Evaluating the performance of anchored hybrid enrichment at the tips of the tree of life: a phylogenetic analysis of Australian Eugongylus group scincid lizards
Evaluating the performance of anchored hybrid enrichment at the tips of the tree of life: a phylogenetic analysis of Australian Eugongylus group scincid lizards
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DOI：
10.1186/s12862-015-0318-0
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发表时间：
2015-04-11
影响因子：
3.4
通讯作者：
Moritz, Craig
中科院分区：
文献类型：
--
作者：
Brandley, Matthew C.;Bragg, Jason G.;Moritz, Craig
背景：使用靶向富集和转录组方法的高通量测序可以快速构建包含数百到数千个位点的系统发育数据集。这些进步使得人们能够获得前所未有的数量的核苷酸序列数据，但它们也提出了新的问题。鉴于富集目标位点通常高度保守，它们在不同分类尺度上的信息量有多大，特别是在种内/系统地理学尺度上？我们利用澳大利亚真蜥属蜥蜴（Squamata：Scincidae）来研究这个问题。我们对 43 个个体的 415 个锚定杂合富集 (AHE) 位点进行了测序，并从 11 个个体的转录组（转录组挖掘）中挖掘了 1650 个外显子（1648 个位点），其中包括 Carlia、Lampropholis 和 Saproscincus 石龙子等几个物种内的多个系统发育谱系。我们在属间、种间和系统发育地理学尺度上评估了这些位点的系统发育信息内容。作为在系统发育地理学尺度上实用性的进一步测试，我们使用锚定杂交富集位点，使用分离与迁移的合并模型来推断谱系分歧参数。结果：两个数据集的系统发育分析在所有分类水平上推断出非常有力支持的树木。此外，AHE 基因座对密切相关的谱系之间的分化时间进行了估计，与之前的群体水平分析大致一致。结论：锚定丰富的基因座在深层系统发育和系统发育地理学尺度上很有用。尽管整个系统发育支持在整个澳大利亚真虫类群系统发育中都很高，但仍然存在一些冲突或未解决的关系，特别是在假眼属、隐斑蜥属的位置以及塔斯马尼亚尼维奥斯石龙子的密切相关物种之间的关系方面。
Background: High-throughput sequencing using targeted enrichment and transcriptomic methods enables rapid construction of phylogenomic data sets incorporating hundreds to thousands of loci. These advances have enabled access to an unprecedented amount of nucleotide sequence data, but they also pose new questions. Given that the loci targeted for enrichment are often highly conserved, how informative are they at different taxonomic scales, especially at the intraspecific/phylogeographic scale? We investigate this question using Australian scincid lizards in the Eugongylus group (Squamata: Scincidae). We sequenced 415 anchored hybrid enriched (AHE) loci for 43 individuals and mined 1650 exons (1648 loci) from transcriptomes (transcriptome mining) from 11 individuals, including multiple phylogeographic lineages within several species of Carlia, Lampropholis, and Saproscincus skinks. We assessed the phylogenetic information content of these loci at the intergeneric, interspecific, and phylogeographic scales. As a further test of the utility at the phylogeographic scale, we used the anchor hybrid enriched loci to infer lineage divergence parameters using coalescent models of isolation with migration.Results: Phylogenetic analyses of both data sets inferred very strongly supported trees at all taxonomic levels. Further, AHE loci yielded estimates of divergence times between closely related lineages that were broadly consistent with previous population-level analyses.Conclusions: Anchored-enriched loci are useful at the deep phylogeny and phylogeographic scales. Although overall phylogenetic support was high throughout the Australian Eugongylus group phylogeny, there were nonetheless some conflicting or unresolved relationships, especially regarding the placement of Pseudemoia, Cryptoblepharus, and the relationships amongst closely-related species of Tasmanian Niveoscincus skinks.