Phylogenetic trees based on genome-wide sequence data may not always represent the true evolutionary history for a variety of reasons. One process that can lead to incorrect reconstruction of species phylogenies is gene flow, especially if interspecific gene flow has affected large parts of the genome. We investigated phylogenetic relationships within a clade comprising eight species of passerine birds (Phylloscopidae, Phylloscopus, leaf warblers) using one de novo genome assembly and 78 resequenced genomes. On the basis of hypothesis-exclusion trials based on D-statistics, phylogenetic network analysis, and demographic inference analysis, we identified ancient gene flow affecting large parts of the genome between one species and the ancestral lineage of a sister species pair. This ancient gene flow consistently caused erroneous reconstruction of the phylogeny when using large amounts of genome-wide sequence data. In contrast, the true relationships were captured when smaller parts of the genome were analyzed, showing that the “winner-takes-all democratic majority tree” is not necessarily the true species tree. Under this condition, smaller amounts of data may sometimes avoid the effects of gene flow due to stochastic sampling, as hidden reticulation histories are more likely to emerge from the use of larger data sets, especially whole-genome data sets. In addition, we also found that genomic regions affected by ancient gene flow generally exhibited higher genomic differentiation but a lower recombination rate and nucleotide diversity. Our study highlights the importance of considering reticulation in phylogenetic reconstructions in the genomic era.[Bifurcation; introgression; recombination; reticulation; Phylloscopus.]

中文翻译：

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由于古代基因流，大多数基因组基因座歪曲了鸟类辐射的系统发育


由于多种原因，基于全基因组序列数据的系统发育树可能并不总是代表真实的进化历史。可能导致物种系统发育不正确重建的一个过程是基因流，特别是当种间基因流影响了基因组的大部分时。我们使用一种从头基因组组装和 78 个重新测序的基因组，研究了由 8 种雀形目鸟类（柳莺科、柳莺属、叶莺）组成的进化枝内的系统发育关系。在基于 D 统计、系统发育网络分析和人口统计推断分析的假设排除试验的基础上，我们确定了影响一个物种和一对姐妹物种的祖先谱系之间大部分基因组的古代基因流。当使用大量全基因组序列数据时，这种古老的基因流始终导致系统发育的错误重建。相比之下，当分析基因组的较小部分时，就捕获了真正的关系，这表明“赢者通吃的民主多数树”不一定是真正的物种树。在这种情况下，较小的数据量有时可能会避免由于随机采样而导致的基因流的影响，因为隐藏的网状历史更有可能从较大的数据集（尤其是全基因组数据集）的使用中出现。此外，我们还发现受古代基因流影响的基因组区域通常表现出较高的基因组分化，但重组率和核苷酸多样性较低。我们的研究强调了在基因组时代的系统发育重建中考虑网状结构的重要性。基因渗入；重组；网状；柳叶属。]