Data from: Ephemeral stream reaches preserve the evolutionary and distributional history of threespine stickleback in the Santa Clara and Ventura River Watersheds of southern California

Much remains to be understood about the evolutionary history and contemporary landscape genetics of unarmored threespine stickleback in southern California, where populations collectively referred to as Gasterosteus aculeatus williamsoni have severely declined over the past 70+ years and are now endangered. We used mitochondrial sequence and microsatellite data to assess the population genetics and phylogeography of unarmored populations sampled immediately downstream from the type locality of G. a. williamsoni in the upper Santa Clara River, and assessed their distinctiveness with respect to low-armor populations in the downstream sections of the river and the adjacent Ventura River. We also characterized the geographic limits of different plate morphs and evaluated the congruence of those boundaries with barriers to dispersal in both river systems and to neutral genetic variation. We show substantial population structuring within the upper reach of the Santa Clara River, but little partitioning between the lower Santa Clara and Ventura Rivers—we attribute these patterns to different ancestry between spatially subdivided populations within the same drainage, a predominance of downstream gene flow, and ability for coastal dispersal between the Santa Clara and Ventura Rivers. We also show that alleles from introduced low-plate stock have infiltrated a native population in at least one upper Santa Clara River tributary, causing this formerly unarmored population to become gradually low-plated over a 30 + year time period. Measures of genetic diversity, census surveys, and severe habitat disturbance all indicate that unarmored stickleback near the type locality are currently at high risk of extinction.

关于加利福尼亚南部无侧装甲三棘刺鱼（unarmored threespine stickleback）的演化历史与当代景观遗传学，仍有诸多问题有待阐明。该区域被统称为三棘刺鱼威廉姆森亚种（Gasterosteus aculeatus williamsoni）的种群在过去70余年中种群数量急剧下降，目前已处于濒危状态。本研究借助线粒体序列与微卫星（microsatellite）数据，对采自圣克拉拉河上游威廉姆森亚种模式产地（type locality）紧邻下游区域的无装甲种群开展了种群遗传学与系统发生地理学（phylogeography）分析，并对比评估了该种群与该河下游及邻近文图拉河的低装甲种群的分化程度。本研究同时明确了不同侧板形态型（plate morphs）的地理分布范围，并验证了这些分布边界与两大河流水系中的扩散障碍（barriers to dispersal）及中性遗传变异（neutral genetic variation）的一致性。研究结果显示，圣克拉拉河上游区域存在显著的种群遗传结构，但圣克拉拉河下游与文图拉河种群间的遗传分化极弱——我们将这一格局归因于同一水系内空间隔离种群间的不同起源、以顺流基因流（gene flow）为主导的扩散模式，以及圣克拉拉河与文图拉河之间存在的沿海扩散能力。本研究同时发现，引入的低装甲种群的等位基因（alleles）已渗入至少一条圣克拉拉河上游支流的本土种群中，使得该原本无装甲的种群在30余年的时间里逐渐演变为低装甲表型。遗传多样性指标、种群普查数据以及严重的栖息地干扰均表明，模式产地附近的无装甲刺鱼种群目前面临极高的灭绝风险。