Rapidly evolving taxa are excellent models for understanding the mechanisms that give rise to biodiversity. However, developing an accurate historical framework for comparative analysis of such lineages remains a challenge due to ubiquitous incomplete lineage sorting and introgression. Here, we use a whole-genome alignment, multiple locus-sampling strategies, and summary-tree and SNP-based species-tree methods to infer a species tree for eastern North American Neodiprion species, a clade of pine-feeding sawflies (Order: Hymenopteran; Family: Diprionidae). We recovered a well-supported species tree that—except for three uncertain relationships—was robust to different strategies for analyzing whole-genome data. Nevertheless, underlying gene-tree discordance was high. To understand this genealogical variation, we used multiple linear regression to model site concordance factors estimated in 50-kb windows as a function of several genomic predictor variables. We found that site concordance factors tended to be higher in regions of the genome with more parsimony-informative sites, fewer singletons, less missing data, lower GC content, more genes, lower recombination rates, and lower D-statistics (less introgression). Together, these results suggest that incomplete lineage sorting, introgression, and genotyping error all shape the genomic landscape of gene-tree discordance in Neodiprion. More generally, our findings demonstrate how combining phylogenomic analysis with knowledge of local genomic features can reveal mechanisms that produce topological heterogeneity across genomes.

中文翻译：

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全基因组揭示了新双齿锯蝇基因-树不一致的进化关系和机制


快速进化的分类群是理解产生生物多样性的机制的极好模型。然而，由于普遍存在的不完整谱系分类和渗入，开发一个准确的历史框架来对此类谱系进行比较分析仍然是一个挑战。在这里，我们使用全基因组比对、多基因座采样策略以及基于摘要树和 SNP 的物种树方法来推断北美东部 Neodiprion 物种的物种树，这是以松树为食的锯蝇的一个分支（订单号：膜翅目;科：Diprionidae）。我们恢复了一个得到充分支持的物种树，除了三个不确定的关系外，该树对分析全基因组数据的不同策略具有鲁棒性。尽管如此，潜在的基因-树不一致程度很高。为了理解这种谱系变异，我们使用多元线性回归对在 50 kb 窗口中估计的位点一致性因子进行建模，作为几个基因组预测变量的函数。我们发现，在基因组中具有更多简洁信息位点、较少单例、较少缺失数据、较低 GC 含量、更多基因、较低重组率和较低 D 统计量（较少渗入）的区域，位点一致性因子往往更高。总之，这些结果表明，不完整的谱系分选、渗入和基因分型错误都塑造了 Neodiprion 中基因-树不一致的基因组景观。更一般地说，我们的研究结果展示了将系统发育分析与局部基因组特征的知识相结合如何揭示产生跨基因组拓扑异质性的机制。