Quaternary history, population genetic structure and diversity of the cold-adapted Alpine newt Ichthyosaura alpestris in peninsular Italy

Abstract

Mediterranean peninsulas are major biodiversity hotspots, and cold-adapted species are an important component of this biodiversity. However, cold-adapted species contributed surprisingly little to our knowledge of the intimate links between Quaternary environmental changes, species' responses to these changes, and current patterns of intraspecific biodiversity. Here, we investigated the genetic structure and evolutionary history of a cold-adapted amphibian, the Alpine newt Ichthyosaura alpestris, within the Italian peninsula. Nuclear and mitochondrial markers consistently identified three distinct genetic lineages, whose divergence dates to the Early Pleistocene (1.9 and 0.8 million years ago). Our results show that the Italian peninsula provided multiple Pleistocene refugia to this cold-adapted species, and suggest that allopatric fragmentation followed by secondary admixture have been key events in the formation of its current pattern of genetic diversity. Indeed, estimates of population genetic diversity clearly identified contact populations as those achieving the highest levels of diversity. Such concordance among cold-adapted and temperate species in terms of processes triggering the formation of regional patterns of genetic diversity provides strong support for the hypothesis that gene exchange between divergent lineages, rather than long-term stability of refugial populations, has been the main step toward the formation of hotspots of intraspecific biodiversity.

Figure 1

Geographical distribution of Ichthyosaura alpestris on the Apennine peninsula and the geographical locations of the 15 populations sampled. The locations are numbered as in Table 1. The inset shows the distribution of I. alpestris within the Western Palearctic region. The map was drawn using the software Canvas 11 (ACD Systems of America, Inc.).

Figure 2

Genetic structure of Ichthyosaura alpestris populations in Italy estimated using TESS based on (a) nuclear sequence dataset and (b) a microsatellite dataset. The bar plots show the admixture proportions of each individual for the three genetic clusters recovered. The pie diagrams on the maps show the frequency distributions of each cluster among the populations. The line charts show mean values of deviance information criterion (DIC) statistics (averaged over 100 runs) that were estimated for the 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 3

Haplotype genealogy based on a maximum likelihood phylogenetic tree of the Ichthyosaura alpestris mtDNA haplotypes found (a). Statistical parsimony network showing genealogical relationships among haplotypes in PDGFR (b), β-FIB (c) and GH (d) genes. Circle sizes are proportional to haplotype frequency; missing intermediate haplotypes are shown as black dots. Pie diagrams show the frequency distributions of the haplogroups among the populations studied. The map was drawn using the software Canvas 11 (ACD Systems of America, Inc.).

Figure 4

Maximum clade credibility tree based on the Ichthyosaura alpestris mtDNA dataset recovered by Bayesian analysis in BEAST, showing the time to the most recent common ancestor (TMRCA) for the major clades. Node bars (grey) represent 95% highest posterior density (HPD) intervals for node ages. The posterior probabilities for each node are also shown (only values >0.9 are shown). The scale is in millions of years before present. The graph was drawn using the software Canvas 11 (ACD Systems of America, Inc.).

Figure 5

Ancestral areas of the two main genetic lineages of Ichthyosaura alpestris at their respective times to the most recent common ancestor (TMRCAs) based on Bayesian phylogeographical analyses conducted independently for both lineages on mtDNA. Polygons represent the highest posterior density (HPD) regions of the geographical locations at 10% to 70% probabilities. The map was drawn using the software Canvas 11 (ACD Systems of America, Inc.).