Consistent loss of genetic diversity in isolated cutthroat trout populations independent of habitat size and quality

Fragmentation and isolation of wildlife populations has reduced genetic diversity worldwide, leaving many populations vulnerable to inbreeding depression and local extinction. Nonetheless, isolation is protecting many native aquatic species from interactions with invasive species, often making reconnection an unrealistic conservation strategy. Isolation management is widely used to protect extant cutthroat trout (Oncorhynchus clarkii) populations from invasive species. Despite this, few studies have empirically examined how predictor variables including habitat length, population size, time since isolation and habitat quality, relate to levels of genetic diversity in isolated trout populations. We compared allelic richness of cutthroat trout across 14 microsatellite loci in two connected and 12 anthropogenically isolated populations of the Flathead River basin, Montana. Isolated populations in habitat fragments <8 km stream length had reduced genetic diversity, but diversity was not significantly related to any of our predictor variables. To broaden our scope, we analyzed seven geologically isolated populations from the same river basin occupying habitat fragments up to 18 km in length. These populations showed reduced diversity, regardless of fragment size. Furthermore, geologically isolated populations had significantly lower average allelic richness compared to streams recently isolated by anthropogenic activities. These results demonstrate a consistent loss of genetic diversity through time in isolated populations, emphasizing the need to explore strategies to minimize risks of inbreeding depression. Testing conservation theory and subsequent assumptions broadly across taxa is necessary to ensure efficacy of conservation efforts.