ddRAD-seq phylogenetics based on nucleotide, indel, and presence-absence polymorphisms: Analyses of two avian genera with contrasting histories
ddRAD-seq phylogenetics based on nucleotide, indel, and presence-absence polymorphisms: Analyses of two avian genera with contrasting histories
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DOI：
10.1016/j.ympev.2015.07.026
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发表时间：
2016-01-01
影响因子：
4.1
通讯作者：
Sorenson, Michael D.
中科院分区：
文献类型：
--
作者：
DaCosta, Jeffrey M.;Sorenson, Michael D.
基因测序(GBS)方法使分子生态学领域发生了革命性的变化，但它们在分子系统发育学中的应用仍然受到一定的限制。此外，大多数基于大型GBS数据集的系统发育研究依赖于对串联数据的分析，而不是明确说明基因座之间的系谱随机性的物种树方法。我们探索了“双酶切”限制性内切酶相关DNA测序技术(ddRAD-seq)在斑翅目火雀(雌蝇科)和维杜亚幼体寄生雀(病毒科)系统发育分析中的应用。正如预期的那样，由于限制性内切酶酶切位点多态性的积累，样本之间共享的同源基因座数量与遗传距离呈负相关。然而，对于每个属，我们获得了所有样本中相似的3000个共有的基因座的数据集，包括一个更远的亲缘关系较远的外群分类单元。对于所有的样本组合，我们获得了1000个同源基因座，尽管在雌雀和寄生雀之间的差异类似于20My。除了核苷酸多态外，ddRAD-seq数据还产生了大量的插入多态和位点有无多态，在串联简约分析的背景下，所有这些数据都比mtDNA序列数据具有更高的一致性指数。使用单个基因树或单核苷酸多态作为输入的物种树方法产生的结果与串联数据的分析大体一致，特别是对似乎具有良好分解的分叉历史的斑节藻类。Vidua的结果在方法和数据集上也大体上是一致的，尽管节点支持和不同树种方法的结果差异更大。Vidua中较低的基因树一致性可能是其独特的进化历史的结果，包括寄主转移导致的快速物种形成，以及由于不完全生殖隔离而偶尔发生的杂交和导入。我们的结论是，ddRAD-seq对于生成稳健的系统发育数据集是一种经济高效的方法，特别是对于密切相关的物种和属的分析。(C)2015 Elsevier Inc.保留所有权利。
Genotype-by-sequencing (GBS) methods have revolutionized the field of molecular ecology, but their application in molecular phylogenetics remains somewhat limited. In addition, most phylogenetic studies based on large GBS data sets have relied on analyses of concatenated data rather than species tree methods that explicitly account for genealogical stochasticity among loci. We explored the utility of "double-digest" restriction site-associated DNA sequencing (ddRAD-seq) for phylogenetic analyses of the Lagonosticta firefinches (family Estrildidae) and the Vidua brood parasitic finches (family Viduidae). As expected, the number of homologous loci shared among samples was negatively correlated with genetic distance due to the accumulation of restriction site polymorphisms. Nonetheless, for each genus, we obtained data sets of similar to 3000 loci shared in common among all samples, including a more distantly related outgroup taxon. For all samples combined, we obtained >1000 homologous loci despite similar to 20 my divergence between estrildid and parasitic finches. In addition to nucleotide polymorphisms, the ddRAD-seq data yielded large sets of indel and locus presence-absence polymorphisms, all of which had higher consistency indices than mtDNA sequence data in the context of concatenated parsimony analyses. Species tree methods, using individual gene trees or single nucleotide polymorphisms as input, generated results broadly consistent with analyses of concatenated data, particularly for Lagonosticta, which appears to have a well resolved, bifurcating history. Results for Vidua were also generally consistent across methods and data sets, although nodal support and results from different species tree methods were more variable. Lower gene tree congruence in Vidua is likely the result of its unique evolutionary history, which includes rapid speciation by host shift and occasional hybridization and introgression due to incomplete reproductive isolation. We conclude that ddRAD-seq is a cost-effective method for generating robust phylogenetic data sets, particularly for analyses of closely related species and genera. (C) 2015 Elsevier Inc. All rights reserved.