Mitochondrial DNA phylogeography of Lissotriton boscai (Caudata, Salamandridae): evidence for old, multiple refugia in an Iberian endemic

Abstract

In Europe, southern peninsulas served as refugia during cold periods in the Pleistocene, acting both as centres of origin of endemisms and as sources from which formerly glaciated areas were recolonized during interglacial periods. Previous studies have revealed that within the main refugial areas, intraspecific lineages often survived in allopatric refugia. We analysed two mitochondrial markers (nad4, control region, approximately 1.4 kb) in 103 individuals representing the entire distribution of Lissotriton boscai, a newt endemic to the western Iberian Peninsula. We inferred the evolutionary history of the species through phylogenetic, phylogeographic and historical demographic analyses. The results revealed unexpected, deep levels of geographically structured genetic variability. We identified two main evolutionary lineages, each containing three well-supported clades. The first historical split involved populations from central-southwestern coastal Portugal and the ancestor of all the remaining populations around 5.8 million years ago. Both lineages were subsequently fragmented into different population groups between 2.5 and 1.2 million years ago. According to nested clade analysis, at lower hierarchical levels the patterns suggest restricted gene flow with isolation by distance, whereas at higher levels the clades exhibit signatures of contiguous range expansion. Bayesian Skyline Plots show recent bottlenecks, followed by demographic expansions in all lineages. The significant genetic structure found is consistent with long-term survival of populations in allopatric refugia, supporting the 'refugia-within-refugia' scenario for southern European peninsulas. The comparison of our results with other co-distributed species highlights the generality of this hypothesis for the Iberian herpetofauna and suggests that Mediterranean refuges had more relevance for the composition and distribution of present biodiversity patterns than currently acknowledged. We briefly discuss the taxonomic and conservation implications of our results.

Patterns of nuclear and mitochondrial DNA variation in Iberian populations of Emys orbicularis (Emydidae): conservation implications

“…As opposed to other genetic patterns in Iberian amphibians and reptiles which show deep genetic intraspecific structure (Alexandrino et al 2001;Godinho et al 2003;Martinez-Solano et al 2006), Iberian populations of E. orbicularis show moderate genetic differentiation (microsatellite data, see results) and also low mtDNA genetic differentiation (0.0-0.1% uncorrected ''p'' distances), However, the management of this species should take into account the moderate genetic structuring (F ST = 0.12; private alleles) of these highly isolated Iberian populations into five main geographic groups (Fig. 5) and therefore, E. orbicularis in the Iberian Peninsula should be handled taking into account five management units for future conservation programs.…”

Amphibian molecular ecology and how it has informed conservation

“…Amphibian populations have a varied history of bottlenecking, with strong evidence of recent population bottlenecks for some populations (Schoville et al 2011). Bayesian skyline estimates of effective population size fluctuations through time have shown the full range of scenarios, with reports of stable or increasing population size for some populations (Nuñez et al 2011) and historical bottlenecks for others (Mart ınez-Solano et al 2006).…”

Cantharidin is conserved across phylogeographic lineages and present in both morphs of Iberian Berberomeloe blister beetles (Coleoptera, Meloidae)

“…PCR reactions were performed as explained in Percino-Daniel et al (2013). Sequencing was as indicated in Martínez-Solano et al (2006).…”