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bioRxiv preprint doi: https://doi.org/10.1101/2020.04.08.030452; this version posted April 9, 2020. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity.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. GARDNER ET AL., PHYLOGENOMICS AND GENERIC REVISION OF

1 Repeated parallel losses of inflexed in : phylogenomics and generic 2 revision of the tribe Moreae and the reinstatement of the tribe Olmedieae (Moraceae) 3

4 Elliot M. Gardner1,2,3,*, Mira Garner1,4, Robyn Cowan5, Steven Dodsworth5,6, Niroshini

5 Epitawalage5, Olivier Maurin5, Deby Arifiani7, S. Sahromi8, William J. Baker5, Felix

6 Forest5, Nyree J.C. Zerega9,10, Alexandre Monro5, and Andrew L. Hipp1,11

7

8 1 The Morton Arboretum, 4100 IL-53, Lisle, Illinois 60532, USA

9 2 Case Western Reserve University, Department of Biology, 2080 Adelbert Road, 10 Cleveland, Ohio 44106, USA (current affiliation)

11 3 Singapore Botanic Gardens, National Parks Board, 1 Cluny Road, 259569, Singapore 12 (current affiliation)

13 4 University of British Columbia, Faculty of Forestry, 2424 Main Mall, Vancouver, British 14 Columbia, V6T 1Z4, Canada (current affiliation)

15 5 Royal Botanic Gardens, Kew, Richmond, TW9 3AE, United Kingdom

16 6 School of Life Sciences, University of Bedfordshire, Luton LU1 3JU, United Kingdom

17 (current affiliation)

18 7 Herbarium Bogoriense, Research Center for Biology, Indonesian Institute of Sciences, 19 Cibinong, Jawa Barat,

20 8 Center for Conservation Botanic Gardens, Indonesian Institute of Sciences, Bogor, 21 Jawa Barat, Indonesia

22 9 Chicago Botanic Garden, Plant Science and Conservation, 1000 Lake Cook Road, 23 Glencoe, IL, 60022, USA

24 10 Northwestern University, Plant Biology and Conservation Program, 2205 Tech Dr., 25 Evanston, IL, 60208, USA

26 11 The Field Museum, 1400 S Lake Shore Dr., Chicago, IL 60605, USA

27 a For correspondence, email [email protected] 28 29 30 Abstract

1 bioRxiv preprint doi: https://doi.org/10.1101/2020.04.08.030452; this version posted April 9, 2020. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity.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. GARDNER ET AL., PHYLOGENOMICS AND GENERIC REVISION OF MOREAE

31 We present a densely-sampled phylogenomic study of the mulberry tribe (Moreae, 32 Moraceae), an economically important clade with a global distribution, revealing multiple 33 losses of inflexed stamens, a character traditionally used to circumscribe Moreae. Inflexed 34 stamens facilitate ballistic release and are associated with wind pollination, and the 35 results presented here suggest that losses of this character state may have evolved 36 repeatedly in Moraceae. Neither Moreae nor several of its major genera (, , 37 ) were found to be monophyletic. A revised system for a monophyletic Moreae is 38 presented, including the reinstatement of the genera Ampalis, Maillardia, Pachytrophe, 39 Taxotrophis, and Paratrophis, and the recognition of the new Afromorus, based on 40 Morus subgenus Afromorus. Pseudostreblus is reinstated and transferred to the 41 Parartocarpeae, and Sloetiopsis is reinstated and transferred to the Dorstenieae. The tribe 42 Olmediae is reinstated, replacing the , owing to the reinstatement of the type 43 genus Olmedia, and its exclusion from Moreae. Streblus s.s. is excluded from Moreae and 44 transferred to the Olmediae, which is characterized primarily by involucrate 45 without regard to position. Eight new combinations are made. 46 47 Keywords: Moraceae, mulberry family; Moreae, Olmedieae, Castilleae, Parartocarpeae, 48 Afromorus, Ampalis, , Maillardia, Milicia, Morus, Olmedia; Pachytrophe, 49 Paratrophis, Pseudostreblus, Sloetiopsis; , Streblus, Taxotrophis, Trophis. 50 51 52 Introduction 53 The preservation of plesiomorphic (ancestral) characters can result in that 54 are similar in appearance but distantly related, connected only by a remote common 55 ancestor. The mulberry family (Moraceae Gaudich., seven tribes, ca. 39 genera and 1,200 56 species) illustrates this principle well. Inflexed stamens in bud—an adaptation to wind 57 pollination that allows explosive pollen dispersal when open—were traditionally 58 used to define a tribe of the family, the Moreae (mulberries and their allies). Yet 59 phylogenetic analyses have revealed that inflexed stamens, an ancestral feature of both 60 Moraceae and their sister family (nettles), have been lost repeatedly (Clement &

2 bioRxiv preprint doi: https://doi.org/10.1101/2020.04.08.030452; this version posted April 9, 2020. 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. GARDNER ET AL., PHYLOGENOMICS AND GENERIC REVISION OF MOREAE

61 Weiblen, 2009). Thus, for example, Cecropiaceae C.C. Berg, traditionally distinguished 62 from the nettle family by the absence of inflexed stamens, is in fact embedded within the 63 Urticaceae Juss. (Berg, 1978; Clement & Weiblen, 2009). Likewise, while mulberries 64 (Morus L.), paper mulberries ( L’Hér. ex Vent.), and osage oranges ( 65 Nutt.) were once treated as tribe Moreae Gaudich. on account of their inflexed stamens, 66 phylogenetic analyses reveal them to belong to three distinct clades, each containing an 67 assemblage of genera with and without inflexed stamens (Clement & Weiblen, 2009; 68 Zerega & Gardner, 2019). 69 This study focuses on the tribe Moreae, a clade of six genera and an estimated 66 70 species (Clement & Weiblen, 2009). This widespread group of contains species of 71 ecological and cultural importance, as well as the economically important white mulberry 72 ( L.), whose sustain mori L. (), the invertebrate 73 proletariat of the industry. 74 75 Morphological basis for higher classification in Moraceae 76 By the end of the nineteenth century, Engler (1889) had circumscribed a Moraceae 77 that is quite similar to the modern concept of the family, with two subfamilies: the 78 Moroideae, comprising tribes Dorstenieae Gaudich., Broussonetieae Gaudich., Fatouae 79 Engler, Moreae, and Strebleae Bureau, characterized by stamens inflexed in bud (broadly 80 construed, including where they straighten gradually rather than spring outward 81 suddenly); and the Artocarpoideae, composed of tribes Brosimae Trécul, Euartocarpeae 82 Trécul, Ficeae Dumort., and Olmedieae Trécul and characterized by stamens straight in 83 bud. The two most influential scholars of Moraceae classification in the 20th century were 84 E.J.H. Corner and C.C. Berg. Corner considered architecture to be the most 85 important character for higher-rank within the family and inflexed stamens 86 consequently of secondary importance(Corner, 1962). Berg by contrast questioned the 87 utility of inflorescence architecture and took into account a variety of characters, especially 88 the presence of inflexed stamens (Berg, 1977b, 2001). 89 The taxonomic history of the family has leaned heavily on this stamen character. 90 Engler’s Moreae (1899), unchanged in substance from Bureau’s (1873), contained six

3 bioRxiv preprint doi: https://doi.org/10.1101/2020.04.08.030452; this version posted April 9, 2020. 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. GARDNER ET AL., PHYLOGENOMICS AND GENERIC REVISION OF MOREAE

91 genera, Ampalis Bojer, Pachytrophe Bureau, Paratrophis Blume, Pseudomorus Bureau, 92 and Morus, all with inflexed stamens that spring out suddenly at anthesis (Table 1). 93 Corner’s expanded Moreae consisted of seven genera with either straight or inflexed 94 stamens, but with pistillate inflorescences never condensed into a head: Gaudich, 95 Morus, Sorocea A. St.-Hil. (apparently including Paraclarisia Ducke), Ruiz & 96 Pav., Ampalis, Pachytrophe, and Streblus Lour. (including Bleekrodea Blume, Paratrophis, 97 Pseudomorus, Taxotrophis Blume, Sloetiopsis Engl. and Neosloetiopsis Engl.). Corner 98 himself, however, found the diversity of his Moreae unsatisfactory, noting that “[t]oo many 99 genera on insufficient and invalid grounds trouble this small tribe” (Corner, 1962). Perhaps 100 in response, Berg’s Moreae comprised all of the genera with inflexed stamens and none 101 without, including Broussonetia and Maclura but excluding Sorocea and Clarisia, 102 providing a simple character with which to delimit the tribe(Berg, 2001; Berg & al., 2006). 103 Recent phylogenetic work has supported a third approach, with the Moreae 104 comprising six genera, including genera with both straight (Sorocea, Bagassa Aubl.) and 105 inflexed (Broussonetia, Maclura) stamens (Clement & Weiblen, 2009). These studies also 106 suggest that the character state of inflexed stamens is plesiomorphic and is the ancestral 107 state for both Moraceae and Urticaceae (Datwyler & Weiblen, 2004; Zerega & al., 2005; 108 Clement & Weiblen, 2009). Inflexed stamens, which are precursors to ballistic pollen 109 release, are associated with wind pollination (Bawa & Crisp, 1980; Berg, 2001), while the 110 loss of inflexed stamens is associated with pollination. Although dominant in the 111 Moreae, inflexed stamens also occur in two other tribes: Maclureae W.L. Clement & G. 112 Weiblen and Dorstenieae. Genera lacking inflexed stamens occur in all seven tribes of 113 Moraceae (Clement & Weiblen, 2009; Zerega & Gardner, 2019). 114 115 Taxonomic summary of Moreae 116 Following Clement & Weiblen (2009), the Moreae comprise six genera and an 117 estimated 66 species: Bagassa (1), Milicia Sim (2), Morus (16), Sorocea (16), Streblus 118 (23), and Trophis P. Browne. (8) (Berg, 1977a, 2001; Berg & al., 2006; Clement & 119 Weiblen, 2009; Filho & al., 2009; Machado & al., 2013; Santos & Neto, 2015). Here, we 120 present an overview of these genera.

4 bioRxiv preprint doi: https://doi.org/10.1101/2020.04.08.030452; this version posted April 9, 2020. 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. GARDNER ET AL., PHYLOGENOMICS AND GENERIC REVISION OF MOREAE

121 Morus L., the true mulberries, is characterized by leaves with crenate margins and 122 trinerved bases, stamens inflexed in bud, and many-flowered pistillate spikes whose four- 123 parted become fleshy in , the aggregations superficially resembling a 124 . Morus comprises approximately 16 species whose delimitation requires further 125 research. There are three subgenera: Morus (ca. 14 species) which is found in temperate to 126 tropical and from North America to ; Gomphomorus Leroy, a single species 127 restricted to tropical ; and Afromorus (Bureau ex Leroy), a single species 128 restricted to tropical . Previous phylogenetic work has suggested that these three 129 subgenera may not form a monophyletic clade (Nepal, 2012). Milicia (2 spp., Africa) has 130 inflorescences which somewhat resemble those of Morus, but the leaves of Milicia, with 131 entire margins and pinnate venation, prevent any confusion of the two genera. 132 Streblus Lour., with 23 species from to and , is 133 morphologically heterogeneous, but its species are all characterized by stamens inflexed in 134 bud and pistillate flowers with more or less free tepals that enclose the fruit loosely or not 135 at all. Initially described by Loureiro based on the widespread S. asper Lour.—notable for 136 its discoid-capitate staminate inflorescences with the rudiments of an involucre—Streblus 137 was broadened by Corner (1962), bringing in as sections Taxotrophis, Phyllochlamys 138 Bureau, Paratrophis (including Pseudomorus), Pseudostreblus Bureau, Bleekrodea, and 139 Sloetia Teijsm. & Binn. (apparently including Sloetiopsis but without making any 140 combinations). None of these have discoid-capitate inflorescences; they mostly have 141 spicate staminate inflorescences, and the latter two can have bisexual inflorescences. 142 Corner viewed these sections as fragments of an ancient lineage preserving ancestral 143 characters (Corner, 1975). Following additional work by Corner (1970, 1975), Berg 144 included the genera Ampalis and Pachytrophe as section Ampalis (Bojer) C.C. Berg, 145 subsumed Sloetiopsis and section Taxotrophis into section Streblus, and excluded section 146 Bleekrodea, reinstating it as a genus (Berg, 1988). Berg later reinstated section Taxotrophis, 147 whose species are unique in bearing axillary spines (Berg, 2005; Berg & al., 2006). In 148 2009, Clement and Weiblen reinstated Sloetia at generic rank and transferred it and 149 Bleekrodea to Dorstenieae based on phylogenetic evidence (Clement & Weiblen, 2009).

5 bioRxiv preprint doi: https://doi.org/10.1101/2020.04.08.030452; this version posted April 9, 2020. 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. GARDNER ET AL., PHYLOGENOMICS AND GENERIC REVISION OF MOREAE

150 Trophis P. Browne is characterized by stamens inflexed in bud, spicate staminate 151 inflorescences, and tubular pistillate perianths, becoming fleshy and enclosing the fruit, 152 except for the monotypic section Olmedia (Ruiz & Pav.) C.C. Berg (T. caucana), which has 153 discoid-capitate staminate inflorescences with an involucre. Trophis (regrettably conserved 154 over Linnaeus’s Bucephalon L.) as recognized by Berg (1988, 2001) had five sections: 155 Trophis, restricted to ; Calpidochlamys (Diels) Corner (previously included 156 in Paratrophis and Uromorus), restricted to Southeast Asia (Corner, 1962); Maillardia 157 (Frapp. ex Duch.) C.C. Berg, restricted to Africa; Malaisia (Blanco) C.C. Berg, restricted to 158 Southeast Asia; and Olmedia, restricted to Latin America. The sinking of Olmedia into 159 Trophis by Berg (1988), requiring the re-typification of the tribe Olmedieae Trécul, which 160 became Castilleae C.C. Berg. Recently, Malaisia Blanco was reinstated as a genus and 161 transferred to Dorstenieae based on phylogenetic evidence (Clement & Weiblen, 2009), 162 reducing the current number of sections to four. 163 Two Neotropical genera included in Moreae by Clement and Weiblen (2009) but 164 not by Berg (2001) have straight stamens. While the monotypic Bagassa Aubl., with its 165 long staminate , is wind pollinated (Bawa & Crisp, 1980), evidence suggests that 166 Sorocea A. St.-Hil. (19 spp.), which produces racemose staminate inflorescences that do 167 not have as many flowers as those of Bagassa, likely contains both wind- and - 168 pollinated species (Zapata & Arroyo, 1978; Bawa & al., 1985; Lewis, 1986). The pistillate 169 perianths are subtended by pluricellular hairs, believed to serve as a substrate for a fungus 170 which, in turn attracts pollinators (Berg, 2001). The staminate flowers of Sorocea affinis 171 Helmsl. are apparently fragrant (fide S. Zona 778, 21 Nov. 1997, FTBG♂♀), suggesting 172 insect pollination for that species. If insect pollination is confirmed in Sorocea, it would 173 likely represent another transition from ancestral wind to derived insect pollination in 174 Moraceae. 175 Disagreement between the two principal recent monographers of the Moraceae, 176 Corner (1962) and Berg (2001, 2005, 2006), over the delimitation of the Moreae has been 177 compounded by a series of phylogenies based on the analysis of molecular (DNA 178 sequence) data that have redefined genera and their relationships. This has resulted in a 179 poorly delimited tribe, both with respect to diagnostic morphological characters, the genera

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180 it comprises, and the rank of several taxa (see above). Ensuring that the tribe and its genera 181 are monophyletic will result in a classification that better reflects evolutionary history, 182 providing a framework for answering broader scientific questions. Our aim, therefore, was 183 to generate a comprehensive phylogeny of the Moreae (Fig. 1) and its near allies by 184 sampling all of the potential genera and species in the tribe sensu Berg, and sensu Clement 185 & Weiblen (2009) and use this to redelimit the tribe and its genera. We aimed to do so 186 through increased taxon and genome sampling compared to previous studies, including a 187 nearly comprehensive sample of the taxa in Moreae (56/66 species) and the allied tribes 188 (76/83 taxa) and Maclureae (12/12). Our data set combines phylogenomic data 189 generated using two largely non-overlapping sets of enrichment baits, one developed 190 specifically for the Moraceae (Gardner et al., 2016), the other for the whole of the 191 Angiosperms (Johnson & al., 2019), allowing us to explore the possibilities and challenges 192 of combining samples based on largely non-overlapping loci. The resulting generic revision 193 lays the groundwork for species-level revisionary work and provides clarity to this 194 economically important clade. 195 We also set out to reconstruct the evolutionary history of inflexed stamens within 196 Moraceae using ancestral state reconstruction. The loss of inflexed stamens in 197 Castilleae+Ficeae and Artocarpeae have been associated with transitions from wind to 198 animal pollination (Momose & al., 1998; Sakai & al., 2000; Datwyler & Weiblen, 2004; 199 Gardner & al., 2018). A more complete picture of evolutionary transitions between inflexed 200 and straight stamens may help focus further research on transitions in pollination biology 201 with Moraceae. 202 203 Materials and Methods 204 We used target enrichment sequencing (HybSeq) (Weitemier & al., 2014) to capture 205 333 genes previously developed for phylogenetic work in Moraceae (the “Moraceae333”) 206 (Gardner & al., 2016; Johnson & al., 2016). This method allows for efficient capture of 207 hundreds of loci and is suitable for both fresh material and degraded DNA from herbarium 208 material (Villaverde & al., 2018; Brewer & al., 2019), which comprises much of the 209 material employed in this study.

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210 211 Taxon sampling, library preparation, and sequencing 212 We sampled 56 out of 66 species (and all genera) in Moreae as well as select outgroup 213 taxa from Artocarpeae using DNA from tissue preserved on silica gel or—in most 214 cases—samples from herbarium specimens (Table S1). In either case, DNA was extracted 215 using a modified CTAB method, usually with increased incubation times to maximize yield 216 from herbarium tissue(Doyle & Doyle, 1987; Hale & al., 2020). Samples were quantified 217 using a Qubit fluorometer (Invitrogen, Life Technologies, California, USA), and herbarium 218 samples were run on a gel to test for degradation. For most samples 200 ng of DNA was 219 used for library preparation; for some low-yield samples, as little as 50 ng was used, and for 220 very degraded samples, as much input as possible was used, up to 400 ng. Undegraded 221 DNA was fragmented either using NEB DNA Fragmentase (New England Biolabs, 222 Ipswich, Massachusetts, USA) or on a Covaris M220 (Covaris, Wobum, Massachusetts, 223 USA). DNA samples with an average fragment size less than 500 bp were not fragmented 224 at all, and partially-degraded samples with an average fragment size of over 500 bp were 225 fragmented on the Covaris M220. TruSeq-style library preparation was carried out using 226 either the KAPA Hyper Prep kit (Kapa Biosystems, Wilmington, MA) or the NEB DNA 227 Ultra 2 kit following the manufacturer’s protocols, except that end repair, A-tailing, and 228 adapter ligation were carried out in reduced-volume reactions (0.25x for KAPA and 0.5x 229 for NEB) to reduce costs. Final products were quantified on the Qubit and combined in 230 equal molecular weights into pools of 16–20 samples. The pools totaled 1,200 µg each if 231 enough library preparation was available. Pools were hybridized for 16–24 hours to custom 232 Moraceae probes (Gardner et al, 2016) using a MYBaits kit (Arbor Biosciences, Ann 233 Arbor, Michigan, USA) following the manufacturer’s protocol, except that the probes were 234 diluted 1:1 with nuclease-free water. Hybridization products were reamplified using KAPA 235 Hot Start PCR reagents following the MYbaits protocol, quantified on the Qubit, and 236 quality-checked on an Agilent BioAnalyzer (Agilent Technologies, Palo Alto, California, 237 USA). Samples with adapter dimer peaks were cleaned using 0.7x SPRI beads and re-run 238 on the Qubit and BioAnalyzer. An initial sequencing run took place on a MiSeq 2 x 300bp 239 run (v3) (Illumina, San Diego, California, USA) at the Field Museum of Natural History,

8 bioRxiv preprint doi: https://doi.org/10.1101/2020.04.08.030452; this version posted April 9, 2020. 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. GARDNER ET AL., PHYLOGENOMICS AND GENERIC REVISION OF MOREAE

240 and then additional samples were sequenced on a HiSeq 4000 2 x 150bp run at the 241 Northwestern University Genomics Core. 242 We also included 47 Moraceae and Urticaceae samples enriched for the 243 Angiosperm353 probes and sequenced as part of the Plant and Fungal of Life project 244 (PAFTOL, RBG Kew; https://www.kew.org/science/our-science/projects/plant-and-fungal- 245 trees-of-life; Table S1). Sample preparation and sequencing followed Johnson et al. (2019). 246 The PAFTOL samples were enriched with a universal probe set developed for angiosperms 247 (the “Angiosperms353”). 248 Finally, we used samples sequenced for previous phylogenetics projects in 249 J.R. Forst. & G. Forst. and Parartocarpeae Zerega & E.M. Gardner to complete our 250 sampling (Johnson & al., 2016; Gardner, 2017; Kates & al., 2018; Zerega & Gardner, 251 2019). The final dataset contained 247 samples. 252 253 Assembly of reads 254 We trimmed reads using Trimmomatic (ILLUMINACLIP: TruSeq3-PE.fa:2:30:10 255 HEADCROP:3 LEADING:30 TRAILING:25 SLIDINGWINDOW:4:25 MINLEN:20) 256 (Bolger & al., 2014) and assembled them with HybPiper, which produces gene-by-gene, 257 reference-guided, de novo assemblies (Johnson & al., 2016). For the samples enriched with 258 the Angiosperms353 baits, we used the reference described by Johnson et al. (2019), and 259 for the samples enriched with the Moraceae333 baits, we used the reference described in 260 Zerega & Gardner (2019). To increase overlap between the two data sets beyond the 5 261 genes they inherently have in common, we used HybPiper to assemble the 262 Angiosperms353-enriched reads using the Moraceae333 targets and vice-versa, in order to 263 capture any additional genes found in off-target reads. The exception was most of the 264 Artocarpus data set, which was previously assembled for another study using only the 265 Moraceae333 targets. We used the HybPiper script “intronerate.py” to build “supercontig” 266 sequences for each gene, consisting of exons as well as any assembled flanking non-coding 267 sequences (intronic or intergenic). To these new assemblies, we added 76 Moraceae333 268 assemblies from Gardner (2017) to complete sampling for the Artocarpeae. 269

9 bioRxiv preprint doi: https://doi.org/10.1101/2020.04.08.030452; this version posted April 9, 2020. 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. GARDNER ET AL., PHYLOGENOMICS AND GENERIC REVISION OF MOREAE

270 Main phylogenetic analyses 271 The full data set was analyzed using the “exon” sequences to ensure good alignment 272 across the entire family. To maximize phylogenetic resolution within Moreae, a smaller 273 data set consisting only of Moreae taxa and a single outgroup taxon (Artocarpus 274 heterophyllus) was analyzed using the “supercontig” sequences but following the same 275 methodology. For each of the 686 genes assembled, we discarded sequences shorter than 276 25% of the average length for the gene and discarded genes containing sequences for less 277 than 30 samples. We aligned each gene with MAFFT (Katoh & Standley, 2013)and used 278 Trimal (Capella-Gutiérrez & al., 2009) to discard sequences with an average pairwise 279 identity of less than 0.5 to all other sequences in the alignment (indicative of poor a poor 280 quality sequence that could not be properly aligned) as well as columns containing more 281 than 75% gaps. We used RAxML 8.2.4 (Stamatakis, 2014) to estimate a maximum- 282 likelihood for a partitioned supermatrix of all genes as well as for each gene 283 individually (GTRCAT model, 200 bootstrap replicates). We then used ASTRAL-III 284 (Zhang & al., 2017), a summary-coalescent method, to estimate a species tree from all gene 285 trees, estimating node support using both bootstrap (160 replicates, resampling across and 286 within genes) and local posterior probability (normalized quartet scores, representing gene 287 tree concordance). Finally, we used ASTRAL-III to test whether, for each node, the null 288 hypothesis of a polytomy could be rejected (Sayyari & Mirarab, 2018). Alignment, 289 trimming, and estimation of gene trees were parallelized using GNU Parallel (Tange, 290 2018). 291 292 Whole 293 We also built a whole-chloroplast phylogenetic tree as follows. Rather than 294 assembling full-length genomes, which can be extremely slow to align, we assembled and 295 aligned the genomes in sections, dramatically speeding up the process. We created 296 HybPiper targets using the chloroplast genome of L. (NCBI RefSeq accession 297 no. NC_008359.1) and the associated gene annotations. Each target consisted of a gene 298 feature concatenated with any internal or subsequent non-coding sequence, terminating one 299 base before the next gene feature began. These intervals were generated by manually

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300 editing the NCBI gff3 file in Excel (Microsoft Corp., Redmond, Washington, USA) and 301 then extracted using BedTools (Quinlan & Hall, 2010). Assemblies for all Moraceae 302 samples and Boehmeria nivea (L.) Gaudich. were carried out in HybPiper using a coverage 303 cutoff of 2 and otherwise with default parameters. Within each target, sequencing less than 304 25% of the average length were discarded, and after alignment with MAFFT, sequences 305 with an average pairwise identity of less than 0.7 were discarded (the higher cutoff 306 reflecting the conserved nature of chloroplast DNA). Alignments were then concatenated 307 into a supermatrix, and samples with more than 50% undetermined characters were 308 discarded. Alignments were then rebuilt, filtered, and concatenated, and columns in the 309 final supermatrix with more than 75% missing characters were discarded. A maximum- 310 likelihood tree was generated using RAxML 8.2.4 under the GTRCAT model, with 200 311 rapid bootstrap replicates. 312 313 Phylogenetic network analysis 314 To further investigate relationships within the Paratrophis clade, including the proper 315 placement of and Trophis philippinensis (Bureau) Corner, we constructed 316 phylogenetic networks based on two reduced 8-taxon datasets (“exon” and “supercontig”) 317 consisting of those taxa plus Streblus anthropophagorum (Seem.) Corner, S. glaber (Merr.) 318 Corner, S. glaber subsp. australianus (C.T. White) C.C. Berg, and S. heterophyllus (Blume) 319 Corner, with S. mauritianus (Jacq.) Blume as the outgroup. Alignment preparation followed 320 the workflow outline above except that only genes with sequences for all eight taxa were 321 retained. Rooted gene trees were used to infer the network in PhyloNet using the 322 “InferNetwork_MPL” command, allowing a maximum of four hybridization events and 323 collapsing gene tree nodes with less than 30% bootstrap support (Yu & Nakhleh, 2015; 324 Wen & al., 2018) (Wen et al., 2018; Yu and Nakhleh, 2015); AIC was scored for the best 325 five networks from 10 runs, using the number of branch lengths and hybridization events 326 calculated as the number of parameters (Kamneva & al., 2017). 327 328 ITS and rbcL phylogenetic trees

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329 While we did not have our own sequences for Streblus tonkinensis (Eberh. & Dubard) 330 Corner, S. ascendens Corner, S. banksii (Cheeseman) C.J. Webb, and S. smithii 331 (Cheeseman) Corner, either ITS or rbcL sequences existed in NCBI GenBank for these taxa 332 (Fig. S2). We were not able to examine the underlying specimens ourselves, but we 333 considered the chances of misidentification low because those species are morphologically 334 and/or geographically distinctive. We constructed ITS and rbcL data sets from our own 335 samples using HybPiper, using Streblus sequences for these loci (obtained from GenBank) 336 as targets and reducing the coverage cutoff at 2 to recover the loci from off-target reads. To 337 these sequences, we added GenBank sequences of Streblus taxa as well as Trophis caucana 338 (Pittier) C.C. Berg. For each locus, we aligned sequences with MAFFT, discarded short 339 sequences (<490 bp), trimmed alignments to remove columns with over 75% gaps, and 340 built maximum-likelihood trees using RAxML (GTRGAMMA, 1000 rapid bootstraps). 341 342 Divergence time estimation 343 The supermatrix maximum-likelihood tree was time calibrated using ape v 5.3 344 (Paradis & Schliep, 2019) in R v 3.5.1 (Team, 2019). First, the tree was pruned of duplicate 345 taxa and non-Moraceae outgroup taxa, and edge lengths (in substitutions per site) were 346 multiplied by the number of sites in the alignment (to convert them to substitutions). The 347 following stem nodes were constrained with minimum ages (in million years, Ma) based on 348 data, following(Zhang & al., 2019): , 56 Ma; Broussonetia, 33.9 Ma; Morus 349 (subg. Morus, based on U.S.S.R. locality of the fossil), 33.9 Ma; and Artocarpus, 64 Ma. 350 The crown node of Moraceae was constrained to a minimum age of 73.2 Ma and a 351 maximum age of 84.7 Ma.(Zhang & al., 2019), which had a more extensive outgroup 352 sampling that we have here. The tree was then time-calibrated using the chronos function 353 under two different models (“relaxed” and “correlated”) (Kim & Sanderson, 2008; Paradis, 354 2013). The smoothing parameter (λ) was chosen using the cross-validation method in the

355 chronopl function (testing λ = 0 and 0-5 through 1015), selecting the value of λ that 356 minimized the cross-validation statistic (Sanderson, 2002). The resulting trees were 357 visualized using the densiTree function in phangorn 2.4.0 (Schliep, 2011), and the time 358 calibrated tree representing the central tendency of these analyses was selected for use in all

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359 further analyses, also taking into account the results of past family-wide studies. As the 360 penalized likelihood approach used does not integrate over model uncertainty or 361 uncertainty in calibration placement and timing, confidence intervals on node ages are not 362 provided in this study. A geologic timescale based on the strat2012 dataset added to tree 363 figures using PHYLOCH v 1.5-3 (Heibl, 2008). 364 365 Ancestral state reconstruction for inflexed stamens 366 All taxa were coded for presence (1) or absence (0) of inflexed stamens in bud. 367 Taxa such as Dorsteniae with stamens that are inflexed in bud but gradually straighten were 368 coded as 0. We reconstructed ancestral character states on the entire phylogeny by 369 stochastic mapping using the make.simmap function in the phytools v 0.6-99 (Revell, 370 2012). We also tested for trait-associated shifts in diversification rates using BAMM v 371 2.5.0 (Rabosky & al., 2013, 2014a; Rabosky, 2014), specifying the amount of missing taxa 372 per clade to account for the high proportion of missing taxa in Ficeae, Castilleae, and 373 Dorstenieae. Parameters were optimized using BAMMtools v 2.1.7 (Rabosky & al., 374 2014b). We also tested for trait-dependent diversification using diversitree v 0.9-13 375 (FitzJohn, 2012). We evaluated BiSSE and trait-independent models on the entire tree and 376 on a pruned tree consisting only of the densely-sampled Maclureae+Moreae+Artocarpeae 377 clade. 378 Reads from have been deposited in Genbank (Non-PAFTOL samples: BioProject 379 PRJNA322184; PAFTOL samples: BioProject PRJEB35285, subprojects PRJEB37667 for 380 Moraceae and PRJEB37665 for Urticaceae). Tree files and scripts outlining the 381 phylogenetic analyses have been deposited in the Dryad Data Repository (###TBA###). 382 383 Results 384 The final data set contained 247 samples, 47 enriched with the Angiosperms353 385 baits, 196 enriched with the Moraceae333 baits, and 4 extracted from whole genomes) and 386 619 genes (286 Angiosperms353 and all of the Moraceae333) (Table S1). The “exon” 387 supermatrix (all taxa) contained 613,126 characters, and the “supercontig” supermatrix

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388 (Moreae and select outgroup taxa only) contained 799,926 characters. The chloroplast data 389 set contained 113 loci. 390 On average, we assembled 39 Moraceae333 genes from the Angiosperms353- 391 enriched samples and 20 Angiosperms353 genes from the Moraceae333-enriched samples, 392 and the average pairwise overlap in assembled loci was 210 (Tables S1, S2). Nineteen taxa 393 were represented in both sets of samples, and 15 of these were always monophyletic (Figs. 394 2, 3). Twelve resolved as sister pairs: decipiens (31 loci overlapping), Bagassa 395 guianensis Aubl. (38), amazonicus (Ducke) Fosberg (22), Batocarpus 396 orinocensis H. Karst. (34), alicastrum Sw. (42), Clarisia racemosa Ruiz & Pav. 397 (59), Maclura africana (Bureau) Corner (213), (Welw.) C.C. Berg (45), 398 (Retz.) Lour. (75), Streblus mauritianus (Jacq.) Blume (40), Streblus 399 usambarensis (Engl.) C.C. Berg (43), and Trophis caucana (32). Three more represented 400 by more than two samples always resolved as a clade: Sorocea bonplandii (Baillon) W.C. 401 Burger, Lanj. & de Boer (3 samples; 19–35 loci overlapping), (L.) D. 402 Don ex Steud. (4 samples; 37–43 loci overlapping), and Malaisia scandens (Lour.) Planch. 403 (3 samples; 27–43 loci overlapping). Three additional taxa resolved as sister pairs in the 404 ASTRAL analysis but as a grade in the supermatrix analysis: 405 (Lour.) Corner (28 loci overlapping), (Blume) Corner (50), and 406 Trophis montana (Leandri) C.C. Berg (56). Only one species, Utsetela gabonensis Pellegr. 407 (18 loci overlapping) was never monophyletic, always forming a grade with U. neglecta 408 Jongkind. 409 The supermatrix and species trees were broadly concordant except within 410 Artocarpus, where the species tree was much more consistent with previous analyses within 411 that genus (Gardner et al., in review) (Figs. 2, 3). Otherwise, most differences were at 412 shallow phylogenetic depths, such as relationships within Streblus section Paratrophis. For 413 both data sets, the polytomy hypothesis was rejected (P < 0.05) for Moraceae and all tribe 414 and genus-level clades (following the revised classification presented below) (Figs. 2, 3). 415 Of the genera in Moreae sensu Clement & Weiblen, only Milicia and Sorocea were 416 monophyletic; Morus, Streblus, and Trophis were not; Bagassa is monotypic and resolved 417 as sister to Sorocea, with which it shares straight stamens. Four Moreae species resolved

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418 with other tribes: Trophis caucana was nested within Castilleae, Streblus asper (Retz.) 419 Lour. was sister to Castilleae, Streblus indicus (Bureau) Corner was sister to 420 Parartocarpeae, and Streblus usambarensis was nested within Dorstenieae. Moreae was 421 otherwise monophyletic, comprising the following subclades: (1) Streblus section 422 Taxotrophis, sister to all other Moreae; (2) (a) Trophis section Maillardia, (b) Milicia + 423 Morus subgenus Afromorus, (c) Streblus section Ampalis, (d) Streblus section Paratrophis 424 in part + Morus subgenus Gomphomorus, (e) Streblus section Paratrophis in part + Trophis 425 section Calpidochlamys; (3) Bagassa + Sorocea; (4) Trophis sections Trophis and 426 Echinocarpa C.C. Berg + Morus. These are roughly geographic clades: (1) Southeast Asia; 427 (2) (a) Madagascar, (b) Southeast Africa, (c) Madagascar, (d) Pacific + South America, (e) 428 Southeast Asia + Pacific; (3) South America; (4) South America. 429 While Trophis philippinensis was inside the Paratrophis clade in all analyses, the 430 position of Morus insignis was not stable. In the “exon” analyses, it was always in 431 Paratrophis (Fig. 2), although the polotomy hypothesis could not be rejected for its 432 position as sister to S. anthropophagorum+S. heterophyllus. In the “supercontig” and 433 chloroplast analyses, it was sister to Paratrophis, and the polotomy test was rejected for 434 that node (Figs. 3, S1). In the five phylogenetic networks reported (Fig. 4, Table S3), M. 435 insignis was inside Paratrophis in three of them, had a hybrid origin involving Paratrophis 436 in one, and was only unambiguously sister to Paratrophis in one network, although even in 437 that one it was involved in a hybridization involving Paratrophis. 438 The chloroplast phylogenetic tree (Fig. S1) was generally in agreement with the 439 nuclear phylogenetic trees, with three notable differences. Streblus indicus and the 440 Parartocarpeae formed a grade paraphyletic to Dorstenieae, Castilleae, and Ficeae, rather 441 than a clade. Streblus zeylanicus (Thwaites) Kurz was sister to S. taxoides (B. Heyne ex 442 Roth) Kurz (instead of sister to all of section Taxotrophis), although with low support 443 (62%), and S. glaber subsp. australianus was not sister to subsp. glaber, although its 444 placement was not strongly supported (80%). Finally, Morus insignis was sister to 445 Paratrophis, agreeing with the “supercontig” analysis but not the “exon” analysis. 446 The ITS and rbcL phylogenetic trees based on few characters, were not very well 447 resolved, with only few nodes attaining 100% bootstrap support (Fig. S2). Nevertheless,

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448 with the exception of a few stray taxa (one Dorstenia sample in ITS and one Streblus 449 indicus samples in rbcL), both phylogenetic trees reconstructed monophyletic tribes with at 450 least moderate support. In the ITS phylogenetic tree, Streblus smithii and S. banksii were 451 both in a well-supported clade comprising section Paratrophis, and S. tonkinensis was part 452 of the Castilleae clade, which also contained S. asper and Trophis caucana. In the rbcL 453 phylogenetic tree, the two Streblus ascendens samples, the four samples of the 454 undetermined Streblus from Papua New , and S. smithii were part of a well- 455 supported clade comprising section Paratrophis. 456 457 Time-calibration and ancestral state reconstruction 458 The cross-validation criterion was minimized by a smoothing parameter (λ) value of

459 106. The tree calibrated under the correlated model (logLik = -17; p-logLik = -17; ΦIC = 460 1108) was less sensitive to changes in λ and generally had younger ages than the tree 461 calibrated under the relaxed model (logLik = -56.7; p-logLik = -53129706, ΦIC = 462 4209013), the latter of which had perhaps implausibly long terminal branches (Table 2, Fig. 463 S3). The crown age of Moreae was Paleocene (59.1 Ma) under the correlated model and 464 late (75.4 Ma) under the relaxed model. Because the correlated tree was more 465 consistent with past family-wide studies (Zerega & al., 2005; Zhang & al., 2019), we used 466 that tree for all further analyses (Fig. 5). The BAMM analysis found a single credible rate 467 shift, not surprisingly at the crown node of Ficus (Fig. S4); that rate shift was—also not 468 surprisingly—associated with a loss of inflexed stamens, which are never found in Ficus (P 469 = 0.035); no rate shifts were found within Moreae. Ancestral reconstruction on the entire 470 tree found that ancestral Moraceae had stamens inflexed in bud; these were lost nine times 471 (in Ficeae, Olmedieae [=Castilleae], Parartocarpeae, twice in Dorstenieae, Maclura section 472 Cudrania (Trécul) Corner, Artocarpeae, Bagassa, and Sorocea) and regained once (in 473 Trophis caucaua) (Fig. 6). Model testing on both the whole tree and on the 474 Moreae+Artocarpeae+Maclureae subtree indicated that a BiSSE model was not 475 substantially better than a trait-independent model (Moreae only: AIC for BiSSE = 1110.4; 476 trait-independent = 1112.8; ΔAIC = 2.4; whole family: AIC for BiSSE = 1488.3; trait-

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477 independent = 1490.4; ΔAIC = 2.1). In any event, the reconstructions were identical (Figs. 478 6). 479 480 481 Discussion 482 483 Sequencing and combination of data sets 484 This study was materially improved by our ability to combine samples enriched 485 with two largely non-overlapping bait sets. Despite minimal by-design overlap, we were 486 able to assemble many overlapping loci for samples with moderate to deep coverage (Table 487 S2), adding taxa that would not otherwise have been included in the study and replicating 488 taxa to confirm unexpected phylogenetic placement (e.g, Streblus indicus). Taxa replicated 489 across the two data sets performed well in phylogenetic analyses, with 15 out of 19 always 490 resolving as monophyletic in supermatrix analyses and 18/19 so resolving in ASTRAL 491 analyses, with only Utsetela gabonensis always forming a grade instead (with a difficult-to- 492 distinguish congener). Our results should embolden others to combine and repurpose data 493 sets in similar ways. 494 495 Higher taxonomy in Moraceae and the delimitation of the tribe Moreae 496 Our results support Corner’s overall approach to the classification of Moraceae, if 497 not all of its details, including the primacy of inflorescence architecture and the 498 unreliability of inflexed stamens for higher taxonomy (Corner, 1962). Inflexed stamens are 499 a plesiomorphy that was lost nine times in Moraceae (Fig. 6), a preserved ancestral 500 character whose past taxonomic importance accounts for the rather extreme non- 501 monophyly of the Moreae. Streblus s.l. provides the best illustration of this principle, 502 appearing in four out of seven tribe-level clades within Moraceae. We may justly call its 503 disparate sections, as Corner did, “fragments of an ancestral Streblus.” (Corner, 1975)—or 504 in modern parlance, a paraphyletic remnant preserving plesiomorphic staminate flowers 505 similar to those likely to have occurred in the ancestor of all Moraceae, with four free tepals 506 and four inflexed stamens (Clement & Weiblen, 2009). If one of the goals of modern

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507 systematics is to establish taxonomic frameworks that reflect as far as possible real 508 evolutionary relationships, our results may serve as a warning to carefully investigate 509 whether characters used for taxonomy are derived (synapomorphic) or ancestral 510 (symplesiomorphic). 511 Broadly speaking, a tribal delimitation based on inflorescence architecture 512 (supplemented with other characters in some cases) agrees best with the phylogenetic trees 513 presented here. Moreae (as revised below) have unisexual spicate or racemose 514 inflorescences (the pistillate ones sometimes uniflorous), with the globose-capitate pistillate 515 inflorescences of the monotypic Bagassa as the sole exception. Stamens may be either 516 inflexed or straight. Elsewhere in the family, racemes and spikes are rare, with the former 517 found in Maclura (in part) and the latter found in the related genera Broussonetia, 518 Allaeanthus Thwaites, and Malaisia and arguably in Batocarpus H. Karst. and Clarisia; all 519 of these have capitate pistillate inflorescences. The taxa of Streblus s.l. and Trophis s.l. that 520 must be excluded from Moreae all have inflorescences that do not fit our general rule: 521 discoid-capitate (Streblus asper and Trophis caucana), cymose (Streblus indicus), or 522 bisexual (Streblus usambarensis). In these cases, perhaps Corner did not take his emphasis 523 on inflorescence architecture quite far enough, including too wide of a variety in this one 524 tribe. In critiquing the utility of inflorescence architecture for classification, Berg (1977b) 525 noted the similarity in the inflorescence structure of Bleekrodea (then part of Moreae, and 526 included in Streblus by Corner) to that of Utsetela and Helianthostylis (Dorstenieae), an 527 observation that proved prescient when Bleekrodea was found to belong to Dorstenieae 528 (Clement & Weiblen, 2009). 529 Olmedieae (as revised below, including Castilleae) can be defined entirely based 530 upon the presence of a discoid inflorescence subtended by an involucre of imbricate bracts. 531 Two species with such involucres previously classified as Moreae, Streblus asper and 532 Trophis caucana (=Olmedia aspera) always appeared in the Olmedieae (=Castilleae) clade 533 in our analyses (Figs. 2–3). Olmedia aspera (=Trophis caucana)—the nomenclatural type 534 of the tribe Olmedieae—was transferred to Moreae because of its inflexed stamens and lack 535 of self-pruning branches (Berg, 1977b). In inflorescence morphology, however, T. caucana 536 closely resembles other Castilleae, always subtended by an involucre of imbricate bracts

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537 (Berg, 1977b, 2001). The staminate inflorescences of Streblus asper are strikingly similar 538 to those of T. caucana, and it is remarkable that the affinity between S. asper and the 539 Olmedieae has not been seriously considered until now. Previous barcoding or phylogenetic 540 studies have placed Trophis caucana (Kress & al., 2009) and Streblus tonkinensis (Chen & 541 al., 2016) (closely allied to S. asper) in the Castilleae clade, but those results went 542 unremarked upon, perhaps because of the broad scale of the studies (respectively, forest 543 community phylogenetics and the vascular plants of ). 544 The remaining five tribes can all be broadly defined based on inflorescence 545 architecture as Corner argued, sometimes supplemented by other characters as Berg 546 preferred, allowing of course for the exceptions made inevitable by the vicissitudes of 547 evolution. Ficeae of course is defined by the (essentially an urceolate disc that 548 has been closed at the top). Maclureae have densely-packed globose infructescences and 549 can be distinguished from Artocarpeae by their four stamens (inflexed in most sections) and 550 armature. Artocarpeae also have densely-packed globose infructescences but only one 551 straight stamen and no armature. Parartocarpeae have a few connate involucral bracts and 552 (in large part) flowers embedded in fleshy receptacles. Dorstenieae are perhaps the most 553 heterogenous group, but in large part they have bisexual inflorescences, often capitate or 554 discoid, and often with ballistically-ejected endocarps. 555 556 The role of inflexed stamens in the evolution of Moraceae 557 The repeated losses of inflexed stamens (Fig. 6), which are associated with wind 558 pollination (Bawa & Crisp, 1980; Berg, 2001), raise the possibility that transitions from 559 wind to animal pollination, which have already been documented in Moraceae (Momose & 560 al., 1998; Sakai & al., 2000; Datwyler & Weiblen, 2004; Gardner & al., 2018), are even 561 more common within the family. Generally considered rare (Culley & al., 2002), the shift 562 from wind to animal pollination may be a repeated feature of Moraceae deserving of further 563 investigation. Further investigation of Sorocea, with its straight stamens and sometimes- 564 scented inflorescences, may reveal that, like Artocarpus, it contains both wind and animal 565 pollination. And while little is known about pollination in the Dorstenieae, the presence of 566 unisexual inflorescences and inflexed stamens (e.g., Broussonetia) as well as bisexual

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567 inflorescences with straight stamens (e.g., Brosimum, Dorstenia) raises the possibility of 568 transitions within that clade as well; taxa with inflexed stamens but bisexual inflorescences 569 such as Bleekrodea and Sloetia (which is visited by bees, EMG pers. obs.) may represent 570 remnants of an intermediate state. Finally, the conclusion that a single transition to insect 571 pollination preceded the split between the Ficeae and Olmedieae (Castilleae) should be 572 reevaluated in light of the position of Streblus asper as sister to the latter (Figs. 2, 3). The 573 only shift in diversification rates our analyses recovered was on the branch leading to the 574 very diverse Ficus, suggesting that the shift away from wind pollination may not by itself 575 lead to increased diversification. 576 577 Explanation of taxonomic revisions 578 We present a generic revision of Moreae (Fig. 7) based on the present phylogenetic 579 study as well as morphological characters. Arranging monophyletic and morphologically 580 coherent genera requires one change of rank and 8 new combinations, but no entirely new 581 names. These revisions provide a framework for within-genus revisionary work, which will 582 require more intensive sampling and review of specimens within the genera circumscribed 583 here. We provide an explanation of the taxonomic changes, followed by a formal 584 presentation of the affected tribes and genera, with complete species lists and synonymy. 585 Trophis and the reinstatement of the Olmedieae — To make Trophis monophyletic, 586 we propose that it be applied strictly to the Neotropical clade that includes the type species 587 Trophis americana L. (=Trophis racemosa (L.) Urb.) . To accomplish this, we reinstate the 588 genus Maillardia and transfer Trophis philippinensis to Paratrophis (discussed below), 589 reinstating its former name Paratrophis philippinensis (Bureau) Fern.-Vill. Because 590 Trophis caucana does not belong in Trophis or Moreae but rather with the members of 591 Castilleae, we reinstate its former name Olmedia aspera Ruiz & Pav. and transfer it to that 592 tribe, whose former name Olmedieae must now be reinstated on account of its priority. 593 Streblus — We restrict the genus Streblus to three species comprising most of 594 section Streblus—Streblus asper, Streblus tonkinensis, and Streblus celebensis C.C. Berg— 595 and transfer the genus to Olmedieae. Although S. celebensis was not included in our 596 phylogeny, the sub-involucrate inflorescences are similar to those of S. asper, with which S.

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597 celebensis differs primarily in vegetative characters, the latter having broadly-toothed 598 margins in the distal half of the leaf. Both occur in , where at least one specimen 599 with intermediate leaf morphology has been collected (Sulawesi, Kendari: Kjellberg 452, 600 24 Feb. 1929, L, det. S. asper by E.J.H. Corner). We therefore retain its taxonomic position 601 in Streblus. The remaining member of section Streblus, S. usambarensis, belongs with 602 Dorstenieae, and we therefore transfer it to that tribe, reinstating its former name 603 Sloetiopsis usambarensis. Streblus indicus is sister to Parartocarpeae, and we therefore 604 reinstate its former name Pseudostreblus indicus and transfer it to Parartocarpeae. 605 The remaining species of Streblus s.l. are properly placed in Moreae but are still 606 paraphyletic. We therefore reinstate the genera Ampalis, Pachytrophe, Paratrophis, and 607 Taxotrophis, largely corresponding to the former sections but requiring some new 608 combinations. Paratrophis as presented here is united by spicate male inflorescences 609 (usually) with peltate or reniform bracts (except for Paratrophis philippinensis (=Trophis 610 philippinensis), which does not have fleshy tepals in fruit). Within Paratrophis we include 611 Paratrophis ascendens (Corner) E.M. Gardner (=Streblus ascendens Corner) based on its 612 inflorescence morphology and phylogenetic position in the rbcL tree (Fig. S2b). Its 613 previous position within the monotypic section Protostreblus was due to the type 614 specimen’s spiral phyllotaxy, but the latter may be atypical, as a more recent collection 615 Womersley NGF 24791 (K, L, BO), has distichous leaves. Berg (1988), recognizing the 616 affinities between Pachytrophe dimepate Bureau and Ampalis mauritiana, included both in 617 Streblus section Ampalis, noting that in light of the diversity found in Streblus s.l., 618 separation at the sectional level was no longer warranted; although our phylogenetic results 619 support this grouping, we provisionally retain them as separate genera because the 620 differences between them in phyllotaxy, stipule amplexicaulity, and embryo characters 621 equal or exceed the distinctions between other genera in Moreae following our atomization 622 of Streblus s.l. Further intensive study of that species complex may of course warrant a 623 different approach, including potentially reducing both to a section of Paratrophis. Our 624 species lists within the former components of Streblus follow Berg’s approach (1988, 625 2006), with two exceptions. We provisionally recognize Taxotrophis zeylanica (Thwaites) 626 Thwaites as distinct from Taxotrophis taxoides (B. Heyne ex Roth) W.L. Chew ex E.M.

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627 Gardner (= (B. Heyne ex Roth) Kurz) based on our phylogenetic work and 628 following the , which recognizes Streblus zeylanicus as distinct from S. 629 taxoides based on its clustered pistillate inflorescences. In addition, we provisionally 630 recognize Paratrophis australiana (=S. glaber subsp. australianus) as distinct from 631 Paratrophis glabra based on its geographic and consistent morphological distinctiveness. 632 Taxotrophis and Paratrophis warrant further investigation to refine species limits. 633 Morus — Morus has never been revised, and the species concepts are often based on 634 minor morphological differences (Berg et al., 2006; Berg 2001), and the paraphyly of 635 several species in our analyses suggests that a broad M. alba similar to Bureau’s (1873) 636 may be worth a second look. The monotypic subgenus Afromorus is sister to Milicia, but 637 the leaf morphology is markedly different, instead resembling other Morus species in its 638 trinerved based and crenate margins. We therefore raise Afromorus to genus level, requiring 639 one new combination. Morus insignis, from western Central and South America, bears a 640 remarkable resemblance to Paratrophis, in particular P. pendulina, especially in leaf 641 morphology, which in M. insignis is not consistently trinerved as in other mulberries. The 642 infructescence appears superficially like a mulberry because of its basally fleshy tepals, 643 although with more loosely-packed flowers, but closer inspection places it firmly within 644 Paratrophis, with drupes protruding from the persistent tepals, peltate bracts, and a sterile 645 groove. Because analyses differ as to whether M. insignis is sister to Paratrophis or part of 646 it, it seems best to treat them as congeners. 647 These changes result in eleven monophyletic genera of Moreae, providing a 648 framework for revisionary work within the genera. Below, we present a complete genus 649 and species list for Moreae with brief descriptions for all genera and synonymies for new 650 combinations and reinstated or recircumscribed taxa. All cited protologues were reviewed, 651 and dates for works published piecemeal were confirmed by reference to Taxonomic 652 Literature 2 online (https://www.sil.si.edu/DigitalCollections/tl-2/index.cfm). 653 654 655 Taxonomic Treatment 656

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657 Key to the tribes of Moraceae

658 This key follows the tribal circumscription of Clement & Weiblen (2009), as subsequently 659 modified by Zerega & al. (2010), Chung & al. (2017), Zerega & Gardner (2019), and this 660 study. 661

662 1. Inflorescences urceolate with the opening entirely closed by ostiolar bracts (i.e. 663 syconium) such that the flowers are enclosed at all stages of development; lamina 664 with waxy glandular spots at the base of the midrib or in the axils of the basal lateral 665 veins beneath – Ficeae (Ficus)

666 1. Inflorescences capitate, spicate, discoid, or urceolate, but flowers are not 667 entirely enclosed at all developmental stages (i.e. mature anthers or stigmas are 668 open to the surrounding environment); lamina without waxy glandular spots. – 2 669 670 2. Inflorescences (at least staminate) with an involucre of imbricate bracts; often 671 with self-pruning horizontal branches (except Olmedia, , Streblus) – 672 Olmedieae (, Antiaropsis, , , , , 673 , Olmedia, , Poulsenia, , Sparattosyce, 674 Streblus) 675 2. Inflorescences not involucrate; plants without self-pruning branches – 3 676 677 3. Plants woody; dioecious; pistillate inflorescences globose-capitate; spines axillary 678 or terminating short shoots; dioecious – Maclureae (Maclura) 679 3. Plants woody, herbaceous, or succulent; dioecious or monoecious; pistillate 680 inflorescences various; spines absent or if present, then pistillate inflorescences 681 not globose capitate – 4 682 683 4. Trees or ; monoecious; inflorescences unisexual; staminate flowers with 684 one stamen (rarely two);– Artocarpeae (Artocarpus, Batocarpus, Clarisia)

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685 4. Trees, shrubs, lianas, herbaceous, or succulent; monoecious or dioecious; 686 inflorescences unisexual or bisexual; staminate flowers with more than one 687 stamen (or if one stamen then dioecious) – 5 688 689 5. Trees or shrubs; monoecious; inflorescences unisexual; stamens straight in bud or 690 staminate flowers 5-parted and inflexed in bud;– Parartocarpeae (Hullettia, 691 , Pseudostreblus) 692 5. Trees, shrubs, lianas, herbaceous, or succulent; not as above but otherwise 693 monoecious or dioecious; bisexual or unisexual inflorescences, stamens straight or 694 inflexed in bud but staminate flowers never 5-parted – 6 695 696 6. Trees, shrubs, lianas, herbaceous, or succulent; bisexual inflorescences (or if 697 unisexual then a climber or herbaceous) – Dorstenieae (Allaeanthus in part, 698 Bleekrodea, Bosqueiopsis, Brosimum, Broussonetia in part, Dorstenia, Fatoua, 699 Helianthostylis, Malaisia, , Sloetia, Sloetiopsis, , Trilepsium, 700 Trymatococcus, Utsetela) 701 6. Trees or shrubs; unisexual inflorescences – 7 702 703 7. Trees; stamens inflexed in bud; pistillate inflorescences globose-capitate – 704 Dorstenieae (Allaeanthus in part, Broussonetia in part) 705 7. Trees or shrubs; stamens inflexed or straight in bud; if stamens inflexed in bud, 706 pistillate inflorescence not globose-capitate – Moreae (Afromorus, Ampalis, 707 Bagassa, Maillardia, Milicia, Morus, Pachytrophe, Paratrophis, Taxotrophis, 708 Sorocea, Trophis) 709 710 711 Revisions 712 713 Tribe MOREAE 714

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715 Moreae Gaudich. in Freyc., Voy. Uranie, Bot. (1830) 509. 716 Moreae subtribe Soroceae Miq in Martius, Fl. Bras. 4, 1, fasc. 12: 111 (1853), p.t. – 717 Soroceae (Miq.) C.C. Berg, Blumea 50: 537 (2005), p.p. 718 Strebleae Bureau in DC., Prodr. 17: 215 (1873), p.p. 719 720 Tree or shrubs, monoecious or dioecious. Leaves alternate or opposite, distichous or 721 spirally arranged; stipules lateral to amplexicaul. Inflorescences unisexual, uniflorous or 722 racemose, spicate, capitate, or globose; bracteate; tepals 4, free to connate; staminate 723 flowers with 4 stamens, filaments straight or inflexed in bud, pistillode usually present; 724 pistillate flowers with (mostly) free , 2 stigmas. drupaceous or achene-like 725 with a fleshy persistent , dehiscent or not. Seeds with or without , testa 726 usually with a thick vascularized part below the hilum, cotyledons equal or unequal, 727 straight or folded. 728 729 Genera and distribution: eleven genera and 63 species with a worldwide distribution. 730 731 732 Afromorus 733 734 Afromorus (A. Chev. ex J.-F. Leroy) E.M. Gardner, stat. nov. — based on Morus L. 735 subg. Afromorus [A. Chev., Rev. Bot. Appl. Agr. Trop. 29 (315–316): 70 (1949), 736 invalidly published]; J.-F. Leroy, Rev. Bot. Appl. Agr. Trop. 29 (323–324): 482 737 (1949) & Bull. Mus. Hist. Nat. Paris, ser. 2, 21: 732 (1949). TYPE: Afromorus 738 mesozygia (Stapf ex A. Chev.) E.M. Gardner. 739 740 Dioecious trees, shoot apices . Leaves distichous, triplinerved or at least trinerved 741 at the base. Stipules free, more or less lateral. Inflorescences solitary or paired, bracts 742 of varying shapes. Staminate inflorescences spicate, to 2.5mm long, 4-parted, 743 tepals imbricate, ciliolate, pistillode small, apiculate. Pistillate inflorescences 744 subglobose, ca. 5 mm across, flowers 4-parted, tepals ciliolate, bifid, equal or

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745 unequal, arms filiform to 5 mm long. Infructescences subglobose or less often slightly 746 elongate, ca. 1 mm across, tepals fleshy, yellowish to greenish, drupes ca. 5 x 3–5 mm. 747 Seeds ca. 4.5 x 2.5–4.5 mm. 748 749 Species and distribution: one species, in tropical Africa. 750 751 Note: The leaves of Afromorus—with crenate margins and trinerved bases—bear a striking 752 resemblance to those of Morus, and it is thus not surprising that the former was heretofore 753 included within the latter. However, leaves of Afromorus are distinct in being usually 754 completely triplinerved, without an upper pinnately-veined portion as in most species of 755 Morus. As the genus is monotypic, the type must be its only species, Afromorus mesozygia 756 (Stapf ex A. Chev.) E.M. Gardner. 757 Leroy’s protologue of Morus subg. Afromorus was published only in French and 758 was therefore not a valid diagnosis or description in 1949. However, because the subgenus 759 was monotypic, the protologue referred to a single name based on a validly-published 760 description, Morus lactea (Sim.) Mildbr. (= lactea Sim.), and was therefore validly 761 published by reference to the latter. 762 763 1. Afromorus mesozygia (Stapf ex A. Chev.) E.M. Gardner, comb. nov. — based on Morus 764 mesozygia Stapf ex A. Chev. [Végétaux utiles de l’Afrique tropicale française 5: 263 765 (1909), nomen solum], J. Bot. (Morot) ser. 2, t. 2: 99 (1909). 766 Celtis lactea Sim, For. Fl. Port. E. Afr. : 97, t. 96 (1909), probably post-dating Morus 767 mesozygia (fide Berg. 1977) – Morus lactea (Sim) Mildbr., Notizbl. Bot. Gart. 768 Berlin 8: 243 (1922) – var. lactea (Sim) A. Chev., Rev. Bot. 769 Appl. Agr. Trop. 29: 72 (1949). 770 Morus mesozygia var. sanda A. Chev., Rev. Bot. Appl. Agr. Trop. 29: 71 (1949), 771 invalidly published (under Art. 39.1, Latin description or diagnosis lacking). 772 Morus mesozygia var. colossea A. Chev., Rev. Bot. Appl. Agr. Trop. 29: 71 (1949), 773 invalidly published (under Art. 39.1, Latin description or diagnosis lacking). 774

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775 Ampalis 776 Ampalis Bojer, Hort. Maurit. 291 (1837) 777 Streblus Lour. subgen. Parastreblus Blume, Mus. Bot. Ludg.-. 2: 89 (1856) 778 Streblus Lous. sect. Ampalis (Bojer) C.C. Berg, Proc. Kon. Ned. Akad. Wetensch. C 779 91(4): 358 (1988), p.p. 780 781 Dioecious trees or shrubs. Leaves spirally arranged to nearly distichous, pinnately veined. 782 Stipules free, nearly lateral. Inflorescences solitary or paired in the leaf axils, spicate, with 783 flowers in longitudinal rows, bracts present but sparse, usually subpeltate. Staminate 784 inflorescences to 9 cm long, flowers 4-parted, decussate-imbricate, stamens 4, inflexed in 785 bud, pistillode present. Pistillate inflorescences to 12 cm long, flowers tepals 4, separate, 786 decussate-imbricate, ovary free, stigmas 2, equal. Infructescences with enlarged fleshy 787 perianths, surrounding drupaceous fruits, the latter ca. 5–6 mm long. Seeds ca. 4 x 4 mm, 788 testa thickened and not distinctly vascularized, cotyledons equal. 789 790 Species and distribution: One species, native to Madagascar and Comoros. 791 792 1. Ampalis mauritiana (Jacq.) Urb., Symb. Antill. 8: 165 (1920) – Morus mauritiana Jacq., 793 Collect. 3: 206 (“1789”, 1791) – Streblus mauritianus (Jacq.) Blume, Mus. Bot. 794 Lugd.-Bat. 2: 80 (1856). 795 Streblus maritimus Palaky, Catal. Pl. Madag. 2: 31 (1907) 796 Morus nitida Willem. In Useri, Ann. Bot. 18: 56 (1796) 797 M. ampalis Poir. In Lam., Encycl. Bot. 4: 380 (1797) 798 Trophis cylindrica Roxb., Fl. Indica 3: 599 (1832), pro syn. M. mauritianae. 799 Ampalis madagascariensis, Bojer, Hort. Maurit. 291 (1837) nom. illeg., pro syn. 800 Ampalis madagascariensis var. occidentalis Léandri, Mém. Inst. Sci. Madag., ser. B, 801 1: 12, pl. (1948). 802 Morus rigida Hassk., Cat. Hort. Bog. 74 (1844). 803

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804 Note: May be considered congeneric with Pachytrophe, with which it shares inflorescence 805 and infructescence morphology. They are distinguished on the basis of phyllotaxy, 806 which is (usually) spiral in Ampalis and distichous in Pachytrophe. 807 808 809 Bagassa 810 811 Bagassa Aubl., Pl. Guiane. Suppl. 15 (1775). 812 813 Dioecious trees. Leaves opposite and decussate, lamina triplinerved, 3-lobed to entire. 814 Stipules free, lateral. Inflorescences solitary or paired in the leaf axils, bracteate. Staminate 815 inflorescences spicate with an abaxial sterile groove, to 12 cm long, flowers in longitudinal 816 rows with, tepals 4, stamens 2, straight in bud, pistillode present. Pistillate inflorescences 817 globose-capitate, ca. 1–1.5 cm across, flowers 4-lobed to 4-parted, stigmas 2, filiform. 818 Infructescences globose, ca. 2.5–3.5 cm across, green, tepals fleshy, yellowish to greenish, 819 drupes ca. 7–8 mm long. Seeds ca. 3 x 2 mm, testa thin and not vascularized, cotyledons 820 equal. 821 822 Species and distribution: One, in tropical South America. 823 824 1. Bagassa guianensis Aubl., Pl. Guiane. Supple. 15 (1775) 825 826 827 Maillardia 828 829 Maillardia Frapp. ex Duch. in Maillard, Notes sur l’île de la Réunion, Annex P. 3 (1862) 830 Trophis P. Br. sect. Maillardia (Duch.) Corner, Gard. Bull. Singapore 19: 230 (1962). 831 832 Dioecious trees or shrubs. Leaves distichous, pinnately veined. Stipules free, semi- 833 amplexicaul. Inflorescences solitary or paired in the leaf axils, bracts subpeltate. Staminate

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834 inflorescences spicate with an abaxial sterile groove, flowers 4-parted, decussate-imbricate, 835 stamens 4, inflexed in bud, pistillode present. Pistillate inflorescences up to three together, 836 uni- or bi-florous, perianth tubular 4-lobed, ovary adnate to the perianth, stigmas 2, equal. 837 Infructescences with enlarged fleshy perianths surrounding drupaceous fruits, the latter to 838 18 mm long. Seeds to 13 mm long, testa thin, with a thickened vascularized part below the 839 hilum, cotyledons unequal. 840 841 Species and distribution: Two species, in Madagascar, Comoros, and the Seychelles. 842 843 1. Maillardia borbonica Duch., Ann. Notes Réunion, Bot. 1: 148 (1862) – Trophis 844 borbonica (Duch.) C.C.Berg, Proc. Kon. Ned. Akad. Wetensch. C 91(4): 355 (1988) 845 Maillardia lancifolia Frapp. ex Duch., Ann. Notes Réunion, Bot. 1: 148 (1862). 846 Trophis borbonica (Duch.) C.C. Berg, Proc. Kon. Ned. Akad. Wetensch. C 91: 355 847 (1988). 848 849 2. Maillardia montana Leandri, Mém. Inst. Sci. Madagascar, Sér. B, Biol. Vég. 1: 25 850 (1948) – Trophis montana (Leandri) C.C.Berg, Proc. Kon. Ned. Akad. Wetensch. C 851 91(4): 355 (1988). 852 Maillardia occidentalis Leandri, Mém. Inst. Sci. Madagascar, Sér. B, Biol. Vég. 1: 26 853 (1948) 854 Maillardia orientalis Léandri, Mém. Inst. Sci. Madagascar, Sér. B, Biol. Vég. 1: 27 855 (1948) 856 Maillardia mandrarensis Léandri, Mém. Inst. Sci. Madagascar, Sér. B, Biol. Vég. 1: 857 28 (1948). 858 Maillardia pendula Fosberg, Kew Bull. 29: 266, t. 2 (1974). 859 860 861 Milicia 862 Milicia Sim, For. Fl. Port. E. Afr. 97 (1909). 863

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864 Dioecious trees. Leaves distichous, lamina pinnately veined. Stipules free, not fully 865 amplexicaul. Inflorescences spicate, usually solitary in the leaf axils or on leafless nodes, 866 spicate, flowers in longitudinal rows alternating with rows of bracts, bracts mostly basally 867 attached, abaxial sterile groove present. Staminate inflorescences to 20 cm long, flowers 4- 868 parted, imbricate, stamens 4, inflexed in bud, pistillode present. Pistillate inflorescences to 869 4.5 cm long, flowers 4-parted, decussate-imbricate, ovary free, stigmas 2, unequal. 870 Infructescences with enlarged fleshy perianths, surrounding slightly flattened drupaceous 871 fruits, the latter to ca. 3 mm long. Seeds ca. 2 mm long, testa thin with a slightly thickened 872 vascularized part below the hilum, cotyledons equal. 873 874 Species and distribution: Two species in tropical Africa. 875 876 1. Milicia excelsa (Welw.) C.C. Berg, Bull. Jard. Bot. Natl. Belg. 52(1-2): 227 (1982) – 877 Morus excelsa Welw., Trans. Linn. Soc. Lond. (Bot.) 27: 69, t. 23 (1869) – Maclura 878 excelsa (Welw.) Bur. In DC., Prodr. 17: 231 (1873) – Chlorophora excelsa (Welw.) 879 Benth. & Hook., Gen. Pl. 3(1): 363 (1880). 880 Chlorophora tenuifolia Engl., Bot. Jahrb. 20: 139 (1894). 881 Milicia africana Sim, For. Fl. Port. E. Afr. 97, t. 122 (1909). 882 Chlorophora alba A. Chev., Bull. Soc. Bot. Fr. 58 (Mém. 8d): 209 (1912). 883 884 2. (A. Chev.) C.C. Berg, Bull. Jard. Bot. Natl. Belg. 52(1-2): 227 (1982) – 885 Chlorophora regia A. Chev., Bull. Soc. Bot. Fr. 58 (Mém. 8d): 209 (1912) – Maclura 886 regia (A. Chev.) Corner, Gard. Bull. Singapore 19: 237 (1962). 887 888 889 Morus 890 Morus L., Sp. Pl. 986 (1753). 891 892 Dioecious trees or shrubs. Leaves trinerved (to five-nerved) at the base. Stipules free, 893 nearly lateral. Inflorescences solitary or paired in the leaf axils, without an obvious sterile

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894 groove, interfloral bracts absent. Staminate inflorescences spicate or racemose, to 8 cm 895 long, flowers 4-parted, imbricate, stamens 4, inflexed in bud, pistillode present. Pistillate 896 inflorescences subcapitate to spicate, up to 16 cm long, flowers tepals 4, separate, 897 decussate-imbricate, ovary free, stigmas 2, equal. Infructescences with enlarged fleshy 898 perianths enclosing achene-like fruits, the latter ca. 1 mm long. Seeds less than 1 mm long, 899 cotyledons equal. 900 901 Species and distribution: Sixteen species, Asia and North to Central America; introduced 902 worldwide. 903 904 1. Morus alba L., Sp. Pl. 2: 986 (1753). 905 var. alba 906 var. multicaulis (Perrottet) Loudon, Arbor. Frutic. Brit. 3: 1348 (1838). 907 2. Poir. in Desrousseaux et al., Encycl. 4: 380 (1797). 908 3. Morus boninensis Koidz., Bot. Mag. (Tokyo) 31: 38 (1917) 909 4. Hemsl., J. Linn. Soc., Bot. 26: 456 (1894) 910 var. cathayana 911 var. gongshanensis (Z. Y. Cao) Z. Y. Cao, Acta Bot. . 17: 154 (1995). 912 5. Kunth, Nov. Gen. Sp. [H.B.K.] 2: 33 (1817). 913 6. Morus liboensis S. S. Chang, Acta Phytotax. Sin. 22: 66 (1984). 914 7. Miq., Pl. Jungh. 1: 42 (1851). 915 var. macroura 916 var. laxiflora G.K.Upadhyay & A.A.Ansari, Rheedea 20: 44 (2010). 917 8. Morus koordersiana J.-F.Leroy, Bull. Mus. Natl. Hist. Nat. sér. 2, 21: 729 (1949) 918 (endemic to and possibly synonymous with M. macroura. However, it was 919 not cited by Berg et al. (2006) either as a good species or as a synonym of the latter). 920 9. Morus microphylla Buckley, Acad. Nat. Sci. Philadelphia 1862: 8 (1863) (recognized in 921 the Flora of North America (Flora of North America Editorial Committee, 1993) but 922 likely conspecific with M. celtidifolia and considered so by Berg (2001)). 923 10. (Bureau) C. K. Schneid. in Sargent, Pl. Wilson. 3: 296 (1916).

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924 11. L. Sp. Pl. 2: 986 (1753). 925 12. C. K. Schneid. in Sargent, Pl. Wilson. 3: 293 (1916). 926 13. L., Sp. Pl. 986 (1753). 927 var. rubra 928 var. murrayana (Saar & Galla) Saar, Phytologia 91: 106 (2009). 929 14. Roxb., Fl. Ind., ed. 1832, 3: 596 (1832). 930 15. Morus trilobata (S. S. Chang) Z. Y. Cao, Acta Phytotax. Sin. 29: 265 (1991). 931 16. Morus wittiorum Hand.-Mazz., Anz. Akad. Wiss. Wien, Math.-Naturwiss. Kl. 58: 88 932 (1921) 933 934 Pachytrophe 935 936 Pachytrophe Bureau, Prodr. [A.P. de Candolle] 17: 234 (1873). – Ampalis Boj. sect. 937 Pachytrophe (Bur.) Baillon, Hist. Pl. 6: 191 (1875–76) 938 Streblus Lour. sect. Ampalis (Boj.) C.C. Berg, Proc. Kon. Ned. Akad. Wetensch. C 91(4): 939 358 (1988), p.p. 940 941 Dioecious trees. Leaves distichous, pinnately veined. Stipules connate, semi-amplexicaul. 942 Inflorescences usually paired in the leaf axils, spicate, with an abaxial sterile groove, 943 flowers sessile in longitudinal rows, tepals 4, decussate-imbricate, ciliolate. Staminate 944 inflorescences up to 5 cm. long, bracts basally attached, flowers with filaments inflexed in 945 bud, anthers introrse, pistillode quadrangular, ca. 0.5 mm long. Pistillate inflorescences up 946 to 2.5 cm long, bracts (sub)peltate, flowers 2–14, tepals free, stigma bifid, arms equal. 947 Infructescences reddish, with enlarged fleshy perianths ca. 6–8 mm long, drupes thinly 948 fleshy. Seeds ca. 4.5 mm long. 949 950 Species and distribution: One, in tropical Africa (Madagascar). 951 952 Note: Pachytrophe could be considered congeneric with Ampalis, within which Baillon 953 treated it as a section (although without making any new specific combinations).

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954 955 1. Pachytrophe dimepate Bureau, Prodr. [A.P. de Candolle] 17: 234 (1873). 956 Pachytrophe obovata Bureau, Prodr. [A.P. de Candolle] 17: 235 (1873). 957 Plecospermum bureaui A.G. Richt., Term. Füzetek 18: 296 (1895), nomen nudum et 958 superfl., pro. syn. nom. ined. “Plecospermum obovatum Bureau” (Boivin 1717, P). 959 Plecospermum (?) laurifolium Baill. in Grandidier, Hist. Madag. Vol. 35, Hist. Nat. 960 Pl., Tome 5, Atlas 3, 2e partie: pl. 294a (1895) – Pachytrophe obovata var. 961 laurifolia (Baill.) Léandri, Mém. Inst. Sci. Madag., ser. B, 1: 16 (1948). 962 Pachytrophe obovata var. montana Léandri, Mém. Inst. Sci. Madag., ser. B, 1: 16 963 (1948). 964 965 966 Paratrophis 967 968 Paratrophis Blume, Ann. Mus. Bot. Lugduno-Batavi 2 (1856) 81. 969 Pseudomorus Bureau, Ann. Sci. Nat., Bot. sér. 5, 11: 371 (1869). 970 Uromorus Bureau in A.DC., Prodr. 17: 236 (1873). 971 Calpidochlamys Diels, Bot. Jahrb. Syst. 67: 172 (1935); — Trophis sect. 972 Calpidochlamys Corner, Gard. Bull. Singapore 19: 230 (1962). 973 Chevalierodendron J.-F. Leroy, Compt. Rend. Hebd. Séances Acad. Sci. 227: 146 974 (1948) . 975 Streblus Lour. sect. Paratrophis (Blume) Corner, Gard. Bull. Singapore 19: 216 976 (1962). 977 Streblus Lour. sect. Protostreblus Corner, Blumea 18: 393 (1970). 978 Morus L. subg. Gomphomorus J.-F. Leroy, Bull. Mus. Hist. Nat. (Paris), Sér. 2, 21: 979 732 (1949) 980 981 Dioecious trees or shrubs. Leaves distichous (or spiral in P. ascendens), pinnately veined, 982 sometimes trinerved at the base. Stipules free, lateral. Inflorescences axillary, solitary or up 983 to 5 together, spicate, with an abaxial sterile groove, interfloral bracts mostly peltate,

33 bioRxiv preprint doi: https://doi.org/10.1101/2020.04.08.030452; this version posted April 9, 2020. 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. GARDNER ET AL., PHYLOGENOMICS AND GENERIC REVISION OF MOREAE

984 flowers sessile in longitudinal rows, tepals 4, valvate, ciliolate. Staminate inflorescences up 985 to at least 20 cm. long, flowers with filaments inflexed in bud, pistillode present. Pistillate 986 inflorescences up to at least 10 cm long, flowers usually at least 2 (to many), tepals free 987 (except in P. philippinensis), stigma bifid, arms equal. Fruits drupaceous, red to black, with 988 tepals persistent but usually not enlarged or fleshy (except in P. philippinensis and P. 989 insignis), up to ca. 1 cm long. Seeds up to ca. 8 x 6 mm, cotyledons equal. 990 991 Species and distribution: Twelve species from the Malesian region to , New 992 Zealand, and Oceania, Central and western South America. 993 994 1. Paratrophis anthropophagorum (Seem.) Benth. & Hook. f. ex Drake, Ill. Fl. Ins. Pacif. 995 296 1892 996 Trophis anthropophagorum Seem. [Bonplandia 9 (17–18): 259 (1861), nomen nudum] 997 Fl. Vit. 258, t. 68 (1868); — Uromorus anthropophagorum (Seem.) Bureau in de 998 Candolle, Prodr. 17 (1873) 236; — Streblus anthropophagorum (Seem.) Corner, 999 Gard. Bull. Sing.19 (1962) 221. 1000 Caturus oblongatus Seem., Fl. Vit. 254 (1868). 1001 Paratrophis ostermeyri Rech., Fedd. Rep. 5: 130 (1908). 1002 Paratrophis viridissima Rech., Fedd. Rep. 5: 130 (1908). 1003 Paratrophis zahlbruckneri Rech., Fedd. Rep. 5: 130 (1908). 1004 Pseudomorus brunoniana (Endl.) Bureau var. tahitensis J. Nadeaud, Énum. Pl. Tahiti 1005 43 (1873) – Uromorus tahitensis (J. Nadeaud) Bureau in de Candolle, Prodr. 17: 237 1006 (1873) – Paratrophis tahitensis (Bureau) Benth. & Hook.f. ex Drake, Ill. Ins. Mar. 1007 Pacif. Fasc. 7: 296 (1892); et Fl. Polyn. Franc. 193 (1892). – Streblus tahitensis (J. 1008 Nadeaud) E.J.H. Corner, Gard. Bull. Singapore 19: 225 (1962). 1009 1010 2. Paratrophis ascendens (Corner) E.M. Gardner comb. nov. — based on Streblus 1011 ascendens Corner, Blumea 18: 395, t.1 (1970). 1012

34 bioRxiv preprint doi: https://doi.org/10.1101/2020.04.08.030452; this version posted April 9, 2020. 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. GARDNER ET AL., PHYLOGENOMICS AND GENERIC REVISION OF MOREAE

1013 3. Paratrophis australiana C.T. White, Contr. Arnold Arbor. 4: 15 (1933) — Streblus 1014 glaber (Merr.) Corner var. australianus (C.T. White) Corner, Gard. Bull. Singapore 1015 19: 221 (1962) — Streblus glaber (Merr.) Corner subsp. australianus (C.T. White) 1016 C.C. Berg, Blumea 50: 548 (2005). 1017 1018 4. Paratrophis banksii Cheeseman, Man. N.Z. Fl. 633 (1906) – 1019 (Cheeseman) C.J. Webb, in Connor & Edgar, J. of Bot. 25 136 (1987). 1020 Paratrophis heterophylla var. elliptica Kirk T.N.Z.L 29: 500, t. 46 (1897); — Streblus 1021 heterophyllus var. ellipticus (Kirk) Corner, Gard. Bull. Singapore 19: 222 (1962). 1022 Note:— Morphologically very close to and not always distinguishable from P. 1023 microphylla. 1024 1025 5. Paratrophis glabra (Merr.) Steenis, J. Bot. 72: 8 (1934) – Gironniera glabra Merr., 1026 Philipp. J. Sci., 1, Suppl. 42 (1906); Enum. Philipp. Flow. Pl. 2: 35 (1923) — 1027 Chevalierodendron glabrum (Merr.) J.-F. Leroy, Compt. Rend. Hebd. Séances Acad. Sci. 1028 227: 146 (1948) — Streblus glaber (Merr.) Corner, Gard. Bull. Singapore 19: 221 (1962). 1029 Aphananthe negrosensis Elmer, Leafl. Philipp. Bot. 2: 575 (1909). 1030 Pseudostreblus caudatus Ridl., J. Fed. Malay States Mus. 6: 54 (1915). 1031 Streblus laevifolius Diels, Bot. Jahrb. Syst. 67: 171 (1935). 1032 Streblus urophyllus Diels, Bot. Jahrb. Syst. 67: 172 (1935) — Streblus glaber (Merr.) 1033 Corner subsp. urophyllus (Diels) C.C. Berg, Blumea 50: 548 (2005); 1034 Streblus urophyllus Diels var. salicifolius Corner, Gard. Bull. Singapore. 19: 225 (1962). 1035 1036 Note: Berg et al. (2006) treated P. australiana and Streblus urophyllus as subspecies of 1037 Streblus glaber. Paratrophis australiana, endemic to Australia, has crenate leaf margins 1038 and somewhat larger staminate inflorescences with more interfloral bracts than P. glabra; 1039 these morphological differences are consistent and geographically confined, and we 1040 therefore reinstate P. australiana. This stands in contrast to Streblus urophyllus, which we 1041 provisionally maintain in synonomy under P. glabra. Although collections from Mt. 1042 Wilhelm in are remarkable for their thick coriaceous leaves and spinose

35 bioRxiv preprint doi: https://doi.org/10.1101/2020.04.08.030452; this version posted April 9, 2020. 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. GARDNER ET AL., PHYLOGENOMICS AND GENERIC REVISION OF MOREAE

1043 margins, similar toothed margins can be found at higher elevations in and Sulawesi, 1044 suggesting that the striking leaf morphology of S. urophyllus is an alpine effect not 1045 indicative of speciation. We reserve judgment on the status of Streblus urophyllus var. 1046 salicifolius Corner, applied by Corner (1962) to specimens with linear leaves, provisionally 1047 maintaining it in synonomy following Berg et al. (2006). 1048 1049 6. Paratrophis insignis (Bureau) E.M. Gardner comb. nov. — based on Morus insignis 1050 Bureau, in De Candolle, Prodr. 17: 247 (1873). 1051 Morus peruviana Planch. ex Koidz., Fl. Symb. Orient.-Asiat. 88 (1930). 1052 Morus trianae J.-F.Leroy, Bull. Mus. Hist. Nat. (Paris) Sér. 2, 21: 731 (1949). 1053 Morus marmolii Legname, Lilloa 33: 334 (1973) 1054 Note: The infructescences differ from most other Paratrophis in their fleshy free tepals and 1055 denser aggregation of flowers, but the staminate inflorescences are typical of the genus. 1056 1057 7. Paratrophis microphylla (Raoul) Cockayne, Bot. Notes Kennedy's Bush & Scenic Res. 1058 Port Hills, Lyttelton (Rep. Scenery Preserv.) 3 (1915) – Epicarpurus microphyllus 1059 Raoul, Choix Pl. Nouv.-Zel. 14. (1846) – Taxotrophis microphylla (Raoul) F. Muell., 1060 Fragm. (Mueller) 6(47): 193 (1868). 1061 Paratrophis heterophylla Blume, Mus. Bot. 2(1-8): 81. (1856). 1062 1063 8. Paratrophis pendulina (Endl.) E.M. Gardner, comb. nov. — based on Morus 1064 pendulina Endl., Prodromus Florae Norfolkicae 40 (1833) – Pseudomorus pendulina 1065 (Endl.) Stearn, J. Arnold Arbor. 28: 427 (1947) – Pseudomorus brunoniana var. 1066 pendulina (Endl.) Bureau, Ann. Sci. Nat. Bot. sér. 5, 11: 372 (1869) – Streblus 1067 pendulinus (Endl.) F. Muell., Fragmenta Phytographiae Australiae (1868). 1068 Morus brunoniana Endl., Atakta Bot. t. 32 (1835) – (Endl.) F. 1069 Muell., Fragm. Phyt. Australiae 6: 192 (1868) – Pseudomorus brunoniana (Endl.) 1070 Bureau, Ann. Sci. Nat., Bot. sér. 5, 11: 372 (1869)

36 bioRxiv preprint doi: https://doi.org/10.1101/2020.04.08.030452; this version posted April 9, 2020. 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. GARDNER ET AL., PHYLOGENOMICS AND GENERIC REVISION OF MOREAE

1071 Pseudomorus brunoniana var. australiana Bureau, Ann. Sci. Nat., Bot. sér. 5, 11: 373 1072 (1869) – Pseudomorus pendulina var. australiana (Bureau) Stearn, J. Arnold Arbor. 1073 28: 427 (1947). 1074 Pseudomorus brunoniana var. australiana subvar. castaneaefolia Bureau, Ann. Sci. 1075 Nat., Bot. sér. 5, 11: 372 (1869). 1076 Pseudomorus brunoniana var. obtusa Bureau, Ann. Sci. Nat., Bot. sér. 5, 11: 373 1077 (1869) – Pseudomorus pendulina var. obtusa (Bureau) Stearn, J. Arnold Arbor. 28: 1078 428 (1947), as var. obtusata. 1079 Pseudomorus sandwicensis O. Deg., Fl. Hawaiiensis fam. 38 (1938) – Pseudomorus 1080 brunoniana var. sandwicensis (O. Deg.) Skottsb., Acta Horti Gothob. 15: 347 1081 (1944) – Pseuomorus pendulina var. sandwicensis (O. Degener) Stearn, J. Arnold 1082 Arbor. 28: 428 (1947) – Streblus sandwicensis (O. Deg.) H. St. John, Pacific Trop. 1083 Bot. Gard. Mem. 1: 374. 1973. 1084 Note: This complex requires further investigation. Although the types of Morus pendulina, 1085 Morus brunoniana, Pseudomorus sandwicensis, and Pseudomorus brunoniana var. obtusa 1086 differ from one another, it is difficult to discern clear geographic patterns that warrant 1087 maintaining separate species, and we therefore provisionally treat them all as one 1088 widespread and variable species. 1089 1090 9. Paratrophis philippinensis (Bureau) Fern.-Vill., Nov. App. 98 (1880) — Uromorus 1091 philippinensis Bureau in A.DC., Prodr. 17: 237 (1873) — Trophis philippinensis (Bureau) 1092 Corner, Gard. Bull. Singapore 19: 231 (1962). 1093 Sloetia minahassae Koord., Versl. Minahasa 645 (1898). 1094 Paratrophis grandifolia Elmer, Leafl. Philipp. Bot. 5: 1814 (1913). 1095 Calpidochlamys branderhorstii Diels, Bot. Jahrb. Syst. 67: 173 (1935) — Trophis 1096 branderhorstii (Diels) Corner, Gard. Bull. Singapore 19: 231 (1962). 1097 Calpidochlamys drupacea Diels, Bot. Jahrb. Syst. 67: 173 (1935) — Trophis drupacea 1098 (Diels) Corner, Gard. Bull. Singapore 19: 231 (1962).

37 bioRxiv preprint doi: https://doi.org/10.1101/2020.04.08.030452; this version posted April 9, 2020. 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. GARDNER ET AL., PHYLOGENOMICS AND GENERIC REVISION OF MOREAE

1099 Note: This species is the only Paratrophis with fused tepals and one of only two whose 1100 tepals develop into a fleshy accessory fruit. The staminate inflorescences, however, are 1101 typical of the genus. 1102 1103 10. Paratrophis sclerophyllus (Corner) E.M. Gardner, comb. nov. — based on Streblus 1104 sclerophyllus Corner, Blumea 18: 399 (1970). 1105 1106 11. Paratrophis smithii Cheeseman T.N.Z.L 20:148 (1888) – Streblus smithii (Cheeseman) 1107 Corner Gard. Bull. Singapore 19: 224 (1962). 1108 Note: Morphologically very close to P. anthropophagorum. 1109 1110 12. Paratrophis solomonensis (Corner) E.M. Gardner, comb. nov. — based on Streblus 1111 solomonensis Corner, Gard. Bull. Singapore 19: 224 (1962). 1112 Note:— Morphologically very close to P. anthropophagorum. 1113 1114 1115 Sorocea 1116 1117 Sorocea A. St-Hil., Mém. Mus. Hist. Nat. 7: 473 (1821). 1118 Balanostreblus Kurz, J. Asiat. Soc. Bengal., Pt. 2, Nat. Hist., 42: 247 (1873), p.p. 1119 Pseudosorocea Baill., Hist. Pl. 6: 210 (1875). 1120 Trophisomia Rojas Acosta, Bull. Acad. Inst. Geogr. Bot. 24: 211 (1914). 1121 Paraclarisia Ducke, Arq. Serv. Florest. 1(1): 2 (1939). 1122 1123 Dioecious trees. Leaves alternate, distichous, lamina pinnately veined, 3-lobed to entire. 1124 Stipules free, lateral. Inflorescences solitary or paired in the leaf axils or below the leaves, 1125 racemose to spicate to subcapitate or uniflorous, bracts basally attached to peltate. 1126 Staminate flowers 4-lobed to 4-parted, tepals decussate-imbricate, stamens (3–)4, straight 1127 in bud, pistillode usually absent. Pistillate flowers tubular, 4-lobed to sub-entire, ovary 1128 basally adnate to the perianth, stigmas 2, short, usually tongue-shaped. Infructescences

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1129 with drupaceous fruits enclosed by fleshy enlarged perianths, the latter red to orange, 1130 turning black at maturity. Seeds large, testa thin, embryo green, cotyledons very unequal, 1131 the smaller one minute and enclosed by the larger. 1132 1133 Species and distribution: 19 species in Central and South America from Mexico to 1134 Argentina. 1135 1136 Note: This species list follows the Flora Neotropica monograph (Berg 2001) with the 1137 addition of four new species and one status change published later. Names synonymized by 1138 Berg (2001) but recognized by Burger et al. (1962) are noted in parentheses. Complete 1139 synonymies can be found in those treatments. 1140 1141 Sorocea subg. Sorocea 1142 Sorocea affinis Hemsl., Biol. Cent.-Amer., Bot. 3: 150 (1883). 1143 Sorocea angustifolia Al.Santos & Romaniuc, Novon 24: 199 (2015). 1144 Sorocea bonplandii (Baill.) W.C. Burger, Lanj. & de Boer, Acta Bot. Neerl. 11: 465 1145 (1962). 1146 Sorocea briquetii J.F.Macbr., Publ. Field Columb. Mus., Bot. Ser. 11: 16 (1931) (incl. 1147 S. pileate W.C. Burger). 1148 Sorocea carautana M.D.M.Vianna, Carrijo & Romaniuc, Novon 19: 549 (2009). 1149 Sorocea ganevii R.M.Castro, Neodiversity 1: 18 (2006). 1150 Gaudich., Voy. Bonite, Bot. 3: t. 74 (1843) (incl. S. 1151 klotzschiana Baill. and S. macrogyna Lanj. & Wess. Boer). 1152 Sorocea hilarii Gaudich., Voy. Bonite, Bot. 3: t. 71 (1843) (incl. S. racemosa 1153 Gaudich.). 1154 Sorocea jaramilloi C.C.Berg, Novon 6: 241 (1996). 1155 Sorocea longipedicellata A.F.P. Machado, M.D.M. Vianna & Romaniuc, Syst. Bot. 1156 38: 687 (2013). 1157 Sorocea muriculata Miq., C.F.P. von Martius & auct. suc. (eds.), Fl. Bras. 4(1): 113 1158 (1853).

39 bioRxiv preprint doi: https://doi.org/10.1101/2020.04.08.030452; this version posted April 9, 2020. 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. GARDNER ET AL., PHYLOGENOMICS AND GENERIC REVISION OF MOREAE

1159 subsp. muriculata (incl. S. amazonica Miq.) 1160 subsp. uaupensis (Baill.) C.C. Berg, Proc. Kon. Ned. Akad. Wetensch. C 88: 387 1161 (1985) (incl. S. guayanensis W.C. Burger). 1162 Sorocea pubivena Hemsl., Biol. Cent.-Amer., Bot. 3: 150 (1883). 1163 subsp. pubivena (incl. S. cufodontii W.C. Burger) 1164 subsp. hirtella (Mildbr.) C.C. Berg, Novon 6: 243 (1996) (incl. S. opima J.F. 1165 Macbr.) 1166 subsp. oligotricha (Akkermans & C.C. Berg) C.C. Berg, Novon 6: 243 (1996). 1167 Sorocea ruminata C.C.Berg, Novon 6: 244 (1996). 1168 Sorocea sarcocarpa Lanj. & Wess. Boer, Acta Bot. Neerl. 11: 452 (1962). 1169 Sorocea steinbachii C.C. Berg, Proc. Kon. Ned. Akad. Wetensch. C 88: 385 (1985). 1170 Sorocea trophoides W.C. Burger, Acta Bot. Neerl. 11: 450 (1962). 1171 1172 Sorocea subg. Paraclarisia (Ducke) W.C. Burger, Lanj. & Wess. Boer, Acta Bot. Neerl. 1173 11: 468 (1962). 1174 Sorocea duckei W.C.Burger, Acta Bot. Neerl. 11: 473 (1962). 1175 Sorocea sprucei (Baill.) J.F.Macbr., Publ. Field Mus. Nat. Hist., Bot. Ser. 11: 16 1176 (1931). 1177 subsp. sprucei (incl. S. arnoldoi Lanj. & Wess. Boer). 1178 subsp. saxicola (Hassl.) C.C.Berg, Proc. Kon. Ned. Akad. Wetensch., Ser. C., 1179 Biol. Med. Sci. 88: 391 (1985). 1180 Sorocea subumbellata (C.C. Berg) Cornejo, Novon 19: 297 (2009). 1181 1182 1183 Taxotrophis 1184 Taxotrophis Blume, Ann. Mus. Bot. Lugduno-Batavi 2 77 (1856); Hutch., Bull. Misc. 1185 Inform. Kew 147 (1918). 1186 Streblus Lour. sect. Taxotrophis (Blume) Corner, Gard. Bull. Singapore 19: 218 (1962); 1187 Berg et al., Fl. Males. Ser. 1, Vol. 17, Pt. 2 (2006). 1188

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1189 Monoecious or dioecious trees or shrubs, usually with lateral or terminal thorns. Leaves 1190 distichous, pinnately veined, petioles adaxially pubescent. Stipules free, lateral. 1191 Inflorescences axillary, solitary or paired, with an abaxial sterile groove, interfloral bracts 1192 basally attached, flowers with 4 free tepals, valvate. Staminate inflorescences spicate to 1193 sub-capitate, flowers with filaments inflexed in bud, pistillode present. Pistillate 1194 inflorescences uniflorous or sub-spicate, flowers usually pedicellate, stigma bifid, arms 1195 equal. Fruits drupaceous, up to ca. 1 cm long, usually loosely enclosed by the enlarged 1196 persistent tepals. Seeds up to ca. 8 x 6 mm, cotyledons subequal to unequal. 1197 1198 Species and distribution: Six species, ranging from Sri Lanka to New Guinea. 1199 1200 1. Taxotrophis ilicifolia S. Vidal, Revis. Pl. Vasc. Filip. 249 (1886). 1201 Balanostreblus ilicifolia Kurz, J. Asiat. Soc. Bengal, Pt. 2, Nat. Hist. 42(4): 248 1202 (1874), p.p. 1203 Pseudotrophis laxiflora Warb., Bot. Jahrb. Syst. 13 294 (1891). 1204 Taxotrophis obtusa Elmer, Leafl. Philipp. Bot. 5 1813 (1913). 1205 Taxotrophis laxiflora Hutch., Bull. Misc. Inform. Kew 151 (1918). – Streblus 1206 laxiflorus (Hutch.) Corner, Gard. Bull. Singapore 19 229 (1962). 1207 Taxotrophis triapiculata Gamble, Bull. Misc. Inform. Kew 188 (1913). 1208 Taxotrophis eberhardtii Gagnep., Fl. Indo-Chine 5 700 (1928). 1209 Taxotrophis macrophylla auct. non Boerl.: Burkill, Dict. Econ. Prod. Malay Penins. 1210 2126 (1935). 1211 Streblus ilicifolius (S. Vidal) Corner, Gard. Bull. Singapore 19: 227 (1962). 1212 1213 2. Taxotrophis macrophylla (Blume) Boerl., Handl. Fl. Ned. Ind. 3: 359 (1900). 1214 Streblus macrophyllus Blume, Ann. Mus. Bot. Lugduno-Batavi 2: 80 (1856) — 1215 Diplocos ? macrophyllus (Blume) Bureau in A.DC., Prodr. 17: 216 (1873). 1216 Pseudotrophis mindanaensis Warb. in Perkins, Fragm. Fl. Philipp. 1: 165 (1905); 1217 Elmer, Leafl. Philipp. Bot. 5: 1815 (1913), ‘Taxatrophis mindanaensis’ in nota. 1218 Paratrophis caudata Merr., Philipp. J. Sci., 1, Suppl. 183 (1906).

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1219 Taxotrophis balansae Hutch., Bull. Misc. Inform. Kew 151 (1918). 1220 Dimerocarpus brenieri Gagnep., Bull. Mus. Hist. Nat. (Paris) 27: 441 (1921). 1221 1222 3. Taxotrophis perakensis (Corner) E.M. Gardner, comb. nov., based on Streblus 1223 perakensis Corner, Gard. Bull. Singapore 19: 223 (1962). 1224 1225 Note: Although Corner (1962) considered S. perakensis species part of section Paratrophis, 1226 albeit with some hesitation, Berg et al. (2006), whom we follow, placed it in Taxotrophis 1227 based on the spines that appear on some specimens. This is a rather variable species that 1228 requires further investigation to properly elucidate its limits and affinities. 1229 1230 4. Taxotrophis spinosa Steenis in Backer & Bakh.f., Fl. 2 (1965) 16. 1231 spinosa Blume, Bijdr. (1825) 507. — Streblus spinosus (Blume) Corner, Gard. 1232 Bull. Singapore 19: 229 (1962). 1233 Taxotrophis javanica Blume, Ann. Mus. Bot. Lugduno-Batavi 2: 77, t. 26 (1856). 1234 1235 5. Taxotrophis taxoides (B. Heyne ex Roth) W.L. Chew ex E.M. Gardner, comb. nov. 1236 Trophis taxoides B. Heyne ex Roth, Nov. Pl. Sp. 368 (1821). — Trophis taxiformis 1237 Spreng., Syst. Veg. 3 902 (1826), nom. nov. illeg. — Streblus taxoides (B. Heyne 1238 ex Roth) Kurz, Forest Fl. Burma 2: 465 (1877) — Phyllochlamys taxoides (B. 1239 Heyne ex Roth) Koord., Exkurs.-Fl. Java 2: 89 (1912). 1240 Trophis spinosa Roxb., Fl. Ind., ed. Carey 3: 762 (1832), non Willd. 1806, nec Blume 1241 1826. — Epicarpurus spinosus (Roxb.) Wight, Icon. Pl. Ind. Orient. 6: 7, t. 1962 1242 (1853), p.p. — Phyllochlamys spinosa (Roxb.) Bureau in A.DC., Prodr. 17: 218 1243 (1873); 1244 Epicarpurus timorensis Decne., Nouv. Ann. Mus. Hist. Nat. 3: 499, t. 21 (1834). 1245 Taxotrophis roxburghii Blume, Ann. Mus. Bot. Lugduno-Batavi 2: 78 (1856) 1246 Streblus microphyllus Kurz, Prelim. Rep. Forest Pegu App. A, cxviii; App. B, 84 1247 (1875); — Streblus taxoides (B. Heyne ex Roth) Kurz var. microphylla (Kurz) 1248 Kurz, Forest Fl. Burma 2: 465 (1877).

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1249 Phyllochlamys wallichii King ex Hook.f., Fl. Brit. India 5: 489 (1888); 1250 Phyllochlamys taxoides (B. Heyne ex Roth) Koord. var. parvifolia Merr., Enum. 1251 Philipp. Flow. Pl. 2: 38 (1923). 1252 Taxotrophis poilanei Gagnep., Fl. Indo-Chine 5: 701 (1928). 1253 Taxotrophis crenata Gagnep., Fl. Indo-chine 5: 702, t. 82 (1928). — Streblus crenatus 1254 (Gagnep.) Corner, Gard. Bull. Singapore 19: 226 (1962). 1255 Phyllochlamys tridentata Gagnep., Fl. Indo-Chine 5: 714 (1928). 1256 1257 Note: In the 1950s, Dr. Chew Wee Lek annotated quite a lot of specimens at K and SING 1258 with the new combination Taxotrophis taxoides. However, the combination was never 1259 published, probably because the need for the combination was obviated in 1962 when 1260 Corner, his doctoral supervisor, reduced Taxotrophis to a section of Streblus. 1261 1262 6. Taxotrophis zeylanica (Thwaites) Thwaites, Enum. Pl. Zeyl. [Thwaites] 264 (1861). 1263 Epicarpurus zeylanicus Thwaites, Hooker’s J. Bot. Kew Gard. Misc. 4: 1 (1852) — 1264 Diplocos zeylanica (Thwaites) Bureau, Prodr. [A. P. de Candolle] 17: 215 (1873) 1265 — Streblus zeylanicus (Thwaites) Kurz, Forest Fl. Burma 2: 464 (1877). 1266 Taxotrophis caudata Hutchinson, Bull. Misc. Inform. Kew 1918(4): 149 (1918). 1267 1268 1269 Trophis 1270 1271 Trophis Lour., P. Browne, Civ. Nat. Hist. Jamaica 357 (1756), nom. cons. 1272 Bucephalon L. Sp. Pl. 1190 (1753), nom. rejic. 1273 Skutchia Pax & K. Hoffm. ex C.V. Morton, J. Wash. Acad. Sci. 27: 306 (1937). 1274 1275 Dioecious trees or shrubs. Leaves distichous, pinnately veined. Stipules free, lateral. 1276 Inflorescences axillary or just below the leaves, solitary or paired, interfloral bracts basally 1277 attached. Staminate inflorescences spicate to racemose with an abaxial sterile groove, tepals 1278 4, basally connate, stamens 4, filaments inflexed in bud, pistillode present. Pistillate

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1279 inflorescences spicate to racemose or subcapitate, tepals 4, connate, forming a tubular 1280 perianth, ovary adnate to the perianth or not, stigma bifid, arms equal. Fruits drupaceous, 1281 up to ca. 1.5 cm long, adnate to the perianth or not, the perianth enlarged and fleshy or not. 1282 Seeds up to ca. 1 cm long, cotyledons equal. 1283 1284 Species and distribution: Five species in the neotropics. 1285 1286 Trophis P. Browne sect. Trophis 1287 1288 1. Trophis cuspidata Lundell, Amer. Midl. Naturalist 19: 427 (1938). 1289 2. Trophis mexicana (Liebm.) Bureau, Prodr. [A. P. de Candolle] 17: 253 (1873). 1290 3. Trophis noraminervae Cuevas & Carvajal, Acta Bot. Mex. 47: 2 (1-7, fig.) (1999). 1291 4. Trophis racemosa Urb., Symb. Antill. (Urban). 4(2): 195 (1905). 1292 1293 Trophis P. Browne sect. Echinocarpa C.C. Berg, Proc. Kon. Ned. Akad. Wetensch., Ser. C, 1294 Biol. Med. Sci. 91: 353 (1988). 1295 1296 5. Trophis involucrata W.C. Burger, Phytologia 26: 432 (1973). 1297 1298 1299 Tribe OLMEDIEAE 1300 1301 Olmedieae Trécul, Ann. Sci. Nat., Bot. sér. 3, 8 (1847) 126 1302 Castilleae C.C. Berg, Acta Bot. Neerl. 26 (1977) 78 1303 Strebleae Bureau in DC., Prodr. 17: 215 (1873), p.p. 1304 1305 Tree or shrubs, monoecious or dioecious (or androdioecious), mostly with self-pruning 1306 branches. Leaves alternate or opposite, distichous or spirally arranged; stipules lateral to 1307 amplexicaul. Inflorescences mostly unisexual, capitate, mostly discoid to urceolate, 1308 involucrate, tepals mostly 4, connate or not. Staminate inflorescences usually many-

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1309 flowered; stamens 4 or fewer, with filaments straight or less often inflexed in bud, pistillode 1310 mostly absent. Pistillate inflorescences one to many-flowered, ovary free or not, stigmas 2, 1311 filiform. Fruits mostly drupaceous, mostly enclosed by a fleshy perianth or embedded in a 1312 fleshy . Seeds with or without endosperm, testa thin, vascularized, cotyledons 1313 mostly equal. 1314 1315 Genera and distribution: 13 genera with 63 species. Eight neotropical genera: Castilla (3 1316 spp.), Helicostylis (7), Maquira (4), Naucleopsis (22), Olmedia (1), Perebea (9), 1317 Poulsenia (1), and Pseudolmedia (9); and five Paleotropical genera: the widespread 1318 Antiaris (1); Antiaropsis (2) in New Guinea; Mesogyne (1) in Africa; Sparattosyce (1) 1319 in New Caledonia; and Streblus (3) in South to Southeast Asia. 1320 1321 Olmedia 1322 1323 Olmedia Ruiz & Pav., Syst. Veg. Fl. Peruv. Chil.1:257.1798. Type — Olmedia aspera Ruiz 1324 & Pav. 1325 Trophis section Olmedia (Ruiz & Pav.) Berg, Proc. Kon. Ned. Acad. Wetensch. C. 91: 1326 354. 1988. 1327 1328 Dioecious trees or shrubs. Leaves distichous, lamina pinnately veined. Stipules free, not 1329 fully amplexicaul. Inflorescences unisexual, with a well-developed involucre. Staminate 1330 inflorescences discoid, multiflorous; tepals 4, valvate, stamens 4, inflexed in bud, pistillode 1331 absent. Pistillate inflorescences usually uniflorous, perianth tubular, 4-dentate, ovary free, 1332 stigmas 2, equal. Fruits drupaceous, surrounded by fleshy persistent perianth and 1333 subtended by spreading, fleshy involucral bracts. Seeds ca. 5 mm long, cotyledons equal. 1334 1335 Species and distribution: One species, in the Neotropics. 1336 1337 1. Olmedia aspera Ruiz & Pav., Syst. Veg. Fl. Peruv. Chil.1:257.1798

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1338 Olmedia caucana Pittier, Contr. U.S. Natl. Herb. 13:434. 1912. — Trophis caucana 1339 (Pitttier) C.C. Berg, Proc. Kon. Ned. Acad. Wetensch. C. 91: 354. 1988 1340 Olmedia poeppigiana Klotzsch, Linnaea 20: 525. 1847, as a synonym of O. aspera 1341 Poeppig & Endlicher, Nov. Gen. 2: 31. 1838, based on Poeppig s.n. or 1267, non 1342 O.poeppigiana Martius Flora (or Bot. Zeit) 24 (Beibl. 2): 93. 1841 (= Helicostylis 1343 tomentosa (Poeppig & Endlicher) Rusby). 1344 Olmedia falcifolia Pittier, Contr. U.S. Natl. Herb. 13: 435. 1912. 1345 Trophis aurantiaca Herzog, Repert. Spec. Nov. 7: 51. 1909 1346 1347 1348 Streblus 1349 1350 Streblus Lour., Fl. Cochinch. (1790) 615. 1351 Achymus Juss., Dict. Sci. Nat. 1, Suppl. 31 (1816) . 1352 Epicarpurus Blume, Bijdr. 488 (1825). 1353 Albrandia Gaudich. in Freyc., Voy. Uranie, Bot. 509 (1830). 1354 Calius Blanco, Fl. Filip. 698 (1837). 1355 Teonongia Stapf, Hooker’s Icon. Pl. 30: t. 2947 (1911). 1356 Diplothorax Gagnep., Bull. Soc. Bot. France 75 98 (1928). 1357 1358 Trees or shrubs, dioecious or monoecious. Leaves distichous, lamina pinnately veined. 1359 Stipules free, lateral. Inflorescences bisexual or unisexual, capitate, with a rudimentary 1360 involucre, bracts basally attached. Staminate inflorescences discoid capitate, multiflorous; 1361 tepals 4, imbricate, stamens 4, inflexed in bud, pistillode present but small. Pistillate 1362 inflorescences usually uniflorous, tepals 4, ovary free, stigmas 2, equal. Fruits drupaceous, 1363 up to ca. 8 mm long, initially enclosed by enlarged but not fleshy tepals, which may open 1364 later. Seeds ca. 5 mm long, cotyledons equal or very unequal. 1365 1366 Species and distribution: three species from India to South China and from mainland 1367 Southeast Asia to the and the Moluccas.

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1368 1369 1. Streblus asper (Retz.) Lour., Fl. Cochinch. 2: 615 (1790). 1370 Trophis aspera Retz., Observ. Bot. 5 (1788) – Epicarpurus asper (Retz.) Steud. 1371 Nomencl. Bot. ed. 2, 1: 556 (1840). 1372 Trophis cochinchinensis Poir., Encycl. 8 (1808) 123. 1373 Epicarpurus orientalis Blume, Bijdr. (1825) 488 1374 Calius lactescens Blanco, Fl. Filip. (1837) 698; ed. 3, 3 (1879) 1103, t. 171. — 1375 Streblus lactescens (Blanco) Blume, Ann. Mus. Bot. Lugduno-Batavi 2 (1856) 80. 1376 Achymus pallens Sol. ex Blume, Ann. Mus. Bot. Lugduno-Batavi 2 (1856) 79. 1377 Cudrania crenata C.H. Wright, J. Linn. Soc., Bot. 26 (1899) 469. — Vanieria crenata 1378 (C.H. Wright) Chun, J. Arnold Arbor. 8 (1927) 21. 1379 Diplothorax tonkinensis Gagnep., Bull. Soc. Bot. France 75 (1928) 98. 1380 1381 Note: Retzius’s Trophis aspera predated Loureiro’s Streblus asper by two years, making 1382 the latter an implied new combination under Article 41.1 of the Code (cf. Ex. 10). 1383 Synonymies of the S. asper have sometimes erroneously included Trophis aculeata Roth, 1384 which is actually Maclura spinosa (Roxb. ex Willd.) C.C. Berg. 1385 1386 2. Streblus celebensis C.C. Berg, Blumea 50 547 (2005). 1387 1388 3. Streblus tonkinensis (Eberh. & Dubard) Corner, Gard. Bull. Singapore 19 (1962): 228. 1389 Bleeokrodea tonkinensis Eberh. & Dubard, Compt. Rend. Hebd. SÈances Acad. Sci. 1390 145 (1907): 632. — Teonongia tonkinensis (Eberh. & Dubard) Stapf. 1391 1392 1393 Tribe DORSTENIEAE 1394 1395 Dorstenieae Gaudich. in Freyc., Voy. Uranie, Bot. (1830). 1396 Broussonetieae Gaudich. in Freyc., Voy. Uranie, Bot. 508 (1830). 1397 Brosimeae Trécul, Ann. Sci. Nat., Bot. sér. 3, 8: 146 (1847).

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1398 Fatoueae Engl., Nat. Pflanzenfam. 3, 1: 71 (1888). 1399 1400 Tree, shrubs, lianas, and herbs, monoecious or less often dioecious. Leaves alternate or less 1401 commonly (sub)opposite, distichous or spirally arranged; stipules lateral to fully 1402 amplexicaul. Inflorescences unisexual or bisexual, cymose, spicate, globose, or discoid to 1403 turbinate or cup-shaped, multiflorous or uniflorous (the latter in pistillate inflorescences 1404 only), bracteate or not, interfloral bracts mostly peltate. Staminate flowers with tepals (1– 1405 )2–4 or absent, stamens 1–4 with filaments straight or inflexed in bud, pistillode present or 1406 (more often) absent. Pistillate flowers free or connate or embedded in the receptacle, tepals 1407 2–4, ovary free or not, stigmas 1 or 1, equal or unequal. Fruits drupaceous or drupe-like 1408 due to a persistent fleshy perianth and/or receptacle, the whole endocarp unit often 1409 ballistically ejected from the infructescence. Seeds with or without endosperm, large or 1410 small; cotyledons equal or unequal. 1411 1412 Genera and distribution: eleven genera and 63 species with a worldwide distribution: 1413 Bleekrodea (Africa and Southeast Asia), Bosqueiopsis (Africa), Brosimum (Neotropics), 1414 Broussonetia (Asia to Oceania; introduced worldwide), Dorstenia (Africa and South 1415 America, with one species in India), Fatoua (Madagascar and Japan to New Caledonia; 1416 introduced worldwide), Helianthostylis (Neotropics), Malaisia (Southeast Asia to New 1417 Caledonia), Scyphosyce (Africa), Sloetia (Southeast Asia), Sloetiopsis (Africa), 1418 (Africa), Trymatococcus (Neotropics), Utsetela (Africa). 1419 1420 1421 Sloetiopsis 1422 1423 Sloetiopsis Engl., Bot. Jahrb. 39: 573 (1907). 1424 Neosloetiopsis Engl., Bot. Jahrb. 51: 426 (1914) 1425 Streblus auct. non Lour., C.C. Berg, Proc. Kon. Ned. Acad. Wetensch. C. 91: 357. 1426 1988. 1427

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1428 Tree or shrubs, dioecious (or monoecious). Leaves distichous, pinnately veined, cystoliths 1429 present; stipules free, nearly amplexicaul. Inflorescences unisexual (or bisexual); staminate 1430 inflorescences spicate with an abaxial sterile groove, bracts mostly peltate, tepals 4, free or 1431 basally connate filaments inflexed in bud, pistillode small; pistillate inflorescences 1432 uniflorous, bracts mostly basally attached, tepals 4, free, imbricate, 2 stigmas. Fruits 1433 drupaceous, fleshy endocarp dehiscent, tepals enlarged and persistent but not fleshy. Seeds 1434 globose, ca. 4 mm, endocarp coriaceous with a hard disc against the hilum, testa 1435 vascularized with a thick apical cap, cotyledons equal. 1436 1437 1. Sloetiopsis usambarensis Engl., Bot. Jahrb. 39: 573 (1907) — Streblus usambarensis 1438 (Engl.) C.C. Berg, Proc. Kon. Ned. Acad. Wetensch. C. 91: 357. 1988. 1439 Neosloetiopsis kamerunensis Engl., Bot. Jahrb. 51: 426 (1914). 1440 1441 Note. The nearly amplexicaul stipules and occasional bisexual inflorescences reflect an 1442 affinity with the Southeast Asian Sloetia, also a member of the Dorstenieae. 1443 1444 1445 Tribe PARARTOCARPEAE 1446 1447 Parartocarpeae N.J.C. Zerega & E.M. Gardner Zerega, Phytotaxa 388, 253–265 (2019). 1448 Shrubs to large trees, monoecious or dioecious; abundant white exudate. Leaves distichous 1449 or spirally arranged; simple; entire; pinnately veined; thin to thick coriaceous; glabrous, 1450 pubescent, scabrid, or hispid pubescent. Stipules axillary, simple or paired, lateral. 1451 Inflorescences solitary or paired in leaf axils, unisexual (or bisexual with a single apical 1452 pistillate flower), uniflorous, cymose, or capitate with stamens or ovaries sunken into the 1453 receptacle; pedunculate; involucre of 3–8 triangular bracts, basally connate. Staminate 1454 inflorescences with numerous flowers, tepals 4–5, stamens 5 and normally positioned or 1– 1455 3 in cavities in the receptacle with the anthers exerted through perforations in the upper 1456 surface of the receptacle, filaments free or united. Pistillate inflorescences uniflorous or 1457 (sub)globose with ovaries solitary in each cavity, unilocular, the style apical with a short

49 bioRxiv preprint doi: https://doi.org/10.1101/2020.04.08.030452; this version posted April 9, 2020. 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. GARDNER ET AL., PHYLOGENOMICS AND GENERIC REVISION OF MOREAE

1458 exerted stigma. Fruits drupaceous, enclosed by persistant tepals, or aggregated into 1459 syncarps formed by the enlargement of the entire inflorescence. 1460 1461 Genera and distribution: Three genera and five species, from Southern China to the 1462 Solomon Islands: Hullettia, Parartocarpus, and Pseudostreblus. 1463 1464 1465 Pseudostreblus 1466 1467 Pseudostreblus Bureau, in A.P. de Candolle, Prodr. 17: 220 (1873). 1468 Streblus Lour. sect. Pseudostreblus (Bureau) Corner, Gard. Bull. Singapore 19: 217 (1962). 1469 1470 Monoecious trees. Leaves distichous, pinnately veined. Stipules free, lateral. 1471 Inflorescences axillary. Staminate inflorescences cymose, tepals 5, imbricate, filaments 1472 inflexed in bud but apparently straightening gradually upon anthesis, pistillode minute, 1473 conical, pubescent, interfloral bracts few, basally attached. Pistillate inflorescences 1474 uniflorous, pedunculate, involucral bracts 3, ±connate, tepals 4, imbricate, stigma bifid, 1475 arms equal. Fruits drupaceous, ca. 1 cm long, with tepals enlarged and loosely enclosing 1476 the fruit. Seeds ellipsoid, ca. 6 x 8 mm, cotyledons unequal. 1477 1478 Species and distribution: One, in South to Southeast Asia and Southern China. 1479 1480 Note: Pseudostreblus is remarkable for its five-parted staminate flowers. 1481 1482 1. Pseudostreblus indicus Bureau, in A.P. de Candolle, Prodr. 17: 220 (1873). 1483 Streblus indicus (Bureau) Corner, Gard. Bull. Singapore 19: 226 (1962). 1484 1485 1486 Conclusion

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1487 The revisions presented here, based on the best phylogenetic evidence available to date, 1488 provide for seven monophyletic tribes of Moraceae and eleven monophyletic genera within 1489 Moreae. We hope that the resulting taxonomic and phylogenetic framework will provide a 1490 solid foundation for further research into the systematics and evolution of Moraceae. 1491 1492 1493 Author contributions 1494 EMG led the writing of the manuscript, did field, lab, and herbarium work, conducted all 1495 phylogenetic analyses, and was responsible for the taxonomic treatment. MG performed lab 1496 work for the Moraceae333 samples. RC, SD, NE, and OM performed lab work for the 1497 PAFTOL samples, and OM curated the PAFTOL data. DA collaborated on all herbarium 1498 work at BO. Sahromi facilitated access and participated in field collections at the Bogor 1499 Botanical Gardens. NJCZ provided overall guidance on Moraceae and facilitated 1500 sequencing at Northwestern University. WJB and FF acquired funding for and supervised 1501 the PAFTOL project. AM performed herbarium sampling at K and supervised the 1502 Moraceae portion of the PAFTOL project. EMG designed the overall study with input from 1503 ALH and NJCZ. ALH supervised the overall study. All authors commented on and 1504 contributed to the manuscript. 1505 1506 1507 Acknowledgements 1508 This work was supported by the United States National Science Foundation (DBI award 1509 number 1711391, and DEB award numbers 0919119 and 1501373); the SYNTHESYS 1510 Project http://www.synthesys.info/ which is financed by European Community Research 1511 Infrastructure Action under the FP7 “Capacities" Program”; the National Parks Board of 1512 Singapore through a Flora of Singapore Fellowship and a Research Fellowship; grants 1513 from the Calleva Foundation and the Sackler Trust to the Plant & Fungal Trees of Life 1514 Project at the Royal Botanic Gardens, Kew. We thank the Pritzker Laboratory for 1515 Molecular Systematics at the Field Museum of Natural History (K. Feldheim) for access to 1516 laboratory and sequencing facilities; S. Knapp and J. Wajer (BM) for helpful consultation

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1517 on nomenclatural issues; W. Clement for helpful comments on the circumscription of the 1518 Olmedieae; the Bogor Botanical Gardens, Singapore Botanic Gardens, and The Morton 1519 Arboretum for access to living collections; and the following herbaria for access to 1520 collections for examination and/or sampling: BM, BKF, BO, F, IBSC, K, FTBG, L, MO, 1521 NY, SING, SAN, SAR, SNP, and U. Finally, we gratefully acknowledge the careful work 1522 of past scholars of Moraceae, in particular the late C.C. Berg and E.J.H. Corner. 1523 1524 Conflicts of interest 1525 The authors are unaware of any conflicts of interest affecting this research. 1526 1527 Literature cited 1528 1529 Bawa, K., & Crisp, J. 1980. Wind-pollination in the understorey of a rain forest in Costa 1530 Rica. J. Ecol., 68: 871–876. Retrieved from 1531 http://www.jstor.org/stable/10.2307/2259462 1532 Bawa, K. S., Bullock, S. H., Perry, D. R., Coville, R. E., & Grayum, M. H. 1985. 1533 Reproductive biology of tropical lowland rain forest trees. II. Pollination systems. Am. 1534 J. Bot., 72: 346–356. https://doi.org/10.2307/2443527 1535 Berg, C. C. 1977a. Revisions of African Moraceae (excluding Dorstenia, Ficus, Musanga 1536 and Myrianthus). Bull. Du Jard. Bot. Natl. Belgique, 47: 267–407. Retrieved from 1537 http://www.jstor.org/stable/10.2307/3667908 1538 Berg, C. C. 1977b. The Castilleae, a tribe of the Moraceae, rename and redefined due tothe 1539 exclusion of the type genus Olmedia from the ‘Olmedieae’. Acta Bot. Neerl., 26: 73– 1540 82. 1541 Berg, C. C. 1978. Cecropiaceae: A new family of the . Taxon, 27: 39–44. 1542 https://doi.org/10.2307/1220477 1543 Berg, C. C. 1988. The genera Trophis and Streblus (Moraceae) remodelled. Proc. K. Ned. 1544 Akad. van Wet. Ser. C, Biol. Med. Sci., 91: 345–362. 1545 Berg, C. C. 2001. Flora Neotropica Monograph 83: Moreae, Artocarpeae, and Dorstenia 1546 (Moraceae), with Introductions to the Family and Ficus and with Additions and

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1697 https://doi.org/10.1111/nph.15312 1698 Weitemier, K., Straub, S. C. K., Cronn, R. C., Fishbein, M., Schmickl, R., McDonnell, 1699 A., & Liston, A. 2014. Hyb-Seq: Combining Target Enrichment and Genome 1700 Skimming for Plant Phylogenomics. Appl. Plant Sci., 2: 1400042. 1701 https://doi.org/10.3732/apps.1400042 1702 Wen, D., Yu, Y., Zhu, J., & Nakhleh, L. 2018. Inferring phylogenetic networks using 1703 PhyloNet. Syst. Biol., 67: 735–740. https://doi.org/10.1093/sysbio/syy015 1704 Yu, Y., & Nakhleh, L. 2015. A maximum pseudo-likelihood approach for phylogenetic 1705 networks. BMC Genomics, 16: 1–10. https://doi.org/10.1186/1471-2164-16-S10-S10 1706 Zapata, T. R., & Arroyo, M. T. K. 1978. Plant Reproductive Ecology of a Secondary 1707 Deciduous Tropical Forest in Venezuela. Biotropica, 10: 221. 1708 https://doi.org/10.2307/2387907 1709 Zerega, N. J. C., Clement, W. L., Datwyler, S. L., & Weiblen, G. D. 2005. 1710 Biogeography and divergence times in the mulberry family (Moraceae). Mol. 1711 Phylogenet. Evol., 37: 402–16. https://doi.org/10.1016/j.ympev.2005.07.004 1712 Zerega, N. J. C., & Gardner, E. M. 2019. Delimitation of the new tribe Parartocarpeae 1713 (Moraceae) is supported by a 333-gene phylogeny and resolves tribal level Moraceae 1714 taxonomy. Phytotaxa, 388: 253–265. 1715 Zerega, N. J. C., Nur Supardi, M. N., & Motley, T. J. 2010. Phylogeny and 1716 Recircumscription of Artocarpeae (Moraceae) with a Focus on Artocarpus. Syst. Bot., 1717 35: 766–782. https://doi.org/10.1600/036364410X539853 1718 Zhang, C., Sayyari, E., & Mirarab, S. 2017. ASTRAL-III: Increased Scalability and 1719 Impacts of Contracting Low Support Branches BT - Comparative Genomics: 15th 1720 International Workshop, RECOMB CG 2017, Barcelona, Spain, October 4-6, 2017, 1721 Proceedings. in: J. Meidanis & L. Nakhleh (eds.). Cham: Springer International 1722 Publishing. https://doi.org/10.1007/978-3-319-67979-2_4 1723 Zhang, Q., Onstein, R. E., Little, S. A., & Sauquet, H. 2019. Estimating divergence 1724 times and ancestral breeding systems in Ficus and Moraceae. Ann. Bot., 123: 191–204. 1725 https://doi.org/10.1093/aob/mcy159 1726

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1729 Tables 1730 1731 Table 1. Overview of the taxonomic history of Moreae.

Engler (1899) Corner (1962) Berg (2001) Clement & Gardner et al. Weiblen (2009)

Afromorusc

Ampalis Ampalis (Ampalis)a (Ampalis)a Ampalis Bagassa Bagassa

(Bleekrodea)a Bleekrodea Broussonetia Clarisia Fatoua Fatoua Maclura

(Maillardia)b (Maillardia)b (Maillardia)b Maillardia

(Malaisia)b Milicia Milicia Milicia Morus Morus Morus Morus Morus

Pachytrophe Pachytrophe (Pachytrophe)a (Pachytrophe)a Pachytrophe

Paratrophis (Paratrophis)a (Paratrophis)a (Paratrophis)a Paratrophis

Pseudomorus (Pseudomorus)a (Pseudomorus)a (Pseudomorus)a (Pseudomorus)d

(Pseudostreblus)a (Pseudostreblus)a (Pseudostreblus)a

(Sloetia) (Sloetia)a

(Sloetiopsis)a (Sloetiopsis)a (Sloetiopsis)a Sorocea Sorocea Sorocea

Streblus Streblus Streblus

(Taxotrophis)a (Taxotrophis)a (Taxotrophis)a Taxotrophis Trophis Trophis Trophis Trophis Trophis

1732 a Included in Streblus.

1733 b Included in Trophis.

1734 c Newly separated from Morus.

1735 d Included in Paratrophis.

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1736 1737 1738 Table 2. Divergence times (in Ma) estimated using penalized likelihood under correlated 1739 and relaxed models. Nomenclature follows the revisions proposed in this study.

Clade Correlated Relaxed

Moraceae 84.7 84.7

Parartocarpeae 75.3 74.7

Ficeae 24 34.5

Olmedieae 36.4 43.4

Dorstenieae 72.5 76.9

Maclureae 44.9 52.1

Artocarpeae 64 64

Moreae 59.1 75.4

1740 1741 1742 1743 1744 1745

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1746 Figures 1747 1748 Figure 1. Representatives of Moreae: Paratrophis pendulina (=) (a) 1749 infructescences and (b) staminate inflorescences, the latter showing the characteristic sterile 1750 groove; Sorocea racemosa (c) infructescences and (d) staminate inflorescence; Morus nigra 1751 (e) pistillate inflorescences with elaborate stigmas and (f) staminate inflorescences with 1752 stamens that, having been inflexed in bud, are substantially longer than the perianth itself; 1753 and a newly-placed member of Olmedieae (=Castilleae), Streblus asper: (g) infructescences 1754 and (h) discoid-capitate staminate inflorescences with the rudiments of an involucre visible 1755 below the unopened flowers. Photo credits: (a) F. & Kim Starr, under a CC-BY-3.0-US licence 1756 (https://commons.wikimedia.org/wiki/File:Starr-051029-5102-Streblus_pendulinus-fruit-Auwahi- 1757 Maui_(24481336159).jpg); (b) M. Marathon, CC-BY-SA-4.0 1758 (https://commons.wikimedia.org/wiki/File:Streblus_brunonianus_flowers.jpg); (c)-(d) A. Popovkin, CC-BY- 1759 2.0 (https://commons.wikimedia.org/wiki/File:Sorocea_racemosa_Gaudich._-_Flickr_- 1760 _Alex_Popovkin,_Bahia,_Brazil_(3).jpg and 1761 https://commons.wikimedia.org/wiki/File:Sorocea_racemosa_Gaudich._-_Flickr_- 1762 _Alex_Popovkin,_Bahia,_Brazil_(9).jpg); (e) E. Gardner; (f) Schurdl, CC-BY-SA-4.0 1763 (https://commons.wikimedia.org/wiki/File:Morus_nigra_100525_02.jpg); (g) D. Valke, CC-BY-SA-2.0

1764 (https://commons.wikimedia.org/wiki/File:Bekar_(Konkani-_बेकर)_(4533519363).jpg); (h) Vinayaraj, CC

1765 BY-SA 4.0 (https://commons.wikimedia.org/wiki/File:Streblus_asper_at_Panamaram_(5).jpg) 1766 1767

62 bioRxiv preprint doi: https://doi.org/10.1101/2020.04.08.030452; this version posted April 9, 2020. 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.

a b c d

e f g h bioRxiv preprint doi: https://doi.org/10.1101/2020.04.08.030452; this version posted April 9, 2020. 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. GARDNER ET AL., PHYLOGENOMICS AND GENERIC REVISION OF MOREAE

1768 Figure 2. Phylogenetic trees from the "exon" dataset. Maximum-likelihood based on a 1769 supermatrix of all loci, with bootstrap support and previous nomenclature (left), and a 1770 species tree based on gene trees from all loci with bootstrap/LPP support and revised 1771 nomenclature (right). Discordant branches are colored in red, and tribal classifications are 1772 shaded without (left) and with (right) the revised classifications presented here. 1773 1774

63 bioRxiv preprint doi: https://doi.org/10.1101/2020.04.08.030452; this version posted April 9, 2020. 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.

● Trema orientale SRR5674478 Trema orientale SRR5674478 ● 100 ● Elatostema retrohirtum Monro7601 Elatostema retrohirtum Monro7601 ● 98.67/85.37 100 ● Urtica urens FayMF173 Urtica urens FayMF173 ● 98.67/59.99 100 ● suaveloens AsmanTA2 Poikilospermum suaveloens AsmanTA2 ● 96.67/92.74 16 ● ficifolia BergCC18418 Cecropia ficifolia BergCC18418 ● 98/63.2 100 ● Leucosyke capitellata LugasL41 Leucosyke capitellata LugasL41 ● 54.67/36.77 100 ● Soleirolia soleirolii Sheahan M C17 Soleirolia soleirolii Sheahan M C17 ● 98.67/63.79 ● Boehmeria nivea HuSY 8113 Boehmeria nivea HuSY 8113 ● 100 ● Streblus indicus Tsang24252 Pseudostreblus indica Tsang24252 ● 100/98.95 Streblus indicus NewmanLA0518 Pseudostreblus indica NewmanLA0518 100 ● ● 78/41.24 100 ● Parartocarpus bracteatus NZ730 Parartocarpus bracteatus NZ730 ● 100/90.43 100 ● Parartocarpus venenosus NZ874 Parartocarpus venenosus NZ874 ● 100/98.42 100 ● Hullettia griffithiana Kerr16886 Hullettia griffithiana Kerr16886 ● 100/81.25 ● Hulletia dumosa NZ242 Hulletia dumosa NZ242 ● 100 ● SRR1405699 SRR1405700 Ficus racemosa SRR1405699 SRR1405700 ● 100/95.48 100 ● EG30 Ficus macrophylla EG30 ● 93.33/66.24 ● Ficus sagittifolia ChaseMW19852 Ficus sagittifolia ChaseMW19852 ● 100/94.01 100 100 100 ● Streblus asper EG696 Streblus asper EG696 ● 100/94.41 100/84.43 ● Streblus asper Townsend73142 Streblus asper Townsend73142 ● 100 100 ● Sparattosyce dioica WeiblenWW1223 Sparattosyce dioica WeiblenWW1223 ● 100/70.87 100/92.29 100 ● Antiaropsis decipiens NZ281 Antiaropsis decipiens NZ281 ● 100/93.36 100 ● Antiaropsis decipiens WeiblenGW1865 Antiaropsis decipiens WeiblenGW1865 ● 100/80.24 ● Poulsenia armata Pennington14600 Poulsenia armata Pennington14600 ● 10082 ● Gomes511 Antiaris toxicaria 5595 ● 99.33/56.92 ● ChaseMW19850 Helicostylis tomentosa Gomes511 ● 43.33/39.4334.67/42.87 97.33/51.63 100 100 41 Antiaris toxicaria 5595 Castilla elastica ChaseMW19850 ● ● 40.67/39.4 92/84.57 100 ● Naucleopsis macrophylla BergP18534 Olmedia aspera Fuentes5323 S41 ● 100● Trophis caucana Fuentes5323 S41 Olmedia aspera AceedoR8833 ● 58/49.16 41 ● Trophis caucana AceedoR8833 Naucleopsis macrophylla BergP18534 ● 62/36.19 ● Pseudolmedia spuria Lobo263 Pseudolmedia spuria Lobo263 ● 87.33/86.57 ● Fatoua pilosa TaylorP218 Fatoua pilosa TaylorP218 ● 100 ● Malaisia scandens EG122 Malaisia scandens GrayB8416 ● 100/91.91 100 ● Malaisia scandens GrayB8416 Malaisia scandens EG122 ● 25.33/38.1 100 100 ● Malaisia scandens Sands sn Malaisia scandens Sands sn ● 100/92.61 100/79.71 100 ● Broussonetia papyrifera SRR1477753 Broussonetia papyrifera SRR1477753 ● 100/81.03 100 ● Broussonetia cf papyrifera Heng14289 Broussonetia cf papyrifera Heng14289 ● 100 100/92.07 100 ● Broussonetia kazinoki ChaseMW17827 Broussonetia kazinoki ChaseMW17827 ● ● Bleekrodea madagascariensis DavisRakotonasolo3117 ChaseMW18153 ● 100 ● Bosqueiopsis gilletii Fronties243 Bleekrodea madagascariensis DavisRakotonasolo3117 ● 99.33/83.93 ● Trilepisium madagascariense Richard403 Dorstenia hildebrandtii NZ311 ● 100100 30/64.42 100 ● Dorstenia barteri ChaseMW18153 Bosqueiopsis gilletii Fronties243 ● 99.33/75.41 21.33/31.51 100 ● Dorstenia hildebrandtii NZ311 Trilepisium madagascariense Richard403 ● 90.67/67.51 100 ● Utsetela gabonensis Lebrun5879 Utsetela gabonensis Lebrun5879 ● 100/99.66 100 100 ● Utsetela gabonenesis Breteler14086 Utsetela gabonenesis Breteler14086 ● 93.33/58.82 32.67/62.4 ● Utsetela neglecta Bissiengen923 Utsetela neglecta Bissiengen923 ● 100 ● Streblus usambarensis Faden77 417 Sloetiopsis usambarensis Faden77 417 ● 100/89.4 Streblus usambarensis CheekM18194 Sloetiopsis usambarensis CheekM18194 100 ● ● 98.67/44.86 100 ● Trymatococcus amazonicus Prance13461 Trymatococcus amazonicus Prance13461 ● 100/74.18 100 ● Helianthostylis sprucei Ribeiro1204 Helianthostylis sprucei Ribeiro1204 ● 100/90.91 100 ● EG23 Brosimum alicastrum EG23 ● 100/94.12 ● Brosimum alicastrum MonroLander7382 Brosimum alicastrum MonroLander7382 ● 100 ● Maclura tinctoria Fernandez314 Maclura tinctoria Fernandez314 ● 100/98.89 100 100 ● Maclura tinctoria mora Nee40044 Maclura tinctoria mora Nee40044 ● 100/85.07 ● Maclura tinctoria tinctoria Campos2679 Maclura tinctoria tinctoria Campos2679 ● 94.67/55.63 Maclura tinctoria Reuvoize3252 Maclura tinctoria Reuvoize3252 ● ● 90.67/78.45 100 100 ● Maclura spinosa Perumal RHT22554 Maclura spinosa Perumal RHT22554 ● 100/96.97 98.67/97.77 100 74 ● Maclura andamanica Maxwell89−436 Maclura andamanica Maxwell89−436 ● 95.33/60.9 74 ● Maclura africana GreenwayKanuri15269 Maclura africana GreenwayKanuri15269 ● 93.33/71.77 ● Maclura africana Manktelow93027 Maclura africana Manktelow93027 ● 100 98.67/95.13 72 ● Maclura brasiliensis NeeVargas45025 Maclura brasiliensis NeeVargas45025 ● 100/89.93 72● EG139 Maclura pomifera EG139 ● 90.67/69.23 ● Maclura pomifera Swannsn Maclura pomifera Swannsn ● 72 98/63.15 58 ● Maclura thorellii Pierre4709 Maclura thorellii Pierre4709 ● Maclura cochinchinensis Guill6841 Maclura fruticosa NMCuong1193 ● ● 99.33/69.8898/79.19 72 100 ● Maclura fruticosa NMCuong1193 Maclura cf cochinchinensis NZ757 ● 100/88.44 100 Maclura cf cochinchinensis NZ757 Maclura amboinensis Takeuchi16578 ● ● 92/55.25 86 ● Maclura amboinensis Takeuchi16578 Maclura cochinchinensis Guill6841 ● 58.67/52.33 70/46.64 86 ● Maclura cochinchinensis SAGBE887 Maclura cochinchinensis SAGBE887 ● 70/40.57 100 ● Maclura aff pubsecens Averyanov1198 Maclura aff pubsecens Averyanov1198 ● ● MOR 68−7917 Maclura tricuspidata MOR 68−7917 ● 100 ● Clarisia ilicifolia Carranta6386 Clarisia ilicifolia Carranta6386 ● 100/97.42 100 ● Clarisia ilicifolia Maguire56675 Clarisia ilicifolia Maguire56675 ● 100/90.94 ● Clarisia ilicifolia Souza2492 Clarisia ilicifolia Souza2492 ● 100/94.39 100100 ● Batocarpus costaricensis GW1463 Batocarpus costaricensis GW1463 ● 69.33/39.07 100 ● Batocarpus amazonicus Salidas1233 Batocarpus amazonicus Salidas1233 ● 100/100 ● Batocarpus amazonicus Berg18524 Batocarpus amazonicus Berg18524 ● 100/58.35 100 100 ● Clarisia racemosa Assuncao690 Clarisia racemosa Assuncao690 ● 100/92.89 100 ● Clarisia racemosa NeilD1291 Clarisia racemosa NeilD1291 ● 31.33/33.46 50 ● Clarisia biflora GW1460 Clarisia biflora GW1460 ● 17.33/35.58 100 ● Batocarpus orinocensis Vasquez27440 Batocarpus oriniceros Vasquez27440 ● 100/84.41 ● Batocarpus orinocensis Palacios3265 Batocarpus orinocensis Palacios3265 ● 100 ● Artocarpus scandens EG411 Artocarpus scandens EG411 ● 100/92.42 100 ● Artocarpus papuanus NZ61 Artocarpus papuanus NZ61 ● 100/79.89 ● Artocarpus limpato NZ609 Artocarpus limpato NZ609 ● 96.67/98.15 100 ● Artocarpus nitidus ssp lingnanensis NZ911 Artocarpus tonkinensis EG174 ● ● Artocarpus fulvicortex EG711 Artocarpus styracifolius EG176 ● 99.33/42.46100/67.51 100 100 ● NZ420 Artocarpus nanchuanensis EGL238 ● 100/66.81 10 ● ssp zeylanicus NZ956 Artocarpus hypargyraeus EG170 ● 100/52.25 95 ● Artocarpus thailandicus NZ402 Artocarpus petelotii DDS14435 ● 100/62.72 ● Artocarpus tonkinensis EG174 Artocarpus pithecogallus LiJianwu3200 ● 98/41.27 100/96.42 10097 ● Artocarpus styracifolius EG176 Artocarpus gongshanensis HAST137747 ● 100 ● Artocarpus nanchuanensis EGL238 Artocarpus nitidus ssp lingnanensis NZ911 ● 100100 ● Artocarpus hypargyraeus EG170 Artocarpus lacucha NZ420 ● 100/84.54 96.67/49.75 100 4 ● Artocarpus petelotii DDS14435 Artocarpus gomezianus ssp zeylanicus NZ956 ● 96.67/85.1 100 98.67/45.47 100 ● Artocarpus pithecogallus LiJianwu3200 Artocarpus thailandicus NZ402 ● 90.67/41.28 93.33/39.76 ● Artocarpus gongshanensis HAST137747 Artocarpus gomezianus ssp gomezianus NZ533 ● 41.33/37.9 ● Artocarpus nitidus ssp humilis EG258 Artocarpus nitidus ssp humilis EG258 ● 10010 100/75.28 100 ● NZ694 Artocarpus dadah NZ694 ● 57.33/39.87 ● Artocarpus nitidus ssp griffithii NZ216 Artocarpus nitidus ssp griffithii NZ216 ● 100 74.67/39.79 ● Artocarpus gomezianus ssp gomezianus NZ533 Artocarpus fulvicortex EG711 ● 9.33/35.32 5 ● Artocarpus cf lacucha NZ517 Artocarpus cf lacucha NZ517 ● 100 100 ● Artocarpus glaucus NZ852 Artocarpus glaucus NZ852 ● ● Artocarpus nitidus ssp borneensis NZ686 Artocarpus nitidus ssp borneensis NZ686 ● 96 15.33/34.85 100 ● Artocarpus primackii NZ687 Artocarpus primackii NZ687 ● 100/75.4621.33/40.39 100 98.67/47.03 100 Artocarpus tomentosulus NZ617 Artocarpus tomentosulus NZ617 27.33/40.36 ● ● 96/45.24 100 ● Artocarpus xanthocarpus Yang15648 Artocarpus xanthocarpus Yang15648 ● 100/70.78 100100 ● Artocarpus vrieseanus var refractus Hoogland4822 Artocarpus vrieseanus refractus Hoogland4822 ● 100/76.1 35.33/41.56 ● Artocarpus vriesianus var vrieseanus GW1229 Artocarpus vriesianus var vrieseanus GW1229 ● 88 100 100/82.24 ● Artocarpus albobrunneus AA2243 Artocarpus albobrunneus AA2243 ● 72/41.4 Artocarpus fretessii NZ929 Artocarpus fretessii NZ929 100 ● ● 38/42.04 86 ● Artocarpus ovatus NZ202 Artocarpus ovatus NZ202 ● 100/72.13 100 ● Artocarpus nitidus ssp nitidus PPI10374 Artocarpus subrotundifolius Wenzel1576 ● 97.33/42.46 99 ● Artocarpus subrotundifolius Wenzel1576 Artocarpus nitidus ssp nitidus PPI10374 ● 54/37.16 ● Artocarpus rubrovenius JSB84 Artocarpus rubrovenius JSB84 ● ● Artocarpus longifolius ssp adpressus Nangkat15511 Artocarpus longifolius ssp adpressus Nangkat15511 ● 100 ● Artocarpus altissimus EG441 Artocarpus altissimus EG441 ● 76.67/39.69 100 ● Artocarpus sepicanus GW1701 Artocarpus sepicanus GW1701 ● 100 ● Artocarpus heterophyllus EG98 Artocarpus heterophyllus EG98 ● 100/93.19 100 ● NZ918 Artocarpus integer NZ918 ● 100/82.41 ● Artocarpus annulatus NZ985 Artocarpus annulatus NZ985 ● 69.33/39.53 100 ● Artocarpus sarawakensis EG527 Artocarpus brevipedunculatus NZ814 ● 100/95.33 100 ● Artocarpus brevipedunculatus NZ814 Artocarpus sarawakensis EG527 ● 98.67/47.87 100 NZ606 Artocarpus anisophyllus NZ606 100/64.67 100 ● ● ● Artocarpus lanceifolius ssp clementis NZ739 Artocarpus lanceifolius ssp clementis NZ739 ● 100/50.86 100 ● NZ953 Artocarpus hirsutus NZ953 ● 96.67/88.58 100 AHJ3283 Artocarpus nobilis AHJ3283 100/85.68 100 ● ● ● NZ354 Artocarpus chama NZ354 ● 44/36.61100/59.32 100 Artocarpus melinoxylus JLS2924 Artocarpus melinoxylus JLS2924 100 ● ● 99.33/47.88 100 ● NZ618 Artocarpus odoratissimus NZ618 ● 100/69.47 100 ● ssp asperulus NZ507 Artocarpus rigidus ssp asperulus NZ507 ● 100/63.04 96/82.72 100 96.67/83.31 100 100 ● Artocarpus rigidus NZ728 Artocarpus rigidus NZ728 ● 100/49.08 ● Artocarpus hispidus NZ258 Artocarpus hispidus NZ258 ● 100 ● Artocarpus treculianus nigrescens Ramos2107 Artocarpus treculianus nigrescens Ramos2107 ● 95.33/50.84 100 ● Artocarpus pinnatisectus Escritor Artocarpus pinnatisectus Escritor ● 90.67/63.16 100 ● Artocarpus multifidus PPI3911 Artocarpus multifidus PPI3911 ● 98/89.81 100 ● Artocarpus treculianus Elmer12468 Artocarpus treculianus Elmer12468 ● 99.33/68.28 84 ● Artocarpus treculianus ovatifolius NZ203 Artocarpus treculianus ovatifolius NZ203 ● 100/44.04 100 ● Ramos42018 Artocarpus blancoi Ramos42018 ● 98/97.43 ● Artocarpus aff excelsus AveryanovVH1819 Artocarpus aff excelsus AveryanovVH1819 ● ● Artocarpus camansi EG149 Artocarpus camansi EG149 ● 88/41.25 100100100 ● Artocarpus altilis K7 UluFiti Artocarpus altilis K7 UluFiti ● 100/98.37 95.33/41.55 100 66 ● Artocarpus cf horridus RM160 Artocarpus cf horridus RM160 ● 46.67/37.42 ● Artocarpus horridus EG437 Artocarpus horridus EG437 ● 71.33/40.1 100 ● DD4 Artocarpus mariannensis DD4 ● 98/43.44 ● Artocarpus excelsus NZ780 Artocarpus obtusus NZ729 ● 97.33/44.16 100 100 ● Artocarpus obtusus NZ729 Artocarpus lowii MWL2 ● ● Artocarpus lowii MWL2 Artocarpus excelsus NZ780 ● 95.33/44.24 7897 ● Artocarpus teijsmannii NZ946 Artocarpus teijsmannii NZ946 ● 95.33/48.71 99 ● Artocarpus sumatranus AA2766 Artocarpus maingayi NZ257 ● 100/72.9358.67/36.41 91 ● Artocarpus maingayi NZ257 Artocarpus sumatranus AA2766 ● 53.33/38.0252.67/41.95 100 ● Artocarpus kemando NZ612 Artocarpus kemando NZ612 ● ● Artocarpus tamaran EG92 Artocarpus jarrettiae SAN120933 ● 83.33/46.44 87 NZ771 Artocarpus tamaran EG92 ● ● 48.67/39.95 8573 ● Artocarpus jarrettiae SAN120933 Artocarpus sericicarpus NZ771 ● 29.33/36.07 90 ● Artocarpus corneri Fuchs21347 Artocarpus corneri Fuchs21347 ● 98.67/63.08 86 ● Artocarpus elasticus EG87 Artocarpus elasticus EG87 ● 100/50.15 ● Artocarpus scortechinii NZ209 Artocarpus scortechinii NZ209 ● ● Streblus zeylanicus Meijer701 Taxotrophis zeylanica Meijer701 ● 100 100 ● Streblus macrophyllus DDS10673 Taxotrophis macrophylla DDS10673 ● 100/97.79 98.67/98.97 ● Streblus macropyllus JLS2916 Taxotrophis macrophylla JLS2916 ● 97 100 ● Streblus ilicifolius deWilde18958 Taxotrophis ilicifolia deWilde18958 ● 99.33/97.45 65.33/45.59 100 ● Streblus ilicifolius Cuong122 Taxotrophis ilicifolia Cuong122 ● 98.67/40.51 96 ● Streblus cf ilicifolius EG720 Taxotrophis ilicifolius EG720 ● 38/36.48 100 ● Streblus taxoides Ridsdale SMHI422 Taxotrophis taxoides Ridsdale SMHI422 ● 100/97.6 99 ● Streblus taxoides EG701 Taxotrophis taxoides EG701 ● 76.67/43.19 100 ● Streblus spinosus Sidiyasa4071 Taxotrophis spinosa Sidiyasa4071 ● 100/91.16 100 ● Streblus spinosus MahyuniRDH 020 Taxotrophis spinosa MahyuniRDH 020 ● 100/90.65 ● Streblus spinosus EG702 Taxotrophis spinosa EG702 ● 100 ● Trophis montana Andrianantoanina 1023 Maillardia borbonica Cadet4518 ● 100/92.81 100 ● Trophis borbonica Cadet4518 Maillardia montana Andrianantoanina 1023 ● 75.33/46.15 ● Trophis montana Nek1882 Maillardia montana Nek1882 ● 100● Morus mesozygia Buckner309 Afromorus mesozygia Buckner309 ● 100/99.48 100100 ● Morus mesozygia Bo330 Afromorus mesozygia Bo330 ● 100/87.12 100 ● Milicia regia Cooper332 Milicia regia Cooper332 ● 100/98.08 100 ● Milicia excelsa McPherson16087 Milicia excelsa McPherson16087 ● 100/77.78 20.67/37.23100/56.95 100 ● Milicia excelsa Williamson187 Milicia excelsa Williamson187 ● 98.67/98.13 100 100 ● Streblus dimepate CasmirZ405 Pachytrophe dimepate CasmirZ405 ● 100/54.6 100 ● Streblus mauritianus Rakotonirina489 Ampalis mauritiana Rakotonirina489 ● 100/93.48 ● Streblus mauritianus Hoffman Ampalis mauritiana Hoffman ● 96 Streblus anthropophagorum Degeer4698 Paratrophis anthropophagorum Degeer4698 63 ● ● 100/95.37 100/52.9 100 ● Streblus heterophyllus Beecher sn Paratrophis microphylla Beecher sn ● 89.33/57.61 ● Streblus heterophyllus ChaseMW17825 Paratrophis microphylla ChaseMW17825 ● 34.67/35.6 100● Trophis philippinensis EG430 Paratrophis insignis Homeier1949 ● 100 100/97.41 98 ● Trophis philippinensis Brambach465 Paratrophis insignis Monteagudo3734 ● 100/59 100 ● Streblus glaber EG78 Paratrophis insignis Vargas4154 ● 98.67/49.64 ● Streblus glaber var australianus Hyland10634 Paratrophis insignis Vasquez28068 ● 100/87.86 67 100/98.59 100 ● Morus insignis Homeier1949 Paratrophis philippinensis EG430 ● 100● Morus insignis Monteagudo3734 Paratrophis philippinensis Brambach465 ● 26.67/35.06 100 100/83.02 35 ● Morus insignis Vargas4154 Paratrophis glabra EG78 ● ● Morus insignis Vasquez28068 Paratrophis australiana Hyland10634 ● 55.33/35.93 100 ● Streblus pendulinus Gray3277 Paratrophis pendulina Gray3277 ● 100/98.72 100 100 ● Streblus pendulinus Degener17839 Paratrophis pendulina Degener17839 ● 100/95.05 100● Streblus pendulinus Wood989 Paratrophis pendulina Wood989 ● 100/60.44 100/98.65 ● Streblus pendulinus Fosberg12877 Paratrophis pendulina Fosberg12877 ● 100 ● Bagassa guianensis GW1677 Bagassa guianensis GW1677 ● 98/93.4 Parartocarpeae ● Bagassa guianensis JansenJacobs3767 Bagassa guianensis JansenJacobs3767 ● 100 ● Sorocea subumbellata Dodson9601 Sorocea subumbellata Dodson9601 ● 100/95.47 68 100 ● Sorocea sprucei saxicola Nee35729 Sorocea sprucei saxicola Nee35729 ● 100/96.95 61.33/39.3 ● Sorocea duckei Stein 3931 Sorocea duckei Stein 3931 ● ● Sorocea trophoides Perea2479 Sorocea trophoides Perea2479 ● 100100 ● Sorocea pubivena pubivena cufodontisii Kernan406 Sorocea pubivena pubivena cufodontisii Kernan406 ● 100/79.66 100/99.12 100100● Sorocea pubivena oligotricha Kennedy2124 Sorocea pubivena oligotricha Kennedy2124 ● 100/46.42100/67.75 100 ● Sorocea pubivena pubivena Galdames4477 Sorocea pubivena pubivena Galdames4477 ● 100/59.07 Ficeae 100100● Sorocea affinis Espinosa706 Sorocea affinis Espinosa706 ● 100/64.27 ● Sorocea trophoides Fuentes304 Sorocea trophoides Fuentes304 ● 100/75.34 ● Sorocea jaramilloi Madison4772 Sorocea jaramilloi Madison4772 ● 81.33/39.47 Sorocea muriculata muriculata Schunke16489 Sorocea muriculata muriculata Schunke16489 100100 ● ● 100/90.34 100 ● Sorocea briquetii Valenzula954 Sorocea briquetii Valenzula954 ● 100/56.76 Sorocea pubivena hirtella Vasquez19236 Sorocea pubivena hirtella Vasquez19236 100/49.96 39 ● ● 100 ● Sorocea steinbachii GW1501 Sorocea steinbachii GW1501 ● 100/87.14 100/55.67 100 ● Sorocea muriculata uaupensis Plowman sn Sorocea muriculata uaupensis Plowman sn ● 100/67.08 Castilleae | Olmedieae 100 ● Sorocea guilieminiana Maguire56625 Sorocea guilleminiana Moya112 S38 ● 100/83.71 10030 ● Sorocea guilleminiana Moya112 S38 Sorocea guilieminiana Maguire56625 ● 38 Sorocea hilarii Pirani1136 Sorocea hilarii Pirani1136 44.67/41.27 ● ● 66/42.05 37 ● Sorocea hilarii Carauta795 Sorocea hilarii Carauta795 ● 56.67/39.26 75 ● Sorocea bonplandii MonroA sn Sorocea bonplandii MonroA sn ● 70.67/73.55 100 ● Sorocea boplandii Tressens6347 Sorocea boplandii Tressens6347 ● 94.67/58.76 ● Sorocea bonplandii Stevens30948 Sorocea bonplandii Stevens30948 ● 100 ● Trophis involucrata Lent2243 Trophis involucrata Lent2243 ● 100/91.33 Dorstenieae 100 ● Trophis involucrata Aguilar4679 Trophis involucrata Aguilar4679 ● 100/96.77 100 ● Trophis racemosa Stevens37196 Trophis racemosa Stevens37196 ● 100/94.63 100 ● Trophis mexicana Stevens27939 Trophis mexicana Stevens27939 ● 100/48.88 ● Trophis cuspidata Gomez−Dominuez774 Trophis cuspidata Gomez−Dominuez774 ● 100/83.28 100 ● Morus notabilis SRR8138828 Morus notabilis SRR8138828 ● 100● Morus rubra MOR 326−784 Morus rubra MOR 326−784 ● 100/98.18 Morus rubra EG141 Morus rubra EG141 100 ● ● 100/70.44100/96.27 100 ● Morus microphylla Stone4225 Morus microphylla Stone4225 ● 100/82.15 100● Morus celtidifolia Sandoval637 Morus celtidifolia Sandoval637 ● 56.67/39.55 Maclureae 100 ● Morus microphylla Fishbein1058 Morus microphylla Fishbein1058 ● 100/67.76 100● Morus macroura Bounhong LAOS366 Morus macroura Bounhong LAOS366 ● 100/65.7 91 ● Morus macroura DDS14088 Morus macroura DDS14088 ● 100/62.84 91● Morus macroura EG28 Morus macroura EG28 ● 100/86.92 10078 ● Morus cathayana Wilson10 Morus serrata Rodin 5315 ● 100/69.61 100 ● Morus serrata Rodin 5315 Morus serrata Koelz4788 ● supermatrix ● Morus serrata Koelz4788 Morus cathayana Wilson10 ● 61.33/40.72 species tree 70 Artocarpeae ● Morus australis Koelz4431 Morus australis Koelz4431 ● 64/46.13 10078 ● Morus australis Tanaka17776 Morus australis Tanaka17776 ● 100/57.68 100● Morus australis Oh110618−012 Morus australis Oh110618−012 ● 100/54.7299.33/60.57 78 ● Morus australis MOR 241−716 Morus australis MOR 241−716 ● 98 ● Morus australis Chung3290 Morus australis Chung3290 ● 99● Morus kagayamai AA20187−A Morus nigra EG29 ● 84/47.3799.33/53.51 62.67/39.72 7070 ● Morus nigra EG29 Morus kagayamai AA20187−A ● ● Morus cathayana Nie92144 Morus cathayana Nie92144 ● 38/37.93 6399● Morus alba var pendula MOR 380−871 Morus alba var pendula MOR 380−871 ● 97.33/40.8929.33/39.7698/51.59 Moreae 100 ● Morus alba var tatarica MOR 523−305 Morus alba var tatarica MOR 523−305 ● 100/50.52 100 ● Morus mongolica MOR 55−951 Morus mongolica MOR 55−951 ● 73.33/36.21 ● Morus alba MOR 920−261 Morus alba MOR 920−261 ● ● Morus cf alba HamiltonMA618 Morus cf alba HamiltonMA618 ● bioRxiv preprint doi: https://doi.org/10.1101/2020.04.08.030452; this version posted April 9, 2020. 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. GARDNER ET AL., PHYLOGENOMICS AND GENERIC REVISION OF MOREAE

1775 Figure 3. Phylogenetic trees of the Moreae clade from the "supercontig" dataset. 1776 Maximum-likelihood based on a supermatrix of all loci, with bootstrap support and 1777 previous nomenclature (left), and a species tree based on gene trees from all loci with 1778 bootstrap/LPP support and revised nomenclature (right). Discordant branches are colored in 1779 red. 1780 1781

64 ● Artocarpus heterophyllus EG98 Artocarpus heterophyllus EG98 ●

● Streblus zeylanicus Meijer701 Taxotrophis macrophylla DDS10673 ● 100/35.6

31 ● Streblus ilicifolius deWilde18958 Taxotrophis macrophylla JLS2916 ● 100 100 ● Streblus ilicifolius Cuong122 Taxotrophis ilicifolia deWilde18958 ● 100/97.51 100/36.47 ● Streblus cf ilicifolius EG720 Taxotrophis ilicifolia Cuong122 ● 88/47.32 86 100 ● Streblus macrophyllus DDS10673 Taxotrophis ilicifolius EG720 ● 30.67/97.83 ● Streblus macropyllus JLS2916 Taxotrophis zeylanica Meijer701 ● 82 100 ● Streblus taxoides Ridsdale SMHI422 Taxotrophis taxoides Ridsdale SMHI422 ● 100/98.62 54.67/36.21 ● Streblus taxoides EG701 Taxotrophis taxoides EG701 ● 100 65.33/84.37 ● Streblus spinosus Sidiyasa4071 Taxotrophis spinosa Sidiyasa4071 ● 100 ● Streblus spinosus MahyuniRDH 020 Taxotrophis spinosa MahyuniRDH 020 ● 100/92.43 100/55.16 100 100/48.57 98 ● Streblus spinosus MahyuniRDH 020 Taxotrophis spinosa MahyuniRDH 020 ● 100/67.62 ● Streblus spinosus EG702 Taxotrophis spinosa EG702 ● ● Trophis montana Andrianantoanina 1023 Maillardia montana Andrianantoanina 1023 ● 100 100/55.66 100 ● Trophis montana Nek1882 Maillardia montana Nek1882 ● 77.33/94.12 ● Trophis borbonica Cadet4518 Maillardia borbonica Cadet4518 ●

100 ● Morus mesozygia Buckner309 Afromorus mesozygia Buckner309 ● 100/100 ● ● 100 100 Morus mesozygia Bo330 Afromorus mesozygia Bo330 100/99.55 100/42.82 ● Milicia regia Cooper332 Milicia regia Cooper332 ● 100 100/69.7 ● Milicia excelsa McPherson16087 Milicia excelsa McPherson16087 ● 100 100 100 ● Milicia excelsa Williamson187 Milicia excelsa Williamson187 ● 100/97.86

100 ● Streblus dimepate CasmirZ405 Pachytrophe dimepate CasmirZ405 ● 100/90.63 100 100/61.2 100 ● Streblus mauritianus Rakotonirina489 Ampalis mauritiana Rakotonirina489 ● 100/52.13 ● Streblus mauritianus Hoffman Ampalis mauritiana Hoffman ● ● Morus insignis Homeier1949 Paratrophis insignis Homeier1949 ● 100 100/54.05 100 ● Morus insignis Monteagudo3734 Paratrophis insignis Monteagudo3734 ● 95.33/56.82 100 100/57.19 100 ● Morus insignis Vasquez28068 Paratrophis insignis Vasquez28068 ● 94/44.53 ● Morus insignis Vargas4154 Paratrophis insignis Vargas4154 ●

100 99 ● Streblus anthropophagorum Degeer4698 Paratrophis anthropophagorum Degeer4698 ● 100/49.34 100/59.96 100 ● Streblus heterophyllus Beecher sn Paratrophis microphylla Beecher sn ● 69.33/35.55 ● Streblus heterophyllus ChaseMW17825 Paratrophis microphylla ChaseMW17825 ● 24/36.4 ● Trophis philippinensis EG430 Paratrophis philippinensis EG430 ● 99 100 100/39.03 100 ● Trophis philippinensis Brambach465 Paratrophis philippinensis Brambach465 ● 56.67/38.65

100 ● Streblus glaber EG78 Paratrophis glabra EG78 ● 100/98.4 86 ● Streblus glaber var australianus Hyland10634 Paratrophis australiana Hyland10634 ● 50.67/45.6 ● Streblus pendulinus Gray3277 Paratrophis pendulina Gray3277 ● bioRxiv preprint doi: https://doi.org/10.1101/2020.04.08.030452100 ; this version posted April 9, 2020. The copyright holder for this preprint (which 100/95.47 100 ● Streblus pendulinus Degener17839 Paratrophis pendulina Degener17839 ● 100/88.96 was not certified by peer review) is the author/funder,100 who has granted bioRxiv a license to display the preprint in perpetuity. It is made 100/45.86 available100● under aCC-BY-NC-ND 4.0 International license. Streblus pendulinus Wood989 Paratrophis pendulina Wood989 ● 100/95.56 ● Streblus pendulinus Fosberg12877 Paratrophis pendulina Fosberg12877 ●

100 ● Bagassa guianensis GW1677 Bagassa guianensis GW1677 ● 93.33/72.1 ● Bagassa guianensis JansenJacobs3767 Bagassa guianensis JansenJacobs3767 ● ● Sorocea subumbellata Dodson9601 Sorocea subumbellata Dodson9601 ● 100 100/92.28 12 100 ● Sorocea sprucei saxicola Nee35729 Sorocea sprucei saxicola Nee35729 ● 100/72.73 90.67/56.25 ● Sorocea duckei Stein 3931 Sorocea duckei Stein 3931 ● ● Sorocea trophoides Perea2479 Sorocea trophoides Perea2479 ● 100 100 100/97.39 ● Sorocea pubivena pubivena cufodontisii Kernan406 Sorocea pubivena pubivena cufodontisii Kernan406 ● 100/97.61 100 100/36.97 100 ● Sorocea pubivena pubivena Galdames4477 Sorocea pubivena pubivena Galdames4477 ● 100/46.43

100 ● Sorocea pubivena oligotricha Kennedy2124 Sorocea pubivena oligotricha Kennedy2124 ● 100/96.18

100 100 ● Sorocea trophoides Fuentes304 Sorocea trophoides Fuentes304 ● 98.67/43.09 ● Sorocea affinis Espinosa706 Sorocea affinis Espinosa706 ● 100/99.11 ● Sorocea jaramilloi Madison4772 Sorocea jaramilloi Madison4772 ● 79.33/98.01 ● Sorocea muriculata muriculata Schunke16489 Sorocea muriculata muriculata Schunke16489 ● 100 100 100/94.66 100 ● Sorocea briquetii Valenzula954 Sorocea briquetii Valenzula954 ● 100/94.64 ● Sorocea pubivena hirtella Vasquez19236 Sorocea pubivena hirtella Vasquez19236 ● 97.33/39.37 100 100 ● Sorocea steinbachii GW1501 Sorocea steinbachii GW1501 ● 100/69.96 100 ● Sorocea muriculata uaupensis Plowman sn Sorocea muriculata uaupensis Plowman sn ● 99.33/94.71 100/NaN 100 ● Sorocea guilleminiana Moya112 S38 Sorocea guilleminiana Moya112 S38 ● ● ● 100/44.07 100 Sorocea guilieminiana Maguire56625 Sorocea guilieminiana Maguire56625 28 86/91.46 87 ● Sorocea hilarii Pirani1136 Sorocea hilarii Pirani1136 ● 74/98.81 100 ● Sorocea hilarii Carauta795 Sorocea hilarii Carauta795 ● 78/95.76 ● Sorocea bonplandii MonroA sn Sorocea bonplandii MonroA sn ● 100 94.67/96.67 94 ● Sorocea boplandii Tressens6347 Sorocea boplandii Tressens6347 ● 81.33/75.46 ● Sorocea bonplandii Stevens30948 Sorocea bonplandii Stevens30948 ●

100 ● Trophis involucrata Lent2243 Trophis involucrata Lent2243 ● 100/60.54 ● ● 100 Trophis involucrata Aguilar4679 Trophis involucrata Aguilar4679 100/71.77 ● Trophis racemosa Stevens37196 Trophis racemosa Stevens37196 ● 100 100/68.24 100 ● Trophis mexicana Stevens27939 Trophis mexicana Stevens27939 ● 100/43.92 ● Trophis cuspidata Gomez−Dominuez774 Trophis cuspidata Gomez−Dominuez774 ● 100 100/81.76 ● Morus notabilis SRR8138828 Morus notabilis SRR8138828 ●

100 ● Morus rubra EG141 Morus rubra EG141 ● 100/61.9 ● ● 100 Morus rubra MOR 326−784 Morus rubra MOR 326−784 100/93.13 100/51.84 100 ● Morus microphylla Stone4225 Morus microphylla Stone4225 ● 100 100/69.92 100 ● Morus celtidifolia Sandoval637 Morus celtidifolia Sandoval637 ● 98/84.12 ● Morus microphylla Fishbein1058 Morus microphylla Fishbein1058 ● 100/41.97 100 ● Morus macroura EG28 Morus macroura EG28 ● 100 100/40.58 100 ● Morus macroura Bounhong LAOS366 Morus macroura Bounhong LAOS366 ● 100/40.99 ● Morus macroura DDS14088 Morus macroura DDS14088 ● 100/84.56 100 100 ● Morus serrata Rodin 5315 Morus serrata Rodin 5315 ● 100/76.58 ● Morus serrata Koelz4788 Morus serrata Koelz4788 ● ● Morus cathayana Wilson10 Morus cathayana Wilson10 ● 98/40.17 7793 ● Morus australis Koelz4431 Morus australis Koelz4431 ● 93.33/42.9 ● Morus australis Tanaka17776 Morus australis Tanaka17776 ● 99100 100/70.2191.33/88.46 100 ● Morus australis Oh110618−012 Morus australis Oh110618−012 ● 100/69.15 ● Morus australis MOR 241−716 Morus australis MOR 241−716 ● 92.67/97.55 100 94 ● Morus cf alba HamiltonMA618 Morus cf alba HamiltonMA618 ● ● Morus nigra EG29 Morus nigra EG29 ● 94.67/98.65 70.67/85.06 100100 ● Morus australis Chung3290 Morus australis Chung3290 ● 43.33/44.58 supermatrix 100 ● Morus cathayana Nie92144 Morus cathayana Nie92144 ● species tree 42.67/87.6 100 ● Morus kagayamai AA20187−A Morus kagayamai AA20187−A ● ● Morus alba MOR 920−261 Morus alba MOR 920−261 ● 56.67/60.77 100 ● Morus mongolica MOR 55−951 Morus mongolica MOR 55−951 ● 100/66.74 35 47.33/47.21 100 ● Morus alba var pendula MOR 380−871 Morus alba var pendula MOR 380−871 ● 98.67/68.62 ● Morus alba var tatarica MOR 523−305 Morus alba var tatarica MOR 523−305 ● bioRxiv preprint doi: https://doi.org/10.1101/2020.04.08.030452; this version posted April 9, 2020. 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. GARDNER ET AL., PHYLOGENOMICS AND GENERIC REVISION OF MOREAE

1782 Figure 4. The best five maximum-pseudo-likelihood phylogenetic networks for the 1783 Paratrophis clade. 1784 1785

65 bioRxiv preprint doi: https://doi.org/10.1101/2020.04.08.030452; this version posted April 9, 2020. 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. bioRxiv preprint doi: https://doi.org/10.1101/2020.04.08.030452; this version posted April 9, 2020. 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. GARDNER ET AL., PHYLOGENOMICS AND GENERIC REVISION OF MOREAE

1786 Figure 5. Time-calibrated phylogenetic tree, with revised nomenclature. 1787 1788

66 Pseudostreblus indica 100 Hulletia dumosa 100 Hulletia griffithiana 100 Parartocarpus venenosus 100 Parartocarpus bracteatus Ficus sagittifolia 100 Ficus racemosa 100 Ficus macrophylla 100 100 Streblus asper Antiaropsis decipiens 100 100 Sparratosyce dioca 100 Poulsenia armata Helicostylis tomentosa 10082 Castilla elastica 100 100 Olmedia aspera 41 Pseudolmedia spuria 100 Naucleopsis macrophylla 41 Antiaris toxicaria Fatoua pilosa Malaisia scandens 100 100 Broussonetia papyrifera 100 Broussonetia cf. papyrifera 100 Broussonetia kazinoki 100 Bleekrodea madagascariensis Sloetiopsis usambarensis 100 100 Brosimum alicastrum 100 Helianthostylis sprucei 100 Trymatococcus amazonicus 100 Bosqueiopsis gilletii 100 Trilepisium madagascariense 100 Utsetela gabonenesis 100 Utsetela neglecta 100 Dorstenia hildebrandtii 100 100 Dorstenia barteri Maclura tinctoria ssp. tinctoria Maclura africana 100 74 Maclura andamanica 100 Maclura spinosa 100 Maclura pomifera 72 Maclura brasiliensis 72 Maclura thorelii Maclura cochinchinensis 72 86 Maclura aff. pubescens 100 86 Maclura tricuspidata Maclura fruticosa 100 Maclura cf. cochinchinensis 100 Maclura amboinensis Taxotrophis zeylanica 100 Taxotrophis macrophylla 97 Taxotrophis ilicifolius 96 Taxotrophis spinosa 99 Taxotrophis taxoides Maillardia borbonica 100 Maillardia montana Afromorus mesozygia 100 100 Milicia excelsa 100 Milicia regia 100 100 Pachytrophe dimepate 100 Ampalis mauritiana 100 63 Paratrophis microphylla 96 Paratrophis anthropophagorum 100 Paratrophis insignis 35 Paratrophis pendulina 67 Paratrophis glabra 98 Paratrophis philippinensis 100 Trophis involucrata 100 Trophis racemosa 100 Trophis mexicana 100 100 Trophis cuspidata Morus notabilis Morus rubra 100 100 Morus microphylla 100 100 Morus celtidifolia Morus macroura 78 Morus serrata 70 Morus australis 100 78 Morus kagayamai 70 Morus cathayana 70 Morus nigra 63 Morus mongolica 100 Morus alba var. alba bioRxiv preprint doi: https://doi.org/10.1101/2020.04.08.030452; this version posted April 9, 2020. The copyright holder forBagassa this preprint guianensis (which 100 Sorocea subumbellata was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the100 preprint in perpetuity. It is made 68 Sorocea duckei available under aCC-BY-NC-ND 4.0 International license. 100 Sorocea sprucei subsp. saxicola Sorocea trophoides 100 100 Sorocea affinis 100 Sorocea pubivena subsp. pubivena 100Sorocea pubivena subsp. oligotricha 100 Sorocea jaramilloi Sorocea muriculata subsp. muriculata 100 100 Sorocea pubivena subsp. hirtella 100 Sorocea briquetii 39 Sorocea muriculata subsp. uaupensis 100 Sorocea steinbachii 100 Sorocea bonplandii 37 Sorocea hilarii 38 Sorocea guilleminiana Clarisia ilicifolia 100 Batocarpus amazonicus 100 Batocarpus costaricensis 100 Batocarpus orinocensis 50 Clarisia racemosa 100 Clarisia biflora Artocarpus scandens 100 Artocarpus papuanus 100 Artocarpus limpato Artocarpus altissimus 100 100 Artocarpus sepicanus Artocarpus longifolius 88 Artocarpus fulvicortex 100 Artocarpus nitidus subsp. lingnanensis 100 Artocarpus thailandicus 10 Artocarpus lacucha 100 95 Artocarpus gomezianus subsp. zeylanicus Artocarpus nitidus subsp. humilis 100 Artocarpus nitidus subsp. griffithii 100 100 Artocarpus dadah 100 4 Artocarpus tonkinensis Artocarpus styracifolius 10097 Artocarpus hypargyraeus 100 100 Artocarpus nanchuanensis 10 Artocarpus petelotii 100 Artocarpus pithecogallus 100 Artocarpus gongshanensis Artocarpus gomezianus subsp. gomezianus Artocarpus rubrisoccatus 5 Artocarpus glaucus 100 100 Artocarpus nitidus subsp. borneensis 96 Artocarpus tomentosulus 100 100 Artocarpus primackii 100 Artocarpus xanthocarpus 100 Artocarpus vrieseanus 100 100 Artocarpus vrieseanus var. refractus Artocarpus albobrunneus 100 Artocarpus fretessii 100 Artocarpus ovatus 86 Artocarpus nitidus subsp. nitidus 100 Artocarpus rubrovenius 99 Artocarpus subrotundifolius Artocarpus heterophyllus 100 Artocarpus annulatus 100 Artocarpus integer Artocarpus sarawakensis 100 Artocarpus brevipedunculatus 100 Artocarpus anisophyllus 100 100 Artocarpus lanceifolius subsp. clementis 100 Artocarpus hirsutus 100 Artocarpus nobilis 100 Artocarpus chama 100 Artocarpus melinoxylus 100 Artocarpus odoratissimus 100 Artocarpus rigidus ssp. asperulus 100 100 Artocarpus hispidus 100 Artocarpus rigidus Artocarpus treculianus (nigrescens) 100 Artocarpus pinnatisectus 100 100 Artocarpus multifidus Artocarpus treculianus 100 Artocarpus treculianus (ovatifolius) 84 100 Artocarpus blancoi Artocarpus montanus Artocarpus camansi 100 Artocarpus mariannensis 100 66 Artocarpus altilis 100 Artocarpus horridus 100 100Artocarpus cf. horridus Artocarpus excelsus Artocarpus obtusus 100100 Artocarpus lowii Artocarpus teijsmannii subsp. teijsmannii 78 97 Artocarpus sumatranus 99 Artocarpus kemando 91 100 Artocarpus maingayi Artocarpus tamaran 87 Artocarpus sericicarpus 85 Artocarpus elasticus 86 Artocarpus scortechinii 90 Artocarpus corneri 73 Artocarpus jarrettiae 84.7 66 56 33.9 23 0 Upper Paleocene Oligocene Miocene Pliocene Plei. Cretaceous Paleogene Neogene Qua. bioRxiv preprint doi: https://doi.org/10.1101/2020.04.08.030452; this version posted April 9, 2020. 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. GARDNER ET AL., PHYLOGENOMICS AND GENERIC REVISION OF MOREAE

1789 Figure 6. Ancestral reconstruction of stamen position, with revised nomenclature. The 1790 reconstruction was identical under a trait-dependent (BiSSE) or a trait-independent model. 1791 Blue = inflexed in bud; yellow = straight in bud. 1792 1793

67 Pseudostreblus indica NewmanLA0518 Hulletia dumosa NZ242 Hullettia griffithiana Kerr16886 Parartocarpus venenosus NZ874 Parartocarpus bracteatus NZ730 Ficus sagittifolia ChaseMW19852 Ficus racemosa SRR1405699 SRR1405700 Ficus macrophylla EG30 Streblus asper EG696 Antiaropsis decipiens NZ281 Sparattosyce dioica WeiblenWW1223 Poulsenia armata Pennington14600 Helicostylis tomentosa Gomes511 Castilla elastica ChaseMW19850 Olmedia aspera Fuentes5323 S41 Pseudolmedia spuria Lobo263 Naucleopsis macrophylla BergP18534 Antiaris toxicaria 5595 Fatoua pilosa TaylorP218 Malaisia scandens EG122 Broussonetia papyrifera SRR1477753 Broussonetia cf papyrifera Heng14289 Broussonetia kazinoki ChaseMW17827 Bleekrodea madagascariensis DavisRakotonasolo3117 Sloetiopsis usambarensis Faden77 417 Brosimum alicastrum EG23 Helianthostylis sprucei Ribeiro1204 Trymatococcus amazonicus Prance13461 Bosqueiopsis gilletii Fronties243 Trilepisium madagascariense Richard403 Utsetela gabonenesis Breteler14086 Utsetela neglecta Bissiengen923 Dorstenia hildebrandtii NZ311 Dorstenia barteri ChaseMW18153 Maclura tinctoria tinctoria Campos2679 Maclura africana GreenwayKanuri15269 Maclura andamanica Maxwell89−436 Maclura spinosa Perumal RHT22554 Maclura pomifera EG139 Maclura brasiliensis NeeVargas45025 Maclura thorellii Pierre4709 Maclura cochinchinensis SAGBE887 Maclura aff pubsecens Averyanov1198 Maclura tricuspidata MOR 68−7917 Maclura fruticosa NMCuong1193 Maclura cf cochinchinensis NZ757 Maclura amboinensis Takeuchi16578 Taxotrophis zeylanica Meijer701 Taxotrophis macrophylla DDS10673 Taxotrophis ilicifolius EG720 Taxotrophis spinosa EG702 Taxotrophis taxoides EG701 Maillardia borbonica Cadet4518 Maillardia montana Andrianantoanina 1023 Afromorus mesozygia Buckner309 Milicia excelsa McPherson16087 Milicia regia Cooper332 Pachytrophe dimepate CasmirZ405 Ampalis mauritiana Hoffman Paratrophis microphylla Beecher sn Paratrophis anthropophagorum Degeer4698 Paratrophis insignis Vasquez28068 Paratrophis pendulina Gray3277 Paratrophis glabra EG78 Paratrophis philippinensis EG430 Trophis involucrata Aguilar4679 Trophis racemosa Stevens37196 Trophis mexicana Stevens27939 Trophis cuspidata Gomez−Dominuez774 bioRxiv preprint doi: https://doi.org/10.1101/2020.04.08.030452; this version posted April 9, 2020.Morus The copyrightnotabilis SRR8138828 holder for this preprint (which Morus rubra EG141 was not certified by peer review) is the author/funder, who has granted bioRxiv a license to displayMorus themicrophylla preprint Fishbein1058 in perpetuity. It is made available under aCC-BY-NC-ND 4.0 International licenseMorus. celtidifolia Sandoval637 Morus macroura EG28 Morus serrata Koelz4788 Morus australis MOR 241−716 Morus kagayamai AA20187−A Morus cathayana Nie92144 Morus nigra EG29 Morus mongolica MOR 55−951 Morus alba MOR 920−261 Bagassa guianensis GW1677 Sorocea subumbellata Dodson9601 Sorocea duckei Stein 3931 Sorocea sprucei saxicola Nee35729 Sorocea trophoides Fuentes304 Sorocea affinis Espinosa706 Sorocea pubivena pubivena Galdames4477 Sorocea pubivena oligotricha Kennedy2124 Sorocea jaramilloi Madison4772 Sorocea muriculata muriculata Schunke16489 Sorocea pubivena hirtella Vasquez19236 Sorocea briquetii Valenzula954 Sorocea muriculata uaupensis Plowman sn Sorocea steinbachii GW1501 Sorocea boplandii Tressens6347 Sorocea hilarii Carauta795 Sorocea guilleminiana Moya112 S38 Clarisia ilicifolia Carranta6386 Batocarpus amazonicus Salidas1233 Batocarpus costaricensis GW1463 Batocarpus oriniceros Vasquez27440 Clarisia racemosa Assuncao690 Clarisia biflora GW1460 Artocarpus scandens EG411 Artocarpus papuanus NZ61 Artocarpus limpato NZ609 Artocarpus altissimus EG441 Artocarpus sepicanus GW1701 Artocarpus longifolius ssp adpressus Nangkat15511 Artocarpus fulvicortex EG711 Artocarpus nitidus ssp lingnanensis NZ911 Artocarpus thailandicus NZ402 Artocarpus lacucha NZ420 Artocarpus gomezianus ssp zeylanicus NZ956 Artocarpus nitidus ssp humilis EG258 Artocarpus nitidus ssp griffithii NZ216 Artocarpus dadah NZ694 Artocarpus tonkinensis EG174 Artocarpus styracifolius EG176 Artocarpus hypargyraeus EG170 Artocarpus nanchuanensis EGL238 Artocarpus petelotii DDS14435 Artocarpus pithecogallus LiJianwu3200 Artocarpus gongshanensis HAST137747 Artocarpus gomezianus ssp gomezianus NZ533 Artocarpus cf lacucha NZ517 Artocarpus glaucus NZ852 Artocarpus nitidus ssp borneensis NZ686 Artocarpus tomentosulus NZ617 Artocarpus primackii NZ687 Artocarpus xanthocarpus Yang15648 Artocarpus vriesianus var vrieseanus GW1229 Artocarpus vrieseanus refractus Hoogland4822 Artocarpus albobrunneus AA2243 Artocarpus fretessii NZ929 Artocarpus ovatus NZ202 Artocarpus nitidus ssp nitidus PPI10374 Artocarpus rubrovenius JSB84 Artocarpus subrotundifolius Wenzel1576 Artocarpus heterophyllus EG98 Artocarpus annulatus NZ985 Artocarpus integer NZ918 Artocarpus sarawakensis EG527 Artocarpus brevipedunculatus NZ814 Artocarpus anisophyllus NZ606 Artocarpus lanceifolius ssp clementis NZ739 Artocarpus hirsutus NZ953 Artocarpus nobilis AHJ3283 Artocarpus chama NZ354 Artocarpus melinoxylus JLS2924 Artocarpus odoratissimus NZ618 Artocarpus rigidus ssp asperulus NZ507 Artocarpus hispidus NZ258 Artocarpus rigidus NZ728 Artocarpus treculianus nigrescens Ramos2107 Artocarpus pinnatisectus Escritor Artocarpus multifidus PPI3911 Artocarpus treculianus Elmer12468 Artocarpus treculianus ovatifolius NZ203 Artocarpus blancoi Ramos42018 Artocarpus aff excelsus AveryanovVH1819 Artocarpus camansi EG149 Artocarpus mariannensis DD4 Artocarpus altilis K7 UluFiti Artocarpus horridus EG437 Artocarpus cf horridus RM160 Artocarpus excelsus NZ780 Artocarpus obtusus NZ729 Artocarpus lowii MWL2 Artocarpus teijsmannii NZ946 Artocarpus sumatranus AA2766 Artocarpus kemando NZ612 Artocarpus maingayi NZ257 Artocarpus tamaran EG92 Artocarpus sericicarpus NZ771 Artocarpus elasticus EG87 Artocarpus scortechinii NZ209 Artocarpus corneri Fuchs21347 Artocarpus jarrettiae SAN120933 bioRxiv preprint doi: https://doi.org/10.1101/2020.04.08.030452; this version posted April 9, 2020. 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. GARDNER ET AL., PHYLOGENOMICS AND GENERIC REVISION OF MOREAE

1794 Figure 7. Revised classification of Moreae on a maximum-likelihood phylogenetic tree of 1795 Moreae based on "supercontig" sequences. 1796 1797

68 bioRxiv preprint doi: https://doi.org/10.1101/2020.04.08.030452; this version posted April 9, 2020. 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.

Taxotrophis zeylanica 100 Taxotrophis macrophylla 97 Taxotrophis ilicifolius Taxotrophis 96 Taxotrophis taxoides 99 Taxotrophis spinosa 100 Taxotrophis spinosa Maillardia borbonica 100 Maillardia Maillardia montana Afromorus mesozygia Afromorus 100 100 Milicia excelsa 100 Milicia 100 Milicia regia 100 Pachytrophe dimepate Pachytrophe 100 Ampalis mauritiana Ampalis Paratrophis microphylla 63 96 Paratrophis anthropophagorum 100 Paratrophis insignis 35 Paratrophis pendulina Paratrophis 67 Paratrophis glabra 98 Paratrophis philippinensis Trophis involucrata 100 100 Trophis racemosa Trophis 100 Trophis mexicana 100 Trophis cuspidata 100 Morus notabilis Morus rubra 100 100 Morus microphylla 100 Morus celtidifolia 100 Morus macroura 78 Morus serrata 70 Morus australis 100 Morus 78 Morus kagayamai Morus cathayana 7070 Morus nigra 63 Morus mongolica 100 Morus alba var. alba Bagassa guianensis Bagassa Sorocea subumbellata 100 Sorocea duckei 68 100 Sorocea sprucei subsp. saxicola Sorocea trophoides 100 100 Sorocea affinis 100 Sorocea pubivena subsp. pubivena 100 Sorocea pubivena subsp. oligotricha 100 Sorocea jaramilloi Sorocea muriculata subsp. muriculata 100 100 Sorocea pubivena subsp. hirtella 100 Sorocea briquetii Sorocea 39 Sorocea muriculata subsp. uaupensis 100 Sorocea steinbachii 100 Sorocea boplandii 37 Sorocea hilarii 38 Sorocea guilleminiana