The Last Glacial Maximum

Population dynamics of caribou shaped by glacial cycles before the last glacial maximum

Pleistocene glacial cycles influenced the diversification of high‐latitude wildlife species through recurrent periods of range contraction, isolation, divergence, and expansion from refugia and subsequent admixture of refugial populations. We investigate population size changes and the introgressive history of caribou (Rangifer tarandus) in western Canada using 33 whole genome sequences coupled with larger‐scale mitochondrial data. We found that a major population expansion of caribou occurred starting around 110,000 years ago (kya), the start of the last glacial period. Additionally, we found effective population sizes of some caribou reaching ~700,000 to 1,000,000 individuals, one of the highest recorded historical effective population sizes for any mammal species thus far. Mitochondrial analyses dated introgression events prior to the LGM dating to 20–30 kya and even more ancient at 60 kya, coinciding with colder periods with extensive ice coverage, further demonstrating the importance of glacial cycles and events prior to the LGM in shaping demographic history. Reconstructing the origins and differential introgressive history has implications for predictions on species responses under climate change. Our results have implications for other whole genome analyses using pairwise sequentially Markovian coalescent (PSMC) analyses, as well as highlighting the need to investigate pre‐LGM demographic patterns to fully reconstruct the origin of species diversity, especially for high‐latitude species.

Divergence in the Aquilegia ecalcarata complex is correlated with geography and climate oscillations: Evidence from plastid genome data

Quaternary climate oscillations and geographical heterogeneity play important roles in determining species and genetic diversity distribution patterns, but how these factors affect the migration and differentiation of East Asian plants species at the population level remains poorly understood. The Aquilegia ecalcarata complex, a group that originated in the Late Tertiary and is widely distributed throughout East Asia, displays high genetic variation that is suitable for studying elaborate phylogeographic patterns and demographic history related to the impact of Quaternary climate and geography. We used plastid genome data from 322 individuals in 60 populations of the A. ecalcarata complex to thoroughly explore the impact of Quaternary climate oscillations and geography on the phylogeographic patterns and demographic history of the A. ecalcarata complex through a series of phylogenetic, divergence time estimation, and demographic history analyses. The dry, cold climate and frequent climate oscillations that occurred during the early Pleistocene and the Mid-Pleistocene transition led to the differentiation of the A. ecalcarata complex, which was isolated in various areas. Geographically, the A. ecalcarata complex can be divided into Eastern and Western Clades and five subclades, which conform to the divergence of the East Asian flora. Our results clearly show the impact of Quaternary climate and geography on evolutionary history at the population level. These findings promote the understanding of the relationship between plant genetic differentiation and climate and geographical factors of East Asia at the population level.

Using charcoal, ATR FTIR and chemometrics to model the intensity of pyrolysis: Exploratory steps towards characterising fire events

This study describes a multivariate statistical model (derived using partial least squares regression, PLS-R) that derives charring intensity (reaction temperature and duration) from the attenuated total reflectance (ATR) Fourier Transform Infrared (FTIR) spectra of charcoal. Data for the model was obtained from a library of charcoal samples produced under laboratory conditions at charring intensities (CI) relevant to wildfires and a series of feedstocks representing common tree species collected from Australia. The PLS-R model developed reveals the potential of FTIR to determine the charring intensity of charcoal. Though limited by the differences between laboratory-produced charcoal and the more heterogeneous and less-structured charcoal produced in a wildfire, the method was tested against fossil charcoal from a well-dated sediment core collected from Thirlmere Lakes National Park, Australia and showed a distinct change in CI that can be related to other climatic and environmental proxies. We suggest that the method has the potential to offer insights into the conditions under which natural charcoal is formed including the modelling of charring intensities of fossil charcoal samples isolated from sediments, archaeological applications or characterisation of contemporary fire events from charcoal in soils.

A new subspecies of Finlayson’s squirrel from an isolated island offshore of the Indochina Peninsula in southern Vietnam

We describe a new subspecies of Finlayson’s squirrel (Callosciurus finlaysonii) from Hon Nghe Island in the Gulf of Thailand. This island is located off the coast of southern Vietnam. In addition, we discussed the phylogenetic relationships among C. finlaysonii subspecies distributed on the isolated islands in the Gulf of Thailand. The new subspecies (C. finlaysonii honnghensis), which is endemic to Hon Nghe Island, differs from other C. finlaysonii subspecies in pelage colouration. The mitochondrial cytochrome b sequences showed that this squirrel is closely related to C. finlaysonii albivexilli and C. finlaysonii frandseni, which are endemic to the Koh Kut and Koh Chang islands, respectively, suggesting that the three subspecies diverged approximately 30,000 years ago. After the last glacial maximum, many small islands were formed by the sea level rise in the Gulf of Thailand, which was a consequence of global warming. Following the continuous fragmentation of the Sunda Continent, each C. finlaysonii subspecies could have evolved in each geographically isolated island in this gulf. Thus, studying C. finlaysonii subspecies may be used to track the recent geological history of the Gulf of Thailand.

Genetic signatures of divergent selection in European beech (Fagus sylvatica L.) are associated with the variation in temperature and precipitation across its distribution range

High genetic variation and extensive gene flow may help forest trees with adapting to ongoing climate change, yet the genetic bases underlying their adaptive potential remain largely unknown. We investigated range-wide patterns of potentially adaptive genetic variation in 64 populations of European beech (Fagus sylvatica L.) using 270 SNPs from 139 candidate genes involved either in phenology or in stress responses. We inferred neutral genetic structure and processes (drift and gene flow) and performed differentiation outlier analyses and gene-environment association (GEA) analyses to detect signatures of divergent selection. Beech range-wide genetic structure was consistent with the species' previously identified postglacial expansion scenario and recolonization routes. Populations showed high diversity and low differentiation along the major expansion routes. A total of 52 loci were found to be putatively under selection and 15 of them turned up in multiple GEA analyses. Temperature and precipitation related variables were equally represented in significant genotype-climate associations. Signatures of divergent selection were detected in the same proportion for stress response and phenology-related genes. The range-wide adaptive genetic structure of beech appears highly integrated, suggesting a balanced contribution of phenology and stress-related genes to local adaptation, and of temperature and precipitation regimes to genetic clines. Our results imply a best-case scenario for the maintenance of high genetic diversity during range shifts in beech (and putatively other forest trees) with a combination of gene flow maintaining within-population neutral diversity and selection maintaining between-population adaptive differentiation.

The Chromosome-Level Genome of Triplophysa dalaica (Cypriniformes: Cobitidae) Provides Insights into Its Survival in Extremely Alkaline Environment

Lake Dali Nur, located in Inner Mongolia, North China, is alkaline, with Triplophysa dalaica one of the three fish species that not only survive, but thrive, in the lake. To investigate the presence of molecular mutations potentially responsible for this adaptation, the whole-genome sequence of the species was sequenced. A total of 126.5 and 106 Gb data, covering nearly 200× of the estimated genome, were generated using long-read sequencing and Hi-C technology, respectively. De novo assembly generated a genome totalled 607.91 Mb, with a contig N50 of 9.27 Mb. Nearly all whole-genome sequences were anchored and oriented onto 25 chromosomes, with telomeres for most chromosomes also being recovered. Repeats comprised approximately 35.01% of the whole genome. A total of 23,925 protein-coding genes were predicted, within which, 98.62% could be functionally annotated. Through comparisons of T. dalaica, T. tibetana, and T. siluroides gene models, a total of 898 genes were identified as likely being subjected to positive selection, with several of them potentially associated with alkaline adaptation, such as sodium bicarbonate cotransporter, SLC4A4. Demographic analyses suggested that the Dali population might have diverged from endemic freshwater Hai River populations, approximately 1 Ma. The high-quality T. dalaica genome, created in this study, not only aids in the analyses of alkaline adaptation, but may also assist in revealing the mysteries of the highly divergent genus Triplophysa in the future.

The role of anthropogenic dispersal in shaping the distribution and genetic composition of a widespread North American tree species

Dispersal and colonization are among the most important ecological processes for species persistence as they allow species to track changing environmental conditions. During the last glacial maximum (LGM), many cold-intolerant Northern Hemisphere plants retreated to southern glacial refugia. During subsequent warming periods, these species expanded their ranges northward. Interestingly, some tree species with limited seed dispersal migrated considerable distances after the LGM ~19,000 years before present (YBP). It has been hypothesized that indigenous peoples may have dispersed valued species, in some cases beyond the southern limits of the Laurentide Ice Sheet. To investigate this question, we employed a molecular genetics approach on a widespread North American understory tree species whose fruit was valued by indigenous peoples. Twenty putative anthropogenic (near pre-Columbian habitations) and 62 wild populations of Asimina triloba (pawpaw), which produces the largest edible fruit of any North American tree, were genetically assayed with nine microsatellite loci. Putative anthropogenic populations were characterized by reduced genetic diversity and greater excess heterozygosity relative to wild populations. Anthropogenic populations in regions that were glaciated during the LGM had profiles consistent with founder effects and reduced gene flow, and shared rare alleles with wild populations hundreds of kilometers away (mean = 723 km). Some of the most compelling evidence for human-mediated dispersal is that putative anthropogenic and wild populations sharing rare alleles were separated by significantly greater distances (mean = 695 km) than wild populations sharing rare alleles (mean = 607 km; p = .014). Collectively, the genetic data suggest that long-distance dispersal played an important role in the distribution of pawpaw and is consistent with the hypothesized role of indigenous peoples.

Ancient DNA reveals multiple origins and migration waves of extinct Japanese brown bear lineages

Little is known about how mammalian biogeography on islands was affected by sea-level fluctuations. In the Japanese Archipelago, brown bears (Ursus arctos) currently inhabit only Hokkaido, the northern island, but Pleistocene fossils indicate a past distribution throughout Honshu, Japan's largest island. However, the difficulty of recovering ancient DNA from fossils in temperate East Asia has limited our understanding of their evolutionary history. Here, we analysed mitochondrial DNA from a 32 500-year-old brown bear fossil from Honshu. Our results show that this individual belonged to a previously unknown lineage that split approximately 160 Ka from its sister lineage, the southern Hokkaido clade. This divergence time and fossil record suggest that brown bears migrated from the Eurasian continent to Honshu at least twice; the first population was an early-diverging lineage (greater than 340 Ka), and the second migrated via Hokkaido after approximately 160 Ka, during the ice age. Thus, glacial-age sea-level falls might have facilitated migrations of large mammals more frequently than previously thought, which may have had a substantial impact on ecosystem dynamics in these isolated islands.

Soil Formation, Subaerial Sedimentation Processes and Ancient Cultures during MIS 2 and the Deglaciation Phase MIS 1 in the Baikal–Yenisei Siberia (Russia)

The time of Sartan glaciation in the Baikal–Yenisei Siberia, is comparable with that of MIS 2 and the deglaciation phase MIS 1. Loess loams, aeolian–colluvial sands and sandy loams represent subaerial sediments. There are four subhorizons (sr1, sr2, sr3 and sr4) in the Sartan horizon (sr). Sedimentary and soil-forming processes at different stratigraphic levels are considered. Differing soil formation types of cold periods are distinguished. Soils of the interstadial type with the A-C profile are represented only in the Early Sartan section of this paper. The soils of the pleniglacial type are discussed throughout the section. Their initial profile is O-C, TJ-C and W-C. Plant detritus remnants or poor thin humus horizons are preserved in places from the upper horizons. We propose for the first time for the interphasial soil formation type of cold stages to be distinguished. This is represented in the sections by the preserved BCm, BCg, Cm and Cg horizons of 15–20 cm thick. The upper horizons are absent in most sections. According to the surviving fragments, these were organogenous (O, TJ and T) and organomineral (AO and W) horizons. The sedimentation and soil formation features are considered from the perspective reconstruction of the Sartan natural and climatic conditions. Buried Sartan soils often contain cultural layers. Soil formation shows a well-defined periodicity of natural condition stabilization, which allowed ancient populations to adapt actively to various situations. Archaeologists’ interest in fossil soils is based on the ability of soils to “record” information about the natural and climatic conditions of human habitation.

First modern human settlement recorded in the Iberian hinterland occurred during Heinrich Stadial 2 within harsh environmental conditions

As the south-westernmost region of Europe, the Iberian Peninsula stands as a key area for understanding the process of modern human dispersal into Eurasia. However, the precise timing, ecological setting and cultural context of this process remains controversial concerning its spatiotemporal distribution within the different regions of the peninsula. While traditional models assumed that the whole Iberian hinterland was avoided by modern humans due to ecological factors until the retreat of the Last Glacial Maximum, recent research has demonstrated that hunter-gatherers entered the Iberian interior at least during Solutrean times. We provide a multi-proxy geoarchaeological, chronometric and paleoecological study on human–environment interactions based on the key site of Peña Capón (Guadalajara, Spain). Results show (1) that this site hosts the oldest modern human presence recorded to date in central Iberia, associated to pre-Solutrean cultural traditions around 26,000 years ago, and (2) that this presence occurred during Heinrich Stadial 2 within harsh environmental conditions. These findings demonstrate that this area of the Iberian hinterland was recurrently occupied regardless of climate and environmental variability, thus challenging the widely accepted hypothesis that ecological risk hampered the human settlement of the Iberian interior highlands since the first arrival of modern humans to Southwest Europe.

Deep classification of cut-marks on bones from Arroyo del Vizcaíno (Uruguay)

The earliest widely accepted presence of humans in America dates to approximately 17.5 cal kyr BP, at the end of the Last Glacial Maximum (LGM). Among other evidence, this presence is attested by stone tools and associated cut-marks and other bone surface modifications (BSM), interpreted as the result of the consumption of animals by humans. Claims of an older human presence in the continent have been made based on the proposed anthropogenic modification of faunal remains; however, these have been controversial due to the highly subjective nature of the interpretations. Here, we employ advanced deep learning algorithms to objectively increase the accuracy of BSM identification on bones. With several models that exhibit BSM classification accuracies greater than 94%, we use ensemble learning techniques to robustly classify a selected sample of BSM from the approximately 30 kyr BP site of Arroyo del Vizcaíno, Uruguay. Our results confidently show the presence of cut-marks imparted by stone tools on bones at the site. This result supports an earlier presence of humans in the American continent, expanding additional genetic and archaeological evidence of a human LGM and pre-LGM presence in the continent.

Phylogeographic reconstructions can be biased by ancestral shared alleles: The case of the polymorphic lichen Bryoria fuscescens in Europe and North Africa

Large phylogeographic studies on lichens are scarce, and none involves a single species within which different lineages show fixed alternative dispersal strategies. We investigated Bryoria fuscescens (including B. capillaris) in Europe and western North Africa by phenotypically characterizing 1400 specimens from 64 populations and genotyping them with 14 microsatellites. We studied population structure and genetic diversity at the local and continental scales, discussed the post-glacial phylogeography, and compared dispersal capacities of phenotypes with and without soralia. Our main hypothesis is that the estimated phylogeography, migration routes, and dispersal capacities may be strongly biased by ancestral shared alleles. Scandinavia is genetically the richest area, followed by the Iberian Peninsula, the Carpathians, and the Alps. Three gene pools were detected: two partially linked to phenotypic characteristics, and the third one genetically related to the American sister species B. pseudofuscescens. The comparison of one gene pool producing soredia and one not, suggested both as panmictic, with similar levels of isolation by distance (IBD). The migration routes were estimated to span from north to south, in disagreement with the assessed glacial refugia. The presence of ancestral shared alleles in distant populations can explain the similar IBD levels found in both gene pools while producing a false signal of panmixia, and also biasing the phylogeographic reconstruction. The incomplete lineage sorting recorded for DNA sequence loci also supports this hypothesis. Consequently, the high diversity in Scandinavia may rather come from recent immigration into northern populations than from an in situ diversification. Similar patterns of ancestral shared polymorphism may bias the phylogeographical reconstruction of other lichen species.

The effects of climate and demographic history in shaping genomic variation across populations of the Desert Horned Lizard (Phrynosoma platyrhinos)

Species often experience spatial environmental heterogeneity across their range, and populations may exhibit signatures of adaptation to local environmental characteristics. Other population genetic processes, such as migration and genetic drift, can impede the effects of local adaptation. Genetic drift in particular can have a pronounced effect on population genetic structure during large-scale geographic expansions, where a series of founder effects leads to decreases in genetic variation in the direction of the expansion. Here, we explore the genetic diversity of a desert lizard that occupies a wide range of environmental conditions and that has experienced post-glacial expansion northwards along two colonization routes. Based on our analyses of a large SNP data set, we find evidence that both climate and demographic history have shaped the genetic structure of populations. Pronounced genetic differentiation was evident between populations occupying cold versus hot deserts, and we detected numerous loci with significant associations with climate. The genetic signal of founder effects, however, is still present in the genomes of the recently expanded populations, which comprise subsets of genetic variation found in the southern populations.

The genome of the Pyrenean desman and the effects of bottlenecks and inbreeding on the genomic landscape of an endangered species

The Pyrenean desman (Galemys pyrenaicus) is a small semiaquatic mammal endemic to the Iberian Peninsula. Despite its limited range, this species presents a strong genetic structure due to past isolation in glacial refugia and subsequent bottlenecks. Additionally, some populations are highly fragmented today as a consequence of river barriers, causing substantial levels of inbreeding. These features make the Pyrenean desman a unique model in which to study the genomic footprints of differentiation, bottlenecks and extreme isolation in an endangered species. To understand these processes, the complete genome of the Pyrenean desman was sequenced and assembled using a Bloom filter-based approach. An analysis of the 1.83 Gb reference genome and the sequencing of five additional individuals from different evolutionary units allowed us to detect its main genomic characteristics. The population differentiation of the species was reflected in highly distinctive demographic trajectories. In addition, a severe population bottleneck during the postglacial recolonization of the eastern Pyrenees created one of the lowest genomic heterozygosity values recorded in a mammal. Moreover, isolation and inbreeding gave rise to a high proportion of runs of homozygosity (ROH). Despite these extremely low levels of genetic diversity, two key multigene families from an eco-evolutionary perspective, the major histocompatibility complex and olfactory receptor genes, showed heterozygosity excess in the majority of individuals, revealing that functional diversity can be maintained up to a certain extent. Furthermore, these two classes of genes were significantly less abundant than expected within ROH. In conclusion, the genomic landscape of each analysed Pyrenean desman turned out to be strikingly distinctive and was a clear reflection of its recent ancestry and current conservation conditions. These results may help characterize the genomic health of each individual, and can be crucial for the conservation and management of the species.

Host tropism determination by convergent evolution of immunological evasion in the Lyme disease system

Pathogens possess the ability to adapt and survive in some host species but not in others-an ecological trait known as host tropism. Transmitted through ticks and carried mainly by mammals and birds, the Lyme disease (LD) bacterium is a well-suited model to study such tropism. Three main causative agents of LD, Borrelia burgdorferi, B. afzelii, and B. garinii, vary in host ranges through mechanisms eluding characterization. By feeding ticks infected with different Borrelia species, utilizing feeding chambers and live mice and quail, we found species-level differences in bacterial transmission. These differences localize on the tick blood meal, and specifically complement, a defense in vertebrate blood, and a polymorphic bacterial protein, CspA, which inactivates complement by binding to a host complement inhibitor, Factor H (FH). CspA selectively confers bacterial transmission to vertebrates that produce FH capable of allele-specific recognition. CspA is the only member of the Pfam54 gene family to exhibit host-specific FH-binding. Phylogenetic analyses revealed convergent evolution as the driver of such uniqueness, and that FH-binding likely emerged during the last glacial maximum. Our results identify a determinant of host tropism in Lyme disease infection, thus defining an evolutionary mechanism that shapes host-pathogen associations.

Climate-induced range shifts shaped the present and threaten the future genetic variability of a marine brown alga in the Northwest Pacific

Glaciation-induced environmental changes during the last glacial maximum (LGM) have strongly influenced species' distributions and genetic diversity patterns in the northern high latitudes. However, these effects have seldom been assessed on sessile species in the Northwest Pacific. Herein, we chose the brown alga Sargassum thunbergii to test this hypothesis, by comparing present population genetic variability with inferred geographical range shifts from the LGM to the present, estimated with species distribution modelling (SDM). Projections for contrasting scenarios of future climate change were also developed to anticipate genetic diversity losses at regional scales. Results showed that S. thunbergii harbours strikingly rich genetic diversity and multiple divergent lineages in the centre-northern range of its distribution, in contrast with a poorer genetically distinct lineage in the southern range. SDM hindcasted refugial persistence in the southern range during the LGM as well as post-LGM expansion of 18 degrees of latitude northward. Approximate Bayesian computation (ABC) analysis further suggested that the multiple divergent lineages in the centre-northern range limit stem from post-LGM colonization from the southern survived lineage. This suggests divergence due to demographic bottlenecks during range expansion and massive genetic diversity loss during post-LGM contraction in the south. The projected future range of S. thunbergii highlights the threat to unique gene pools that might be lost under global changes.

Phylogenetics and phylogeography of red deer mtDNA lineages during the last 50 000 years in Eurasia

The present phylogeographic pattern of red deer in Eurasia is not only a result of the contraction of their distribution range into glacial refugia and postglacial expansion, but probably also an effect of replacement of some red deer s.l. mtDNA lineages by others during the last 50 000 years. To better recognize this process, we analysed 501 sequences of mtDNA cytochrome b, including 194 ancient and 75 contemporary samples newly obtained for this study. The inclusion of 161 radiocarbon-dated samples enabled us to study the phylogeny in a temporal context and conduct divergence-time estimation and molecular dating. Depending on methodology, our estimate of divergence between Cervus elaphus and Cervus canadensis varied considerably (370 000 or 1.37 million years BP, respectively). The divergence times of genetic lineages and haplogroups corresponded to large environmental changes associated with stadials and interstadials of the Late Pleistocene. Due to the climatic oscillations, the distribution of C. elaphus and C. canadensis fluctuated in north–south and east–west directions. Some haplotypes dated to pre-Last Glacial Maximum periods were not detected afterwards, representing possibly extinct populations. We indicated with a high probability the presence of red deer sensu lato in south-eastern Europe and western Asia during the Last Glacial Maximum.

Biogeography of Italy revisited: genetic lineages confirm major phylogeographic patterns and a pre-Pleistocene origin of its biota

Warm-adapted species survived the cold stages of the past glacial-interglacial cycles in southern European peninsulas and recolonized major parts of Central and Northern Europe in the wake of postglacial warming. However, many of the genetic lineages which differentiated within these refugia predate even the Pleistocene. One of these refugia is the Italian Peninsula with its surrounding islands. In this meta-analysis, we compiled phylogeographic patterns of multiple species across this region. We transformed existing geographic information on 78 animal and plant species (with a total of 471 genetic lineages) within 17 predefined areas into presence/absence matrices. We elaborated three matrices: (i) only old lineages exclusively distinguished by deep splits, (ii) only young lineages distinguished by shallow (i.e. recent) splits, and (iii) presence/absence of the respective species. To infer biogeographic relationships between the predefined areas, we performed bootstrapped neighbour joining cluster analyses on these three matrices. In addition, we reviewed the geological history of Italy to identify causes of the observed biogeographic patterns. We found Sardinia and Corsica to be biogeographically closely linked with each other, and that they diverge strongly from all other regions. Sicily also diverges strongly from all other regions, while the intra-island differentiation was comparatively low. On the Italian mainland, Calabria exhibited the most pronounced biogeographic differentiation, often with several lineages present, resulting from old vicariance events within the region. Furthermore, southern Apulia and the Po Plain with adjoining areas of northern peninsular Italy displayed considerable distinctiveness. Admixture prevailed in the areas between these three regions. The ancient isolation of Sicily, as well as Sardinia plus Corsica, resulted in endemic lineages with only moderate recent exchange with adjacent mainland regions. Pronounced diversification occurs within the Italian Peninsula. The complex tectonic activities, such as shifting (micro)plates, submergence of major parts of peninsular Italy with the genesis of numerous Pliocene islands, in combination with the climatic cycles during the Pleistocene have most likely generated the current biogeographic pattern of species. Immigrations from the Balkan Peninsula into northern Italy partly accounted for the distinctiveness of this region.

Vocal phenotype of male rutting roars and genetic markers delineate East European red deer (Cervus elaphus) from Central and West European populations

This study investigates a population of red deer Cervus elaphus, founded by 10 individuals introduced in the nineteenth century from Germany to the Voronezh region of the European part of Southern Russia and then developed without further introductions. We characterize for the first time the vocal phenotype of the Voronezh red deer male rutting calls in comparison with similar data on the Pannonian (native Central European) and Iberian (native West European) red deer obtained by the authors during preceding studies. In addition, we provide for the first time the genetic data on Pannonian red deer. In Voronezh stags, the number of roars per bout (2.85 ± 1.79) was lower than in Pannonian (3.18 ± 2.17) but higher than in Iberian (2.11 ± 1.71) stags. In Voronezh stags, the duration of main (the longest within bouts) roars was longer (2.46 ± 1.14 s) than in Pannonian (1.13 ± 0.50 s) or Iberian (1.90 ± 0.50 s) stags. The maximum fundamental frequency of main roars was similar between Voronezh (175 ± 60 Hz) and Pannonian (168 ± 61 Hz) but higher in Iberian stags (223 ± 35 Hz). Mitochondrial cytochrome b gene analysis of red deer from the three study populations partially supports the bioacoustical data, of closer similarity between Voronezh and Pannonian populations. In contrast, microsatellite DNA analysis delineates Voronezh red deer from either Pannonian or Iberian red deer. We discuss that population bottlenecking might affect the acoustics of the rutting roars, in addition to genotype.

Mitogenomes Reveal Two Major Influxes of Papuan Ancestry across Wallacea Following the Last Glacial Maximum and Austronesian Contact

The tropical archipelago of Wallacea contains thousands of individual islands interspersed between mainland Asia and Near Oceania, and marks the location of a series of ancient oceanic voyages leading to the peopling of Sahul—i.e., the former continent that joined Australia and New Guinea at a time of lowered sea level—by 50,000 years ago. Despite the apparent deep antiquity of human presence in Wallacea, prior population history research in this region has been hampered by patchy archaeological and genetic records and is largely concentrated upon more recent history that follows the arrival of Austronesian seafarers ~3000–4000 years ago (3–4 ka). To shed light on the deeper history of Wallacea and its connections with New Guinea and Australia, we performed phylogeographic analyses on 656 whole mitogenomes from these three regions, including 186 new samples from eight Wallacean islands and three West Papuan populations. Our results point to a surprisingly dynamic population history in Wallacea, marked by two periods of extensive demographic change concentrated around the Last Glacial Maximum ~15 ka and post-Austronesian contact ~3 ka. These changes appear to have greatly diminished genetic signals informative about the original peopling of Sahul, and have important implications for our current understanding of the population history of the region.

Confirmed archaeological evidence of water deer in Vietnam: relics of the Pleistocene or a shifting baseline?

Studies of archaeological and palaeontological bone assemblages increasingly show that the historical distributions of many mammal species are unrepresentative of their longer-term geographical ranges in the Quaternary. Consequently, the geographical and ecological scope of potential conservation efforts may be inappropriately narrow. Here, we consider a case-in-point, the water deer Hydropotes inermis, which has historical native distributions in eastern China and the Korean peninsula. We present morphological and metric criteria for the taxonomic diagnosis of mandibles and maxillary canine fragments from Hang Thung Binh 1 cave in Tràng An World Heritage Site, which confirm the prehistoric presence of water deer in Vietnam. Dated to between 13 000 and 16 000 years before the present, the specimens are further evidence of a wider Quaternary distribution for these Vulnerable cervids, are valuable additions to a sparse Pleistocene fossil record and confirm water deer as a component of the Upper Pleistocene fauna of northern Vietnam. Palaeoenvironmental proxies suggest that the Tràng An water deer occupied cooler, but not necessarily drier, conditions than today. We consider if the specimens represent extirpated Pleistocene populations or indicate a previously unrecognized, longer-standing southerly distribution with possible implications for the conservation of the species in the future.

The deep population history of northern East Asia from the Late Pleistocene to the Holocene

Northern East Asia was inhabited by modern humans as early as 40 thousand years ago (ka), as demonstrated by the Tianyuan individual. Using genome-wide data obtained from 25 individuals dated to 33.6-3.4 ka from the Amur region, we show that Tianyuan-related ancestry was widespread in northern East Asia before the Last Glacial Maximum (LGM). At the close of the LGM stadial, the earliest northern East Asian appeared in the Amur region, and this population is basal to ancient northern East Asians. Human populations in the Amur region have maintained genetic continuity from 14 ka, and these early inhabitants represent the closest East Asian source known for Ancient Paleo-Siberians. We also observed that EDAR V370A was likely to have been elevated to high frequency after the LGM, suggesting the possible timing for its selection. This study provides a deep look into the population dynamics of northern East Asia.

A vertebrate adaptive radiation is assembled from an ancient and disjunct spatiotemporal landscape

To investigate the origins and stages of vertebrate adaptive radiation, we reconstructed the spatial and temporal histories of adaptive alleles underlying major phenotypic axes of diversification from the genomes of 202 Caribbean pupfishes. On a single Bahamian island, ancient standing variation from disjunct geographic sources was reassembled into new combinations under strong directional selection for adaptation to the novel trophic niches of scale-eating and molluscivory. We found evidence for two longstanding hypotheses of adaptive radiation: hybrid swarm origins and temporal stages of adaptation. Using a combination of population genomics, transcriptomics, and genome-wide association mapping, we demonstrate that this microendemic adaptive radiation of novel trophic specialists on San Salvador Island, Bahamas experienced twice as much adaptive introgression as generalist populations on neighboring islands and that adaptive divergence occurred in stages. First, standing regulatory variation in genes associated with feeding behavior (prlh, cfap20, and rmi1) were swept to fixation by selection, then standing regulatory variation in genes associated with craniofacial and muscular development (itga5, ext1, cyp26b1, and galr2) and finally the only de novo nonsynonymous substitution in an osteogenic transcription factor and oncogene (twist1) swept to fixation most recently. Our results demonstrate how ancient alleles maintained in distinct environmental refugia can be assembled into new adaptive combinations and provide a framework for reconstructing the spatiotemporal landscape of adaptation and speciation.

Circumpolar phylogeography and demographic history of beluga whales reflect past climatic fluctuations

Several Arctic marine mammal species are predicted to be negatively impacted by rapid sea ice loss associated with ongoing ocean warming. However, consequences for Arctic whales remain uncertain. To investigate how Arctic whales responded to past climatic fluctuations, we analysed 206 mitochondrial genomes from beluga whales (Delphinapterus leucas) sampled across their circumpolar range, and four nuclear genomes, covering both the Atlantic and the Pacific Arctic region. We found four well-differentiated mitochondrial lineages, which were established before the onset of the last glacial expansion ~110 thousand years ago. Our findings suggested these lineages diverged in allopatry, reflecting isolation of populations during glacial periods when the Arctic sea-shelf was covered by multiyear sea ice. Subsequent population expansion and secondary contact between the Atlantic and Pacific Oceans shaped the current geographic distribution of lineages, and may have facilitated mitochondrial introgression. Our demographic reconstructions based on both mitochondrial and nuclear genomes showed markedly lower population sizes during the Last Glacial Maximum (LGM) compared to the preceding Eemian and current Holocene interglacial periods. Habitat modelling similarly revealed less suitable habitat during the LGM (glacial) than at present (interglacial). Together, our findings suggested the association between climate, population size, and available habitat in belugas. Forecasts for year 2100 showed that beluga habitat will decrease and shift northwards as oceans continue to warm, putatively leading to population declines in some beluga populations. Finally, we identified vulnerable populations which, if extirpated as a consequence of ocean warming, will lead to a substantial decline of species-wide haplotype diversity.

Integrating Linguistics, Social Structure, and Geography to Model Genetic Diversity within India

India represents an intricate tapestry of population substructure shaped by geography, language, culture, and social stratification. Although geography closely correlates with genetic structure in other parts of the world, the strict endogamy imposed by the Indian caste system and the large number of spoken languages add further levels of complexity to understand Indian population structure. To date, no study has attempted to model and evaluate how these factors have interacted to shape the patterns of genetic diversity within India. We merged all publicly available data from the Indian subcontinent into a data set of 891 individuals from 90 well-defined groups. Bringing together geography, genetics, and demographic factors, we developed Correlation Optimization of Genetics and Geodemographics to build a model that explains the observed population genetic substructure. We show that shared language along with social structure have been the most powerful forces in creating paths of gene flow in the subcontinent. Furthermore, we discover the ethnic groups that best capture the diverse genetic substructure using a ridge leverage score statistic. Integrating data from India with a data set of additional 1,323 individuals from 50 Eurasian populations, we find that Indo-European and Dravidian speakers of India show shared genetic drift with Europeans, whereas the Tibeto-Burman speaking tribal groups have maximum shared genetic drift with East Asians.

Genomic vulnerability and socio-economic threats under climate change in an African rainforest bird

Preserving biodiversity under rapidly changing climate conditions is challenging. One approach for estimating impacts and their magnitude is to model current relationships between genomic and environmental data and then to forecast those relationships under future climate scenarios. In this way, understanding future genomic and environmental relationships can help guide management decisions, such as where to establish new protected areas where populations might be buffered from high temperatures or major changes in rainfall. However, climate warming is only one of many anthropogenic threats one must consider in rapidly developing parts of the world. In Central Africa, deforestation, mining, and infrastructure development are accelerating population declines of rainforest species. Here we investigate multiple anthropogenic threats in a Central African rainforest songbird, the little greenbul (Andropadus virens). We examine current climate and genomic variation in order to explore the association between genome and environment under future climate conditions. Specifically, we estimate Genomic Vulnerability, defined as the mismatch between current and predicted future genomic variation based on genotype-environment relationships modeled across contemporary populations. We do so while considering other anthropogenic impacts. We find that coastal and central Cameroon populations will require the greatest shifts in adaptive genomic variation, because both climate and land use in these areas are predicted to change dramatically. In contrast, in the more northern forest-savanna ecotones, genomic shifts required to keep pace with climate will be more moderate, and other anthropogenic impacts are expected to be comparatively low in magnitude. While an analysis of diverse taxa will be necessary for making comprehensive conservation decisions, the species-specific results presented illustrate how evolutionary genomics and other anthropogenic threats may be mapped and used to inform mitigation efforts. To this end, we present an integrated conceptual model demonstrating how the approach for a single species can be expanded to many taxonomically diverse species.

Past connections with the mainland structure patterns of insular species richness in a continental-shelf archipelago (Aegean Sea, Greece)

Recent research in island biogeography has highlighted the important role of late Quaternary sea-level fluctuations in shaping biogeographic patterns in insular systems but focused on oceanic systems. Through this study, we aim investigate how late Quaternary sea-level fluctuations shaped species richness patterns in continental-shelf island systems. Focusing on the Aegean archipelago, we first compiled maps of the area's geography using published data, under three sea-level stands: (a) current; (b) median sea-level over the last nine glacial-interglacial cycles (MSL); and (c) Last Glacial Maximum (LGM). We gathered taxon-island occurrences for multiple chorotypes of angiosperms, butterflies, centipedes, and reptiles. We investigated the impact of present-day and past geographic settings on chorological groups by analyzing island species-area relationships (ISARs) and using generalized linear mixed models (GLMMs) selection based on multiple metrics of goodness of fit. Our results confirm that the Aegean's geography has changed dramatically since the LGM, whereas the MSL only modestly differs from the present configuration. Apart for centipedes, paleogeographic changes affected both native and endemic species diversity through altering connections between land-bridge islands and the mainland. On land-bridge islands, we detected over-representation of native species and under-representation of endemics. Unlike oceanic islands, sea-level-driven increase of isolation and area contraction did not strongly shape patterns of species richness. Furthermore, the LGM configurations rather than the MSL configuration shaped patterns of endemic species richness. This suggests that even short episodes of increased connectivity with continental populations are sufficient to counteract the genetic differentiation of insular populations. On the other hand, the over-representation of native nonendemic species on land-bridge islands reflected MSL rather than LGM mainland connections. Our study shows that in terms of processes affecting species richness patterns, continental archipelagos differ fundamentally from oceanic systems because episodic connections with the mainland have profound effects on the biota of land-bridge islands.

Phylogeographic and demographic modeling analyses of the multiple origins of the rheophytic goldenrod Solidago yokusaiana Makino

Understanding adaptation mechanisms is important in evolutionary biology. Parallel adaptation provides good opportunities to investigate adaptive evolution. To confirm parallel adaptation, it is effective to examine whether the phenotypic similarity has one or multiple origins and to use demographic modeling to consider the gene flow between ecotypes. Solidago yokusaiana is a rheophyte endemic to the Japanese Archipelago that diverged from Solidago virgaurea. This study examined the parallel origins of S. yokusaiana by distinguishing between multiple and single origins and subsequent gene flow. The haplotypes of noncoding chloroplast DNA and genotypes at 14 nuclear simple sequence repeat (nSSR) loci and single-nucleotide polymorphisms (SNPs) revealed by double-digest restriction-associated DNA sequencing (ddRADseq) were used for phylogeographic analysis; the SNPs were also used to model population demographics. Some chloroplast haplotypes were common to S. yokusaiana and its ancestor S. virgaurea. Also, the population genetic structures revealed by nSSR and SNPs did not correspond to the taxonomic species. The demographic modeling supported the multiple origins of S. yokusaiana in at least four districts and rejected a single origin with ongoing gene flow between the two species, implying that S. yokusaiana independently and repeatedly adapted to frequently flooding riversides.

Evolutionary effects of geographic and climatic isolation between Rhododendron tsusiophyllum populations on the Izu Islands and mainland Honshu of Japan

Geographic and environmental isolations of islands and the mainland offer excellent opportunity to investigate colonization and survival dynamics of island populations. We inferred and compared evolutionary processes and the demographic history of Rhododendron tsusiophyllum, in the Izu Islands and the much larger island Honshu, treated here as the mainland, using thousands of nuclear SNPs obtained by ddRAD-seq from eight populations of R. tsusiophyllum and three populations of R. tschonoskii as an outgroup. Phylogenetic relationships and their habitats suggest that R. tsusiophyllum had evolved and migrated from cold north to warm south regions. We detected clear genetic divergence among populations in three regions of Honshu and the Izu Islands, suggesting restricted migration between them due to isolated habitats on mountains even in the mainland. The three regions have different changes in effective population size, especially, genetic diversity and population size of the Izu Islands are small compared to the others. Further, habitats of populations in the Izu Islands are warmer than those in Honshu, suggesting that they have undergone adaptive evolution. Our study provides evidences of montane rather than insular isolation on genetic divergence, survival of populations and significance of adaptive evolution for island populations with small population size and low genetic diversity, despite close proximity to mainland populations.

Analysis of whole-genome re-sequencing data of ducks reveals a diverse demographic history and extensive gene flow between Southeast/South Asian and Chinese populations

BACKGROUND

The most prolific duck genetic resource in the world is located in Southeast/South Asia but little is known about the domestication and complex histories of these duck populations.

RESULTS

Based on whole-genome resequencing data of 78 ducks (Anas platyrhynchos) and 31 published whole-genome duck sequences, we detected three geographic distinct genetic groups, including local Chinese, wild, and local Southeast/South Asian populations. We inferred the demographic history of these duck populations with different geographical distributions and found that the Chinese and Southeast/South Asian ducks shared similar demographic features. The Chinese domestic ducks experienced the strongest population bottleneck caused by domestication and the last glacial maximum (LGM) period, whereas the Chinese wild ducks experienced a relatively weak bottleneck caused by domestication only. Furthermore, the bottleneck was more severe in the local Southeast/South Asian populations than in the local Chinese populations, which resulted in a smaller effective population size for the former (7100-11,900). We show that extensive gene flow has occurred between the Southeast/South Asian and Chinese populations, and between the Southeast Asian and South Asian populations. Prolonged gene flow was detected between the Guangxi population from China and its neighboring Southeast/South Asian populations. In addition, based on multiple statistical approaches, we identified a genomic region that included three genes (PNPLA8, THAP5, and DNAJB9) on duck chromosome 1 with a high probability of gene flow between the Guangxi and Southeast/South Asian populations. Finally, we detected strong signatures of selection in genes that are involved in signaling pathways of the nervous system development (e.g., ADCYAP1R1 and PDC) and in genes that are associated with morphological traits such as cell growth (e.g., IGF1R).

CONCLUSIONS

Our findings provide valuable information for a better understanding of the domestication and demographic history of the duck, and of the gene flow between local duck populations from Southeast/South Asia and China.

The forensic landscape and the population genetic analyses of Hainan Li based on massively parallel sequencing DNA profiling

Due to the formation of the Qiongzhou Strait by climate change and marine transition, Hainan island was isolated from the mainland southern China during the Last Glacial Maximum. Hainan island, located at the southernmost part of China and separated from the Leizhou Peninsula by the Qiongzhou Strait, laid on one of the modern human northward migration routes from Southeast Asia to East Asia. The Hlai language-speaking Li minority, the second largest population after Han Chinese in Hainan island, is the direct descendants of the initial migrants in Hainan island and has unique ethnic properties and derived characteristics; however, the forensic-associated studies on Hainan Li population are still insufficient. Hence, 136 Hainan Li individuals were genotyped in this study using the MPS-based ForenSeq™ DNA Signature Prep Kit (DNA Primer Set A, DPMA) to characterize the forensic genetic polymorphism landscape, and DNA profiles were obtained from 152 different molecular genetic markers (27 autosomal STRs, 24 Y-STRs, 7 X-STRs, and 94 iiSNPs). A total of 419 distinct length variants and 586 repeat sequence sub-variants, with 31 novel alleles (at 17 loci), were identified across the 58 STR loci from the DNA profiles of Hainan Li population. We evaluated the forensic characteristics and efficiencies of DPMA, demonstrating that the STRs and iiSNPs in DPMA were highly polymorphic in Hainan Li population and could be employed in forensic applications. In addition, we set up three datasets, which included the genetic data of (i) iiSNPs (27 populations, 2640 individuals), (ii) Y-STRs (42 populations, 8281 individuals), and (iii) Y haplogroups (123 populations, 4837 individuals) along with the population ancestries and language families, to perform population genetic analyses separately from different perspectives. In conclusion, the phylogenetic analyses indicated that Hainan Li, with a southern East Asia origin and Tai-Kadai language-speaking language, is an isolated population relatively. But the genetic pool of Hainan Li influenced by the limited gene flows from other Tai-Kadai populations and Hainan populations. Furthermore, the establishment of isolated population models will be beneficial to clarify the exquisite population structures and develop specific genetic markers for subpopulations in forensic genetic fields.

Genetic characteristics of the amphidromous fish Ayu Plecoglossus altivelis altivelis (Osmeriformes: Plecoglossidae) on Yaku-shima Island in Japan, the southernmost population of the subspecies

The Ayu (Plecoglossus altivelis altivelis) population on Yaku-shima Island, Kagoshima Prefecture, Japan represents the southernmost population of the subspecies and is considered to be facing extinction. We investigated the genetic characteristics of Ayu in the Miyanoura River (MYU) in the northeast of the island and the Kurio River (KRO) in the southwest of the island, using partial sequences of mitochondrial (mt) control region and polymorphic microsatellite (simple sequence repeat: SSR) loci. The mtDNA analysis revealed that the Yaku-shima Island population was significantly differentiated from other Ayu populations; additionally, the MYU and KRO populations were significantly different from each other in terms of mtDNA (pairwise Φ_ST = 0.5826, P < 0.01) and SSR (pairwise Φ_ST = 0.1598, P < 0.01) analyses, indicating very little or no gene flow between them. The mtDNA haplotype diversity values were minimal for KRO and somewhat lower for MYU (h = 0.8176) than for each population from the mainland of Japan (Honshu-Kyushu) and the Korean Peninsula (h = 0.9905-1.0000). The mean values of expected heterozygosity (He) of SSRs were also lower in KRO (mean He = 0.555) than in MYU (mean He = 0.649). A considerably small effective population size (N_e = 100.1 for MYU, 151.2 for KRO) and a bottleneck effect for Yaku-shima Island population were suggested by SSR analysis. These findings underscore the importance of monitoring the genetic diversity of Ayu on Yaku-shima Island and the necessity of designing conservation policies for each river's population.

The Effect of the Recombination Rate between Adaptive Loci on the Capacity of a Population to Expand Its Range

AbstractPrevious theoretical work on range expansions over heterogeneous environments showed that there is a critical environmental gradient where range expansion stops. For populations with freely recombining loci underlying the trait under selection (hereafter, "adaptive loci"), the critical gradient in one-dimensional habitats depends on the fitness cost of dispersal and the strength of selection relative to genetic drift. Here, we extend the previous work in two directions and ask, What is the role of the recombination rate between the adaptive loci during range expansions? And what effect does the ability of selfing as opposed to obligate outcrossing have on range expansions? To answer these questions, we use computer simulations. We demonstrate that while reduced recombination rates between adaptive loci slow down range expansions as a result of poor purging of locally deleterious alleles at the expansion front, they may also allow a species to occupy a greater range. In addition, we find that the allowance of selfing may improve the ability of populations to expand their ranges, for example, because selfing among potentially rare high-fitness individuals facilitates the establishment and maintenance of locally well-adapted genotypes. We conclude that during range expansions there is a trade-off between positive and negative effects of recombination within and between individuals.

Inferring the Demographic History of Inbred Species from Genome-Wide SNP Frequency Data

Demographic inference using the site frequency spectrum (SFS) is a common way to understand historical events affecting genetic variation. However, most methods for estimating demography from the SFS assume random mating within populations, precluding these types of analyses in inbred populations. To address this issue, we developed a model for the expected SFS that includes inbreeding by parameterizing individual genotypes using beta-binomial distributions. We then take the convolution of these genotype probabilities to calculate the expected frequency of biallelic variants in the population. Using simulations, we evaluated the model's ability to coestimate demography and inbreeding using one- and two-population models across a range of inbreeding levels. We also applied our method to two empirical examples, American pumas (Puma concolor) and domesticated cabbage (Brassica oleracea var. capitata), inferring models both with and without inbreeding to compare parameter estimates and model fit. Our simulations showed that we are able to accurately coestimate demographic parameters and inbreeding even for highly inbred populations (F = 0.9). In contrast, failing to include inbreeding generally resulted in inaccurate parameter estimates in simulated data and led to poor model fit in our empirical analyses. These results show that inbreeding can have a strong effect on demographic inference, a pattern that was especially noticeable for parameters involving changes in population size. Given the importance of these estimates for informing practices in conservation, agriculture, and elsewhere, our method provides an important advancement for accurately estimating the demographic histories of these species.

Environmental and Oceanographic Conditions at the Continental Margin of the Central Basin, Northwestern Ross Sea (Antarctica) Since the Last Glacial Maximum

The continental margin is a key area for studying the sedimentary processes related to the advance and retreat of the Ross Ice Shelf (Antarctica); nevertheless, much remains to be investigated. The aim of this study is to increase the knowledge of the last glacial/deglacial dynamics in the Central Basin slope–basin system using a multidisciplinary approach, including integrated sedimentological, micropaleontological and tephrochronological information. The analyses carried out on three box cores highlighted sedimentary sequences characterised by tree stratigraphic units. Collected sediments represent a time interval from 24 ka Before Present (BP) to the present time. Grain size clustering and data on the sortable silt component, together with diatom, silicoflagellate and foraminifera assemblages indicate the influence of the ice shelf calving zone (Unit 1, 24–17 ka BP), progressive receding due to Circumpolar Deep Water inflow (Unit 2, 17–10.2 ka BP) and (Unit 3, 10.2 ka BP–present) the establishment of seasonal sea ice with a strengthening of bottom currents. The dominant and persistent process is a sedimentation controlled by contour currents, which tend to modulate intensity in time and space. A primary volcanic ash layer dated back at around 22 ka BP is correlated with the explosive activity of Mount Rittmann.

Phylogeography of Cedros and Tiburón Island Mule Deer in North America's Desert Southwest

Though mule deer (Odocoileus hemionus) persist in robust populations throughout most of their North American distribution, habitat loss, unregulated hunting, and other factors have reduced their historical range in México. Two of the 6 putative subspecies inhabiting México's deserts and Baja California peninsula are of conservation concern, occupying islands in the Pacific Ocean (Odocoileus hemionus cerrosensis on Cedros Island: endangered) and Sea of Cortés (Odocoileus hemionus sheldoni on Tiburón Island: threatened). Focusing on the desert southwest (n = 448), we sampled Tiburón (n = 22) and Cedros (n = 15) Island mule deer using contemporary samples and natural history museum specimens to complete a phylogeographic evaluation of the species complex, and assess the phylogeography of these insular subspecies. Both insular subspecies formed endemic haplotype lineages, consistent with island biogeographic theory. Bayesian skyline plots were consistent with Holocene demographic expansion. Cedros Island deer were genetically most similar to adjacent mainland Baja California deer, but exhibited a suite of unique haplotypes and reduced genetic variation. Tiburón Island deer haplotypes unexpectedly nested within a mainland lineage found in distant New Mexico, rather than the adjacent mainland Sonoran lineage. Such findings suggest the importance of postglacial climate fluctuations and biotic community turnover in the phylogeographic history of mule deer in the desert southwest. Our genetic data corroborates cultural, archaeological, and phenotypic evidence supporting Cedros and Tiburón deer endemicity and subspecies status. Reduced genetic variation, divergence from mainland populations, and demographic trends on both islands indicate that conservation, monitoring, and management are critical to ensure persistence of these endemic insular subspecies.

Origin and diffusion of human Y chromosome haplogroup J1-M267

Human Y chromosome haplogroup J1-M267 is a common male lineage in West Asia. One high-frequency region-encompassing the Arabian Peninsula, southern Mesopotamia, and the southern Levant-resides ~ 2000 km away from the other one found in the Caucasus. The region between them, although has a lower frequency, nevertheless demonstrates high genetic diversity. Studies associate this haplogroup with the spread of farming from the Fertile Crescent to Europe, the spread of mobile pastoralism in the desert regions of the Arabian Peninsula, the history of the Jews, and the spread of Islam. Here, we study past human male demography in West Asia with 172 high-coverage whole Y chromosome sequences and 889 genotyped samples of haplogroup J1-M267. We show that this haplogroup evolved ~ 20,000 years ago somewhere in northwestern Iran, the Caucasus, the Armenian Highland, and northern Mesopotamia. The major branch-J1a1a1-P58-evolved during the early Holocene ~ 9500 years ago somewhere in the Arabian Peninsula, the Levant, and southern Mesopotamia. Haplogroup J1-M267 expanded during the Chalcolithic, the Bronze Age, and the Iron Age. Most probably, the spread of Afro-Asiatic languages, the spread of mobile pastoralism in the arid zones, or both of these events together explain the distribution of haplogroup J1-M267 we see today in the southern regions of West Asia.

Increased autumn and winter precipitation during the Last Glacial Maximum in the European Alps

The culmination of the glaciers in the European Alps during the Last Glacial Maximum (LGM) is one of the most intensively studied paleoglaciological events, but its trigger and forcing remain incompletely understood. Here, we provide evidence that the timing of this glacier maximum coincided within age uncertainties with a 3100 yr-long interval of subsurface warming (26.6 to 23.5 ka BP) as recorded by an archive preserved in caves, cryogenic carbonates. This interval of sustained permafrost degradation during one of the coldest intervals of the last glacial period calls for a fundamental change in the dry Arctic-style precipitation regime. Instead, heavy snowfall during autumn and early winter led to the accumulation of a seasonal snowpack insulating the ground from the winter chill. Combined with thermal modelling, the data provide compelling evidence that the LGM glacier advance in the Alps was fueled by intensive snowfall late in the year, likely sourced from the Mediterranean Sea.

What controlled changes of glaciers in the European Alps at the time of their largest extent, about 25,000 years ago, is not well known. Here, the authors use cryogenic carbonates in caves to show that heavy snowfall during autumn and early winter was the main source of glacier growth.

Molecular Phylogeny of the Subgenus Karstomys Reveals Genetic Signature of Post-Glacial Colonization of Apodemus mystacinus (Rodentia: Muridae) in the Zagros Mountains from Different Refugia

Eastern broad-toothed field mouse, Apodemus mystacinus, is a rocky habitat dwelling rodent distributed in Asia Minor, the Levant, the Caucasus, and the Zagros Mountains. In this study, we investigated the phylogenetic relationship between different populations of A. mystacinus throughout its range, based on the mitochondrial cytb marker. Phylogenetic analyses revealed the existence of five separately evolving lineages within A. mystacinus, of which two previously unrecognized lineages were identified in the Zagros Mountains and the Levant. Divergence between two major clades of the subgenus Karstomys, corresponding to A. mystacinus and Apodemus epimelas, is inferred to coincide with the Messinian Salinity Crisis (Late Miocene), whereas the splits between major lineages of A. mystacinus are inferred to have occurred during the Pleistocene. Colonization of the Zagros may have occurred from different refugia via eastward migration of the Turkish population and then again by a more recent colonization from the Caucasus, after reopening of the land corridor between the Caucasus and the Zagros Mountains during the Holocene drought.

Mitogenomics and the genetic differentiation of contemporary Balaena mysticetus (Cetacea) from Svalbard

Full mitochondrial genomes were assembled for 12 recently sampled animals from the Svalbard bowhead whale (Balaena mysticetus) stock via high-throughput sequencing data, facilitating analysis of the demographic history of the population for the first time. The Svalbard population has retained noticeable amounts of mitochondrial genome diversity despite extreme historical harvest levels. Haplotype and nucleotide diversities were similar to those estimated earlier for other bowhead whale populations. The reconstructed demographic history was in accordance with a boom–bust scenario, combining a slight Pleistocene population growth 25 000–35 000 years ago and a Holocene decline. Employing a mutation rate of 3.418 × 10–8 substitutions per site per year, the time to the most recent common ancestor for the mitochondrial genomes of the contemporary Svalbard bowhead whales was estimated to be 68 782 (54 353–83 216) years before the present. Based on 370 bp fragments of the D-loop region, significant genetic differentiation was detected between all extant bowhead whale populations across the circumpolar Arctic. Thus, the Svalbard bowhead whales can be regarded as a population with its own genetic legacy.

Collapse of the endemic lizard Podarcis pityusensis on the island of Ibiza mediated by an invasive snake

The invasive snake Hemorrhois hippocrepis colonized the island of Ibiza (Balearic Islands) in 2003 as stowaways inside trunks of olive trees imported for gardening. It has quickly spread since 2010, posing a threat to the island’s only remaining endemic vertebrate, the Ibiza wall lizard Podarcis pityusensis. We map the yearly expansion rate of the snake and estimate via transect surveys how severely it affects the distribution and abundance of the endemic lizard. As well, we surveyed 9 of 30 small lizard populations on islets surrounding Ibiza that have been isolated since the Last Glacial Maximum. Snakes had invaded 49% of Ibiza’s land area by 2018, and censuses show a critical contrast in lizard abundance between areas with and without snakes; almost all censuses in areas without snakes show lizard presence whereas nearly all censuses in areas with H. hippocrepis lack lizard sightings. Moreover, at least one subspecies previously thriving on one of the offshore islets has become extinct, and there have been several snakes recorded swimming between Ibiza and the surrounding islets. Therefore, lizard populations have been dramatically reduced or have vanished within the range of the snake, and our results quantitatively support upgrading this species’ threat level for extinction. This study can inform to programs to manage invasive snake populations and to conservation actions to recover the endemic lizard.

Climate-driven flyway changes and memory-based long-distance migration

Millions of migratory birds occupy seasonally favourable breeding grounds in the Arctic¹, but we know little about the formation, maintenance and future of the migration routes of Arctic birds and the genetic determinants of migratory distance. Here we established a continental-scale migration system that used satellite tracking to follow 56 peregrine falcons (Falco peregrinus) from 6 populations that breed in the Eurasian Arctic, and resequenced 35 genomes from 4 of these populations. The breeding populations used five migration routes across Eurasia, which were probably formed by longitudinal and latitudinal shifts in their breeding grounds during the transition from the Last Glacial Maximum to the Holocene epoch. Contemporary environmental divergence between the routes appears to maintain their distinctiveness. We found that the gene ADCY8 is associated with population-level differences in migratory distance. We investigated the regulatory mechanism of this gene, and found that long-term memory was the most likely selective agent for divergence in ADCY8 among the peregrine populations. Global warming is predicted to influence migration strategies and diminish the breeding ranges of peregrine populations of the Eurasian Arctic. Harnessing ecological interactions and evolutionary processes to study climate-driven changes in migration can facilitate the conservation of migratory birds.

A geo-chemo-mechanical study of a highly polluted marine system (Taranto, Italy) for the enhancement of the conceptual site model

The paper presents the results of the analysis of the geo-chemo-mechanical data gathered through an innovative multidisciplinary investigation campaign in the Mar Piccolo basin, a heavily polluted marine bay aside the town of Taranto (Southern Italy). The basin is part of an area declared at high environmental risk by the Italian government. The cutting-edge approach to the environmental characterization of the site was promoted by the Special Commissioner for urgent measures of reclamation, environmental improvements and redevelopment of Taranto and involved experts from several research fields, who cooperated to gather a new insight into the origin, distribution, mobility and fate of the contaminants within the basin. The investigation campaign was designed to implement advanced research methodologies and testing strategies. Differently from traditional investigation campaigns, aimed solely at the assessment of the contamination state within sediments lying in the top layers, the new campaign provided an interpretation of the geo-chemo-mechanical properties and state of the sediments forming the deposit at the seafloor. The integrated, multidisciplinary and holistic approach, that considered geotechnical engineering, electrical and electronical engineering, geological, sedimentological, mineralogical, hydraulic engineering, hydrological, chemical, geochemical, biological fields, supported a comprehensive understanding of the influence of the contamination on the hydro-mechanical properties of the sediments, which need to be accounted for in the selection and design of the risk mitigation measures. The findings of the research represent the input ingredients of the conceptual model of the site, premise to model the evolutionary contamination scenarios within the basin, of guidance for the environmental risk management. The study testifies the importance of the cooperative approach among researchers of different fields to fulfil the interpretation of complex polluted eco-systems.

Climate change, not human population growth, correlates with Late Quaternary megafauna declines in North America

The disappearance of many North American megafauna at the end of the Pleistocene is a contentious topic. While the proposed causes for megafaunal extinction are varied, most researchers fall into three broad camps emphasizing human overhunting, climate change, or some combination of the two. Understanding the cause of megafaunal extinctions requires the analysis of through-time relationships between climate change and megafauna and human population dynamics. To do so, many researchers have used summed probability density functions (SPDFs) as a proxy for through-time fluctuations in human and megafauna population sizes. SPDFs, however, conflate process variation with the chronological uncertainty inherent in radiocarbon dates. Recently, a new Bayesian regression technique was developed that overcomes this problem-Radiocarbon-dated Event-Count (REC) Modelling. Here we employ REC models to test whether declines in North American megafauna species could be best explained by climate changes, increases in human population densities, or both, using the largest available database of megafauna and human radiocarbon dates. Our results suggest that there is currently no evidence for a persistent through-time relationship between human and megafauna population levels in North America. There is, however, evidence that decreases in global temperature correlated with megafauna population declines.

Trans-marine dispersal inferred from the saltwater tolerance of lizards from Taiwan

Dehydration and hypersalinity challenge non-marine organisms crossing the ocean. The rate of water loss and saltwater tolerance thus determine the ability to disperse over sea and further influence species distribution. Surprisingly, this association between physiology and ecology is rarely investigated in terrestrial vertebrates. Here we conducted immersion experiments to individuals and eggs of six lizard species differently distributed across Taiwan and the adjacent islands to understand if the physiological responses reflect the geographical distribution. We found that Plestiodon elegans had the highest rate of water loss and the lowest saltwater tolerance, whereas Eutropis longicaudata and E. multifasciata showed the lowest rate of water loss and the highest saltwater tolerance. Diploderma swinhonis, Hemidactylus frenatus, and Anolis sagrei had medium measurements. For the eggs, only the rigid-shelled eggs of H. frenatus were incubated successfully after treatments. While, the parchment-shelled eggs of E. longicaudata and D. swinhonis lost or gained water dramatically in the immersions without any successful incubation. Combined with the historical geology of the islands and the origin areas of each species, the inferences of the results largely explain the current distribution of these lizards across Taiwan and the adjacent islands, pioneerly showing the association between physiological capability and species distribution.

Effect of the Central American Isthmus on gene flow and divergence of the American crocodile (Crocodylus acutus)

The final formation of the Central American Isthmus (CAI) about 3.5 million years ago altered global ocean circulation, connected North and South America terrestrial biotas, and established the Caribbean Sea. The nature of this event creates a natural scenario to test vicariance, divergence, and speciation by allopatry. Studies have shown the effect of the CAI on marine and terrestrial species, but none have examined a large-bodied amphibious taxon. We used RAD sequencing on populations of the American crocodile (Crocodylus acutus) to study the genomic variation of C. acutus on both sides of the CAI, infer its demographic history, and measure the effect of the opening of the Panama Canal. Our results showed three genomic clusters: (1) Caribbean and the Panama Canal, (2) Pacific coast, and (3) Coiba island. The estimated divergence times between the Caribbean and Pacific populations are about 20,000 years ago, which is younger than the formation of the CAI, coinciding with the Last Glacial Maximum. We hypothesize the glacial/interglacial cycles facilitated gene flow between the Caribbean and Pacific crocodile populations after the formation of the CAI, masking any genomic divergence the CAI may have caused. There is no evidence of gene flow associated with the opening of the Panama Canal.