Brandley Matthew C, Bragg Jason G, Singhal Sonal, Chapple David G, Jennings Charlotte K, Lemmon Alan R, Lemmon Emily Moriarty, Thompson Michael B, Moritz Craig
School of Biological Sciences, Heydon-Laurence Building A08, University of Sydney, Sydney, NSW, 2006, Australia.
New York University - Sydney, The Rocks, NSW, 2000, Australia.
BMC Evol Biol. 2015 Apr 11;15:62. doi: 10.1186/s12862-015-0318-0.
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.
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.
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.
使用靶向富集和转录组学方法的高通量测序能够快速构建包含数百到数千个基因座的系统发育基因组数据集。这些进展使得能够获取前所未有的核苷酸序列数据，但也带来了新的问题。鉴于靶向富集的基因座通常高度保守，它们在不同分类尺度上，特别是在种内/系统地理学尺度上的信息含量如何？我们使用澳大拉西亚石龙子科优功石龙子属（有鳞目：石龙子科）的蜥蜴来研究这个问题。我们对43个个体的415个锚定杂交富集（AHE）基因座进行了测序，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个基因座），包括卡氏石龙子属、闪光石龙子属和腐食石龙子属几个物种内的多个系统地理学谱系。我们在属间、种间和系统地理学尺度上评估了这些基因座的系统发育信息含量。作为对系统地理学尺度实用性的进一步测试，我们使用锚定杂交富集基因座，通过带有迁移的溯祖模型来推断谱系分化参数。
两个数据集的系统发育分析在所有分类水平上都推断出了支持度非常高的树。此外，AHE基因座对密切相关谱系之间分歧时间的估计与先前的种群水平分析大致一致。
锚定富集基因座在深层系统发育和系统地理学尺度上是有用的。尽管在整个澳大拉西亚优功石龙子属系统发育中总体系统发育支持度很高，但仍存在一些相互矛盾或未解决的关系，特别是关于伪莫氏石龙子属、隐睑石龙子属的位置以及塔斯马尼亚岛雪石龙子属密切相关物种之间的关系。
