Fine-scale phylogeography of Rana temporaria (Anura: Ranidae) in a putative secondary contact zone in the southern Alps

Are glacial refugia hotspots of speciation and cytonuclear discordances? Answers from the genomic phylogeography of Spanish common frogs

“…The first hypothesis is consistent with the biogeography of the Cantabrian Range, which hosts endemic refugial clades in other amphibians with a broad European distribution (e.g., Recuero & García‐París, ). The T6 evolutionary lineage could have thus arisen in R. temporaria during the Pleistocene, and then merged with T4 until complete fusion (as seen among Alpine lineages: Marchesini et al, ), to the point that only its mitochondrial legacy remains. Subsequent glacial expansions (Figure ) would have then spread T6 mtDNA in most of Cantabria and the west of the Basque Country.…”

“…For the cold-tolerant Rana frogs, this outcome is remarkable because Spanish populations expanded and thrived during the prolonged glacials rather than during the short interglacial cycles only (Figures 4 and 5; see also Galán et al, 2010 for the Galician populations of R. parvipalmata), thus experiencing longer opportunities for lineage fusion compared to species with Mediterranean affinities. Such ecological flexibility is today reflected in the high levels of genetic variation in R. temporaria range wide (Vences et al, 2013), and by a complex history of divergences and subsequent fusions of lineages in some regions (Marchesini, Ficetola, Cornetti, Battisti, & Vemesi, 2017, see next section). Finally, it is worth noting that the phylogeography of Spanish common frogs shows similar patterns of west-east fragmentation to those reported in other Iberian amphibians associated with the Atlantic region, including Salamandra salamandra (García-París, Alcobendas, Buckley, & Wake, 2003), Lissotriton helveticus (Recuero & García-París, 2011), Ichthyosaura alpestris (Recuero et al, 2014), and Alytes obstetricans (Maia-Carvalho et al, 2018), which are thus also good candidates for cryptic speciation events.…”

Deciphering the drivers of negative species–genetic diversity correlation in Alpine amphibians

“…Sampling sites matched the areas of amphibian community monitoring. We collected one fertilized egg from each clutch to avoid full‐sibs, as each female lays only one clutch per year (Schmeller & Merilä, ; see Marchesini et al, , for more details on sampling). Overall, we collected 700 samples (minimum: 15 samples per site).…”

“…COI data for the selected populations were derived from Marchesini et al. (). Analyses with different proxies of historical factors (frequency of the Alp1 mitochondrial lineage, included as linear or quadratic term; Supporting Information ) yielded identical results.…”

“…GLS are regression models that successfully incorporate spatial structure in the error term (correlation function depending on the geographical distance among sites) and are suitable to analyse spatially explicit data, controlling for potential issues of spatial autocorrelation (Beale, Lennon, Yearsley, Brewer, & Elston, 2010). A previous phylogeographic study (using the mitochondrial COI gene) revealed a complex scenario, with different evolutionary lineages of common frog colonizing the study region after glaciations (Marchesini et al, 2017). Past evolutionary processes can strongly influence present-day genetic diversity (Ficetola, Garner, & De Bernardi, 2007;Petit et al, 2003;Roberts & Hamann, 2015); thus, we repeated SGDC including the number of mitochondrial lineages as covariate, under the assumption that admixture among lineages can increase genetic diversity (see Supporting Information Appendix S1).…”