Phylogenomics of a rapid radiation: is chromosomal evolution linked to increased diversification in north american spiny lizards (Genus Sceloporus)?
Phylogenomics of a rapid radiation: is chromosomal evolution linked to increased diversification in north american spiny lizards (Genus Sceloporus)?
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DOI：
10.1186/s12862-016-0628-x
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发表时间：
2016-03-22
影响因子：
3.4
通讯作者：
de Oca AN
中科院分区：
文献类型：
--
作者：
Leaché AD;Banbury BL;Linkem CW;de Oca AN
解决快速进化多样化导致的短系统发育分支通常需要大量的基因座。我们收集了来自585个核位点（541个超保守元件和44个蛋白质编码基因）的靶向序列捕获数据，以估计北美属Sceloporus中鬣蜥之间的系统发育关系。我们测试了多样化率的变化，以确定快速辐射的属与染色体进化。我们获得的Sceloporus使用连接和基于聚结的物种树推理的单系和几乎所有主要群体之间的相互关系提供了强有力的支持。多样性分析支持了大约2000万至2500万年前Sceloporus物种发生的一个速率变化，这与物种形成速率从0.06种/百万年（Ma）增加到0.15种/Ma有关。后验概率为这个率移发生在分支导致Sceloporus物种组表现出增加的染色体多样性是高的（后验概率= 0.997）。尽管高水平的基因树的不一致性，我们能够估计的Sceloporus，解决了以前的分析较少的位点所造成的一些分类学问题的一个基因组树。我们建议使用这个新的基因组树的分类变化有助于澄清属中主要物种群的数量和组成。我们的研究为染色体进化与北美Sceloporus的快速分化和辐射之间的假定联系提供了新的证据。本文的在线版本（doi：10.1186/s12862-016-0628-x）包含补充材料，可供授权用户使用。
Resolving the short phylogenetic branches that result from rapid evolutionary diversification often requires large numbers of loci. We collected targeted sequence capture data from 585 nuclear loci (541 ultraconserved elements and 44 protein-coding genes) to estimate the phylogenetic relationships among iguanian lizards in the North American genus Sceloporus. We tested for diversification rate shifts to determine if rapid radiation in the genus is correlated with chromosomal evolution. The phylogenomic trees that we obtained for Sceloporus using concatenation and coalescent-based species tree inference provide strong support for the monophyly and interrelationships among nearly all major groups. The diversification analysis supported one rate shift on the Sceloporus phylogeny approximately 20–25 million years ago that is associated with the doubling of the speciation rate from 0.06 species/million years (Ma) to 0.15 species/Ma. The posterior probability for this rate shift occurring on the branch leading to the Sceloporus species groups exhibiting increased chromosomal diversity is high (posterior probability = 0.997). Despite high levels of gene tree discordance, we were able to estimate a phylogenomic tree for Sceloporus that solves some of the taxonomic problems caused by previous analyses of fewer loci. The taxonomic changes that we propose using this new phylogenomic tree help clarify the number and composition of the major species groups in the genus. Our study provides new evidence for a putative link between chromosomal evolution and the rapid divergence and radiation of Sceloporus across North America. The online version of this article (doi:10.1186/s12862-016-0628-x) contains supplementary material, which is available to authorized users.