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.

本研究旨在探讨长期存在的核心学术问题：需要多少个基因座（loci）才能准确推断系统发育关系（phylogenetic relationships），以及具有特定属性（即简约信息性（parsimony informativeness）、变异性（variability）、基因树分辨率（gene tree resolution））的基因座是否优于其他基因座。为此，我们采用一套经验数据集展开分析，该数据集涵盖7种山雀科（Paridae）鸟类，该类群具备分析易处理性、近期分化的特征，且生态学研究较为充分，但目前尚未建立核基因组系统发育框架。我们借助40个核基因座与线粒体DNA（mitochondrial DNA），采用4种基于溯祖理论的物种树推断方法（coalescent-based species tree inference methods，即BEST、BEAST、STEM、STELLS）对物种间亲缘关系进行估算。总体而言，本研究的分析结果与既往研究存在差异，支持黑顶山雀（Black-capped Chickadee）与卡罗莱纳山雀（Carolina Chickadee）互为姐妹群的关系——这两种外观相似的物种在广阔的接触带内存在杂交现象。基因流可能是核基因树与线粒体基因树之间产生冲突的潜在诱因，但我们仍检测到了显著且程度较低的基因流信号。本研究结果表明，仅需相对少量高信息含量的基因座即可准确估算物种树，但要实现参数的精准估计则需要显著更多的基因座。本研究为旨在推断近缘类群系统发育与种群参数的研究者设计采样方案提供了经验参考基准。