Data from: Heterogeneity in genetic diversity among non-coding loci fails to fit neutral coalescent models of population history

Inferring aspects of the population histories of species using coalescent analyses of non-coding nuclear DNA has grown in popularity. These inferences, such as divergence, gene flow, and changes in population size, assume that genetic data reflect simple population histories and neutral evolutionary processes. However, violating model assumptions can result in a poor fit between empirical data and the models. We sampled 22 nuclear intron sequences from at least 19 different chromosomes (a genomic transect) to test for deviations from selective neutrality in the gadwall (Anas strepera), a Holarctic duck. Nucleotide diversity among these loci varied by nearly two orders of magnitude (from 0.0004 to 0.029), and this heterogeneity could not be explained by differences in substitution rates. Using two different coalescent methods to infer models of population history and then simulating neutral genetic diversity under these models, we found that the among-locus heterogeneity in nucleotide diversity was significantly higher than expected for these simple models. Defining more complex models of population history demonstrated that a pre-divergence bottleneck was also unlikely to explain this heterogeneity. However, both selection and interspecific hybridization could account for the heterogeneity observed among loci. Regardless of the cause of the deviation, our results illustrate that violating key assumptions of coalescent models can mislead inferences of population history.

利用核非编码DNA（non-coding nuclear DNA）的溯祖分析（coalescent analyses）推断物种种群历史特征的研究日益受到关注。此类推断——诸如物种分化、基因流以及种群规模变化等——均预设遗传数据能够反映简单的种群历史与中性进化过程。然而，若违背模型假设，则可能导致实证数据与模型间适配性不佳。
本研究针对全北界鸭类赤膀鸭（Anas strepera），从至少19条不同染色体上采集了22个核内含子序列（nuclear intron sequences），构建基因组断面（genomic transect）以检验其是否偏离选择中性（selective neutrality）。这些位点间的核苷酸多样性（nucleotide diversity）差异跨度接近两个数量级（范围为0.0004至0.029），且该异质性无法通过替换速率（substitution rates）的差异加以解释。
本研究采用两种不同的溯祖方法（coalescent methods）推断种群历史模型，并基于这些模型模拟中性遗传多样性（neutral genetic diversity），结果发现，相较于这些简单模型的预期值，位点间的核苷酸多样性异质性显著更高。通过构建更为复杂的种群历史模型可知，分化前瓶颈效应（pre-divergence bottleneck）同样无法解释该异质性。但选择作用与种间杂交（interspecific hybridization）均能够解释观测到的位点间异质性。无论该偏离的成因为何，本研究结果均表明，违背溯祖模型的关键假设，可能会误导种群历史的推断结果。