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47 results for “plastid phylogenomics”
Untying the Gordian Knot of plastid phylogenomic conflict: a case from ferns
<p>Phylogenomic studies based on plastid genome have resolved the recalcitrant relationships among various plants, yet the phylogeny of Dennstaedtiaceae at the taxonomic level remains unresolved due to conflicting plastid genes, limited molecular data and incomplete taxon sampling of previous studies. The present study generated 31 new plastid genomes of Dennstaedtiaceae (9 genera, 30 species) and combined 41 publicly available sequences of plastid genome (including 24 families, 26 genera, 41 species) to solve and explore the evolution of Dennstaedtiaceae. In order to minimize the impact of systematic errors on the resolution of phylogenetic inference, we applied six strategies to generate 30 datasets based on CDS, Spacer, and All datasets, and two tree inference methods (maximum-likelihood, ML; and multispecies coalescent, MSC) to comprehensively analyze the plastome-scale data. Besides, the phylogenetic signal among all loci was quantified for the controversial node using the ML framework, and the phylogenetic hypotheses among all datasets were tested. In the species tree based on different data sets and methods, obvious conflicts were detected at the base of the polypod ferns. Meanwhile, the topology of the "CDS-codon-align-rm3" (CDS removed the third codon) matrix was selected as the primary reference or summary tree due to its analysis results are consistent, and similar to the topological structure of the amino-acid matrix. The final phylogenetic tree supported Dennstaedtiaceae as the sister group to eupolypods, and<em> Dennstaedtia</em> (sen. lat.) can divided into smaller genera, which was also supported by geographical distribution and plastid structure. This robust reconstructed phylogenetic backbone established a framework for future studies on Dennstaedtiaceae classification, evolution and diversification. The present study suggests considering plastid phylogenomic conflict when using plastid genomes. From our results, reducing saturated genes or sites can effectively mitigate the tree conflicts of distantly related taxa. Moreover, amino acid sequences may verify the accuracy of nucleotide-based phylogeny.</p>
Plastid phylogenomics of tribe Perseeae (Lauraceae) yields insights into the evolution of East Asian subtropical evergreen broad-leaved forests
<p><b>Background:</b> The East Asian subtropical evergreen broad-leaved forests (EBLFs) harbor remarkable biodiversity. However, their historical assembly remains unclear. To gain new insights into the assembly of this biome, we generated a molecular phylogeny of one of its essential elements, the tribe Perseeae (Lauraceae).</p> <p><b>Results: </b>Our plastid tree topologies were robust to analyses based on different plastid regions, data partitioning, nucleotide substitution saturation and gap handling strategies. We found that Perseeae comprised six major clades and started to colonize the subtropical EBLFs of east Asia in the early Miocene. The diversification rates of Perseeae accelerated twice in the late Miocene.</p> <p><b>Conclusions: </b>Our findings suggest that the intensified precipitation in East Asia in the early Miocene might have facilitated range expansions of the drought-sensitive subtropical EBLFs and establishment of Perseeae within this biome. By the late Miocene, assembly and diversification within the EBLFs had become rapid.</p>
FIGURE 3 in Plastid phylogenomic study of grape species and its implications for evolutionary study and conservation of Vitis
FIGURE 3. Phylogenetic tree of Vitis based on large single copy region inferred from maximum likelihood (ML) analysis based on IQTREE website. Purple branches represent species from North America, yellow branch represent species from Europe, and green branches represent species from Asia. Value of ultrafast bootstrap approximation are indicated on the branches.
FIGURE 2 in Plastid phylogenomic study of grape species and its implications for evolutionary study and conservation of Vitis
FIGURE 2. Sliding window analysis of the complete chloroplast genome of 13 Vitis taxa (window length: 600 bp, step size: 50 bp). X- axis: position of the midpoint of a window, Y-axis: nucleotide diversity of each window.
Table 1 in Plastid phylogenomics of the Eriostemon group (Rutaceae; Zanthoxyloideae): support for major clades and investigation of a backbone polytomy
<p>Table 1. Accession details for all samples.</p><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><i>Acronychia laevis</i></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><i>Asterolasia asteriscophora</i></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><i>Asterolasia drummondii</i></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><i>Boronia edwardsii</i></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><i>Boronia imlayensis</i></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><i>Boronia ternata</i></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><i>Brombya platynema</i></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><i>Chorilaena anceps</i></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><i>Chorilaena euphemiae</i></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><i>Chorilaena quercifolia</i></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><i>Correa alba</i></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><i>Correa glabra</i></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><i>Correa lawrenceana</i> var. <i>grampiana</i></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><i>Correa lawrenceana</i> var. <i>latrobeana</i></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><i>Crowea angustifolia</i> var. <i>platyphylla</i></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><i>Crowea exalata</i> subsp. <i>exalata</i></th><td>D.J.Ohlsen <i>s.n</i>.</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><i>Crowea exalata</i> var. <i>revoluta</i></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><i>Crowea saligna</i></th><td>D.J.Ohlsen <i>s.n</i>.</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><i>Cyanothamnus anemonifolius</i></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><i>Diplolaena drummondii</i></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><i>Diplolaena obovata</i></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><i>Drummondita calida</i></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><i>Drummondita fulva</i></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><i>Drummondita hassellii</i></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><i>Drummondita hassellii</i></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><i>Eriostemon australasius</i></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><i>Eriostemon banksii</i></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><i>Euodia pubifolia</i></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><i>Geleznowia verrucosa</i></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><i>Geleznowia verrucosa</i></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><i>Geleznowia verrucosa</i></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><i>Halfordia kendack</i></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><i>Halfordia kendack</i></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><i>Halfordia kendack</i></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><i>Halfordia kendack</i></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><i>Halfordia kendack</i></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><i>Leionema beckleri</i></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><i>Leionema ellipticum</i></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><i>Leionema lamprophyllum</i> subsp. <i>obovatum</i></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><i>Leionema rotundifolium</i></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><i>Medicosma cunninghamii</i></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><i>Melicope hayesii</i></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><i>Muiriantha hassellii</i></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><i>Myrtopsis</i> 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><i>Nematolepis phebalioides</i></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><i>Nematolepis squamea</i></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><i>Nematolepis wilsonii</i></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><i>Neobyrnesia suberosa</i></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><i>Neoschmidia pallida</i></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><i>Phebalium clavatum</i></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><i>Phebalium elegans</i></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><i>Phebalium longifolium</i></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><i>Phebalium multiflorum</i></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><i>Phebalium stenophyllum</i></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><i>Phebalium tuberculosum</i></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><i>Phebalium whitei</i></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><i>Philotheca acrolopha</i></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><i>Philotheca angustifolia</i> subsp. <i>angustifolia</i></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><i>Philotheca angustifolia</i> subsp. <i>montana</i></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><i>Philotheca apiculata</i></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><i>Philotheca basistyla</i></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><i>Philotheca brevifolia</i></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><i>Philotheca ciliata</i></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><i>Philotheca coateana</i></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><i>Philotheca coccinea</i></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><i>Philotheca cuticularis</i></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><i>Philotheca deserti</i> subsp. <i>deserti</i></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><i>Philotheca difformis</i> subsp. <i>difformis</i></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><i>Philotheca difformis</i> subsp. <i>smithiana</i></th><td>M.J.Bayly <i>s.n</i>.</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><i>Philotheca ericifolia</i></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><i>Philotheca fitzgeraldii</i></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><i>Philotheca gardneri</i></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><i>Philotheca glabra</i></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><i>Philotheca linearis</i></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><i>Philotheca linearis</i></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><i>Philotheca myoporoides</i> subsp. <i>myoporoides</i></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><i>Philotheca nodiflora</i> subsp. <i>lasiocalyx</i></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><i>Philotheca pachyphylla</i></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><i>Philotheca pinoides</i></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><i>Philotheca pungens</i></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><i>Philotheca rhomboidea</i></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><i>Philotheca salsolifolia</i> subsp. <i>salsolifolia</i></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><i>Philotheca sericea</i></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><i>Philotheca spicata</i></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><i>Philotheca sporadica</i></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><i>Philotheca thryptomenoides</i></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><i>Philotheca tomentella</i></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><i>Philotheca trachyphylla</i></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><i>Philotheca tubiflora</i></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><i>Philotheca verrucosa</i></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><i>Philotheca virgata</i></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><i>Picrella glandulosa</i></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><i>Zanthoxylum simulans</i></th><td>see Hou <i>et al.</i> (2018)</td><td>NC037482</td><td></td><td></td><td></td><td></td><td></td></tr><tr><th><i>Zieria arborescens</i> subsp. <i>arborescens</i></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><p>Genbank numbers for Sanger sequences are listed in the order: <i>psb</i> A– <i>trn</i> H; <i>rpl</i> 32– <i>trn</i> L; <i>trn</i> L– <i>trn</i> F; <i>trn</i> Q– <i>rps</i> 16. Samples included from previous existing sequences on GenBank are in bold.</p>
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.
Data from: First plastid phylogenomic study reveals potential cyto-nuclear discordance in the evolutionary history of Ficus L. (Moraceae)
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Untying the Gordian Knot of plastid phylogenomic conflict: a case from ferns
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Plastid phylogenomics of tribe Perseeae (Lauraceae) yields insights into the evolution of East Asian subtropical evergreen broad-leaved forests
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Data from: Organellar phylogenomics inform systematics in the green algal family Hydrodictyaceae (Chlorophyceae) and provide clues to the complex evolutionary history of plastid genomes in the green algal Tree of Life.
Premise of the study: Phylogenomic analyses across the green algae are resolving relationships at the class, order and family levels, and highlighting dynamic patterns of evolution in organellar genomes. Here we present a within-family phylogenomic study to resolve genera and species relationships in the family Hydrodictyaceae (Chlorophyceae), for which poor resolution in previous phylogenetic studies, along with divergent morphological traits, have precluded taxonomic revisions. Methods: Complete plastome sequences and mitochondrial protein-coding gene sequences were acquired from representatives of the Hydrodictyaceae using Next-Generation sequencing methods. Plastomes were characterized and gene order and content were compared with plastomes spanning the Sphaeropleales. Single-gene and concatenated-gene phylogenetic analyses of plastid and mitochondrial genes were performed. Key results: The Hydrodictyaceae contain the largest sphaeroplealean plastomes thus far fully sequenced. Conservation of plastome gene order within Hydrodictyaceae is striking compared with more dynamic patterns revealed across Sphaeropleales. Phylogenetic analyses resolve Hydrodictyon sister to a monophyletic Pediastrum, though the morphologically distinct P. angulosum and P. duplex continue to be polyphyletic. Analyses of plastid data supported the neochloridacean genus Chlorotetraëdron as sister to Hydrodictyaceae, while conflicting signal was found in the mitochondrial data. Conclusions: A phylogenomic approach resolved within-family relationships not obtainable with previous phylogenetic analyses. Denser taxon sampling across Sphaeropleales is necessary to capture patterns in plastome evolution, and further taxa and studies are needed to fully resolve sister lineage to Hydrodictyaceae and polyphyly of Pediastrum angulosum and P. duplex.
Plastid genome structure and phylogenomics of Nymphaeales: conserved gene order and new insights into relationships
<p>The plastid genomes of early-diverging angiosperms were among the first land plant plastomes investigated. Despite their importance to understanding angiosperm evolution, no investigation has so far compared gene content or gene synteny of these plastid genomes with a focus on the Nymphaeales. Here, we report an evaluation and comparison of gene content, gene synteny and inverted repeat length for a set of 15 plastid genomes of early-diverging angiosperms. Seven plastid genomes of the Nymphaeales were newly sequenced for this investigation. We compare gene order and inverted repeat (IR) length across all genomes, review the gene annotations of previously published genomes, generate a multi-gene alignment of 77 plastid-encoded genes and reconstruct the phylogenetic relationships of the taxa under study. Our results show that gene content and synteny are highly conserved across early-diverging angiosperms: All species analyzed display complete gene synteny when accounting for expansions and contractions of the IRs. This conservation was initially obscured by ambiguous and potentially incorrect gene annotations in previously published genomes. We also report the presence of intact open reading frames across all taxa analyzed. The multi-gene phylogeny displays maximum support for the families Cabombaceae and Hydatellaceae, but no support for a clade of all Nymphaeaceae. It further indicates that the genus <em>Victoria</em> is embedded within <em>Nymphaea</em>. Plastid genomes of <em>Trithuria</em> were found to deviate by numerous substitutions and length changes in the IRs. Phylogenetic analyses further indicate that a previously published plastome named <em>Nymphaea mexicana</em> falls into a clade of <em>N. odorata</em> and should be re-evaluated.</p>
Nuclear and plastid phylogenomic analyses provide insights into the reticulate evolution, species delimitation and biogeography of the Sino-Japanese disjunctive Diabelia (Caprifoliaceae)
<p>Understanding biological diversity and the mechanisms of the Sino-Japanese disjunctions are major challenge<span>s in</span><span> </span><span>eastern Asia biogeography</span><span>. </span><span>The Sino-Japanese flora has been broadly studied as an ideal model</span><span> for plant phylogeography</span><span>. </span><span>Diabelia</span><span> (Caprifoliaceae) is an</span><span> East Asian genus, </span><span>with a disjunctive distribution across </span><span>the </span><span>Sino-</span><span>J</span><span>apanese region.</span><span> However, </span><span>relationships within </span><span>Diabelia</span><span> remain elusive. In this study, </span><span>we reconstructed</span><span> the </span><span>phylogeny of </span><span>Diabelia</span><span> </span><span>and </span><span>inferred historical biogeography and evolutionary patterns</span><span> based on nuclear and </span><span>plastid</span><span> sequence</span><span>s</span><span> from </span><span>target enrichment</span><span> and genome skimming approaches, respectively</span><span>.</span><span> We found that the </span><span>main </span><span>clades</span><span> within </span><span>Diabelia</span><span> were</span><span> </span><span>discordant between nuclear and plastid trees</span><span>. </span><span>Both </span><span>nuclear and plastid </span><span>phylogenetic analys</span><span>e</span><span>s </span><span>supported</span><span> five main clades: </span><span>D. serrata</span><span>, </span><span>D. </span><span>tetrasepala</span><span>, </span><span>D. </span><span>sanguinea</span><span>, </span><span>D. </span><span>spathulata</span><span> </span><span>var. </span><span>stenophylla</span><span> and </span><span>D. </span><span>spathulata</span><span> </span><span>var. </span><span>spathulata</span><span>. Species network analyses revealed that </span><span>Diabelia</span><span> </span><span>tetrasepala</span><span> </span><span>is likely the </span><span>result </span><span>of a</span><span> hybridization event</span><span>. Divergence time estimation</span><span> and </span><span>ancestral area reconstructions</span><span> showed that </span><span>Diabelia</span><span> originated in</span><span> </span><span>Japan during </span><span>the </span><span>early Miocene, with subsequent vicariance </span><span>and dispersal </span><span>events between Japan and Korea, and between Japan and China</span><span>.</span><span> </span><span>Overall</span><span>, </span><span>our results support the division of</span><span> </span><span>Diabelia</span><span> into five main clades and </span><span>the recognition of five species in the genus.</span><span> </span><span>T</span><span>his research </span><span>provides new insights in the species delimitation and</span><span> </span><span>speciation processes of</span><span> </span><span>taxonomically complex lineages such as </span><span>Diabelia</span><span>.</span></p>
FIGURE 4 in Plastid phylogenomic study of grape species and its implications for evolutionary study and conservation of Vitis
FIGURE 4. Leaves and seeds of Vitis amurensis (A–B) and V. baihuashanensis (C–D).
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