Phylogenomic discordance suggests polytomies along the backbone of the large genus Solanum.
Phylogenomic discordance suggests polytomies along the backbone of the large genus Solanum.
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DOI：
10.1002/ajb2.1827
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发表时间：
2022-04
影响因子：
3
通讯作者：
Sarkinen, Tiina
中科院分区：
文献类型：
--
作者：
Gagnon, Edeline;Hilgenhof, Rebecca;Orejuela, Andres;McDonnell, Angela;Sablok, Gaurav;Aubriot, Xavier;Giacomin, Leandro;Gouvea, Yuri;Bragionis, Thamyris;Stehmann, Joao Renato;Bohs, Lynn;Dodsworth, Steven;Martine, Christopher;Poczai, Peter;Knapp, Sandra;Sarkinen, Tiina
关键词：
进化研究需要坚实的系统发育框架，但越来越多的基因组数据揭示了许多生物体基因组之间和基因组内部的基因树之间的不一致拓扑结构。其中一些不一致表明可能仍然无法解决的多分割。在这里，我们调查了茄属中基因树不一致的程度，茄属是最大的开花植物属之一，包括栽培的马铃薯，番茄和茄子，以及24种次要作物植物。使用未发表和公开可用的桑格序列构建了一个密集采样的茄属物种水平的遗传学，该序列占所有可接受物种（742种）的60%。9个区域（ITS、蜡质和7个质体标记）。通过检查具有140种物种的完整质体组数据集和具有39种茄属物种的核靶捕获数据集（被子植物353探针集）来测试该拓扑结构的稳健性。虽然茄属的分类框架保持稳定，但观察到从靶捕获和质体组数据集生成的系统发育树之间的基因树冲突和不一致。后者对应于短节间分支的区域，网络分析和多分支测试表明，骨干是由三个多分支发现在不同的进化深度。最强烈的不一致区域，靠近茄属植物的冠节，可能代表硬多形分裂。我们认为，不完整的血统排序，由于快速多样化是最有可能的原因，这些多分支，拥抱的不确定性，他们是至关重要的理解大型和快速辐射谱系的进化。
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. A densely sampled species‐level phylogeny of Solanum is built using unpublished and publicly available Sanger sequences comprising 60% of all accepted species (742 spp.)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). 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. 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.
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DOI：
10.1093/bioinformatics/btx063
发表时间：
2017-06-15
期刊：
Bioinformatics (Oxford, England)
影响因子：
--
作者：
Brown JW;Walker JF;Smith SA
通讯作者：
Smith SA
影响因子：
2.4
作者：
Duvall, Melvin R.;Burke, Sean, V;Clark, Dylan C.
通讯作者：
Clark, Dylan C.
影响因子：
10.7
作者：
Darriba, Diego;Posada, David;Flouri, Tomas
通讯作者：
Flouri, Tomas
影响因子：
3.7
作者：
Amiryousefi A;Hyvönen J;Poczai P
通讯作者：
Poczai P
影响因子：
6.5
作者：
Baker WJ;Bailey P;Barber V;Barker A;Bellot S;Bishop D;Botigué LR;Brewer G;Carruthers T;Clarkson JJ;Cook J;Cowan RS;Dodsworth S;Epitawalage N;Françoso E;Gallego B;Johnson MG;Kim JT;Leempoel K;Maurin O;Mcginnie C;Pokorny L;Roy S;Stone M;Toledo E;Wickett NJ;Zuntini AR;Eiserhardt WL;Kersey PJ;Leitch IJ;Forest F
通讯作者：
Forest F