Data from: Considering gene flow when using coalescent methods to delimit lineages of North American pitvipers of the genus Agkistrodon

Examining species diversity and mechanisms of speciation using coalescent models provides a framework for how regional diversity is accrued, even in well-studied areas such as the Nearctic. It is likely, that gene flow among closely-related species with adjacent distributions may be common. However, the absence of gene flow is a primary assumption of many phylogeographical methods that produce species trees and delimit species using Bayesian or likelihood functions in a coalescent framework. In the present study, we examine delimitation when gene flow between species is present using empirical datasets from two species of North American pitvipers of the genus Agkistrodon. We also use niche modelling to determine whether these young lineages occur in distinct environmental niches. To manage the problem of gene flow between species, we first identify admixed individuals, demonstrate that gene flow has occurred, and then identify the impact of alternative population assignments of admixed individuals on delimitation posterior probabilities. In addition, we examine the influence of mitochondrial genes relative to other loci combined in coalescent analyses that delimit species. Here, we find that the copperheads (Agkistrodon contortrix) and the cottonmouths (Agkistrodon piscivorus) are each composed of two distinct species, with each occupying different niches. Importantly, we find that species can be delimited when the amount of gene flow between lineages is low, although the methods are acutely sensitive to population assignment of individuals.利用溯祖模型（coalescent models）研究物种多样性与物种形成机制，可为区域物种多样性的积累过程提供理论框架，即便在新北区（Nearctic）这类已被充分研究的区域亦不例外。亲缘关系相近且分布相邻的物种间存在基因流，这一情况大概率较为普遍。然而，诸多基于溯祖框架、借助贝叶斯（Bayesian）方法或似然函数（likelihood functions）构建物种树并开展物种界定的系统地理学（phylogeographical）研究方法，均以物种间不存在基因流为核心前提假设。本研究以蝮属（Agkistrodon）的两种北美颊窝蝰蛇的经验数据集（empirical datasets）为基础，针对物种间存在基因流的场景开展物种界定研究。此外，我们通过生态位建模（niche modelling）分析这些年轻演化支是否占据独特的环境生态位。为解决物种间基因流带来的分析难题，我们首先识别混血个体（admixed individuals）并证实基因流确实发生，随后探究混血个体的不同种群归属方案对物种界定后验概率（posterior probabilities）的影响。此外，我们还分析了线粒体基因在用于物种界定的联合多位点溯祖分析中的相对影响力。本研究发现，铜头蝮（Agkistrodon contortrix）与棉口蝮（Agkistrodon piscivorus）各自均包含两个独立物种，且二者分别占据不同的环境生态位。值得注意的是，尽管相关方法对个体的种群归属方案极为敏感，但当演化支间的基因流水平较低时，仍可实现准确的物种界定。