The influence sampling design on species tree inference: a new relationship for the New World chickadees (Aves: Poecile)

In this study, we explore the long-standing issue of how many loci are needed to infer accurate phylogenetic relationships, and whether loci with particular attributes (i.e., parsimony informativeness, variability, gene tree resolution) outperform others. To do so, we use an empirical dataset consisting of the seven species of chickadees (Aves: Paridae), an analytically tractable, recently diverged group, and well studied ecologically but lacking a nuclear phylogeny. We estimate relationships using 40 nuclear loci and mitochondrial DNA using four coalescent-based species tree inference methods (BEST, *BEAST, STEM, STELLS). Collectively, our analyses contrast with previous studies and support a sister relationship between the Black-capped and Carolina Chickadee, two superficially similar species that hybridize along a long zone of contact. Gene flow is a potential source of conflict between nuclear and mitochondrial gene trees, yet, we find a significant, albeit low, signal of gene flow....本研究旨在探讨一个长期存在的科学议题：需多少个基因座方可推断出准确的系统发育关系，以及具备特定属性（即简约信息量、变异度、基因树分辨率）的基因座是否优于其他基因座。为此，我们采用一套实证数据集，该数据集涵盖7种山雀（鸟纲：山雀科）。该类群在分析上易于处理、分化时间较近，且生态研究较为充分，但目前尚未构建其核基因组系统发育。我们利用40个核基因座与线粒体DNA序列，结合四种基于溯祖理论的物种树推断方法（BEST、*BEAST、STEM、STELLS），对物种间的系统发育关系进行估算。综合而言，本研究的分析结果与既往研究存在分歧，支持黑顶山雀（Black-capped Chickadee）与卡罗莱纳山雀（Carolina Chickadee）互为姐妹群的结论；这两个物种外观相似度较高，且在漫长的接触带区域内发生杂交。基因流或为核基因树与线粒体基因树之间产生冲突的潜在诱因，然而本研究仍检测到了虽强度较低但统计学显著的基因流信号……