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Whole genome phylogeny of Gallus : introgression and data-type effects

机译：全部基因组血症：血栓增长和数据类型效应

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BackgroundPrevious phylogenetic studies that include the four recognized species of Gallus have resulted in a number of distinct topologies, with little agreement. Several factors could lead to the failure to converge on a consistent topology, including introgression, incomplete lineage sorting, different data types, or insufficient data.MethodsWe generated three novel whole genome assemblies for Gallus species, which we combined with data from the published genomes of Gallus gallus and Bambusicola thoracicus (a member of the sister genus to Gallus ). To determine why previous studies have failed to converge on a single topology, we extracted large numbers of orthologous exons, introns, ultra-conserved elements, and conserved non-exonic elements from the genome assemblies. This provided more than 32 million base pairs of data that we used for concatenated maximum likelihood and multispecies coalescent analyses of Gallus .ResultsAll of our analyses, regardless of data type, yielded a single, well-supported topology. We found some evidence for ancient introgression involving specific Gallus lineages as well as modest data type effects that had an impact on support and branch length estimates in specific analyses. However, the estimated gene tree spectra for all data types had a relatively good fit to their expectation given the multispecies coalescent.ConclusionsOverall, our data suggest that conflicts among previous studies probably reflect the use of smaller datasets (both in terms of number of sites and of loci) in those analyses. Our results demonstrate the importance of sampling large numbers of loci, each of which has a sufficient number of sites to provide robust estimates of gene trees. Low-coverage whole genome sequencing, as we did here, represents a cost-effective means to generate the very large data sets that include multiple data types that enabled us to obtain a robust estimate of Gallus phylogeny.
机译：背景技术包括四种公认的巨大巨大的巨大物种已经导致了许多不同的拓扑，几乎没有一致。有几个因素可能导致未能收敛于一致的拓扑，包括迟滞，不完整的谱系分类，不同的数据类型或数据不足。方法为巨大的GALLUS物种生成了三种新的全基因组组件，我们将其与来自公开的基因组的数据相结合Gallus Gallus和Bambusicola Thoracicus（Gallus姐妹属的成员）。为了确定为什么先前的研究未能收敛在单一拓扑上，我们从基因组组件中提取了大量的外显子，内含子，超保守元件和保守的非外部元素。这提供了3200多亿基对数据，我们用于汇编的最大可能性和多数巨大的通池分析我们的分析，无论数据类型如何，都产生了单一，良好支持的拓扑。我们发现了一些涉及特定Gallus谱系的古代迟滞的证据以及适度的数据类型效应，对特定分析的支持和分支长度估计产生了影响。然而，给予所有数据类型的估计基因树谱对其对其期望相对较好地符合它们的期望.ConclusOverall，我们的数据表明，以前研究中的冲突可能反映了较小数据集的使用（两者都在网站数量和网站数量方面在那些分析中的基因座。我们的结果表明了采样大量基因座的重要性，每个基因座都有足够数量的基因植物的基因树。低覆盖整个基因组测序，正如我们在此，它代表了一种成本效益的方法，可以生成包括多种数据类型的非常大的数据集，使我们能够获得血管发育的鲁棒估计。

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