REPORTS reduction in chemical potential by forming the are already in positions similar to those in the un- 25. The reaction volume was calculated by assuming a ring crystalline phase. In the second scenario, we derlying bulk sapphire. The oxygen collected of triangular cross section. Calculation of the volume yields ~1.7 × 10−20 cm3. Given that the number of assume that oxygen has first adsorbed to the on the LV surface is used to eradicate the facets 22 oxygen atoms per unit volume of a-Al2O3 is 8.63 × 10 LS interface, driven by the reduction in inter- at the outer, top rim of the nanowires once a atoms cm−3, the number of oxygen atoms contained face energy (24, 28), having diffused along the complete (0006) layer is formed. It is this process within the reaction volume is ~1.46 × 103 atoms. The interface from the triple junction. Once oxygen that is the rate-limiting step. number of oxygen atoms needed to deposit a monolayer of close-packed oxygen at the LS (0001) interface was adsorbs, a critical-size nucleus (in the form of calculated by assuming a square and a circular shape a step) forms at the triple junction and sweeps of the interfaces. The area density of a hexagonal close- References and Notes − across the LS (0001) interface, forming a new packed oxygen layer is 1.6 × 1015 atoms cm 2. The 1. E. I. Givargizov, J. Cryst. Growth 31, 20 (1975). a amount of oxygen needed to deposit a monolayer of (0006) layer of -Al2O3 in its wake. Oxygen then 2. F. M. Ross, J. Tersoff, M. C. Reuter, Phys. Rev. Lett. 95, close-packed oxygen is ~1.6 × 103 and ~1.2 × 103 again adsorbs to the new LS interface, supplied 146104 (2005). atoms for the square and the circular interfaces, 3. Y. Hao, G. Meng, Z. L. Wang, C. Ye, L. Zhang, Nano Lett. from the dissolving outer rim of the nanowire. respectively. 6, 1650 (2006). The nucleation rate of steps is relatively low un- 26. S. M. Roper et al., J. Appl. Phys. 102, 034304 4. L. E. Jensen et al., Nano Lett. 4, 1961 (2004). (2007). der the present experimental conditions, leading 5. S. Kodambaka, J. Tersoff, M. C. Reuter, F. M. Ross, 27. K. W. Schwarz, J. Tersoff, Phys. Rev. Lett. 102, to single steps that sweep across the interface (no Science 316, 729 (2007). 206101 (2009). 6. V. Valcárcel, A. Souto, F. Guitián, Adv. Mater. defects resulting from the intersection of steps 28. G. Levi, W. D. Kaplan, J. Am. Ceram. Soc. 85, 1601 10, 138 (1998). or multiple nucleation events were detected). (2002). 7. W. F. Li et al., Phys. Stat. Sol. A 203, 294 (2006). 29. The in situ TEM experiments were carried out using the Both of these reactions would be very fast; the 8. T. Kuykendall et al., Nat. Mater. 3, 524 (2004). Stuttgart high-voltage microscope (JEM-ARM 1250) at the formation of a new (0006) layer after oxygen 9. E. A. Stach et al., Nano Lett. 3, 867 (2003). Max-Planck-Institut für Metallforschung. We thank 10. Y. Wu, P. Yang, J. Am. Chem. Soc. 123, 3165 diffusion has started requires only ~0.16 s. Our F. Phillipp, R. Höschen, and U. Salzberger for technical (2001). experimental observations cannot distinguish support, and D. Chatain and the participants of the 3 11. S. Hofmann et al., Nat. Mater. 7, 372 (2008). Phase, Interface, Component Systems (PICS3) meeting for between these two scenarios. 12. G. Lee et al., Angew. Chem. 48, 7366 (2009). stimulating discussions. Supported by the German Our in situ HRTEM observations have re- 13. B. Tian, P. Xie, T. J. Kempa, D. C. Bell, C. M. Lieber, Science Foundation via the Graduiertenkolleg Innere Nat. Nanotechnol. 4, 824 (2009). vealed an oscillatory growth process that is not Grenzflächen (GRK 285/3), the German-Israel Fund 14.S.H.Oh,Y.Kauffmann,C.Scheu,W.D.Kaplan,M.Rühle, obvious from ex situ observations of grown nano- (grant I-779-42.10/2003), the Nano and Steel Fusion Science 310, 661 (2005); published online wires. These observations provide an explanation Research Program funded by the POSCO (S.H.O.) Basic 6 October 2005 (10.1126/science.1118611). Science Research Institute grant 2.0006028 (S.H.O.), the for the (0001) growth mechanism and why it is 15. See supporting material on Science Online. on October 21, 2010 Basic Science Research Program through the National not continuous. What distinguishes this reaction 16. V. Laurent, D. Chatain, C. Chatillon, N. Eustathopoulos, Research Foundation funded by the Ministry of Acta Metall. 36, 1797 (1988). from most VLS processes is that the catalyst Education, Science and Technology (grant 2010- 17. D. Chatain, W. C. Carter, Nat. Mater. 3, 843 droplet is not directly involved in supplying all 0005834) (S.H.O.), the excellence cluster Nanosystems (2004). Initiative Munich (C.S. and S.H.O.), and the Materials the necessary components for growth. Instead, 18. E. J. Siem, W. C. Carter, D. Chatain, Philos. Mag. 84, Sciences and Engineering Division of the U.S. oxygen for the new (0006) layer is supplied by 991 (2004). Department of Energy (M.F.C. and W.L.). transient sacrificial dissolution of the top rim of 19. H. Wang, G. S. Fischman, J. Appl. Phys. 76, 1557 the nanowires via facet formation. The compo- (1994). 20. H. Saka, K. Sasaki, S. T. Tsukimoto, S. Arai, J. Mater. Res. nents of interface tensions at the triple junction Supporting Online Material 20, 1629 (2005). www.sciencemag.org/cgi/content/full/330/6003/489/DC1

also promote formation of the facets and probably www.sciencemag.org 21. D. J. Siegel, L. G. Hector Jr., J. B. Adams, Phys. Rev. B 65, SOM Text drive the nucleation of steps of solid (0006), 085415 (2002). Figs. S1 to S5 which sweep across the LS (0001) interface, re- 22. W. D. Kaplan, Y. Kauffmann, Annu. Rev. Mater. Res. 36, References 1 (2006). Movies S1 to S3 sulting in growth of a new (0006) layer. Forma- 23. A. Hashibon, J. Adler, M. W. Finnis, W. D. Kaplan, tion of the (0006) layer is relatively fast because Interface Sci. 9, 175 (2001). 7 April 2010; accepted 16 September 2010 the Al atoms on the liquid side of the LS surface 24. G. Levi, W. D. Kaplan, Acta Mater. 50, 75 (2002). 10.1126/science.1190596

may have been overlooked because of method- Downloaded from Species Selection Maintains ological shortcomings (5, 6). The overwhelming majority of flowering Self-Incompatibility plants function as both males and females, but despite the potential for self-fertilization in her- Emma E. Goldberg,1 Joshua R. Kohn,2 Russell Lande,3 Kelly A. Robertson,1 maphrodites, most of these plants predominantly Stephen A. Smith,4 Boris Igic´1* or exclusively mate with other individuals (out- cross) (7, 8). Outcrossing is often enforced by Identifying traits that affect rates of speciation and extinction and, hence, explain differences in self-incompatibility (SI): the ability of individual species diversity among clades is a major goal of evolutionary biology. Detecting such traits is plants to recognize and reject their own pollen. especially difficult when they undergo frequent transitions between states. Self-incompatibility, Each SI system characterized to date relies on the ability of hermaphrodites to enforce outcrossing, is frequently lost in flowering plants, enabling self-fertilization. We show, however, that in the nightshade plant family (Solanaceae), species with functional self-incompatibility diversify at a significantly higher rate than those without it. 1Department of Biological Sciences, University of Illinois at The apparent short-term advantages of potentially self-fertilizing individuals are therefore offset Chicago, 840 West Taylor Street, M/C 067, Chicago, IL 60607, USA. 2Division of Biological Sciences, University of California at by strong species selection, which favors obligate outcrossing. San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA. 3Division of Biology, Imperial College London, Silwood Park 4 1–4 Campus,Ascot,Berkshire,SL57PY,UK. National Evolutionary he astonishing diversity of flowering plants acteristics ( ). Although it is clear that no Synthesis Center 2024 West Main Street, Durham, NC 27705, has led to numerous hypotheses linking single character can entirely explain the variation USA. 2, 4 Tthe propensity for diversification to mor- in plant diversity ( ), many traits potentially *To whom correspondence should be addressed. E-mail: phological, life history, and physiological char- associated with an increase in species richness [email protected]

www.sciencemag.org SCIENCE VOL 330 22 OCTOBER 2010 493 REPORTS

complex genetic mechanisms (9). Their value is many agriculturally important species (such as (Fig. 1). This sample did not statistically differ in primarily attributed to the avoidance of inbreed- tomato, potato, chile, and tobacco), so phyloge- SI frequency from the total available data set of ing depression (10), but the short-term disad- netic and breeding system data are extensive. 616 species (P > 0.3), and our analyses accounted vantages of SI, which limits an individual plant's Among the estimated 2700 species in the fam- for sampling incompleteness (21). ability to reproduce if outcross pollen is not avail- ily, approximately 57% are SC, 41% are SI, and Irreversible loss of SI in Solanaceae will able, is expected to result in frequent transitions to less than 2% have separate male and female cause the frequency of SI to decline to zero if rI ≤ self-compatibility (SC) (8). Mate limitation and plants (19). rC + qIC,whererI and rC are net diversification the automatic advantage of selfing (10, 11) each We constructed a phylogeny through an ini- rates (the difference between speciation and favor the spread of mutants that break down SI. tial alignment matrix of 998 species and eight extinction rates) for SI and SC lineages, respec- Indeed, angiosperm families in which SI is found genes, and we assigned character states (SI or SC) tively, and qIC is the per-lineage rate of transition also contain significant proportions of SC species for 616 species (19). Subsequent analyses con- from SI to SC. Alternatively, the loss of SI may (12). The two states are commonly interspersed centrated on a monophyletic clade termed “x = be offset by more rapid diversification of SI within clades, implying frequent evolutionary tran- 12” for its uniform base chromosome number, lineages when rI > rC + qIC. In this latter case, sitions. Independent data, both genetic and phylo- containing approximately 2300 species, including the equilibrium proportion of SI species, pSI,is genetic (12, 13), suggest that the transition from the subfamilies Solanoideae and Nicotianoideae positive and equal to 1 − qIC/(rI − rC)(17). SI to SC is one of the most common evolutionary (20) [we also conducted analyses on the whole We analyzed character evolution and diversi- shifts in flowering plants (14). Studies of the ge- family (19)]. Both character states and phylo- fication on the maximum likelihood tree (Fig. 1) netic basis of SI indicate that novel SI systems genetic data are better sampled in this clade than and also on 100 bootstrap trees to assess robust- originate very rarely (9, 15). The combined evi- in the rest of the family, yielding 356 species ness to phylogenetic uncertainty (19). Rates of dence implies that SI is frequently lost by species present in the tree and with known mating systems speciation (lI and lC; the subscripts denote SI and that an identical form of SI is only rarely, if ever, regained (12). In Solanaceae species with SI, strong negative frequency-dependent selection maintains dozens of alleles at the locus controlling self-recognition (S-locus), where it has preserved ancestral poly- 13 16 17 morphism over 40 million years ( , , ). After on October 21, 2010 pollination, if the haploid pollen allele matches either allele of the diploid female reproductive organ, fertilization is prevented. Individuals with common alleles therefore have fewer potential mates, and those with rare alleles more, so that alleles ordinarily lost by drift are instead main- tained over long time scales (16). The outcome is a pattern of ancestral polymorphism shared not

only across species boundaries but among distant- www.sciencemag.org ly related genera. Randomly sampled alleles from different SI species of Solanaceae are often more closely related than those within species (16, 17). This provides strong evidence that a polymorphic and therefore functional S-locus was present in thecommonancestorandpassedontodescend- ent SI species in the family (17).

Although the SI mechanism has been fre- Downloaded from quently lost and not regained within Solanaceae (13), it occurs at an intermediate frequency. The proportion of SI species is declining with each transitiontoSC,soSImaybedestinedforex- tinction. But the SI mechanism of Solanaceae is ~90 million years old, nearly as old as eudicots (15), and SI may instead persist if the diversifi- cation rate of SI lineages exceeds that of SC lineages by at least the SI-to-SC transition rate (17). In this scenario, the loss of SI may be count- ered by a greater difference between speciation and extinction rates associated with the presence of SI relative to SC. A strong association between SI and increased diversification would provide Fig. 1. Maximum likelihood tree of phylogenetic relationships among 356 species of Solanaceae. unusually compelling evidence for a causal re- Higher ranks are indicated around the perimeter of the tree. Purple and turquoise tip colors denote SI lationship, because frequent character changes to and SC extant species, respectively. The root age is 36 million years. Inset panels display posterior SC uncouple the evolution of the focal character probability distributions and 95% credibility intervals of reconstructed rates of character evolution (the from others and reduce the chance that an inferred time unit is millions of years). (A) BiSSE estimates of transition, speciation, and extinction parameters 18 connection is spurious ( ). (qIC << mI < lI << lC < mC). (B) Net diversification rate—the difference between speciation and We examined the effect of SI on diversifi- extinction rates—associated with each state. (C) Schematic summary of estimated rate parameters. For cation in Solanaceae. The nightshades contain methods, species names, character states, and further results, see (19).

494 22 OCTOBER 2010 VOL 330 SCIENCE www.sciencemag.org REPORTS and SC states, respectively), extinction (mI and mC), Our results point to a strong role for species relationship between traits, including SI, and specia- and loss of SI (qIC) were estimated with Markov selection in determining the evolutionary dynam- tion and extinction may result in the uneven chain Monte Carlo analyses under the binary- ics and distribution of mating systems among patterns of diversification rates observed among state speciation and extinction (BiSSE) model species. Both theoretical and empirical studies on clades of flowering plants (2, 4), especially when (19, 22), which explicitly incorporates differing the shape of outcrossing rate distributions have coupled with time heterogeneity and historical speciation and extinction rates associated with overlooked the possibility that species selection contingency. These results provide evidence that the two states of a binary character. Because SI may produce an arbitrary proportion of selfing, the evolutionary origin and maintenance of SI has apparently not been regained in this clade mixed-mating, and outcrossing species (8, 27). mayplayanimportantroleinshapingtheimmense (13), we fixed the rate of transitions from SC to It remains unknown why strict avoidance of extant diversity of flowering plants (18, 33). SI, qCI, to be zero in our main analyses [although self-fertilization yields such strong long-term evo- we also considered bidirectional transitions (19)]. lutionary advantages. Outcrossing plants, which References and Notes We find a higher rate of speciation for SC generally maintain high effective population sizes 1. C. Darwin, F. Darwin, A. C. Seward, More Letters of Charles Darwin: A Record of His Work in a Series of than SI lineages, but this apparent advantage is and recombination rates, may have increased poly- Hitherto Unpublished Letters (J. Murray, London, 1903). erased by an SC extinction rate that exceeds that morphism, lower linkage disequilibrium, more 2. S. Magallón, M. J. Sanderson, Evolution 55, 1762 (2001). of SI lineages and even the SC speciation rate efficient response to purifying selection, more 3. S. C. H. Barrett, Philos. Trans. R. Soc. London Ser. B 358, 991 (2003). [mI < lI < lC < mC, with posterior probability 0.99 extensive geographic distribution of genetic di- 28–31 4. T. J. Davies et al., Proc. Natl. Acad. Sci. U.S.A. 101, (Fig. 1A)]. SI lineages consequently show a versity, and lower rates of extinction ( ). 1904 (2004). substantially higher rate of net diversification Various mechanisms other than SI, such as the 5. W. P. Maddison, Evolution 60, 1743 (2006). ć than do SC lineages [rI > rC, with posterior prob- physical and temporal separation of sexes within 6. E. E. Goldberg, B. Igi , Evolution 62, 2727 (2008). ability 1.0 (Fig. 1B)]. Furthermore, this diversi- hermaphrodite flowers, or single-sex individuals, 7. C. Goodwillie, S. Kalisz, C. G. Eckert, Annu. Rev. Ecol. 3 Evol. Syst. 36, 47 (2005). fication difference is large enough to counter the can effect outcrossing in the absence of SI ( ). 8. B. Igić, J. R. Kohn, Evolution 60, 1098 (2006). irreversible loss of SI [rI > rC + qIC, with posterior Moreover, although SI may be a relatively ef- 9. V. Franklin-Tong, Self-Incompatibility in Flowering probability 1.0 (Fig. 2A)]. The equilibrium fre- ficient mechanism for obligate outcrossing (32), Plants: Evolution, Diversity, and Mechanisms quency of SI is therefore positive [p > 0.25, delayed selfing ability and plastic sex expression (Springer, Berlin, 2008). SI 10. E. Porcher, R. Lande, Evolution 59, 46 (2005). with posterior probability 0.99 (Fig. 2B)], demon- afforded by other breeding systems may addi- 11. J. W. Busch, D. J. Schoen, Trends Plant Sci. 13, 128 (2008). strating that the macroevolutionary advantage of tionally provide reproductive assurance (7). 12. B. Igić, R. Lande, J. R. Kohn, Int. J. Plant Sci. 169,93 (2008).

SI is enough for it to persist indefinitely, despite At short time scales, the expression of inbreed- on October 21, 2010 ć its loss through transitions to SC. These results ing depression can oppose the spread of muta- 13. B. Igi , L. Bohs, J. R. Kohn, Proc. Natl. Acad. Sci. U.S.A. 103, 1359 (2006). are robust to phylogenetic uncertainty and against tions that break down SI, but many ecological 14. G. L. Stebbins, Flowering Plants (Belknap Press, the assumption that SI is not regained (19). factors favor their rapid and frequent fixation (7). Cambridge, MA, 1974). The higher rate of diversification associated This is problematic because natural selection 15. J. E. Steinbachs, K. E. Holsinger, Mol. Biol. Evol. 19, 825 (2002). with SI means that selection is acting among cannot maintain features slated for future use 16. T. R. Ioerger, A. G. Clark, T. H. Kao, Proc. Natl. Acad. Sci. species, which can produce trends that are not (18). We find that SC is associated with a macro- U.S.A. 87, 9732 (1990). predictable from studies of selection among in- evolutionary disadvantage from high extinction 17. B. Igić, L. Bohs, J. R. Kohn, New Phytol. 161, 97 (2004). dividuals within species. Natural selection can act rates, despite its high speciation rates relative to 18. G. C. Williams, Natural Selection: Domains, Levels, and Challenges (Oxford Univ. Press, New York, 1992). on many levels of evolutionary hierarchy (includ- SI. Both theoretical and empirical evidence link 19. Materials, methods, and further results are available as www.sciencemag.org ing genes, individuals, populations, and species), inbreeding with an increased probability of ex- supporting material on Science Online. with the potential for cascading effects of se- tinction (27, 29, 31). Self-fertilization and increased 20. R. G. Olmstead, L. Bohs, Acta Hortic. 745, 255 (2007). lection from any level to those above and below inbreeding are also closely tied to higher among- 21. R. G. FitzJohn, W. P. Maddison, S. P. Otto, Syst. Biol. 58, 18 23–26 30 595 (2009). ( , ). Species, as units, may vary in her- population differentiation ( ), which may in turn 22. W. P. Maddison, P. E. Midford, S. P. Otto, Syst. Biol. 56, itable traits associated with different rates of mul- lead to escalating speciation rates. 701 (2007). tiplication. A higher form of selection may thus We conclude that species selection opposes 23. R. C. Lewontin, Annu. Rev. Ecol. Syst. 1, 1 (1970). be manifested as a trait-dependent net diversifica- the short-term advantages provided by the ability 24. S. J. Gould, Science 216, 380 (1982). 25. D. Jablonski, Annu. Rev. Ecol. Evol. Syst. 39, 501 (2008). tion rate. There is wide acceptance of the existence of flowering plants to self-fertilize, and that vol- 26. D. L. Rabosky, A. R. McCune, Trends Ecol. Evol. 25, 68 (2010). Downloaded from of higher-order selection (18, 25, 26) but rela- atile dynamics underlie the scattered phyloge- 27. D. J. Schoen, J. W. Busch, Int. J. Plant Sci. 169, tively sparse data on its importance (25, 26). netic distribution of SC plant species. A strong 119 (2008). 28. G. L. Stebbins, Am. Nat. 91, 337 (1957). 29. D. J. Schoen, A. H. Brown, Proc. Natl. Acad. Sci. U.S.A. 88, 4494 (1991). A B 30. J. L. Hamrick, M. J. W. Godt, Philos. Trans. R. Soc. London rI − rC − qIC pSI Ser. B 351, 1291 (1996). 8 31. S. Glémin, E. Bazin, D. Charlesworth, Proc. R. Soc. London Ser. B 273, 3011 (2006). 32. K. Karoly, Am. Nat. 144, 677 (1994). 33. M. S. Zavada, T. N. Taylor, Am. Nat. 128, 538 (1986). 34. We thank R. FitzJohn, A. Mooers, R. Olmstead, T. Paape,

46 L. Popović, D. L. Shade, and R. Ree for help and discussions. Data are deposited in the Dryad database with accession no. 1888. Funded by NSF grant DEB-

probability density 0919089 to B.I. Supporting Online Material 02 0123456 www.sciencemag.org/cgi/content/full/330/6003/493/DC1 Materials and Methods 0.0 0.2 0.4 0.6 0.8 1.0 0.0 0.1 0.2 0.3 0.4 0.5 SOM Text rate frequency Figs. S1 and S2 Tables S1 to S4 Fig. 2. Further analyses of the posterior rate distributions in Fig. 1. (A) The diversification rate of SI is References sufficiently higher than that of SC for it to persist deterministically (shown by positive values here) despite 1 July 2010; accepted 25 August 2010 frequent and irreversible loss. (B) The equilibrium frequency of SI is consequently always positive. 10.1126/science.1194513

www.sciencemag.org SCIENCE VOL 330 22 OCTOBER 2010 495 www.sciencemag.org/cgi/content/full/330/6003/493/DC1

Supporting Online Material for

Species Selection Maintains Self-Incompatibility E. E. Goldberg, J. R. Kohn, R. Lande, K. A. Robertson, S. A. Smith, B. Igic∗

*To whom correspondence should be addressed. E-mail: [email protected]

Published 22 October 2010, Science 330, 493 (2010) DOI: 10.1126/science.1194513

This PDF file includes:

Materials and Methods SOM Text Figs. S1 and S2 Tables S1 to S4 References Materials and methods

Phylogeny construction Alignment and tree construction pipeline

The procedure for reconstructing phylogenetic relationships among a subset of Solanaceae closely followed the one developed and reported in detail by Smith and colleagues (S1, S2).

We implemented this pipeline in Python (v2.5) with the BioPython (v1.48) module (S3) and using the BioSQL (v1.0.1) database schema (S4). Here, we present the most important aspects of this procedure.

We found eight loci within Solanaceae with more than 200 taxa represented in GenBank. Six of these genes are encoded in the chloroplast genome: atpB (ca. 300 entries), matK (520), ndhF (500), rbcL (220), trnK (210), trnL-trnF (700), and two in the nuclear genome: GBSSI

(790), ITS (910). We removed taxa with identical (duplicated) names and produced a first- pass multiple alignment using MAFFT (S5), which resulted in a 1084-taxon, 16,405bp (eight- gene) matrix. Gene-partitioned phylogenetic reconstructions were performed using RAxML

(v7.0.4) (S6). Subsequent analyses were performed on the maximum likelihood (ML) tree found in a heuristic search and on 100 bootstrap replicates. We manually curated the tree obtained after the initial pass. The resulting matrix contained 995 ingroup taxa, plus five outgroup species of

Convolvulaceae (Fig. S1). The resulting trees were then pruned to include only those species contained within the “x=12” clade, the best-sampled monophyletic group in the family. Cultivars and known hybrid varieties were removed from the analyses, as were those species for which the self-incompatibility status is unknown. The final dataset contained 356 species (Fig. S2). In addition, we present below abbreviated results for the dataset consisting of all 397 species in the family on the tree and with known character states.

1 Relaxed molecular clock implementation

In order to ultrametricize our phylogenetic trees and obtain node and tip dates proportional to true time (rather than substitutions per site), we used the semiparametric method developed by Sanderson (S7). This method accommodates rate variation among lineages by combining a parametric model with different nucleotide substitution rates on every branch with a nonpara- metric roughness penalty. The λ parameter for penalized likelihood calculations determines the contribution of this penalty. It was estimated using a cross-validation procedure implemented in r8s (v1.71) (S7). We applied 13 values of λ, spaced evenly on a logarithmic scale from 1 to 1000, after randomly pruning the ML tree to 71 taxa (for computational feasibility) 10 times. In each pruned set, the best estimate was log10 λ = 2.25, which we used for penalized likelihood rate-smoothing on the ML and bootstrap trees. Accurate absolute divergence dates are not crucial for our analyses. Nevertheless, we ob- tained approximate values in order to make the units of the results of our character evolution analyses meaningful for comparative study. We constrained the age of the focal crown group (“x=12” clade) to 36 Ma based on the node date obtained by Paape and colleagues (S8). This dating procedure relies on the use of two key constraints derived from dating and identification of Solanum- and Physalis-like seeds (S9). Those two dates were used to anchor a normally distributed age prior (µ = 10.0 Ma, σ = 4.0 Ma; 95% CI = [3.4, 16.6]), along with the date for stem group age of Solanaceae (divergence from Convolvulaceae; µ = 52 Ma, σ = 5.2 Ma; 95% CI = [43, 60]). The divergence dates we obtained are comparable to others recovered with different strategies [e.g., (S10, S11)].

Character evolution analyses

Testing for a correlation between character state and net diversification rate has commonly relied on associations of clade age and number of species, either through the use of sister clade

2 or regression analyses (S12–S14). These methods consider only clades in which most tips are in the same state and assume that ancestors within the clade had that state. Because the transition rate from SI to SC is high relative to the family’s age (S15), few non-polymorphic clades are available, and such tests will have low statistical power (S13, S16). We therefore employ the recently-developed BiSSE method for estimating from a phylogeny speciation and extinction rates that depend on character states (S17). We include the correction for incomplete sampling (S18): the probability of being sampled in the tree is 0.162 for SI species and 0.150 for SC species. By explicitly modeling speciation and extinction associated with the two states of a binary character, BiSSE allows us to quantify the effects of state-dependent diversification and state transitions.

Character state encoding

For macroevolutionary models of binary character evolution to be applied to breeding system evolution, each species must be classified as either SI or SC, and this can be difficult (S19). We use the same general principles as described elsewhere (S20). The best available data, however sparse, indicate that the breakdown of SI is so common that no SI species studied in any detail fails to reveal segregating SC mutants, SC populations, or sister species. Our intention is to measure the average rate at which an entire lineage, ancestrally SI (see main text and (S20)), transitions to SC. Therefore, we encode as SI all “polymorphic” taxa that have not entirely transitioned to SI. This encoding should yield a conservative estimate of the advantage of SI lineages. The breeding system data were available for 356 species represented on the phylogeny of “x=12” Solanaceae. Of those, 196 were described in the literature and encoded by us as SC.

Of the remaining species encoded as SI, 116 were unambiguously described as SI, 17 as both SI and SC, 25 as dioecious, and one each as SI/SC/dioecious and SI/dioecious.

3 Bayesian analysis

We performed a Bayesian analysis of BiSSE on the Solanaceae ML phylogeny. Compared with maximum likelihood parameter estimation, this approach better handles the potentially- rough likelihood surfaces and provides a natural means of testing how meaningful parameter differences are. Although a Bayesian analysis across a posterior set of trees would be more philosophically consistent, obtaining such a set was not computational feasible due to the large number of species and sites in the phylogenetic analysis. We obtained 1,000,000 post-burn-in samples of slice-sampling Markov chain Monte Carlo (MCMC) on the maximum likelihood tree and 10,000 samples on each of the 100 bootstrap trees. Priors on each parameter were exponentially distributed and broad, with rate 0.3. We used the conditional likelihood root state assumption (S18): because the rate of gain of SI was fixed to zero, this effectively fixes as SI the root and hence the other internal nodes leading to

SI tips. Analyses were conducted with the R package diversitree (S21, S22). Once posterior distributions of the five model parameters were obtained (Fig. 1A), further analyses (Fig. 1B, Fig. 2) simply involved computing additional quantities from each MCMC sample. Reported posterior probabilities are the proportion of MCMC samples for which a statement was true.

Supporting text

Additional character evolution results Results from maximum likelihood tree

Mean values, standard deviations, and the standard errors of the mean (determined from time series analysis as implemented in the R package coda (S23)) are reported in Table S1. The results for λC − λI and µC − µI provide further quantification of our finding that SC lineages have a higher rate of speciation and an even higher rate of extinction than do self-incompatible lineages. The results for rI , rC and their difference show not only a higher rate of net diversifi-

4 cation for SI lineages, but in fact negative net diversification for SC lineages. The equilibrium frequency of SI is only slightly less than the observed frequency and is certainly positive, show- ing that SI is not bound for deterministic extinction due to its loss through transitions to SC. Correlations between the five directly estimated parameters are reported in Table S2. The speciation and extinction rates for each state are very strongly correlated, consistent with the much tighter estimates of net diversification rates than of speciation and extinction rates sep- arately (Fig. 1AB, Table S1). The moderate correlations between the transition rate and the rest of the rates reflects the balance between state change and diversification in explaining the observed state frequencies.

Results from bootstrap trees

The results reported above include uncertainty from the parameter estimation process but not uncertainty in the tree topology or branch lengths. Variation in individual parameter estimates across the bootstrap trees is comparable to uncertainties in estimation on the ML tree (Table S3). For net diversification rates, however, variation across bootstrap trees is much less (Table S3), likely because diversification rate is determined largely by the frequency of tip states and the root age, both of which are constant across the bootstrap set. Our main results are robust to phylogenetic uncertainty. On 92 out of the 100 bootstrap trees, µI < λI < λC < µC is true with a posterior probability of at least 0.90. On all 100 bootstrap trees, the following statements are true with posterior probability 0.90: rI > 0.35, rC < −0.01, rI − rC − qIC > 0.12, pSI > 0.27.

Results with regain of SI allowed

Although we feel we are justified in fixing the rate of SI gain, qCI , to zero in our analyses, we understand that results without that restriction may be of interest. We therefore also ran the

BiSSE MCMC analysis on the ML tree without the general qCI = 0 constraint, but incorporat-

5 ing information on specific lineages in which reversals were shown not to occur. For the seven- teen species on our tree in which trans-specific polymorphism has been documented (Solanum chilense, S. peruvianum, S. carolinense, S. chacoense, Lycium californicum, L. andersonii, L. parishii, L. ferocissimum, L. cestroides, Physalis cinerascens, P. crassifolia, P. longifolia,

Witheringia solanacea, Nicotiana alata, N. glauca, Iochroma australe, Eriolarynx lorentzii), every node that is an ancestor of that species was fixed to the SI state by setting its conditional likelihood of SC to zero in all tree likelihood calculations.

The estimate of qCI is positive but small, and the estimates for other parameters (Table S4) are similar to those with qCI = 0 (Table S1). Our main conclusions all hold under this anal- ysis. The ordering of the speciation and extinction rates is the same (the posterior probability of µI < λI < λC < µC is 0.99). Diversification is greater for SI lineages (rI > rC with pos- terior probability 1.0). The equilibrium frequency of SI is positive (pSI > 0.30 with posterior probability 0.90; the pSI computation is somewhat more complicated than the expression given in the main text when reversals are allowed (S17)). Compared with the results in which qCI is fixed to zero, the diversification advantage of SI is smaller when regain of SI is allowed but the equilibrium frequency of SI is slightly larger because the rate of loss of SI is smaller.

Results from whole-family analysis

On the full Solanaceae tree, pruned only to contain species with known SI status, overall sam- pling intensity is somewhat less than that of the “x=12” clade used in the main analyses: the sampling proportions are 0.123 for SI and 0.168 for SC. Inclusion in the tree is much less uniform outside of the “x=12” clade (e.g., Petunia is very well represented but the other deep genera are not), so we did not use the whole-family in the main analyses. Nevertheless, it is worthwhile to ask if our results for the clade spanning Solanum and Nicotiana also hold for what is known of the entire family. We find that the ordering of the

6 speciation and extinction rates is not as clear (on the ML tree, the posterior probability of

µI < λI < λC < µC is only 0.61), but the transition rate qIC is always much less than these rates, and all of our other conclusions hold. Specifically, with posterior probabilities of at least

0.99, rC < −0.09, rI > 0.26, rI > rC + qIC , and pSI > 0.32.

7 Solanum chomatophilu

munaellodnac munal munaellodnac

S

Solanum pampasense

o

S

naloS

loS Solanum commersonii

aloS

esnesaniram munalo esnesaniram Solanum achacachens Solanum acroscopicum

Solanum demissum

Solanum lycopersicum musor

Solanum multiinterruptu Solanum santolallae munaloS

Solanum acaule

Solanum circaeifolium muna

munisob

Solanum albicans

i

i e c aloiv m u n alo S Solanum stoloniferum mutnodorcim munalo mutnodorcim

apbus mu

Solanum habrochaites m vosakub Solanum lignicaule e

n e Solanum scabrifolium Solanum spegazzinii Solanum incamayoens

Solanum hjertingii rga mun Solanum cardiophyllum hpar es Solanum palustre Solanum schenckii bu d Solanum bulbocastanu Solanum immite eluaciver

m Solanum guerreroense Solanum andreanum Solanum moscopanum t ne

munaloS

ienrev munalo ienrev

Solanum lycopersicoide Solanum piurae Solanum stenophyllidiu Solanum ehrenbergii jirat

oS Solanum cheesmaniae munalo ma Solanum pascoense Solanum morelliforme Solanum iopetalum

lofina

i

Solanum alandiae Solanum hougasii mutaru Solanum pimpinellifoliu aromrami Solanum galapagense Solanum pinnatisectum Solanum etuberosum m u cin o cig n ol Solanum polyadenium mu

t esn e m ola d n ut m u n al Solanum kurtzianumSolanum Solanum chmielewskii Solanum doddsii

u

m u n aib m oloc m u n alo

un Solanum lycopersicum b munaloS m uilofin o m i

m

munaloS

Solanum sparsipilum Solanum neorickii Solanum jamesii m u pracyxo m u n alo S

e var cerasiforme aloS Solanum leptophyes m u m issix al m u n alo S

S SolanumSolanum peruvianum chilense Solanum sitiens Solanum oplocense Solanum ugentii m

S Solanum clarum

Solanum avilesii

SolanumSolanum juglandifolium ochranthum Solanum pennellii S Solanum okadae S

e Solanum chacoense Solanum yungasense

m Solanum arnezii Solanum infundibuliform Solanum verrucosum

Solanum muricatum Solanum berthaultii s Solanum taeniotrichum m Solanum laxum m

Solanum appendiculatu

Solanum fraxinifolium bsp guianensis Solanum phaseoloides bsp circinatum bsp ramosum

m

Solanum allophyllum Solanum seaforthianum Solanum ptychanthumSolanum trizygum n um Capsicum annuum var Solanum stuckertii Solanum physalifolium Solanum fusiforme Solanum delitescens Solanum tripartitum Solanum amotapense Solanum calileguaeSolanum palitansSolanum americanum subsp nodiflorum Capsicum minutiflorum Solanum dulcamaraSolanum ipomoeoides Solanum hibernum Solanum uleanum Solanum evolvulifolium Solanum exiguum Solanum glaucophyllum Solanum opacum Solanum nemorense Solanum luteoalbum Solanum obliquum Solanum fiebrigii Solanum cylindricum Solanum mammosum Capsicum coccineum Solanum mapiriense Solanum riojense Solanum cacosmum Solanum palinacanthum Capsicum ceratocalyxCapsicum frutescens m Solanum tenuisetosum Solanum polygamum m var inerme Solanum diploconos Solanum confusum Solanum diversifolium Solanum pendulum Solanum roseum Solanum melissarum Solanum tegore Capsicum baccatum Solanum tobagense Solanum calidumSolanum endopogon suSolanum circinatum Solanum wallacei Solanum hoehnei Solanum sciadostylis Solanum circinatum su Capsicum chinense Solanum reptans Solanum pinetorum SolanumSolanum circinatum sibundoyense su Solanum morellifolium lianum SolanumSolanumSolanum platenseSolanum incarceratum myriacanthum aculeatissimu Solanum oxyphyllum SolanumSolanum fallax cajanumense Solanum proteanthum m Capsicum chacoense Solanum latiflorum Solanum occultum Solanum corymbiflorum SolanumSolanum unilobum betaceum Solanum viarum Lycianthes pseudolycio Capsicum galapagoens Solanum maternum SolanumSolanum capsicoides atropurpureum annuum Solanum arboreum Solanum ochrophyllumSolanum argentinum Solanum acerifolium Solanum tenuispinum CapsicumCapsicum annuum pubescens Solanum aphyodendroSolanum pseudocapsic Solanum amygdalifoliu Solanum anomalum Solanum americanum Lycianthes glandulosa Solanum rovirosanum Lycianthes furcatistella Solanum adscendens Solanum abutiloides Solanum sessiliflorum CapsicumCapsicum cardenasii tovarii Solanum inelegans Solanum retroflexum Solanum havanenseSolanum capsicastrumSolanum turneroides SolanumSolanum stramoniifoliu felinum CapsicumCapsicum hunzikerianu eximium Solanum herculeum Solanum villosum SolanumSolanum quitoense candidum Solanum hirsutissimum Lycianthes jalicensis Solanum nigrum SolanumSolanum clandestinum wendlandii Solanum lasiocarpum Solanum tequilense Lycianthes multiflora Solanum linearifoliumSolanum pubigerum Solanum rugosumSolanum bicorne Solanum repandum Lycianthes surotatensis Solanum triflorum SolanumSolanum cordovenseSolanum mauritianum refractum ides SolanumSolanum uporo stramoniifoliu Capsicum schottianum Solanum laciniatum Solanum lepidotum e Solanum aviculare Solanum schlechtenda Capsicum recurvatum Solanum trisectum SolanumSolanum nitidum aligerum Lycianthes heteroclitaLycianthes nitida Solanum vestissimum Solanum crispum Solanum hyporhodium Lycianthes geminiflora Solanum caesium Solanum pseudolulo ta Lycianthes synanthera Solanum symonii SolanumSolanum pectinatumSolanum microphyllum agrarium Lycianthes stephanoca Capsicum flexuosum SolanumSolanum thelopodium multifidum m Solanum hirtum Lycianthes tricolor Solanum montanum Lycianthes sanctaeclarLycianthes beckneriana CapsicumCapsicum pereirae villosum Solanum quadrangular Lycianthes pringlei Solanum terminale e Lycianthes lenta Capsicum campylopod Solanum aggregatum Solanum stenandrum m Solanum accrescens Capsicum parvifolium Solanum stagnaleSolanumSolanum citrullifolium rostratum Lycianthes denticulata Solanum robustum Solanum bahamense Lycianthes lysimachioid lyx Solanum wrightii ae Solanum sisymbriifolium Solanum drymophilum

Capsicum rhomboideu SolanumSolanum crinitumSolanum lycocarpum campechiens ium SolanumSolanum comptum conditum Lycianthes biflora Capsicum ciliatum JaltomataJaltomata dentata hunzikerie Solanum carolinense Lycianthes shanesii Solanum mitlense Solanum jamaicense es CapsicumCapsicumCapsicum lanceolatum lycianthoide geminifolium SolanumSolanum adhaerens aturense Solanum multispinum

m Solanum crotonoides Solanum lanceolatum2426 SolanumSolanum torvum paniculatum Solanum glutinosum Solanum racemosum Solanum crinitipes Solanum hieronymi s Solanum hispidum Solanum elaeagnifolium Solanum pyracanthos Solanum hindsianum Solanum sp Goldblatt 1 Solanum tridynamum Solanum erianthum SolanumSolanum myoxotrichum mahoriense Solanum coactiliferum Solanum toliaraea SolanumSolanum heinianum giganteum Solanum renschii

m Lycianthes moziniana v Solanum aculeastrum SolanumSolanum virginianum thruppii Solanum marginatum Solanum coagulans Lycianthes pedunculari Solanum kwebense reum Physalis campanulata Lycianthes dejecta SolanumSolanum schimperianuSolanum richardii manaense Lycianthes rzedowskii Physalis hederifoliaPhysalis greenmanii var Solanum dasyphyllum Lycianthes acutifoliaar margaretiana Lycianthes inaequilater Solanum macrocarpon Physalis hintonii LycianthesLycianthes acapulcens ciliolata Solanum hastifolium Lycianthes amatitlanen Solanum cyaneopurpu Physalis longifolia s Lycianthes saltensis Solanum aethiopicum Physalis caudella puberula Lycianthes fasciculata Solanum anguivi Lycianthes rantonneiLycianthesLycianthes jelskii radiata Physalis hederifolia Lycianthes asarifolia SolanumSolanum lidii vespertilio Physalis glutinosa Lycianthes lycioides a is Solanum tomentosum Solanum capense um sis Solanum rigescens Physalis angustifoliaPhysalis sordida Physalis coztomatl Salpichroa origanifolia SolanumSolanum supinum violaceum Physalis walteri Nectouxia formosa Solanum incanum m Physalis cinerascens Lycianthes pilifera Solanum panduriforme Physalis viscosa Salpichroa tristis Solanum campylacanth Solanum arundo Solanum lichtensteinii Physalis aff heterophylPhysalis heterophyllaPhysalis mollis Solanum sessilistellatu Physalis pumila Solanum linnaeanum Physalis virginiana H 1 Solanum cumingii m Physalis arenicola Solanum melongena la MW 2004 Solanum ovigerum Physalis lanceolata Solanum esuriale PhysalisPhysalis chenopodiifoli angustiphysaPhysalis lassa Solanumllum cf centrale AM Solanum quadriloculatu Physalis aff philadelphi Solanum sejunctum Physalis Physalisnicandroides peruviana Solanum centrale a Solanum asymmetriphy Physalis patula Solanum orbiculatum Physalisca philadelphica MW 2004 995 Solanaceae + five outgroup Convolvulaceae taxa Solanum tetrathecum Bohs 2727 Physalis microcarpa m Solanum eremophilum Physalis philadelphica Solanum echinatum Solanum aff echinatum Solanum cleistogamumSolanum pugiunculiferu Physalis fuscomaculata Physalis sp P149 Solanum ellipticum Physalis Physalismendocinavar curassavica immaculata from a sparse eight-gene, 16405-site alignment SolanumSolanum nemophilum nummularium Physalis ixocarpa SolanumSolanum dioicum cunninghamii Physalis mexicana Solanum leopoldense PhysalisPhysalis angulata aequata Physalis pubescens Solanum carduiforme nse Fryxell 3421 Physalis longifolia var s SolanumSolanum petraeum cataphractum Physalis lagascae Solanum aff vansittarte 5 Physalis pruinosaubglabrata Solanum tudununggae Solanum vansittartense Physalis ignota SolanumSolanum sp Martine hoplopetalum 80 Physalis cordata Solanum hystrix Physalis minimaculata um Physalis minima Solanum clarkiae Physalis lanceifolia Solanum melanosperm Physalis acutifolia Solanum oedipus Solanum heteropodium Margaranthus solanacePhysalis crassifolia Solanum beaugleholei us Chamaesaracha coron Solanum phlomoides Chamaesaracha sordid Physalis sp P099 Solanum lasiophyllum opus Solanum diversiflorum Physalis arborescensa Solanum chippendalei Physalis melanocystis Solanum petrophilum Quincula lobata Solanum prinophyllum Solanum campanulatum Physalis alkekengiPhysalis microphysa Solanum cinereum Solanum furfuraceum Physalis carpenteri Solanum stelligerum Leucophysalis grandiflo Solanum chenopodinum Leucophysalis nanara Solanum cookii Oryctes nevadensis Solanum parvifolium Witheringia meiantha Solanum ferocissimum Witheringia macrantha Solanum corifolium Witheringia solanacea Solanum stupefactum Brachistus stramonifoli Solanum pancheri Leucophysalis viscosaus Solanum vaccinioides Tzeltalia amphitricha Solanum incompletum Tzeltalia calidaria Solanum sandwicense Witheringia mexicana Solanum nobile Withania frutescens Solanum brownii Withania somnifera Solanum neoanglicum Withania sp W009 Solanum curvicuspe Dinetus truncatus Withania coagulans Evolvulus glomeratus Mellissia begoniifolia Convolvulus arvensis Athenaea sp Bohs 91 Ipomoea purpureaIpomoea batatas Aureliana fasciculata Schizanthus hookeri Nothocestrum latifolium Schizanthus grahamii Nothocestrum longifolium Schizanthus alpestris ium Schizanthus candidus Discopodium penninerv m Schizanthus integrifoliu Tubocapsicum anomalu Schizanthus lacteus s Deprea sylvarum Schizanthus laetus Schizanthus litoralis Larnax subtriflora Schizanthus porrigens Larnax sachapapa Duckeodendron cestro Schizanthus pinnatus Larnax sylvarum Schizanthus parvulus r fasciculata ides Schizanthus tricolor Aureliana fasciculata va Deprea bitteriana Deprea paneroi Metternichia principis Deprea glabra Coeloneurum ferrugine Larnax cuyacensis Tsoala tubiflora Henoonia myrtifoliaum Deprea orinocensis Salpiglossis sinuataPantacantha ameghino Espadaea amoena Goetzea ekmanii Combera paradoxa Goetzea elegans Larnax grandiflora Larnax psilophyta Dunalia fasciculata i Larnax suffruticosa Vassobia breviflora Vassobia fasciculata Protoschwenkia mando VassobiaEriolarynx dichotoma lorentzii Larnax hawkesiiLarnax peruviana Iochroma australe Vestia foetida Browallia eludensnii Eriolarynx fasciculata Sessea stipulata Browallia speciosa Dunalia brachyacantha Iochroma Dunaliaparvifolium spinosa Sessea vestita Streptosolen jamesonii Dunalia obovata Vestia lycioides Dunalia spathulata CestrumSessea strigilatum corymbiflora DunaliaSaracha solanacea quitensis Cestrum megalophyllum Saracha punctata Cestrum acutifolium Iochroma loxense Cestrum Cestrumvirgaurea macrophyllum Iochroma cyaneum Cestrum milciomejiae Cestrum inclusum Iochroma cornifolium 0.02 substitutions / site Cestrum sphaerocarpu Iochroma stenanthum Cestrum violaceum Iochroma squamosum Iochroma lehmannii Cestrum glanduliferum Iochroma sp Smith 337 m IochromaIochroma sp Smith edule 353 Cestrum tuerckheimii Iochroma salpoanum Cestrum parqui CestrumCestrum rigidum pittieri IochromaAcnistus confertiflorum arborescens CestrumCestrum nocturnum mortonianum Iochroma ellipticum CestrumCestrum luteovirescens tomentosum IochromaIochroma sp Smith calycinum 476 Cestrum aurantiacum Cestrum aurantiacum v Iochroma fuchsioides Cestrum regelii IochromaIochroma gesnerioides grandiflorum Cestrum dasyanthum Cestrum pacayense Iochroma sp Smith 370 des Cestrum guatemalense IochromaIochroma umbellatum nitidum Cestrum sp Montero 21 Iochroma sp SmithCuatresia 317 riparia Cestrum fragile ar macrocalyx Larnax hunzikeriana CestrumCestrum chiriquianum irazuense Cuatresia exiguiflora Cestrum poasanum Cuatresia colombianaWitheringia coccoloboi Cestrum fulvescens Witheringia cuneata Cestrum laxum 3 Calibrachoa sellowiana Cestrum oblongifolium Datura inoxia CestrumCestrum thyrsoideum roseum Datura metel m Fabiana imbricata Cestrum miradorense Datura Daturastramonium leichhardtii Calibrachoa pygmaea Cestrum fasciculatum Petunia secreta Petunia axillaris Cestrum endlicheri s Cestrum elegans Brugmansia sanguineasis PetuniaPetunia altiplana mantiqueirensiCalibrachoa parviflora Brugmansia Nicandraaurea physalodes Petunia riograndensis Petunia bajeensis IochromaMandragora cardenasianu officinarum Petunia exserta Petunia axillaris subsp PetuniaPetunia guarapuavensi occidentalis Schwenckia glabrata Markea MarkeapanamensisJuanulloa uleinthum mexicanaSolandra grandiflora Petunia axillaris subsp Schwenckia lateriflora Mandragora caulescen Solandra brachycalyx PetuniaPetunia integrifolia interior sub Juanulloa aurantiaca Petunia integrifolia var s Mandragora chinghaien Petunia axillaris subsp thus Petunia scheideana Hawkesiophyton Dyssochromaulei andrus viridiflora Petunia bonjardinensis JaltomataJaltomata auriculata sinuosa PetuniaPetuniaPetunia integrifolia reitzii saxicola subandina JaltomataJaltomata procumbens grandiflora Merinthopodium neuraLyciumLycium texanum torreyi s Schwenckia americana Lycium sp 202 Petunia littoralis axillaris Lycium parishii Petunia integrifolia var sp inflata Melananthus guatemal integrifolia Schultesianthus leucanLycium andersonii parodii Schultesianthus megalsp parviflorumsp berlandieri Nierembergia frutescen LyciumLycium berlandieri exsertum Lycium fremontii Leptoglossis linifolia Lycium athium Brunfelsia americana Lycium minimum Brunfelsia uniflora ensis Nierembergia calycina r quadrifidum depauperata

Lycium Lyciumberlandieri berlandieri sub subLycium sandwicense s Lycium brevipes Nierembergia linariifoliaLeptoglossis darcyana Lycium infaustum Nierembergia ericoides Lycium tenuispinosum Nierembergia scoparia Lycium rachidocladumr carolinianum Symonanthus aromatic LyciumLycium americanum elongatumLycium cestroides Nierembergia pulchella Lycium leiospermum Symonanthus bancroft Nierembergia tucuman LyciumLycium cuneatum morongii Nierembergia browallio Lycium minutifoliumLycium deserti NierembergiaNierembergia boliviana pulchella Lycium carolinianum va Lycium fuscum Bouchetia erecta Lycium stenophyllumLycium chanar Nierembergia veitchii NierembergiaNierembergia aristata angustifo Hunzikeria texana Lycium gilliesianum NierembergiaNierembergia micranth hatschba Lycium ameghinoi AnthocercisAnthocercisAnthocercis Anthocercisangustifolia viscosa ilicifolia gracilis var linariifolia Bouchetia anomala LyciumLycium chilense ciliatum Anthocercis littorea Nierembergia graveole AnthocercisAnthocercis sylvicola intricata NierembergiaNierembergia rigida pinifolia Lycium carolinianum va Lycium nodosum Nierembergia spathula Plowmania nyctaginoid Anthotroche pannosa us Nierembergia rivularis var pulchella Lycium vimineumLycium cooperi Anthocercis myosotideAnthotroche myoporoid Nierembergia repens ensis Lycium californicum AnthotrocheAnthotroche blackii walcottii ii ides PhrodusLycium microphyllus macrodon Nicotiana wigandioides Cyphanthera odgersii var macrocalyx Phrodus bridgesii lia LyciumLycium shockleyi pallidum Nicotiana thyrsiflora Anthocercis racemosa Lycium puberulum Grammosolen dixonii Browallia americana NicotianaNicotianaNicotiana solanifolia benavidesii Nicotianaraimondii glutinosa Grammosolen truncatu lia Cyphanthera microphy Nicotiana trigonophyllaNicotianaNicotiana paniculata cordifolia Lycium amoenumLycium tenue Nicotiana undulata a chii Nicotiana knightiana Nicotiana arentsii Cyphanthera anthocerc ns Grabowskia glaucaLycium grandicalyx Nicotiana clevelandii CyphantheraDuboisia albicans hopwoodii Lycium australe Nicotiana rustica Duboisia myoporoides Lycium sp N 309 Nicotiana pauciflora Nicotiana bigelovii Crenidium spinescens Nierembergia hippomaes Grabowskia obtusa Duboisia leichhardtii ta Lycium horridum Nicotiana acuminataNicotianaNicotiana miersiiNicotiana linearis palmeri GrabowskiaLycium duplicata strandveldense Nicotiana attenuata Nicotiana obtusifolia LyciumLycium arenicola afrum Lycium gariepense Nicotiana corymbosaNicotiana spegazzinii a Lycium schizocalyxLycium cinereum es Grabowskia boerhaviifo Lycium pilifolium Lycium ferocissimum Nicotiana alata Nicotiana sylvestris NicotianaNicotiana tabacum digluta Nicotiana langsdorffii s Lycium oxycarpum Nicotiana tomentosa Lycium europaeum Nicotiana nesophila lla Lycium depressumLycium pumilum Nicotiana stocktoniiNicotiana nudicaulis Nicotiana acaulis Lycium ruthenicumLycium tetrandrumLycium eenii NicotianaNicotiana x sanderae bonariensis Nicotiana glauca Lycium chinense Latua pubiflora Nicotiana debneyi Nicotiana tomentosiform Lycium barbarum Nicotiana africana Nicotiana repanda nica Lycium shawii Nicotiana forgetiana Nicotiana kawakamiiNicotiana setchellii idea Nicotiana otophora Lycium decumbens Nicotiana fragrans Nicotiana occidentalis Nicotiana longiflora Nicotiana hesperis Exodeconus miersii Nicotiana petunioides Nicotiana gossei Nicotiana picilla Lycium hirsutum Nicotiana amplexicaulis Nicotiana plumbaginifo Lycium intricatum Lycium villosum Nicotiana noctiflora Nicotiana suaveolens Nicotiana velutina Nicotiana didepta Nicotiana rosulata Nicotiana megalosipho Nicotiana exigua Nicotiana simulans Nicotiana cavicola Nicotiana rotundifolia Nicotiana ingulba Lycium acutifolium Nicotiana goodspeedii Lycium bosciifolium Nicotiana eastii Nicotiana umbratica Lycium schweinfurthii Lycium prunus spinosa

Atropa belladonna Nicotiana maritima Lycium mascarenense

inA

s

aciloinrac ailopocS aciloinrac

o

is Nicotiana excelsior

sediolasyhp anialhco sediolasyhp silatneiro anialhcosy silatneiro

Jaborosa integrifolia

lia

siralu rul s u d o sin A Nicotiana benthamiana

Hyoscyamus muticus n

iis

ailofitanda xalyhporel ailofitanda

wezrP

snecs hylla 7 sudi

nis e htn a p ort A

Jaborosa sativa

580 eillig xalyhporelcS eillig Jaborosa squarrosa

citu g n at s u d Scopolia japonica Scopolia

bidnufni anialhcosyh bidnufni

su

5

sh e Nolana villosa sisne

arolfilisses analoN arolfilisses yH Nolana flaccida xaly nips

Nolana glauca at aiksla

ycsoyH

n o

a

B d B m NolanaNolana leptophylla peruviana NolanaNolana albescens diffusa Nolana mollis u Nolana tocopillensis

aycsoyH Nolana sp Dillon 5729 Nolana clivicola n

hP

syhP

m

s a

acitug

hporelcS Hyoscyamus albus n Nolana sedifolia p eeN

Bargemontia sphaerop Nolana salsoloides 212

785 egi

su

Nolana ramosissima cS r

Nolana aplocaryoides Nolana incana csoyH

P Nolana sp Dillon 8591 xalyhpo s Nolana divaricata

resed

t Nolana sp 413 Nolana confinisNolana ivaniana Nolana laxa o Nolana pallida Nolana pilosa Nolana inflata Nolana lycioides Nolana plicata sun a evo b su m aycso

Nolana intonsa r Nolana johnstonii Nolana thinophila Nolana humifusa Nolana volcanica sup su m aycsoy H Nolana aticoana Nolana tarapacana Nolana scaposa Nolana crassulifolia mu i Nolana weissiana

Nolana cerrateana a sumay Nolana filifolia Nolana tomentella Nolana urubambae Nolana gayana Nolana rostrataNolana carnosa r sull

Nolana spathulata elcS

Nolana galapagensis Nolana elegans Nolana arenicola Nolana sp 414 Nolana linearifolia Nolana sp Dillon 8790 Nolana sp Dillon 8789 sueru

Nolana werdermannii Nolana stenophylla

Nolana adansonii Nolana rupicola Nolana sp Leiva et al 2 Nolana baccata

Nolana coelestis Nolana acuminata Nolana sp Quipuscoa 2

Nolana parviflora Nolana paradoxa Nolana balsamiflua

Nolana pterocarpa

Nolana sp Dillon 8690

Figure S1: Phylogenetic relationships among 995 species of Solanaceae, rooted with five species of Convolvulaceae.

8 Solan

Solan Solan Solan Solan Solan Solan

Solan Solan Solan

Solan m

ense Solan

Solan Solan u y um

t um

Solan um div um

a S um

um glaucoph umense ense um mater um o um tobagense um betaceum

Solan um cor n odendron

Solan o v Solan um amotapense um luteoalb um unilob i um ob Solan Solan y itian l c um hiber undo Solan um confusum a um roseum r

i utiloides Solan n Solan um stuck um Solan c xyph u um ersif pureum um cacosm endlandii Solan um latiflor iacanthum um sciadostylis m

um pinetor um e ymbiflor m um Solan um diploconos liquum yr

u um caja n um melissar um sib um occultum f um aph olium um pseudocapsicum Solan um argentin n um pendulum a um adscendens Solan Solan yllum n um ab uispin um alloph um cordo olium Solan um maur um um pum l um w Solan n a um polygam um leptoph l l um mammosum um um xiguum a yllum um um palinacanthum um um platense um oplocense er o Solan x um m Solan um aculeatissim Sola n um chacoense S um viar um infundib Solan Solan um v Solan elin Solan um tii Solan um capsicoides um tar Solan um Solan um atropur um sparsipilum Solan Solan Solan um ten amoniif um Solan um Solan um sessiliflor Solan um quitoense um microdontum Solan um ber err yllum Solan um f estissim SolaSolan n Solan um candidum Solan um Solan yporhodium olium Solan Solan Solan Solan um repandum ucosum ijense Solan um lasiocar iif SolaSolan n y Solan tum es Solan um str um b Solan um v ustum olium um colombiaum tuberosumn ulif Solan um h um violaceimar um kur um v thaultii Solan um pseudolulo pum Solaumn agumr longiconicum Solan um pectinatum ullif atum or Solan ukaso Solan um hir me Solan um stagnale Solan er Solan um rob um o tzian Solan um sisymbr Solan imonif nei Solan initum Solan Solan um citr Solan vii Solan um rostr ymophilum um santolallaexycar um Solan um lycocar um laxissim Solan um stenoph mor olium um um cr Solaumn demissum Solan um campechiense pum Solan um dr SolanSolan atum Solan vum Solan Solan um carolinense um acaule Solan um jamaicense um umum guerreroense stolonium hjef r Solan um crotonoidesianthum um um Solan um tor SolaSolan nSolan yllidium Solan um paniculatum Solan um er um andreaum hougasiin tingii Solan um hispidumidynam Solaumn moscopan Solan acanthosum SolanSolan er um hindsiayr n um Solan um tr um iopetalum Solan um um chomatophilumum spegazzinii Solan um p Solan um giganteum Solan um um virginian um Solan um Solan um SolaSolan num commersonii Solan um marginatum Solan um piur Solan um aculeastr um umcardiop ehrenbergiih Solan um incan yllumpon um b Solan um linnaean pureum Solan ae Solan um melongena Solaulbocastan n Solan um dasyph Solanum pinnatisectum Solan aneopur um jamesiiyllum um macrocar Solan um poly Solan um cy um Solan um aethiopicum um morelliadeniumf Solan um anguivi Solan Solan tilio Solan Solan um tomentosum Solan um claorr um lidiiesper yllum Solan Solan um palustreme Solan inoph ulatum um lycopersicum v um etuberosumum Solan um v Solanum cheesmaniae 356 “x=12” Solanaceae taxa Solan um pr um galapagense Solan um campan Solan ar cer Solan um cinereum um pimpinellif Solan um incompletum Solan asifor mum um chmiele me with known breeding system status Solan um sandwicensekiae Solan olium Solan um clar Solan um neorwskii Solan um melanospeumr Solan um chilenseickii Solan um beaugleholeiersiflor um per Solan um div yllum Solan uvian Solan um chippendaleiiph Solan um pennelliium Solan Solan um habrochaites um asymmetr um lycopersicoides Solan um echinatum um Solanum cleistogam Solanum sitiens Solan Solanum ochr Solanum nemophilum Solanum juglandianthumf Solanum dioicum Solanum appendiculatumolium Solanum cunninghamii um leopoldense Solanum taeniotr Solan orme ichum Solanum carduif Solanum muricatum Solanum tudununggae Solanum fraxinifolium Solanum vansittartense Solanum trizygum Solanum petraeum Solanum ptychanthum Solanum cataphractum Solanum opacum Symonanthus aromaticus Solanum americanum 10 million years Symonanthus bancroftii ysalifolium Nicotiana wigandioides Solanum ph Nicotiana undulata Solanum palitans Nicotiana glutinosa um tripartitum Solan allacei Nicotiana bena Solanum w um Nicotiana solanividesiif orthian a Nicotiana cordif olia Solanum seaf Nicotiana paniculata Solanum dulcamaxumr olia um retrofle um Nicotiana r Solan um nigr Nicotiana knightianaustica Solan Nicotiana obtusif Solanum villosumiflorum Nicotiana cle um tr ispum Nicotiana bigelo Solan um cr olia Solan viculare Nicotiana lineavrelandii um a Nicotiana miersii vii Solanum laciniatum Nicotiana cor is Solan um symoniiisectum Nicotiana atten Solan i Nicotiana otophoymbosar um tr minaleer Nicotiana setchellii Solan um ter Nicotiana tomentosiuataf Solan Nicotiana tomentosa Jaltomata hunzik Nicotiana acaulis a Jaltomata dentata Nicotiana glauca Nicotiana petunioides Capsicum baccatum or utescens Nicotiana noctiflor mis Capsicum chacoense Nicotiana sylv Capsicum chinense Nicotiana n uumarii Nicotiana stocktonii Capsicum fr v Nicotiana repanda Nicotiana alataudicaulisestr a Capsicum galapagoense um Nicotiana langsdorffii is CapsicumCapsicum pubescens ann ximium Nicotiana plumbaginif Capsicum to Nicotiana longiflor Nicotiana f Capsicum cardenasiixuosumolium Nicotiana bonar Capsicum e vif Nicotiana afr Nicotiana fr CapsicumCapsicum schottia villosumn Nicotiana hesperorgetiana ifolia Nicotiana debne Capsicum fle Nicotiana occidentalis a olia olia Nicotiana umbr icana Capsicum par antonnei Nicotiana sim agr iensis ylla Nicotiana ingulba Capsicumycianthes lanceolatum ciliolataiganif olia Nicotiana megalosiphon ans L Nicotiana rotundif Capsicumycianthes rhomboideum asar Nicotiana rosulata is L Nicotiana e yi ycianthesysalis r viscosaascens Nicotiana v L Ph Nicotiana gossei Nicotiana goodspeedii ulansatica Salpichroa orysalis longif olia Nicotiana ample ysalis heteroph uinosa olia Nicotiana ca Ph Nicotiana sua Ph Nicotiana mar ysalis cineysalisr angulata Nicotiana benthamiana xigua assif antha Nicotiana e elutina Ph a J olia ysalisP hphiladelphica olius Atropaaborosa belladonna integr ysalisysalis pubescens pr er Hy Ph Hy Ph Ph ysalis lanceif xicana Hy e ale Anisodus tanguticusoscy ysalisingia cr meiantha a Nolana iv oscy vicola Ph Nolana r oscy amonif Nolana elegans Ph Nolana acuminata v xicaulis ingia macr Nolana par ingia solanacea Nolana adansonii am eolens viflor Nolana rostr am xcelsior itima acantha ia Nolana plicata Wither ingia m a Nolana laxa am y Nolana humifusa ynx lorentzii aneum Nolana aticoana us alb L Gr us m ioides L Wither L ycium pallidum us niger a L ipar L if L ycium calif upicolaaniana Wither ach L ycium cestroides L L L ycium minim L abo L olia L ycium fremontii iolar ycium e Withania somnif xia ycium ber ycium par ycium andersonii ycium villosum ycium hirsutum uosa ycium tetr y achistusWithe strr e a a uticusus WithaniaEr coagulans iculata

c Iochroma austr xiguiflor s Br um

i wskia duplicata ado um

n assobia bre u

a ino idum e V andiflor a metel m ata Dunalia solanacea d

l xa idiflor Iochroma cy amonium xser ingia cuneata p Dunalia br e

Cuatresia r andiflor iepense

v u or

landier Datur ishii

d m

Acnistus arborescens Datur andr a str a leichhardtii nicum n tum um a gr Iochroma fuchsioides i altomata sin a officinar

Iochroma gesner l erocissim Cuatresiaingia e coccoloboides a J u Wither altomata aur r

t J ugmansia aurea m

ycium horr um s

ycium arenicola

ycium cinereum altomata gr Datur Datur L i agor Br L altomataJ procumbens L

m J ycium ga r

Wither L u Solandr ugmansia sanguinea ycium f i

L c

Br y

Mandr Dyssochroma vir L

Figure S2: Phylogenetic relationships among 356 species of Solanaceae used in the analyses of character evolution. Branch lengths were obtained with penalized likelihood smoothing, implemented in r8s (S7), with the crown group age fixed at 36 Ma.

9 mean std dev std err λI 2.933 0.467 0.049 λC 5.199 0.738 0.063 µI 2.319 0.556 0.059 µC 5.433 0.757 0.065 qIC 0.555 0.138 0.010 λC − λI 2.266 0.899 0.083 µC − µI 3.114 1.011 0.095 rI 0.613 0.141 0.010 rC −0.234 0.075 0.002 rI − rC 0.847 0.200 0.012 rI − rC − qIC 0.292 0.075 0.002 pSI 0.345 0.043 0.002

Table S1: Summary of MCMC results from the ML tree, showing the mean, standard deviation, and standard error from time-series analysis. The first five quantities are the parameters directly estimated by the BiSSE analysis.

λI λC µI µC qIC λI — λC −0.067 — µI 0.977 −0.142 — µC −0.076 0.995 −0.165 — qIC −0.510 0.352 −0.677 0.414 —

Table S2: Parameter correlations on the ML tree. Correlations between qIC and net diversifica- tion are 0.984 and −0.719 for rI and rC , respectively.

10 λI λC µI µC qIC rI rC ML 0.467 0.738 0.556 0.757 0.138 0.141 0.075 BS 0.548 0.812 0.547 0.869 0.124 0.059 0.033

Table S3: Standard deviations of estimated parameters, computed from MCMC on the ML tree (upper row) and from the median values on the set of bootstrap trees (lower row).

mean std dev std err λI 3.031 0.486 0.013 λC 5.108 0.744 0.018 µI 2.516 0.563 0.015 µC 5.284 0.769 0.018 qIC 0.484 0.128 0.002 qCI 0.021 0.011 0.000 rI − rC 0.690 0.187 0.003 pSI 0.355 0.044 0.000

Table S4: Summary of MCMC results from the ML tree when regain of SI is not prohibited.

11 Supporting references

S1. S. A. Smith, C. W. Dunn, Bioinformatics 24, 715 (2008).

S2. S. A. Smith, J. M. Beaulieu, M. J. Donoghue, BMC Evol Biol 9, 37 (2009).

S3. P. J. A. Cock, et al., Bioinformatics 25, 1422 (2009).

S4. http://www.biosql.org.

S5. K. Katoh, K.-i. Kuma, H. Toh, T. Miyata, Nucleic Acids Res 33, 511 (2005).

S6. A. Stamatakis, Bioinformatics 22, 2688 (2006).

S7. M. J. Sanderson, Mol Biol Evol 19, 101 (2002).

S8. T. Paape, et al., Mol Biol Evol 25, 655 (2008).

S9. M. J. Benton, The fossil record 2 (Chapman and Hall (London), 1993).

S10. S. Magallon,´ M. J. Sanderson, Evolution 55, 1762 (2001).

S11. Y. Wang, et al., Genetics 180, 391 (2008).

S12. C. Mitter, B. Farrell, W. B. J, Am Nat 132, 107 (1988).

S13. M. J. Sanderson, M. J. Donoghue, Trends Ecol Evol 11 (1996).

S14. R. E. Ricklefs, Ecology 87, 2468 (2006).

S15. B. Igic,´ R. Lande, J. R. Kohn, Int J Plant Sci 169, 93 (2008).

S16. J. C. Heilbuth, Am Nat 156, 221 (2000).

S17. W. P. Maddison, P. E. Midford, S. P. Otto, Syst Biol 56, 701 (2007).

12 S18. R. G. FitzJohn, W. P. Maddison, S. P. Otto, Syst Biol 58, 595 (2009).

S19. C. Goodwillie, S. Kalisz, C. G. Eckert, Ann Rev Ecol Evol Syst 36, 47 (2005).

S20. B. Igic,´ L. Bohs, J. R. Kohn, Proc Natl Acad Sci USA 103, 1359 (2006).

S21. R Development Core Team, R: A Language and Environment for Statistical Computing, R Foundation for Statistical Computing, Vienna, Austria (2009). ISBN 3-900051-07-0.

S22. R. G. FitzJohn, diversitree: diversitree: comparative phylogenetic tests of diversification

(2010). R package version 0.4-5.

S23. M. Plummer, N. Best, K. Cowles, K. Vines, coda: Output analysis and diagnostics for MCMC (2010). R package version 0.13-5.

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