Unexpected early extinction of the European pond turtle (Emys orbicularis) in Sweden and climatic impact on its Holocene range

Variation in shell morphology of the European pond turtle, Emys orbicularis, in fragmented central European populations

The European pond turtle (Emys orbicularis) is a widely distributed freshwater species inhabiting much of Europe, but it is often in population decrease or is locally extinct. In this study, we sampled five central European populations, of which four were autochthonous and one was introduced outside the native range. Moreover, two of the native populations were relatively isolated and at the periphery of the species, range. Using the frequency of shell anomalies, a geometric morphometric framework and an analysis of fluctuating asymmetry, we aimed to determine the degree of morphological differentiation among different populations. Significantly, a smaller number of individuals with a malformed shell or scutes occurred in the native core range population, which potentially has a high level of gene flow (Hungary). Although neither canonical variate analysis nor the morphological disparity analysis showed distinct differences between populations, we found significantly higher shell asymmetry in the two marginal populations (Austria and Slovakia) compared with the core range populations. Our results might thus support the central–marginal hypothesis and indicate potential genetically based conservation problems owing to demographic bottlenecks and/or isolation in marginal populations.

Origin, extinction and ancient DNA of a new fossil insular viper: molecular clues of overseas immigration

Viperinae is a subfamily of viperid snakes whose fossil record in the Mediterranean islands is, until now, restricted to 12 palaeontological deposits on seven islands. Revision of the material excavated 30 years ago from the Middle/Late Pleistocene–Holocene deposit of Es Pouàs [Eivissa (= Ibiza), Balearic Islands, western Mediterranean] revealed about 6000 bones of a small-sized viper across different stratigraphic levels. Its morphological characteristics are different enough to known species of Vipera to warrant the description of a new species, but the nearly complete mitochondrial genome obtained from this snake based on a sample dated to 16 130 ± 45 bp, suggested it belonged to a new insular population of Lataste’s viper (Vipera latastei), Vipera latastei ebusitana subsp. nov. Phylogenetic analysis indicates that the dispersal of the ancestors of V. l. ebusitana to Eivissa, most probably from a north-east Iberian population, occurred via overwater colonization < 1.5 Mya, well after the Messinian Salinity Crisis (5.97–5.32 Mya) when land bridges allowed terrestrial colonization of the Balearic Islands by mainland faunas. The morphological differences between V. l. ebusitana and the Iberian populations suggest that it is a new dwarf taxon resulting from insular evolutionary processes, becoming extinct shortly after the first human arrival to this island about 4000 years ago.

Complex hybridization patterns in European pond turtles (Emys orbicularis) in the Pyrenean Region

Hybrid zones are natural laboratories allowing insights in genetic processes like lineage diversification, speciation and introgression. Using large sampling, 15 microsatellite loci and a mitochondrial marker, we examined the Pyrenean contact zone of three pond turtle taxa (Emys orbicularis orbicularis, E. o. galloitalica, E. o. occidentalis). The Pyrenees are a biogeographically important region separating many lineages endemic to the Iberian Peninsula from their Western European counterparts. We discovered limited admixture, reflecting a complex biogeographic scenario. Simulations using Approximate Bayesian Computing supported that E. o. orbicularis invaded the Iberian Peninsula in the Holocene, circumventing the Pyrenees along the Mediterranean coast, and hybridized in the northern peninsula with the local coastal subspecies galloitalica, and to a lesser extent, with occidentalis. While E. o. occidentalis, and in particular E. o. orbicularis, expanded their ranges considerably during Holocene warming, E. o. galloitalica remained largely confined to its former Iberian refuge. Admixture among the three taxa is surprisingly low, and a future taxonomic investigation that includes the unstudied subspecies of E. orbicularis from North Africa, Eastern Europe and Asia has to determine whether their current status properly reflects their evolutionary divergence or whether certain taxa should be regarded as full species.

Tracing the maternal origin of the common wall lizard (Podarcis muralis) on the northern range margin in Central Europe

The maternal origin of isolated populations of the common wall lizard (Podracis muralis) in the Czech Republic, representing the north-eastern range border of the species, was addressed. We compared mitochondrial DNA sequences of the cytochrome b gene of samples from these populations with those from within the continuous range in Slovakia, the northern Balkan region, and those available from previous studies. We recorded five main haplogroups in the studied region, with all available Central European samples belonging to the same haplogroup. The star-like structure of this haplogroup suggests a scenario of relatively recent, post-glacial population expansion, which is further supported by a coalescent-based demographic analysis. The presence of unique haplotypes in two of the three isolated Czech populations together with close phylogenetic relationships to adjacent Slovak populations suggests either autochthonous origin or human-mediated introductions from geographically and genetically closest populations. We therefore support conservation programs for all three isolated Czech populations.

Tropical ancient DNA reveals relationships of the extinct Bahamian giant tortoise Chelonoidis alburyorum

Ancient DNA of extinct species from the Pleistocene and Holocene has provided valuable evolutionary insights. However, these are largely restricted to mammals and high latitudes because DNA preservation in warm climates is typically poor. In the tropics and subtropics, non-avian reptiles constitute a significant part of the fauna and little is known about the genetics of the many extinct reptiles from tropical islands. We have reconstructed the near-complete mitochondrial genome of an extinct giant tortoise from the Bahamas (Chelonoidis alburyorum) using an approximately 1 000-year-old humerus from a water-filled sinkhole (blue hole) on Great Abaco Island. Phylogenetic and molecular clock analyses place this extinct species as closely related to Galápagos (C. niger complex) and Chaco tortoises (C. chilensis), and provide evidence for repeated overseas dispersal in this tortoise group. The ancestors of extant Chelonoidis species arrived in South America from Africa only after the opening of the Atlantic Ocean and dispersed from there to the Caribbean and the Galápagos Islands. Our results also suggest that the anoxic, thermally buffered environment of blue holes may enhance DNA preservation, and thus are opening a window for better understanding evolution and population history of extinct tropical species, which would likely still exist without human impact.

Phylogeography and postglacial colonization of Central Europe by Anguis fragilis and Anguis colchica

Five slow-worm species are distributed in the Palearctic region. Two species, Anguis fragilis and A. colchica, are native to Central Europe, where only limited information on the phylogeography of the genus exists. Here, we examined the situation in Poland and surrounding regions, where a mitochondrial contact zone between the species is expected. We used new mitochondrial DNA sequences and available published data from Central Europe and the northern Balkans. Haplotypes of both species were recorded in the study area. Anguis fragilis is represented by a single haplogroup, while A. colchica by three haplogroups. This suggests four independent sources/refugia for postglacial colonization of northern Central Europe. The mitochondrial contact zone seems to mirror the borders between lowlands of the North European Plain and East European Plain, and the south-eastern Poland uplands, while the Vistula River does not constitute a barrier. The presence of both species, A. fragilis and A. colchica, in Poland should also be considered for protection by the Polish conservation legislation.

Archaeological evidence for the introduction of Emys orbicularis (Testudines: Emydidae) in the Balearic Islands, Western Mediterranean

Among the different anthropogenic processes that affected the current distribution of the European pond turtle (Emys orbicularis), the timing of the human-mediated translocations is rarely known. Here we present data derived from an archaeological specimen ofE. orbicularisobtained at the Roman site of Pollentia (Mallorca, Balearic Islands) using direct radiocarbon dating. These remains correspond to the early Roman period and represent the first reliable evidence for the ancient introduction of this turtle species in a Western Mediterranean Island.

Genetic structure and differentiation of the fire salamander Salamandra salamandra at the northern margin of its range in the Carpathians

Amphibian populations occurring at the margin of the species range exhibit lower genetic variation due to strong genetic drift and long-term isolation. Limited mobility and site fidelity together with habitat changes may accelerate genetic processes leading to local extinction. Here, we analyze genetic variation of the fire salamander subspecies Salamandra s. salamandra inhabiting the Outer Carpathian region in Poland, at the northern border of its distribution. Nuclear DNA polymorphism based on 10 microsatellite loci of 380 individuals sampled in 11 populations were analysed to measure gene flow between subpopulations and possible long-term isolation. Mitochondrial DNA control region analysis among 17 individuals representing 13 localities was used to detect the origin of populations which colonized Northern Europe after the last glaciation. Overall, pairwise FST’s and AMOVA test of ‘among group’ variation showed little differences in the allele frequencies and relatively high local gene flow. However, Bayesian clustering results revealed subtle structuring between eastern and western part of the studied region. Two extreme marginal populations from the Carpathian Piedmont revealed reduced genetic variation which may be attributed to strong influence of genetic drift. Only one mitochondrial DNA haplotype (type IIb) was found in all individuals and suggest that after the Last Glacial Maximum Salamandra salamandra migrated to the North-Western Europe from the single glacial refugium placed in the Balkan Peninsula.

Faunal histories from Holocene ancient DNA

Recent studies using ancient DNA have been instrumental in advancing understanding of the impact of Holocene climate change on biodiversity. Ancient DNA has been used to track demography, migration and diversity, and is providing new insights into the long-term dynamics of species and population distributions. The Holocene is key to understanding how the past has impacted on the present, as it bridges the gap between contemporary phylogeographic studies and those with inference on Pleistocene patterns, based on ancient DNA studies. Here, we examine the major patterns of Holocene faunal population dynamics and connectivity; highlighting the dynamic nature of species and population responses to Holocene climatic change, thereby providing an 'analogue' for understanding potential impacts of future change.

Relics of the Europe's warm past: phylogeography of the Aesculapian snake

Understanding how species responded to past climate change can provide information about how they may respond to the current global warming. Here we show how a European reptile species responded to the last natural global warming event at the Pleistocene-Holocene transition that led to the Holocene climatic optimum approximately 5000-8000 years ago. The Aesculapian snake, Zamenis longissimus, is a thermophilous species whose present-day distribution in the southern half of Europe is a remnant of much wider range during the Holocene climatic optimum when populations occurred as far north as Denmark. These northern populations went extinct as the climate cooled, and presently the species is extinct from all central Europe, except few relic populations in locally suitable microhabitats in Germany and the Czech Republic. Our phylogenetic and demographic analyses identified two major clades that expanded from their respective western and eastern refugia after the last glacial maximum (18,000-23,000 years ago) and contributed approximately equally to the present range. Snakes from the relic northern populations carried the Eastern clade, showing that it was primarily the snakes from the eastern, probably Balkan, refugium that occupied the central and northern Europe during the Holocene climatic optimum. Two small, deep-branching clades were identified in near the Black Sea and in Greece. These clades provide evidence for two additional refugia, which did not successfully contribute to the colonization of Europe. If, as our results suggest, some populations responded to the mid-Holocene global warming by shifting their ranges further north than other populations of the same species, knowing what populations were able to expand in different species may provide information about what populations will be important for the species' ability to cope with the current global warming.