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opencc-zeroNov 2023View details →

Phylogenomics reveals an almost perfect polytomy among the almost ungulates (Paenungulata)

Phylogenetic studies have resolved most relationships among Eutherian Orders. However, the branching order of elephants (Proboscidea), hyraxes (Hyracoidea), and sea cows (Sirenia) (i.e., the Paenungulata) has remained uncertain since at least 1758, when Linnaeus grouped elephants and manatees into a single Order (Bruta) to the exclusion of hyraxes. Subsequent morphological, molecular, and large-scale phylogenomic datasets have reached conflicting conclusions on the branching order within Paenungulates. We use a phylogenomic dataset of alignments from 13,388 protein-coding genes across 261 Eutherian mammals to infer phylogenetic relationships within Paenungulates. We find that gene trees almost equally support the three alternative resolutions of Paenungulate relationships, and that despite strong support for a Proboscidea+Hyracoidea split in the multispecies coalescent (MSC) tree, there is significant evidence for gene tree uncertainty, incomplete lineage sorting, and introgression among Proboscidea, Hyracoidea, and Sirenia. Indeed, only 8-10% of genes have statistically significant phylogenetic signal to reject the hypothesis of a Paenungulate polytomy. These data indicate little support for any resolution for the branching order Proboscidea, Hyracoidea, and Sirenia within Paenungulata and suggest that Paenungulata may be as close to a real, or at least unresolvable, polytomy as possible.

opencc-zeroFeb 2022View details →

Between a rock and a hard polytomy: phylogenomics of the rock-dwelling mbuna cichlids of Lake Malawi

Whole genome sequences are beginning to revolutionise our understanding of phylogenetic relationships. Yet, even whole genome sequences can fail to resolve the evolutionary history of the most rapidly radiating lineages, where incomplete lineage sorting, standing genetic variation, introgression, and other factors obscure the phylogenetic history of the group. To overcome such challenges, one emerging strategy is to integrate results across different methods. Most such approaches have been implemented on reduced representation genomic datasets, but whole genomes should provide the maximum possible evidence approach. Here, we test the ability of SNPs extracted from whole genome resequencing data, implemented in an integrative genomic approach, to resolve key nodes in the phylogeny of the mbuna, rock-dwelling cichlid fishes of Lake Malaŵi, which epitomise the phylogenetic intractability that often accompanies explosive lineage diversification. This monophyletic radiation has diversified at an unparalleled rate into several hundred species in less than two million years. Using an array of phylogenomic methods, we consistently recovered four major clades of mbuna, but a large basal polytomy among them. Although introgression between clades apparently contributed to the challenge of phylogenetic reconstruction, reduction of the dataset to non-introgressed sites still did not help to resolve the basal polytomy. On the other hand, relationships among six congeneric species pairs were resolved without ambiguity, even in one case where existing data led us to predict that resolution would be difficult. We conclude that the bursts of diversification at the earliest stages of the mbuna radiation may be phylogenetically unresolvable, but other regions of the tree are phylogenetically clearly supported. Integration of multiple phylogenomic approaches will continue to increase confidence in relationships inferred from these and other whole-genome datasets.

publicFeb 2022View details →

Between a rock and a hard polytomy: phylogenomics of the rock-dwelling mbuna cichlids of Lake Malawi

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publicNov 2023View details →

Phylogenomics reveals an almost perfect polytomy among the almost ungulates (Paenungulata)

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dryad32/100

Phylogenomic discordance suggests polytomies along the backbone of the large genus Solanum

Premise of the study: Evolutionary studies require solid phylogenetic frameworks, but increased volumes of phylogenomic data have revealed incongruent topologies among gene trees in many organisms both between and within genomes. Some of these incongruences indicate polytomies that may remain impossible to resolve. Here we investigate the degree of gene-tree discordance in Solanum, one of the largest flowering plant genera that includes the cultivated potato, tomato, and eggplant, as well as 24 minor crop plants. Methods: A densely sampled species-level phylogeny of Solanum is built using unpublished and publicly available Sanger sequences comprising 60% of all accepted species (742 spp.) and nine regions (ITS, waxy, and seven plastid markers). The robustness of this topology is tested by examining a full plastome dataset with 140 species and a nuclear target-capture dataset with 39 species of Solanum (Angiosperms353 probe set). Key results: While the taxonomic framework of Solanum remained stable, gene tree conflicts and discordance between phylogenetic trees generated from the target-capture and plastome datasets were observed. The latter correspond to regions with short internodal branches, and network analysis and polytomy tests suggest the backbone is composed of three polytomies found at different evolutionary depths. The strongest area of discordance, near the crown node of Solanum, could potentially represent a hard polytomy. Conclusions: We argue that incomplete lineage sorting due to rapid diversification is the most likely cause for these polytomies, and that embracing the uncertainty that underlies them is crucial to understand the evolution of large and rapidly radiating lineages.

opencc-zeroNov 2021View details →

Table 1 in Plastid phylogenomics of the Eriostemon group (Rutaceae; Zanthoxyloideae): support for major clades and investigation of a backbone polytomy

Table 1. Accession details for all samples.<table><tbody><tr><th>Taxon name</th><th>Collector number</th><th>Herbarium voucher number(s)</th><th>GenBank number (full plastome)</th><th>GenBank numbers (Sanger)</th><th>Latitude</th><th>Longitude</th><th>Collection locality</th></tr></tbody><tbody><tr><th>Acronychia laevis</th><td>P.I.Forster 33410</td><td>BRI AQ0752244</td><td>OL591157</td><td>–</td><td>−25.93</td><td>152.1</td><td>Australia: Queensland, Grongah National Park.</td></tr><tr><th>Asterolasia asteriscophora</th><td>M.J.Bayly 2564</td><td>MELUD114862a</td><td>OL591158</td><td>–</td><td>−37.58</td><td>145.49</td><td>Australia: Victoria, Healesville.</td></tr><tr><th>Asterolasia drummondii</th><td>B.J.Mole 330</td><td>NSW 1003537</td><td>OL591159</td><td>–</td><td>−30.8</td><td>115.6</td><td>Australia: New South Wales.</td></tr><tr><th>Boronia edwardsii</th><td>M.J.Bayly 1974</td><td>MEL 2383596A</td><td>OL591160</td><td>–</td><td>−35.6</td><td>138.4</td><td>Australia: South Australia, Yankalilla.</td></tr><tr><th>Boronia imlayensis</th><td>M.J.Bayly 2005</td><td>MELUD105861a</td><td>OL591161</td><td>–</td><td>–</td><td>–</td><td>Australia: Cultivated, Australian National Botanic Garden (loc. 23a, Prop ID 749585).</td></tr><tr><th>Boronia ternata</th><td>M.J.Bayly 1931</td><td>MEL 2383603A</td><td>OL591162</td><td>–</td><td>−31.26</td><td>120.05</td><td>Australia: Western Australia, Boorabbin National Park.</td></tr><tr><th>Brombya platynema</th><td>P.I.Forster 34088</td><td>HO550407</td><td>OL591163</td><td>–</td><td>−17.58</td><td>145.7</td><td>Australia: Queensland, Wooroonooran National Park.</td></tr><tr><th>Chorilaena anceps</th><td>B.J.Mole 475</td><td>NSW 1003674</td><td>OL591221</td><td>–</td><td>−35.01</td><td>117.92</td><td>Australia: Western Australia, Albany.</td></tr><tr><th>Chorilaena euphemiae</th><td>B.J.Mole 424</td><td>NSW 1003630</td><td>OL591222</td><td>–</td><td>−33.99</td><td>122.14</td><td>Australia: Western Australia, Mount Le Grand.</td></tr><tr><th>Chorilaena quercifolia</th><td>M.J.Bayly 1954</td><td>MEL 2383575A</td><td>OL591164</td><td>–</td><td>−34.1</td><td>115.98</td><td>Australia: Western Australia, Netic State Forest.</td></tr><tr><th>Correa alba</th><td>M.J.Bayly 1876</td><td>MELUD105867a</td><td>OL591165</td><td>–</td><td>−38.4</td><td>144.18</td><td>Australia: Victoria, Anglesea.</td></tr><tr><th>Correa glabra</th><td>M.J.Bayly 2476</td><td>MELUD127019a</td><td>OL591166</td><td>–</td><td>−36.08</td><td>143.23</td><td>Australia: Victoria, Mount Wycheproof.</td></tr><tr><th>Correa lawrenceana var. grampiana</th><td>M.J.Bayly 1988</td><td>MEL 2383594A</td><td>OL591167</td><td>–</td><td>−37.29</td><td>142.59</td><td>Australia: Victoria, Grampians.</td></tr><tr><th>Correa lawrenceana var. latrobeana</th><td>M.J.Bayly 2567</td><td>MELUD114861a</td><td>OL591168</td><td>–</td><td>−37.53</td><td>145.51</td><td>Australia: Victoria, Toolangi.</td></tr><tr><th>Crowea angustifolia var. platyphylla</th><td>M.J.Bayly 1953</td><td>MEL 2383618A</td><td>OL591169</td><td>–</td><td>−34.58</td><td>116.4</td><td>Australia: Western Australia, Shannon National Park.</td></tr><tr><th>Crowea exalata subsp. exalata</th><td>D.J.Ohlsen s.n.</td><td>MELUD121723a</td><td>OL591170</td><td>–</td><td>−37.37</td><td>148.22</td><td>Australia: Victoria, W Tree.</td></tr><tr><th>Crowea exalata var. revoluta</th><td>M.J.Bayly 1992</td><td>MELUD105865a</td><td>OL591171</td><td>–</td><td>−36.67</td><td>144.25</td><td>Australia: Victoria, Greater Bendigo National Park.</td></tr><tr><th>Crowea saligna</th><td>D.J.Ohlsen s.n.</td><td>MELUD121722a</td><td>OL591172</td><td>–</td><td>−33.73</td><td>151.24</td><td>Australia: New South Wales, Sydney.</td></tr><tr><th>Cyanothamnus anemonifolius</th><td>M.J.Bayly 2562</td><td>MELUD114859a</td><td>OL591173</td><td>–</td><td>−37.74</td><td>144.31</td><td>Australia: Victoria, Brisbane Ranges National Park.</td></tr><tr><th>Diplolaena drummondii</th><td>M.J.Bayly 1956</td><td>MEL 2383571A</td><td>OL591174</td><td>–</td><td>−33.37</td><td>115.97</td><td>Australia: Western Australia, Wellington National Park.</td></tr><tr><th>Diplolaena obovata</th><td>M.J.Bayly 1908</td><td>MEL 2383570A</td><td>OL591175</td><td>–</td><td>−30.05</td><td>115.07</td><td>Australia: Western Australia.</td></tr><tr><th>Drummondita calida</th><td>P.I.Forster 22556</td><td>BRI AQ0605109</td><td>OL591176</td><td>–</td><td>−17.52</td><td>143.75</td><td>Australia: Queensland Bulleringa National Park.</td></tr><tr><th>Drummondita fulva</th><td>A.S.Markey 6212</td><td>MELUD105908a</td><td>OL591177</td><td>–</td><td>−29.1</td><td>116.9</td><td>Australia: Western Australia, Blue Hills Range.</td></tr><tr><th>Drummondita hassellii</th><td>M.J.Bayly 1925</td><td>MEL 2383612A</td><td>OL591178</td><td>–</td><td>−31.32</td><td>117.94</td><td>Australia: Western Australia, Trayning.</td></tr><tr><th>Drummondita hassellii</th><td>M.J.Bayly 1928</td><td>MEL 2383568A</td><td>–</td><td>OL660700; OM744163; OL660675; OL697857</td><td>−31.28</td><td>119.83</td><td>Australia: Western Australia, Yellowdine Nature Reserve.</td></tr><tr><th>Eriostemon australasius</th><td>P.I.Forster 34192</td><td>BRI AQ0743514</td><td>OL591179</td><td>–</td><td>−26.01</td><td>153.05</td><td>Australia: Queensland, Great Sandy NP.</td></tr><tr><th>Eriostemon banksii</th><td>P.I.Forster 33960</td><td>BRI AQ0743323</td><td>OL591180</td><td>–</td><td>−11.71</td><td>142.86</td><td>Australia: Queensland, Cape York Peninsula.</td></tr><tr><th>Euodia pubifolia</th><td>P.I.Forster 25751</td><td>BRI AQ0607159</td><td>OL591181</td><td>–</td><td>−16.14</td><td>145.43</td><td>Australia: Queensland, Daintree National Park.</td></tr><tr><th>Geleznowia verrucosa</th><td>B.J.Mole 344</td><td>NSW 1003545</td><td>OL591182</td><td>–</td><td>−29.99</td><td>115.91</td><td>Australia: Western Australia, Coorow.</td></tr><tr><th>Geleznowia verrucosa</th><td>M.J.Bayly 1910</td><td>MEL 2383587A</td><td>OL591183</td><td>–</td><td>−29.8</td><td>115.49</td><td>Australia: Western Australia, Tathra National Park.</td></tr><tr><th>Geleznowia verrucosa</th><td>M.J.Bayly 1909</td><td>MEL 2383586A</td><td>–</td><td>OL660701; OM744150; OM803177; OL697858</td><td>−29.8</td><td>115.49</td><td>Australia: Western Australia, Tathra National Park.</td></tr><tr><th>Halfordia kendack</th><td>D.G.Fell 10829</td><td>CNS 149723.1</td><td>OL591184</td><td>–</td><td>−10.18</td><td>142.23</td><td>Australia: Queensland, Moa Island.</td></tr><tr><th>Halfordia kendack</th><td>G.&N.Sankowksy 3019</td><td>MELUD105887a</td><td>OL591188</td><td>–</td><td>–</td><td>–</td><td>Australia: Cultivated Tolga. Arboretum number 276.</td></tr><tr><th>Halfordia kendack</th><td>P.I.Forster 34073</td><td>BRI AQ0743506</td><td>OL591185</td><td>–</td><td>−17.41</td><td>145.7</td><td>Australia: Queensland, Topaz.</td></tr><tr><th>Halfordia kendack</th><td>P.I.Forster 34090</td><td>BRI AQ0743446</td><td>OL591186</td><td>–</td><td>−17.45</td><td>145.48</td><td>Australia: Queensland, Herberton Range Forest Reserve.</td></tr><tr><th>Halfordia kendack</th><td>P.I.Forster 34580</td><td>BRI AQ0745524</td><td>OL591187</td><td>–</td><td>−12.25</td><td>143.09</td><td>Australia: Queensland, Cape York Peninsula.</td></tr><tr><th>Leionema beckleri</th><td>P.I.Forster 33439</td><td>BRI AQ0752479</td><td>OL591189</td><td>–</td><td>−28.22</td><td>153.21</td><td>Australia: Queensland, Lamington National Park.</td></tr><tr><th>Leionema ellipticum</th><td>P.I.Forster 25021</td><td>BRI AQ0606667</td><td>OL591190</td><td>–</td><td>−15.82</td><td>145.28</td><td>Australia: Queensland, Cedar Bay National Park.</td></tr><tr><th>Leionema lamprophyllum subsp. obovatum</th><td>M.J.Bayly 2563</td><td>MELUD114858a</td><td>OL591191</td><td>–</td><td>−37.74</td><td>144.31</td><td>Australia: Victoria, Brisbane Ranges National Park.</td></tr><tr><th>Leionema rotundifolium</th><td>P.I.Forster 34469</td><td>BRI AQ0745286</td><td>OL591192</td><td>–</td><td>−28.83</td><td>151.96</td><td>Australia: Queensland, Girraween National Park.</td></tr><tr><th>Medicosma cunninghamii</th><td>P.I.Forster 33501</td><td>BRI AQ0752476</td><td>OL591193</td><td>–</td><td>−26.45</td><td>152.97</td><td>Australia: Queensland, Sunshine Coast.</td></tr><tr><th>Melicope hayesii</th><td>P.I.Forster 36183</td><td>BRI AQ0813873</td><td>OL591194</td><td>–</td><td>−28.26</td><td>153.16</td><td>Australia: Queensland, Lamington National Park.</td></tr><tr><th>Muiriantha hassellii</th><td>B.J.Mole 474</td><td>NSW 1003673</td><td>OL591196</td><td>–</td><td>−34.4</td><td>118</td><td>Australia: Western Australia, Plantagenet.</td></tr><tr><th>Myrtopsis sp.</th><td>J.Munzinger 3458</td><td>NOU014250; MNHN-P- P04759709</td><td>OL591197</td><td>–</td><td>−22.1</td><td>166.64</td><td>New Caledonia: Riviére Bleu.</td></tr><tr><th>Nematolepis phebalioides</th><td>A.S.Markey 6215</td><td>MEL 2337320A; PERTH 8114846</td><td>OL591198</td><td>–</td><td>−33.66</td><td>120.28</td><td>Australia: Western Australia, Ravensthorpe Range.</td></tr><tr><th>Nematolepis squamea</th><td>P.I.Forster 34811</td><td>BRI AQ745513</td><td>OL591199</td><td>–</td><td>–</td><td>–</td><td>Australia: New South Wales, Wooyung, near Billinudgel.</td></tr><tr><th>Nematolepis wilsonii</th><td>M.J.Bayly 2568</td><td>MELUD114864a</td><td>OL591200</td><td>–</td><td>−37.83</td><td>144.98</td><td>Australia: Cultivated Royal Botanic Gardens Victoria.</td></tr><tr><th>Neobyrnesia suberosa</th><td>M.J.Bayly 1904</td><td>MEL 2383567A</td><td>OL591201</td><td>–</td><td>−12.44</td><td>132.97</td><td>Australia: Northern Territory, Kakadu National Park.</td></tr><tr><th>Neoschmidia pallida</th><td>P.H.Weston 3303</td><td>NSW783008</td><td>OL591202</td><td>–</td><td>–</td><td>–</td><td>New Caledonia: Cultivated Royal Botanic Garden Sydney, ex. Mount Dore.</td></tr><tr><th>Phebalium clavatum</th><td>B.J.Mole 398</td><td>NSW 1003609</td><td>OL591203</td><td>–</td><td>−31.2</td><td>121.3</td><td>Australia: Western Australia, Coolgardie.</td></tr><tr><th>Phebalium elegans</th><td>B.J.Mole 403</td><td>NSW 1003615</td><td>OL591204</td><td>–</td><td>−32.06</td><td>122.72</td><td>Australia: Western Australia, east of Norseman.</td></tr><tr><th>Phebalium longifolium</th><td>P.I.Forster 25088</td><td>BRI AQ0678653</td><td>OL591205</td><td>–</td><td>−17.32</td><td>145.42</td><td>Australia: Queensland, Mount Baldy State Forest.</td></tr><tr><th>Phebalium multiflorum</th><td>R.Butcher 1280</td><td>MELUD105904A; PERTH 8143110</td><td>OL591195</td><td>–</td><td>−33.66</td><td>120.27</td><td>Australia: Western Australia, Ravensthorpe Range.</td></tr><tr><th>Phebalium stenophyllum</th><td>M.J.Bayly 2560</td><td>MELUD127020a</td><td>OL591206</td><td>–</td><td>−36.61</td><td>141.75</td><td>Australia: Victoria, Little Desert.</td></tr><tr><th>Phebalium tuberculosum</th><td>B.J.Mole 375</td><td>NSW 1003583</td><td>OL591207</td><td>–</td><td>−31.48</td><td>118.33</td><td>Australia: Western Australia, east of Merridin.</td></tr><tr><th>Phebalium whitei</th><td>P.I.Forster 34467</td><td>BRI AQ0745285</td><td>OL591208</td><td>–</td><td>−28.83</td><td>151.96</td><td>Australia: Queensland, Girraween National Park.</td></tr><tr><th>Philotheca acrolopha</th><td>W.W.Cooper 2048</td><td>BRI AQ0745516; CNS 134918.1</td><td>–</td><td>OL660702; OM744164; OL660676; OL697859</td><td>−12.75</td><td>143.21</td><td>Australia: Queensland, Mount Tozer, Iron Range.</td></tr><tr><th>Philotheca angustifolia subsp. angustifolia</th><td>M.J.Bayly 1990</td><td>MEL 2383589A</td><td>OL591209</td><td>–</td><td>−36.55</td><td>144.35</td><td>Australia: Victoria, Greater Bendigo National Park.</td></tr><tr><th>Philotheca angustifolia subsp. montana</th><td>M.J.Bayly 1871</td><td>MELUD105857a</td><td>–</td><td>OL660703; OM744155; OL660677; OL697860</td><td>−36.88</td><td>142.37</td><td>Australia: Victoria, Mount Zero, northern Grampians.</td></tr><tr><th>Philotheca apiculata</th><td>M.J.Bayly 1939</td><td>MELUD105856a</td><td>–</td><td>OL660704; OM744147; OL660678; OL697861</td><td>−32.2</td><td>121.8</td><td>Australia: Western Australia.</td></tr><tr><th>Philotheca basistyla</th><td>M.J.Bayly 1924</td><td>PERTH 7810989</td><td>–</td><td>OL660705; OM744165; OL660679; OL697862</td><td>−31.3</td><td>118</td><td>Australia: Western Australia.</td></tr><tr><th>Philotheca brevifolia</th><td>M.J.Bayly 322</td><td>PERTH 7421087</td><td>–</td><td>OL660706; OM744167; OL660680; OL697863</td><td>−33.97</td><td>146.17</td><td>Australia: New South Wales, Cocoparra Nature Reserve.</td></tr><tr><th>Philotheca ciliata</th><td>P.I.Forster 29594</td><td>BRI AQ0647786; HO538812; NE 86281</td><td>–</td><td>OL660707; OM744168; OL660681; OL697864</td><td>−28.39</td><td>151.27</td><td>Australia: Queensland, Biggs Road, 18 km east of Inglewood.</td></tr><tr><th>Philotheca coateana</th><td>M.J.Bayly 1936</td><td>MELUD105855a</td><td>–</td><td>OL660708; OM744156; OL660682; OL697865</td><td>−29.2</td><td>120.1</td><td>Australia: Western Australia.</td></tr><tr><th>Philotheca coccinea</th><td>M.J.Bayly 1929</td><td>MEL 2383614A</td><td>–</td><td>OL660709; OM744149; OL660683; OL697866</td><td>−31.27</td><td>120.02</td><td>Australia: Western Australia, Boorabbin National Park.</td></tr><tr><th>Philotheca cuticularis</th><td>P.I.Forster 35315</td><td>BRI AQ0813977; MEL 2340118A</td><td>–</td><td>OL660710; OM744145; OL660684; OL697867</td><td>−25.71</td><td>144.46</td><td>Australia: Queensland, near Little Hell Hole Waterhole, Milo Station.</td></tr><tr><th>Philotheca deserti subsp. deserti</th><td>M.J.Bayly 1919</td><td>MEL 2383584A</td><td>–</td><td>OL660711; OM744144; OL660685; OL697868</td><td>−29.78</td><td>117.03</td><td>Australia: Western Australia, Great Northern Highway, 93.8 km south-west of Paynes Find.</td></tr><tr><th>Philotheca difformis subsp. difformis</th><td>M.T.Mathieson 274</td><td>MEL 2339553A</td><td>–</td><td>OL660712; OM744159; OL660686; OL697869</td><td>−26.11</td><td>147.64</td><td>Australia: Queensland, western end of ‘Currawarra’.</td></tr><tr><th>Philotheca difformis subsp. smithiana</th><td>M.J.Bayly s.n.</td><td>MELUD121708a</td><td>OL591210</td><td>–</td><td>−26.41</td><td>152.98</td><td>Australia: Queensland, Tinbeerwah.</td></tr><tr><th>Philotheca ericifolia</th><td>M.J.Bayly 203</td><td>MEL 2278545A</td><td>–</td><td>OL660713; OM744161; OL660687; OL697870</td><td>−30.61</td><td>149.32</td><td>Australia: New South Wales, Pilliga East State Forest.</td></tr><tr><th>Philotheca fitzgeraldii</th><td>M.J.Bayly 1942</td><td>MEL 2383574A</td><td>OL591211</td><td>–</td><td>−32.63</td><td>121.55</td><td>Australia: Western Australia.</td></tr><tr><th>Philotheca gardneri</th><td>M.J.Bayly 1949</td><td>MEL 2383569A</td><td>OL591212</td><td>–</td><td>−33.46</td><td>119.99</td><td>Australia: Western Australia, Ravensthorpe.</td></tr><tr><th>Philotheca glabra</th><td>M.J.Bayly 1917</td><td>MEL 2383617A</td><td>–</td><td>OL660714; OM744146; OL660688; OL697871</td><td>−29.59</td><td>117.15</td><td>Australia: Western Australia, Great Northern Highway, 1 km south of White Wells turn-off.</td></tr><tr><th>Philotheca linearis</th><td>J.J.Bruhl 2864</td><td>NE 113630</td><td>–</td><td>OL660715; OM744157; OL660689; OL697872</td><td>–</td><td>–</td><td>–</td></tr><tr><th>Philotheca linearis</th><td>M.J.Bayly 186</td><td>MELUD105844a</td><td>–</td><td>OL660716; OM744158; OL660690; OL697873</td><td>−31.05</td><td>145.24</td><td>Australia: New South Wales, Beside Gidgee Road, 17.7 km west of Louth-Cobar Road.</td></tr><tr><th>Philotheca myoporoides subsp. myoporoides</th><td>M.J.Bayly 2565</td><td>MELUD114860a</td><td>OL591213</td><td>–</td><td>−37.53</td><td>145.52</td><td>Australia: Victoria, Toolangi.</td></tr><tr><th>Philotheca nodiflora subsp. lasiocalyx</th><td>M.J.Bayly 1962</td><td>MELUD105840a</td><td>OL591214</td><td>–</td><td>–</td><td>–</td><td>Australia: Cultivated ex. Kuranga.</td></tr><tr><th>Philotheca pachyphylla</th><td>M.J.Bayly 1932</td><td>MEL 2383619A</td><td>–</td><td>OL660717; OM744153; OL660691; OL697874</td><td>−31.04</td><td>120.84</td><td>Australia: Western Australia, 3.8 km west of Bullabulling on Great Eastern Highway.</td></tr><tr><th>Philotheca pinoides</th><td>M.J.Bayly 11</td><td>MELUD105845a</td><td>OL591215</td><td>–</td><td>−29.8</td><td>115.47</td><td>Australia: Western Australia, east of Eneabba.</td></tr><tr><th>Philotheca pungens</th><td>M.J.Bayly 1872</td><td>MELUD105849a</td><td>OL591216</td><td>–</td><td>−36.92</td><td>142.43</td><td>Australia: Victoria, Grampians.</td></tr><tr><th>Philotheca rhomboidea</th><td>M.J.Bayly 1950</td><td>MEL 2383576A</td><td>–</td><td>OL660718; OM744154; OL660692; OL697875</td><td>−33.36</td><td>119.87</td><td>Australia: Western Australia, Lake King-Ravensthorpe Road, near Lake Chidnup.</td></tr><tr><th>Philotheca salsolifolia subsp. salsolifolia</th><td>M.J.Bayly 1961</td><td>MELUD105841a</td><td>–</td><td>OL660719; OM744169; OL660693; OL697876</td><td>–</td><td>–</td><td>Australia: Victoria, Cultivated in Rosanna.</td></tr><tr><th>Philotheca sericea</th><td>M.J.Bayly 1916</td><td>MEL 2383579A</td><td>–</td><td>OL660720; OM744151; OL660694; OL697877</td><td>−29.29</td><td>117.48</td><td>Australia: Western Australia, ~20 km west-south-west of Paynes Find.</td></tr><tr><th>Philotheca spicata</th><td>M.J.Bayly 1907</td><td>MEL 2383588A</td><td>OL591217</td><td>–</td><td>−30.07</td><td>115.53</td><td>Australia: Western Australia.</td></tr><tr><th>Philotheca sporadica</th><td>M.T.Mathieson 217</td><td>MEL 2339573A</td><td>–</td><td>OL660721; OM744160; OL660695; OL697878</td><td>−27.07</td><td>150.84</td><td>Australia: Queensland, Condamine Highway, east of Kogan.</td></tr><tr><th>Philotheca thryptomenoides</th><td>M.J.Bayly 1921</td><td>MEL 2383582A</td><td>–</td><td>OL660722; OM744162; OL660696; OL697879</td><td>−29.78</td><td>117.03</td><td>Australia: Western Australia, Great Northern Highway 93.8 km south-west of Paynes Find.</td></tr><tr><th>Philotheca tomentella</th><td>M.J.Bayly 1913</td><td>MEL 2383616A</td><td>OL591218</td><td>–</td><td>−28.44</td><td>116.04</td><td>Australia: Western Australia, Pindar.</td></tr><tr><th>Philotheca trachyphylla</th><td>M.J.Bayly 1900</td><td>MELUD105850a</td><td>OL591219</td><td>–</td><td>−37.73</td><td>148.09</td><td>Australia: Victoria, Nowa Nowa.</td></tr><tr><th>Philotheca tubiflora</th><td>M.J.Bayly 1934</td><td>MELUD105854a</td><td>–</td><td>OL660723; OM744152; OL660697; OL697880</td><td>−28.3</td><td>122.6</td><td>Australia: Western Australia.</td></tr><tr><th>Philotheca verrucosa</th><td>M.J.Bayly 2199</td><td>MELUD121711a</td><td>–</td><td>OL660724; OM744166; OL660698; OL697881</td><td>−37.89</td><td>144.22</td><td>Australia: Victoria, Brisbane Ranges.</td></tr><tr><th>Philotheca virgata</th><td>M.J.Bayly 266</td><td>MELUD105843a</td><td>–</td><td>OL660725; OM744148; OL660699; OL697882</td><td>−37.4</td><td>149.26</td><td>Australia: Victoria, Coopracambra National Park, Mount Kaye walking track.</td></tr><tr><th>Picrella glandulosa</th><td>M.J.Bayly 2104</td><td>MEL 2383678A</td><td>OL591220</td><td>–</td><td>−20.32</td><td>164.42</td><td>New Caledonia: Province Nord.</td></tr><tr><th>Zanthoxylum simulans</th><td>see Hou et al. (2018)</td><td>NC037482</td><td></td><td></td><td></td><td></td><td></td></tr><tr><th>Zieria arborescens subsp. arborescens</th><td>M.J.Bayly 2566</td><td>MELUD114863a</td><td>OL591223</td><td>–</td><td>−37.53</td><td>145.51</td><td>Australia: Victoria, Toolangi.</td></tr></tbody></table>Genbank numbers for Sanger sequences are listed in the order: psb A– trn H; rpl 32– trn L; trn L– trn F; trn Q– rps 16. Samples included from previous existing sequences on GenBank are in bold.

Fig. 8 in Plastid phylogenomics of the Eriostemon group (Rutaceae; Zanthoxyloideae): support for major clades and investigation of a backbone polytomy

Fig. 8. Seed morphology in Clade 1, showing the adaxially central raphe in Philotheca section Philotheca, Drummondita and Geleznowia, and the basal raphe in Philotheca section Erionema. (a–c) Seeds typical of P. section Philotheca [P. linearis; G.J. White s.n., NE 52727]. (d–f) Seeds typical of Drummondita [D. longifolia; H. Demarz 10361, PERTH 959707]. (g–i) Seeds typical of Geleznowia [G. verrucosa; L. Broadhurst 14, PERTH 5547822]. (j–l) Seeds typical of P. section Erionema [P. verrucosa; MJB 249, HO523410]. (a, d, g, j) Lateral views. (b, e, h, k) Adaxial views. (c, f, i, l) Longitudinal sections through the raphe. (a, g) Drawn with the placental portion of endocarp still attached to the seed; for all other drawings the placental endocarp was removed. Drawings are modified from Bayly (2001) and are not to scale.

Fig. 1 in Plastid phylogenomics of the Eriostemon group (Rutaceae; Zanthoxyloideae): support for major clades and investigation of a backbone polytomy

Fig. 1. Distributions of (a) Geleznowia, (b) Drummondita, (c) Philotheca section Philotheca, (d) Philotheca section Erionema, (e) Philotheca section Cyanochlamys, (f) Philotheca section Corynonema. Distributions are also indicated for (b) D. borealis and D. calida (the only species of Drummondita outside of Western Australia, (d) P. brucei (the only species of section Erionema in Western Australia, and (f) the three disjunct species comprising section Corynonema. Maps are based on filtered specimen records from The Australasian Virtual Herbarium (see https://avh.chah.org.au).

Fig. 7 in Plastid phylogenomics of the Eriostemon group (Rutaceae; Zanthoxyloideae): support for major clades and investigation of a backbone polytomy

Fig. 7. Flowers, carpels (with pitted surfaces), and fasciculate stem hairs of Muiriantha and Philotheca section Cyanochlamys (voucher numbers indicated in brackets): (a, d, f) Muiriantha hassellii [MJB 2574, MELUD155083a], (b, e, h) Philotheca nodiflora subsp. lasiocalyx [b, e, MJB 108, MELU; h, MJB 1962, MELUD105840a], (c, f, i) Philotheca spicata [c, f, MJB 9, MELU; i, MJB 10, MELU]. Scale bars: 500 μm, in micrographs of carpels (inset close-up images of pits are not to scale), and 100 μm, in micrographs of hairs (arrows indicate fasciculate hairs in h, i that are obscured by other hairs).

Fig. 6 in Plastid phylogenomics of the Eriostemon group (Rutaceae; Zanthoxyloideae): support for major clades and investigation of a backbone polytomy

Fig. 6. Results of topology tests for the backbone polytomy in the Eriostemon group. (a) The 15 possible resolutions of the polytomy (for the four supported clades) that testing was conducted on, ordered by most likely to least likely from left to right, top to bottom (note: the hard polytomy resolution is not depicted). (b) Plot of log likelihoods for each possible topology. The topology matching the most likely tree is denoted by a star, and the hard polytomy topology is denoted by a triangle.

Fig. 5 in Plastid phylogenomics of the Eriostemon group (Rutaceae; Zanthoxyloideae): support for major clades and investigation of a backbone polytomy

Fig. 5. Results of the likelihood-mapping analysis of loci. (a) Plot of phylogenetic informativeness of individual loci, where a higher percentage of fully resolved quartets for a locus indicates greater support for tree-like evolution. Dashed lines on the plot indicate the three cut-off values that were tested for potentially improving phylogenetic resolution of the polytomy (i.e. 50, 60 and 70%). Bars along the x-axis denote the cluster that each locus was placed in during the analysis of tree space; some loci were excluded from the tree-space analysis, owing to incomplete representation of samples. (b) Phylogenetic network (NeighborNet) showing splits of the backbone polytomy; constructed from a concatenated alignment of all loci with>60% of quartets fully resolved. For Crowea, EA, eastern Australia; WA, western Australia.

Fig. 3 in Plastid phylogenomics of the Eriostemon group (Rutaceae; Zanthoxyloideae): support for major clades and investigation of a backbone polytomy

Fig. 3. Maximum-likelihood phylogeny of the Eriostemon group produced from IQ-TREE analysis of the unpartitioned 'phylogenomic' alignment of samples with full plastome data. UFboot and SH-aLRT support for branches are denoted by dots at nodes, where open circles denote 100% UFboot and 100% SH-aLRT support and closed circles denote 100% UFboot and <100% SH-aLRT support, and no dot present on the node indicates <100% for both metrics. Concordance factors are provided next to node dots, with gene concordance (gCF) positioned above site concordance (sCF). Posterior probabilities from the MrBayes 50% majority-rule consensus tree are superimposed to the left of the concordance factors in bold type at nodes where branch support is not maximal (i.e. <1; dashes occur where a branch was non-existent in the MrBayes tree). Short, unsupported branches that effectively form a polytomy in the backbone of the tree are coloured red. Red asterisks at nodes indicate branches that are well supported in our phylogeny but were unsupported in the plastid sequence phylogeny of Duretto et al. (2023). Sections of Philotheca are listed in grey, and are linked to corresponding taxa by dashed lines.

Fig. 4 in Plastid phylogenomics of the Eriostemon group (Rutaceae; Zanthoxyloideae): support for major clades and investigation of a backbone polytomy

Fig. 4. Phylogenetic relationships in Clade 1. Maximum-likelihood phylogeny produced from IQ-TREE analysis of the 'supermatrix' alignment of combined full plastome and Sanger sequences. UFboot support for branches is positioned above posterior probabilities from the MrBayes 50% majority-rule consensus tree of the same dataset. Relationships in other clades are identical to those in Fig. 3. Unsupported short branches in the backbone of the Eriostemon group have been manually collapsed to a polytomy. Asterisks denote samples represented only by Sanger sequence data. The MrBayes and IQ-TREE phylogenies differed in the placement of Philotheca angustifolia; this incongruence is shown by red-dashed branches that indicate the topology recovered by MrBayes (posterior probability value relevant to this is in red). Black triangle, Philotheca s.str. (largely equivalent to Philotheca sensu Wilson 1971); black square, Philotheca 'Nigrostipulae' (largely equivalent to Eriostemon section Nigrostipulae sensu Wilson 1970), as discussed in the text.

Fig. 2 in Plastid phylogenomics of the Eriostemon group (Rutaceae; Zanthoxyloideae): support for major clades and investigation of a backbone polytomy

Fig. 2. Flowers of Drummondita, Geleznowia and Philotheca section Philotheca: (a) Geleznowia verrucosa, (b) Drummondita hassellii, (c) D. longifolia, (d) Philotheca basistyla, (e) P. difformis subsp. smithiana, (f) P. tubiflora, (g) P. coccinea, and (h) P. salsolifolia. Photographs: Michael Bayly.

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Figure 2 in Model-based approach to test hard polytomies in the Eulaemus clade of the most diverse South American lizard genus Liolaemus (Liolaemini, Squamata)

Figure 2. Description of hypothesis-testing procedures. Models were constructed in MESQUITE v. 2.74 and simulations of 1000 gene trees were generated for each of the 13 loci for each of the eight models (step 1). We then compared the simulated trees for each locus against the corresponding model in order to obtain an approximation of a probability distribution of expected deep coalescence events (step 2). Finally, we counted the number of deep coalescences of the real gene tree within the model and obtained the probability of observing that value given the model (step 3). If the empirical data fell outside the 95% confidence interval, then the hypothesized number of deep coalescence events for that gene tree (real data) is not expected under the specified model, thus rejecting that hypothesis.

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Figure 4 in Model-based approach to test hard polytomies in the Eulaemus clade of the most diverse South American lizard genus Liolaemus (Liolaemini, Squamata)

Figure 4. Simulation results. Total number of loci supporting each model after comparisons of the data against 1000 simulated data sets for each locus for each model, and compared with data. We compared the 1000 simulated trees against the model and obtained an approximation of a probability distribution of the deep coalescences expected, and then compared the number of deep coalescences on the observed tree (real data) against the probability distribution. Here, we the show number of loci that fell within the 95% confidence intervals of those probability distributions.

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Figure 3 in Model-based approach to test hard polytomies in the Eulaemus clade of the most diverse South American lizard genus Liolaemus (Liolaemini, Squamata)

Figure 3. Empirical Eulaemus phylogenetic hypotheses. Phylogenetic results using the full matrix of 188 taxa (A, B) and a reduced set of 40 taxa chosen to subsample the largest clades (C to F). A, topology recovered from the concatenated matrix; B, species tree recovered by the minimizing deep coalescence (MDC) approach; C, *BEAST results of partial matrix with representatives of largest clades; values on branches are estimated divergences times (upper) and posterior probability values estimated (lower) or separated by a slash; bold branches represent nodal support> 0.90; D, BEST result; E, MDC result of partial matrix; and F, partial concatenated matrix. In (A), (D), and (F) nodes with support <0.90 were collapsed. The calibration point for estimation of divergence times is shown with a white circle in the node corresponding to the divergence of the Eulaemus and Liolaemus clades.

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Phylogenomic discordance suggests polytomies along the backbone of the large genus Solanum

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Table 3 in Plastid phylogenomics of the Eriostemon group (Rutaceae; Zanthoxyloideae): support for major clades and investigation of a backbone polytomy

Table 3. Alignment Information.<table><tbody><tr><th>Item</th><th>Number of variable sites</th><th>Number of parsimony-informative sites</th><th>Number of constant sites</th><th>Total length (bp)</th></tr></tbody><tbody><tr><th>Phylogenomic alignment</th><td>30 038</td><td>16 845</td><td>76 847</td><td>106 885</td></tr><tr><th>Supermatrix alignment</th><td>30 057</td><td>16 895</td><td>76 657</td><td>106 714</td></tr></tbody></table>

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Table 2 in Plastid phylogenomics of the Eriostemon group (Rutaceae; Zanthoxyloideae): support for major clades and investigation of a backbone polytomy

Table 2. Taxonomic coverage of sampling from the Eriostemon group.<table><tbody><tr><th>Genus</th><th>Section</th><th>Number of species sampled (full plastome data)</th><th>Number of species sampled (Sanger data)</th><th>Total number of species</th></tr></tbody><tbody><tr><th>Asterolasia</th><td></td><td>2</td><td></td><td>19</td></tr><tr><th>Chorilaena</th><td></td><td>3</td><td></td><td>4</td></tr><tr><th>Correa</th><td></td><td>3</td><td></td><td>11</td></tr><tr><th>Crowea</th><td></td><td>3</td><td></td><td>3</td></tr><tr><th>Diplolaena</th><td></td><td>2</td><td></td><td>15</td></tr><tr><th>Drummondita</th><td></td><td>3</td><td>(1)</td><td>11</td></tr><tr><th>Eriostemon</th><td></td><td>2</td><td></td><td>2</td></tr><tr><th>Geleznowia</th><td></td><td>1</td><td>(1)</td><td>2</td></tr><tr><th>Halfordia</th><td></td><td>1</td><td></td><td>1–3</td></tr><tr><th>Leionema</th><td></td><td>4</td><td></td><td>28</td></tr><tr><th>Muiriantha</th><td></td><td>1</td><td></td><td>1</td></tr><tr><th>Myrtopsis</th><td></td><td>1</td><td></td><td>~9</td></tr><tr><th>Nematolepis</th><td></td><td>3</td><td></td><td>7</td></tr><tr><th>Neoschmidia</th><td></td><td>1</td><td></td><td>2</td></tr><tr><th>Phebalium</th><td></td><td>7</td><td></td><td>38</td></tr><tr><th>Philotheca</th><td>Corynonema</td><td>3</td><td></td><td>3</td></tr><tr><th></th><td>Cyanochlamys</td><td>2</td><td></td><td>2</td></tr><tr><th></th><td>Erionema</td><td>2</td><td>2</td><td>15</td></tr><tr><th></th><td>Philotheca</td><td>4</td><td>20 (2)</td><td>34</td></tr><tr><th>Total</th><td></td><td>48</td><td>22 (4)</td><td>~206–209</td></tr></tbody></table>Numbers in parentheses indicate where the same species was sampled in both the full plastome and Sanger datasets. Total number of species includes described taxa only (i.e. phrase-named species are excluded).