Garrett Molly J, Conway Courtney J, Waits Lisette P, Hohenlohe Paul A
Department of Fish and Wildlife Sciences, College of Natural Resources, University of Idaho, Moscow, ID 83844, USA.
U.S. Geological Survey, Idaho Cooperative Fish & Wildlife Research Unit, University of Idaho, Moscow, ID 83844, USA.
Genes (Basel). 2025 Jun 8;16(6):694. doi: 10.3390/genes16060694.
Monitoring genetic parameters is important for setting effective conservation and management strategies, particularly for small, fragmented, and isolated populations. Small, isolated populations face increased rates of genetic drift and inbreeding, which increase extinction risk especially when gene flow is limited.
Here, we applied a Genotyping-in-Thousands by sequencing (GT-seq) panel to inform recovery action for the federally threatened northern Idaho ground squirrel (). We evaluated genetic diversity, structure, connectivity, and effective population size to address species recovery goals.
We delineated three types of conservation units: (1) three evolutionarily significant units that represent long-term population structure and variation, (2) nine management units that reflect current demographic connectivity and restrictions to gene flow, and (3) three adaptive units that capture adaptive differentiation across the species range. Effective population sizes per management unit were small overall (mean 38.16, range 2.3-220.9), indicating that recovery goals of 10 subpopulations with > 500 have not been reached.
Our results support the maintenance of connectivity within evolutionarily significant units through the restoration of dispersal corridors. Next steps could include further sampling of some subpopulations with low sample sizes, unsampled subpopulations, and subpopulations that are geographically isolated. Genotyping future samples with the same GT-seq panel would help to detect dispersal, assess effective population size, monitor the effects of inbreeding, and evaluate adaptive differentiation to monitor the effects of management action and environmental change.
监测遗传参数对于制定有效的保护和管理策略至关重要，特别是对于小型、碎片化和孤立的种群。小型孤立种群面临着遗传漂变和近亲繁殖率增加的问题，这会增加灭绝风险，尤其是在基因流动有限的情况下。
在这里，我们应用了一种测序数千样本的基因分型（GT-seq）面板，为联邦政府列为受威胁物种的爱达荷州北部地松鼠（）的恢复行动提供信息。我们评估了遗传多样性、结构、连通性和有效种群大小，以实现物种恢复目标。
我们划定了三种类型的保护单元：（1）三个具有进化意义的单元，代表长期的种群结构和变异；（2）九个管理单元，反映当前的种群统计学连通性和对基因流动的限制；（3）三个适应性单元，捕捉整个物种范围内的适应性分化。每个管理单元的有效种群大小总体较小（平均38.16，范围2.3 - 220.9），这表明尚未达到拥有超过500个个体的10个亚种群的恢复目标。
我们的结果支持通过恢复扩散走廊来维持具有进化意义单元内的连通性。接下来的步骤可能包括对一些样本量低的亚种群、未采样的亚种群以及地理上孤立的亚种群进行进一步采样。使用相同的GT-seq面板对未来样本进行基因分型将有助于检测扩散、评估有效种群大小、监测近亲繁殖的影响以及评估适应性分化，以监测管理行动和环境变化的影响。
