Phylogenomics of phrynosomatid lizards: conflicting signals from sequence capture versus restriction site associated DNA sequencing.
Phylogenomics of phrynosomatid lizards: conflicting signals from sequence capture versus restriction site associated DNA sequencing.
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DOI：
10.1093/gbe/evv026
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发表时间：
2015-02-07
影响因子：
3.3
通讯作者：
Linkem CW
中科院分区：
文献类型：
--
作者：
Leaché AD;Chavez AS;Jones LN;Grummer JA;Gottscho AD;Linkem CW
序列捕获和限制性位点相关DNA测序（RADseq）是用于获得大量基因座以用于系统发育分析的流行方法。这些方法通常用于收集不同进化时间尺度的数据;序列捕获主要用于获得保守的基因座，而RADseq被设计用于发现适合于群体遗传学或地理学分析的单核苷酸多态性（SNP）。跨越“最近”和“深层”时间尺度的系统发育问题可以从任何一种类型的数据中受益，但缺乏直接比较这两种方法的研究。我们比较了序列捕获和双消化RADseq（ddRADseq）数据估计的北美phrynosomatid蜥蜴，一个物种丰富和多样化的组，包含9个属，开始多样化约55马。序列捕获导致584个位点，提供了一个一致的和强大的同源性使用串联和物种树推断。然而，从ddRADseq数据估计的同源性对用于确定同源性、检测旁系同源物和过滤缺失数据的生物信息学步骤敏感。SNP树之间的拓扑冲突不限于任何特定的时间尺度，而是与短的内部分支相关。最大SNP组装的物种树分析，其中也包括最缺失的数据，支持匹配序列捕获树的拓扑结构。这种偏好的进化史为无耳蜥蜴属Holbrookia和Copphosaurus的并系性提供了强有力的支持，表明无耳蜥蜴的形态要么进化了两次，要么进化了一次，随后在Callisaurus中消失了。
Sequence capture and restriction site associated DNA sequencing (RADseq) are popular methods for obtaining large numbers of loci for phylogenetic analysis. These methods are typically used to collect data at different evolutionary timescales; sequence capture is primarily used for obtaining conserved loci, whereas RADseq is designed for discovering single nucleotide polymorphisms (SNPs) suitable for population genetic or phylogeographic analyses. Phylogenetic questions that span both “recent” and “deep” timescales could benefit from either type of data, but studies that directly compare the two approaches are lacking. We compared phylogenies estimated from sequence capture and double digest RADseq (ddRADseq) data for North American phrynosomatid lizards, a species-rich and diverse group containing nine genera that began diversifying approximately 55 Ma. Sequence capture resulted in 584 loci that provided a consistent and strong phylogeny using concatenation and species tree inference. However, the phylogeny estimated from the ddRADseq data was sensitive to the bioinformatics steps used for determining homology, detecting paralogs, and filtering missing data. The topological conflicts among the SNP trees were not restricted to any particular timescale, but instead were associated with short internal branches. Species tree analysis of the largest SNP assembly, which also included the most missing data, supported a topology that matched the sequence capture tree. This preferred phylogeny provides strong support for the paraphyly of the earless lizard genera Holbrookia and Cophosaurus, suggesting that the earless morphology either evolved twice or evolved once and was subsequently lost in Callisaurus.