Jessica Fenker

and 3 more

Differences in the geographic scale and depth of phylogeographic structure across co-distributed taxa can reveal how microevolutionary processes such as population isolation and persistence drive diversification. In turn, environmental heterogeneity, species’ traits and historical biogeographic barriers may influence the potential for isolation and persistence. Using extensive SNP data and a combination of population genetic summary statistics and landscape genomic analyses, we explore predictors of the scale and depth of phylogeographic structure in co-distributed lizard taxa from the topographically and climatically complex monsoonal tropics (AMT) of Australia. We first resolve intraspecific lineages and then test whether genetic divergence across space within lineages is related to isolation by distance, resistance and/or environment, and whether these factors differ across genera or between rock-related versus habitat generalist taxa. We then test whether microevolutionary processes within lineages explain differences in the geographic scale and depth of intraspecific phylogeographic lineages. Results indicate that landscape predictors of phylogeographic structure differ between taxa. Within lineages, there was prevalent isolation by distance, but the strength of isolation by distance is independent of the taxonomic family, habitat specialization and climate. Isolation by environment is the strongest predictor of landscape-scale genetic divergence for all taxa, with both temperature and precipitation acting as limiting factors. The strength of isolation by distance does not predict the geographic scale of phylogeographic structure. However localized lineages had higher mean individual heterozygosity and less negative Tajima’s D. This implies that finer-scale phylogeographic structuring within species is associated with larger and more stable populations and, hence, persistence.
Reduced representation genome sequencing has popularized the application of single nucleotide polymorphisms (SNPs) to address evolutionary and conservation questions in non-model organisms. Patterns of genetic structure and diversity based on SNPs often diverge from those obtained with microsatellites to different degrees, but few studies have explicitly compared their performance under similar sampling regimes in a shared analytical framework. We compared range-wide patterns of genetic structure and diversity in two amphibians endemic to the Iberian Peninsula: Hyla molleri and Pelobates cultripes, based on microsatellite (18 and 14 loci) and SNP (15,412 and 33,140 loci) datasets of comparable sample size and spatial extent. Model-based clustering analyses with STRUCTURE revealed minor differences in genetic structure between marker types, but inconsistent values of the optimal number of populations (K) inferred. SNPs yielded more repeatable and less admixed ancestries with increasing K compared to microsatellites. Genetic diversity was weakly correlated between marker types, with SNPs providing a better representation of southern refugia and of gradients of genetic diversity congruent with the demographic history of both species. Our results suggest that the larger number of loci in a SNP dataset can provide more reliable inferences of patterns of genetic structure and diversity than a typical microsatellite dataset, at least at the spatial and temporal scales investigated.