Objective choice of phylogeographic models

Phylogeography seeks to discover the evolutionary processes that have given rise to organismal and genetic diversity. This requires explicit hypotheses (i.e., models) to be evaluated with genetic data in order to identify those hypotheses that best explain the data. In recent years, advancements in the model-based tools used to estimate phylogeographic parameters of interest such as gene flow, divergence time, and relationships among groups have been made. However, given the complexity of these models, available methods can typically only compare a handful of possible hypotheses, requiring researchers to specify in advance the small set of models to consider. Without formal quantitative approaches to model selection, researchers must rely on their intuition to formulate the model space to be explored.We explore the adequacy of intuitive choices made by researchers during the process of data analysis by reanalyzing 20 empirical phylogeographic datasets using PHRAPL, an objective tool for...系统发育地理学（Phylogeography）旨在揭示催生生物与遗传多样性的进化过程。该领域需借助遗传数据对明确的假说（即模型）进行评估，以筛选出最能解释该数据的假说。近年来，用于估算目标系统发育地理学参数（如基因流、分化时间及类群间亲缘关系）的基于模型的工具已取得进展。然而，鉴于此类模型的复杂性，现有方法通常仅能比对少量潜在假说，这要求研究者提前指定待考察的小型模型集合。若缺乏用于模型选择的正式定量方法，研究者只能依靠直觉构建待探索的模型空间。本研究通过使用PHRAPL——一款客观的……工具——重新分析20套实证系统发育地理学数据集，以此探究研究者在数据分析流程中所做出的直觉性选择的合理性。