Data from: 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. Our results suggest that relatively few loci with high information content may be sufficient for estimating an accurate species tree, but that substantially more loci are necessary for accurate parameter estimation. We provide an empirical reference point for researchers designing sampling protocols with the purpose of inferring phylogenies and population parameters of closely related taxa.本研究旨在探讨一个长期存在的科学问题：需要多少个基因座（locus）才能推断出准确的系统发育关系，以及具有特定属性（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，我们采用了一套实证数据集，其研究对象为山雀科（Paridae）山雀属的7个物种——该类群易于分析、分化时间较近，且已有较为充分的生态学研究，但目前尚无核基因组系统发育相关研究。我们利用40个核基因座与线粒体DNA，结合4种基于溯祖理论的物种树推断方法（BEST、*BEAST、STEM、STELLS）对物种间的演化关系进行推断。综合来看，本研究的分析结果与以往研究存在差异，并支持黑头山雀与卡罗莱纳山雀互为姊妹支系的结论——这两个物种外形相似，且在较长的接触带内发生杂交。核基因树与线粒体基因树之间的冲突可能源于基因流，但本研究仍检测到了虽强度较低却显著的基因流信号。研究结果表明，仅需数量相对较少的高信息量基因座即可准确推断物种树，但要实现准确的参数估计，则需要大幅增加基因座的数量。本研究可为旨在推断近缘类群系统发育关系与群体参数的研究者设计采样方案提供实证参考依据。