Habitat loss and fragmentation have caused population decline across taxa through impacts on life history diversity, dispersal patterns, and gene flow. Yet, intentional isolation of native fish populations is a frequently used management strategy to protect against negative interactions with invasive fish species. We evaluated the population viability and genetic diversity of 12 isolated populations of Oncorhynchus clarkii lewisi located on the Flathead Indian Reservation in Montana, USA. Length-structured integral projection models (IPMs) were used to project population growth rate (lambda) and its sensitivity to underlying vital rates and parameters. We examined relationships between lambda, genetic diversity, and habitat size and quality. Lambda ranged from 0.68 to 1.1 with 10 of 12 populations projected to be in decline. A sensitivity analysis of lambda with respect to projection matrix elements indicated that lambda was generally sensitive to changes in early life history stages (survival/growth), but patterns differed among populations. Another sensitivity analysis with respect to underlying model parameters showed highly consistent pattern across populations, with lambda being most sensitive to the slope of probability of maturity (estimated from published literature), generally followed by adult survival, and the slope of somatic growth rate (directly measured from each population). Lambda was not correlated with genetic diversity. For populations residing in small isolated streams (≤5 km of occupied habitat), lambda significantly increased with base flow discharge (r2=0.50, p<0.02). Our results highlight the potential importance of local adaptation for persistence of small, isolated populations. Specifically we saw evidence for higher probability of maturity at smaller sizes in the smallest, coldest isolated systems, increasing probability of persistence for these populations. Climate change threatens to further fragment populations of aquatic organisms and reduce summertime base flows in much of western North America. Insights from studies such as ours will inform management strategies for long-term persistence of species facing these challenges.
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