Hybridization of two ancient salamander lineages: molecular evidence for endemic spectacled salamanders on the Apennine peninsula

Different Traits, Different Evolutionary Pathways: Insights from Salamandrina (Amphibia, Caudata)

Species delimitation is often based on a single or very few genetic or phenetic traits, something which leads to misinterpretations and often does not provide information about evolutionary processes. Here, we investigated the diversity pattern of multiple phenetic traits of the two extant species of Salamandrina, a genus split only after molecular traits had been studied but the two species of which are phenetically very similar. The phenetic traits we studied are size, external body shape and head colour pattern, in a model comparison framework using non-linear mixed models and unsupervised and supervised clustering. Overall, we found high levels of intra-specific variability for body size and shape, depending on population belonging and habitat, while differences between species were generally lower. The habitat the salamanders dwell in also seems important for colour pattern. Basing on our findings, from the methodological point of view, we suggest (i) to take into account the variability at population level when testing for higher level variability, and (ii) a semi-supervised learning approach to high dimensional data. We also showed that different phenotypic traits of the same organism could result from different evolutionary routes. Local adaptation is likely responsible for body size and shape variability, with selective pressures more similar across species than within them. Head colour pattern also depends on habitat, differently from ventral colour pattern (not studied in this paper) which likely evolved under genetic drift.

Evidences for a shared history for spectacled salamanders, haplotypes and climate

The so-called glacial refugia, formed during the Pleistocene climatic oscillations, played a major role in shaping the distribution of European species, triggering migrations or isolating populations. Many of these events were recently investigated by genetic data, mainly for the European Last Glacial stage, in the Iberic, Italian and Greek-Balkan peninsulas. The amphibian genus Salamandrina, the most ancient living salamandrid lineage, was widespread in Europe until the climatic oscillations of Miocene probably forced it to shelter in the only suitable territory at that time, the Apennines. Nowadays this genus is endemic of peninsular Italy with two parapatric species, S. perspicillata and S. terdigitata, sharing an area of secondary contact formed after the Last Glacial Maximum. Climate is generally identified as the key factor for the interpretation of genetic data. In this research, we directly measure climate influences on the two Salamandrina known species through Ensemble Modelling techniques and post-modelling GIS analyses, integrating updated genetic data in this process. Our results confirm the hypotheses of southwards (and subsequent northwards) shifts, identify glacial refugia and corridors used for the post-glacial re-colonization. Finally, we map a contact zone deserving more sampling effort to disentangle the introgression and hybridization observed.

Seven at one blow: the origin of major lineages of the viviparous Lycian salamanders (Lyciasalamandra Veith and Steinfartz, 2004) was triggered by a single paleo-historic event

The number of tectonic and climatic events that are used to explain speciation processes in the eastern Mediterranean region is low compared to the western Mediterranean. Among them, the emergence of the mid-Aegean trench and the Messinian Salinity Crisis (MSC) often concurred with speciation time estimates that were inferred from molecular data. We here present a dated molecular phylogeny of Lyciasalamandra from Turkey and Greece based on ca. 4500 bp of the mitochondrial genome (3000 bp of three nuclear genes appeared to be completely inconclusive due to their extremely low degree of variation among taxa). Seven major lineages emerged simultaneously from a basal hard polytomy. A scenario that dates this polytomy to 12.3 and 10.2 million years ago, around the final emergence of the mid-Aegean trench, appears to be most plausible. The MSC can be made responsible for first intraspecific divergence events within L. luschani, L. fazilae and L. flavimembris. Further diversification can be explained by Pliocene and Pleistocene glaciations. Based on levels of molecular differentiation we suggest the recently described species L. arikani, L. irfani and L. yehudahi to be treated as subspecies of L. billae.

Extensive unidirectional introgression between two salamander lineages of ancient divergence and its evolutionary implications

Hybridization and introgression, contrary to previous beliefs, are now considered to be widespread processes even among animal species. Nonetheless, the range of their possible outcomes and roles in moulding biodiversity patterns are still far from being fully appraised. Here we investigated the pattern of hybridization and introgression between Salamandrina perspicillata and S. terdigitata, two salamanders endemic to the Italian peninsula. Using a set of diagnostic or differentiated genetic markers (9 nuclear and 1 mitochondrial), we documented extensive unidirectional introgression of S. terdigitata alleles into the S. perspicillata gene pool in central Italy, indicating that barriers against hybridization were permeable when they came into secondary contact, and despite their ancient divergence. Nonetheless, purebred S. terdigitata, as well as F1, F2, and backcrosses were not found within the hybrid zone. Moreover, Bayesian analyses of population structure identified admixed populations belonging to a differentiated gene pool with respect to both parental populations. Overall, the observed genetic structure, together with their geographic pattern of distribution, suggests that Salamandrina populations in central Italy could have entered a distinct evolutionary pathway. How far they have gone along this pathway will deserve future investigation.

Radically different phylogeographies and patterns of genetic variation in two European brown frogs, genus Rana

We reconstruct range-wide phylogeographies of two widespread and largely co-occurring Western Palearctic frogs, Rana temporaria and R. dalmatina. Based on tissue or saliva samples of over 1000 individuals, we compare a variety of genetic marker systems, including mitochondrial DNA, single-copy protein-coding nuclear genes, microsatellite loci, and single nucleotide polymorphisms (SNPs) of transcriptomes of both species. The two focal species differ radically in their phylogeographic structure, with R. temporaria being strongly variable among and within populations, and R. dalmatina homogeneous across Europe with a single strongly differentiated population in southern Italy. These differences were observed across the various markers studied, including microsatellites and SNP density, but especially in protein-coding nuclear genes where R. dalmatina had extremely low heterozygosity values across its range, including potential refugial areas. On the contrary, R. temporaria had comparably high range-wide values, including many areas of probable postglacial colonization. A phylogeny of R. temporaria based on various concatenated mtDNA genes revealed that two haplotype clades endemic to Iberia form a paraphyletic group at the base of the cladogram, and all other haplotypes form a monophyletic group, in agreement with an Iberian origin of the species. Demographic analysis suggests that R. temporaria and R. dalmatina have genealogies of roughly the same time to coalescence (TMRCA ~3.5 mya for both species), but R. temporaria might have been characterized by larger ancestral and current effective population sizes than R. dalmatina. The high genetic variation in R. temporaria can therefore be explained by its early range expansion out of Iberia, with subsequent cycles of differentiation in cryptic glacial refugial areas followed by admixture, while the range expansion of R. dalmatina into central Europe is a probably more recent event.

Cryptic diversity among Western Palearctic tree frogs: postglacial range expansion, range limits, and secondary contacts of three European tree frog lineages (Hyla arborea group)

We characterize divergence times, intraspecific diversity and distributions for recently recognized lineages within the Hyla arborea species group, based on mitochondrial and nuclear sequences from 160 localities spanning its whole distribution. Lineages of H. arborea, H. orientalis, H. molleri have at least Pliocene age, supporting species level divergence. The genetically uniform Iberian H. molleri, although largely isolated by the Pyrenees, is parapatric to H. arborea, with evidence for successful hybridization in a small Aquitanian corridor (southwestern France), where the distribution also overlaps with H. meridionalis. The genetically uniform H. arborea, spread from Crete to Brittany, exhibits molecular signatures of a postglacial range expansion. It meets different mtDNA clades of H. orientalis in NE-Greece, along the Carpathians, and in Poland along the Vistula River (there including hybridization). The East-European H. orientalis is strongly structured genetically. Five geographic mitochondrial clades are recognized, with a molecular signature of postglacial range expansions for the clade that reached the most northern latitudes. Hybridization with H. savignyi is suggested in southwestern Turkey. Thus, cryptic diversity in these Pliocene Hyla lineages covers three extremes: a genetically poor, quasi-Iberian endemic (H. molleri), a more uniform species distributed from the Balkans to Western Europe (H. arborea), and a well-structured Asia Minor-Eastern European species (H. orientalis).