Rangewide landscape genetics of an endemic Pacific northwestern salamander

Abstract

A species' genetic structure often varies in response to ecological and landscape processes that differ throughout the species' geographic range, yet landscape genetics studies are rarely spatially replicated. The Cope's giant salamander (Dicamptodon copei) is a neotenic, dispersal-limited amphibian with a restricted geographic range in the Pacific northwestern USA. We investigated which landscape factors affect D. copei gene flow in three regions spanning the species' range, which vary in climate, landcover and degree of anthropogenic disturbance. Least cost paths and Circuitscape resistance analyses revealed that gene flow patterns vary across the species' range, with unique combinations of landscape variables affecting gene flow in different regions. Populations in the northern coastal portions of the range had relatively high gene flow, largely facilitated by stream and river networks. Near the southeastern edge of the species' range, gene flow was more restricted overall, with relatively less facilitation by streams and more limitation by heat load index and fragmented forest cover. These results suggested that the landscape is more difficult for individuals to disperse through at the southeastern edge of the species' range, with terrestrial habitat desiccation factors becoming more limiting to gene flow. We suggest that caution be used when attempting to extrapolate landscape genetic models and conservation measures from one portion of a species' range to another.

Finding the Genomic Basis of Local Adaptation: Pitfalls, Practical Solutions, and Future Directions

“…When there are no specific hypotheses about the nature of local adaptation, researchers can choose explanatory environmental variables and avoid problems with multicollinearity by selecting one environmental variable as a representative of a correlated set (e.g., Trumbo et al 2013). An alternative strategy is to summarize correlated environmental variables in a dimensionality reduction analysis such as principle components analysis (or others; see Lasky et al 2012) and correlate allele frequencies with those principal components.…”

“…Optimal design requires considering the geographic scale at which local adaptation occurs in the study system, which can be established using ecological knowledge, reciprocal transplants, natural history, and knowledge from similar systems. Investigators should also consider the geographic coverage of their study: when genetic data cover only a small portion of the species range, it may be inappropriate to extrapolate results to the entire species’ range (Short Bull et al 2011; Trumbo et al 2013). …”

Amphibian molecular ecology and how it has informed conservation

“…A key finding of several of the studies in Table 2 is the different patterns seen over diverse scales and sampling regimes. For instance, researchers have found differing effects of landscapes on amphibians by looking at different regions inhabited by a single species (Johansson et al 2005;Wang et al 2009aWang et al , 2011Moore et al 2011;Trumbo et al 2013), different species within the same region (Goldberg & Waits 2010;Richardson 2012), different time periods for the same metapopulation (Savage et al 2010) and different spatial scales for the same analysis (Angelone et al 2011). These results collectively challenge the generality of results that stem from landscape genetic studies, and suggest that results from molecular studies of amphibian-landscape interactions should generally be interpreted within the scope of a specific study or region, but not beyond.…”

Ditch network sustains functional connectivity and influences patterns of gene flow in an intensive agricultural landscape

“…Although resistance distances based on circuit theory have been shown to be good predictors of gene flow among populations (McRae, 2006), resistance distances across the ditch network performed poorly when compared with shortest pathoriented distances along the network. Two recent studies found a significant effect of resistance distances calculated on linear stream networks (Blair et al, 2013;Trumbo et al, 2013). However, both studies were conducted on reptiles and amphibians, which have different dispersal patterns as compared with plant species.…”