Search Results (39)

During the Pleistocene, the successive ice ages prompted the southward expansion of the “Mammoth Steppe” ecosystem, a prevalent habitat that supported species adapted to cold environments such as the mammoth, woolly rhinoceros, and reindeer. Previously, the earliest evidence for such cold-adapted species in the Iberian Peninsula dated back to Marine Isotope Stage 6 (MIS 6, ~191–123 ka). This paper reports the discovery of a reindeer (Rangifer) tooth from Unit GIII of the Galería site at the Atapuerca-Trinchera site complex, dated to MIS 8 (~300–243 ka). This find is significant as it represents not only the oldest evidence of glacial fauna in the Iberian Peninsula but also the southernmost occurrence of reindeer in Europe of this age. The presence of Rangifer at this latitude (42°21′ N) during MIS 8 suggests that the glacial conditions affected the Iberian fauna earlier and with greater intensity than previously understood. Over the subsequent climatic cycles, cold-adapted species spread further south, reaching Madrid (40°20′) during the penultimate glacial period and the province of Granada (37°01′) during the last glacial maximum. The coexistence of human fossils and lithic artefacts within Units GII and GIII at Galería indicates that early humans also inhabited these glacial environments at Atapuerca. This study elaborates on the morphological and archaeological significance of the reindeer fossil, emphasizing its role in understanding the biogeographical patterns of glacial fauna and the adaptability of Middle Pleistocene human populations. Full article

In the traditional classification system of the Lauraceae family based on morphology and anatomy, the phylogenetic position of the genus Sassafras has long been controversial. Chloroplast (cp) evolution of Sassafras has not yet been illuminated. In this study, we first sequenced and assembled the complete cp genomes of Sassafras, and conducted the comparative cp genomics, phylogenomics, and divergence time estimation of this ecological and economic important genus. The whole length of cp genomes of the 10 Sassafras ranged from 151,970 bp to 154,011 bp with typical quadripartite structure, conserved gene arrangements and contents. Variations in length of cp were observed in the inverted repeat regions (IRs) and a relatively high usage frequency of codons ending with T/A was detected. Four hypervariable intergenic regions (ccsA-ndhD, trnH-psbA, rps15-ycf1, and petA-psbJ) and 672 cp microsatellites were identified for Sassafras. Phylogenetic analysis based on 106 cp genomes from 30 genera within the Lauraceae family demonstrated that Sassafras constituted a monophyletic clade and grouped a sister branch with the Cinnamomum sect. Camphora within the tribe Cinnamomeae. Divergence time between S. albidum and its East Asian siblings was estimated at the Middle Miocene (16.98 Mya), S. tzumu diverged from S. randaiense at the Pleistocene epoch (3.63 Mya). Combined with fossil evidence, our results further revealed the crucial role of the Bering Land Bridge and glacial refugia in the speciation and differentiation of Sassafras. Overall, our study clarified the evolution pattern of Sassafras cp genomes and elucidated the phylogenetic position and divergence time framework of Sassafras. Full article

Fourteen Ameletus species are recognized in the eastern Nearctic (south of the Artic zone), including six described as new. Keys to adult males and full-grown larvae are provided. Taxonomic decisions were based on morphologic and genetic evidence. Their justification is discussed in depth and four species groups are proposed. The vast majority of Ameletus encountered in the eastern Nearctic are members of one of three triploid, clonal parthenogenetic species, at least two of which are of hybrid origin. Bisexual progenitors of the parthenogens were inferred using a combination of mitochondrial and nuclear genetic markers. The parthenogens likely arose during the Late Pleistocene when glacial advances brought previously allopatric species/populations into contact, and as glaciers retreated the parthenogens rapidly expanded their range while the sexual lineages remained in presumed glacial refugia. Although parthenogenesis is relatively common in Ephemeroptera, these Ameletus represent the first known cases of polyploidy and hybrid origin. Full article

Located at the crossroads of two continents and at the southeastern edge of the Mediterranean Basin, Anatolia was one of the most important Pleistocene glacial refugia in the Western Palaearctic. As part of the Irano-Anatolian, Caucasus and Mediterranean Basin biodiversity hotspots, this region is also home to a rich avian community including nearly 400 breeding species. Nevertheless, research addressing the genetic structure and diversity of local bird populations is limited, and information on glacial refugia in this region is still scant, especially when compared to other large Mediterranean peninsulas, namely the Balkan, Italian and Iberian ones. In this study, we contribute to filling this gap by addressing the biogeographic pattern of four common resident songbirds—the Eurasian blue tit (Cyanistes caeruleus), the great tit (Parus major), the Eurasian chaffinch (Fringilla coelebs) and the Eurasian blackbird (Turdus merula)—and one endemic species—the Krüper’s nuthatch (Sitta krueperi)—by amplifying two mitochondrial DNA genes in individuals from Anatolia (n = 329) and comparing their sequences to those of conspecifics from the rest of their distribution range across the western Palaearctic (n = 357) deposited in public databases. The overall genetic structure of these species is consistent with a scenario of isolation for multiple populations in different refugia across Anatolia and subsequent secondary contact in the wake of ice retreat, which makes this region a hotspot of genetic diversity for both widespread and endemic avian species. Full article

Studying the distribution of morphologically cryptic animal species is always a very difficult task. Because most marsh frog species (the Pelophylax ridibundus complex) are cryptic, we used molecular markers to identify them. Three marsh frog species (P. ridibundus, P. kurtmuelleri and P. cf. bedriagae) inhabit the northern part of Western Palearctic. We created a database of localities and built models of their modern distribution. These models showed that the most suitable habitats are on the north of the Mediterranean region for P. cf. bedriagae, temperate Europe for P. ridibundus, and the Balkan coastal areas for P. kurtmuelleri. The projection of the modern ecological niches under the late-Quaternary climatic conditions showed that the range of P. kurtmuelleri remained largely unchanged during the period, whereas the ranges of P. cf. bedriagae and especially P. ridibundus changed greatly over time. During the Last Glacial Maximum, the presumed range of P. cf. bedriagae covered a relatively large area in the north of the Mediterranean region and the south of European Russia. Glacial refugia of P. ridibundus were apparently located in the northern Balkans, the northern coast of the Black and Azov seas, and possibly in Western Europe. The northward long-distance post-glacial dispersal of P. ridibundus occurred from refugia in the northeastern Balkans and the Black-Azov seas region. Since the Late Pleistocene, suitable habitats for P. cf. bedriagae in southern Russia began to decline, but local habitats for P. ridibundus become more suitable. Therefore, a mosaic of populations consisting of these both species and their hybrids has now been found here. Full article

The Italian fauna includes about 170 species/subspecies of dung beetles, being one of the richest in Europe. We used data on dung beetle distribution in the Italian regions to investigate some macroecological patterns. Specifically, we tested if species richness decreased southward (peninsula effect) or northward (latitudinal gradient). We also considered the effects of area (i.e., the species–area relationship), topographic complexity, and climate in explaining dung beetle richness. Finally, we used multivariate techniques to identify biotic relationships between regions. We found no support for the peninsula effect, whereas scarabaeines followed a latitudinal gradient, thus supporting a possible role of southern areas as Pleistocene refuges for this group of mainly thermophilic beetles. By contrast, aphodiines were more associated with cold and humid climates and do not show a distinct latitudinal pattern. In general, species richness was influenced by area, with the Sardinian fauna being however strongly impoverished because of its isolation. Faunal patterns for mainland regions reflect the influence of current ecological settings and historical factors (Pleistocene glaciations) in determining species distributions. Full article

Petrolisthes lamarckii (Leach, 1821) and P. haswelli Miers, 1884 are a pair of sister species of porcelain crabs, both of which are common in the intertidal zone of southern China, typically found under rocks and in the crevices of coral reefs. However, the distribution, genetic relationship and diversity of the two species in China have not been rigorously studied. Meanwhile, P. lamarckii is considered as a complex of cryptic species due to their diverse morphological features. In this study, we identified 127 specimens of the P. lamarckii–P. haswelli complex (LH complex) and recognised a new species through morphological and molecular analysis. Furthermore, we constructed a time-calibrated phylogeny of the LH complex using three mitochondrial and two nuclear genes from all three species, finding that the divergence of the LH complex can be traced back to the Miocene epoch, and that the genetic diversity increased during the Mid-Pleistocene transition period. Glacial refugia formed during the Pleistocene climatic oscillations has been regarded as one of the contributing factors to the diversification of marine organisms in the north-western Pacific. Petrolisthes haswelli demonstrates a wide distribution along the southern coast of China, while other lineages display more restricted distributions. The research on the demographic history and gene flow of P. haswelli revealed that the Chinese coastal populations experienced an expansion event approximately 12.5 thousand years ago (Kya) and the asymmetrical gene flows were observed between the two sides of the Taiwan Strait and Qiongzhou Strait, respectively, which is likely influenced by the restriction of ocean currents. Full article

Pleistocene glaciations had profound impact on the spatial distribution and genetic makeup of species in temperate ecosystems. While the glacial period trapped several species into glacial refugia and caused abrupt decline in large populations, the interglacial period facilitated population growth and range expansion leading to allopatric speciation. Here, we analyzed 40 genomes of four species of ibex and found that Himalayan ibex in the Pamir Mountains evolved independently after splitting from its main range about 0.1 mya following the Pleistocene species pump concept. Demographic trajectories showed Himalayan ibex experienced two historic bottlenecks, one each c. 0.8–0.5 mya and c. 50–30 kya, with an intermediate large population expansion c. 0.2–0.16 mya coinciding with Mid-Pleistocene Transitions. We substantiate with multi-dimensional evidence that Himalayan ibex is an evolutionary distinct phylogenetic species of Siberian ibex which need to be prioritized as Capra himalayensis for taxonomic revision and conservation planning at a regional and global scale. Full article

The depressed river mussel Pseudanodonta complanata (Rossmässler, 1835) is an endangered freshwater bivalve with sparse distribution across Europe. Despite its high conservation priority, available data on the current population genetics and biogeography of P. complanata are very limited. In this paper, we studied the genetic diversity and differentiation of P. complanata based on newly sequenced COI and ND1 gene fragments, and on available sequences from the NCBI GenBank. We discovered a localized and highly divergent lineage in the Don River basin and a widespread but low diversified lineage distributed from the Volga River basin to the Oise River in France. A star-like haplotype network, results of mismatch analysis, and significant negative values of neutrality tests reveal that the pan-European lineage went through a bottleneck event. The discovery of the separate lineage in the Don River basin is and additional evidence of the existence of Pleistocene glacial refugia in the south of the Russian Plain. Moreover, this finding confirms the significance of the Azov Sea drainage as a freshwater biodiversity hotspot of great conservation importance. Full article

Phylogeographic and paleoclimatic modelling studies have been combined to infer the role of Pleistocene climatic oscillations as drivers of the genetic structure and distribution of Mediterranean taxa. For the European whip snake, Hierophis viridiflavus, previous studies based on paleoclimatic modelling have depicted a low reliability in the pattern of past climatic suitability across the central Mediterranean Basin, which barely fits the species’ genetic structure. In this study, we combined phylogeographic and paleoclimatic modelling tools to improve our understanding of the biogeographic history of H. viridiflavus, particularly extending the sampling and phylogeographic inferences to previously under-sampled regions. Phylogeographic analyses recovered two major clades that diverged at the beginning of the Pleistocene and had diversified in different ways by the late Pleistocene: the east clade (composed of three subclades) and the west clade (with no further structure). Paleoclimatic models highlighted the temperate character of H. viridiflavus, indicating range contractions during both the last inter-glacial and last glacial maximum periods. Range expansions from southern-located climatic refugia likely occurred in the Bølling–Allerød and Middle Holocene periods, which are supported by signals of demographic growth in the west clade and South–East–North subclade. Overall, this work improves our understanding of the historical biogeography of H. viridiflavus, providing further insights into the evolutionary processes that occurred in the Mediterranean Basin hotspot. Full article

Climatic changes during the Pleistocene were responsible for dramatic redistributions of plant species worldwide. On the rugged southern hemisphere island of Tasmania, temperature increases following the last glaciation saw upslope migration of climatically suitable species from lowland refugia and the expansion of eucalypt-dominated forests and woodlands in the Central Highlands. We integrate multiple lines of evidence (chloroplast and nuclear DNA markers, seedling morphology, and survival in common garden experiments) from a group of closely related endemic eucalypts (the alpine white gums) to argue that (i) the Central Highlands of the island were colonised by multiple glacial refugia with hybridisation among species and previously separated populations, and (ii) natural selection has filtered the admixed populations, resulting in local adaptation to the harsh sub-alpine environment. Chloroplast haplotype diversity decreased and nuclear microsatellite diversity increased with altitude, chloroplast sharing among taxa was common, and nuclear DNA differentiation of morphologically distinct taxa was lower in the Central Highlands compared with lowland regions. Local adaptation in the highlands was signalled by evidence from (i) a glasshouse trial in which directional selection (Q_ST > F_ST) had shaped seedling morphological trait variation and (ii) population survival differences in 35-year-old reciprocal plantings along the major environmental gradients. We conclude that the evolutionary response of these island endemic trees to past climate change has involved the interplay of both hybridisation and natural selection, highlighting the importance of maintaining species interactions under future climate change. Full article

The Pleistocene climatic oscillations (PCO) that provoked several cycles of glacial–interglacial periods are thought to have profoundly affected species distribution, richness and diversity around the world. While the effect of the PCO on population dynamics at temperate latitudes is well known, considerable questions remain about its impact on the biodiversity of neotropical mountains. Here, we use amplified fragment length polymorphism molecular markers (AFLPs) to investigate the phylogeography and genetic structure of 13 plant species belonging to the gentian genus Macrocarpaea (Gentianaceae) in the tropical Andes. These woody herbs, shrubs or small trees show complex and potentially reticulated relationships, including cryptic species. We show that populations of M. xerantifulva in the dry system of the Rio Marañón in northern Peru have lower levels of genetic diversity compared to other sampled species. We suggest that this is due to a recent demographic bottleneck resulting from the contraction of the montane wet forests into refugia because of the expansion of the dry system into the valley during the glacial cycles of the PCO. This may imply that the ecosystems of different valleys of the Andes might have responded differently to the PCO. Full article

Sustainable management of exploited and endangered species is facilitated by knowledge of their geographic genetic structure. Lake sturgeon (Acipenser fulvescens) epitomizes both categories, but genetic information has largely been limited to the Laurentian Great Lakes basin. We assessed the hierarchical geographic genetic structure of lake sturgeon across their Canadian range using a variation at 14 microsatellite loci. Observed patterns showed evidence of two ancestral groups which originated from Mississippian and Missourian glacial refugia. Coalescent analysis indicates the two lineages most recently shared common ancestry during the late Pleistocene and were likely isolated by the late Wisconsinan ice advance, with subsequent interpopulation divergences within each lineage reflecting their reciprocal isolation as glacial meltwaters receded. Hierarchical patterns of genetic relationships among contemporary populations largely reflect colonization histories and connections within primary and secondary watersheds. Populations in western Canada showed strong similarities based on their shared Missourian origins and colonization from glacial Lake Agassiz. By contrast, populations in the Great Lakes–St. Lawrence River drainage were largely founded from a Mississippian source. Sturgeon populations in northern parts of Ontario and Quebec showed evidence of mixed ancestry from secondary contact between the two refugial groups through Holocene meltwater lakes. Within major watersheds, the strong similarity among geographically separate populations reflects their shared ancestry during postglacial colonization. The general lack of structure within major river systems highlights historically continuous habitat (connectivity) and gene flow rather than contemporary barriers (dams). These data highlight the importance of Quaternary and prehistoric events on patterns of genetic diversity and divergence within and among contemporary populations, as well as the importance of these populations for conserving the species’ evolutionary legacy. Full article

Disentangling phylogenetic and phylogeographic patterns is fundamental to reconstruct the evolutionary histories of taxa and assess their actual conservation status. Therefore, in this study, for the first time, the most exhaustive biogeographic history of European wildcat (Felis silvestris) populations was reconstructed by typing 430 European wildcats, 213 domestic cats, and 72 putative admixed individuals, collected across the entire species’ distribution range, at a highly diagnostic portion of the mitochondrial ND5 gene. Phylogenetic and phylogeographic analyses identified two main ND5 lineages (D and W) roughly associated with domestic and wild polymorphisms. Lineage D included all domestic cats, 83.3% of putative admixed individuals, and also 41.4% of wildcats; these latter mostly showed haplotypes belonging to sub-clade Ia, that diverged about 37,700 years ago, long pre-dating any evidence for cat domestication. Lineage W included all the remaining wildcats and putative admixed individuals, spatially clustered into four main geographic groups, which started to diverge about 64,200 years ago, corresponding to (i) the isolated Scottish population, (ii) the Iberian population, (iii) a South-Eastern European cluster, and (iv) a Central European cluster. Our results suggest that the last Pleistocene glacial isolation and subsequent re-expansion from Mediterranean and extra-Mediterranean glacial refugia were pivotal drivers in shaping the extant European wildcat phylogenetic and phylogeographic patterns, which were further modeled by both historical natural gene flow among wild lineages and more recent wild x domestic anthropogenic hybridization, as confirmed by the finding of F. catus/lybica shared haplotypes. The reconstructed evolutionary histories and the wild ancestry contents detected in this study could be used to identify adequate Conservation Units within European wildcat populations and help to design appropriate long-term management actions. Full article

Placed in the center of the Mediterranean biodiversity hotspot, Italy plays a central role for the study of Europe’s biogeography. In this paper, the influence of climatic, spatial, and historical factors on current patterns of variation in earwig species richness and composition is investigated. The Italian earwig fauna is mainly composed of species which are either widely distributed in Europe and the Palearctic region or that are endemic to the Alps and the Apennines. Variation in species richness does not follow any obvious geographical patterns, but a positive influence of precipitation on richness is consistent with earwig preferences for humid climates. European mainland territories did not contribute substantially to the current biodiversity of Italian earwigs, which explains the lack of a distinct peninsula effect, although a southward decrease in similarity with the central European fauna was observed. However, southern areas did not exert a pivotal role during Pleistocene glaciations in determining current patterns of species richness. Variation in species composition among Italian regions can be mostly explained by geographical proximity, while climatic differences and historical (paleogeographical and paleoecological) events seem to have played a minor role. However, the isolation of ancient earwig stocks on Italian mountains led to the origin of a relatively large number of endemics, which makes the Italian earwig fauna one of the richest in Europe. Full article