Interaction Between Ploidy, Breeding System, and Lineage Diversification

Home , Anisodus, Anthocercis, Anthocercis littorea, Anthocercis viscosa, Anthotroche, Atropanthe

bioRxiv preprint doi: https://doi.org/10.1101/709329; this version posted July 22, 2019. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-NC-ND 4.0 International license.

INTERACTIONBETWEEN PLOIDY,BREEDING SYSTEM, AND LINEAGE DIVERSIFICATION

Rosana Zenil-Ferguson1,†, J. Gordon Burleigh2, William A. Freyman3, Boris Igic´4, Itay Mayrose5, and Emma E. Goldberg3

1Department of Biology, University of Hawai’i Manoa,¯ Honolulu, HI 96822, U.S.A. 2Department of Biology, University of Florida, Gainesville, FL 32611, U.S.A. 3Department of Ecology, Evolution, and Behavior, University of Minnesota, Saint Paul, MN 55108, U.S.A. 4Department of Biological Sciences, University of Illinois at Chicago, Chicago, IL 60607, U.S.A. 5School of Plant Sciences and Food Security, Tel Aviv University, Tel Aviv 6997801, Israel. †Author for correspondence.

Running head: Ploidy and Breeding Systems in Solanaceae Keywords: Polyploidy, Breeding Systems, Self-incompatibility, Diversiﬁcation, Ploidy, SSE models, Diploidization.

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Abstract

If particular traits consistently affect rates of speciation and extinction, broad macroevolutionary patterns can be understood as consequences of selection at high levels of the biological hierarchy. Identifying traits associated with diversiﬁcation rate differences is complicated by the wide variety of characters under consid-

5 eration and the statistical challenges of testing for associations from comparative phylogenetic data. Ploidy (diploid vs. polyploid states) and breeding system (self-incompatible vs. self-compatible states) have been repeatedly suggested as possible drivers of differential diversiﬁcation. We investigate the connections of these traits, including their interaction, to speciation and extinction rates in Solanaceae. We show that the effect of ploidy on diversiﬁcation can be largely explained by its correlation with breeding system and that

10 additional unknown factors, alongside breeding system, influence diversification rates. These results are largely robust to allowing for diploidization. Finally, we find that the most common evolutionary pathway to polyploidy in Solanaceae occurs via direct breakdown of self-incompatibility by whole genome duplication, rather than indirectly via breakdown followed by polyploidization.

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“Among life history traits, reproductive characters that determine mating patterns are perhaps

15 the most inﬂuential in governing macroevolution." Barrett et al. (1996)

Introduction

Species accumulate across the tree of life at different rates. One possible explanation for this phenomenon is that various traits differentially affect rates of diversiﬁcation. Dramatic increases in phylogenetic and

20 phenotypic data, along with methodological advances, have greatly accelerated the search for traits that influence diversification. Nevertheless, identifying focal traits associated with rates of speciation and extinction remains a challenge (e.g., Maddison and FitzJohn 2015; Rabosky and Goldberg 2015; Beaulieu and O’Meara 2016; Rabosky and Goldberg 2017). One difficulty is that speciation and extinction likely do not depend on a single character, so the biological and environmental contexts in which traits occur can lead to

25 complex interactions that affect lineage diversification (Beaulieu and O’Meara 2016; Caetano et al. 2018; Herrera-Alsina et al. 2018). Consequently, examining the association of only one character with diversification patterns can be misleading. Here, we embrace this challenge by jointly investigating two characters thought to influence speciation and extinction rates—ploidy level and breeding system—while allowing for their interactions, and other confounding factors, to change diversification. We also test whether adding one

30 more trait and increasing model complexity is worthwhile. Polyploidization is a remarkably common mutation in plants (Husband et al. 2013; Zenil-Ferguson et al. 2017). The widespread variation in ploidy has long been considered a salient feature of ﬂowering plant lineages (Stebbins 1938). An increase in ploidy can alter many traits and affect a variety of evolutionary and ecological processes (Ramsey and Schemske 2002; Sessa 2019). At shallow evolutionary time scale,

35 polyploids were found to have an overall lower net diversiﬁcation rate than diploids across many vascular plant clades (Mayrose et al. 2011, 2015). However, recent genomic studies have inferred numerous paleo- polyploidizations, including some preceding the emergence of highly diverse plant clades (Soltis et al. 2014; Landis et al. 2018), suggesting that whole genome duplications may have played an important role driving innovation and diversiﬁcation in plants. Evidence of paleo-polyploidy within the genomes of diploid extant

40 plants also implies pervasive diploidization, the return of polyploids to the diploid state, throughout the angiosperm phylogeny (Soltis et al. 2015; Dodsworth et al. 2015). Our analyses re-examine the association between ploidy and lineage diversiﬁcation by extending the approach of Mayrose et al. (2011, 2015) to include transitions from polyploid to diploid states and potential unobserved factors affecting diversiﬁcation patterns.

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45 Breeding system shifts—changes in the collection of physiological and morphological traits that determine the likelihood that any two gametes unite—are also remarkably common and crucially affect the distribution and amount of genetic variation in populations (Barrett 2013). In particular, a variety of genetic self-incompatibility (SI) systems cause plants to reject their own pollen, and the loss of such mechanisms, yielding self-compatibility (SC), is a commonly observed transition in ﬂowering plant evolution (Stebbins

50 1974; Igic´ et al. 2008). Previous analyses reported higher rates of diversification for SI than for SC lineages in Solanaceae (Goldberg et al. 2010). Similarly, heterostylous SI lineages in Primulaceae seem to diversify faster than SC lineages (de Vos et al. 2014), as do outcrossing lineages in Onagraceae (Freyman and Höhna 2019). Although these findings suggest a consistent macroevolutionary role of breeding system, it is unlikely to be the sole character determining lineage diversification. We investigate the relationship of breeding

55 system to speciation and extinction rates in the context of ploidy and other unobserved factors. Polyploidy and self-fertilization are widely thought to be associated (Stebbins 1950). Whole genome duplication may facilitate the transition to selﬁng by masking inbreeding depression, or self- fertilization may facilitate polyploidy establishment by by avoiding the lower ﬁtness that characterize early-forming polyploids (Levin 1975; Ramsey and Schemske 1998; Barringer 2007; Barrett 2008;

60 Husband et al. 2008).Additionally, in RNase-based gametophytic SI systems, polyploidization directly causes the loss of SI (Stout and Chandler 1942; Lewis 1947). In these systems, SI occurs because haploid self-pollen grains, with one S-allele at the locus controlling the SI response, are unable to detoxify the S-RNase produced by the same S-allele in the style (Kubo et al. 2010). The unreduced pollen of diploids, however, can contain two S-alleles expressed in pollen, which jointly gain the ability to detoxify the

65 S-RNases produced by any maternal genotype (Entani et al. 1999; Tsukamoto et al. 2005; Kubo et al. 2010). Initial mutant individuals with pollen containing doubled haploid genomes are consequently capable of self-fertilization, with exceedingly few exceptions (Hauck et al. 2002; Nunes et al. 2006). RNase-based SI is regarded as ancestral in eudicots (Igic´ and Kohn 2001; Steinbachs and Holsinger 2002), and it is expressed in all SI species of Solanaceae examined to date. The absence of SI polyploids in this family

70 yields a strong correlation between ploidy and breeding system (Robertson et al. 2011). We address two macroevolutionary questions about the correlated evolution of ploidy and breeding system. First, we investigate their joint inﬂuence on rates of speciation and extinction. Each character alone has been shown to be associated with differential lineage diversiﬁcation, but if their effects are not additive, studying them separately may not reveal their combined effect. Second, we examine the order

75 of transitions in the two characters. Evolution commonly proceeds from diploid to polyploid, and from SI to SC states, but there are two paths by which diploid SI lineages can eventually become SC polyploids.

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Loss of SI in diploids could be directly caused by polyploidization (as explained above, for RNase-based SI systems), resulting in a one-step pathway to SC polyploids. Alternatively, SI diploids could ﬁrst transition to SC without an increase in ploidy, and subsequently undergo polyploidization, resulting in a two-step

80 pathway to SC polyploids. Robertson et al. (2011) compared the contributions of these two paths, ﬁnding that evolution from SI diploids to SC polyploids is more likely to proceed via the one-step pathway over short timescales, but via the two-step pathway over long timescales. They considered only transitions among the states, however, and we investigate whether these results hold true when allowing for differences in lineage diversiﬁcation.

85 In the present study, we employ an extended framework of state speciation and extinction models, which simultaneously model transitions between the discrete states of a trait and different rates of speciation and extinction associated with each of those states (‘SSE’ models; Maddison et al. 2007; FitzJohn 2012). We start by ﬁtting binary state speciation and extinction models to ploidy and breeding system independently (Maddison et al. 2007). We follow by ﬁtting models that incorporate hidden states, which reduce the chance

90 that the effect of the focal trait (ploidy or breeding system) on diversification is found to be significant when in reality, it is simply background heterogeneity in the diversification process what produces the diversification patterns in the phylogeny (Beaulieu and O’Meara 2016). We compare the proposed models against their character independent counterparts (Beaulieu and O’Meara 2016) to investigate whether ploidy or breeding system are actually affect the diversification process. Next, we model ploidy and breeding system jointly

95 to assess their combined influence on diversification, with or without an additional hidden state. Using the ploidy and breeding system model without hidden states, we quantify the relative contributions of the two pathways from SI diploids to SC polyploids. We also aggregate states within these joint models of ploidy and breeding system in order to test whether increasing complexity from one trait to two traits significantly improves our understanding of the diversification process. Furthermore, we extend all the models involving

100 ploidy to investigate the potential effects of including diploidization. Our results highlight the importance of considering non-additive effects of traits on net diversiﬁcation rates under the presence of unobserved factors, in order to detect strong biologically-driven processes dictating the diversiﬁcation patterns.

Methods

Data

105 Chromosome number data were obtained for all Solanaceae taxa in the Chromosome Counts Database (CCDB; Rice et al. 2015), and the ca. 14,000 records were curated semi-automatically using the CCDBcurator R package (Rivero et al. 2019). CCDB contains records from original sources that have

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multiple complex symbol patterns denoting multivalence, or irregularites of chromosome counts. After a ﬁrst round of automatic cleaning, we examined results by hand and corrected records as necessary. Our

110 hand-curated records were also contrasted against the ploidy dataset from Robertson et al. (2011), original references therein, and against ploidy data in the C-value DNA dataset from Bennett and Leitch (2005). By comparing three different sources of information, we were able to code taxa as diploid, D, or polyploid, P. For the majority of species, ploidy was assigned according to information from the original publications included in the C-value DNA dataset (Bennett and Leitch 2005). For taxa without ploidy information but

115 with information about chromosome number, we assigned ploidy based on the multiplicity of chromosomes within the genus/family, or based on SI/SC classiﬁcation. For example, Solanum betaceum did not have information about ploidy level but it has 2n=24 chromosomes, so since x = 12 is the base chromosome number of the genus Solanum (Olmstead and Bohs 2007), we assigned S. betaceum as diploid. Additionally, because of the absence of SI polyploids (explained above and below), species known to be SI could be

120 scored as diploid. Species with more than one ploidy level were assigned the most frequent ploidy level recorded or the smallest ploidy in case of frequency ties. Breeding system states were scored as self-incompatible, I, or self-compatible, C, based on results curated from the literature (as compiled in Igic´ et al. 2006; Goldberg et al. 2010; Robertson et al. 2011; Goldberg and Igic´ 2012). Most species could unambiguously be coded as either I or C (Raduski et al.

125 2012). Following previous work, we coded any species with a functional SI system as I, even if SC or dioecy was also reported. Dioecious species without functional SI were coded as C. Resolution of taxonomic synonymy followed Solanaceae Source (PBI Solanum Project 2012). Hy- brids and cultivars were excluded because ploidy and breeding system can be affected by artiﬁcial selection during domestication. Following the reasoning outlined in Robertson et al. (2011), we closely examined

130 the few species for which the merged ploidy and breeding system data indicated the presence of self- incompatible polyploids. Although SI populations frequently contain some SC individuals, and diploid populations frequently contain some polyploid individuals, in no case did we ﬁnd convincing data for a naturally occurring SI polyploid population (discussed in Robertson et al. 2011). Because of the resulting absence of polyploid SI populations, as well as the functional explanation for polyploidy disabling gameto-

135 phytic SI systems with non-self recognition (see the Introduction), we consider only three observed character states: self-incompatible diploids (ID), self-compatible diploids (CD), and self-compatible polyploids (CP). Matching our character state data to the largest time-calibrated phylogeny of Solanaceae (Särkinen et al. 2013) yielded 651 species with ploidy and/or breeding system information on the tree. Of these,

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140 368 had information for both states. The number of species in each combination of states is summarized in Fig. 1A. We retained all 651 species in each of the analyses below because pruning away tips lacking breeding system in the ploidy-only analyses (and vice versa) would discard data that could inform the diversiﬁcation models. A total of 372 taxa without any information about breeding system or ploidy were excluded.

145 The Supplementary Information contains citations for the numerous original data sources. The Dryad archive contains the data and tree ﬁles used for analyses.

Models

In order to test our hypotheses about lineage diversiﬁcation and trait macroevolution, we ﬁt 29 state- dependent speciation and extinction models (BiSSE, MuSSE, HiSSE; Maddison et al. 2007; FitzJohn 2012;

150 Beaulieu and O’Meara 2016). SSE models contain parameters that describe per-lineage rates of speciation and extinction, speciﬁc to each character state (denoted λ and µ, respectively, with subscripts to indicate the state), along with rates of transitions between states (denoted ρ for polyploidization, δ for diploidization,

and qIC for loss of self-incompatibility). The full set of models and all their rate parameters are detailed in Fig. S1. Here, we summarize how each model allows us to assess whether diversiﬁcation is best explained

155 by variation in ploidy, breeding system, their combination, or some unknown factor.

Ploidy and diversiﬁcation

In order to investigate the association between ploidy level and diversification, we first employed a model (labeled M1), previously used by Mayrose et al. (2011), with each species classified as diploid (D) or polyploid (P). Although this model can be powerful in studies of trait evolution, it is prone to incorrectly

160 reporting that a trait is associated with diversification differences (Maddison and FitzJohn 2015; Rabosky and Goldberg 2015). We therefore define several models that incorporate additional forms of diversification rate heterogeneity. The second ploidy model (M2) includes a binary hidden trait that subdivides each observed state. In this trait-independent model known as CID (Beaulieu and O’Meara 2016), hidden traits can affect diver-

165 sification but the observed traits do not. Comparing M1 and M2 allows us to test whether diversification rate heterogeneity is better explained by ploidy or by some unknown factor. We additionally fit three models in which both ploidy and a hidden trait could influence diversification (M3–M5). These models differ in whether transitions between the hidden states are symmetric (M3) or asymmetric(M4), and whether the polyploidization rate depends on the hidden state(M5). Comparing M1–

170 M5 allows us to test whether ploidy is associated with diversiﬁcation differences on top of the differences

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potentially explained by an unknown factor. We further fit the analogues of these five models but including a rate parameter δ for transitions from polyploid to diploid (M6–M10). These comparisons allow us to assess whether our conclusions about ploidy and diversification are robust to the possibility of diploidization.

175 Breeding system and diversiﬁcation

We propose five breeding system models following the same logic as the ploidy models above. Under the simplest breeding system and diversification model (M11), species are classified as self-incompatible (I) or self-compatible (C). This is the same model as in the analysis presented in Goldberg et al. (2010) but with an updated phylogeny (Särkinen et al. 2013) and a larger aggregated dataset.

180 We then add models to allow diversification to be influenced by only a hidden trait (M12), or by both breeding system and a hidden trait (M13–M15, with varying degrees of complexity in the hidden trait transitions Table 2). Similar models were used by Freyman and Höhna (2019) to study diversification in Onagraceae. Self-incompatibility is homologous in all Solanaceae species in which S-alleles have been cloned

185 and controlled crosses performed. All species sampled to date possess a non-self recognition, RNase-based gametophytic self-incompatibility (shared even with other euasterid families; Ramanauskas and Igic´ 2017). Furthermore, species that are distantly related within this family carry closely-related alleles, with deep trans-speciﬁc polymorphism at the locus that controls the SI response (Ioerger et al. 1990; Igic´ et al. 2006). Thus, there is strong evidence in Solanaceae that the I state is ancestral in the family, and that the SI

190 mechanism was not regained. For all breeding system models, we estimated a transition rate from I to

C but not the reverse (qCI = 0).

Ploidy, breeding system, and diversiﬁcation

Ploidy and breeding system might inﬂuence lineage diversiﬁcation individually, but these two traits also have an intricate association (discussed in the Introduction). Therefore, we considered several multi-state

195 models that investigate the contribution of both traits and the allowable transitions between them. The simplest model (M16) classiﬁes each species as either SI diploid (ID), SC diploid (CD), or SC polyploid (CP); recall that SI polyploids do not occur. Each of these states may again be associated with different rates of speciation and extinction, and the allowable transitions are loss of SI within the diploid state (from ID to CD), loss of SI via polyploidization (from ID to CP), and polyploidization while SC (from

200 CD to CP). As for the previous models of only one trait, we then allow diversiﬁcation to be inﬂuenced by only

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a hidden trait (M17), or by ploidy, breeding system, and a hidden trait (M18–M20) with varying degrees of complexity in the hidden trait transitions (similar to Caetano et al. 2018; Huang et al. 2018). We also ﬁt the analogous models but allowing for diploidization (M21–M25).

205 Lumped models

The models described so far allow us to assess the contributions of our two focal characters—ploidy and breeding system—to lineage diversiﬁcation, but they do not reveal whether it is valuable to include both characters in the analysis. To answer this question with statistical model comparisons requires comparing the likelihood of the data given each model. This is impossible for the ploidy and breeding system models

210 presented so far, however, because the data are different for the different models: they use either the D/P or the I/C or the ID/CD/CP state spaces. Therefore, the use of different data results in incomparable models. In order to compare ﬁts of ploidy-only vs. breeding system-only vs. combined trait models, we use the technique of ‘lumping’ states together (Tarasov 2019). We use the state space of the ID/CD/CP model but constrain the rate parameters to mimic the behavior of the single-trait models. To lump states

215 requires that the transition rates from the lumped state to the singular state be equal (Tarasov 2019). First we lump together ID and CD to form the diploid state, mimicking the D/P model (M26). Proposing a lumped ploidy model by aggregating ID and CD requires forcing the rate of polyploidization from ID and CD to

CP to be equal (i.e. ρ0 = ρI = ρc), but also requires assuming that the rates of speciation and extinciton

for ID and CD to be equal. Therefore, we deﬁne the new parameters λD and µD that are the same for each

220 of the two diploid states ID and CD.We used the same procedure to lump together CD and CP to form the self-compatible state, mimicking the I/C model (M28). In this particular case, the rate from CD to CP back to ID is zero and equal for both, so the model is lumpable. However, to fully mimic the breeding system

model, we assume that the rate of selﬁng is equal (i.e. q0 = qIC = rhoI) and the rates of speciation and

extinction for both CD and CP are the same (new parameters λC and µC). We further add a hidden character

225 to each of these models (M27 and M29), and then compare this group of models (Table 3). We do not include additional models with diploidization because this reverse ploidy transition ren- ders the models non-lumpable. When including diploidization, transitions from CP to CD are at rate δ but transitions from CP to ID do not occur. Because ID and CD would be lumped to mimic the D/P model, this model is non-lumpable when δ 6= 0. Thus, we can compare models to test whether it is advantageous to

230 include both traits, but only when ignoring diploidization.

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Pathways to polyploidy

Considering ploidy and breeding system together, there are two evolutionary pathways from SI diploid to SC polyploid (Brunet and Liston 2001; Robertson et al. 2011). In the one-step pathway, the CP state is produced directly from the ID state when whole genome duplication disables SI. In the two-step pathway,

235 the CD state is an intermediate: SI is ﬁrst lost, and later the SC diploid undergoes polyploidization. We quantify the relative contribution of these pathways to polyploidy in two ways, each using the median estimates of rates from the simplest model that includes both traits (M16). Our results will differ from those of Robertson et al. (2011) because our transition rate estimates come from a dated phylogeny and a model that allows for state-dependent diversiﬁcation.

240 Both of our methods are based on a propagation matrix that describes ﬂow from ID to CP, as in Robertson et al. (2011). We insert an artiﬁcial division in the CP state, so that one sub-state contains the CP species that arrived via the one-step pathway and the other substate contains the CP species that arrived via the two-step pathway. We consider unidirectional change along each step of the pathway in order to separate them into clear alternatives, and because in this family there is no support for regain of SI, and no strong

245 support for diploidization (see below). First, we consider only the rates of transitions between these states, placing them in the propagation matrix Q. The matrix P = exp(Qt) then provides the probabilities of changing from one state to any other state after time t. Closed-form solutions for the two pathway probabilities are provided in Robertson et al. (2011).

250 Second, we consider not only transitions between states but also diversification within each state. State-dependent diversification can change the relative contributions of the two pathways. For example, if the net diversification rate is small for CD, the two-step pathway will contribute relatively less. We therefore include the difference between speciation and extinction along the diagonal elements of the propagation matrix. As before, matrix exponentiation provides the relative chance of changing from one state to any other

255 state after time t. The calculations of the propagation matrix are not probabilities because diversiﬁcation changes the number of lineages as time passes. We can still use ratios, however, to consider the relative contribution of each pathway, analogous to the normalized age structure in a growing population (Leslie 1945).

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Statistical inference

260 Model ﬁtting

Parameters for each of the 29 models were coded as graphical models and Bayesian statistical inference was performed with RevBayes (Höhna et al. 2016). Scripts for analyses and key results are available as Supplementary Information. We accounted for incomplete sampling in all analyses by setting the probability of sampling a species at the present to 651/3000 (using the method of FitzJohn et al. 2009) since

265 the Solanaceae family has approximately 3,000 species (PBI Solanum Project 2012). For all models, we assumed that speciation and extinction parameters had log-normal prior distributions with means equal to the expected net diversiﬁcation rate (number of taxa/[2 × root age]) and standard deviation 0.5. Priors for parameters deﬁning trait changes were assumed to be gamma distributed with parameters k = 0.5 and θ = 1. For each model, a Markov chain Monte Carlo (MCMC; Metropolis et al. 1953; Hastings 1970) was run in

270 the high-performance computational cluster at the Minnesota Supercomputing Institute, which allowed for 5,000 generations of burn-in and a minimum of 200,000 generations of MCMC for each of the models. Convergence and mixing of each MCMC chain was determined by ensuring the effective sample size of each parameter was over 200. We report posterior distributions for the model parameters in Fig. 2, and also for the compound pa-

275 rameters of net diversiﬁcation (λ − µ) and extinction fraction (µ/λ) for each state. Additionally, ancestral states at each node in the phylogeny were sampled jointly during the MCMC analyses every 100 generations. Ancestral state estimations for all models show the maximum a posteriori estimates of the marginal probability distributions for each of the 650 internal nodes for each of the models in Fig. 2. (Figs. S6, S8, S10, S12, S14 and S16).

280 Model selection key questions

We calculated the marginal log-likelihood for each of the models using ﬁfty stepping stone steps under the methodology of Xie et al. (2010), implemented in RevBayes (Höhna et al. 2016). Each stepping stone step was found by calculating at least 500 generations of burn-in followed by a total of 1,000 MCMC steps (Table 1).

285 Using the marginal likelihood values, we calculated Bayes factors to answer ﬁve key biological and methodological questions:

1. Are diversiﬁcation patterns only determined by hidden states and not the traits of interest?— Comparison of character independent models against hidden state (Tables 1 and 2 and Tables S1–S3).

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2. Are hidden states necessary to explain diversiﬁcation rate heterogeneity?—Comparison of simple

290 models against hidden state models (Table S4).

3. Does a second focal trait add information about the diversiﬁcation process?—Comparison of lumped models against IC/CD/CP models (Fig. 3 and Table 3).

4. Are conclusions robust to assumptions about hidden state transitions?—Comparison amongst hidden states models with equal hidden rates and asymmetrical rates (Fig. S5 and Table S6).

295 5. Is there evidence for diploidization?—Comparison amongst models with and without diploidization (Fig. S2 and Table S5).

Each model comparison is reported with a Bayes factor on the natural log scale: the comparison

between models M0 and M1 is K = ln(BF(M1, M0)) = ln[P(X|M1) − P(X|M0)]. There is ‘strong evidence’

for M1 when this value is more than 10, moderate support if the value is more than 1, and no evidence if

300 the value is between -1 and 1. If the value of K is negative the evidence goes towards M0 (Kass and Raftery 1995).

Results

Trait-dependent diversiﬁcation

Ploidy only

305 When considering ploidy alone, we found a larger net diversiﬁcation rate for diploids than for polyploids, in agreement with Mayrose et al. (2011, 2015). This result holds with (model M1, Fig. 2A) or without the diploidization parameter (M6, Fig. S2A). Incorporating a hidden state in this model, however, reduces the clear separation in diversiﬁcation rate estimates between diploids and polyploids (M4, Fig. 2B; M9, Fig. S2B). Statistical model comparisons show a clear preference for models in which only a hidden state

310 affects diversification or a hidden state as well as ploidy (M2 and M4; Table 1). Results are similar when diploidization is included (Table S1). Thus, when other traits are ignored, the role of ploidy in net diversification is unclear, with marginal support for diploids having higher diversification rates, but rate differences perhaps better explained by another factor.

Breeding system only

315 When considering breeding system alone (M11, Fig. 2C), we found a larger net diversiﬁcation rate for SI than for SC species, in agreement with Goldberg et al. (2010). When a hidden state is included, the large net diversiﬁcation rate difference persists for one hidden state but is diminished for the other (M14, Fig. 2D). In

12 bioRxiv preprint doi: https://doi.org/10.1101/709329; this version posted July 22, 2019. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-NC-ND 4.0 International license.

the statistical model comparisons, the best two supported models include diversiﬁcation differences due to both breeding system and to a hidden trait (M14 and M15, Table 2). Breeding system seems to play a role

320 in diversiﬁcation differences, though a hidden factor does as well.

Ploidy and breeding system together

When considering ploidy and breeding system together, the net diversiﬁcation rate for SI diploids was greater than for either SC diploids or SC polyploids, with or without diploidization (M16, Fig. 2E; M21, Fig. S2E). Thus, the difference in net diversiﬁcation associated with breeding system persists even when

325 ploidy is included in the model. The reverse is not true: the association of ploidy with net diversification in the simplest ploidy-only model (M1, Fig. 2A, Fig. S2A) appears to be driven by the subset of diploids that are SI, while among SC species, net diversification rates for diploids and polyploids are similar. When a hidden state is included, the separation in net diversification rate of ID vs. CD and CP persists within one hidden state but is reduced in the other (M19, Fig. 2F). The same general pattern remains

330 when diploidization is included (Fig. S2F). Model comparisons clearly favor models that include ploidy, breeding system, and the hidden trait, against the character-independent model in which the focal traits do not influence diversification (Table S2; Table S3 with diploidization). Using the lumped models, we find moderate support for obtaining a significantly better fit by adding breeding system to the ploidy-only model (M26 vs. M16, Table 3, Fig. 3BC). This is also true when a hidden

335 trait is included (M27 vs. M23, Table 3, Fig. S3EF). A similar comparison in which ploidy is added to the breeding system-only model shows no preference for the model that also includes ploidy (M28 vs. M16, Table 3, Fig. 3CE). When including a hidden state, however, the model with both focal traits is moderately preferred over the model with only breeding system (M29 vs. M18, Table 3, Fig. S4EF). From all of these types of statistical evidence, we conclude that breeding system (and a hidden

340 factor) are strongly associated with diversiﬁcation differences, and that ploidy plays a smaller role.

Key questions about diversiﬁcation and transitions

The above results include several of our statistical model comparison findings. Here we return to the five specific questions we targeted with our model comparisons.

1. Are diversiﬁcation patterns only determined by hidden states and not the traits of interest? No, our

345 focal traits are supported as having associations with diversiﬁcation differences. In most cases, we ﬁnd moderate to strong preference for models with the focal traits as well as hidden states, over models with only hidden states (Tables 1 and 2 and Tables S1–S3).

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2. Are hidden states necessary to explain diversification rate heterogeneity? Yes, models with hidden states that influence diversification are strongly preferred over models containing only the focal traits

350 (Table S4). This means that there are potentially many factors underlying diversiﬁcation shifts within the family.

3. Does a second focal trait add information about the diversiﬁcation process? Yes, in most cases models with both ploidy and breeding system are preferred over models with only one of the focal traits (Table 3 and Figs. S3 and S4).

355 4. Are conclusions robust to assumptions about hidden state transitions? Yes, we found that allowing different types of asymmetry in transitions within and between hidden states did not change our conclusions about net diversiﬁcation differences. Hidden state models with asymmetric rates are, however, strongly preferred over models with equal rates between hidden states (Table S6), and they show stronger differences between some net diversiﬁcation rates (Fig. S5). The effect of the asym-

360 metry of the hidden rate transitions is better observed in the ancestral state estimations (Figs. S8, S12 and S16), which show that moving out of state A (dark colors) happens quickly with rate α, whereas evolving out of hidden state B (light colors) is slow with rate β.

5. Is there evidence for diploidization? Perhaps: when comparing models with diploidization against models without it, we found moderate evidence that models containing diploidization are preferred

365 (Table S5). We discuss later some further challenges in identifying diploidization. We further found that our main conclusions about net diversiﬁcation differences are not dependent on whether diploidization is included (Fig. S2).

Pathways to polyploidy

There are two pathways by which SI diploid lineages eventually—given enough time—become SC poly-

370 ploids. In the one-step pathway, polyploidization directly disables SI. In the two-step pathway, SI is ﬁrst lost within the diploid state, followed by polyploidization. Determining the relative contribution of these pathways based on our transition rate estimates (median transition rate values from M16), we ﬁnd that the one-step pathway is more likely on short timescales and the two-step pathway is more likely on long timescales (Fig. 4, left panels). Beginning with a single SI diploid lineage, when not much time has elapsed,

375 the one-step pathway is more likely because it only necessitates a single event to reach the SC polyploid state. When more time has elapsed, the two-step pathway is more likely because the rate of loss of SI within

diploids, qIC, is greater than the rate of polyploidization for SI species, ρI (Fig. S15). That is, an ID lineage

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is more likely to begin its path to polyploidy with a transition to CD, but completing this path to CP takes longer. Robertson et al. (2011) reached the same conclusion. Our result is qualitatively unchanged when

380 using transition rate estimates from the model that does not allow diversiﬁcation differences related to the observed states (M17). The preceding conclusions, however, ignore the changes in numbers of lineages in each state due to speciation and extinction. By analogy, envisioning the states as stepping stones, the extent to which each stone grows or shrinks over time affects the utility of each possible path. Allowing different net

385 diversification rates for each state (again using median rate estimates from M16), we find a qualitative difference in the relative pathway contributions. The lower rate of net diversification in the CD state, relative to ID, means that relatively fewer lineages are available to complete the second step of the two-step pathway, ending in CP. Consequently, even over long timescales, we find that the two-step pathway contributes less to the formation of polyploids (Fig. 4, right panels) when considering diversification as well as transitions.

390 Discussion

Species are composed of vast assemblages of variable traits. Many traits are both heritable and possibly affect the propensity of species to perish or multiply (Lewontin 1970). Examining the effects of complex trait combinations on lineage diversiﬁcation, however, remains challenging. Focusing ﬁrst on ploidy and then on breeding system, we found that considering each trait in isolation provides an incomplete story. Con-

395 sidering them together, and in conjunction with another hidden factor, provides a more complete picture of macroevolutionary dynamics within Solanaceae. We hope our work serves as an example of how phylogenetic comparative methods can be used to disentangle the contributions of interacting traits to heterogeneous lineage diversiﬁcation, and how to statistically argue for increasing complexity in diversiﬁcation modeling.

Interacting traits and lineage diversiﬁcation

400 Previous analyses of the effects of ploidy on diversification found that diploids are associated with greater net diversification rates than polyploids across many angiosperm clades (Mayrose et al. 2011, 2015). We obtain a similar outcome when examining ploidy alone in Solanaceae (Fig. 2A), but a consistent effect of ploidy on diversification is not clear when we incorporate a hidden factor linked to diversification (Fig. 2B). Previous analyses of breeding system in this family found that SI may cause higher diversification rates,

405 compared with SC (Goldberg et al. 2010; Fig. 2C). Our analyses that include a hidden trait recover the same pattern, with one important difference. On the background of one hidden state, we recover a net diversiﬁcation rate for SC species that is positive and greater than the diversiﬁcation rate of SI species on the background of the other hidden state (Fig. 2D). Therefore, SC may not be a ‘dead end’ when coupled with

15 bioRxiv preprint doi: https://doi.org/10.1101/709329; this version posted July 22, 2019. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-NC-ND 4.0 International license.

some unknown trait combinations or processes not modeled by these two traits. Our analyses also reveal

410 that models of joint evolution of ploidy and breeding system are statistically preferred, and hint at how various trait combinations may be linked with diversification. We find that the highest net diversification rate is associated with SI diploids, while SC diploids have a lower diversification rate that overlaps with the net diversification of SC polyploids (Fig. 2E). Thus, breeding system appears to provide a relatively better explanation of diversification rate differences, with ploidy providing a secondary effect within SC species.

415 Throughout our numerous model comparisons, we ﬁnd that inclusion of hidden states provides a considerably better ﬁt (Table S4). This is consistent with the expectation that many processes, beyond those associated with the focal traits, can affect inference of speciation and extinction. It is, however, unclear exactly which processes are captured by the hidden states. For example, our results show that, to a varying extent, breeding system functions as a hidden state in the ploidy-centered analysis, and vice

420 versa (Figs. S3 and S4). But the strong statistical support for processes not well explained by ploidy and breeding system (Table S4) tempts one to interpret the remaining variation as the effect of other measurable traits. For example, our data appear to show a rapidly-diversifying Australasian clade of mostly SC species within Solanum, which suggests that geography may play a role. Nevertheless, it is also possible that the addition of hidden states instead explains variation stemming from any of a number of unrelated processes

425 or methodological artifacts, as previously discussed by Beaulieu and O’Meara (2016). In the absence of additional information, the hidden states can be viewed as a statistical trick, providing an easy way to model extra heterogeneity without directly representing a speciﬁc trait. As more trait information becomes available for macroevolutionary studies, it is not only important to recognize the role of hidden states as a part of a general modeling approach, but also to question whether

430 adding more traits to diversification studies is justified. More generally, we find that lumped models are useful for assessing the value of adding additional traits to already complex diversification models(Fig. 3 and Table 3). Although we fit an extensive set of models in order to relax a variety of assumptions, we did not explore the process of trait change in conjunction with speciation. That is, our models all assume anagenetic

435 trait evolution and ignore cladogenetic shifts. Anagenetic and cladogenetic changes can be separated with phylogenetic models (Mayrose et al. 2011; Goldberg and Igic´ 2012; Magnuson-Ford and Otto 2012). These have been applied to estimate the relative contribution of anagenetic and cladogenetic shifts in breeding system (Goldberg and Igic´ 2012) and polyploidization (Zhan et al. 2016; Freyman and Höhna 2019). We did not explore cladogenetic trait change because they would greatly increase in state space and model

440 number of our already complex and extensive modeling framework. Although Goldberg and Igic´ (2012)

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found that allowing cladogenetic changes did not substantially affect inference of net diversiﬁcation rates associated with breeding system, future work could test whether this process affects diversiﬁcation rate estimates with the more complex state and parameter spaces of our other models.

Pathways to polyploidy

445 With evolution predominantly in the direction from diploid to polyploid, and from SI to SC, surviving lineages will tend to become SC polyploids. We ﬁnd that in Solanaceae, the pathway to this state is more likely to consist of a single step (ID → CP) than two steps (ID → CD → CP; Fig. 4). Although this question focuses on the process of state transitions, we also show that its answer is affected by the process of lineage diversiﬁcation. We used a simple mathematical approach to investigate the contributions of the two path-

450 ways, but future work could instead rely on stochastic character mapping to estimate the numbers of each type of transition more directly. Macroevolutionary transition rates represent a combination of time spent waiting for individuals with a new character state, and for that new state to become widespread within the species. For our traits, this consists of mutations that break SI or generate polyploid individuals, and selective pressures that cause

455 ﬁxation (or loss) of these mutants. Estimates of mutation rates are highly uncertain, but the chance of breakdown of SI within diploids is perhaps 10−5 per pollen grain; this includes breakdown by autopoly- ploidization (Lewis 1979), which is by itself estimated to occur approximately within the same order of magnitude (Ramsey and Schemske 1998). In contrast, we infer a macroevolutionary transition rate from ID to CP that is 2. 5 times greater than the rate from ID to CD, indicating that selection restricts the ﬁxation of

460 new polyploids more than of new SC mutants (Fig. 4, Robertson et al. 2011). Our ﬁndings prompt several further questions about the macroevolutionary pathways of ploidy and breeding system. First, our support for the direct pathway is consistent with the idea that breakdown of SI by whole genome duplication—via diploid ‘heteroallelic’ pollen—may trigger the evolution of gender dimorphism as a different mechanism of inbreeding avoidance (Miller and Venable 2000). A further test of

465 this hypothesis would additionally examine the propensity of polyploids generated through either pathway to become dioecious (Robertson et al. 2011). Second, we might wonder whether the propensity for a polyploid species to diversify depends on whether it arose via the one-step or two-step pathway. This could be tested with a different form of a hidden state model, in which the polyploid state is subdivided into parts, reﬂecting the arriving path taken to that state. Such an estimate of path-dependence could also include the possibility

470 of different diversiﬁcation rates for the subdivided CP substates. Third, the generality of our ﬁndings in other families remains to be assessed. An identical procedure could be used in other families with gametophytic

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SI. In clades with sporophytic SI systems, however, SI is not disabled by whole genome duplication, so there is no one-step pathway (Miller and Venable 2000; Mable 2004). The correlation between breeding system and ploidy may therefore be different in sporophytic systems, and it is unclear whether one of the two-step

475 pathways might predominate.

Diploidization

Polyploidization is known to be common in plants, but the pace and relative frequency of the reverse process—diploidization—remains unclear, and it is under active investigation (Dodsworth et al. 2015; Man- dakova and Lysak 2018). Ignoring diploidization, if it is common, could cause underestimation and increase

480 of uncertainty in the polyploidization rate. Therefore, we included a slate of models with a diploidization parameter, and show that our main conclusions are robust to this process (Fig. S2). These models also suggest modest statistical support for diploidization (Table S5), although our estimates of its rate were highly uncertain. Furthermore, additional lines of evidence for classifying species as diploid or polyploid (beyond the genus-level chromosome multiplicity that we primarily relied on) are needed for more reliable conclusions.

485 Other lines of evidence about the prevalence of diploidization within Solanaceae or its ancestors are mixed or even conﬂicting. On the one hand, polyploidy may have occurred prior to the origin of Solanaceae, rendering all extant ‘diploids’ secondarily derived. Ku et al. (2000) and Blanc and Wolfe (2004) posited that the lineage leading to cultivated tomato, Solanum lycopersicum, may have experienced one or more whole genome duplications. A subsequent analysis of synteny between grape and Solanum genomes, as well as

490 genetic distances (Ks) between inferred paralogs within genomes of Solanum (tomato and potato), each suggested that this lineage experienced a likely round of ancient genome duplication or triplication (71±19 My; Tomato Genome Consortium 2012) likely pre-dating the origin of the family (49 ± 3 My; Särkinen et al. 2013). On the other hand, there is little evidence for the occurrence of diploidization after the origin of

495 Solanaceae itself. Studies comparing genetic map-based genome synteny within a number of species in this family ﬁnd no evidence for diploidization (Wu and Tanksley 2010). Instead, simple genome re-arrangements appear sufﬁcient to explain chromosomal evolution within species in the cytogenetically conserved ‘x=12’ group, which includes tomato, potato, eggplant, pepper, and tobacco. Recovery of comparatively few rear- rangements would require outstanding convergent loss of duplicated segments. Furthermore, whole genome

500 duplication in a eudicot lineage ancestral to Solanaceae would clash with the evidence that the homologous mechanism of SI, which has been present continually in many families (Igic´ et al. 2006), breaks down nearly invariably in natural and induced tetraploids (Stone 2002; McClure 2009). Most problematically in

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this context, it is unclear how to explain the maintenance of trans-generic polymorphism at the orthologous S-loci in Solanaceae and other families if SI was previously broken down by polyploidization. Regardless

505 of whether genome polyploidization, followed by widespread diploidization, is a dominant mechanism of genome evolution in Solanaceae, it is clear that more work is needed for a complete understanding of the joint evolution of ploidy and breeding systems.

Conclusion

Heterogeneity in lineage diversiﬁcation across time and clades is the rule, rather than the exception. This

510 background heterogeneity makes it difficult to test for the association of any one, isolated trait with different rates of speciation or extinction. Our study provides an example of how diversification linked to a particular trait can be better assessed by a suite of more inclusive models that allow for alternative explanations— whether other traits or unknown factors. Additionally, our analysis of evolutionary pathways to polyploidy shows the importance of including diversification effects even when addressing questions that focus on trait

515 evolution. Finally, although a growing number of plant traits have been studied to date, breeding systems indeed seem to be among the most inﬂuential in governing macroevolution (Barrett et al. 1996).

Acknowledgements

Special thanks to Bob Thomson for donating computational resources that made possible testing the convergence of the models. We also thank Sergei Tarasov for clarifying lumpability concepts, and Carrie Tribble

520 for troubleshooting some ancestral estimate ﬁgures. The computing resources were provided by the Min- nesota Supercomputing Institute (MSI) at the University of Minnesota. This work was supported by the National Science Foundation grant DEB-1655478 (to EEG and IM), DEB-1655692 and NESCent sabbat- ical scholar award EF-0905606 (to BI), and the Israel Science Foundation 961/17 (to IM). We thank Dan Schoen and three anonymous reviewers for providing uncommonly thoughtful and helpful reviews, as well

525 as Spencer Barrett for continually inspiring our work.

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(A) ID CD C? CP I? ?D ?P

num species = 124 170 157 70 85 +20 +23

(B) Ploidy-only ID models ?D CD C? CP (M1-M10) I? ?P

Breeding system- ID only models ?D CD C? CP (M11-M15) I? ?P

Ploidy and breeding system models & ID CD C? CP Lumped models I? ?D ?P M16-M29

Figure 1: Character states used in the models. (A) Each species retained on the phylogeny belonged to one of ﬁve possible categories, depending on whether ploidy and/or breeding system were known. Number of species in each category is indicated; for example, 70 species are self-compatible with unknown ploidy. Character state abbreviations are: I for self-incompatible, C for self-compatible, D for diploid, P for polyploid, ? for unknown. Because polyploidization breaks this form of self-incompatibility, self-incompatible species with unobserved ploidy (I?) are taken to be diploid (ID), and polyploid species with unobserved breeding system (?P) are taken to be SC (CP). (B) Category groupings into states for each model class. In the ploidy-only models (M1- M10), states are coded as D & P when uncertain/consistent with either state; in the breeding system-only models (M11-M15) such states are coded as C; in the ploidy and breeding system models (M16-M29), they are coded as CD & CP. In the hidden-trait models, all species could take on either of two ‘hidden’ character states. Two species, Lycium californicum and Solanum bulbocastanum, are simultaneously ID and CP, and by adding them the sample adds to the total of 651 taxa used for analyses.

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(A) M1. D/P (B) M4. D/P + asymetric A/B

μD μ P μD A μPA ρ ρ λ λD D λ D D P λP A A PA PA 15 4 Posterior Density λDA -μ DA λ -μ D D α β α β λ -μ 3 DB DB 10 λ -μ P P λ -μ ρ PA PA λ 2 λDB DB PB PB λPB -μ PB 5 μ PB 1 μDB Posterior Density Posterior 0 0 -0.2 0.0 0.2 0.4 -2 -1 0 1 Rate Rate (C) M9. I/C (D) M11. I/C + asymmetric A/B

μI μC μ IA μCA

λI -μ I λI I C λC λ IA CA λC A A IA qIC A qIC λ -μ λI -μ I Posterior Density IB IB α β α β λ -μ 10 λC -μ C 4 CA CA

λCB -μ CB λI B λC IB q CB B 5 IC 2 μI B μCB Posterior Density Posterior 0 0 0.0 0.2 0.4 0.6 0.8 -2 -1 0 1 Rate Rate (E) M13. ID/CD/CP (F) M16. ID/CD/CP + asymmetric A/B ρI ρI μ μ CD λCD CDA λCD μ μID A μID P A μCPA ρ qIC ρC qIC C λID IDA CDA CPA ID CD CP λP A λCPA λID 10.0 λIDA -μ IDA 6 α β α β α β Posterior Density λIDB -μ IDB 7.5 λID -μ ID λCD -μ CD 4 A A λCD -μ CD qIC ρC λID CD λ λ -μ 5.0 B IDB B CPB CPB CDB CDB λCP -μ CP μID μCP λ -μ B μCD B CPA CPA B λCDB 2 2.5 λ -μ ρI CPB CPB Posterior Density Posterior 0.0 0 -0.3 0.0 0.3 0.6 -1 0 1 2 Rate Rate

Figure 2: Net diversiﬁcation rates for SSE models of focal traits with or without hidden state. Each panel contains a graphical summary of estimated model parameters and displays posterior distributions for net diversiﬁcation estimates.

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Equivalent Comparable

(A) M1. D/P (B)M26. Lumped D/P

μD μP μD μP λD qIC ρ0 λP ρ ID CD CP λ D D P λP (C) M16. ID/CD/CP

15 15 ρI μ CD λCD μID μP q ρC 10 10 IC ID CD CP λP λD -μ D λD -μ D λID

λP -μ P λP -μ P

5 5 Posterior Density Posterior Density Posterior 10.0

0 0 -0.2 0.0 0.2 0.4 -0.2 0.0 0.2 Rate Rate 7.5

5.0

(D) M11. I/C (E) M28. Lumped I/C μ μ

C Density Posterior I 2.5 μC μI

λ λC λC I I C λ ρ q I q0 C IC ID CD CP 0.0 -0.3 0.0 0.3 0.6 Rate

λID -μ ID λCD -μ CD λCP -μ CP

10 10

λI -μI λI -μI

λC -μC λC -μC 5 5 Posterior Density Posterior Density Posterior

0 0 0.0 0.2 0.4 0.6 0.8 0.00 0.25 0.50 Rate Rate

Figure 3: Comparing two and three state models is possible via lumpable models (M26, M28). These models used the same classiﬁcations as the three-state model M16 which allow for comparisons via Bayes Factors as shown in Table 3.

26 bioRxiv preprint doi: https://doi.org/10.1101/709329; this version posted July 22, 2019. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-NC-ND 4.0 International license.

ID ID

one-step two-step

CD CP CD CP

without diversification with diversification 1.0 one−step 1e+04 one−step two−step two−step 0.8 100 0.6 1 0.4 0.2 contribution of each pathway contribution 0.01 0.0

0 10 20 30 40 50 0 10 20 30 40 50 1.0 1.0 0.8 0.8 0.6 0.6 0.4 0.4 0.2 0.2 proportion of one−step 0.0 0.0

0 10 20 30 40 50 0 10 20 30 40 50

elapsed time (My) elapsed time (My)

Figure 4: Contributions of the two pathways to polyploidy. The one-step pathway is direct ID→CP transitions. The two-step pathway consists of ID→CD→CP transitions. When considering only rates of transitions among the states (ignoring the diversiﬁcation rate parameters), the one-step pathway dominates on short timescales and the two-step on long timescales (left panels). When also considering diversiﬁcation within each state, the one-step pathway, in which polyploidization breaks down SI, dominates over any timescale (right panels). The top panels show the separate contributions of each pathway. The bottom panels show the proportional contribution of the one-step pathway (i.e., one-step / [one-step + two-step]).

27 bioRxiv preprint doi: https://doi.org/10.1101/709329; this version posted July 22, 2019. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-NC-ND 4.0 International license.

Marginal Model M2 M3 M4 M5 Evidence log-likelihood Every model strongly M1. D/P -1283.76 59.90 49.23 60.48 58.82 preferred over M1 Strong preference for M2. CID D/P -1223.86 -10.66 0.579 -1.079 M2 over M1 Asymmetric rates strongly M3. D/P+A/B -1234.52 11.24 9.58 preferred over symmetric Moderate evidence for M4. D/P+A/B asym -1223.28 -1.658 only asymmetric hidden rates M5. D/P+A/B all asym -1224.93

Table 1: Bayes factors of ploidy-only models without diplodization. Numbers greater that 1 mean moderate support relative to the model in the row label. Conventional threshold for ‘strong’ support is 10. The best models are written in bold.

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Marginal Model M12 M13 M14 M15 Evidence log-likelihood Every model strongly M11. I/C -1309.07 41.13 38.59 61.34 61.40 preferred over M11 Models with asymmetric rates M12. CID I/C -1267.93 -2.53 20.21 20.37 are preferred over M12 Asymmetric rates strongly M13. I/C+A/B -1270.47 22.75 22.80 preferred over symmetric M14. I/C+A/B asym -1247.72 0.05 No evidence M15. I/C+A/B all asym -1247.66

Table 2: Bayes factors of breeding system-only models. Results indicate that the HiSSE models with asymmetric rates (M14, M15) are strongly preferred over every other model.

29 bioRxiv preprint doi: https://doi.org/10.1101/709329; this version posted July 22, 2019. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-NC-ND 4.0 International license.

Marginal Preferred Model Comparison K=ln(BF(M ,M )) log-likelihood i ii Model (Evidence) M26. Lumped D/P -1463.22 M26 vs. M16 4.10 M16 (Moderate) M16. ID/CD/CP -1459.11 M27. Lumped D/P+A/B -1417.67 M27 vs. M23 3.678 M23 (Moderate) M23. ID/CD/CP +A/B -1414.00 M28. Lumped I/C -1458.41 M28 vs. M16 -0.69 No evidence M16. ID/CD/CP -1459.11 M29. Lumped I/C+ A/B -1416.60 M29 vs. M23 2.60 M23 (Moderate) M23. IC/CD/CP+A/B -1414.00

Table 3: Test for adding a focal trait to a binary state model via Bayes factors. Three-state models are moderately preferred over two-state models. The evidence is stronger towards the inclusion of breeding systems in ploidy models (M26, M27) than the inclusion of ploidy in breeding system models (M29, M29)

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Figure S1: All models. [This ﬁgure is provided as a separate, large-format page.]

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(A) M6. D/P+δ (B) M9. D/P+A/B+δ asym μD μP ρ μD μ λD D P λ A PA P ρ δ λD A DA PA λPA Posterior Density δ 6 10 λD -μ D α β α β A A λD -μ D λDB -μ DB λ -μ 4 P P ρ λ -μ λ PA PA 5 λDB DB PB PB λ -μ δ 2 PB PB μPB μDB Posterior Density Posterior 0 0 0.0 0.2 0.4 -2 -1 0 1 Rate Rate (C) M11. I/C (D) I/C + A/B asym μ μI C μ IA μCA

λ IA CA λC λI I C λC IA qIC A qIC λI -μ I λIA -μ IA α β α β Posterior Density λC -μ C λIB -μ IB 10 4 λI λC -μ C B λC A A IB CB B qIC λ -μ μ CB CB IB μC 5 B 2 Posterior Density Posterior 0 0 0.0 0.2 0.4 0.6 0.8 -2 -1 0 1 Rate Rate (E) M21. ID/CD/CP+δ ρ (F)M24. IC/CD/CP +A/B +δ asym I ρ μ I CD λCD μ μ μP CDA λCD ID μID A μ ρ A CPA qIC C q ρC ID CD CP λ IC λ P λID IDA CDA CPA λ ID δ A δ CPA 10.0 λIDA -μ IDA

β Posterior Density α α β α β 6 λIDB -μ IDB 7.5 λID -μ ID λCD -μ CD qIC ρC A A λCD -μ CD λID ID CD λ 4 B B B CPB CPB λ -μ 5.0 δ CDB CDB λCP -μ CP μ μ IDB μ CPB CDB λ λCP -μ CP CDB 2 A A 2.5 ρI λCPB -μ CPB Posterior Density Posterior 0.0 0 0.0 0.2 0.4 0.6 0.8 -2 -1 0 1 2 Rate Rate

Figure S2: Posterior distribution for all the best models with diploidization

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Equivalent Comparable (A) M1. D/P (B) M26. Lumped D/P (C) M16. IC/CD/CP

ρ μD I μ μ μP D P μ CD λCD ρ μID μP λD qIC ρ0 λP λD D P λ ρC P ID CD CP qIC ID CD CP λP λID

10.0

15 15

7.5

10 10 λD -μ D λ -μ λID -μ ID D D 5.0 λP -μ P λP -μ P λCD -μ CD

λCP -μ CP 5 5 Posterior Density Posterior Density Posterior Density Posterior 2.5

0 0 0.0 -0.2 0.0 0.2 0.4 -0.2 0.0 0.2 -0.3 0.0 0.3 0.6 Rate Rate Rate (D) M3. D/P+A/B (E) M27. Lumped D/P+A/B (F) M18. ID/CD/CP +A/B ρ λ μ I μD μ DA PA A PA μCD λ μD μ A CDA ρ A λ IDA μCP ρ0 PA A qIC qIC ρC λDA DA PA λP ID CD CP A A A A λID IDA CDA CPA A λCPA

α α α α α α α α α α α α α α α α qIC ρC ρ λID ID CD λ λ B B B CPB CPB λD D PB PB B B μ μ IDB μ CPB q ρ CDB λCD μPB IC 0 B μ IDB CDB CPB DB ρI λD B λPB

μP 15 B μDB 6

10 4 10

λIDA -μ IDA λ -μ λD -μ D DA DA A A λIDB -μ IDB 5 λ -μ λD -μ D 2 DB DB B B λCDA -μ CDA Posterior Density Posterior 5 Density Posterior Density Posterior λ -μ λP -μ P PA PA A A λCDB -μ CDB λ -μ λP -μ P PB PB B B λCPA -μ CPA λ -μ 0 0 0 CPB CPB -0.5 0.0 0.5 1.0 1.5 -0.5 0.0 0.5 1.0 1.5 -1 0 1 2 Rate Rate Rate

Figure S3: Lumped ploidy models to assess the effect of adding breeding system to create a three-state model. Moderate evidence exists that adding a breeding system is necessary Table 3

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Equivalent Comparable

(A) M11. I/C (B) M2. Lumped I/C (C) M16. ID/CD/CP μI μC ρI μC μI μ λ CD λCD λI I C C μID μP λC qIC ρC λI q0 ρC qIC ID CD CP λP ID CD CP λID

10.0 ρI

10 10 7.5

λI -μ I λI -μ I 5.0 λID -μ ID λ -μ λ -μ C C C C λ -μ 5 5 CD CD λCP -μ CP Posterior Density Posterior Density Posterior Density Posterior 2.5

0 0 0.0 0.0 0.2 0.4 0.6 0.8 0.00 0.25 0.50 -0.3 0.0 0.3 0.6 Rate Rate Rate

(D) M13. I/C+A/B (E) M29. Lumped I/C+A/B (F) M18. ID/CD/CP + A/B μCA μIA λ μI μC λ CA ρ A A IA q0 ρC I IDA CDA CPA μCD λ I C λC A CDA λIA A q A A μID IC A μCPA qIC ρC λID IDA CDA CPA α α α α A λCPA α α α α α α α α α α α α λI B λC IB CB B qIC μI μ q ρ B CB q0 ρ λ IC C C IDB IDB CDB CP λCP IDB CDB CPB B B λIB λC μID μCP B B μCD B B λCDB μIB μCB 8 6

9 6 λ -μ 4 IDA IDA λ -μ IA IA λI -μ I λID -μ ID 6 A A B B 4 λI -μ I λ -μ B B λIB -μ IB CDA CDA λC -μ C λ -μ A A CA CA λCDB -μ CDB 2 λC -μ C Posterior Density Posterior B B Density Posterior λC -μ C Density Posterior λCP -μ CP 2 3 B B A A λCPB -μ CPB

0 0 0 -0.5 0.0 0.5 1.0 -0.5 0.0 0.5 1.0 -1 0 1 2 Rate Rate Rate

Figure S4: Lumped breeding system models to assess the effect of adding ploidy to create a three-state model. Moderate to insigniﬁcant evidence exists that adding ploidy is necessary Table 3

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Preferred Models

M3. D/P + A/B M4. D/P+A/B asym M5. D/P + A/B all asymm μD μ μ μD μ A PA DA μP A PA ρ A A ρ ρ λD DA P λP λ λD A A A DA DA PA λP A DA PA λPA A α β α α α α α β α β α β

ρ ρB ρ λ P λP λ DB DB B B λD D P λP λDB DB PB PB B B B B μP μ μP μ B PB B DB μD μDB B 4 15 4 λDA -μ DA 3 3 λDB -μ DB 10 λ -μ 2 2 PA PA λ -μ 5 PB PB 1 1 Posterior Density Posterior Density Posterior Density Posterior 0 0 0 -0.5 0.0 0.5 1.0 1.5 -2 -1 0 1 -2 -1 0 1 2 Rate Rate Rate

M13. I/C+A/B M14. I/C+A/B asym M15. I/C+ A/B asym μ μ μI μC μ IA CA A A IA μCA I C λ λ IA CA λC λI A q A CA IA A A λ IA CA λC A IC q IC IA qIC A α β α β α β α β α α α α

λ λI IB λ λ B λC I CB CB IB λ IB CB B B I CB CB qIC B B μ q IC qIC μI IB μC B μCB B μI B μCB 8 4

6 4 3 λIA -μ IA 4 2 λIB -μ IB 2 λC -μ C 2 1 A A

Posterior Density Posterior Density Posterior Density Posterior λCB -μ CB 0 0 0 -0.5 0.0 0.5 1.0 -2 -1 0 1 -1 0 1 2 Rate Rate Rate M18. IC/CD/CP+ A/B M19. IC/CD/CP+A/B asym M20. IC/CD/CP+ A/B all asym A ρI ρI ρ I

μCD μCD λCD μCD λ A λCDA A A A CDA μID μ μIDA μCP μID μ A CPA A A A A CPA q ρC qIC ρC q ρ IC ID CD CP IC C λID IDA CDA CPA λID A A A λCP λID IDA CDA CPA λ A λCPA A A A CPA

α α α α α α α β α β α β α β α β α β

q qIC ρ B B IC ρC λ C q IC ρ C λID CD IDB ID CDB λCP λID CD λ B IDB B CPB λCPB B CPB B B IDB B CPB CPB μ μ μCP μ μID CPB IDB μ B μIDB CPB B μCD CDB λCD μCDB λ B λCDB B CDB ρI ρI B ρ I

6 5 λIDA -μ IDA 7.5 4 λIDB -μ IDB 4 3 λCDA -μ CDA 5.0 λ -μ 2 CDB CDB 2 2.5 λCPA -μ CPA 1

Posterior Density Posterior Density Posterior λCPB -μ CPB 0.0 0 0 -0.5 0.0 0.5 1.0 -1 0 1 2 -1 0 1 2 Rate Rate Rate

Figure S5: Effect of asymmetric rates in hidden models. Models with asymmetric rates are preferred over models with equal rates Table S6

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aCC-BY-NC-ND 4.0 International license.

Nolana rupicola Nolana

Nolana acuminata Nolana Nolana elegans

Nolana rostrata Nolana Sclerophylax arnottii

Nolana adansonii Nolana Physochlaina orientalis

Nolana galapagensis Nolana Physochlaina praealta

Nolana plicata Nolana Przewalskia tangutica

Nolana laxa Nolana Scopolia parviflora

Nolana aticoana Nolana Scopolia carniolica

Nolana humifusa Nolana Scopolia japonica

Lycium depressum Lycium Atropanthe sinensis

Lycium ruthenicum Lycium Hyoscyamus niger

Lycium tetrandrum Lycium Hyoscyamus albus

Lycium acutifolium Lycium Hyoscyamus pusillus

Lycium bosciifolium Lycium Hyoscyamus turcomanicus

Lycium hirsutum Lycium Hyoscyamus desertorum

Lycium villosum Lycium Hyoscyamus muticus

Lycium eenii Lycium Anisodus acutangulus

Lycium schweinfurthii Lycium Anisodus carniolicoides

Lycium shawii Lycium Anisodus tanguticus

Lycium decumbens Lycium Atropa komarovii

Lycium pumilum Lycium Atropa belladonna

Lycium oxycarpum Lycium Jaborosa sativa

Lycium pilifolium Lycium Jaborosa integrifolia

Lycium gariepense Lycium Latua pubiflora

Lycium tenue Lycium Nicotiana velutina

Lycium strandveldense Lycium Nicotiana rosulata

Lycium amoenum Lycium Nicotiana rotundifolia

Lycium grandicalyx Lycium Nicotiana gossei

Lycium arenicola Lycium Nicotiana goodspeedii

Lycium cinereum Lycium Nicotiana cavicola

Lycium afrum Lycium Nicotiana suaveolens

Lycium ferocissimum Lycium Nicotiana eastii

Lycium horridum Lycium Nicotiana amplexicaulis

Lycium schizocalyx Lycium Nicotiana maritima

Lycium boerhaviifolium Lycium Nicotiana excelsior

Lycium pallidum Lycium Nicotiana simulans

Lycium cooperi Lycium Nicotiana megalosiphon

Lycium macrodon Lycium Nicotiana umbratica

Lycium puberulum Lycium Nicotiana occidentalis

Lycium californicum Lycium Nicotiana forsteri

Lycium nodosum Lycium Nicotiana petunioides

Lycium vimineum Lycium Nicotiana noctiflora

Lycium gilliesianum Lycium Nicotiana glauca

Lycium ameghinoi Lycium Nicotiana acaulis

Lycium chanar Lycium Nicotiana africana

Lycium fuscum Lycium Nicotiana plumbaginifolia

Lycium minutifolium Lycium Nicotiana longiflora

Lycium stenophyllum Lycium Nicotiana forgetiana

Lycium cestroides Lycium Nicotiana bonariensis

Lycium cuneatum Lycium Nicotiana langsdorffii

Lycium morongii Lycium Nicotiana alata

Lycium brevipes Lycium Nicotiana stocktonii

Lycium carolinianum Lycium Nicotiana nesophila

Lycium rachidocladum Lycium Nicotiana repanda

Lycium tenuispinosum Lycium Nicotiana nudicaulis

Lycium elongatum Lycium Nicotiana sylvestris

Lycium americanum Lycium Nicotiana pauciflora

Lycium infaustum Lycium Nicotiana acuminata

Lycium minimum Lycium Nicotiana corymbosa

Lycium parishii Lycium Nicotiana miersii

Lycium torreyi Lycium Nicotiana spegazzinii

Lycium andersonii Lycium Nicotiana linearis

Lycium berlandieri Lycium Nicotiana obtusifolia

Lycium exsertum Lycium Nicotiana quadrivalvis

Lycium fremontii Lycium Nicotiana clevelandii

Exodeconus miersii Exodeconus Nicotiana rustica

Solandra grandiflora Solandra Nicotiana knightiana

Dyssochroma viridiflora Dyssochroma Nicotiana paniculata

Mandragora caulescens Mandragora Nicotiana solanifolia

Nicandra physalodes Nicandra Nicotiana cordifolia

Brugmansia sanguinea Brugmansia Nicotiana raimondii

Brugmansia arborea Brugmansia Nicotiana benavidesii

Brugmansia aurea Brugmansia Nicotiana undulata

Datura discolor Datura Nicotiana arentsii

Datura metel Datura Nicotiana glutinosa

Datura inoxia Datura Nicotiana wigandioides

Datura leichhardtii Datura Nicotiana thyrsiflora

Datura ferox Datura Nicotiana tomentosiformis

M1. D/P quercifolia Datura Nicotiana tomentosa

Datura stramonium Datura Nicotiana kawakamii

Datura ceratocaula Datura Nicotiana otophora

Salpichroa origanifolia Salpichroa Nicotiana tabacum

Lycianthes shanesii Lycianthes Duboisia myoporoides

Lycianthes biflora Lycianthes Cyphanthera albicans

Lycianthes multiflora Lycianthes Duboisia hopwoodii

Lycianthes jalicensis Lycianthes Duboisia leichhardtii

Lycianthes heteroclita Lycianthes Cyphanthera anthocercidea

Lycianthes lycioides Lycianthes Crenidium spinescens

Lycianthes rantonnetii Lycianthes Cyphanthera microphylla

Lycianthes asarifolia Lycianthes Anthotroche myoporoides

Lycianthes acapulcensis Lycianthes Anthotroche pannosa Lycianthes ciliolata Lycianthes Anthotroche walcottii

μ moziniana Lycianthes Grammosolen truncatus

D μ rzedowskii Lycianthes Grammosolen dixonii

P dejecta Lycianthes Cyphanthera odgersii

Lycianthes peduncularis Lycianthes Anthocercis viscosa

Capsicum geminifolium Capsicum Anthocercis angustifolia

Capsicum lanceolatum Capsicum Anthocercis intricata

Capsicum ciliatum Capsicum Anthocercis littorea

Capsicum rhomboideum Capsicum Anthocercis ilicifolia

Capsicum campylopodium Capsicum Anthocercis gracilis

Capsicum villosum Capsicum Symonanthus bancroftii Capsicum schottianum Capsicum Symonanthus aromaticus

ρ recurvatum Capsicum Nierembergia pulchella

Capsicum flexuosum Capsicum Nierembergia browallioides

Capsicum cardenasii Capsicum Nierembergia tucumanensis

Capsicum eximium Capsicum Nierembergia ericoides

Capsicum pubescens Capsicum Nierembergia scoparia Capsicum tovarii Capsicum Nierembergia linariifolia

λ D P chacoense Capsicum Nierembergia calycina D baccatum Capsicum

λ Nierembergia veitchii

P coccineum Capsicum Nierembergia aristata

Capsicum annuum Capsicum Nierembergia graveolens

Capsicum chinense Capsicum Nierembergia repens

Capsicum frutescens Capsicum Nierembergia rivularis

Capsicum galapagoensis Capsicum Bouchetia erecta

Cuatresia cuneata Cuatresia Bouchetia anomala

Cuatresia exiguiflora Cuatresia Hunzikeria texana

Cuatresia riparia Cuatresia Brunfelsia americana

Deprea paneroi Deprea Petunia saxicola

Nothocestrum longifolium Nothocestrum Petunia reitzii

Withania coagulans Withania Petunia altiplana

Withania somnifera Withania Petunia secreta

Iochroma gesnerioides Iochroma Petunia scheideana

Iochroma fuchsioides Iochroma Petunia bonjardinensis

Iochroma lehmannii Iochroma Petunia mantiqueirensis

Acnistus arborescens Acnistus Petunia integrifolia

Iochroma cyaneum Iochroma Petunia exserta

Dunalia solanacea Dunalia Petunia axillaris

Dunalia obovata Dunalia Calibrachoa pygmea

Vassobia breviflora Vassobia Calibrachoa parviflora

Dunalia brachyacantha Dunalia Calibrachoa sellowiana

Eriolarynx lorentzii Eriolarynx Fabiana imbricata

Iochroma australe Iochroma Schizanthus lacteus

Leucophysalis grandiflora Leucophysalis Schizanthus integrifolius

Leucophysalis nana Leucophysalis Schizanthus candidus

Schraderanthus viscosa Schraderanthus Schizanthus alpestris

Brachistus stramoniifolius Brachistus Schizanthus hookeri

Witheringia macrantha Witheringia Schizanthus grahamii

Witheringia meiantha Witheringia Schizanthus tricolor

Physalis alkekengi Physalis Schizanthus parvulus

Posterior Probability carpenteri Calliphysalis Schizanthus pinnatus

Quincula lobata Quincula Schizanthus porrigens

Physalis melanocystis Physalis Schizanthus litoralis

Physalis acutifolia Physalis Schizanthus laetus

Physalis crassifolia Physalis Goetzea elegans

Physalis philadelphica Physalis Espadaea amoena

Physalis longifolia Physalis Metternichia princeps

Physalis glutinosa Physalis Schwenckia lateriflora

Physalis sordida Physalis Cestrum fasciculatum

Physalis nicandroides Physalis Cestrum elegans

0.6 patula Physalis

Cestrum aurantiacum

Physalis peruviana Physalis Cestrum nocturnum

Physalis angustiphysa Physalis Cestrum tomentosum

Physalis cordata Physalis Cestrum diurnum

Physalis ignota Physalis Cestrum strigilatum

hslsminima Physalis Cestrum megalophyllum

Physalis pruinosa Physalis Sessea corymbiflora

Physalis lagascae Physalis Streptosolen jamesonii

Physalis angulata Physalis Browallia speciosa

0.7 pubescens Physalis Salpiglossis sinuata

Physalis lanceolata Physalis Combera paradoxa

Physalis heterophylla Physalis Pantacantha ameghinoi

Physalis virginiana Physalis Solanum ferocissimum

Physalis arenicola Physalis Solanum chenopodinum

Physalis walteri Physalis Solanum stelligerum

Physalis pumila Physalis Solanum nemophilum

Physalis cinerascens Physalis Solanum densevestitum Physalis mollis Physalis Solanum furfuraceum

0.8 viscosa Physalis Solanum stupefactum

Jaltomata darcyana Jaltomata Solanum corifolium

Jaltomata repandidentata Jaltomata Solanum cookii

Jaltomata bohsiana Jaltomata Solanum sandwicense

Jaltomata procumbens Jaltomata Solanum incompletum

Jaltomata chihuahuensis Jaltomata Solanum semiarmatum

Jaltomata grandiflora Jaltomata Solanum viridifolium

Jaltomata antillana Jaltomata Solanum dimorphispinum

Jaltomata auriculata Jaltomata Solanum inaequilaterum

Jaltomata oppositifolia Jaltomata Solanum quadriloculatum

0.9 salpoensis Jaltomata Solanum ellipticum

Jaltomata aspera Jaltomata Solanum dianthophorum

Jaltomata lojae Jaltomata Solanum esuriale

Jaltomata lanata Jaltomata Solanum centrale

Jaltomata paneroi Jaltomata Solanum cinereum

Jaltomata bernardelloana Jaltomata Solanum sturtianum

Jaltomata sagastegui Jaltomata Solanum petrophilum

Jaltomata herrerae Jaltomata Solanum pungetium

Jaltomata yacheri Jaltomata Solanum prinophyllum

Jaltomata weberbaueri Jaltomata Solanum campanulatum

1.0 ventricosa Jaltomata

Solanum vicinum

Jaltomata sanchez-vegae Jaltomata Solanum ditrichum

Jaltomata andersonii Jaltomata Solanum elachophyllum

Jaltomata lezamae Jaltomata Solanum tetrathecum

Jaltomata sinuosa Jaltomata Solanum orbiculatum

Jaltomata viridiflora Jaltomata Solanum nummularium

Jaltomata yungayensis Jaltomata Solanum oligacanthum

Jaltomata contumacensis Jaltomata Solanum hystrix

Jaltomata leivae Jaltomata Solanum hoplopetalum

Jaltomata biflora Jaltomata Solanum sejunctum

Jaltomata dentata Jaltomata Solanum asymmetriphyllum

Jaltomata bicolor Jaltomata Solanum diversiflorum

Jaltomata umbellata Jaltomata Solanum chippendalei

Jaltomata cajacayensis Jaltomata Solanum phlomoides

Jaltomata lomana Jaltomata Solanum beaugleholei

Jaltomata mionei Jaltomata Solanum melanospermum

Solanum valdiviense Solanum Solanum clarkiae

Solanum guineense Solanum Solanum oedipus

Solanum terminale Solanum Solanum vansittartense

Solanum herculeum Solanum Solanum tudununggae

Solanum trisectum Solanum Solanum petraeum

Solanum capsiciforme Solanum Solanum cataphractum

Solanum simile Solanum Solanum leopoldensis

Solanum symonii Solanum Solanum carduiforme

Solanum vescum Solanum Solanum dioicum

Solanum linearifolium Solanum Solanum cunninghamii

Solanum laciniatum Solanum Solanum lucani

Solanum aviculare Solanum Solanum echinatum

Solanum multivenosum Solanum Solanum horridum

Solanum aligerum Solanum Solanum cleistogamum

Solanum laxum Solanum Solanum lasiophyllum

Solanum amygdalifolium Solanum Solanum gabrielae

Solanum crispum Solanum Solanum coactiliferum

Solanum dulcamara Solanum Solanum oldfieldii

Solanum lyratum Solanum Solanum pyracanthos

Solanum wallacei Solanum Solanum tomentosum

Solanum palitans Solanum Solanum capense

Solanum tripartitum Solanum Solanum humile

Solanum triflorum Solanum Solanum vespertilio

Solanum physalifolium Solanum Solanum lidii

Solanum pallidum Solanum Solanum anguivi

Solanum fiebrigii Solanum Solanum aethiopicum

Solanum villosum Solanum Solanum cyaneopurpureum

Solanum scabrum Solanum Solanum macrocarpon

Solanum opacum Solanum Solanum dasyphyllum

Solanum ptychanthum Solanum Solanum incanum

Solanum americanum Solanum Solanum linnaeanum

Solanum nigrum Solanum Solanum melongena

Solanum taeniotrichum Solanum Solanum insanum

Solanum caripense Solanum Solanum supinum

Solanum fraxinifolium Solanum Solanum violaceum

Solanum appendiculatum Solanum Solanum giganteum

Solanum brevifolium Solanum Solanum marginatum

Solanum etuberosum Solanum Solanum coagulans

Solanum palustre Solanum Solanum aculeastrum

Solanum lycopersicoides Solanum Solanum houstonii

Solanum sitiens Solanum Solanum hindsianum

Solanum juglandifolium Solanum Solanum elaeagnifolium

Solanum ochranthum Solanum Solanum torvum

Solanum habrochaites Solanum Solanum chrysotrichum

Solanum neorickii Solanum Solanum asperolanatum

Solanum chilense Solanum Solanum bonariense

Solanum peruvianum Solanum Solanum paniculatum

Solanum chmielewskii Solanum Solanum donianum

Solanum pennellii Solanum Solanum crotonoides

Solanum galapagense Solanum Solanum lanceifolium

Solanum lycopersicum Solanum Solanum jamaicense

Solanum cheesmaniae Solanum Solanum aridum

Solanum pimpinellifolium Solanum Solanum carolinense

Solanum chomatophilum Solanum Solanum ensifolium

Solanum scabrifolium Solanum Solanum davisense

Solanum pinnatisectum Solanum Solanum citrullifolium

Solanum piurae Solanum Solanum heterodoxum

Solanum bulbocastanum Solanum Solanum tribulosum

Solanum jamesii Solanum Solanum rostratum

Solanum clarum Solanum Solanum fructu-tecto

Solanum morelliforme Solanum Solanum angustifolium

Solanum polyadenium Solanum Solanum lumholtzianum

Solanum cardiophyllum Solanum Solanum grayi

Solanum ehrenbergii Solanum Solanum johnstonii

Solanum andreanum Solanum Solanum tenuipes

Solanum schenckii Solanum Solanum wrightii

Solanum doddsii Solanum Solanum crinitum

Solanum stenophyllidium Solanum Solanum mitlense

Solanum iopetalum Solanum Solanum lycocarpum

Solanum violaceimarmoratum Solanum Solanum sisymbriifolium

Solanum albicans Solanum Solanum vestissimum

Solanum acaule Solanum Solanum pseudolulo

Solanum boliviense Solanum Solanum hyporhodium

Solanum raphanifolium Solanum Solanum pectinatum

Solanum lignicaule Solanum Solanum hirtum

Solanum laxissimum Solanum Solanum stramoniifolium

Solanum maglia Solanum Solanum repandum

Solanum longiconicum Solanum Solanum lasiocarpum

Solanum oxycarpum Solanum Solanum candidum

Solanum agrimoniifolium Solanum Solanum felinum

Solanum colombianum Solanum Solanum quitoense

Solanum stipuloideum Solanum Solanum sessiliflorum

Solanum vernei Solanum Solanum viarum

Solanum candolleanum Solanum Solanum aculeatissimum

Solanum microdontum Solanum Solanum myriacanthum

Solanum demissum Solanum Solanum incarceratum

Solanum kurtzianum Solanum Solanum tenuispinum

Solanum chacoense Solanum Solanum atropurpureum

Solanum berthaultii Solanum Solanum acerifolium

Solanum infundibuliforme Solanum Solanum capsicoides

Solanum okadae Solanum Solanum platense

Solanum stoloniferum Solanum Solanum mammosum

Solanum hjertingii Solanum Solanum palinacanthum

Solanum verrucosum Solanum Solanum stagnale

Solanum guerreroense Solanum Solanum robustum

Solanum hougasii Solanum Solanum paludosum

Solanum latiflorum Solanum Solanum microphyllum

Solanum cacosmum Solanum Solanum gardneri

Solanum exiguum Solanum Solanum hoehnei

Solanum diploconos Solanum Solanum wendlandii

Solanum pinetorum Solanum Solanum allophyllum

Solanum sciadostylis Solanum Solanum diphyllum

Solanum cylindricum Solanum Solanum aphyodendron

Solanum glaucophyllum Solanum Solanum arboreum

Solanum fusiforme Solanum Solanum rovirosanum

Solanum melissarum Solanum Solanum pseudocapsicum

Solanum confusum Solanum Solanum argentinum

Solanum hibernum Solanum Solanum reductum

Solanum luteoalbum Solanum Solanum mauritianum

oau stuckertii Solanum Solanum asperum

oau oxyphyllum Solanum Solanum rugosum

Solanum pendulum Solanum Solanum cordovense

Solanum tobagense Solanum Solanum abutiloides

Solanum obliquum Solanum Solanum turneroides

Solanum roseum Solanum Solanum adscendens

Solanum maternum Solanum Solanum tenuisetosum

Solanum betaceum Solanum Solanum circinatum

Solanum unilobum Solanum Solanum tegore

Solanum cajanumense Solanum Solanum proteanthum

Solanum fallax Solanum Solanum sibundoyense Solanum endopogon Solanum Solanum occultum

Figure S6: Ancestral state estimation using the maximum a posteriori for each node of theM1. D/P ploidy model

36 bioRxiv preprint doi: https://doi.org/10.1101/709329; this version posted July 22, 2019. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-NC-ND 4.0 International license.

Speciation Extinction

3 3

Type 2 Type 2 Diploid Diploid Polyploid Polyploid 1 1 Posterior Density Posterior Density Posterior 0 0 1.0 1.5 2.0 2.5 0.5 1.0 1.5 2.0 2.5 Rate Rate Net Diversification Relative Extinction 15 15

Type 10 Type 10 Diploid Diploid

5 Polyploid 5 Polyploid Posterior Density Posterior Density Posterior 0 0 -0.2 0.0 0.2 0.4 0.7 0.8 0.9 1.0 1.1 Rate Rate Trait change

30 Type

20 Polyploidization

10 Posterior Density Posterior 0 0.025 0.050 0.075 0.100 Rate

Figure S7: Posterior distribution for each of the parameters in the M1. D/P model

37 bioRxiv preprint doi: https://doi.org/10.1101/709329; this version posted July 22, 2019. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-NC-ND 4.0 International license.

M4. D/P + A/B asym

Nolana rupicola Nolana

Nolana acuminata Nolana Nolana elegans

Nolana rostrata Nolana Sclerophylax arnottii

Nolana adansonii Nolana Physochlaina orientalis

Nolana galapagensis Nolana Physochlaina praealta

Nolana plicata Nolana Przewalskia tangutica

Nolana laxa Nolana Scopolia parviflora

Nolana aticoana Nolana Scopolia carniolica

Nolana humifusa Nolana Scopolia japonica

Lycium depressum Lycium Atropanthe sinensis

Lycium ruthenicum Lycium Hyoscyamus niger

Lycium tetrandrum Lycium Hyoscyamus albus

Lycium acutifolium Lycium Hyoscyamus pusillus

Lycium bosciifolium Lycium Hyoscyamus turcomanicus

Lycium hirsutum Lycium Hyoscyamus desertorum

Lycium villosum Lycium Hyoscyamus muticus

Lycium eenii Lycium Anisodus acutangulus

Lycium schweinfurthii Lycium Anisodus carniolicoides

Lycium shawii Lycium Anisodus tanguticus

Lycium decumbens Lycium Atropa komarovii

Lycium pumilum Lycium Atropa belladonna

Lycium oxycarpum Lycium Jaborosa sativa

Lycium pilifolium Lycium Jaborosa integrifolia

Lycium gariepense Lycium Latua pubiflora

Lycium tenue Lycium Nicotiana velutina

Lycium strandveldense Lycium Nicotiana rosulata

Lycium amoenum Lycium Nicotiana rotundifolia

Lycium grandicalyx Lycium Nicotiana gossei

Lycium arenicola Lycium Nicotiana goodspeedii

Lycium cinereum Lycium Nicotiana cavicola

Lycium afrum Lycium Nicotiana suaveolens

Lycium ferocissimum Lycium Nicotiana eastii

Lycium horridum Lycium Nicotiana amplexicaulis

Lycium schizocalyx Lycium Nicotiana maritima

Lycium boerhaviifolium Lycium Nicotiana excelsior

Lycium pallidum Lycium Nicotiana simulans

Lycium cooperi Lycium Nicotiana megalosiphon

Lycium macrodon Lycium Nicotiana umbratica

Lycium puberulum Lycium Nicotiana occidentalis

Lycium californicum Lycium Nicotiana forsteri

Lycium nodosum Lycium Nicotiana petunioides

Lycium vimineum Lycium Nicotiana noctiflora

Lycium gilliesianum Lycium Nicotiana glauca μ ameghinoi Lycium Nicotiana acaulis

D chanar Lycium Nicotiana africana

Lycium fuscum Lycium Nicotiana plumbaginifolia μ minutifolium Lycium

Nicotiana longiflora

A P stenophyllum Lycium Nicotiana forgetiana Lycium cestroides Lycium Nicotiana bonariensis

A cuneatum Lycium Nicotiana langsdorffii

Lycium morongii Lycium Nicotiana alata

Lycium brevipes Lycium Nicotiana stocktonii

Lycium carolinianum Lycium Nicotiana nesophila

Lycium rachidocladum Lycium Nicotiana repanda

Lycium tenuispinosum Lycium Nicotiana nudicaulis

Lycium elongatum Lycium Nicotiana sylvestris

Lycium americanum Lycium Nicotiana pauciflora

Lycium infaustum Lycium Nicotiana acuminata

ρ minimum Lycium Nicotiana corymbosa

Lycium parishii Lycium Nicotiana miersii

Lycium torreyi Lycium Nicotiana spegazzinii

Lycium andersonii Lycium Nicotiana linearis

Lycium berlandieri Lycium Nicotiana obtusifolia Lycium exsertum Lycium Nicotiana quadrivalvis

λ fremontii Lycium Nicotiana clevelandii

D miersii Exodeconus Nicotiana rustica D P λ grandiflora Solandra Nicotiana knightiana

A A A P viridiflora Dyssochroma Nicotiana paniculata

Mandragora caulescens Mandragora Nicotiana solanifolia

A physalodes Nicandra

Nicotiana cordifolia

Brugmansia sanguinea Brugmansia Nicotiana raimondii

Brugmansia arborea Brugmansia Nicotiana benavidesii

Brugmansia aurea Brugmansia Nicotiana undulata

Datura discolor Datura Nicotiana arentsii

Datura metel Datura Nicotiana glutinosa

Datura inoxia Datura Nicotiana wigandioides

Datura leichhardtii Datura Nicotiana thyrsiflora

Datura ferox Datura Nicotiana tomentosiformis

Datura quercifolia Datura Nicotiana tomentosa

Datura stramonium Datura Nicotiana kawakamii

Datura ceratocaula Datura Nicotiana otophora

Salpichroa origanifolia Salpichroa Nicotiana tabacum

Lycianthes shanesii Lycianthes Duboisia myoporoides

Lycianthes biflora Lycianthes Cyphanthera albicans

Lycianthes multiflora Lycianthes Duboisia hopwoodii

Lycianthes jalicensis Lycianthes Duboisia leichhardtii

Lycianthes heteroclita Lycianthes Cyphanthera anthocercidea

Lycianthes lycioides Lycianthes Crenidium spinescens

α β α β rantonnetii Lycianthes Cyphanthera microphylla

Lycianthes asarifolia Lycianthes Anthotroche myoporoides

Lycianthes acapulcensis Lycianthes Anthotroche pannosa

Lycianthes ciliolata Lycianthes Anthotroche walcottii

Lycianthes moziniana Lycianthes Grammosolen truncatus

Lycianthes rzedowskii Lycianthes Grammosolen dixonii

Lycianthes dejecta Lycianthes Cyphanthera odgersii

Lycianthes peduncularis Lycianthes Anthocercis viscosa

Capsicum geminifolium Capsicum Anthocercis angustifolia

Capsicum lanceolatum Capsicum Anthocercis intricata

Capsicum ciliatum Capsicum Anthocercis littorea

Capsicum rhomboideum Capsicum Anthocercis ilicifolia

Capsicum campylopodium Capsicum Anthocercis gracilis

Capsicum villosum Capsicum Symonanthus bancroftii

Capsicum schottianum Capsicum Symonanthus aromaticus

Capsicum recurvatum Capsicum Nierembergia pulchella

Capsicum flexuosum Capsicum Nierembergia browallioides

ρ cardenasii Capsicum Nierembergia tucumanensis

Capsicum eximium Capsicum Nierembergia ericoides Capsicum pubescens Capsicum Nierembergia scoparia

λ tovarii Capsicum Nierembergia linariifolia

λ P chacoense Capsicum Nierembergia calycina P baccatum Capsicum

D D B B Nierembergia veitchii

B B coccineum Capsicum Nierembergia aristata

Capsicum annuum Capsicum Nierembergia graveolens

Capsicum chinense Capsicum Nierembergia repens

Capsicum frutescens Capsicum Nierembergia rivularis

Capsicum galapagoensis Capsicum Bouchetia erecta

Cuatresia cuneata Cuatresia Bouchetia anomala Cuatresia exiguiflora Cuatresia Hunzikeria texana

μ riparia Cuatresia Brunfelsia americana

P paneroi Deprea Petunia saxicola

B longifolium Nothocestrum Petunia reitzii Withania coagulans Withania Petunia altiplana

μ somnifera Withania Petunia secreta D gesnerioides Iochroma Petunia scheideana

B fuchsioides Iochroma Petunia bonjardinensis

Iochroma lehmannii Iochroma Petunia mantiqueirensis

Acnistus arborescens Acnistus Petunia integrifolia

Iochroma cyaneum Iochroma Petunia exserta

Dunalia solanacea Dunalia Petunia axillaris

Dunalia obovata Dunalia Calibrachoa pygmea

Vassobia breviflora Vassobia Calibrachoa parviflora

Dunalia brachyacantha Dunalia Calibrachoa sellowiana

Eriolarynx lorentzii Eriolarynx Fabiana imbricata

Iochroma australe Iochroma Schizanthus lacteus

Leucophysalis grandiflora Leucophysalis Schizanthus integrifolius

Leucophysalis nana Leucophysalis Schizanthus candidus

Posterior Probability viscosa Schraderanthus Schizanthus alpestris

Brachistus stramoniifolius Brachistus Schizanthus hookeri

Witheringia macrantha Witheringia Schizanthus grahamii

Witheringia meiantha Witheringia Schizanthus tricolor

Physalis alkekengi Physalis Schizanthus parvulus

Calliphysalis carpenteri Calliphysalis Schizanthus pinnatus

Quincula lobata Quincula Schizanthus porrigens

Physalis melanocystis Physalis Schizanthus litoralis

Physalis acutifolia Physalis Schizanthus laetus

Physalis crassifolia Physalis Goetzea elegans

0.5 philadelphica Physalis Espadaea amoena

Physalis longifolia Physalis Metternichia princeps

Physalis glutinosa Physalis Schwenckia lateriflora

Physalis sordida Physalis Cestrum fasciculatum

Physalis nicandroides Physalis Cestrum elegans

Physalis patula Physalis Cestrum aurantiacum

Physalis peruviana Physalis Cestrum nocturnum

Physalis angustiphysa Physalis Cestrum tomentosum Physalis cordata Physalis Cestrum diurnum

0.6 ignota Physalis Cestrum strigilatum

Physalis minima Physalis Cestrum megalophyllum

Physalis pruinosa Physalis Sessea corymbiflora

Physalis lagascae Physalis Streptosolen jamesonii

Physalis angulata Physalis Browallia speciosa

Physalis pubescens Physalis Salpiglossis sinuata

Physalis lanceolata Physalis Combera paradoxa

Physalis heterophylla Physalis Pantacantha ameghinoi

Physalis virginiana Physalis Solanum ferocissimum

Physalis arenicola Physalis Solanum chenopodinum

0.7 walteri Physalis Solanum stelligerum

Physalis pumila Physalis Solanum nemophilum

Physalis cinerascens Physalis Solanum densevestitum

Physalis mollis Physalis Solanum furfuraceum

Physalis viscosa Physalis Solanum stupefactum

Jaltomata darcyana Jaltomata Solanum corifolium

Jaltomata repandidentata Jaltomata Solanum cookii

Jaltomata bohsiana Jaltomata Solanum sandwicense

atmt procumbens Jaltomata Solanum incompletum

0.8 chihuahuensis Jaltomata Solanum semiarmatum

Jaltomata grandiflora Jaltomata Solanum viridifolium

Jaltomata antillana Jaltomata Solanum dimorphispinum

Jaltomata auriculata Jaltomata Solanum inaequilaterum

Jaltomata oppositifolia Jaltomata Solanum quadriloculatum

Jaltomata salpoensis Jaltomata Solanum ellipticum

Jaltomata aspera Jaltomata Solanum dianthophorum

Jaltomata lojae Jaltomata Solanum esuriale

Jaltomata lanata Jaltomata Solanum centrale

Jaltomata paneroi Jaltomata Solanum cinereum

0.9 bernardelloana Jaltomata Solanum sturtianum

Jaltomata sagastegui Jaltomata Solanum petrophilum

Jaltomata herrerae Jaltomata Solanum pungetium

Jaltomata yacheri Jaltomata Solanum prinophyllum

Jaltomata weberbaueri Jaltomata Solanum campanulatum

Jaltomata ventricosa Jaltomata Solanum vicinum

Jaltomata sanchez-vegae Jaltomata Solanum ditrichum

Jaltomata andersonii Jaltomata Solanum elachophyllum Jaltomata lezamae Jaltomata Solanum tetrathecum

1.0 sinuosa Jaltomata Solanum orbiculatum

Jaltomata viridiflora Jaltomata Solanum nummularium

Jaltomata yungayensis Jaltomata Solanum oligacanthum

Jaltomata contumacensis Jaltomata Solanum hystrix

Jaltomata leivae Jaltomata Solanum hoplopetalum

Jaltomata biflora Jaltomata Solanum sejunctum

Jaltomata dentata Jaltomata Solanum asymmetriphyllum

Jaltomata bicolor Jaltomata Solanum diversiflorum

Jaltomata umbellata Jaltomata Solanum chippendalei

Jaltomata cajacayensis Jaltomata Solanum phlomoides

Jaltomata lomana Jaltomata Solanum beaugleholei

Jaltomata mionei Jaltomata Solanum melanospermum

Solanum valdiviense Solanum Solanum clarkiae

Solanum guineense Solanum Solanum oedipus

Solanum terminale Solanum Solanum vansittartense

Solanum herculeum Solanum Solanum tudununggae

Solanum trisectum Solanum Solanum petraeum

Solanum capsiciforme Solanum Solanum cataphractum

Solanum simile Solanum Solanum leopoldensis

Solanum symonii Solanum Solanum carduiforme

Solanum vescum Solanum Solanum dioicum

Solanum linearifolium Solanum Solanum cunninghamii

Solanum laciniatum Solanum Solanum lucani

Solanum aviculare Solanum Solanum echinatum

Solanum multivenosum Solanum Solanum horridum

Solanum aligerum Solanum Solanum cleistogamum

Solanum laxum Solanum Solanum lasiophyllum

Solanum amygdalifolium Solanum Solanum gabrielae

Solanum crispum Solanum Solanum coactiliferum

Solanum dulcamara Solanum Solanum oldfieldii

Solanum lyratum Solanum Solanum pyracanthos

Solanum wallacei Solanum Solanum tomentosum

Solanum palitans Solanum Solanum capense

Solanum tripartitum Solanum Solanum humile

Solanum triflorum Solanum Solanum vespertilio

Solanum physalifolium Solanum Solanum lidii

Solanum pallidum Solanum Solanum anguivi

Solanum fiebrigii Solanum Solanum aethiopicum

Solanum villosum Solanum Solanum cyaneopurpureum

Solanum scabrum Solanum Solanum macrocarpon

Solanum opacum Solanum Solanum dasyphyllum

Solanum ptychanthum Solanum Solanum incanum

Solanum americanum Solanum Solanum linnaeanum

Solanum nigrum Solanum Solanum melongena

Solanum taeniotrichum Solanum Solanum insanum

Solanum caripense Solanum Solanum supinum

Solanum fraxinifolium Solanum Solanum violaceum

Solanum appendiculatum Solanum Solanum giganteum

Solanum brevifolium Solanum Solanum marginatum

Solanum etuberosum Solanum Solanum coagulans

Solanum palustre Solanum Solanum aculeastrum

Solanum lycopersicoides Solanum Solanum houstonii

Solanum sitiens Solanum Solanum hindsianum

Solanum juglandifolium Solanum Solanum elaeagnifolium

Solanum ochranthum Solanum Solanum torvum

oau habrochaites Solanum Solanum chrysotrichum

Solanum neorickii Solanum Solanum asperolanatum

Solanum chilense Solanum Solanum bonariense

Solanum peruvianum Solanum Solanum paniculatum

Solanum chmielewskii Solanum Solanum donianum

Solanum pennellii Solanum Solanum crotonoides

Solanum galapagense Solanum Solanum lanceifolium

Solanum lycopersicum Solanum Solanum jamaicense

Solanum cheesmaniae Solanum Solanum aridum

Solanum pimpinellifolium Solanum Solanum carolinense

Solanum chomatophilum Solanum Solanum ensifolium

Solanum scabrifolium Solanum Solanum davisense

Solanum pinnatisectum Solanum Solanum citrullifolium

Solanum piurae Solanum Solanum heterodoxum

Solanum bulbocastanum Solanum Solanum tribulosum

Solanum jamesii Solanum Solanum rostratum

Solanum clarum Solanum Solanum fructu-tecto

Solanum morelliforme Solanum Solanum angustifolium

Solanum polyadenium Solanum Solanum lumholtzianum

Solanum cardiophyllum Solanum Solanum grayi

Solanum ehrenbergii Solanum Solanum johnstonii

Solanum andreanum Solanum Solanum tenuipes

Solanum schenckii Solanum Solanum wrightii

Solanum doddsii Solanum Solanum crinitum

Solanum stenophyllidium Solanum Solanum mitlense

Solanum iopetalum Solanum Solanum lycocarpum

Solanum violaceimarmoratum Solanum Solanum sisymbriifolium

Solanum albicans Solanum Solanum vestissimum

Solanum acaule Solanum Solanum pseudolulo

Solanum boliviense Solanum Solanum hyporhodium

Solanum raphanifolium Solanum Solanum pectinatum

Solanum lignicaule Solanum Solanum hirtum

Solanum laxissimum Solanum Solanum stramoniifolium

Solanum maglia Solanum Solanum repandum

Solanum longiconicum Solanum Solanum lasiocarpum

Solanum oxycarpum Solanum Solanum candidum

Solanum agrimoniifolium Solanum Solanum felinum

Solanum colombianum Solanum Solanum quitoense

Solanum stipuloideum Solanum Solanum sessiliflorum

Solanum vernei Solanum Solanum viarum

Solanum candolleanum Solanum Solanum aculeatissimum

Solanum microdontum Solanum Solanum myriacanthum

Solanum demissum Solanum Solanum incarceratum

Solanum kurtzianum Solanum Solanum tenuispinum

Solanum chacoense Solanum Solanum atropurpureum

Solanum berthaultii Solanum Solanum acerifolium

Solanum infundibuliforme Solanum Solanum capsicoides

Solanum okadae Solanum Solanum platense

Solanum stoloniferum Solanum Solanum mammosum

Solanum hjertingii Solanum Solanum palinacanthum

Solanum verrucosum Solanum Solanum stagnale

Solanum guerreroense Solanum Solanum robustum

Solanum hougasii Solanum Solanum paludosum

Solanum latiflorum Solanum Solanum microphyllum

Solanum cacosmum Solanum Solanum gardneri

Solanum exiguum Solanum Solanum hoehnei

Solanum diploconos Solanum Solanum wendlandii

Solanum pinetorum Solanum Solanum allophyllum

Solanum sciadostylis Solanum Solanum diphyllum

Solanum cylindricum Solanum Solanum aphyodendron

Solanum glaucophyllum Solanum Solanum arboreum

Solanum fusiforme Solanum Solanum rovirosanum

Solanum melissarum Solanum Solanum pseudocapsicum

Solanum confusum Solanum Solanum argentinum

Solanum hibernum Solanum Solanum reductum

Solanum luteoalbum Solanum Solanum mauritianum

Solanum stuckertii Solanum Solanum asperum

Solanum oxyphyllum Solanum Solanum rugosum

Solanum pendulum Solanum Solanum cordovense

Solanum tobagense Solanum Solanum abutiloides

Solanum obliquum Solanum Solanum turneroides

Solanum roseum Solanum Solanum adscendens

Solanum maternum Solanum Solanum tenuisetosum

Solanum betaceum Solanum Solanum circinatum

Solanum unilobum Solanum Solanum tegore

Solanum cajanumense Solanum Solanum proteanthum

Solanum fallax Solanum Solanum sibundoyense Solanum endopogon Solanum Solanum occultum

Figure S8: Ancestral state estimation using the maximum a posteriori for each node of the M4. D/P+A/B asym model

38 bioRxiv preprint doi: https://doi.org/10.1101/709329; this version posted July 22, 2019. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-NC-ND 4.0 International license.

Speciation Extinction

3 2.0 Type Type 1.5 2 Diploid A Diploid A Diploid_B 1.0 Diploid_B

1 Polyploid_A Polyploid_A 0.5 Polyploid_B Polyploid_B Posterior Density Posterior Density Posterior 0 0.0 0 1 2 3 0 1 2 3 Rate Rate Net Diversification Relative Extinction

4 Type Type 2 3 Diploid A Diploid A Diploid_B Diploid_B 2 1 Polyploid_A Polyploid_A 1 Polyploid_B Polyploid_B Posterior Density Posterior Density Posterior 0 0 -2 -1 0 1 0 1 2 3 4 Rate Rate Trait change Hidden trait change

30 60 Type 20 Type 40 alpha Polyploidy beta 10 20 Posterior Density Posterior Density Posterior 0 0 0.05 0.10 0.15 0.0 0.5 1.0 1.5 Rate Rate

Figure S9: Posterior distribution for each of the parameters in the M4. D/P+A/B asym model

39 bioRxiv preprint doi: https://doi.org/10.1101/709329; this version posted July 22, 2019. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under

aCC-BY-NC-ND 4.0 International license.

Nolana rupicola Nolana

Nolana acuminata Nolana Nolana elegans

Nolana rostrata Nolana Sclerophylax arnottii

Nolana adansonii Nolana Physochlaina orientalis

Nolana galapagensis Nolana Physochlaina praealta

Nolana plicata Nolana Przewalskia tangutica

Nolana laxa Nolana Scopolia parviflora

Nolana aticoana Nolana Scopolia carniolica

Nolana humifusa Nolana Scopolia japonica

Lycium depressum Lycium Atropanthe sinensis

Lycium ruthenicum Lycium Hyoscyamus niger

Lycium tetrandrum Lycium Hyoscyamus albus

Lycium acutifolium Lycium Hyoscyamus pusillus

Lycium bosciifolium Lycium Hyoscyamus turcomanicus

Lycium hirsutum Lycium Hyoscyamus desertorum

Lycium villosum Lycium Hyoscyamus muticus

Lycium eenii Lycium Anisodus acutangulus

Lycium schweinfurthii Lycium Anisodus carniolicoides

Lycium shawii Lycium Anisodus tanguticus

Lycium decumbens Lycium Atropa komarovii

Lycium pumilum Lycium Atropa belladonna

Lycium oxycarpum Lycium Jaborosa sativa

Lycium pilifolium Lycium Jaborosa integrifolia

Lycium gariepense Lycium Latua pubiflora

Lycium tenue Lycium Nicotiana velutina

Lycium strandveldense Lycium Nicotiana rosulata

Lycium amoenum Lycium Nicotiana rotundifolia

Lycium grandicalyx Lycium Nicotiana gossei

Lycium arenicola Lycium Nicotiana goodspeedii

Lycium cinereum Lycium Nicotiana cavicola

Lycium afrum Lycium Nicotiana suaveolens

Lycium ferocissimum Lycium Nicotiana eastii

Lycium horridum Lycium Nicotiana amplexicaulis

Lycium schizocalyx Lycium Nicotiana maritima

Lycium boerhaviifolium Lycium Nicotiana excelsior

Lycium pallidum Lycium Nicotiana simulans

Lycium cooperi Lycium Nicotiana megalosiphon

yimmacrodon Lycium Nicotiana umbratica

Lycium puberulum Lycium Nicotiana occidentalis

Lycium californicum Lycium Nicotiana forsteri

Lycium nodosum Lycium Nicotiana petunioides

Lycium vimineum Lycium Nicotiana noctiflora

Lycium gilliesianum Lycium Nicotiana glauca

Lycium ameghinoi Lycium Nicotiana acaulis

Lycium chanar Lycium Nicotiana africana

Lycium fuscum Lycium Nicotiana plumbaginifolia

Lycium minutifolium Lycium Nicotiana longiflora

Lycium stenophyllum Lycium Nicotiana forgetiana

Lycium cestroides Lycium Nicotiana bonariensis

Lycium cuneatum Lycium Nicotiana langsdorffii

Lycium morongii Lycium Nicotiana alata

Lycium brevipes Lycium Nicotiana stocktonii

Lycium carolinianum Lycium Nicotiana nesophila

Lycium rachidocladum Lycium Nicotiana repanda

Lycium tenuispinosum Lycium Nicotiana nudicaulis

Lycium elongatum Lycium Nicotiana sylvestris

Lycium americanum Lycium Nicotiana pauciflora

Lycium infaustum Lycium Nicotiana acuminata

Lycium minimum Lycium Nicotiana corymbosa

Lycium parishii Lycium Nicotiana miersii

Lycium torreyi Lycium Nicotiana spegazzinii

yimandersonii Lycium Nicotiana linearis

Lycium berlandieri Lycium Nicotiana obtusifolia

Lycium exsertum Lycium Nicotiana quadrivalvis

Lycium fremontii Lycium Nicotiana clevelandii

Exodeconus miersii Exodeconus Nicotiana rustica

Solandra grandiflora Solandra Nicotiana knightiana

Dyssochroma viridiflora Dyssochroma Nicotiana paniculata

Mandragora caulescens Mandragora Nicotiana solanifolia

Nicandra physalodes Nicandra Nicotiana cordifolia

Brugmansia sanguinea Brugmansia Nicotiana raimondii

Brugmansia arborea Brugmansia Nicotiana benavidesii

M11. I/C aurea Brugmansia Nicotiana undulata

Datura discolor Datura Nicotiana arentsii

Datura metel Datura Nicotiana glutinosa

Datura inoxia Datura Nicotiana wigandioides

Datura leichhardtii Datura Nicotiana thyrsiflora

Datura ferox Datura Nicotiana tomentosiformis

Datura quercifolia Datura Nicotiana tomentosa

Datura stramonium Datura Nicotiana kawakamii

Datura ceratocaula Datura Nicotiana otophora μ origanifolia Salpichroa

μ Nicotiana tabacum C shanesii Lycianthes

I Duboisia myoporoides

Lycianthes biflora Lycianthes Cyphanthera albicans

Lycianthes multiflora Lycianthes Duboisia hopwoodii

Lycianthes jalicensis Lycianthes Duboisia leichhardtii

Lycianthes heteroclita Lycianthes Cyphanthera anthocercidea

Lycianthes lycioides Lycianthes Crenidium spinescens

Lycianthes rantonnetii Lycianthes Cyphanthera microphylla

Lycianthes asarifolia Lycianthes Anthotroche myoporoides

yinhsacapulcensis Lycianthes Anthotroche pannosa

Lycianthes ciliolata Lycianthes Anthotroche walcottii

Lycianthes moziniana Lycianthes Grammosolen truncatus

Lycianthes rzedowskii Lycianthes Grammosolen dixonii

Lycianthes dejecta Lycianthes Cyphanthera odgersii

Lycianthes peduncularis Lycianthes Anthocercis viscosa

Capsicum geminifolium Capsicum Anthocercis angustifolia

Capsicum lanceolatum Capsicum Anthocercis intricata

Capsicum ciliatum Capsicum Anthocercis littorea

Capsicum rhomboideum Capsicum Anthocercis ilicifolia

Capsicum campylopodium Capsicum Anthocercis gracilis

λ villosum Capsicum Symonanthus bancroftii

C schottianum Capsicum

λ Symonanthus aromaticus C recurvatum Capsicum

I I Nierembergia pulchella

Capsicum flexuosum Capsicum Nierembergia browallioides

Capsicum cardenasii Capsicum Nierembergia tucumanensis

Capsicum eximium Capsicum Nierembergia ericoides

Capsicum pubescens Capsicum Nierembergia scoparia

q tovarii Capsicum Nierembergia linariifolia

IC chacoense Capsicum Nierembergia calycina

Capsicum baccatum Capsicum Nierembergia veitchii

Capsicum coccineum Capsicum Nierembergia aristata

Capsicum annuum Capsicum Nierembergia graveolens

Capsicum chinense Capsicum Nierembergia repens

Capsicum frutescens Capsicum Nierembergia rivularis

Capsicum galapagoensis Capsicum Bouchetia erecta

Cuatresia cuneata Cuatresia Bouchetia anomala

utei exiguiflora Cuatresia Hunzikeria texana

Cuatresia riparia Cuatresia Brunfelsia americana

Deprea paneroi Deprea Petunia saxicola

Nothocestrum longifolium Nothocestrum Petunia reitzii

Withania coagulans Withania Petunia altiplana

Withania somnifera Withania Petunia secreta

Iochroma gesnerioides Iochroma Petunia scheideana

Iochroma fuchsioides Iochroma Petunia bonjardinensis

Iochroma lehmannii Iochroma Petunia mantiqueirensis

Acnistus arborescens Acnistus Petunia integrifolia

Iochroma cyaneum Iochroma Petunia exserta

Dunalia solanacea Dunalia Petunia axillaris

Dunalia obovata Dunalia Calibrachoa pygmea

Vassobia breviflora Vassobia Calibrachoa parviflora

Dunalia brachyacantha Dunalia Calibrachoa sellowiana

Eriolarynx lorentzii Eriolarynx Fabiana imbricata

Iochroma australe Iochroma Schizanthus lacteus

Leucophysalis grandiflora Leucophysalis Schizanthus integrifolius

Leucophysalis nana Leucophysalis Schizanthus candidus

Schraderanthus viscosa Schraderanthus Schizanthus alpestris

Brachistus stramoniifolius Brachistus Schizanthus hookeri

Witheringia macrantha Witheringia Schizanthus grahamii

Witheringia meiantha Witheringia Schizanthus tricolor

Physalis alkekengi Physalis Schizanthus parvulus

Posterior Probability carpenteri Calliphysalis Schizanthus pinnatus

Quincula lobata Quincula Schizanthus porrigens

Physalis melanocystis Physalis Schizanthus litoralis

Physalis acutifolia Physalis Schizanthus laetus

Physalis crassifolia Physalis Goetzea elegans

Physalis philadelphica Physalis Espadaea amoena

Physalis longifolia Physalis Metternichia princeps

Physalis glutinosa Physalis Schwenckia lateriflora

Physalis sordida Physalis Cestrum fasciculatum

Physalis nicandroides Physalis Cestrum elegans

0.6 patula Physalis

Cestrum aurantiacum

Physalis peruviana Physalis Cestrum nocturnum

Physalis angustiphysa Physalis Cestrum tomentosum

Physalis cordata Physalis Cestrum diurnum

Physalis ignota Physalis Cestrum strigilatum

Physalis minima Physalis Cestrum megalophyllum

Physalis pruinosa Physalis Sessea corymbiflora

Physalis lagascae Physalis Streptosolen jamesonii

Physalis angulata Physalis Browallia speciosa

0.7 pubescens Physalis Salpiglossis sinuata

Physalis lanceolata Physalis Combera paradoxa

Physalis heterophylla Physalis Pantacantha ameghinoi

Physalis virginiana Physalis Solanum ferocissimum

Physalis arenicola Physalis Solanum chenopodinum

Physalis walteri Physalis Solanum stelligerum

Physalis pumila Physalis Solanum nemophilum

Physalis cinerascens Physalis Solanum densevestitum Physalis mollis Physalis Solanum furfuraceum

0.8 viscosa Physalis Solanum stupefactum

Jaltomata darcyana Jaltomata Solanum corifolium

Jaltomata repandidentata Jaltomata Solanum cookii

Jaltomata bohsiana Jaltomata Solanum sandwicense

Jaltomata procumbens Jaltomata Solanum incompletum

Jaltomata chihuahuensis Jaltomata Solanum semiarmatum

Jaltomata grandiflora Jaltomata Solanum viridifolium

atmt antillana Jaltomata Solanum dimorphispinum

Jaltomata auriculata Jaltomata Solanum inaequilaterum

Jaltomata oppositifolia Jaltomata Solanum quadriloculatum

0.9 salpoensis Jaltomata Solanum ellipticum

Jaltomata aspera Jaltomata Solanum dianthophorum

Jaltomata lojae Jaltomata Solanum esuriale

Jaltomata lanata Jaltomata Solanum centrale

Jaltomata paneroi Jaltomata Solanum cinereum

Jaltomata bernardelloana Jaltomata Solanum sturtianum

Jaltomata sagastegui Jaltomata Solanum petrophilum

Jaltomata herrerae Jaltomata Solanum pungetium

Jaltomata yacheri Jaltomata Solanum prinophyllum

Jaltomata weberbaueri Jaltomata Solanum campanulatum

1.0 ventricosa Jaltomata

Solanum vicinum

Jaltomata sanchez-vegae Jaltomata Solanum ditrichum

Jaltomata andersonii Jaltomata Solanum elachophyllum

Jaltomata lezamae Jaltomata Solanum tetrathecum

Jaltomata sinuosa Jaltomata Solanum orbiculatum

Jaltomata viridiflora Jaltomata Solanum nummularium

Jaltomata yungayensis Jaltomata Solanum oligacanthum

Jaltomata contumacensis Jaltomata Solanum hystrix

Jaltomata leivae Jaltomata Solanum hoplopetalum

Jaltomata biflora Jaltomata Solanum sejunctum

Jaltomata dentata Jaltomata Solanum asymmetriphyllum

Jaltomata bicolor Jaltomata Solanum diversiflorum

Jaltomata umbellata Jaltomata Solanum chippendalei

Jaltomata cajacayensis Jaltomata Solanum phlomoides

Jaltomata lomana Jaltomata Solanum beaugleholei

Jaltomata mionei Jaltomata Solanum melanospermum

Solanum valdiviense Solanum Solanum clarkiae

Solanum guineense Solanum Solanum oedipus

Solanum terminale Solanum Solanum vansittartense

Solanum herculeum Solanum Solanum tudununggae

Solanum trisectum Solanum Solanum petraeum

Solanum capsiciforme Solanum Solanum cataphractum

Solanum simile Solanum Solanum leopoldensis

Solanum symonii Solanum Solanum carduiforme

Solanum vescum Solanum Solanum dioicum

Solanum linearifolium Solanum Solanum cunninghamii

Solanum laciniatum Solanum Solanum lucani

Solanum aviculare Solanum Solanum echinatum

Solanum multivenosum Solanum Solanum horridum

Solanum aligerum Solanum Solanum cleistogamum

Solanum laxum Solanum Solanum lasiophyllum

Solanum amygdalifolium Solanum Solanum gabrielae

Solanum crispum Solanum Solanum coactiliferum

Solanum dulcamara Solanum Solanum oldfieldii

Solanum lyratum Solanum Solanum pyracanthos

Solanum wallacei Solanum Solanum tomentosum

Solanum palitans Solanum Solanum capense

Solanum tripartitum Solanum Solanum humile

Solanum triflorum Solanum Solanum vespertilio

Solanum physalifolium Solanum Solanum lidii

Solanum pallidum Solanum Solanum anguivi

Solanum fiebrigii Solanum Solanum aethiopicum

Solanum villosum Solanum Solanum cyaneopurpureum

Solanum scabrum Solanum Solanum macrocarpon

Solanum opacum Solanum Solanum dasyphyllum

Solanum ptychanthum Solanum Solanum incanum

Solanum americanum Solanum Solanum linnaeanum

Solanum nigrum Solanum Solanum melongena

Solanum taeniotrichum Solanum Solanum insanum

Solanum caripense Solanum Solanum supinum

Solanum fraxinifolium Solanum Solanum violaceum

Solanum appendiculatum Solanum Solanum giganteum

Solanum brevifolium Solanum Solanum marginatum

Solanum etuberosum Solanum Solanum coagulans

Solanum palustre Solanum Solanum aculeastrum

Solanum lycopersicoides Solanum Solanum houstonii

Solanum sitiens Solanum Solanum hindsianum

Solanum juglandifolium Solanum Solanum elaeagnifolium

Solanum ochranthum Solanum Solanum torvum

Solanum habrochaites Solanum Solanum chrysotrichum

Solanum neorickii Solanum Solanum asperolanatum

Solanum chilense Solanum Solanum bonariense

Solanum peruvianum Solanum Solanum paniculatum

Solanum chmielewskii Solanum Solanum donianum

Solanum pennellii Solanum Solanum crotonoides

Solanum galapagense Solanum Solanum lanceifolium

Solanum lycopersicum Solanum Solanum jamaicense

Solanum cheesmaniae Solanum Solanum aridum

Solanum pimpinellifolium Solanum Solanum carolinense

Solanum chomatophilum Solanum Solanum ensifolium

Solanum scabrifolium Solanum Solanum davisense

Solanum pinnatisectum Solanum Solanum citrullifolium

Solanum piurae Solanum Solanum heterodoxum

Solanum bulbocastanum Solanum Solanum tribulosum

Solanum jamesii Solanum Solanum rostratum

Solanum clarum Solanum Solanum fructu-tecto

Solanum morelliforme Solanum Solanum angustifolium

Solanum polyadenium Solanum Solanum lumholtzianum

Solanum cardiophyllum Solanum Solanum grayi

Solanum ehrenbergii Solanum Solanum johnstonii

Solanum andreanum Solanum Solanum tenuipes

Solanum schenckii Solanum Solanum wrightii

Solanum doddsii Solanum Solanum crinitum

Solanum stenophyllidium Solanum Solanum mitlense

Solanum iopetalum Solanum Solanum lycocarpum

Solanum violaceimarmoratum Solanum Solanum sisymbriifolium

Solanum albicans Solanum Solanum vestissimum

Solanum acaule Solanum Solanum pseudolulo

Solanum boliviense Solanum Solanum hyporhodium

Solanum raphanifolium Solanum Solanum pectinatum

Solanum lignicaule Solanum Solanum hirtum

Solanum laxissimum Solanum Solanum stramoniifolium

Solanum maglia Solanum Solanum repandum

Solanum longiconicum Solanum Solanum lasiocarpum

Solanum oxycarpum Solanum Solanum candidum

oau agrimoniifolium Solanum Solanum felinum

Solanum colombianum Solanum Solanum quitoense

Solanum stipuloideum Solanum Solanum sessiliflorum

Solanum vernei Solanum Solanum viarum

Solanum candolleanum Solanum Solanum aculeatissimum

Solanum microdontum Solanum Solanum myriacanthum

Solanum demissum Solanum Solanum incarceratum

Solanum kurtzianum Solanum Solanum tenuispinum

Solanum chacoense Solanum Solanum atropurpureum

Solanum berthaultii Solanum Solanum acerifolium

Solanum infundibuliforme Solanum Solanum capsicoides

Solanum okadae Solanum Solanum platense

Solanum stoloniferum Solanum Solanum mammosum

Solanum hjertingii Solanum Solanum palinacanthum

Solanum verrucosum Solanum Solanum stagnale

Solanum guerreroense Solanum Solanum robustum

Solanum hougasii Solanum Solanum paludosum

Solanum latiflorum Solanum Solanum microphyllum

Solanum cacosmum Solanum Solanum gardneri

Solanum exiguum Solanum Solanum hoehnei

Solanum diploconos Solanum Solanum wendlandii

Solanum pinetorum Solanum Solanum allophyllum

Solanum sciadostylis Solanum Solanum diphyllum

Solanum cylindricum Solanum Solanum aphyodendron

Solanum glaucophyllum Solanum Solanum arboreum

Solanum fusiforme Solanum Solanum rovirosanum

Solanum melissarum Solanum Solanum pseudocapsicum

Solanum confusum Solanum Solanum argentinum

Solanum hibernum Solanum Solanum reductum

Solanum luteoalbum Solanum Solanum mauritianum

Solanum stuckertii Solanum Solanum asperum

Solanum oxyphyllum Solanum Solanum rugosum

Solanum pendulum Solanum Solanum cordovense

Solanum tobagense Solanum Solanum abutiloides

Solanum obliquum Solanum Solanum turneroides

Solanum roseum Solanum Solanum adscendens

Solanum maternum Solanum Solanum tenuisetosum

Solanum betaceum Solanum Solanum circinatum

Solanum unilobum Solanum Solanum tegore

Solanum cajanumense Solanum Solanum proteanthum

Solanum fallax Solanum Solanum sibundoyense Solanum endopogon Solanum Solanum occultum

Figure S10: Ancestral state estimation using the maximum a posteriori for each node of the M11.I/C model

40 bioRxiv preprint doi: https://doi.org/10.1101/709329; this version posted July 22, 2019. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-NC-ND 4.0 International license.

Speciation Extinction 2.5

2.0 2 Type Type 1.5 SC SC 1.0 1 SI SI 0.5 Posterior Density Posterior Density Posterior 0 0.0 1.0 1.5 2.0 0.0 0.5 1.0 1.5 2.0 2.5 Rate Rate Net Diversification Relative Extinction

20 10 Type 15 Type

C SC 10 5 I SI 5 Posterior Density Posterior Density Posterior 0 0 0.0 0.2 0.4 0.6 0.8 0.0 0.3 0.6 0.9 Rate Rate Trait change

4 Type SI to SC 2 Posterior Density Posterior 0 0.2 0.3 0.4 0.5 0.6 Rate

Figure S11: Posterior distribution for each of the parameters in the M11. I/C model

41 bioRxiv preprint doi: https://doi.org/10.1101/709329; this version posted July 22, 2019. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under

aCC-BY-NC-ND 4.0 International license.

Nolana rupicola Nolana

Nolana acuminata Nolana Nolana elegans

Nolana rostrata Nolana Sclerophylax arnottii

Nolana adansonii Nolana Physochlaina orientalis

Nolana galapagensis Nolana Physochlaina praealta

Nolana plicata Nolana Przewalskia tangutica

Nolana laxa Nolana Scopolia parviflora

Nolana aticoana Nolana Scopolia carniolica

Nolana humifusa Nolana Scopolia japonica

yimdepressum Lycium Atropanthe sinensis

Lycium ruthenicum Lycium Hyoscyamus niger

Lycium tetrandrum Lycium Hyoscyamus albus

Lycium acutifolium Lycium Hyoscyamus pusillus

Lycium bosciifolium Lycium Hyoscyamus turcomanicus

Lycium hirsutum Lycium Hyoscyamus desertorum

Lycium villosum Lycium Hyoscyamus muticus

Lycium eenii Lycium Anisodus acutangulus

Lycium schweinfurthii Lycium Anisodus carniolicoides

Lycium shawii Lycium Anisodus tanguticus

Lycium decumbens Lycium Atropa komarovii

yimpumilum Lycium Atropa belladonna

Lycium oxycarpum Lycium Jaborosa sativa

Lycium pilifolium Lycium Jaborosa integrifolia

Lycium gariepense Lycium Latua pubiflora

Lycium tenue Lycium Nicotiana velutina

Lycium strandveldense Lycium Nicotiana rosulata

Lycium amoenum Lycium Nicotiana rotundifolia

Lycium grandicalyx Lycium Nicotiana gossei

Lycium arenicola Lycium Nicotiana goodspeedii

Lycium cinereum Lycium Nicotiana cavicola

Lycium afrum Lycium Nicotiana suaveolens

Lycium ferocissimum Lycium Nicotiana eastii

Lycium horridum Lycium Nicotiana amplexicaulis

M14. I/C + A/B asym schizocalyx Lycium Nicotiana maritima

Lycium boerhaviifolium Lycium Nicotiana excelsior

Lycium pallidum Lycium Nicotiana simulans

Lycium cooperi Lycium Nicotiana megalosiphon

yimmacrodon Lycium Nicotiana umbratica

Lycium puberulum Lycium Nicotiana occidentalis

Lycium californicum Lycium Nicotiana forsteri

Lycium nodosum Lycium Nicotiana petunioides

Lycium vimineum Lycium Nicotiana noctiflora

Lycium gilliesianum Lycium Nicotiana glauca

Lycium ameghinoi Lycium Nicotiana acaulis

Lycium chanar Lycium Nicotiana africana

Lycium fuscum Lycium Nicotiana plumbaginifolia

Lycium minutifolium Lycium Nicotiana longiflora

Lycium stenophyllum Lycium Nicotiana forgetiana

Lycium cestroides Lycium Nicotiana bonariensis

Lycium cuneatum Lycium Nicotiana langsdorffii

Lycium morongii Lycium Nicotiana alata Lycium brevipes Lycium Nicotiana stocktonii

μ μ carolinianum Lycium Nicotiana nesophila

I rachidocladum Lycium Nicotiana repanda C tenuispinosum Lycium Nicotiana nudicaulis

A elongatum Lycium Nicotiana sylvestris

A americanum Lycium Nicotiana pauciflora

Lycium infaustum Lycium Nicotiana acuminata

Lycium minimum Lycium Nicotiana corymbosa

Lycium parishii Lycium Nicotiana miersii

Lycium torreyi Lycium Nicotiana spegazzinii

Lycium andersonii Lycium Nicotiana linearis

Lycium berlandieri Lycium Nicotiana obtusifolia

Lycium exsertum Lycium Nicotiana quadrivalvis

Lycium fremontii Lycium Nicotiana clevelandii

Exodeconus miersii Exodeconus Nicotiana rustica

Solandra grandiflora Solandra Nicotiana knightiana

Dyssochroma viridiflora Dyssochroma Nicotiana paniculata

Mandragora caulescens Mandragora Nicotiana solanifolia

Nicandra physalodes Nicandra Nicotiana cordifolia Brugmansia sanguinea Brugmansia Nicotiana raimondii

I C λ arborea Brugmansia Nicotiana benavidesii

λ A A C aurea Brugmansia Nicotiana undulata

I discolor Datura Nicotiana arentsii

A metel Datura Nicotiana glutinosa

A q inoxia Datura Nicotiana wigandioides

IC leichhardtii Datura Nicotiana thyrsiflora

Datura ferox Datura Nicotiana tomentosiformis

Datura quercifolia Datura Nicotiana tomentosa

Datura stramonium Datura Nicotiana kawakamii

Datura ceratocaula Datura Nicotiana otophora

Salpichroa origanifolia Salpichroa Nicotiana tabacum

Lycianthes shanesii Lycianthes Duboisia myoporoides

Lycianthes biflora Lycianthes Cyphanthera albicans

Lycianthes multiflora Lycianthes Duboisia hopwoodii

Lycianthes jalicensis Lycianthes Duboisia leichhardtii

Lycianthes heteroclita Lycianthes Cyphanthera anthocercidea

Lycianthes lycioides Lycianthes Crenidium spinescens

Lycianthes rantonnetii Lycianthes Cyphanthera microphylla

Lycianthes asarifolia Lycianthes Anthotroche myoporoides

Lycianthes acapulcensis Lycianthes Anthotroche pannosa Lycianthes ciliolata Lycianthes Anthotroche walcottii

α moziniana Lycianthes Grammosolen truncatus α β rzedowskii Lycianthes

β Grammosolen dixonii

Lycianthes dejecta Lycianthes Cyphanthera odgersii

Lycianthes peduncularis Lycianthes Anthocercis viscosa

Capsicum geminifolium Capsicum Anthocercis angustifolia

Capsicum lanceolatum Capsicum Anthocercis intricata

Capsicum ciliatum Capsicum Anthocercis littorea

Capsicum rhomboideum Capsicum Anthocercis ilicifolia

Capsicum campylopodium Capsicum Anthocercis gracilis

Capsicum villosum Capsicum Symonanthus bancroftii

Capsicum schottianum Capsicum Symonanthus aromaticus

Capsicum recurvatum Capsicum Nierembergia pulchella

Capsicum flexuosum Capsicum Nierembergia browallioides

Capsicum cardenasii Capsicum Nierembergia tucumanensis

Capsicum eximium Capsicum Nierembergia ericoides

Capsicum pubescens Capsicum Nierembergia scoparia

Capsicum tovarii Capsicum Nierembergia linariifolia

Capsicum chacoense Capsicum Nierembergia calycina

Capsicum baccatum Capsicum Nierembergia veitchii

Capsicum coccineum Capsicum Nierembergia aristata

λ annuum Capsicum Nierembergia graveolens I chinense Capsicum

Nierembergia repens

B λ frutescens Capsicum Nierembergia rivularis C galapagoensis Capsicum Bouchetia erecta

I B B cuneata Cuatresia Bouchetia anomala C exiguiflora Cuatresia

B Hunzikeria texana Cuatresia riparia Cuatresia Brunfelsia americana

q paneroi Deprea Petunia saxicola

IC longifolium Nothocestrum Petunia reitzii

Withania coagulans Withania Petunia altiplana

Withania somnifera Withania Petunia secreta

Iochroma gesnerioides Iochroma Petunia scheideana μ fuchsioides Iochroma Petunia bonjardinensis

I μ lehmannii Iochroma Petunia mantiqueirensis

B C arborescens Acnistus Petunia integrifolia

B cyaneum Iochroma Petunia exserta

Dunalia solanacea Dunalia Petunia axillaris

Dunalia obovata Dunalia Calibrachoa pygmea

Vassobia breviflora Vassobia Calibrachoa parviflora

Dunalia brachyacantha Dunalia Calibrachoa sellowiana

Eriolarynx lorentzii Eriolarynx Fabiana imbricata

Iochroma australe Iochroma Schizanthus lacteus

Leucophysalis grandiflora Leucophysalis Schizanthus integrifolius

Leucophysalis nana Leucophysalis Schizanthus candidus

Schraderanthus viscosa Schraderanthus Schizanthus alpestris

Brachistus stramoniifolius Brachistus Schizanthus hookeri

Witheringia macrantha Witheringia Schizanthus grahamii

Witheringia meiantha Witheringia Schizanthus tricolor

Physalis alkekengi Physalis Schizanthus parvulus

Calliphysalis carpenteri Calliphysalis Schizanthus pinnatus

Quincula lobata Quincula Schizanthus porrigens

Physalis melanocystis Physalis Schizanthus litoralis Physalis acutifolia Physalis Schizanthus laetus

Posterior Probability crassifolia Physalis Goetzea elegans

Physalis philadelphica Physalis Espadaea amoena

Physalis longifolia Physalis Metternichia princeps

Physalis glutinosa Physalis Schwenckia lateriflora

Physalis sordida Physalis Cestrum fasciculatum

Physalis nicandroides Physalis Cestrum elegans

Physalis patula Physalis Cestrum aurantiacum

Physalis peruviana Physalis Cestrum nocturnum

Physalis angustiphysa Physalis Cestrum tomentosum Physalis cordata Physalis Cestrum diurnum

0.4 ignota Physalis Cestrum strigilatum

Physalis minima Physalis Cestrum megalophyllum

Physalis pruinosa Physalis Sessea corymbiflora

Physalis lagascae Physalis Streptosolen jamesonii

Physalis angulata Physalis Browallia speciosa

Physalis pubescens Physalis Salpiglossis sinuata

Physalis lanceolata Physalis Combera paradoxa

Physalis heterophylla Physalis Pantacantha ameghinoi

Physalis virginiana Physalis Solanum ferocissimum

Physalis arenicola Physalis Solanum chenopodinum

0.6 walteri Physalis Solanum stelligerum

Physalis pumila Physalis Solanum nemophilum

Physalis cinerascens Physalis Solanum densevestitum

Physalis mollis Physalis Solanum furfuraceum

Physalis viscosa Physalis Solanum stupefactum

Jaltomata darcyana Jaltomata Solanum corifolium

Jaltomata repandidentata Jaltomata Solanum cookii

Jaltomata bohsiana Jaltomata Solanum sandwicense

Jaltomata procumbens Jaltomata Solanum incompletum

0.8 chihuahuensis Jaltomata Solanum semiarmatum

atmt grandiflora Jaltomata Solanum viridifolium

atmt antillana Jaltomata Solanum dimorphispinum

Jaltomata auriculata Jaltomata Solanum inaequilaterum

Jaltomata oppositifolia Jaltomata Solanum quadriloculatum

Jaltomata salpoensis Jaltomata Solanum ellipticum

Jaltomata aspera Jaltomata Solanum dianthophorum

Jaltomata lojae Jaltomata Solanum esuriale

Jaltomata lanata Jaltomata Solanum centrale

Jaltomata paneroi Jaltomata Solanum cinereum

1.0 bernardelloana Jaltomata Solanum sturtianum

Jaltomata sagastegui Jaltomata Solanum petrophilum

Jaltomata herrerae Jaltomata Solanum pungetium

Jaltomata yacheri Jaltomata Solanum prinophyllum

Jaltomata weberbaueri Jaltomata Solanum campanulatum

Jaltomata ventricosa Jaltomata Solanum vicinum

Jaltomata sanchez-vegae Jaltomata Solanum ditrichum

Jaltomata andersonii Jaltomata Solanum elachophyllum

Jaltomata lezamae Jaltomata Solanum tetrathecum

Jaltomata sinuosa Jaltomata Solanum orbiculatum

Jaltomata viridiflora Jaltomata Solanum nummularium

Jaltomata yungayensis Jaltomata Solanum oligacanthum

Jaltomata contumacensis Jaltomata Solanum hystrix

Jaltomata leivae Jaltomata Solanum hoplopetalum

Jaltomata biflora Jaltomata Solanum sejunctum

Jaltomata dentata Jaltomata Solanum asymmetriphyllum

Jaltomata bicolor Jaltomata Solanum diversiflorum

Jaltomata umbellata Jaltomata Solanum chippendalei

Jaltomata cajacayensis Jaltomata Solanum phlomoides

Jaltomata lomana Jaltomata Solanum beaugleholei

Jaltomata mionei Jaltomata Solanum melanospermum

Solanum valdiviense Solanum Solanum clarkiae

Solanum guineense Solanum Solanum oedipus

Solanum terminale Solanum Solanum vansittartense

Solanum herculeum Solanum Solanum tudununggae

Solanum trisectum Solanum Solanum petraeum

Solanum capsiciforme Solanum Solanum cataphractum

Solanum simile Solanum Solanum leopoldensis

Solanum symonii Solanum Solanum carduiforme

Solanum vescum Solanum Solanum dioicum

Solanum linearifolium Solanum Solanum cunninghamii

Solanum laciniatum Solanum Solanum lucani

Solanum aviculare Solanum Solanum echinatum

Solanum multivenosum Solanum Solanum horridum

Solanum aligerum Solanum Solanum cleistogamum

Solanum laxum Solanum Solanum lasiophyllum

Solanum amygdalifolium Solanum Solanum gabrielae

Solanum crispum Solanum Solanum coactiliferum

Solanum dulcamara Solanum Solanum oldfieldii

Solanum lyratum Solanum Solanum pyracanthos

Solanum wallacei Solanum Solanum tomentosum

Solanum palitans Solanum Solanum capense

Solanum tripartitum Solanum Solanum humile

Solanum triflorum Solanum Solanum vespertilio

Solanum physalifolium Solanum Solanum lidii

Solanum pallidum Solanum Solanum anguivi

Solanum fiebrigii Solanum Solanum aethiopicum

Solanum villosum Solanum Solanum cyaneopurpureum

Solanum scabrum Solanum Solanum macrocarpon

Solanum opacum Solanum Solanum dasyphyllum

Solanum ptychanthum Solanum Solanum incanum

Solanum americanum Solanum Solanum linnaeanum

Solanum nigrum Solanum Solanum melongena

Solanum taeniotrichum Solanum Solanum insanum

Solanum caripense Solanum Solanum supinum

Solanum fraxinifolium Solanum Solanum violaceum

Solanum appendiculatum Solanum Solanum giganteum

Solanum brevifolium Solanum Solanum marginatum

Solanum etuberosum Solanum Solanum coagulans

Solanum palustre Solanum Solanum aculeastrum

Solanum lycopersicoides Solanum Solanum houstonii

Solanum sitiens Solanum Solanum hindsianum

Solanum juglandifolium Solanum Solanum elaeagnifolium

Solanum ochranthum Solanum Solanum torvum

Solanum habrochaites Solanum Solanum chrysotrichum

Solanum neorickii Solanum Solanum asperolanatum

Solanum chilense Solanum Solanum bonariense

Solanum peruvianum Solanum Solanum paniculatum

Solanum chmielewskii Solanum Solanum donianum

Solanum pennellii Solanum Solanum crotonoides

Solanum galapagense Solanum Solanum lanceifolium

Solanum lycopersicum Solanum Solanum jamaicense

Solanum cheesmaniae Solanum Solanum aridum

Solanum pimpinellifolium Solanum Solanum carolinense

Solanum chomatophilum Solanum Solanum ensifolium

Solanum scabrifolium Solanum Solanum davisense

Solanum pinnatisectum Solanum Solanum citrullifolium

Solanum piurae Solanum Solanum heterodoxum

Solanum bulbocastanum Solanum Solanum tribulosum

Solanum jamesii Solanum Solanum rostratum

Solanum clarum Solanum Solanum fructu-tecto

Solanum morelliforme Solanum Solanum angustifolium

Solanum polyadenium Solanum Solanum lumholtzianum

Solanum cardiophyllum Solanum Solanum grayi

Solanum ehrenbergii Solanum Solanum johnstonii

Solanum andreanum Solanum Solanum tenuipes

Solanum schenckii Solanum Solanum wrightii

Solanum doddsii Solanum Solanum crinitum

Solanum stenophyllidium Solanum Solanum mitlense

Solanum iopetalum Solanum Solanum lycocarpum

Solanum violaceimarmoratum Solanum Solanum sisymbriifolium

Solanum albicans Solanum Solanum vestissimum

Solanum acaule Solanum Solanum pseudolulo

Solanum boliviense Solanum Solanum hyporhodium

Solanum raphanifolium Solanum Solanum pectinatum

Solanum lignicaule Solanum Solanum hirtum

Solanum laxissimum Solanum Solanum stramoniifolium

Solanum maglia Solanum Solanum repandum

Solanum longiconicum Solanum Solanum lasiocarpum

Solanum oxycarpum Solanum Solanum candidum

Solanum agrimoniifolium Solanum Solanum felinum

Solanum colombianum Solanum Solanum quitoense

Solanum stipuloideum Solanum Solanum sessiliflorum

Solanum vernei Solanum Solanum viarum

Solanum candolleanum Solanum Solanum aculeatissimum

Solanum microdontum Solanum Solanum myriacanthum

Solanum demissum Solanum Solanum incarceratum

Solanum kurtzianum Solanum Solanum tenuispinum

Solanum chacoense Solanum Solanum atropurpureum

Solanum berthaultii Solanum Solanum acerifolium

Solanum infundibuliforme Solanum Solanum capsicoides

Solanum okadae Solanum Solanum platense

Solanum stoloniferum Solanum Solanum mammosum

Solanum hjertingii Solanum Solanum palinacanthum

Solanum verrucosum Solanum Solanum stagnale

Solanum guerreroense Solanum Solanum robustum

Solanum hougasii Solanum Solanum paludosum

Solanum latiflorum Solanum Solanum microphyllum

Solanum cacosmum Solanum Solanum gardneri

Solanum exiguum Solanum Solanum hoehnei

Solanum diploconos Solanum Solanum wendlandii

Solanum pinetorum Solanum Solanum allophyllum

Solanum sciadostylis Solanum Solanum diphyllum

Solanum cylindricum Solanum Solanum aphyodendron

Solanum glaucophyllum Solanum Solanum arboreum

Solanum fusiforme Solanum Solanum rovirosanum

Solanum melissarum Solanum Solanum pseudocapsicum

Solanum confusum Solanum Solanum argentinum

Solanum hibernum Solanum Solanum reductum

Solanum luteoalbum Solanum Solanum mauritianum

Solanum stuckertii Solanum Solanum asperum

Solanum oxyphyllum Solanum Solanum rugosum

Solanum pendulum Solanum Solanum cordovense

Solanum tobagense Solanum Solanum abutiloides

Solanum obliquum Solanum Solanum turneroides

Solanum roseum Solanum Solanum adscendens

Solanum maternum Solanum Solanum tenuisetosum

Solanum betaceum Solanum Solanum circinatum

Solanum unilobum Solanum Solanum tegore

Solanum cajanumense Solanum Solanum proteanthum

Solanum fallax Solanum Solanum sibundoyense Solanum endopogon Solanum Solanum occultum

Figure S12: Ancestral state estimation using the maximum a posteriori for each node of the M14. I/C+A/B asym model

42 bioRxiv preprint doi: https://doi.org/10.1101/709329; this version posted July 22, 2019. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-NC-ND 4.0 International license.

Speciation Extinction 6 4 Type Type

3 SC A 4 SC A SC B SC B 2 SI A 2 SI A 1 SI B SI B Posterior Density Posterior Density Posterior 0 0 0 1 2 3 0 1 2 3 Rate Rate Net Diversification Relative Extinction 8 Type Type 4 6 SC A SC A

SC B 4 SC B 2 SI A SI A 2 SI B SI B Posterior Density Posterior Density Posterior 0 0 -2 -1 0 1 0 1 2 3 4 Rate Rate Trait change Hidden trait change

6 75 Type 4 Type 50 alpha SI to SC beta 2 25 Posterior Density Posterior Density Posterior 0 0 0.2 0.3 0.4 0.5 0.6 0.0 0.5 1.0 1.5 Rate Rate

Figure S13: Posterior distribution for each of the parameters in the M14. I/C+A/B asym model

43 bioRxiv preprint doi: https://doi.org/10.1101/709329; this version posted July 22, 2019. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under

aCC-BY-NC-ND 4.0 International license.

Nolana rupicola Nolana

Nolana acuminata Nolana Nolana elegans

Nolana rostrata Nolana Sclerophylax arnottii

Nolana adansonii Nolana Physochlaina orientalis

Nolana galapagensis Nolana Physochlaina praealta

Nolana plicata Nolana Przewalskia tangutica

Nolana laxa Nolana Scopolia parviflora

Nolana aticoana Nolana Scopolia carniolica

Nolana humifusa Nolana Scopolia japonica

Lycium depressum Lycium Atropanthe sinensis

Lycium ruthenicum Lycium Hyoscyamus niger

Lycium tetrandrum Lycium Hyoscyamus albus

Lycium acutifolium Lycium Hyoscyamus pusillus

Lycium bosciifolium Lycium Hyoscyamus turcomanicus

Lycium hirsutum Lycium Hyoscyamus desertorum

Lycium villosum Lycium Hyoscyamus muticus

Lycium eenii Lycium Anisodus acutangulus

Lycium schweinfurthii Lycium Anisodus carniolicoides

Lycium shawii Lycium Anisodus tanguticus

Lycium decumbens Lycium Atropa komarovii

Lycium pumilum Lycium Atropa belladonna

Lycium oxycarpum Lycium Jaborosa sativa

Lycium pilifolium Lycium Jaborosa integrifolia

Lycium gariepense Lycium Latua pubiflora

Lycium tenue Lycium Nicotiana velutina

Lycium strandveldense Lycium Nicotiana rosulata

Lycium amoenum Lycium Nicotiana rotundifolia

Lycium grandicalyx Lycium Nicotiana gossei

Lycium arenicola Lycium Nicotiana goodspeedii

Lycium cinereum Lycium Nicotiana cavicola

Lycium afrum Lycium Nicotiana suaveolens

Lycium ferocissimum Lycium Nicotiana eastii

Lycium horridum Lycium Nicotiana amplexicaulis

Lycium schizocalyx Lycium Nicotiana maritima

Lycium boerhaviifolium Lycium Nicotiana excelsior

Lycium pallidum Lycium Nicotiana simulans

Lycium cooperi Lycium Nicotiana megalosiphon

Lycium macrodon Lycium Nicotiana umbratica

Lycium puberulum Lycium Nicotiana occidentalis

Lycium californicum Lycium Nicotiana forsteri

Lycium nodosum Lycium Nicotiana petunioides

Lycium vimineum Lycium Nicotiana noctiflora

Lycium gilliesianum Lycium Nicotiana glauca

Lycium ameghinoi Lycium Nicotiana acaulis

Lycium chanar Lycium Nicotiana africana

Lycium fuscum Lycium Nicotiana plumbaginifolia

Lycium minutifolium Lycium Nicotiana longiflora

Lycium stenophyllum Lycium Nicotiana forgetiana

Lycium cestroides Lycium Nicotiana bonariensis

Lycium cuneatum Lycium Nicotiana langsdorffii

Lycium morongii Lycium Nicotiana alata

Lycium brevipes Lycium Nicotiana stocktonii

Lycium carolinianum Lycium Nicotiana nesophila

Lycium rachidocladum Lycium Nicotiana repanda

Lycium tenuispinosum Lycium Nicotiana nudicaulis

Lycium elongatum Lycium Nicotiana sylvestris

Lycium americanum Lycium Nicotiana pauciflora

Lycium infaustum Lycium Nicotiana acuminata

Lycium minimum Lycium Nicotiana corymbosa

Lycium parishii Lycium Nicotiana miersii

M16. ID/CD/CP torreyi Lycium Nicotiana spegazzinii

Lycium andersonii Lycium Nicotiana linearis

Lycium berlandieri Lycium Nicotiana obtusifolia

Lycium exsertum Lycium Nicotiana quadrivalvis

Lycium fremontii Lycium Nicotiana clevelandii

Exodeconus miersii Exodeconus Nicotiana rustica

Solandra grandiflora Solandra Nicotiana knightiana

Dyssochroma viridiflora Dyssochroma Nicotiana paniculata

Mandragora caulescens Mandragora Nicotiana solanifolia

Nicandra physalodes Nicandra Nicotiana cordifolia

Brugmansia sanguinea Brugmansia Nicotiana raimondii

Brugmansia arborea Brugmansia Nicotiana benavidesii

Brugmansia aurea Brugmansia Nicotiana undulata

ρ discolor Datura

Nicotiana arentsii

I metel Datura Nicotiana glutinosa

Datura inoxia Datura Nicotiana wigandioides

Datura leichhardtii Datura Nicotiana thyrsiflora

Datura ferox Datura Nicotiana tomentosiformis

Datura quercifolia Datura Nicotiana tomentosa

Datura stramonium Datura Nicotiana kawakamii

Datura ceratocaula Datura Nicotiana otophora

Salpichroa origanifolia Salpichroa Nicotiana tabacum

Lycianthes shanesii Lycianthes Duboisia myoporoides Lycianthes biflora Lycianthes Cyphanthera albicans

μ multiflora Lycianthes Duboisia hopwoodii

CD jalicensis Lycianthes Duboisia leichhardtii

Lycianthes heteroclita Lycianthes Cyphanthera anthocercidea

λ lycioides Lycianthes Crenidium spinescens

CD rantonnetii Lycianthes Cyphanthera microphylla Lycianthes asarifolia Lycianthes Anthotroche myoporoides

μ acapulcensis Lycianthes Anthotroche pannosa

P ciliolata Lycianthes Anthotroche walcottii μ moziniana Lycianthes

ID Grammosolen truncatus

Lycianthes rzedowskii Lycianthes Grammosolen dixonii

Lycianthes dejecta Lycianthes Cyphanthera odgersii

Lycianthes peduncularis Lycianthes Anthocercis viscosa

Capsicum geminifolium Capsicum Anthocercis angustifolia

Capsicum lanceolatum Capsicum Anthocercis intricata

ρ ciliatum Capsicum Anthocercis littorea

C rhomboideum Capsicum Anthocercis ilicifolia

q campylopodium Capsicum Anthocercis gracilis

IC villosum Capsicum Symonanthus bancroftii

Capsicum schottianum Capsicum Symonanthus aromaticus

Capsicum recurvatum Capsicum Nierembergia pulchella Capsicum flexuosum Capsicum Nierembergia browallioides

ID CP λ cardenasii Capsicum Nierembergia tucumanensis

CD P eximium Capsicum Nierembergia ericoides

Capsicum pubescens Capsicum Nierembergia scoparia

λ tovarii Capsicum Nierembergia linariifolia

ID chacoense Capsicum Nierembergia calycina

Capsicum baccatum Capsicum Nierembergia veitchii

Capsicum coccineum Capsicum Nierembergia aristata

Capsicum annuum Capsicum Nierembergia graveolens

Capsicum chinense Capsicum Nierembergia repens

Capsicum frutescens Capsicum Nierembergia rivularis

Capsicum galapagoensis Capsicum Bouchetia erecta

Cuatresia cuneata Cuatresia Bouchetia anomala

Cuatresia exiguiflora Cuatresia Hunzikeria texana

Cuatresia riparia Cuatresia Brunfelsia americana

Deprea paneroi Deprea Petunia saxicola

Nothocestrum longifolium Nothocestrum Petunia reitzii

Withania coagulans Withania Petunia altiplana

Withania somnifera Withania Petunia secreta

Iochroma gesnerioides Iochroma Petunia scheideana

Iochroma fuchsioides Iochroma Petunia bonjardinensis

Iochroma lehmannii Iochroma Petunia mantiqueirensis

Acnistus arborescens Acnistus Petunia integrifolia

Iochroma cyaneum Iochroma Petunia exserta

Dunalia solanacea Dunalia Petunia axillaris

Dunalia obovata Dunalia Calibrachoa pygmea

Vassobia breviflora Vassobia Calibrachoa parviflora

Dunalia brachyacantha Dunalia Calibrachoa sellowiana

Eriolarynx lorentzii Eriolarynx Fabiana imbricata

Iochroma australe Iochroma Schizanthus lacteus

Leucophysalis grandiflora Leucophysalis Schizanthus integrifolius

Leucophysalis nana Leucophysalis Schizanthus candidus

Schraderanthus viscosa Schraderanthus Schizanthus alpestris

Brachistus stramoniifolius Brachistus Schizanthus hookeri

Witheringia macrantha Witheringia Schizanthus grahamii

Witheringia meiantha Witheringia Schizanthus tricolor

Physalis alkekengi Physalis Schizanthus parvulus

Posterior Probability carpenteri Calliphysalis Schizanthus pinnatus

Quincula lobata Quincula Schizanthus porrigens

Physalis melanocystis Physalis Schizanthus litoralis

Physalis acutifolia Physalis Schizanthus laetus

Physalis crassifolia Physalis Goetzea elegans

Physalis philadelphica Physalis Espadaea amoena

Physalis longifolia Physalis Metternichia princeps

Physalis glutinosa Physalis Schwenckia lateriflora

Physalis sordida Physalis Cestrum fasciculatum

Physalis nicandroides Physalis Cestrum elegans

0.6 patula Physalis

Cestrum aurantiacum

Physalis peruviana Physalis Cestrum nocturnum

Physalis angustiphysa Physalis Cestrum tomentosum

Physalis cordata Physalis Cestrum diurnum

Physalis ignota Physalis Cestrum strigilatum

Physalis minima Physalis Cestrum megalophyllum

Physalis pruinosa Physalis Sessea corymbiflora

Physalis lagascae Physalis Streptosolen jamesonii

Physalis angulata Physalis Browallia speciosa

0.7 pubescens Physalis Salpiglossis sinuata

Physalis lanceolata Physalis Combera paradoxa

Physalis heterophylla Physalis Pantacantha ameghinoi

Physalis virginiana Physalis Solanum ferocissimum

Physalis arenicola Physalis Solanum chenopodinum

Physalis walteri Physalis Solanum stelligerum

Physalis pumila Physalis Solanum nemophilum

Physalis cinerascens Physalis Solanum densevestitum Physalis mollis Physalis Solanum furfuraceum

0.8 viscosa Physalis Solanum stupefactum

Jaltomata darcyana Jaltomata Solanum corifolium

Jaltomata repandidentata Jaltomata Solanum cookii

Jaltomata bohsiana Jaltomata Solanum sandwicense

Jaltomata procumbens Jaltomata Solanum incompletum

Jaltomata chihuahuensis Jaltomata Solanum semiarmatum

Jaltomata grandiflora Jaltomata Solanum viridifolium

Jaltomata antillana Jaltomata Solanum dimorphispinum

Jaltomata auriculata Jaltomata Solanum inaequilaterum

Jaltomata oppositifolia Jaltomata Solanum quadriloculatum

0.9 salpoensis Jaltomata Solanum ellipticum

Jaltomata aspera Jaltomata Solanum dianthophorum

Jaltomata lojae Jaltomata Solanum esuriale

Jaltomata lanata Jaltomata Solanum centrale

Jaltomata paneroi Jaltomata Solanum cinereum

Jaltomata bernardelloana Jaltomata Solanum sturtianum

Jaltomata sagastegui Jaltomata Solanum petrophilum

Jaltomata herrerae Jaltomata Solanum pungetium

Jaltomata yacheri Jaltomata Solanum prinophyllum

Jaltomata weberbaueri Jaltomata Solanum campanulatum

1.0 ventricosa Jaltomata

Solanum vicinum

Jaltomata sanchez-vegae Jaltomata Solanum ditrichum

Jaltomata andersonii Jaltomata Solanum elachophyllum

Jaltomata lezamae Jaltomata Solanum tetrathecum

Jaltomata sinuosa Jaltomata Solanum orbiculatum

Jaltomata viridiflora Jaltomata Solanum nummularium

Jaltomata yungayensis Jaltomata Solanum oligacanthum

Jaltomata contumacensis Jaltomata Solanum hystrix

Jaltomata leivae Jaltomata Solanum hoplopetalum

Jaltomata biflora Jaltomata Solanum sejunctum

Jaltomata dentata Jaltomata Solanum asymmetriphyllum

Jaltomata bicolor Jaltomata Solanum diversiflorum

Jaltomata umbellata Jaltomata Solanum chippendalei

Jaltomata cajacayensis Jaltomata Solanum phlomoides

Jaltomata lomana Jaltomata Solanum beaugleholei

Jaltomata mionei Jaltomata Solanum melanospermum

Solanum valdiviense Solanum Solanum clarkiae

Solanum guineense Solanum Solanum oedipus

Solanum terminale Solanum Solanum vansittartense

Solanum herculeum Solanum Solanum tudununggae

Solanum trisectum Solanum Solanum petraeum

Solanum capsiciforme Solanum Solanum cataphractum

Solanum simile Solanum Solanum leopoldensis

Solanum symonii Solanum Solanum carduiforme

Solanum vescum Solanum Solanum dioicum

Solanum linearifolium Solanum Solanum cunninghamii

Solanum laciniatum Solanum Solanum lucani

Solanum aviculare Solanum Solanum echinatum

Solanum multivenosum Solanum Solanum horridum

Solanum aligerum Solanum Solanum cleistogamum

Solanum laxum Solanum Solanum lasiophyllum

Solanum amygdalifolium Solanum Solanum gabrielae

Solanum crispum Solanum Solanum coactiliferum

Solanum dulcamara Solanum Solanum oldfieldii

Solanum lyratum Solanum Solanum pyracanthos

Solanum wallacei Solanum Solanum tomentosum

Solanum palitans Solanum Solanum capense

Solanum tripartitum Solanum Solanum humile

Solanum triflorum Solanum Solanum vespertilio

Solanum physalifolium Solanum Solanum lidii

Solanum pallidum Solanum Solanum anguivi

Solanum fiebrigii Solanum Solanum aethiopicum

Solanum villosum Solanum Solanum cyaneopurpureum

Solanum scabrum Solanum Solanum macrocarpon

Solanum opacum Solanum Solanum dasyphyllum

Solanum ptychanthum Solanum Solanum incanum

Solanum americanum Solanum Solanum linnaeanum

Solanum nigrum Solanum Solanum melongena

Solanum taeniotrichum Solanum Solanum insanum

Solanum caripense Solanum Solanum supinum

Solanum fraxinifolium Solanum Solanum violaceum

Solanum appendiculatum Solanum Solanum giganteum

Solanum brevifolium Solanum Solanum marginatum

Solanum etuberosum Solanum Solanum coagulans

Solanum palustre Solanum Solanum aculeastrum

Solanum lycopersicoides Solanum Solanum houstonii

Solanum sitiens Solanum Solanum hindsianum

Solanum juglandifolium Solanum Solanum elaeagnifolium

Solanum ochranthum Solanum Solanum torvum

Solanum habrochaites Solanum Solanum chrysotrichum

Solanum neorickii Solanum Solanum asperolanatum

Solanum chilense Solanum Solanum bonariense

Solanum peruvianum Solanum Solanum paniculatum

Solanum chmielewskii Solanum Solanum donianum

Solanum pennellii Solanum Solanum crotonoides

Solanum galapagense Solanum Solanum lanceifolium

Solanum lycopersicum Solanum Solanum jamaicense

Solanum cheesmaniae Solanum Solanum aridum

Solanum pimpinellifolium Solanum Solanum carolinense

Solanum chomatophilum Solanum Solanum ensifolium

Solanum scabrifolium Solanum Solanum davisense

Solanum pinnatisectum Solanum Solanum citrullifolium

Solanum piurae Solanum Solanum heterodoxum

Solanum bulbocastanum Solanum Solanum tribulosum

Solanum jamesii Solanum Solanum rostratum

Solanum clarum Solanum Solanum fructu-tecto

Solanum morelliforme Solanum Solanum angustifolium

Solanum polyadenium Solanum Solanum lumholtzianum

Solanum cardiophyllum Solanum Solanum grayi

Solanum ehrenbergii Solanum Solanum johnstonii

Solanum andreanum Solanum Solanum tenuipes

Solanum schenckii Solanum Solanum wrightii

Solanum doddsii Solanum Solanum crinitum

Solanum stenophyllidium Solanum Solanum mitlense

Solanum iopetalum Solanum Solanum lycocarpum

Solanum violaceimarmoratum Solanum Solanum sisymbriifolium

Solanum albicans Solanum Solanum vestissimum

Solanum acaule Solanum Solanum pseudolulo

Solanum boliviense Solanum Solanum hyporhodium

Solanum raphanifolium Solanum Solanum pectinatum

Solanum lignicaule Solanum Solanum hirtum

Solanum laxissimum Solanum Solanum stramoniifolium

Solanum maglia Solanum Solanum repandum

Solanum longiconicum Solanum Solanum lasiocarpum

Solanum oxycarpum Solanum Solanum candidum

Solanum agrimoniifolium Solanum Solanum felinum

Solanum colombianum Solanum Solanum quitoense

Solanum stipuloideum Solanum Solanum sessiliflorum

Solanum vernei Solanum Solanum viarum

Solanum candolleanum Solanum Solanum aculeatissimum

Solanum microdontum Solanum Solanum myriacanthum

Solanum demissum Solanum Solanum incarceratum

Solanum kurtzianum Solanum Solanum tenuispinum

Solanum chacoense Solanum Solanum atropurpureum

Solanum berthaultii Solanum Solanum acerifolium

Solanum infundibuliforme Solanum Solanum capsicoides

Solanum okadae Solanum Solanum platense

Solanum stoloniferum Solanum Solanum mammosum

Solanum hjertingii Solanum Solanum palinacanthum

Solanum verrucosum Solanum Solanum stagnale

Solanum guerreroense Solanum Solanum robustum

Solanum hougasii Solanum Solanum paludosum

Solanum latiflorum Solanum Solanum microphyllum

Solanum cacosmum Solanum Solanum gardneri

Solanum exiguum Solanum Solanum hoehnei

Solanum diploconos Solanum Solanum wendlandii

Solanum pinetorum Solanum Solanum allophyllum

Solanum sciadostylis Solanum Solanum diphyllum

Solanum cylindricum Solanum Solanum aphyodendron

Solanum glaucophyllum Solanum Solanum arboreum

Solanum fusiforme Solanum Solanum rovirosanum

Solanum melissarum Solanum Solanum pseudocapsicum

Solanum confusum Solanum Solanum argentinum

Solanum hibernum Solanum Solanum reductum

Solanum luteoalbum Solanum Solanum mauritianum

Solanum stuckertii Solanum Solanum asperum

Solanum oxyphyllum Solanum Solanum rugosum

Solanum pendulum Solanum Solanum cordovense

Solanum tobagense Solanum Solanum abutiloides

Solanum obliquum Solanum Solanum turneroides

Solanum roseum Solanum Solanum adscendens

Solanum maternum Solanum Solanum tenuisetosum

Solanum betaceum Solanum Solanum circinatum

Solanum unilobum Solanum Solanum tegore

Solanum cajanumense Solanum Solanum proteanthum

Solanum fallax Solanum Solanum sibundoyense Solanum endopogon Solanum Solanum occultum

Figure S14: Ancestral state estimation using the maximum a posteriori for each node of the M16. ID/CD/CP model

44 bioRxiv preprint doi: https://doi.org/10.1101/709329; this version posted July 22, 2019. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-NC-ND 4.0 International license.

Speciation Extinction

3 2.0 Type Type 2 1.5 Polyploid Polyploid SC-Diploid 1.0 SC-Diploid 1 SI-Diploid 0.5 SI-Diploid Posterior Density Posterior Density Posterior 0 0.0 1.0 1.5 2.0 2.5 0 1 2 3 Rate Rate Net Diversification Relative Extinction 10.0 15 7.5 Type Type

Polyploid 10 Polyploid 5.0 SC-Diploid SC-Diploid 5 2.5 SI-Diploid SI-Diploid Posterior Density Posterior Density Posterior 0.0 0 -0.3 0.0 0.3 0.6 0.25 0.50 0.75 1.00 Rate Rate Trait change 40

30 Type

Polyploidization from SC 20 Polyploidization from SI 10 SI to SC Posterior Density Posterior 0 0.0 0.1 0.2 0.3 0.4 Rate

Figure S15: Posterior distribution for each of the parameters in the M16. ID/CD/CP model

45 bioRxiv preprint doi: https://doi.org/10.1101/709329; this version posted July 22, 2019. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-NC-ND 4.0 International license.

M19. ID/CD/CP + A/B asym

ρI

Nolana rupicola Nolana

Nolana acuminata Nolana Nolana elegans

Nolana rostrata Nolana Sclerophylax arnottii

Nolana adansonii Nolana Physochlaina orientalis

Nolana galapagensis Nolana Physochlaina praealta

Nolana plicata Nolana Przewalskia tangutica

Nolana laxa Nolana Scopolia parviflora

Nolana aticoana Nolana Scopolia carniolica

Nolana humifusa Nolana Scopolia japonica

Lycium depressum Lycium Atropanthe sinensis

Lycium ruthenicum Lycium Hyoscyamus niger

Lycium tetrandrum Lycium Hyoscyamus albus

Lycium acutifolium Lycium Hyoscyamus pusillus

Lycium bosciifolium Lycium Hyoscyamus turcomanicus

Lycium hirsutum Lycium Hyoscyamus desertorum

Lycium villosum Lycium Hyoscyamus muticus

Lycium eenii Lycium Anisodus acutangulus

yimschweinfurthii Lycium Anisodus carniolicoides

Lycium shawii Lycium Anisodus tanguticus

Lycium decumbens Lycium Atropa komarovii

Lycium pumilum Lycium Atropa belladonna

Lycium oxycarpum Lycium Jaborosa sativa

Lycium pilifolium Lycium Jaborosa integrifolia

Lycium gariepense Lycium Latua pubiflora

Lycium tenue Lycium Nicotiana velutina

Lycium strandveldense Lycium Nicotiana rosulata

Lycium amoenum Lycium Nicotiana rotundifolia

Lycium grandicalyx Lycium Nicotiana gossei

Lycium arenicola Lycium Nicotiana goodspeedii

Lycium cinereum Lycium Nicotiana cavicola

Lycium afrum Lycium Nicotiana suaveolens

Lycium ferocissimum Lycium Nicotiana eastii

Lycium horridum Lycium Nicotiana amplexicaulis Lycium schizocalyx Lycium Nicotiana maritima

μ boerhaviifolium Lycium Nicotiana excelsior

Lycium pallidum Lycium Nicotiana simulans

Lycium cooperi Lycium Nicotiana megalosiphon CD macrodon Lycium

λ Nicotiana umbratica

Lycium puberulum Lycium Nicotiana occidentalis

CD californicum Lycium Nicotiana forsteri

A nodosum Lycium Nicotiana petunioides

Lycium vimineum Lycium Nicotiana noctiflora

A gilliesianum Lycium Nicotiana glauca Lycium ameghinoi Lycium Nicotiana acaulis

μ chanar Lycium Nicotiana africana

Lycium fuscum Lycium Nicotiana plumbaginifolia

ID minutifolium Lycium Nicotiana longiflora μ stenophyllum Lycium Nicotiana forgetiana

CP cestroides Lycium Nicotiana bonariensis A cuneatum Lycium

Nicotiana langsdorffii

Lycium morongii Lycium Nicotiana alata

A brevipes Lycium Nicotiana stocktonii

Lycium carolinianum Lycium Nicotiana nesophila

Lycium rachidocladum Lycium Nicotiana repanda yimtenuispinosum Lycium Nicotiana nudicaulis

ρ elongatum Lycium Nicotiana sylvestris

Lycium americanum Lycium Nicotiana pauciflora C infaustum Lycium

q Nicotiana acuminata

IC minimum Lycium Nicotiana corymbosa

Lycium parishii Lycium Nicotiana miersii

Lycium torreyi Lycium Nicotiana spegazzinii

Lycium andersonii Lycium Nicotiana linearis

Lycium berlandieri Lycium Nicotiana obtusifolia

Lycium exsertum Lycium Nicotiana quadrivalvis

Lycium fremontii Lycium Nicotiana clevelandii ID CD CP miersii Exodeconus Nicotiana rustica

λ A A A grandiflora Solandra Nicotiana knightiana

ID viridiflora Dyssochroma Nicotiana paniculata

λ caulescens Mandragora Nicotiana solanifolia

A CP physalodes Nicandra Nicotiana cordifolia

Brugmansia sanguinea Brugmansia Nicotiana raimondii

A arborea Brugmansia

Nicotiana benavidesii

Brugmansia aurea Brugmansia Nicotiana undulata

Datura discolor Datura Nicotiana arentsii

Datura metel Datura Nicotiana glutinosa

Datura inoxia Datura Nicotiana wigandioides

Datura leichhardtii Datura Nicotiana thyrsiflora

Datura ferox Datura Nicotiana tomentosiformis

Datura quercifolia Datura Nicotiana tomentosa

Datura stramonium Datura Nicotiana kawakamii

Datura ceratocaula Datura Nicotiana otophora

Salpichroa origanifolia Salpichroa Nicotiana tabacum

Lycianthes shanesii Lycianthes Duboisia myoporoides

Lycianthes biflora Lycianthes Cyphanthera albicans

Lycianthes multiflora Lycianthes Duboisia hopwoodii

Lycianthes jalicensis Lycianthes Duboisia leichhardtii

Lycianthes heteroclita Lycianthes Cyphanthera anthocercidea Lycianthes lycioides Lycianthes Crenidium spinescens

α β β rantonnetii Lycianthes Cyphanthera microphylla α α asarifolia Lycianthes

β Anthotroche myoporoides

Lycianthes acapulcensis Lycianthes Anthotroche pannosa

Lycianthes ciliolata Lycianthes Anthotroche walcottii

Lycianthes moziniana Lycianthes Grammosolen truncatus

Lycianthes rzedowskii Lycianthes Grammosolen dixonii

Lycianthes dejecta Lycianthes Cyphanthera odgersii

Lycianthes peduncularis Lycianthes Anthocercis viscosa

Capsicum geminifolium Capsicum Anthocercis angustifolia

Capsicum lanceolatum Capsicum Anthocercis intricata

Capsicum ciliatum Capsicum Anthocercis littorea

Capsicum rhomboideum Capsicum Anthocercis ilicifolia

Capsicum campylopodium Capsicum Anthocercis gracilis

Capsicum villosum Capsicum Symonanthus bancroftii

Capsicum schottianum Capsicum Symonanthus aromaticus

Capsicum recurvatum Capsicum Nierembergia pulchella

Capsicum flexuosum Capsicum Nierembergia browallioides

Capsicum cardenasii Capsicum Nierembergia tucumanensis Capsicum eximium Capsicum Nierembergia ericoides

q pubescens Capsicum Nierembergia scoparia

IC ρ tovarii Capsicum Nierembergia linariifolia C chacoense Capsicum Nierembergia calycina

λ baccatum Capsicum Nierembergia veitchii

ID coccineum Capsicum Nierembergia aristata

ID CD λ annuum Capsicum Nierembergia graveolens B chinense Capsicum

B B CP CP Nierembergia repens B frutescens Capsicum

B Nierembergia rivularis

Capsicum galapagoensis Capsicum Bouchetia erecta

Cuatresia cuneata Cuatresia Bouchetia anomala

Cuatresia exiguiflora Cuatresia Hunzikeria texana

Cuatresia riparia Cuatresia Brunfelsia americana

Deprea paneroi Deprea Petunia saxicola

Nothocestrum longifolium Nothocestrum Petunia reitzii

Withania coagulans Withania Petunia altiplana μ somnifera Withania

μ CP Petunia secreta

ID gesnerioides Iochroma Petunia scheideana B fuchsioides Iochroma

B μ Petunia bonjardinensis

CD lehmannii Iochroma Petunia mantiqueirensis

B λ arborescens Acnistus Petunia integrifolia

CD cyaneum Iochroma Petunia exserta

B solanacea Dunalia Petunia axillaris

Dunalia obovata Dunalia Calibrachoa pygmea

Vassobia breviflora Vassobia Calibrachoa parviflora

Dunalia brachyacantha Dunalia Calibrachoa sellowiana

Eriolarynx lorentzii Eriolarynx Fabiana imbricata Iochroma australe Iochroma Schizanthus lacteus

ρ grandiflora Leucophysalis Schizanthus integrifolius

I nana Leucophysalis Schizanthus candidus

Schraderanthus viscosa Schraderanthus Schizanthus alpestris

Brachistus stramoniifolius Brachistus Schizanthus hookeri

Witheringia macrantha Witheringia Schizanthus grahamii

Witheringia meiantha Witheringia Schizanthus tricolor

Physalis alkekengi Physalis Schizanthus parvulus

Calliphysalis carpenteri Calliphysalis Schizanthus pinnatus

Quincula lobata Quincula Schizanthus porrigens

Physalis melanocystis Physalis Schizanthus litoralis Physalis acutifolia Physalis Schizanthus laetus

Posterior Probability crassifolia Physalis Goetzea elegans

Physalis philadelphica Physalis Espadaea amoena

Physalis longifolia Physalis Metternichia princeps

Physalis glutinosa Physalis Schwenckia lateriflora

Physalis sordida Physalis Cestrum fasciculatum

Physalis nicandroides Physalis Cestrum elegans

Physalis patula Physalis Cestrum aurantiacum

Physalis peruviana Physalis Cestrum nocturnum

Physalis angustiphysa Physalis Cestrum tomentosum Physalis cordata Physalis Cestrum diurnum

0.4 ignota Physalis Cestrum strigilatum

Physalis minima Physalis Cestrum megalophyllum

Physalis pruinosa Physalis Sessea corymbiflora

Physalis lagascae Physalis Streptosolen jamesonii

Physalis angulata Physalis Browallia speciosa

Physalis pubescens Physalis Salpiglossis sinuata

Physalis lanceolata Physalis Combera paradoxa

Physalis heterophylla Physalis Pantacantha ameghinoi

Physalis virginiana Physalis Solanum ferocissimum

Physalis arenicola Physalis Solanum chenopodinum

0.6 walteri Physalis Solanum stelligerum

Physalis pumila Physalis Solanum nemophilum

Physalis cinerascens Physalis Solanum densevestitum

Physalis mollis Physalis Solanum furfuraceum

Physalis viscosa Physalis Solanum stupefactum

Jaltomata darcyana Jaltomata Solanum corifolium

Jaltomata repandidentata Jaltomata Solanum cookii

Jaltomata bohsiana Jaltomata Solanum sandwicense

Jaltomata procumbens Jaltomata Solanum incompletum

0.8 chihuahuensis Jaltomata Solanum semiarmatum

Jaltomata grandiflora Jaltomata Solanum viridifolium

Jaltomata antillana Jaltomata Solanum dimorphispinum

Jaltomata auriculata Jaltomata Solanum inaequilaterum

Jaltomata oppositifolia Jaltomata Solanum quadriloculatum

Jaltomata salpoensis Jaltomata Solanum ellipticum

Jaltomata aspera Jaltomata Solanum dianthophorum

Jaltomata lojae Jaltomata Solanum esuriale

Jaltomata lanata Jaltomata Solanum centrale

Jaltomata paneroi Jaltomata Solanum cinereum

1.0 bernardelloana Jaltomata Solanum sturtianum

Jaltomata sagastegui Jaltomata Solanum petrophilum

Jaltomata herrerae Jaltomata Solanum pungetium

Jaltomata yacheri Jaltomata Solanum prinophyllum

Jaltomata weberbaueri Jaltomata Solanum campanulatum

Jaltomata ventricosa Jaltomata Solanum vicinum

Jaltomata sanchez-vegae Jaltomata Solanum ditrichum

Jaltomata andersonii Jaltomata Solanum elachophyllum

Jaltomata lezamae Jaltomata Solanum tetrathecum

Jaltomata sinuosa Jaltomata Solanum orbiculatum

Jaltomata viridiflora Jaltomata Solanum nummularium

Jaltomata yungayensis Jaltomata Solanum oligacanthum

Jaltomata contumacensis Jaltomata Solanum hystrix

Jaltomata leivae Jaltomata Solanum hoplopetalum

Jaltomata biflora Jaltomata Solanum sejunctum

Jaltomata dentata Jaltomata Solanum asymmetriphyllum

Jaltomata bicolor Jaltomata Solanum diversiflorum

Jaltomata umbellata Jaltomata Solanum chippendalei

Jaltomata cajacayensis Jaltomata Solanum phlomoides

Jaltomata lomana Jaltomata Solanum beaugleholei

Jaltomata mionei Jaltomata Solanum melanospermum

Solanum valdiviense Solanum Solanum clarkiae

Solanum guineense Solanum Solanum oedipus

Solanum terminale Solanum Solanum vansittartense

Solanum herculeum Solanum Solanum tudununggae

Solanum trisectum Solanum Solanum petraeum

Solanum capsiciforme Solanum Solanum cataphractum

Solanum simile Solanum Solanum leopoldensis

Solanum symonii Solanum Solanum carduiforme

Solanum vescum Solanum Solanum dioicum

Solanum linearifolium Solanum Solanum cunninghamii

Solanum laciniatum Solanum Solanum lucani

Solanum aviculare Solanum Solanum echinatum

Solanum multivenosum Solanum Solanum horridum

Solanum aligerum Solanum Solanum cleistogamum

Solanum laxum Solanum Solanum lasiophyllum

Solanum amygdalifolium Solanum Solanum gabrielae

Solanum crispum Solanum Solanum coactiliferum

Solanum dulcamara Solanum Solanum oldfieldii

Solanum lyratum Solanum Solanum pyracanthos

Solanum wallacei Solanum Solanum tomentosum

Solanum palitans Solanum Solanum capense

Solanum tripartitum Solanum Solanum humile

Solanum triflorum Solanum Solanum vespertilio

Solanum physalifolium Solanum Solanum lidii

Solanum pallidum Solanum Solanum anguivi

Solanum fiebrigii Solanum Solanum aethiopicum

Solanum villosum Solanum Solanum cyaneopurpureum

Solanum scabrum Solanum Solanum macrocarpon

Solanum opacum Solanum Solanum dasyphyllum

Solanum ptychanthum Solanum Solanum incanum

Solanum americanum Solanum Solanum linnaeanum

Solanum nigrum Solanum Solanum melongena

Solanum taeniotrichum Solanum Solanum insanum

Solanum caripense Solanum Solanum supinum

Solanum fraxinifolium Solanum Solanum violaceum

Solanum appendiculatum Solanum Solanum giganteum

Solanum brevifolium Solanum Solanum marginatum

Solanum etuberosum Solanum Solanum coagulans

Solanum palustre Solanum Solanum aculeastrum

Solanum lycopersicoides Solanum Solanum houstonii

Solanum sitiens Solanum Solanum hindsianum

Solanum juglandifolium Solanum Solanum elaeagnifolium

Solanum ochranthum Solanum Solanum torvum

Solanum habrochaites Solanum Solanum chrysotrichum

Solanum neorickii Solanum Solanum asperolanatum

Solanum chilense Solanum Solanum bonariense

Solanum peruvianum Solanum Solanum paniculatum

Solanum chmielewskii Solanum Solanum donianum

Solanum pennellii Solanum Solanum crotonoides

Solanum galapagense Solanum Solanum lanceifolium

Solanum lycopersicum Solanum Solanum jamaicense

Solanum cheesmaniae Solanum Solanum aridum

Solanum pimpinellifolium Solanum Solanum carolinense

Solanum chomatophilum Solanum Solanum ensifolium

Solanum scabrifolium Solanum Solanum davisense

Solanum pinnatisectum Solanum Solanum citrullifolium

Solanum piurae Solanum Solanum heterodoxum

Solanum bulbocastanum Solanum Solanum tribulosum

Solanum jamesii Solanum Solanum rostratum

Solanum clarum Solanum Solanum fructu-tecto

Solanum morelliforme Solanum Solanum angustifolium

Solanum polyadenium Solanum Solanum lumholtzianum

Solanum cardiophyllum Solanum Solanum grayi

Solanum ehrenbergii Solanum Solanum johnstonii

Solanum andreanum Solanum Solanum tenuipes

Solanum schenckii Solanum Solanum wrightii

Solanum doddsii Solanum Solanum crinitum

Solanum stenophyllidium Solanum Solanum mitlense

Solanum iopetalum Solanum Solanum lycocarpum

Solanum violaceimarmoratum Solanum Solanum sisymbriifolium

Solanum albicans Solanum Solanum vestissimum

Solanum acaule Solanum Solanum pseudolulo

Solanum boliviense Solanum Solanum hyporhodium

Solanum raphanifolium Solanum Solanum pectinatum

Solanum lignicaule Solanum Solanum hirtum

Solanum laxissimum Solanum Solanum stramoniifolium

Solanum maglia Solanum Solanum repandum

Solanum longiconicum Solanum Solanum lasiocarpum

Solanum oxycarpum Solanum Solanum candidum

Solanum agrimoniifolium Solanum Solanum felinum

Solanum colombianum Solanum Solanum quitoense

Solanum stipuloideum Solanum Solanum sessiliflorum

Solanum vernei Solanum Solanum viarum

Solanum candolleanum Solanum Solanum aculeatissimum

Solanum microdontum Solanum Solanum myriacanthum

Solanum demissum Solanum Solanum incarceratum

Solanum kurtzianum Solanum Solanum tenuispinum

Solanum chacoense Solanum Solanum atropurpureum

Solanum berthaultii Solanum Solanum acerifolium

Solanum infundibuliforme Solanum Solanum capsicoides

Solanum okadae Solanum Solanum platense

Solanum stoloniferum Solanum Solanum mammosum

Solanum hjertingii Solanum Solanum palinacanthum

Solanum verrucosum Solanum Solanum stagnale

Solanum guerreroense Solanum Solanum robustum

Solanum hougasii Solanum Solanum paludosum

Solanum latiflorum Solanum Solanum microphyllum

Solanum cacosmum Solanum Solanum gardneri

Solanum exiguum Solanum Solanum hoehnei

Solanum diploconos Solanum Solanum wendlandii

Solanum pinetorum Solanum Solanum allophyllum

Solanum sciadostylis Solanum Solanum diphyllum

Solanum cylindricum Solanum Solanum aphyodendron

Solanum glaucophyllum Solanum Solanum arboreum

Solanum fusiforme Solanum Solanum rovirosanum

Solanum melissarum Solanum Solanum pseudocapsicum

Solanum confusum Solanum Solanum argentinum

Solanum hibernum Solanum Solanum reductum

Solanum luteoalbum Solanum Solanum mauritianum

Solanum stuckertii Solanum Solanum asperum

Solanum oxyphyllum Solanum Solanum rugosum

Solanum pendulum Solanum Solanum cordovense

Solanum tobagense Solanum Solanum abutiloides

Solanum obliquum Solanum Solanum turneroides

Solanum roseum Solanum Solanum adscendens

Solanum maternum Solanum Solanum tenuisetosum

Solanum betaceum Solanum Solanum circinatum

Solanum unilobum Solanum Solanum tegore

Solanum cajanumense Solanum Solanum proteanthum

Solanum fallax Solanum Solanum sibundoyense Solanum endopogon Solanum Solanum occultum

Figure S16: Ancestral state estimation using the maximum a posteriori for each node of the M19. ID/CD/CP+A/B asym model

46 bioRxiv preprint doi: https://doi.org/10.1101/709329; this version posted July 22, 2019. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-NC-ND 4.0 International license.

Speciation Extinction Type Type

Polyploid A 6 Polyploid A 4 Polyploid B Polyploid B 4 SC-D A SC-D A 2 SC-D B SC-D B 2 SI-Diploid A SI-Diploid A Posterior Density Posterior Density Posterior 0 SI-Diploid B 0 SI-Diploid B 1 2 3 0.0 0.5 1.0 1.5 2.0 Rate Rate Net Diversification Relative Extinction Type Type 6 Polyploid A 7.5 Polyploid A

4 Polyploid B Polyploid B SC-D A 5.0 SC-D A

2 SC-D B SC-D B 2.5 SI-Diploid A SI-Diploid A Posterior Density Posterior Density Posterior 0 SI-Diploid B 0.0 SI-Diploid B -1 0 1 2 0 1 2 3 Rate Rate Trait change Hidden trait change 25 80

20 Type 60 Type 15 Polyploidization from SC 40 alpha 10 Polyploidization from SI beta SI to SC 20 5 Posterior Density Posterior Density Posterior 0 0 0.0 0.2 0.4 0.0 0.5 1.0 1.5 Rate Rate

Figure S17: Posterior distribution for each of the parameters in the M19. ID/CD/CP+A/B asym model

47 bioRxiv preprint doi: https://doi.org/10.1101/709329; this version posted July 22, 2019. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-NC-ND 4.0 International license.

Marginal Model M7 M8 M9 M10 Evidence log-likelihood Every model strongly M6. D/P+δ -1268.83 55.41 42.78 53.37 52.85 preferred over M6 Model M7 moderately M7. CID D/P+δ -1212.42 -12.62 -2.04 -2.04 preferred over M9 and M10 Asymmetric rates strongly M8. D/P+A/B δ -1214.46 10.58 10.07 preferred over symmetric M9. D/P+A/B +δ asym -1214.46 -0.51 No evidence M10. D/P+A/B +δ all asym -1214.97

Table S1: Bayes factors of ploidy-only models with diplodization. Results indicate that a character independent model (M6) is strongly preferred over BiSSE (M1) model. M6 is moderately preferred over any of the HiSSE models with asymmetric hidden rates (M9, M10).

48 bioRxiv preprint doi: https://doi.org/10.1101/709329; this version posted July 22, 2019. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-NC-ND 4.0 International license.

Marginal Model M18 M19 M20 Evidence log-likelihood Every model strongly M16. ID/CP/CD -1459.11 45.11 65.91 63.98 preferred over M16 M17. CID ID/CP/CD * Asymmetric rates strongly M18. ID/CP/CD+A/B -1414 20.79 18.87 preferred over symmetric Asymmetric hidden rates moderately M19. ID/CP/CD +A/B asym -1393.20 -1.92 preferred over all asymmetric M20. ID/CP/CD +A/B all asym -1393.12

Table S2: Bayes factors of ploidy and breeding system without diploidization. Results indicate that the MuHiSSE model with asymmetric hidden rates (17) is strongly preferred over M16 and M18 and moderately preferred over the MuHiSSe with all rates asymetric (M20). *Marginal log-likelihood for M17 could not be calculated within allotted computer time.

49 bioRxiv preprint doi: https://doi.org/10.1101/709329; this version posted July 22, 2019. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-NC-ND 4.0 International license.

Marginal Model M22 M23 M24 M25 Evidence log-likelihood Every model strongly M21. ID/CP/CD+δ -1454.68 55.48 46.031 67.94 65.15 preferred over M21 Model M24 strongly preferred M22. CID ID/CP/CD+δ -1399.201 -9.452 12.45 9.675 over M22 Asymmetric rates strongly M23. ID/CP/CD+A/B δ -1408.65 21.91 19.12 preferred over symmetric Asymmetric hidden rates M24. ID/CP/CD +δ asym -1386.74 -2.78 preferred over all asymmetric M25. ID/CP/CD +δ all asym -1389.52

Table S3: Bayes factors of ploidy and breeding system with diploidization. Results indicate that the MuHiSSE model with asymmetric hidden rates (M24) is strongly preferred over M21-M23 and moderately preferred over the MuHiSSe with all rates asymmetric (M25).

50 bioRxiv preprint doi: https://doi.org/10.1101/709329; this version posted July 22, 2019. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-NC-ND 4.0 International license.

Marginal Preferred Model Comparison K=log(BF(M1,M2) log-likelihood Model (Evidence) M1. D/P -1238.76 M1 vs. M4 60.47 M4 (Strong) M4. D/P+A/B asym -1223.28 M11. I/C -1309.07 M11 vs. M14 61.35 M14 (Strong) M14. I/C+A/B asym -1247.72 M16. ID/CD/CP -1459.11 M16 vs. M19 65.90 M19 (Strong) M19. ID/CD/CP+A/B asym -1393.20 M6. D/P+δ -1283.76 M6 vs. M9 69.3 M9 (Strong) M9. D/P+A/B+δ asym -1214.46 M21. IC/CD/CP+δ -1454.68 M21 vs. M24 68.48 M24 (Strong) M24. IC/CD/CP+A/B+δ asym -1386.20

Table S4: Test for addition of hidden states in models via Bayes factors. Models with hidden states are strongly preferred over simpler models

51 bioRxiv preprint doi: https://doi.org/10.1101/709329; this version posted July 22, 2019. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-NC-ND 4.0 International license.

Marginal Preferred Model Comparison K=log(BF(M1,M2) log-likelihood Model (Evidence) M1. D/P -1238.76 M1 vs. M6 65.92 M6 (Strong) M6. D/P+δ -1267.84 M4. D/P+A/B asym -1223.28 M4 vs. M9 8.81 M9 (Moderate) M9. D/P+A/B+δ asym -1214.46 M16. ID/CD/CP -1459.11 M16 vs. M21 4.41 M21 (Moderate) M21. ID/CD/CP+δ -1454.68 M19. IC/CD/CP +A/B asym -1393.20 M19 vs. M24 6.46 M24 (Moderate) M24. IC/CD/CP+A/B+δ asym -1386.20

Table S5: Test for inclusion of a diploidization rate via Bayes factors. Models with diploidization are moderately preferred over models that do not include a diploidization rate

52 bioRxiv preprint doi: https://doi.org/10.1101/709329; this version posted July 22, 2019. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-NC-ND 4.0 International license.

Marginal Preferred Model Comparison K=log(BF(M1,M2) log-likelihood Model (Evidence) M3. D/P+A/B -1234.52 M3 vs. M4 11.239 M4 (Strong) M4. D/P+ A/B asym -1223.28 M4 vs. M5 -1.658 M4 (Moderate) M5. D/P+A/B all asym -1224.93 M13. I/C+ A/B -1270.47 M13 vs. M14 22.75 M14 (Strong) M14. I/C+ A/B asym -1247.72 M14 vs. M15 0.05 No evidence M15. I/C+ A/B all asym -1247.67 M18. IC/CD/CP+A/B -1414.00 M18 vs. M19 20.79 M19 (Strong) M19. IC/CD/CP+ A/B asym -1393.21 M19 vs. M20 -1.919 M19 (Moderate) M20. IC/CD/CP+ A/B all asym -1395.129 M8. D/P +A/B+δ -1225.05 M8 vs. M9 10.58 M9 (Strong) M9. D/P+ A/B+ δ asym -1214.46 M9 vs. M10 -0.52 M10 (Moderate) M10. D/P+A/B+δ all asym -1214.98 M23. IC/CD/DP+A/B+δ -1408.65 M23 vs M24 21.91 M24(Strong) M24. IC/CD/DP+A/B+δ asym -1386.74 M24 vs M25 -2.78 M24 (Moderate) M25. IC/CD/DP+A/B+ δ all asym -1389.52

Table S6: Test for symmetry of the hidden and trait rates via Bayes factors. For all models asymmetric hidden transition rates are preferred over models with equal hidden rates. Adding more complexity by assuming asymmetry in the trait rate within hidden states does not improve models.

53 What is the focal trait?

Ploidy only Br eeding sy stem only Ploidy and br eeding sy stem Ploidy only (lumped) Breeding system only (lumped)

no diploidization with diploidization no diploidization with diploidization

M1. D/P M6. D/P+ δ M11. I/C M16. ID/CD/CP M21. ID/CD/CP + δ M26. Lumped D/P M28. Lumped I/C

ρ ρ μD μC I I μP μI μ μC μD μ μD μP I P μCD λ μCD λ Focal trait onl y CD μ CD μ λC ρ μID P μID P λD q ρ0 λP ρ IC λI q0 ρC λ λD D P λ ρC ρC D D P λP λP λI I C C qIC qIC ID CD CP ID CP ID CP λ ID CP λ CD δ qIC λ CD P λ CD P ID ID δ

M17 . CID ID/CD/CP M22. CID ID/CD/CP + δ

μ λ M2. CID D/P M7. CID D/P + δ M12. CID I/C A A μA λA

μA λA μA λA μA λA ρI ρI

qIC ρC qIC ρC ρ ρ IDA CDA CPA IDA CDA CPA DA PA DA PA IA CA δ qIC Hidden trait onl y δ α β α β α β α β α β α β α β α β α β α β α β α β

ρ ρ bioRxiv preprint doi: https://doi.org/10.1101/709329; this version posted July D22, 2019. The copyrightP holder for this preprint (which was not D P I CB B B B B B q q ρ q ρC certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under IC IC CD C IC aCC-BY-NC-ND 4.0 International license. δ IDB B CPB IDB CDB CPB δ

μB λ μB λ μB λ B B B ρI ρI

μ μB λB B λB

M3. D/P + A/B M8. D/P + A/B + δ M13. I/C + A/B M18. ID/CD/CP + A/B M23. ID/CD/CP + A/B + δ

ρI ρI

μCD λ μCD λ μ μ μ μ A CDA A CDA DA μP DA μP IA CA μID μID A A A μCPA A μCPA ρ ρ q ρC q ρC λ λ I C λ IC IC DA DA PA λP DA DA PA λP λI A A CA λID IDA CDA CPA λID IDA CDA CPA A A A qIC A λCPA A λCPA δ δ α α α α α α α α α α α α α α α α α α α α α α α α

ρ ρ λ ρC λ P λP λ P λP IB λ qIC ρC qIC DB DB B B DB DB B B I CB CB λID CD λ λID CD λ B q B IDB B CPB CPB B IDB B CPB CPB δ IC δ μPB μPB μD μD μIB μ μID μCP μID μCP B B CB B μCD B B μCD B

B λCDB B λCDB What affects diversification? affects What ρI ρI M27. Lumped D/P + A/B M29. Lumped I/C + A/B λ DA μPA μ μ M4. D/P + A/B asym M9. D/P + A/B + δ asym M14. I/C + A/B asym M19 . ID/CD/CP + A/B asym M24. ID/CD/CP + A/B + δ asym DA μ CA λ IA q ρ0 PA ρ IC λ ρ I IDA CDA CPA CA I q0 ρC μCD λCD IDA CDA CPA μD μ μD μ μ μ μCD λ μ A A A PA A PA IA CA μ A CDA IDA μCP IDA μCP ρ A Focal trait ρ ρ A qIC C qIC ρC λD D P λP λD D P λP λ I C λC λ IDA CDA CPA A A A A A A A A IA A q A A λ ID CD CP IDA λCP IC IDA A A A λCP δ A δ A α α α α α and α α α α α α α α β α β α β α β α β α β α β α β α hidden trait α β α β α β β ρ ρ λ λ λ qIC ρC λD D PB PB λD D PB PB IB λ q B B B B I B CB IC ρC λID ID CD λ qIC ρ0 q B C λID CD λ B B B CPB CPB 0 ρC qIC B IDB B CPB CPB IDB CDB CP ID CD μP δ μP δ B B B CPB B B μI μ μ λI μD μD B CB μID CPB B λ B B μID μCP B μCD λ λD λP CB B μCD λ B B CDB B B B CDB μ ρ IB I μPB μCB μDB M5. D/P + A/B all asym M10. D/P + A/B + δ all asym M15. I/C + A/B all asym M20. ID/CD/CP + A/B all asym M25. ID/CD/CP + A/B + δ all asym

A A ρ I ρ I

μD μCD λCD μCD λCD μD A μP μ μ μ A A μ A A A μP A A IA CA IDA μCP IDA μCP A A ρ A A A A A A ρ q IC ρ C q IC ρ C λD DA P λP λD DA P λP A A A λ IA CA λC λ IDA CDA CPA λ IDA CDA CPA A A A IA A A IDA λCP IDA A λCP δA q IC A δ A α β α β α β α β α β α β α β α β α β α β α β α β

B ρB ρ B λ λP B B B ρ C λ P λP DB DB PB B λI q ρ q DB DB B B B λC λID IC CD C λID IC CD B IB CB B B IDB B CPB λCPB B IDB B CPB λCPB δ B δB μPB μ q IC μPB IB μ μ μ μDB CB μID CPB μID CPB μDB B μCD B μCD B λCDB B λCDB B B ρ I ρ I