Data from: Fuzzy boundaries: color and gene flow patterns among parapatric lineages of the Western shovel-nosed snake and taxonomic implication

Accurate delineation of lineage diversity is increasingly important, as species distributions are becoming more reduced and threatened. During the last century, the subspecies category was often used to denote phenotypic variation within a species range and to provide a framework for understanding lineage differentiation, often considered incipient speciation. While this category has largely fallen into disuse, previously recognized subspecies often serve as important units for conservation policy and management when other information is lacking. In this study, we evaluated phenotypic subspecies hypotheses within shovel-nosed snakes on the basis of genetic data and considered how evolutionary processes such as gene flow influenced possible incongruence between phenotypic and genetic patterns. We used both traditional phylogenetic and Bayesian clustering analyses to infer range-wide genetic structure and spatially explicit analyses to detect possible boundary locations of lineage contact. Multilocus analyses supported three historically isolated groups with low to moderate levels of contemporary gene exchange. Genetic data did not support phenotypic subspecies as exclusive groups, and we detected patterns of discordance in areas where three subspecies are presumed to be in contact. Based on genetic and phenotypic evidence, we suggested that species-level diversity is underestimated in this group and we proposed that two species be recognized, Chionactis occipitalis and C. annulata. In addition, we recommend retention of two subspecific designations within C. annulata (C. a. annulata and C. a. klauberi) that reflect regional shifts in both genetic and phenotypic variation within the species. Our results highlight the difficultly in validating taxonomic boundaries within lineages that are evolving under a time-dependent, continuous process.精准划定谱系多样性（lineage diversity）的边界愈发关键，当前物种种群的分布范围正持续缩减且面临生存威胁。在过去一个世纪中，亚种（subspecies）这一分类单元常被用于指代物种种群范围内的表型变异（phenotypic variation），并为理解谱系分化——通常被视为初期物种形成（incipient speciation）——提供分析框架。尽管该分类单元如今已基本不再使用，但在缺乏其他相关信息的情况下，此前被认定的亚种往往仍是保护政策与管理工作中的重要单元。本研究基于遗传数据（genetic data）对铲鼻蛇类的表型亚种假说进行了评估，并探讨了基因流（gene flow）等进化过程如何影响表型与遗传模式间可能存在的不一致性。研究采用传统系统发育（phylogenetic）分析与贝叶斯聚类（Bayesian clustering）分析来推断全分布范围的遗传结构，并借助空间显式分析（spatially explicit analyses）检测谱系接触的潜在边界位置。多位点（multilocus）分析结果支持存在三个历史上相互隔离的类群，它们之间存在低至中等程度的当代基因交流（contemporary gene exchange）。遗传数据并不支持将表型亚种划分为排他性类群，且研究团队在三个亚种疑似接触的区域检测到了模式不一致的现象。基于遗传与表型证据，本研究认为该类群的物种多样性被低估，并提议认可两个有效物种：枕鳞铲鼻蛇（Chionactis occipitalis）与环纹铲鼻蛇（C. annulata）。此外，研究建议保留环纹铲鼻蛇（C. annulata）内的两个亚种分类单元（C. a. annulata与C. a. klauberi），这两个单元能够反映该物种种内遗传与表型变异的区域分化特征。本研究结果凸显了在随时间推移持续演化的谱系中验证分类学边界（taxonomic boundaries）的难度。