Late Pleistocene-dated divergence between South Hemisphere populations of the non-conventional yeast L. cidri.

Most organisms belonging to the Saccharomycotina subphylum have high genetic diversity and a vast repertoire of metabolisms and lifestyles, which explains its ecological versatility. The yeast Lachancea cidri is an ideal model for exploring the interplay between genetics, ecological function and evolution. L. cidri is a species that diverged from the Saccharomyces lineage before the whole-genome duplication and exhibits a broad distribution across the South Hemisphere, thus displaying an important ecological success. Here, we applied phylogenomics to investigate the adaptive genetic variation of L. cidri isolates obtained from natural environments in Australia and South America. Our approach revealed the presence of two main lineages according to their geographic distribution (Aus and SoAm). Estimation of the divergence time suggest that South American and Australian lineages diverged near the last glacial maximum event during the Pleistocene (64-8 KYA), consistent with the presence of multiple glacial refugia. Interestingly, we found that the French reference strain belongs to the Australian lineage, with a recent divergence (405-51 YA), likely associated to human movements. Additionally, species delimitation analysis identified different evolutionary units within the South American lineage and, together with parameters like Pi (π) and FST, revealed that Patagonia contains most of the genetic diversity of this species. These results agree with phenotypic characterizations, demonstrating a greater phenotypic diversity in the South American lineage. These findings support the idea of a Pleistocene-dated divergence between South Hemisphere lineages, where the Nothofagus and Araucaria ecological niches likely favored the extensive distribution of L. cidri in Patagonia.

Ancient mitochondrial genomes recovered from small vertebrate bones through minimally destructive DNA extraction: phylogeography of the New Zealand gecko genus Hoplodactylus.

Methodological and technological improvements are continually revolutionizing the field of ancient DNA. Most ancient DNA extraction methods require the partial (or complete) destruction of finite museum specimens, which disproportionately impacts small or fragmentary subfossil remains, and future analyses. We present a minimally destructive ancient DNA extraction method optimized for small vertebrate remains. We applied these methods to detect lost mainland genetic diversity in the large New Zealand diplodactylid gecko genus Hoplodactylus, which is presently restricted to predator-free island sanctuaries. We present the first mitochondrial genomes for New Zealand diplodactylid geckos, recovered from 19 modern, six historic/archival (1898 to 2011) and 16 Holocene Hoplodactylus duvaucelii sensu latu specimens, and one modern Woodworthia sp. specimen. No obvious damage was observed in post-extraction micro-CT reconstructions. All ‘large gecko’ specimens examined from extinct populations were found to be conspecific with extant Hoplodactylus species, suggesting their large relative size evolved only once in the New Zealand diplodactylid radiation. Phylogenetic analyses of Hoplodactylus samples recovered two genetically (and morphologically) distinct North and South Island clades, probably corresponding to distinct species. Finer phylogeographic structuring within Hoplodactylus spp. highlighted the impacts of Late-Cenozoic biogeographic barriers, including the opening and closure of Pliocene marine straits, fluctuations in size and suitability of glacial refugia, and eustatic sea-level change. Recent mainland extinction obscured these signals from the modern tissue derived data. These results highlight the utility of minimally destructive DNA extraction in genomic analyses of less well studied small vertebrate taxa, and the conservation of natural history collections.

The interaction of climate history and evolution impacts alpine biodiversity assembly differently in freshwater and on land

Quaternary climate fluctuations can affect biodiversity assembly through speciation in two non-mutually-exclusive ways: a glacial species pump, where isolation in glacial refugia accelerates allopatric speciation, and adaptive radiation during ice-free periods. Here we detected biogeographic and genetic signatures associated with both mechanisms in the generation of the European Alps biodiversity. Age distributions of endemic and widespread species within aquatic and terrestrial taxa (amphipods, fishes, amphibians, butterflies and flowering plants) revealed that endemic fish evolved only in lakes, are highly sympatric and mainly of Holocene age, consistent with adaptive radiation. Endemic amphipods are ancient, suggesting preglacial radiation with limited range expansion and local Pleistocene survival, perhaps facilitated by a groundwater-dwelling lifestyle. Terrestrial endemics are mostly of Pleistocene age, and are thus more consistent with the glacial species pump. The lack of evidence for Holocene adaptive radiation in the terrestrial biome may be attributable to a faster range expansion of these taxa after glacial retreats, though fewer stable environments may also have contributed to differences between terrestrial areas and lakes. The high proportion of young, endemic species make the Alps vulnerable to climate change, but the mechanisms and consequences of species loss will likely differ between biomes because of their distinct histories.

It takes two to tango – Phylogeography, taxonomy and hybridization in grass snakes and dice snakes (Serpentes: Natricidae: Natrix natrix, N. tessellata)

Using two mitochondrial DNA fragments and 13 microsatellite loci, we examined the phylogeographic structure and taxonomy of two codistributed snake species (Natrix natrix, N. tessellata) in their eastern distribution area, with a focus on Turkey. We found evidence for frequent interspecific hybridization, previously thought to be extremely rare, and for backcrosses. This underscores that closely related sympatric species should be studied together because otherwise the signal of hybridization will be missed. Furthermore, the phylogeographic patterns of the two species show many parallels, suggestive of a shared biogeographic history. In general, the phylogeographies follow the paradigm of southern richness to northern purity, but the dice snake has some additional lineages in the south and east in regions where grass snakes do not occur. For both species, the Balkan Peninsula and the Caucasus region served as glacial refugia, with several mitochondrial lineages occurring in close proximity. Our results show that the mitochondrial divergences in both species match nuclear genomic differentiation. Yet, in the former glacial refugia of grass snakes there are fewer nuclear clusters than mitochondrial lineages, suggesting that Holocene range expansions transformed the glacial hotspots in melting pots where only the mitochondrial lineages persisted, bearing witness of former diversity. On the other hand, the deep mitochondrial divergences in N. tessellata across its entire range indicate that more than one species could be involved, even though lacking microsatellite data outside of Turkey prevent firm conclusions. On the contrary, our microsatellite and mitochondrial data corroborate that N. megalocephala is invalid and not differentiated from sympatric populations of N. natrix. For Cypriot grass snakes, our analyses yielded conflicting results. A critical assessment of the available evidence suggests that N. natrix is a genetically impoverished recent invader on Cyprus and taxonomically not distinct from a subspecies also occurring in western Anatolia and the southern Balkans. Based on combined mitochondrial and nuclear genomic evidence we propose that for grass snakes the following subspecies should be recognized in our study region: (1) Natrix natrix vulgaris Laurenti, 1768, southeastern Central Europe and northern Balkans; (2) Natrix natrix moreoticus (Bedriaga, 1882), southern Balkans, western Anatolia, and Cyprus; and (3) Natrix natrix scutata (Pallas, 1771), eastern Anatolia, Caucasus region, Iran, northeastern distribution range (from eastern Poland and Finland to Kazakhstan and the Lake Baikal region). Thus, Natrix natrix cypriaca (Hecht, 1930) becomes a junior synonym of N. n. moreoticus and Natrix natrix persa (Pallas, 1814) becomes a junior synonym of N. n. scutata. Due to insufficient material, we could not resolve the status of Natrix natrix syriaca (Hecht, 1930) from the Gulf of İskenderun, southeastern Turkey.

Phylogeography of Myrica nana: the Wumeng Mountains as a natural geographical isolation boundary on the Yunnan-Guizhou Plateau

The Yunnan-Guizhou Plateau (YGP) is characterized by the distinctive isolated habitat of limestone Karst Islands and features the Wumeng Mountains (Mts), which divide the YGP into the two Plateaus of Yunnan and Guizhou. This study aims to assess the effects of past geographic and environmental isolation and climate fluctuation on the flora distribution in the YGP. To this effect, we analyzed the phylogeographical pattern and genetic structure for Myrica nana, a vulnerable species endemic to the YGP, based on chloroplast and nuclear ribosomal DNA sequence. The results suggest that the genetic and haplotype network structures are divided into at least two groups—cpDNA haplotype H2 (or nrDNA haplotypes h1, h2, and the native haplotype) mainly distributed to the east of the Wumeng Mts, and cpDNA haplotype H1 and haplotypes H3–H10 (or nrDNA haplotype h3) distributed to the west of the Wumeng Mts. A deep genetic split was noted within the two groups to reach 25 steps, especially for the cpDNA fragment variation. The east–west divergence reveals the existence of a natural geographical isolation boundary in the form of the Wumeng Mts, which divides the YGP into the Yunnan and Guizhou Plateaus. Therefore, there existed at least two glacial refugia during the Quaternary glacial period, along with a genetic diversity center, and at least two large geographic protection units for the vulnerable species of M. nana, distributed throughout the eastern and western sides of the Wumeng Mts. This study not only clarifies that the phylogeographical pattern and genetic structure for M. nana can be attributed to geographic and environmental isolation and climate fluctuation, but it also proposes an effective strategy to protect vulnerable species and the important wild flora of the YGP.

Pleistocene allopatric differentiation followed by recent range expansion explains the distribution and molecular diversity of two congeneric crustacean species in the Palaearctic

Pleistocene glaciations had a tremendous impact on the biota across the Palaearctic, resulting in strong phylogeographic signals of range contraction and rapid postglacial recolonization of the deglaciated areas. Here, we explore the diversity patterns and history of two sibling species of passively dispersing taxa typical of temporary ponds, fairy shrimps (Anostraca). We combine mitochondrial (COI) and nuclear (ITS2 and 18S) markers to conduct a range-wide phylogeographic study including 56 populations of Branchinecta ferox and Branchinecta orientalis in the Palaearctic. Specifically, we investigate whether their largely overlapping ranges in Europe resulted from allopatric differentiation in separate glacial refugia followed by a secondary contact and reconstruct their postglacial recolonization from the inhabited refugia. Our results suggest the existence of distinct refugia for the two species, with genetic divergence among intraspecific lineages consistent with late Pleistocene glacial cycles. While B. ferox lineages originated from Mediterranean refugia, the origin of B. orientalis lineages was possibly located on the Pannonian Plain. We showed that most dispersal events predominantly happened within 100 km, coupled with several recent long-distance events (> 1000 km). Hence the regional habitat density of suitable habitats in Central Europe is possibly a key to the co-existence of the two species. Overall, our study illustrates how isolation in combination with stochastic effects linked to glacial periods are important drivers of the allopatric differentiation of Palaearctic taxa.

A cosmogenic nuclide chronology of Cordilleran Ice Sheet configuration during the Last Glacial Maximum in the northern Alexander Archipelago, Alaska

The late-Pleistocene history of the coastal Cordilleran Ice Sheet (CIS) remains relatively unstudied compared to chronologies of the Laurentide Ice Sheet. Yet accurate reconstructions of CIS extent and timing of ice retreat along the Pacific Coast are essential for a variety of reasons including paleoclimate modeling, assessing meltwater contribution to the North Pacific, and determining the availability of ice-free land along the coastal CIS margin for human migration from Beringia into the Americas. To improve the chronology of CIS history in the Alexander Archipelago, Alaska, we applied 10Be and 36Cl dating to boulders and glacially sculpted bedrock outcrops in areas previously hypothesized to have remained ice-free throughout the local Last Glacial Maximum (lLGM; 20–17 ka). Results indicate that these sites, and more generally the coastal northern Alexander Archipelago, became ice-free by 15.1 ± 0.9 ka (n = 12 boulders; 1 SD). We also provide further age constraints on deglaciation along the southern Alexander Archipelago and combine our new ages with data from two previous studies. We determine that ice retreated from the outer coast of the southern Alexander Archipelago at 16.3 ± 0.8 ka (n = 14 boulders; 1 SD). These results collectively indicate that areas above modern sea level that were previously mapped as glacial refugia were covered by ice during the lLGM until between ~16.3 and 15.1 ka. As no evidence was found for ice-free land during the lLGM, our results suggest that previous ice-sheet reconstructions underestimate the regional maximum CIS extent, and that all ice likely terminated on the continental shelf. Future work should investigate whether presently submerged areas of the continental shelf were ice-free.

Past, present, and future climate space of the only endemic vertebrate genus of the Italian peninsula

The two extant Salamandrina species represent a unique case of morphology, ecology, and ethology among urodeles. The range of this genus is currently limited to Italy, where it represents the only endemic vertebrate genus, but its past range extended over a much broader area of Europe, including the Iberian and Balkan peninsulas. ENM analyses using modern occurrences of Salamandrina demonstrate that the current climate of the majority of Europe, and especially areas where fossils of this genus were found, is currently not suitable for this genus, neither was it suitable during the last 3.3 million years. This result allows possible assumptions about the climatic influence on the former extirpation of this salamander from several areas of Europe. Furthermore, it shows that, during Pliocene–Pleistocene climatic oscillations, Mediterranean peninsulas, despite being generally considered together because of similar latitude, had different potential to effectively become glacial refugia for this salamander, and possibly for other species as well. Future projections using different CO2 emission scenarios predict that climatic suitability will be even more drastically reduced during the next 50 years, underlining once more the importance of conservation strategies and emission-reducing policies.