Orthologous repeats and mammalian phylogenetic inference
Orthologous repeats and mammalian phylogenetic inference
复制标题
DOI：
10.1101/gr.3493405
复制
发表时间：
2005-07-01
期刊：
影响因子：
7
通讯作者：
Bafna, V
中科院分区：
文献类型：
--
作者：
Bashir, A;Ye, C;Bafna, V
确定物种之间的系统发育关系是一个困难的问题，许多系统发育关系仍然没有解决，即使在真兽类哺乳动物之间也是如此。重复元件为系统发育分析提供了极好的标记，因为它们的进化模式主要是无同质性和单向的。历史上，使用重复元件的系统发育研究一直依赖于生物学方法，如聚合酶链式反应分析，而计算推理仅限于几个孤立的重复序列。在这里，我们提出了一种新的计算方法，用于从部分序列数据中使用同源重复来推断系统发育关系。我们应用我们的方法重建了28种哺乳动物的系统发育，使用了从NISC比较测序计划获得的序列数据中获得的1000多个同源重复序列。由此产生的系统发育具有强大的自举数字，并与使用完全不同的数据和方法获得的先前研究的结果大体一致。此外，我们还阐明了进化史上一些有争议的方面。随着可用部分序列数据的快速扩展，重复元件的计算分析为系统发育推断的未来带来了巨大的希望。
Determining phylogenetic relationships between species is a difficult problem, and many phylogenetic relationships remain unresolved, even among eutherian mammals. Repetitive elements provide excellent markers for phylogenetic analysis, because their mode of evolution is predominantly homoplasy-free and unidirectional. Historically, phylogenetic studies using repetitive elements have relied on biological methods Such as PCR analysis, and computational inference is limited to a few isolated repeats. Here, we present a novel computational method for inferring phylogenetic relationships from partial sequence data using orthologous repeats. We apply our method to reconstructing the phylogeny of 28 mammals, using more than 1000 orthologous repeats obtained from sequence data available from the NISC Comparative Sequencing Program. The resulting phylogeny has robust bootstrap numbers, and broadly matches results from previous studies which were obtained using entirely different data and methods. In addition, we shed light on some of the debatable aspects of the phylogeny. With rapid expansion of available partial sequence data, Computational analysis of repetitive elements holds great promise for the future of phylogenetic inference.