Different genomic regions may reflect conflicting phylogenetic topologies primarily due to incomplete lineage sorting and/or gene flow. Genomic data are necessary to reconstruct the true species tree and explore potential causes of phylogenetic conflict. Here, we investigate the phylogenetic relationships of four Emberiza species (Aves: Emberizidae) and discuss the potential causes of the observed mitochondrial non-monophyly of Emberiza godlewskii (Godlewski's bunting) using phylogenomic analyses based on whole genome resequencing data from 41 birds. Analyses based on both the whole mitochondrial genome and ~39 kilobases from the non-recombining W chromosome reveal sister relationships between each the northern and southern populations of E. godlewskii with E. cioides and E. cia, respectively. In contrast, the monophyly of E. godlewskii is reflected by the phylogenetic signal of autosomal and Z chromosomal sequence data as well as demographic inference analyses, which – in combination – support the following tree topology: (((E. godlewskii, E. cia), E. cioides), E. jankowskii). Using D-statistics, we detected multiple gene flow events among different lineages, indicating pervasive introgressive hybridization within this clade. Introgression from an unsampled lineage that is sister to E. cioides or introgression from an unsampled mitochondrial + W chromosomal lineage of E. cioides into northern E. godlewskii may explain the phylogenetic conflict between the species tree estimated from genome-wide data versus mtDNA/W tree topologies. These results underscore the importance of using genomic data for phylogenetic reconstruction and species delimitation.

中文翻译：

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Emberiza鹀分支中物种树和母系遗传基因树之间的系统发育冲突（鸟纲：Emberizidae）


不同的基因组区域可能反映了冲突的系统发育拓扑，这主要是由于不完整的谱系排序和/或基因流。基因组数据对于重建真实的物种树和探索系统发育冲突的潜在原因是必要的。在这里，我们研究了四种 Emberiza 物种（鸟纲：Emberizidae）的系统发育关系，并使用基于 41 只鸟类的全基因组重测序数据的系统发育分析，讨论了观察到的 Emberiza godlewskii（Godlewski's patting）线粒体非单系的潜在原因。基于整个线粒体基因组和非重组 W 染色体约 39 KB 的分析揭示了 E. godlewskii 的北部和南部群体分别与 E. cioides 和 E. cia 之间的姐妹关系。相比之下，E. godlewskii 的单系性通过常染色体和 Z 染色体序列数据的系统发育信号以及人口统计推断分析来反映，这些分析结合起来支持以下树拓扑：(((E. godlewskii, E. cia )、E. cioides)、E. jankowskii)。使用 D 统计，我们检测到不同谱系之间的多个基因流事件，表明该进化枝内普遍存在渐渗杂交。来自 E. cioides 姐妹的未采样谱系的基因渗入，或者来自 E. cioides 的未采样线粒体 + W 染色体谱系的基因渗入到北部 E. godlewskii 中，可以解释根据全基因组数据估计的物种树与 mtDNA/W 之间的系统发育冲突树形拓扑。这些结果强调了使用基因组数据进行系统发育重建和物种界定的重要性。