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Figure 7 in Phylogenomics of Characidae, a hyper-diverse Neotropical freshwater fish lineage, with a phylogenetic classification including four families (Teleostei: Characiformes)

Figure 7. Phylogeny of Acestrorhamphidae and subfamilies Thayeriinae, Rhoadsiinae, Grundulinae, and Acestrorhamphinae based on 1348 nuclear loci of ultraconserved elements (538 472 bp). Numbers near nodes represent bootstrap support.

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Figure 1 in Phylogenomics of Characidae, a hyper-diverse Neotropical freshwater fish lineage, with a phylogenetic classification including four families (Teleostei: Characiformes)

Figure 1. Accumulation curve of the original descriptions of current valid genera of Characidae s.l. highlighting the three periods of active descriptions of genera: (i) 1777–1900, (ii) 1900–1955, and (iii) 1955–present.

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Figure 5 in Phylogenomics of Characidae, a hyper-diverse Neotropical freshwater fish lineage, with a phylogenetic classification including four families (Teleostei: Characiformes)

Figure 5. Phylogeny of Acestrorhamphidae and subfamilies Oxybryconinae, Trochilocharacinae, Stygichthyinae, Megalamphodinae, and Stichonodontinae based on 1348 nuclear loci of ultraconserved elements (538 472 bp). Numbers near nodes represent bootstrap support.

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.

opencc-zeroDec 2016View details →

Data from: Phylogenomics using target-restricted assembly resolves intra-generic relationships of parasitic lice (Phthiraptera: Columbicola)

Parasitic "wing lice" (Phthiraptera: Columbicola) and their dove and pigeon hosts are a well-recognized model system for coevolutionary studies at the intersection of micro- and macroevolution. Selection on lice in microevolutionary time occurs as pigeons and doves defend themselves against lice by preening. In turn, behavioral and morphological adaptations of the lice improve their ability to evade host defense. Over macroevolutionary time wing lice tend to cospeciate with their hosts; yet, some species of Columbicola have switched to new host species. Understanding the ecological and evolutionary factors that influence coadaptation and codiversification in this system will substantially improve our understanding of coevolution in general. However, further work is hampered by the lack of a robust phylogenetic framework for Columbicola spp. and their hosts. Previous attempts to resolve the phylogeny of Columbicola based on sequences from a few genes provided limited support. Here we apply a new approach, target restricted assembly, to assemble 977 orthologous gene sequences from whole-genome sequence data generated from very small, ethanol-preserved specimens, representing up to 61 species of wing lice. Both concatenation and coalescent methods were used to estimate the species tree. These two approaches yielded consistent and well-supported trees with 90% of all relationships receiving 100% support, which is a substantial improvement over previous studies. We used this new phylogeny to show that biogeographic ranges are generally conserved within clades of Columbicola wing lice. Limited inconsistencies are probably attributable to intercontinental dispersal of hosts, and host switching by some of the lice.

opencc-zeroDec 2014View details →

Data from: Orchid phylogenomics and multiple drivers of their extraordinary diversification

Orchids are the most diverse family of angiosperms, with over 25 000 species, more than mammals, birds and reptiles combined. Tests of hypotheses to account for such diversity have been stymied by the lack of a fully resolved broad-scale phylogeny. Here, we provide such a phylogeny, based on 75 chloroplast genes for 39 species representing all orchid subfamilies and 16 of 17 tribes, time-calibrated against 17 angiosperm fossils. A supermatrix analysis places an additional 144 species based on three plastid genes. Orchids appear to have arisen roughly 112 million years ago (Mya); the subfamilies Orchidoideae and Epidendroideae diverged from each other at the end of the Cretaceous; and the eight tribes and three previously unplaced subtribes of the upper epidendroids diverged rapidly from each other between 37.9 and 30.8 Mya. Orchids appear to have undergone one significant acceleration of net species diversification in the orchidoids, and two accelerations and one deceleration in the upper epidendroids. Consistent with theory, such accelerations were correlated with the evolution of pollinia, the epiphytic habit, CAM photosynthesis, tropical distribution (especially in extensive cordilleras), and pollination via Lepidoptera or euglossine bees. Deceit pollination appears to have elevated the number of orchid species by one-half but not via acceleration of the rate of net diversification. The highest rate of net species diversification within the orchids (0.382 sp sp−1 My−1) is 6.8 times that at the Asparagales crown.

opencc-zeroDec 2013View details →

Data from: A hybrid phylogenetic–phylogenomic approach for species tree estimation in African Agama lizards with applications to biogeography, character evolution, and diversification

Africa is renowned for its biodiversity and endemicity, yet little is known about the factors shaping them across the continent. African Agama lizards (45 species) have a pan-continental distribution, making them an ideal model for investigating biogeography. Many species have evolved conspicuous sexually dimorphic traits, including extravagant breeding coloration in adult males, large adult male body sizes, and variability in social systems among colorful versus drab species. We present a comprehensive time-calibrated species tree for Agama, and their close relatives, using a hybrid phylogenetic-phylogenomic approach that combines traditional Sanger sequence data from five loci for 57 species (146 samples) with anchored phylogenomic data from 215 nuclear genes for 23 species. The Sanger data are analyzed using coalescent-based species tree inference using *BEAST, and the resulting posterior distribution of species trees is attenuated using the phylogenomic tree as a backbone constraint. The result is a time-calibrated species tree for Agama that includes 95% of all species, multiple samples for most species, strong support for the major clades, and strong support for most of the initial divergence events. Diversification within Agama began approximately 23 million years ago (Ma), and separate radiations in Southern, East, West, and Northern Africa have been diversifying for > 10 Myr. A suite of traits (morphological, coloration, and sociality) are tightly correlated and show a strong signal of high morphological disparity within clades, whereby the subsequent evolution of convergent phenotypes has accompanied diversification into new biogeographic areas.

opencc-zeroJul 2021View details →

UCE phylogenomics, detection of a putative hybrid population, and one older mitogenomic node age of Batrachuperus salamanders

The prevalence of incomplete lineage sorting complicates the examination of hybridization and species-level paraphyly with gene trees of a small number of loci. In Asian mountain salamanders of the genus Batrachuperus, possible hybridization and species paraphyly had been identified by utilizing mitochondrial genealogy and fixed allozyme differences. Here we sampled 2909 UCEs in 44 local populations from all six Batrachuperus species, inferred gene and species trees, compared them with mitochondrial and allozyme results, and examined the potential hybridization and species paraphyly. The clustering pattern of single-locus trees, increased proportion of heterozygous SNPs, allele frequency-based migration edge estimation, and intrapopulation long branches (as expected from an increase of genetic lineage and nucleotide diversity) support that an eastern B. karlschmidti population has experienced admixture with B. tibetanus. On the 2909-UCE concatenated and species trees, lower nodal supports were observed when similar proportions of loci agreed with alternative topologies, i.e., a reciprocal monophyly between a Pengxian lineage and the remainder of B. pinchonii (0.379) or a paraphyly of the latter with respect to Pengxian (0.362). The UCE phylogenomics agreed with the relatively recent groupings in the allozyme dendrogram. Despite incomplete lineage sorting, the mitochondrial trees were similar to the UCE trees for deeper relationships of the genus. However, one significant branch-length level discordance was identified. The branch between the common ancestor of B. daochengensis and B. yenyuanensis and common ancestor of the genus was approximately three times shorter on the mitochondrial tree than on the UCE tree, suggesting that the split of the mitochondrial lineages was likely a few million years earlier than the split of species. This finding supports considering possible ancestral polymorphism when interpreting different divergence dates estimated from mitochondrial and genome-wide data.

opencc-zeroDec 2017View details →

Data from: Phylogenomic signatures of ancient introgression in a rogue lineage of darters (Teleostei: Percidae)

Evolutionary history is typically portrayed as a branching phylogenetic tree, yet not all evolution proceeds in a purely bifurcating manner. Introgressive hybridization is one process that results in reticulate evolution. Most known examples of genome-wide introgression occur among closely related species with relatively recent common ancestry; however, we present evidence for ancient hybridization and genome-wide introgression between major stem lineages of darters, a species-rich clade of North American freshwater fishes. Previous attempts to resolve the relationships of darters have been confounded by the uncertain phylogenetic resolution of the lineage Allohistium. In this study we investigate the phylogenomics of darters, specifically the relationships of Allohistium, through analyses of ~30,000 RADseq loci sampled from 112 species. Our phylogenetic inferences are based on traditional approaches in combination with strategies that accommodate reticulate evolution. These analyses result in a novel phylogenetic hypothesis for darters that includes ancient introgression involving Allohistium and other two major darter lineages, minimally occurring 20 million years ago. Darters offer a compelling case for the necessity of incorporating phylogenetic networks in reconstructing the evolutionary history of diversification in species-rich lineages. We anticipate that the growing wealth of genomic data for clades of non-model organisms will reveal more examples of ancient hybridization, eventually requiring a re-evaluation of how evolutionary history is visualized and utilized in macroevolutonary investigations.

opencc-zeroDec 2017View details →

Data from: A comprehensive and dated phylogenomic analysis of butterflies

Butterflies (Papilionoidea), with over 18,000 described species [1], have captivated naturalists and scientists for centuries. They play a central role in the study of speciation, community ecology, biogeography, climate change, and plant-insect interactions and include many model organisms and pest species [2, 3]. However, a robust higher-level phylogenetic framework is lacking. To fill this gap, we inferred a dated phylogeny by analyzing the first phylogenomic dataset, including 352 loci (> 150,000 bp) from 207 species representing 98% of tribes, a 35-fold increase in gene sampling and 3-fold increase in taxon sampling over previous studies [4]. Most data were generated with a new anchored hybrid enrichment (AHE) [5] gene kit (BUTTERFLY1.0) that includes both new and frequently used (e.g., [6]) informative loci, enabling direct comparison and future dataset merging with previous studies. Butterflies originated around 119 million years ago (mya) in the late Cretaceous, but most extant lineages diverged after the Cretaceous-Paleogene (K-Pg) mass-extinction 65 mya. Our analyses support swallowtails (Papilionidae) as sister to all other butterflies, followed by skippers (Hesperiidae) + the nocturnal butterflies (Hedylidae) as sister to the remainder, indicating a secondary reversal from diurnality to nocturnality. The whites (Pieridae) were strongly supported as sister to brush-footed butterflies (Nymphalidae) and blues + metalmarks (Lycaenidae and Riodinidae). Ant association independently evolved once in Lycaenidae and twice in Riodinidae. This study overturns prior notions of the taxon's evolutionary history, as many long-recognized subfamilies and tribes are para- or polyphyletic. It also provides a much-needed backbone for a revised classification of butterflies and for future comparative studies including genome evolution and ecology.

opencc-zeroJul 2021View details →

Data from: Phylogenomic species delimitation dramatically reduces species diversity in an Antarctic adaptive radiation

Application of genetic data to species delimitation often builds confidence in delimitations previously hypothesized using morphological, ecological, and geographic data and frequently yields recognition of previously-undescribed cryptic diversity. However, a recent critique of genomic data-based species delimitation approaches is that they have the potential to conflate population structure with species diversity, resulting in taxonomic oversplitting. The need for an integrative approach to species delimitation, in which molecular, morphological, ecological, and geographic lines of evidence are evaluated together, is becoming increasingly apparent. Here, we integrate phylogenetic, population genetic, and coalescent analyses of genome-wide sequence data with investigation of variation in multiple morphological traits to delimit species within the Antarctic barbeled plunderfishes (Artedidraconidae: Pogonophryne). Pogonophryne currently comprises 29 valid species, most of which are distinguished solely by variation in ornamentation of the mental barbel that projects from the lower jaw, a structure previously shown to vary widely within a single species. However, our genomic and phenotypic analyses result in a dramatic reduction in the number of distinct species recognized within the clade, providing evidence to support the recognition of no more than six species. We propose to synonymize 24 of the currently recognized species with five species of Pogonophryne. We find genomic and phenotypic evidence for a new species of Pogonophryne from specimens collected in the Ross Sea. Our findings represent a rare example in which application of molecular data provides evidence of taxonomic oversplitting on the basis of morphology, clearly demonstrating the utility of an integrative species delimitation framework.