Data from: Inferring the geographic origin of a range expansion: latitudinal and longitudinal coordinates inferred from genomic data in an ABC framework with the program X-ORIGIN

Climatic or environmental change is not only driving distributional shifts in species today, but it has also caused distributions to expand and contract in the past. Inferences about the geographic locations of past populations, especially regions that served as refugia (i.e., source populations) and migratory routes are a challenging endeavor. Refugial areas may be evidenced from fossil records or regions of temporal stability inferred from ecological niche models. Genomic data offer an alternative and broadly applicable source of information about the locality of refugial areas, especially relative to fossil data, which are either unavailable or incomplete for most species. Here we present a pipeline we developed (called x-origin) for statistically inferring the geographic origin of range expansion using a spatially explicit coalescent model and an Approximate Bayesian Computation testing framework. In addition to assessing the probability of specific latitudinal and longitudinal coordinates of refugial or source populations, such inferences can also be made accounting for the effects of temporal and spatial environmental heterogeneity, which may impact migration routes. We demonstrate x-origin with an analysis of genomic data collected in the Collared pika that underwent post-glacial expansion across Alaska, as well as present an assessment of its accuracy under a known model of expansion to validate the approach.气候或环境变化不仅正驱动当代物种的分布范围发生位移，也曾在地质历史时期推动物种分布区发生扩张与收缩。推断过去种群的地理分布位置——尤其是作为避难区（refugia，即源种群）与迁徙通道的区域——是一项极具挑战性的研究课题。避难区的存在可通过化石记录，或是基于生态位模型（ecological niche model）推断得到的长期稳定区域来佐证。相较于多数物种难以获取或残缺不全的化石数据，基因组数据为推断避难区的地理位置提供了一种替代性且普适性极强的信息来源。本文介绍了我们开发的一款名为x-origin的分析流程：该流程基于空间显式溯祖模型（spatially explicit coalescent model）与近似贝叶斯计算（Approximate Bayesian Computation, ABC）检验框架，通过统计学方法推断物种分布扩张的地理起源。该流程不仅可评估避难种群或源种群的特定经纬度坐标的概率，还能纳入时空环境异质性的影响进行推断——这类异质性可能会对物种迁徙通道产生影响。我们通过对曾在阿拉斯加地区经历冰期后扩张的领鼠兔（Collared pika）的基因组数据开展分析，演示了x-origin流程的实际应用；同时还基于已知的物种扩张模型对该方法的准确性进行评估，以验证其有效性。