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.

本研究聚焦于两个长期存在的学术问题：其一，需要多少个基因座（loci）方可推断出准确的系统发育关系；其二，具备特定属性（即简约信息量、变异性、基因树分辨率）的基因座是否相较于其他基因座更具优势。为解答上述问题，本研究采用一套经验数据集，该数据集涵盖7种山雀（Aves: Paridae）——这是一类分析上易于处理、近期分化且生态学研究充分，但尚未构建核基因组系统发育树的类群。研究中，我们利用40个核基因座与线粒体DNA，结合4种基于溯祖模型的物种树推断方法（BEST、BEAST、STEM、STELLS）对物种间亲缘关系进行推断。整体分析结果与既往研究存在差异，支持黑顶山雀与卡罗莱纳山雀互为姐妹群；这两个外观相似的物种沿狭长的接触带发生自然杂交。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，但本研究仍检测到了显著且虽程度较低的基因流信号。研究结果显示，仅需相对少量高信息量基因座即可构建准确的物种树，但要实现准确的参数估计，则需要显著更多的基因座。本研究可为旨在推断近缘类群系统发育关系与种群参数的研究者设计采样方案提供经验参考依据。