Reconstructing hotspots of genetic diversity from glacial refugia and subsequent dispersal in Italian common toads (Bufo bufo)

Abstract

Genetic diversity feeds the evolutionary process and allows populations to adapt to environmental changes. However, we still lack a thorough understanding of why hotspots of genetic diversity are so 'hot'. Here, we analysed the relative contribution of bioclimatic stability and genetic admixture between divergent lineages in shaping spatial patterns of genetic diversity in the common toad Bufo bufo along the Italian peninsula. We combined population genetic, phylogeographic and species distribution modelling (SDM) approaches to map ancestral areas, glacial refugia, and secondary contact zones. We consistently identified three phylogeographic lineages, distributed in northern, central and southern Italy. These lineages expanded from their ancestral areas and established secondary contact zones, before the last interglacial. SDM identified widespread glacial refugia in peninsular Italy, sometimes located under the present-day sea-level. Generalized linear models indicated genetic admixture as the only significant predictor of the levels of population genetic diversity. Our results show that glacial refugia contributed to preserving both levels and patterns of genetic diversity across glacial-interglacial cycles, but not to their formation, and highlight a general principle emerging in Mediterranean species: higher levels of genetic diversity mark populations with substantial contributions from multiple genetic lineages, irrespective of the location of glacial refugia.

Figure 1

Maximum likelihood phylogenetic network of the Bufo bufo mitochondrial haplotypes found in Italy, and geographic distribution of the main haplotype groups. Circle sizes are proportional to haplotype frequency, and black dots represents missing intermediate haplotypes. Populations are numbered as in Table 1. The map was drawn using the software Canvas 11 (ACD Systems of America, Inc.).

Figure 2

Ancestral areas of the genetic lineages of Bufo bufo at their respective time to the most recent common ancestor (TMRCA), as estimated by the Bayesian phylogeographical analyses. Polygons represent 10% to 70% highest posterior density (HPD) regions of the geographical locations of the ancestral areas. The map was drawn using the software Canvas 11 (ACD Systems of America, Inc.); photo: Bufo bufo (from https://www.dreamstime.com).

Figure 3

Genetic structure of the Italian Bufo bufo populations, as inferred by the Bayesian clustering analysis implemented in TESS based on eight microsatellite loci. The bar plot on the left shows the admixture proportions of each individual for the four genetic clusters identified; the pie diagrams on the maps show the frequency of each cluster within the studied populations. Populations are numbered as in Table 1. The line chart shows values of the deviance information criterion (DIC) statistics estimated for models with the number of genetic clusters (K) ranging from 2 to 10. The map was drawn using the software Canvas 11 (ACD Systems of America, Inc.).

Figure 4

Putative Pleistocene glacial refugia for the central (A) and southern (B) lineages of Bufo bufo, as inferred by the species distribution modelling (SDM) calibrated under current bioclimatic conditions and projected at the last glacial maximum (21 kya). Orange: areas of at least two out of three general circulation models (GCMs); red: areas of concordance among all the GCMs; black: areas of “stability”, defined as regions of overlap between current, glacial (two out of three GCMs) and ancestral (Bayesian phylogeographic analysis) areas of species presence. The map was drawn using the software Canvas 11 (ACD Systems of America, Inc.).