Slow and steady wins the race: contrasted phylogeographic signatures in two Alpine amphibians

Abstract

A deeper phylogeographic structure is expected for slow-dispersing habitat specialists compared to widespread adaptable species, especially in topographically complex regions. We tested this classic assumption by comparing the genomic (RAD-sequencing) phylogeographies of 2 amphibians inhabiting the Swiss Alps: the mobile, cosmopolitan common frog (Rana temporaria) against the stationary, mountain endemic Alpine salamander (Salamandra atra). Our results ran opposite of predictions: the frog displayed significantly higher genetic divergences and lower within-population variation compared to the salamander. This implies a prominent role for their distinctive glacial histories in shaping intraspecific diversity and structure: diversification and recolonization from several circum-Alpine micro-refugia for the frog versus a single refugium for the salamander, potentially combined with better population connectivity and stability. These striking differences emphasize the great variability of phylogeographic responses to the Quaternary glaciations, hence the complexity to predict general patterns of genetic diversity at the regional scale, and the forces that underlie them.

Inferring genetic structure when there is little: population genetics versus genomics of the threatened bat Miniopterus schreibersii across Europe

“…A comprehensive picture of the genetic structure of populations is instrumental to any ecological, evolutionary and conservation research 1 . Patterns of genetic variation, differentiation and admixture inform on the history of populations and thus help understanding the ecological and geographic processes shaping biodiversity in space and time 2 – 4 . Molecular assessments also offer a swift alternative to traditional monitoring techniques (e.g., mark-recapture), especially when it comes to measuring individual movements, population fragmentation and other key parameters relevant for conservation such as inbreeding and local adaptation 5 – 7 .…”

“…Patterns of population differentiation may be difficult to detect for mobile organisms, as populations are homogenized by recurrent episodes of gene flow 13 , 14 . The issue is also characteristic of genetically impoverished species that experienced range-wide demographic changes, such as refugial bottlenecks and post-glacial expansions, and for which the remaining diversity might be too low to quantify population connectivity 4 . Moreover, at times in the life cycle, momentary gatherings of individuals from various geographic origins might also blur the appreciations of genetic diversity and between-population differentiation, as seasonal migration confound with dispersal 15 .…”

“…In recent years, molecular ecologists benefit from high-throughput sequencing technology to access unprecedented numbers of loci, as prepared by genomic libraries 25 , 26 . In particular, restriction-site associated DNA sequencing (RAD-seq 27 ; double-digest ddRAD-seq 28 ) have become a popular method to genotype hundreds to thousands single nucleotide polymorphisms (SNPs) across conspecific or interspecific populations for multiple applications, such as high-resolution phylogeography 29 and population genetic studies of weakly structured species 4 , 28 . The number of alleles of a single microsatellite locus is much higher than that of SNPs, but microsatellite analyses rarely include more than 10–20 loci due to practical constraints.…”