Ancient Refugia Research Articles

Cytochrome b mitochondrial gene analysis-based phylogeography of a Sand lizard in the Crimea: ancient refugium at the peninsula, late expansion from the North, and first evidence of Lacerta agilis tauridica and L. a. exigua (Lacertidae: Sauria) hybridization

The contact zones of the distribution ranges of closely related reptile taxa are the source of valuable data on the microevolutionary processes in populations, the history of regional faunas origin, and the environmental preferences of the studied forms. Our study is focused on the genetic structure of the populations of sand lizard, Lacerta agilis Linnaeus, 1758, at the Crimean peninsula. This lacertid species inhabits the mountain (afforested) and plain (steppe) parts of the Crimea, being abundant or common in many areas. Lacerta agilis is represented in the Crimea by two subspecies: the widely distributed Eastern (L. a. exigua Eichwald, 1831) inhabiting a large part of Northern Eurasia, and the endemic (L. a. tauridica Suchow, 1927) residing in the Crimean mountains. Mitochondrial haplogroup affiliation corresponding to one of the subspecies (L. a. tauridica, L. a. exigua or L. a. chersonensis) was established for 225 L. agilis individuals from 81 localities in the Crimea and adjacent mainland territories. The nucleotide sequences of the complete cytochrome b gene of mitochondrial DNA (1143 bp) were studied in 75 L. agilis individuals from 68 localities. The genetic distance between both subspecies inhabiting the Crimea revealed by used molecular marker comprised 2.8%, which indicates their early divergence approximately at the transition of Early to Middle Pleistocene (ca. 1 Mya). L. a. tauridica is characterized by a comparatively deep genetic structure. Haplotypes occupying isolated positions on the phylogenetic tree of this subspecies were found in the south-western part of the Crimean Mountains, what might be explained by the localization of L. agilis microrefugia in areas least affected by the Late Pleistocene cooling. Genetic structure of L. a. exigua is more homogeneous. Another important result of our study was an identification of zones of haplogroups «exigua» and «tauridica» coexistence localized along the northern and eastern margins of the Crimean Mountains. The portion of the «exigua» haplogroup in local populations decreases southward and westward. The observed pattern of the spatial distribution of haplogroups seems to be a result of the hybridization zone formation between the sand lizard subspecies during the Holocene expansion of L. a. exigua. Ecological niches modeling for L. agilis subspecies and analysis of morphological variability of the lizards support the hypothesis of L. a. exigua and L. a. tauridica hybridization in the area of contact of their ranges in the eastern part of the Crimean Mountains.

Ancient refugia and present‐day habitat suitability of native laurophylls in Italy

AbstractQuestionsEuropean native laurophyllous species are interesting for their biogeography and evolutionary history, as well as for their responses to global changes. We identified Italian native laurophylls on the basis of morphology, biogeographical history and ecological niche to study whether these species are in equilibrium with the present‐day climate. Furthermore, we localized Quaternary refugia and areas of potential spread of native laurophylls using distribution patterns of realized and potential aggregations of native laurophylls, respectively.LocationItaly.MethodsWe extracted data for 17 087 forest plots from a phytosociological database. Detrended Correspondence Analysis of these plots with overlay of climatic and environmental variables was performed to identify native laurophylls, i.e., evergreen broad‐leaved species of late Tertiary radiation, occupying a warm and humid niche. Potential ranges of laurophylls were calculated using Beals’ index of sociological favourability. The realized/potential range‐size ratio was calculated for each single laurophyll to understand whether it is in equilibrium with the present‐day climate. Distribution patterns of realized and potential aggregations of laurophylls were mapped.ResultsOrdination analysis provided a selection of 11 species as Italian native laurophylls. Most of them occupied less than half of their estimated potential range. Realized aggregations richest in native laurophylls were localized in the central Apennines. However, the Italian forests showed high potential for native laurophylls with the richest potential aggregations in the whole Apennines and in the southern Alps.ConclusionsMost of the Italian native laurophylls showed non‐equilibrium with the current climate, suggesting that late‐Quaternary events could better explain their present‐day distribution than on‐going climate change. Furthermore, their refugia in central Italy suggest the persistence in sites with temperate climate during Quaternary environmental changes. The high suitability of Italian forests for laurophylls, along with global changes, suggests possible future spreading of these species.

Phylogeographic diversification and postglacial range dynamics shed light on the conservation of the kelp Saccharina japonica.

Studies of postglacial range shifts could enhance our understanding of seaweed species’ responses to climate change and hence facilitate the conservation of natural resources. However, the distribution dynamics and phylogeographic diversification of the commercially and ecologically important kelp Saccharina japonica in the Northwest Pacific (NWP) are still poorly surveyed. In this study, we analyzed the evolutionary history of S. japonica using two mitochondrial markers and 24 nuclear microsatellites. A STRUCTURE analysis revealed two partially isolated lineages: lineage H, which is scattered along the coast of Japan; and lineage P, which occurs along the west coast of the Japan Sea. Ecological niche modeling projections to the Last Glacial Maximum (LGM) revealed that the southern coasts of the Japan Sea and the Pacific side of the Oshima and Honshu Peninsulas provided the most suitable habitats for S. japonica, implying that these regions served as ancient refugia during the LGM. Ancient isolation in different refugia may explain the observed divergence between lineages P and H. An approximate Bayesian computation analysis indicated that the two lineages experienced post‐LGM range expansion and that postglacial secondary contact occurred in Sakhalin. Model projections into the year 2,100 predicted that S. japonica will shift northwards and lose its genetic diversity center on the Oshima Peninsula in Hokkaido and Shimokita Peninsula in Honshu. The range shifts and evolutionary history of S. japonica improve our understanding of how climate change impacted the distribution range and diversity of this species and provide useful information for the conservation of natural resources under ongoing environmental change in the NWP.

All quiet in the East: molecular analysis RetrievesChionomys layias part ofC. nivalis

Snow voles from Zard Kuh in Zagros Mts., Western Iran, were identified as distinct from the European snow vole Chionomys nivalis and described as a species new to science under the name C. layi Zykov, 2004. This description was missed in subsequent years by majority of authors dealing with the genus Chionomys, and taxonomic identity of the new species remains uncertain. In this study we conducted the first testing ever performed on taxonomic status of C. layi. We sequenced cytochrome b (1140 bp) and nuclear growth hormone receptor ghr (870 bp) in topotypes of layi and used them, together with all available haplotypes for snow voles, in phylogenetic reconstructions. Topology of phylogenetic trees accorded published results and topotypes of layi nested within reference samples of C. nivalis. They hold a supported sister position against sequences from the geographically nearby Caucasus and Alborz. Kimura-2 parameter metrics retrieved relatively low divergence (3.2 ± 0.5) between samples from the Zagros and the Alborz Caucasus. We conclude that layi is synonymous with C. nivalis. Our results also show that the ancient refugium for the European snow vole in the Kopet Dagh was detached from the Hyrcanian refugium in the mesic mountains to the south of the Caspian Sea.

Biogeography of the Kimberley, Western Australia: a review of landscape evolution and biotic response in an ancient refugium

AbstractAimWe review the biogeography of the Kimberley, with a particular focus on the geological and landscape history of the region. We identified broad geological and biogeographical discontinuities across the Kimberley, and propose a number of testable hypotheses concerning how the evolution of these land‐forms may have harboured and structured genetic diversity across the region.LocationThe Kimberley region, north‐western Australia.MethodsThe literature available on the Kimberley is summarized, in particular regarding the evolution of Kimberley landscapes and climate. Previous genetic work was assessed in order to establish whether common patterns exist, and to identify concordance with four putative broad‐scale biogeographical breaks to be tested when appropriate fine‐scale genetic data become available: (1) the geological division between the Kimberley Plateau and surrounding deformation zones of the King Leopold and Halls Creek orogens; (2) the east–west geological divide between different sandstone units of the Kimberley Plateau; (3) major drainage divisions and river courses; and (4) the previously defined bioregions and subregions of the Interim Biogeographical Regionalisation for Australia (IBRA), the Northern and Central Kimberley.ResultsGenetic patterns across a number of taxonomic groups in the Kimberley lend support to the four biogeographical scenarios we outline, and these now need to be tested with additional data.Main conclusionsThe biogeographical patterns emerging from studies of Kimberley biota are characterized by high endemism and deep divergences. In addition, a complex relationship between the Kimberley and other monsoon tropical bioregions and the adjacent deserts suggests multiple expansions into the arid zone, and vicariance and isolation in upland refugia within the topographically complex region. Fine‐scale genetic data are beginning to be accumulated for Kimberley taxa, and concordant phylogeographical patterns across disparate groups suggest that regional differences in geological structure and land‐forms may have played an important role in shaping the distribution and evolutionary patterns of extant biota. Future palaeoecological, geomorphological and finer scale phylogenetic investigations based on increased sampling and emerging genetic technologies will shed more light on the evolution of the Kimberley biome amidst one of the greatest environmental changes in the Cenozoic: the widespread aridification of the Australian continent.

Population genetics of Blanding’s turtle (Emys blandingii) in the midwestern United States

Blanding’s turtle (Emys blandingii) has declined substantially in North America due to anthropogenic activities, leaving populations smaller and increasingly fragmented spatially. We sampled 212 turtles to evaluate variation at eight microsatellite loci within and among 18 populations of E. blandingii across its primary range in the midwestern United States (Illinois, Iowa, Minnesota, and Nebraska). All loci and populations were highly polymorphic. Our analyses also detected considerable genetic structure within and among the sampled localities, and revealed ancestral gene flow of E. blandingii in this region north and east from an ancient refugium in the central Great Plains, concordant with post-glacial recolonization timescales. The data further implied unexpected ‘links’ between geographically disparate populations in Nebraska and Illinois. Our study encourages conservation decisions to be mindful of the genetic uniqueness of populations of E. blandingii across its primary range.

Geodiversity and endemism in the iconic Australian Pilbara region: a review of landscape evolution and biotic response in an ancient refugium

AbstractAimWe review the biogeography of the Pilbara, synthesize information on the geological and landscape history of this region and surrounds, and assess fine‐scale genetic structure across multiple taxa to examine hypotheses concerning the distribution of genetic lineages. We use this to provide a baseline for future biological studies in an ancient area of endemism.LocationThe Pilbara region, Western Australia.MethodsLiterature is summarized, including the history of Pilbara landscapes and climate, and previous biogeographical work. We used mitochondrial DNA phylogenetic datasets of seven co‐distributed gecko (diplodactyline and gekkonine) lineages to assess the monophyly of Pilbara lineages, and concordance with geological and habitat divisions.ResultsThe Pilbara harbours taxa genetically distinct from their non‐Pilbara relatives, despite close geographical proximity of populations. This is emphasized at the eastern and southern margins of the Pilbara, where habitat gradients are pronounced. In contrast, the northern margin, where sandy substrates of the Pilbara meet the dunes of the northern deserts, exhibits little genetic differentiation. Within the Pilbara, diversification patterns are idiosyncratic and may reflect species‐specific ecological differences. However, a repeated north/south partitioning of genetic diversity is evident across taxa. An additional emerging pattern is an east/west genetic division in the northern Pilbara, which may relate to major drainage divides and geological discontinuities associated with east and west Pilbara terrains.Main conclusionsThe Pilbara is an area of exceptionally high biotic diversity and endemism. The broader biogeographical patterns revealed in our molecular analyses are consistent with those recently identified using species richness patterns of invertebrates. Future studies of additional taxa using multiple molecular markers will provide the means to test and refine the biogeographical hypotheses presented here. Understanding the biogeography of the Pilbara and the partitioning of genetic diversity across the ancient and heterogeneous landscape is of paramount importance in the face of rapidly expanding economic and developmental pressures.

Phylogeography of the greater horseshoe bat,Rhinolophus ferrumequinum: contrasting results from mitochondrial and microsatellite data

Phylogeographical studies are typically based on haplotype data, occasionally on nuclear markers such as microsatellites, but rarely combine both. This is unfortunate because the use of markers with contrasting modes of inheritance and rates of evolution might provide a more accurate and comprehensive understanding of a species' history. Here we present a detailed study of the phylogeography of the greater horseshoe bat, Rhinolophus ferrumequinum, using 1098 bp of the mitochondrial ND2 gene from 45 localities from across its Palaearctic range to infer population history. In addition, we re-analysed a large microsatellite data set available for this species and compared the results of both markers to infer population relationships and the historical processes influencing them. We show that mtDNA, the most popular marker in phylogeography studies, yielded a misleading result, and would have led us to conclude erroneously that a single expansion had taken place in Europe. Only by combining the mitochondrial and microsatellite data sets are we able to reconstruct the species' history and show two colonization events in Europe, one before the Last Glacial Maximum (LGM) and one after it. Combining markers also revealed the importance of Asia Minor as an ancient refugium for this species and a source population for the expansion of the greater horseshoe bat into Europe before the LGM.

The colonization of Europe by the freshwater crustaceanAsellus aquaticus(Crustacea: Isopoda) proceeded from ancient refugia and was directed by habitat connectivity

Recent continental-scale phylogeographic studies have demonstrated that not all freshwater fauna colonized Europe from the classic Mediterranean peninsular refugia, and that northern or central parts of the continent were occupied before, and remained inhabited throughout the Pleistocene. The colonization history of the ubiquitous aquatic isopod crustacean Asellus aquaticus was assessed using mitochondrial COI and a variable part of nuclear 28S rDNA sequences. Phylogeographic analysis of the former suggested that dispersion proceeded possibly during late Miocene from the western part of the Pannonian basin. Several areas colonized from here have served as secondary refugia and/or origins of dispersion, well before the beginning of the Pleistocene. Postglacial large-scale range expansion was coupled with numerous separate local dispersions from different refugial areas. Connectivity of the freshwater habitat has played an important role in shaping the current distribution of genetic diversity, which was highest in large rivers. The importance of hydrographic connections for the maintenance of genetic contact was underscored by a discordant pattern of mtDNA and nuclear rDNA differentiation. Individuals from all over Europe, differing in their mtDNA to a level normally found between species or even genera (maximal within population nucleotide divergence reached 0.16 +/- 0.018), shared the same 28S rRNA gene sequence. Only populations from hydrographically isolated karst water systems in the northwestern Dinaric Karst had distinct 28S sequences. Here isolation seemed to be strong enough to prevent homogenization of the rRNA gene family, whereas across the rest of Europe genetic contact was sufficient for concerted evolution to act.