Data from: Reconstructing the evolutionary history of an endangered subspecies across the changing landscape of the Great Central Valley of California.

Identifying historic patterns of population genetic diversity and connectivity is a primary challenge in efforts to re-establish the processes that have generated and maintained genetic variation across natural landscapes. The challenge of reconstructing pattern and process is even greater in highly altered landscapes where population extinctions and dramatic demographic fluctuations in remnant populations may have substantially altered, if not eliminated, historic patterns. Here, we seek to reconstruct historic patterns of diversity and connectivity in an endangered subspecies of woodrat that now occupies only 1-2 remnant locations within the highly altered landscape of the Great Central Valley of California. We examine patterns of diversity and connectivity using 14 microsatellite loci and sequence data from a mitochondrial locus and a nuclear intron. We reconstruct temporal change in habitat availability to establish several historical scenarios that could have led to contemporary patterns of diversity, and use an approximate Bayesian computation approach to test which of these scenarios is most consistent with our observed data. We find that the Central Valley populations harbour unique genetic variation coupled with a history of admixture between two well-differentiated species of woodrats that are currently restricted to the woodlands flanking the Valley. Our simulations also show that certain commonly used analytical approaches may fail to recover a history of admixture when populations experience severe bottlenecks subsequent to hybridization. Overall our study shows the strength of combining empirical and simulation analyses to recover the history of populations occupying highly altered landscapes.

识别种群遗传多样性与连通性的历史模式，是重建自然景观中产生并维持遗传变异过程的核心研究挑战。在高度受人类活动改造的景观中，种群灭绝与残存种群的剧烈种群数量波动即便未彻底消除历史遗传模式，也可能大幅改变其原有特征，此时重建种群模式与演化过程的难度将进一步提升。本研究以加州大中央谷（Great Central Valley of California）这一高度受人类活动改造的景观为研究区域，针对目前仅存1至2个残存分布位点的濒危林鼠（woodrat）亚种，旨在重建其历史遗传多样性与连通性模式。研究采用14个微卫星位点（microsatellite loci）、1个线粒体位点（mitochondrial locus）及1个核内含子（nuclear intron）的序列数据，分析该亚种的遗传多样性与连通性模式。我们通过重建栖息地可利用性的时序变化，构建了数种可能塑造当代遗传多样性模式的历史演化情景，并借助近似贝叶斯计算（approximate Bayesian computation）方法，检验与观测数据最契合的情景。研究结果显示，中央谷种群携带有独特的遗传变异，且经历了目前仅分布于谷旁林地的两种高度分化林鼠物种间的遗传混合（admixture）历史。模拟分析还表明，当种群在杂交后遭遇严重瓶颈效应时，部分常用的种群遗传学分析方法可能无法正确还原其遗传混合历史。综上，本研究证实了结合实证研究与模拟分析，对于还原受高度人类活动改造景观中种群演化历史的重要价值与方法优势。