Given the availability of genomic data to identify separately evolving groups of organisms, many researchers establish species limits based on assessments of the extent of gene flow among populations and often use analytical approaches to identify species in which gene flow is explicitly disallowed. Strictly considering lack of—or limited—gene flow as the main or only criterion to delimit species involves two main complications in practice. First, approaches often used to analyze genome-wide data cannot by themselves distinguish species limits from within-species population structure, particularly in allopatric organisms. Second, recognizing as species only those lineages one can identify using such approaches fails to embrace the role of other evolutionary forces (i.e. various forms of selection) in defining evolutionary lineages. Using examples from various groups of birds, we call for the importance of considering evolutionary forces additional to gene flow in species delimitation and explain why genomic approaches commonly used in taxonomic studies may be insufficient by themselves to properly uncover species limits. By considering the processes that structure genotypic and phenotypic variation during speciation, we argue that rigorous analyses of phenotypic variation remain crucial for species delimitation in the genomics era because phenotypes uniquely inform us about the role of selection maintaining the cohesion of evolutionary lineages. Evolutionary theory describing the roles of gene flow, genetic drift and natural and sexual selection in the origin and maintenance of species calls for an integration of genomics with phenomics in avian species delimitation.

中文翻译：

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鸟类（和其他生物）的基因组革命和物种划分：为什么不应忽视表型

鉴于基因组数据可用于识别单独进化的生物群，许多研究人员根据对种群间基因流动程度的评估确定物种限制，并经常使用分析方法来识别明确不允许基因流动的物种。严格考虑缺乏或有限的基因流作为划分物种的主要或唯一标准在实践中涉及两个主要并发症。首先，通常用于分析全基因组数据的方法本身无法将物种限制与物种内种群结构区分开来，特别是在异域生物中。其次，仅将那些可以使用这种方法识别的谱系识别为物种，无法接受其他进化力量（即各种形式的选择）在定义进化谱系中的作用。使用来自不同鸟类群体的例子，我们呼吁在物种划分中考虑除基因流动之外的进化力量的重要性，并解释为什么分类学研究中常用的基因组方法本身可能不足以正确揭示物种限制。通过考虑在物种形成过程中构建基因型和表型变异的过程，我们认为对表型变异的严格分析对于基因组学时代的物种划分仍然至关重要，因为表型独特地告诉我们选择在维持进化谱系凝聚力方面的作用。描述基因流动、遗传漂变以及自然和性选择在物种起源和维持中的作用的进化理论要求在鸟类物种划界中将基因组学与表型学相结合。