Southern Refugia Research Articles

Genome-wide SNP assessment of contemporary European red deer genetic structure highlights the distinction of peripheral populations and the main admixture zones in Europe.

Genome-wide technologies open up new possibilities to clarify questions on genetic structure and phylogeographic history of taxa previously studied with microsatellite loci and mitochondrial sequences. Here, we used 736 individual red deer (Cervus elaphus) samples genotyped at 35,701 single nucleotide polymorphism loci (SNPs) to assess the population structure of the species throughout Europe. The results identified 28 populations, with higher degrees of genetic distinction in peripheral compared to mainland populations. Iberian red deer show high genetic differentiation, with lineages in Western and Central Iberia maintaining their distinctiveness, which supports separate refugial ranges within Iberia along with little recent connection between Iberian and the remaining Western European populations. The Norwegian population exhibited the lowest variability and the largest allele frequency differences from mainland European populations, compatible with a history of bottlenecks and drift during post-glacial colonization from southern refugia. Scottish populations showed high genetic distance from the mainland but high levels of diversity. Hybrid zones were found between Eastern and Western European lineages in Central Europe as well as in the Pyrenees, where red deer from France are in close contact with Iberian red deer. Anthropogenic restocking has promoted the Pyrenean contact zone, admixture events in populations on the Isle of Rum and in the Netherlands, and at least partly the admixture of the two main lineages in central-eastern Europe. Our analysis enabled detailed resolution of population structure of a large mammal widely distributed throughout Europe and contributes to resolving the evolutionary history, which can also inform conservation and management policies.

Do northern species of amphibians and reptiles of Eurasia need southern refugia?

Abstract I do not support modern ideas regarding the sheltering of northern species of amphibians and reptiles in southern refugia during glacial periods. The current article presents arguments that reject the traditional point of view. The northern species did not fall within southern refugia, and therefore new forms (haplotypes) appeared within the periglacial hyperzone. I describe how these processes may have taken place.

Origins of hatchery-reared lake trout Salvelinus namaycush to Lake Michigan’s sport fishery reflect trends in regional relative survival

Fisheries management depends on understanding fish movements, especially in large systems. In Lake Michigan, lake trout are stocked for rehabilitation and to support a diverse, multi-million dollar sport fishery. We described the contributions of lake trout stocked at offshore and onshore locations to Lake Michigan’s sport fishery at multiple spatial scales. We also assessed lake trout relative survival and age-related seasonal movements. Offshore reefs, which historically were important sources of lake trout recruitment and are currently fishery refuges, served as source-populations for nearshore fisheries, as offshore-stocked lake trout comprised 58% of recoveries lakewide and were predominant in fisheries from 9 of 13 management units. By contrast, lake trout stocked onshore primarily had local importance, consistent with the management aim to directly benefit nearshore fisheries. Lake trout relative survival significantly differed among stocking regions but not between the two genetic strains compared. Lake trout stocked at two of the three offshore regions, Julian’s Reef and Southern Refuge, had higher relative survival (0.022–0.038 fish/sampling day/100,000 fish stocked) compared to the three onshore stocking regions (0.001–0.013) and the offshore Northern Refuge (0.011), which helps explain the predominance of offshore-stocked fish in fisheries at most locations. In addition, offshore-stocked fish were most available to sport fisheries in multiple regions during summer, while mature fish generally returned to their stocking region in fall, presumably to spawn. This study demonstrated that stocking at offshore locations in Lake Michigan supported both lake trout rehabilitation efforts and sport fisheries, and illustrates how spatial ecology can help inform fisheries management.

Evolutionary history and seascape genomics of Harbour porpoises (Phocoena phocoena) across environmental gradients in the North Atlantic and adjacent waters.

The Harbour porpoise (Phocoena phocoena) is a highly mobile cetacean species primarily occurring in coastal and shelf waters across the Northern hemisphere. It inhabits heterogeneous seascapes broadly varying in salinity and temperature. Here, we produced 74 whole genomes at intermediate coverage to study Harbour porpoise's evolutionary history and investigate the role of local adaptation in the diversification into subspecies and populations. We identified ~6 million high quality SNPs sampled at eight localities across the North Atlantic and adjacent waters, which we used for population structure, demographic and genotype-environment association analyses. Our results suggest a genetic differentiation between three subspecies (P.p. relicta, P.p. phocoena and P.p. meridionalis), and three distinct populations within P.p. phocoena: Atlantic, Belt Sea and Proper Baltic Sea. Effective population size and Tajima's D suggest population contraction in Black Sea and Iberian porpoises, but expansion in the P.p. phocoena populations. Phylogenetic trees indicate post-glacial colonization from a southern refugium. Genotype-environment association analysis identified salinity as major driver in genomic variation and we identified candidate genes putatively underlying adaptation to different salinity. Our study highlights the value of whole genome resequencing to unravel subtle population structure in highly mobile species, shows how strong environmental gradients and local adaptation may lead to population differentiation, and how neutral and adaptive markers can give different perspectives on population subdivision. The results have great conservation implications as we found inbreeding and low genetic diversity in the endangered Black Sea subspecies and identified the critically endangered Proper Baltic Sea porpoises as a separate population.

A small survey of introduced Zaprionus indianus (Diptera: Drosophilidae) in orchards of the eastern United States.

The African fig fly, Zaprionus indianus (Gupta), is a generalist fruit fly that typically breeds in decaying fruits from over 70 plant species. The species has spread globally from its native range in tropical Africa, becoming an invasive pest on ripening figs in Brazil. First reported in the United States in 2005 in Florida, Z. indianus has since been documented as far north as Canada and is hypothesized to recolonize northwards from southern refugia each year. We sampled drosophilid communities over the growing season at 2 orchards in Virginia from 2020 to 2022 and 11 orchards along the East Coast during the fall of 2022 to quantify the abundance of Z. indianus relative to other drosophilids across locations, seasons, and fruit crops. Massachusetts had the northernmost population, with no Z. indianus detected in Maine and no correlation between latitude and relative abundance. Variation in Z. indianus relative abundance was high between nearby orchards and abundance was higher on peaches relative to apples within orchards. Comparisons of seasonal abundance curves between 2 Virginia orchards showed similar dynamics across years with individuals first detected around July and becoming absent around December, with peaks in late summer and mid-fall. The variation in seasonal and latitudinal abundance shown here highlights a need for broader sampling to accurately characterize the range, spread, and environmental tolerances of Z. indianus in North America.

Biogeographic barriers and historic climate shape the phylogeography and demography of the common gartersnake

AbstractAimCurrent distributions of widespread North American (NA) species have been shaped by Pleistocene glacial cycles, latitudinal temperature gradients, sharp longitudinal habitat transitions and the vicariant effects of major mountain and river systems that subdivide the continent. Within these transcontinental species, genetic diversity patterns might not conform to established biogeographic breaks compared to more spatially restricted taxa due to intrinsic differences or spatiotemporal differences. In this study, we highlight the effects of these extrinsic variables on genetic structuring by investigating the phylogeographic history of a widespread generalist squamate found throughout NA.LocationNorth America.TaxonCommon gartersnake, Thamnophis sirtalis.MethodsWe evaluate the effects of major river basins and the forest‐grassland transition into the Interior Plains on genetic structure patterns using phylogenetic, spatially informed population structure and demographic analyses of single nucleotide polymorphism data and address range expansion history with ecological niche modelling using locality and historic climate data.ResultsWe identify four phylogeographic lineages with varying degrees of connectivity between them. We find discordant population structure patterns between sex‐linked and autosomal loci with respect to the relationship between the central NA lineage relative to coastal lineages. We find support for southeast Pleistocene refugia where recent secondary contact occurred during the Last Glacial Maximum and evidence for both northern and southern refugia in western NA.Main ConclusionOur results provide strong evidence for a Pliocene origin for T. sirtalis in central‐southeastern NA preceding its rapid expansion across the continent prior to middle Pleistocene climate‐mediated lineage formation. We implicate major riverine networks within the Mississippi watershed in likely repeated westward expansion events across the Interior Plains. Finally, we corroborate prior conclusions that phenotypic differences between subspecies do not reflect shared evolutionary history and note that the degree of separation between inferred lineages warrants further investigation before any taxonomic revisions are proposed.

Phylogeography and distribution modelling reveal the history and future of a saproxylic beetle of European conservation concern

AbstractAimThe biogeography of European forests presents many interesting case studies, as inferred from phylogeography, contemporary population genetics, and distribution modelling of saproxylic species. Here, we pose four main hypotheses: (i) the phylogeographic paradigm known for temperate species in Europe is also applicable for saproxylic taxa; (ii) current expansion is occurring only in some genetic lineages; (iii) genetic diversity decreases from east to west, reflecting differences in forest naturalness and management; and (iv) climatic changes will force a northward range shift.LocationEurope.TaxonThe saproxylic beetle, Cucujus cinnaberinus (Scopoli, 1763).MethodsBeetles from 37 locations throughout the species range were genotyped using microsatellites and mtDNA (468 and 237 individuals, respectively). Molecular data were analysed to describe population diversity, structure, and demography. 200 records were used to model distribution based on climate data.ResultsmtDNA analyses revealed three clades: the most divergent in Italy and two less distinct in north‐western and central‐to‐southeastern Europe. Microsatellites showed no clear geographic distribution pattern except for a distinct lineage in Italy. The highest genetic diversity was found in southern refugia, in natural forests of Central‐Eastern Europe, and in a mixing zone in Pannonia. During the Holocene, the Italian population declined, whereas populations in the rest of Europe showed no clear changes. Distribution models revealed the existence of glacial refugia along the coasts of the Adriatic and Black Seas, and northward dispersal in the Holocene continued in the XXI century.ConclusionsC. cinnaberinus has a complex historical biogeography, discordant with patterns known for temperate or boreal taxa. The current expansion occurs only in populations from mainland Europe, whereas southernmost populations are in decline. Current genetic diversity is shaped by recent forest management, which is the least intensive in Eastern Europe. Climate change will most likely enhance northward dispersal and threaten the survival of the southernmost populations.

Regional environmental and climatic concerns on preserving native gene pools of a least concern species: Brown trout lineages in Mediterranean streams

The European brown trout, Salmo trutta, is a cold-adapted fish reported as a Least Concern species in the IUCN Red List. This species colonized new territories from southern refuges during the last glacial melting, but during the 20th century suffered from anthropic impacts on its habitats. The long-time survival of the species relies on the genetic diversity within and among populations. Brown trout is among the genetically most diverse vertebrate species; however, native populations in Mediterranean rivers have dramatically suffered of introgressive hybridization from extensive releases of evolutionary distant non-native Atlantic stocks. In addition, in Mediterranean rivers climate change will result in unsuitable conditions for the species during the 21st century. Using brown trout populations at the headstreams of a Pyrenean river as a model, this paper revised how hatchery releases have affected the native gene pools and how environmental and climatic variables controlled the amount of local introgression at intra-basin level. Introgressive hybridization was detected in all studied sites. Ten times larger divergence was observed among populations at tributaries than among populations along the main stem. A highly impacted population distributed in a long transect in the main stem suggested that hatchery fish move towards the main stem wherever released. From already highly impacted populations and despite the cessation of hatchery releases, warmer temperatures and lower precipitation expected from climate change will extend the introgressive hybridization along the basin, contributing to the extinction of the native gene pools. Based on available morphological distinction of native, hatchery and hybrid brown trout, we advocate the involvement of regional social groups (e.g. riverside dwellers, anglers, conservationists, hikers) in citizen science programs to detect the spread of non-native phenotypes along the rivers. These are cheap and fast methods to collaborate with fishery managers in the preservation and recovery of the regional native populations.

A southern refugium for temperate tree species in the Mediterranean mountains of El Port massif (NE Iberia): Charcoal analysis at Cova Del Vidre

This study focuses on the analysis of wood charcoal from Cova del Vidre (Roquetes, Tarragona, Spain). This cave, located at an altitude of 1000 m a.s.l., is a key site for understanding the transition from hunting and gathering to farming in a mountainous region of north-eastern Iberia so far unexplored by archaeobotany. The anthracological study is based on four archaeological levels from the Epipalaeolithic to the Early Neolithic dated between 12.9 and 6.8 kyr cal BP, that is, from the Late Glacial period to the Middle Holocene. During the Younger Dryas, the record is dominated by a little varied spectrum of cryophilous pines ( Pinus tp. sylvestris) and thorny shrubs revealing an open landscape where Prunus may prefigure the spread of temperate taxa. In the Early Holocene, a significant change in temperature and precipitation is evidenced, which promoted successional changes in plant communities, with a decline of pine and the sudden rise of temperate/Mediterranean taxa, such as Prunus and Quercus coccifera/ilex. During the Middle Holocene, other temperate taxa appear, such as Quercus deciduous, Buxus sempervirens and Taxus baccata, with yew finally dominating the anthracological record. The appearance and early development of temperate or Mediterranean species as early as the Younger Dryas and the Early Holocene periods, in a mountain context that had long been favourable for Scots pine, allows us to argue the local existence of a glacial refugium. Differences with the nearby sites in the lowlands demonstrate that altitudinal differences in vegetation were already established in the Holocene. Furthermore, the site helps to define the palaeodistribution of Taxus baccata, Abies alba and Fagus sylvatica in southern Europe.

Genetic evidence for post-glacial expansion from a southern refugium in the eastern moa (Emeus crassus).

Cycles of glacial expansion and contraction throughout the Pleistocene drove increases and decreases, respectively, in the geographical range and population size of many animal species. Genetic data have revealed that during glacial maxima the distribution of many Eurasian animals was restricted to small refugial areas, from which species expanded to reoccupy parts of their former range as the climate warmed. It has been suggested that the extinct eastern moa (Emeus crassus)-a large, flightless bird from New Zealand-behaved analogously during glacial maxima, possibly surviving only in a restricted area of lowland habitat in the southern South Island of New Zealand during the Last Glacial Maximum (LGM). However, previous studies have lacked the power and geographical sampling to explicitly test this hypothesis using genetic data. Here we analyse 46 ancient mitochondrial genomes from Late Pleistocene and Holocene bones of the eastern moa from across their post-LGM distribution. Our results are consistent with a post-LGM increase in the population size and genetic diversity of eastern moa. We also demonstrate that genetic diversity was higher in eastern moa from the southern extent of their range, supporting the hypothesis that they expanded from a single glacial refugium following the LGM.

Genome-Scale Data Reveal Deep Lineage Divergence and a Complex Demographic History in the Texas Horned Lizard (Phrynosoma cornutum) throughout the Southwestern and Central United States.

The southwestern and central United States serve as an ideal region to test alternative hypotheses regarding biotic diversification. Genomic data can now be combined with sophisticated computational models to quantify the impacts of paleoclimate change, geographic features, and habitat heterogeneity on spatial patterns of genetic diversity. In this study, we combine thousands of genotyping-by-sequencing (GBS) loci with mtDNA sequences (ND1) from the Texas horned lizard (Phrynosoma cornutum) to quantify relative support for different catalysts of diversification. Phylogenetic and clustering analyses of the GBS data indicate support for at least three primary populations. The spatial distribution of populations appears concordant with habitat type, with desert populations in AZ and NM showing the largest genetic divergence from the remaining populations. The mtDNA data also support a divergent desert population, but other relationships differ and suggest mtDNA introgression. Genotype–environment association with bioclimatic variables supports divergence along precipitation gradients more than along temperature gradients. Demographic analyses support a complex history, with introgression and gene flow playing an important role during diversification. Bayesian multispecies coalescent analyses with introgression (MSci) analyses also suggest that gene flow occurred between populations. Paleo-species distribution models support two southern refugia that geographically correspond to contemporary lineages. We find that divergence times are underestimated and population sizes are overestimated when introgression occurred and is ignored in coalescent analyses, and furthermore, inference of ancient introgression events and demographic history is sensitive to inclusion of a single recently admixed sample. Our analyses cannot refute the riverine barrier or glacial refugia hypotheses. Results also suggest that populations are continuing to diverge along habitat gradients. Finally, the strong evidence of admixture, gene flow, and mtDNA introgression among populations suggests that P. cornutum should be considered a single widespread species under the General Lineage Species Concept.

Complex and divergent histories gave rise to genome-wide divergence patterns amongst European whitefish (Coregonus lavaretus).

Pleistocene glaciations dramatically affected species distribution in regions that were impacted by ice cover and subsequent postglacial range expansion impacted contemporary biodiversity in complex ways. The European whitefish, Coregonus lavaretus, is a widely distributed salmonid fish species on mainland Europe, but in Britain it has only seven native populations, all of which are found on the western extremes of the island. The origins and colonization routes of the species into Britain are unknown but likely contributed to contemporary genetic patterns and regional uniqueness. Here, we used up to 25,751 genome‐wide polymorphic loci to reconstruct the history and to discern the demographic and evolutionary forces underpinning divergence between British populations. Overall, we found lower genetic diversity in Scottish populations but high differentiation (F ST = 0.433–0.712) from the English/Welsh and other European populations. Differentiation was elevated genome‐wide rather than in particular genomic regions. Demographic modelling supported a postglacial colonization into western Scotland from northern refugia and a separate colonization route for the English/Welsh populations from southern refugia, with these two groups having been separated for more than ca. 50 Ky. We found cyto‐nuclear discordance at a European scale, with the Scottish populations clustering closely with Baltic population in the mtDNA analysis but not in the nuclear data, and with the Norwegian and Alpine populations displaying the same mtDNA haplotype but being distantly related in the nuclear tree. These findings suggest that neutral processes, primarily drift and regionally distinct pre‐glacial evolutionary histories, are important drivers of genomic divergence in British populations of European whitefish. This sheds new light on the establishment of the native British freshwater fauna after the last glacial maximum.

Evidence for multiple colonisations and Wolbachia infections shaping the genetic structure of the widespread butterfly Polyommatus icarus in the British Isles

The paradigm of isolation in southern refugia during glacial periods followed by expansions during interglacials, producing limited genetic differentiation in northern areas, dominates European phylogeography. However, the existence of complex structured populations in formerly glaciated areas, and islands connected to mainland areas during glacial maxima, call for alternative explanations. We reconstructed the mtDNA phylogeography of the widespread Polyommatus Icarus butterfly with an emphasis on the formerly glaciated and connected British Isles. We found distinct geographical structuring of CO1haplogroups, with an ancient lineage restricted to the marginal European areas, including Northern Scotland and Outer Hebrides. Population genomic analyses, using ddRADSeq genomic markers, also reveal substantial genetic structuring within Britain. However, there is negligble mito-nuclear concordance consistent with independent demographic histories of mitochondrial versus nuclear DNA. While mtDNA-Wolbachia associations in northern Britain could account for the geographic structuring of mtDNA across most of the British Isles, for nuclear DNA markers (derived from ddRADseq data) butterflies from France cluster between northern and southern British populations - an observation consistent with a scenario of multiple recolonisation. Taken together our results suggest that contemporary mtDNA structuring in the British Isles (and potentially elsewhere in Europe) largely results from Wolbachia infections, however, nuclear genomic structuring suggests a history of at least two distinct colonisations. This two-stage colonisation scenario has previously been put forth to explain genetic diversity and structuring in other British flora and fauna. Additionally, we also present preliminary evidence for potential Wolbachia-induced feminization in the Outer Hebrides.

Genomic footprints of Quaternary colonization and population expansion in the Patagonian‐Fuegian region rules out a separate southern refugium in Tierra del Fuego

AbstractAimDuring the glacial phases, the Andean slopes of southern South America were covered by ice sheets, causing the isolation of many species in glacial refugia. This work aimed to test the number and putative location of glacial refugia in southern South America and establish the sources, timing and direction of post‐glacial colonization events.LocationSouthern South America, Patagonia.TaxonOlive mouse (Abrothrix olivacea).MethodsUsing exome capture, we genotyped 7339 SNPs in 172 specimens of A. olivacea collected at 21 localities distributed across the steppe, grasslands, and forests in the Patagonian‐Fuegian region and seven specimens from two other species of Abrothrix. Based on the effective migration rate, principal component analysis, and admixture composition, we first study the population structure of A. olivacea. The source and direction of colonization events were inferred using the directionality index and standard population genetic analyses. To study the role of the glacial phases, we performed a bayesian demographic analysis to infer divergences times and ancestral population sizes.ResultsPopulation genomic analyses based on SNPs of more than 7000 exons identified three Patagonian genetic clusters: Valdivian forests, continental Magellan forests, and a combination of continental open biomes and Tierra del Fuego. The directionality index supports a single source in northwestern forests, in line with a Valdivian forest refugium, from which the post‐glacial colonization may have started. The effective diversity rate, the onset of population expansions and divergence times also support a Valdivian forest refugium and rule out a separate southern refugium in Tierra del Fuego.Main conclusionsOur results support a coastal refugium located in or near the previously proposed Valdivian refugium and reject in situ differentiation in Tierra del Fuego. More in general, our demographical analysis reveals the role of the Last Glacial Maximum in affecting the population dynamics (i.e., contraction and expansion) of A. olivacea and in fostering the geographical diversification of populations.

Surviving in southern refugia: the case of Veronica aragonensis, a rare endemic from the Iberian Peninsula

Surviving in southern refugia: the case of Veronica aragonensis, a rare endemic from the Iberian Peninsula

Impact of Quaternary climatic oscillations on phylogeographic patterns of three habitat‐segregated Cerastium taxa endemic to the Dinaric Alps

AbstractAimThe Balkan Peninsula has served as source for the colonisation of large parts of Europe after the Pleistocene, but the processes driving the intraspecific diversification within the Balkan Peninsula are much less understood. To fill this gap, we investigated the phylogeography and evolutionary history of three habitat‐segregated Cerastium taxa endemic to the Dinaric Alps and explored whether they responded differently to the Quaternary climatic oscillations in the Balkan Peninsula.LocationEurope, Balkan Peninsula, Dinaric Alps.TaxonCerastium (Caryophyllaceae, angiosperms).MethodsWe combined climatic niche comparisons and species distribution modelling (SDM) on the one hand, with cytological (relative genome size, RGS) and genetic / genomic approaches such as amplified fragment length polymorphism (AFLP) fingerprinting, phylogenetic analyses of nuclear ribosomal internal transcribed spacer (ITS) and plastid (trnT–ndhJ) sequences on the other hand, in order to investigate how the Pleistocene glaciations and the Holocene warming influenced the phylogeographic structure of the studied taxa. SDM was used to reconstruct past, present and future habitat suitability.ResultsDespite nonequivalent climatic niches, we detected climatic niche similarity amongst the three Cerastium taxa. Nonhierarchical K‐means clustering of AFLP data revealed an optimal split into two geographically segregated groups in all three taxa. Genetic divergence between the northwestern and the southeastern populations can be explained by isolation in northern and southern refugia, as suggested by SDM. The ITS and plastid sequences revealed similar, although more complex, patterns of genetic differentiation, and RGS differentiation was mainly geography‐correlated.Main conclusionsDespite the pronounced habitat segregation amongst the studied taxa, their overall phylogeographic structure is similar, suggesting comparable underlying processes and similar responses to the same historical events. However, we anticipate that the three taxa will respond differently to ongoing climate warming.

Genetic diversity and population structure in Vitis species illustrate phylogeographic patterns in eastern North America.

Geographical distribution and diversity of current plant species have been strongly shaped by climatic oscillations during the Quaternary. Analysing the resulting divergence among species and differentiation within species is crucial to understand the evolution of taxa like the Vitis genus, which provides very useful genetic resources for grapevine improvement and might reveal original recolonization patterns due to growth habit and dispersal mode. Here, we studied the genetic structure in natural populations of three species from eastern North America: Vitis aestivalis, V.cinerea and V.riparia using different marker types. Vitis aestivalis and V.cinerea showed higher diversity than V.riparia. The two former species are less differentiated, confirming an earlier divergence of V.riparia. V.aestivalis and V.riparia exhibited different genetic groups on both sides of the Appalachian Mountains that could mirror different recolonization routes from southern refugia. Genetic structure was stronger in V.cinerea, for which two varieties (var. berlandieri and var. cinerea) are morphologically recognized. Our results confirm this distinction and suggest the existence of three other lineages within var. cinerea. These discontinuities appear linked to adaptation of var. berlandieri to dry and limy areas of Texas and partially to the Mississippi River Valley. Rapid range expansions from refugia upon climate warming are also suggested by the low linkage disequilibrium values observed. Furthermore, large variation for downy mildew resistance was observed in the three species. Our findings appeared consistent with the vegetation history of eastern North America.

Historical migration and taxonomic entity of Korean endemic shrub Lespedeza maritima (Fabaceae) based on microsatellite loci.

Various plant species are endemic to the Korean Peninsula, but their evolutionary divergence and establishment are poorly understood. One of these, Lespedeza maritima, has been proposed as either a hybrid (L. cyrtobotrya × L. maximowiczii) or a synonym of L. thunbergii. A distinct taxon, L. uekii, has been proposed for inland populations. We investigated genetic diversity and structure in L. maritima and related taxa to resolve this. Genotypes of L. maritima (n = 244, including L. uekii) were determined using 12 microsatellite loci, then compared with those of related species. Genetic diversity within L. maritima was estimated, and Bayesian clustering analysis was used to represent its genetic structure and that of related taxa. Its distribution during the last glacial maximum (LGM) was predicted using ecological niche modelling (ENM). Neighbour-joining (NJ) analysis and principal coordinate analysis (PCoA) were used to investigate relationships among species. Bayesian tree based on nuclear ribosomal internal transcribed spacers (nrITS) was also reconstructed to show relationships and divergence time among species. Morphological features were examined using flower characteristics. In result, expected heterozygosity (HE) and allelic richness (AR) within L. maritima were higher in southern than northern populations. Bayesian clustering analysis largely assigned populations to two clusters (K = 2) (south vs. north). The ENM showed that L. maritima occurred around the East China Sea and Korean Strait land bridge during the LGM. Compared with other Lespedeza species, L. maritima was assigned to an independent cluster (K = 2–5), supported by the NJ, PCoA, Bayesian tree and morphological examination results. Lespedeza maritima and L. uekii were clustered to one clade on Bayesian tree. Given results, current L. maritima populations derive from post-LGM colonization away from southern refugia. The type L. uekii, which grows inland, is thought synonym of L. maritima. In addition, L. maritima is considered a distinct species, compared with related taxa.

Investigating the exploitation pattern of a newly established species, the case of the Late-Glacial roe deer (Capreolus capreolus) at La Fru (Savoie, France)

The Late-Glacial period offers a key window into the expansion of temperate species from southern refugia towards northern areas and the impact of faunal change on hunting strategies. In the Jura and in the Alps, the arrival of red deer and the withdrawal of reindeer are coeval with the warming of the GI-1e. Very little is known about roe deer, however. A high-resolution study of the rich archaeofauna from the Early Azilian occupation at the Northern Alpine site of La Fru provides data on the habitat and exploitation of roe deer. Roe deer populations were already established in the region in the early Bolling (~GI-1e), as is shown by the earliest radiocarbon date of roe deer bones (14.7–14.3 ky cal BP, 1σ). This is the earliest post-Last Glacial Maximum evidence of this species in northern France. The specimens from the site show the highest δ15N values among the deer species present in the areas. This is probably linked to the roe deer’s selective foraging of highly nutritious vegetation already available in the open habitat at that time. Our zooarchaeological study shows that roe deer was a key resource at La Fru and was intensively hunted between May and September. The mortality profile indicates a “deliberate” targeting of inexperienced subadults and weaker older animals. These new data provide further evidence that there was both a reorganization of the animal environment and a reorientation of hunting on red deer and roe deer associated with the Early Azilian culture during the Bolling chronozone.

Contrasting patterns of phylogenetic diversity across climatic zones of Western Ghats: A biodiversity hotspot in peninsular India

AbstractThis study attempts to understand the biogeographic history of the Western Ghats forests by investigating decoupling between phylogenetic and taxonomic diversity. We specifically test whether the deciduous forests have been recently established, whether the southern region was a refuge, and whether the deciduous and evergreen forest species have disparate evolutionary histories. We used species composition data from 23 forest types along the Western Ghats for all woody angiosperms above 10‐cm diameter at breast height. Forests were broadly grouped as either evergreen or deciduous. Mean phylogenetic distances corrected for species richness and mean phylogenetic beta diversity corrected for shared species were assessed using z‐scores from null distributions. Null distributions were generated by randomizing the species relationships on the phylogeny. We found that all evergreen forests showed a greater phylogenetic diversity as compared with null expectations. Deciduous forests showed the inverse pattern. Within the evergreen belt, there was a decreasing phylogenetic diversity from south to north, as predicted by the southern refuge hypothesis. The phylogenetic beta diversity across evergreen–deciduous forests was lesser than the null expectation, whereas it was much higher across forests within the evergreen belt. This study provides the first phylogenetic evidence for the antiquity of evergreen forests as well as the southern refuge hypothesis in the Western Ghats. The deciduous forests species have shared evolutionary histories with the evergreen forest species, suggesting multiple shifts between evergreen and deciduous states through the lineages. Conversely, the evergreen species exhibited a disparate evolutionary history across these forests, possibly owing to sharper ecological or climatic gradients.