Cui Yuwei, Nunney Leonard
Department of Evolution, Ecology, and Organismal Biology, University of California Riverside, Riverside, CA, USA.
Heredity (Edinb). 2025 Aug 25. doi: 10.1038/s41437-025-00789-3.
Karyotype variation within Pacific kangaroo rat Dipodomys agilis motivated its division in 1997 into the agile kangaroo rat (AKR, D. agilis, 2N = 62) in the north of its range in California, and Dulzura kangaroo rat (DKR, D. simulans, 2N = 60) to the south, with a suspected sympatric zone south of the San Gabriel and San Bernardino Mountains. This division was supported by our whole genome sequencing that sampled a ~120 km transect from north of the mountains to SW Riverside County. The taxa showed marked genetic differentiation, with no evidence of hybridization or sympatry. AKR was found at the southern edge of the mountains, precluding the mountain barrier driving isolation, suggesting ecological separation linked to habitat differences between the mountains and the arid area to the south. Adding four additional Dipodomys species, we estimated genetic divergence times in the genus back to ∼3.5 mya. AKR and DKR diverged from D. stephensi ∼1.7 mya, and from each other ∼0.5 mya, when their joint effective population size (N) was ~100,000. After separation, DKR's N declined to ~20,000, while AKR's was little changed. More recently their N converged at ~50,000. Runs of homozygosity were longer in AKR, indicating a smaller neighborhood size, which may have promoted the karyotype change; however, nucleotide diversity was higher in AKR, but both had levels typical for rodents, indicating neither experienced recent bottlenecks. These patterns provide a baseline for any future conservation efforts. More generally, this study shows how a detailed genomic study can resolve taxonomic and demographic questions among morphologically indistinguishable taxa.
太平洋更格卢鼠（Dipodomys agilis）的核型变异促使其在1997年被划分为：分布于加利福尼亚州其分布范围北部的敏捷更格卢鼠（AKR，D. agilis，2N = 62），以及南部的杜尔祖拉更格卢鼠（DKR，D. simulans，2N = 60），在圣盖博山和圣贝纳迪诺山以南存在一个疑似同域分布区。我们的全基因组测序对从山脉以北到西南河滨县的约120公里样带进行了采样，支持了这一划分。这两个分类单元显示出明显的遗传分化，没有杂交或同域分布的证据。在山脉南缘发现了敏捷更格卢鼠，排除了山脉屏障导致隔离的可能性，这表明生态隔离与山脉和南部干旱地区之间的栖息地差异有关。增加另外四种更格卢鼠物种后，我们估计该属的遗传分化时间可追溯到约350万年前。敏捷更格卢鼠和杜尔祖拉更格卢鼠在约170万年前与斯蒂芬斯更格卢鼠（D. stephensi）分化，彼此之间在约50万年前分化，当时它们的联合有效种群大小（N）约为100,000。分离后，杜尔祖拉更格卢鼠的N下降到约20,000，而敏捷更格卢鼠的N变化不大。最近它们的N收敛到约50,000。敏捷更格卢鼠的纯合子片段更长，表明其邻域大小更小，这可能促进了核型变化；然而，敏捷更格卢鼠的核苷酸多样性更高，但两者都具有啮齿动物的典型水平，表明两者都没有经历近期的瓶颈效应。这些模式为未来的任何保护工作提供了基线。更广泛地说，这项研究展示了详细的基因组研究如何解决形态上难以区分的分类单元之间的分类学和种群统计学问题。
