Sensitivity of the polyDetect computational pipeline for phylogenetic analyses
Sensitivity of the polyDetect computational pipeline for phylogenetic analyses
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DOI：
10.1016/j.ab.2019.113516
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发表时间：
2020-03-15
影响因子：
2.9
通讯作者：
Batzer, Mark A.
中科院分区：
文献类型：
--
作者：
Storer, Jessica M.;Walker, Jerilyn A.;Batzer, Mark A.
Alu元素是一种强大的系统发育标记。最近开发的计算流水线PolyDetect与高拷贝数Alu插入相结合，以前曾被用来帮助解析Papio狒狒的系统发育，具有很高的统计学支持。在这里，PolyDetect方法被应用于新大陆猴子(NWM)内极具争议的Cebiae系统发育。PolyDetect方法依赖于被比较物种之间短读取序列数据的保守同源性/同一性，以准确地将预测的共享AlU插入映射到每个唯一的侧翼序列。综合评估的结果表明，在本研究中分析的四个宿科属之间的非重复DNA序列中没有足够的序列同源性/同源性延伸，从而使这一策略在系统发育上是可行的。近2000万年的进化分化导致了短小的读数数据中随机序列的衰减，掩盖了测试物种中潜在的同源元素。这些分析表明，当高质量的组装基因组无法用于感兴趣的分类群时，PolyDetect管道最适合于解决最近出现分歧的谱系的系统发育问题。
Alu elements are powerful phylogenetic markers. The combination of a recently-developed computational pipeline, polyDetect, with high copy number Alu insertions has previously been utilized to help resolve the Papio baboon phylogeny with high statistical support. Here, the polyDetect method was applied to the highly contentious Cebidae phylogeny within New World monkeys (NWM). The polyDetect method relies on conserved homology/identity of short read sequence data among the species being compared to accurately map predicted shared Alu insertions to each unique flanking sequence. The results of this comprehensive assessment indicate that there were insufficient sequence homology/identity stretches in non-repeated DNA sequences among the four Cebidae genera analyzed in this study to make this strategy phylogenetically viable. The similar to 20 million years of evolutionary divergence of the Cebidae genera has resulted in random sequence decay within the short read data, obscuring potentially orthologous elements in the species tested. These analyses suggest that the polyDetect pipeline is best suited to resolving phylogenies of more recently diverged lineages when high-quality assembled genomes are not available for the taxa of interest.