Resolving the phylogeny of rapidly radiating lineages presents a challenge when building the Tree of Life. An Old World avian family Prunellidae (Accentors) comprises twelve species that rapidly diversified at the Pliocene–Pleistocene boundary. Here we investigate the phylogenetic relationships of all species of Prunellidae using a chromosome-level de novo assembly of Prunella strophiata and 36 high-coverage resequenced genomes. We use homologous alignments of thousands of exonic and intronic loci to build the coalescent and concatenated phylogenies and recover four different species trees. Topology tests show a large degree of gene tree-species tree discordance but only 40–54% of intronic gene trees and 36–75% of exonic genic trees can be explained by incomplete lineage sorting and gene tree estimation errors. Estimated branch lengths for three successive internal branches in the inferred species trees suggest the existence of an empirical anomaly zone. The most common topology recovered for species in this anomaly zone was not similar to any coalescent or concatenated inference phylogenies, suggesting presence of anomalous gene trees. However, this interpretation is complicated by the presence of gene flow because extensive introgression was detected among these species. When exploring tree topology distributions, introgression, and regional variation in recombination rate, we find that many autosomal regions contain signatures of introgression and thus may mislead phylogenetic inference. Conversely, the phylogenetic signal is concentrated to regions with low-recombination rate, such as the Z chromosome, which are also more resistant to interspecific introgression. Collectively, our results suggest that phylogenomic inference should consider the underlying genomic architecture to maximize the consistency of phylogenomic signal.

中文翻译：

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基因流和异常区使快速辐射鸟类家族（Prunellidae）的系统发育学推断变得复杂

在构建生命之树时，解决快速辐射谱系的系统发育是一个挑战。旧大陆鸟类 Prunellidae (Accentors) 包括 12 个物种，它们在上新世-更新世边界迅速多样化。在这里，我们使用夏枯草的染色体水平从头组装和 36 个高覆盖率重测序基因组来研究所有夏枯草科物种的系统发育关系。我们使用数千个外显子和内含子基因座的同源比对来构建合并和串联的系统发育并恢复四种不同的物种树。拓扑测试显示基因树与物种树存在很大程度的不一致，但只有 40-54% 的内含子基因树和 36-75% 的外显子基因树可以通过不完整的谱系排序和基因树估计错误来解释。推断物种树中三个连续内部分支的估计分支长度表明存在经验异常区域。该异常区域中物种恢复的最常见拓扑与任何合并或串联推理系统发育并不相似，表明存在异常基因树。然而，这种解释因基因流的存在而变得复杂，因为在这些物种中检测到了广泛的基因渗入。在探索树拓扑分布、基因渗入和重组率的区域变异时，我们发现许多常染色体区域包含基因渗入的特征，因此可能会误导系统发育推断。相反，系统发育信号集中在重组率低的区域，例如 Z 染色体，这些区域也更能抵抗种间渗入。总的来说，我们的结果表明系统发育基因组推断应考虑潜在的基因组结构，以最大限度地提高系统发育信号的一致性。