A Phylogenomic Perspective on the Radiation of Ray-Finned Fishes Based upon Targeted Sequencing of Ultraconserved Elements (UCEs).
A Phylogenomic Perspective on the Radiation of Ray-Finned Fishes Based upon Targeted Sequencing of Ultraconserved Elements (UCEs).
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DOI：
10.1371/journal.pone.0065923
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发表时间：
2013
期刊：
影响因子：
3.7
通讯作者：
Alfaro ME
中科院分区：
文献类型：
--
作者：
Faircloth BC;Sorenson L;Santini F;Alfaro ME
鳐鱼是脊椎动物的主要辐射物种，种类超过32,000种。尽管分子系统发育学已经开始在生命之树的这一巨大部分中解开主要的进化关系，但目前还没有广泛可用的方法来有效地收集鱼类的系统发育数据，这使得大规模平行测序技术在解决射线鳍鱼类主要辐射方面的巨大潜力尚未实现。在这里，我们通过靶向富集超保守核DNA元件（UCEs）及其侧翼序列，为长期存在的关于鳐鱼主要类群多样化的问题提供了基因组视角。我们的工作流程产生的数据集比传统方法产生的数据集大几个数量级，非常适合与博物馆标本一起工作。对UCE数据集的分析恢复了在浅时间尺度和深时间尺度上得到充分支持的系统发育，支持了Amia和Lepisosteus （Holostei）之间的单系关系，并揭示了骨舌形和骨舌形是最早分化的硬骨鱼谱系。我们的方法还揭示了UCE区域及其侧翼序列的序列捕获为解决鳐鱼的系统发育关系提供了巨大的潜力。
Ray-finned fishes constitute the dominant radiation of vertebrates with over 32,000 species. Although molecular phylogenetics has begun to disentangle major evolutionary relationships within this vast section of the Tree of Life, there is no widely available approach for efficiently collecting phylogenomic data within fishes, leaving much of the enormous potential of massively parallel sequencing technologies for resolving major radiations in ray-finned fishes unrealized. Here, we provide a genomic perspective on longstanding questions regarding the diversification of major groups of ray-finned fishes through targeted enrichment of ultraconserved nuclear DNA elements (UCEs) and their flanking sequence. Our workflow efficiently and economically generates data sets that are orders of magnitude larger than those produced by traditional approaches and is well-suited to working with museum specimens. Analysis of the UCE data set recovers a well-supported phylogeny at both shallow and deep time-scales that supports a monophyletic relationship between Amia and Lepisosteus (Holostei) and reveals elopomorphs and then osteoglossomorphs to be the earliest diverging teleost lineages. Our approach additionally reveals that sequence capture of UCE regions and their flanking sequence offers enormous potential for resolving phylogenetic relationships within ray-finned fishes.
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DOI：
10.1073/pnas.0607004104
发表时间：
2007-04-03
影响因子：
11.1
作者：
Edwards, Scott V.;Liu, Liang;Pearl, Dennis K.
通讯作者：
Pearl, Dennis K.
影响因子：
12.3
作者：
Davidson WS;Koop BF;Jones SJ;Iturra P;Vidal R;Maass A;Jonassen I;Lien S;Omholt SW
通讯作者：
Omholt SW
影响因子：
12.3
作者：
Adey A;Morrison HG;Asan;Xun X;Kitzman JO;Turner EH;Stackhouse B;MacKenzie AP;Caruccio NC;Zhang X;Shendure J
通讯作者：
Shendure J
影响因子：
14.9
作者：
Katoh K;Kuma K;Toh H;Miyata T
通讯作者：
Miyata T
影响因子：
10.7
作者：
Genner, Martin J.;Seehausen, Ole;Turner, Georg F.
通讯作者：
Turner, Georg F.