Biology subjects

Sinding, M.-H. S.

Publications and source records attributed to Sinding, M.-H. S..

At least 19 recordsLinked to original sources

bioRxiv2026

Telomere-to-telomere, accurate, and gapless genome assembly (TTAGGA) of the Korean Jindo dog with a single-contig Y chromosome

Complete canine reference genomes are essential for studies of structural variation, sex-chromosome evolution, and breed-specific architecture, yet existing references remain incomplete on the Y chromosome and retain internal gaps across multiple chromosomes. Here, we introduce TTAGGA (Telomere-to-Telomere, Accurate, Gapless Genome Assembly), a stricter completeness standard requiring chromosomes assembled end-to-end with zero internal gaps and Merqury consensus QV [≥] 50, and present Jindo1-G-TTAGGA, the first canine assembly to meet this standard, achieved under a stringent QV [≥] 60 threshold. From 813 Gb ([~]340x coverage) of multi-platform data (PacBio HiFi [~]150x, ONT ultra-long [~]103x, parental Illumina [~]40x per parent) generated from a male Korean Jindo dog, trio binning with hifiasm produced two haplotype-resolved assemblies of 2,441.6 Mb (Hap1, maternal, chrX-carrying) and 2,340.5 Mb (Hap2, paternal, chrY-carrying). Both haplotypes are gap-free at every internal position, with canonical telomeric repeats verified at both ends of all 39 chromosomes (tidk), Merqury consensus QV of 78.0 (Hap1) and 76.8 (Hap2), trio switch-error rates below 0.13%, BUSCO completeness of 99.3% (Hap1) and 96.4% (Hap2; the lower value reflects absent X-linked orthologues in the Y-bearing haplotype), and Genome Continuity Index values of 98.2 (Hap1) and 94.7 (Hap2). Hap2 carries a single 21,255,890 bp gap-free Y chromosome with TTAGGG telomeric repeats at the q-arm terminus and an acrocentric satellite-rich p-arm, representing a 5.4-fold increase over the 3.94 Mb chrY of ROS_Cfam_1.0 and adding approximately 14 Mb of newly resolved Y-linked sequence; this corresponds to roughly 79% of the cytogenetically estimated 27 Mb full-length canine chrY. Jindo1-G-TTAGGA provides a chromosome-scale, haplotype-resolved, gap-free canine reference for studies of canine structural variation, sex-chromosome evolution, and canid phylogenomics.

genomics↗

bioRxiv2026

Evolutionary history and genomic vulnerability of the extinct giant deer Megaloceros giganteus

The extinct giant deer (Megaloceros giganteus) was one of the most striking megafaunal species of the Late Quaternary, distinguished by its enormous palmated antlers reaching up to 3.5 m across, the largest known among both living and extinct cervids. Despite its iconic status, little is known about its genomic history prior to extinction [~]8 thousand years ago (kya). We generated the first nuclear palaeogenomes for Megaloceros, represented by nine individuals from Germany ([~]40 kya) and Ireland ([~]11 kya), mapped to a new chromosome-level reference genome of the fallow deer (Dama dama). Phylogenomic analyses placed Megaloceros as sister to Dama (divergence [~]3.5 Ma) and revealed evidence of gene flow with ancestral Cervus lineages. Population analyses identified clear differentiation between German and Irish lineages, with higher genetic diversity in the German individuals. Two genes under strong positive selection, BNIPL and SLC10A7, are associated with apoptosis regulation and skeletal development/bone mineralisation, respectively, and may relate to the species large body and antler size. Demographic reconstructions indicate a long-term decline in effective population size, extremely low heterozygosity, little evidence of extensive runs of homozygosity, and an elevated burden of predicted deleterious alleles. Together, these results suggest that Megaloceros entered the terminal Pleistocene in a genomically fragile state, offering new insight into the biology and evolutionary legacy of one of the largest and most distinctive cervids that ever lived.

evolutionary biology↗

bioRxiv2025

Human-Mediated Dispersal and Breeding Reshape Global Genomic Patterns in Black Soldier Flies

Human activities, either intentional or unintentional, have significantly influenced the global distribution and genetic composition of many species. Black soldier fly (Hermetia illucens; BSF) is a species that has rapidly gained commercial importance due to its bioconversion efficiency of upcycling organic waste into new products of higher value and quality through a circular economy approach. Despite its global distribution, the current Old-World demography of the wild and captive BSF populations remains poorly understood. This work combined whole-genome sequencing and population genomic analyses to determine the genetic diversity, population structure, and historical spread of global wild and captive BSF populations. Our results reveal that most global captive BSF lines were largely derived from a single primary captive lineage, likely from North America. In contrast to the genetically diverse and geographically structured wild populations, captive populations consistently exhibited reduced heterozygosity, elevated inbreeding, and extensive runs of homozygosity. These patterns reflect demographic processes such as founder effects and genetic drift, rather than intentional selection or domestication. This strongly highlights the lasting genomic impact of human-mediated dispersal and uncoordinated breeding practices. Thus, there is an urgent need for genetically informed management strategies to ensure long-term viability, adaptability, and productivity of BSF for sustainable organic waste bioconversion.

genomics↗

bioRxiv2025

Genomics of sable (Martes zibellina) x pine marten (Martes martes) hybridization

The sable (Martes zibellina) and pine marten (Martes martes) are two Palearctic mustelids with long-recognized hybrids (kidases), whose fertility was controversial for years. Early genetic studies confirmed hybrids beyond F1, but details remained unclear due to low-resolution methods. Both species were hunted for centuries, but anthropogenic pressures during the 20th-century caused severe bottlenecks in the sable followed by hunting bans and large-scale reintroduction programs across much of its range, including the sympatric zone, potentially affecting hybridization. We resequenced 30 individuals from most of the sables range and Eastern part of pine martens. Among samples, we found a broad spectrum of hybrid types with mosaic recombinant chromosomes that confirm hybrid fertility and indicate crossover is not suppressed in kidases. This necessitates re-evaluation of previous research, as we detected notable discrepancies between STR-based ancestry and whole-genome analysis. In pine martens, we revealed mitochondrial DNA introgression from sables, indicating displacement of native pine marten mitochondrial sequences. Pine marten heterozygosity is relatively low ([~]0.5-0.6 hetSNPs/kbp) while sable diversity ([~]1.5-1.8 hetSNPs/kbp) is unexpectedly high for a species with its demographic history, likely reflecting successful reintroduction programs. We dated species divergence at 1.52 (CI: 1.05-2.06) Mya and identified candidate genes associated with ecological, morphological, and dietary differences, as well as hybrid fertility issues. This study is the first to elucidate marten hybridization at the whole-genome level, opening new research directions for understanding hybridization among Holarctic martens, the genetic consequences of reintroduction programs, and comparative adaptomics.

genomics↗

bioRxiv2025

On the ancestry and evolution of the extinct dire wolf

Dire wolves (Aenocyon dirus) are extinct predators of Pleistocene North America. Although phenotypically similar to living wolves (Canis lupus), dire wolves have yet to be placed confidently in the canid family tree. We generated 3.4x and 12.8x paleogenomes from two well-preserved dire wolves dating to > 13,000 and > 72,000 years ago, and estimated consensus species trees for these and 10 canid species. Our results revealed that [~]2/3 of dire wolf ancestry is derived from a lineage sister to the clade comprising the gray wolf, coyote, and dhole, and the remaining [~]1/3 from a lineage near the base of Canini diversity. We identified 80 genes evolving under diversifying selection in dire wolves. Our results underscore the power of paleogenomes to resolve long-standing taxonomic questions and contribute to growing evidence of the role of post-speciation gene flow as an evolutionary force.

evolutionary biology↗

bioRxiv2025

Population structure and domestication history of the Javan banteng (Bos javanicus javanicus)

The domestication of the banteng in Southeast Asia is one of the Worlds least known livestock domestications, yet a vital component of the agricultural system in Indonesia and surrounding countries. Here we generated the first reference genome of the banteng and used it to analyze a set of 78 resequenced wild and domesticated bantengs, including 19 newly generated whole-genome sequenced samples of which three are historical samples. We found low heterozygosity and significant differentiation, the latter primarily driven by recent genetic drift and inbreeding in two populations, and clearly attributable to anthropogenically driven founder events or ex-situ breeding. Population structure when excluding these two populations was limited, and we found that the evolutionary divergence between wild and domestic banteng is moderate (FST = 0.14), relatively young (10,356 years), and with post-divergence gene flow. We found only weak signals of a domestication bottleneck between [~]6100-2900 years ago, and genetic diversity is on average higher in domestic than in wild banteng. Despite the soft domestication history, we found 56 candidate genes under selection during domestication, with the leptin receptor gene (LEPR) of particular interest due to the robust selection signal across methods, and its known association to metabolism, obesity and energy homeostasis. Finally, genetic load estimation revealed that Bali cattle in Australia have high realized load, while Bali cattle from Bali have high masked load. These findings provide the first genomic insights into an understudied bovine that is Critically Endangered in its wild form, and agriculturally important in its domesticated form.

evolutionary biology↗

bioRxiv2024

Complex genomic ancestry in southern regions and drivers of continental-level genetic diversity in the wolves of Asia

Gray wolves (Canis lupus) in Asia encompass most of the species global genetic diversity and many endangered populations. However, a clear understanding of the evolutionary history of wolves from many parts of Asia, especially southern regions, is lacking. We used 98 whole genomes of wolves sampled across Eurasia to better resolve their evolutionary history by investigating phylogenetic and gene flow histories across the genome, and to characterize their demographic history and genetic diversity. The strongest barriers to gene flow coincided with boundaries separating the three major extant wolf lineages - Indian, Tibetan, and Holarctic. Wolves in the central Asian mountain ranges belonged to the Holarctic lineage, and despite their geographic adjacency only share minimal ancestry with the Tibetan lineage. In contrast, wolves from eastern Asia share population-wide ancestry with the Tibetan lineage, which may reflect an unsampled lineage similar, but not exactly to, the modern-day Tibetan lineage. Wolves from southwestern Asia also share population-wide ancestry with the Indian lineage, likely due to old (>6kya) admixture events. Long-term historical declines over the last 100,000 years, geographic isolation, and recent inbreeding have resulted in the Indian and Tibetan wolves having some of the lowest levels of genetic diversity and highest realized genetic loads. In contrast, adjacent populations exhibit some of the highest genetic diversity, due in part to admixture along contact zones. Our study illustrates how using multiple approaches that consider heterogenous signals across the genome can more fully resolve the historical and contemporary processes that have led to present-day species diversity.

evolutionary biology↗

bioRxiv2023

African bush pigs exhibit porous species boundaries and appeared in Madagascar concurrently with human arrival

Several African mammals exhibit a phylogeographic pattern where closely related taxa are split between West/Central and East/Southern Africa, but their evolutionary relationships and histories remain controversial. Bushpigs (Potamochoerus larvatus) and red river hogs (P. porcus) are recognised as separate species due to morphological distinctions, a perceived lack of interbreeding at contact, and putatively old divergence times, but historically, they were considered conspecific. Moreover, the presence of Malagasy bushpigs as the sole large terrestrial mammal shared with the African mainland raises intriguing questions about its origin and arrival in Madagascar. Analyses of 67 whole genomes revealed a genetic continuum between the two species, with putative signatures of historical gene flow, variable FST values, and a recent divergence time (<500,000 years). Thus, our study challenges key arguments for splitting Potamochoerus into two species and suggests their speciation might be incomplete. Our findings also indicate that Malagasy bushpigs diverged from southern African populations and underwent a limited bottleneck 1,000-5,000 years ago, concurrent with human arrival in Madagascar. These results shed new light on the evolutionary history of an iconic and widespread African genus and provide insight into the longstanding biogeographic puzzle surrounding the bushpigs presence in Madagascar.

evolutionary biology↗

bioRxiv2023

Redefining rock doves, Columba livia, using historical whole genome sequences

The domestic pigeons exceptional phenotypic diversity was key in developing Darwins Theory of Evolution and establishing the concept of artificial selection in domestic species. However, unlike its domestic counterpart, its wild progenitor, the rock dove Columba livia, has received considerably less attention. Therefore, questions regarding their domestication, evolution, taxonomy, and conservation status remain unresolved. We generated whole-genome sequencing data from 65 historical rock dove samples representing all currently recognised subspecies and spanning the species original geographic distribution. Our dataset includes three specimens from Darwins collection and the type specimens of five different taxa. We characterised rock doves population structure, genomic diversity and gene-flow patterns. We show the West African subspecies C. l. gymnocyclus is basal to rock doves and domestic pigeons. Our results show gene-flow signals between the rock doves sister species C. rupestris and all rock doves except the West African populations. Our results led us to propose an evolutionary model for the rock dove considering the Pleistocene refugia theory. We propose that todays rock dove genetic diversity and introgression patterns derive from a history of allopatric cycles and dispersion waves during the Quaternary glacial and interglacial periods. To explore the rock dove domestication history, we combined our new dataset with available genomes from domestic pigeons. Our results point to at least one domestication event in the Levant region that gave rise to all domestic breeds analysed in this study. Finally, we propose a species-level taxonomic arrangement to reflect the evolutionary history of the West African rock dove populations.

evolutionary biology↗

bioRxiv2023

Conservation implications of elucidating the Korean wolf taxonomic ambiguity through whole-genome sequencing

The taxonomic status of the now likely extirpated Korean Peninsula wolf has been extensively debated, with some arguing it represents an independent wolf lineage, Canis coreanus. To investigate the Korean wolf genetic affiliations and their taxonomic implications, we sequenced and analysed the genomes of a historical Korean wolf dated to the beginning of the 20th century, and a captive wolf originally located at the Pyongyang Central Zoo. Our results indicated that the Korean wolf bears similar genetic ancestry to other regional East Asian populations, therefore suggesting it is not a distinct taxonomic lineage. We identified regional patterns of wolf population structure and admixture in East Asia with potential conservation consequences in the Korean Peninsula and on a regional scale. We find the Korean wolf has similar diversity and inbreeding to other East Asian wolves. Finally, we show that, in contrast to the historical sample, the captive wolf is more genetically similar to wolves from the Tibetan Plateau, hence, Korean wolf conservation programs might not benefit from the inclusion of this specimen.

evolutionary biology↗

bioRxiv2022

Ancient dolphin genomes reveal rapid repeated adaptation to coastal waters

Parallel evolution provides among the strongest evidence of the role of natural selection in shaping adaptation to the local environment. Yet, the chronology, mode and tempo of the process of parallel evolution remains broadly debated and discussed in the field of evolutionary biology. In this study, we harness the temporal resolution of paleogenomics to understand the tempo and independence of parallel coastal ecotype adaptation in common bottlenose dolphins (Tursiops truncatus). For this, we generated whole genome resequencing data from subfossil dolphins (8,610-5,626 years BP) originating from around the formation time of new coastal habitat and compared them with data from contemporary populations. Genomic data revealed a shift in genetic affinity, with the oldest ancient sample being closer to the pelagic populations, while the younger samples had intermediate ancestry that showed greater affinity with the local contemporary coastal populations. We found coastal-associated genotypes in the genome of our highest coverage ancient sample, SP1060, providing rare evidence of rapid adaptation from standing genetic variation. Lastly, using admixture graph analyses, we found a reticulate evolutionary history between pelagic and coastal populations. Ancestral gene flow from coastal populations was the probable source of standing genetic variation present in the pelagic populations that enabled rapid adaptation to newly emerged coastal habitat. The genetic response to past climatic warming provides an understanding of how bottlenose dolphins will respond to ongoing directional climate change and shifting coastlines.

evolutionary biology↗

bioRxiv2022

Genomes of the extinct Sicilian wolf reveal a complex history of isolation and admixture with ancient dogs

The Sicilian wolf represented the only population of wolves living on a Mediterranean island until the first half of the twentieth century (1930s-1960s) 1-7. Previous studies hypothesised that they remained isolated from mainland wolves from the end of the Last Glacial Maximum (LGM) 8,9, until human persecutions led them to extinction 1-7. There are only seven known Sicilian wolf specimens from the 19th and 20th century preserved in museums in Italy and recent morphometric analyses assigned them to the new subspecies Canis lupus cristaldii 10. To better understand the origins of the Sicilian wolf, and its relationship to other wolf populations, we sequenced four whole genomes (3.8x-11.6x) and five mitogenomes. We investigated the relationship between Sicilian wolves and other modern breeds to identify potential admixture. Furthermore, considering that the last land-bridge between Sicily and Italy disappeared after the LGM 11, around 17 kya, we explored the possibility that the Sicilian wolf retained ancestry from ancient wolf and dog lineages. Additionally, we explored whether the long-term isolation might have affected the genomic diversity, inbreeding levels and genetic load of the Sicilian wolf. Our findings show that the Sicilian wolves shared most ancestry with the modern Italian wolf population but are better modelled as admixed with European dog breeds, and shared traces of Eneolithic and Bronze age European dogs. We also find signatures of severe inbreeding and low genomic diversity at population and individual levels due to long-term isolation and drift, suggesting also low effective population size.

genomics↗

bioRxiv2021

Genomic analyses of the extinct Sardinian dhole (Cynotherium sardous) reaveal its evolutionary history

The Sardinian dhole (Cynotherium sardous)1 was an iconic and unique canid species of canid that was endemic of Sardinia and Corsica until it became extinct at the end of the Late Pleistocene2-5. Given its peculiar dental morphology, small body size and high level of endemism, several canids have been proposed as possible ancestors of the Sardinian dhole, including the Asian dhole and African hunting dog ancestor 3,6-9. Morphometric analyses3,6,8-12 have failed to clarify the evolutionary relationship with other canids. We sequenced the genome of a ca 21,100 year old Sardinian dhole in order to understand its genomic history and clarify its phylogenetic position. We found it represents a separate taxon from all other living canids from Eurasia, Africa and North America, and that the Sardinian and Asian dhole lineages diverged ca 885 ka. We additionally detected historical gene flow between the Sardinian and Asian dhole lineages, that ended approximately 500-300 ka, when the landbridge between Sardinia and mainland Italy was broken, severing their population connectivity. Our sample showed low genome-wide diversity compared to other extant canids - probably a result of the long-term isolation - that could have contributed to the subsequent extinction of the Sardinian dhole.

genomics↗

bioRxiv2020

The germline mutational process in rhesus macaque and its implications for phylogenetic dating

Understanding the rate and pattern of germline mutations is of fundamental importance for understanding evolutionary processes. Here we analyzed 19 parent-offspring trios of rhesus macaques (Macaca mulatta) at high sequencing coverage of ca. 76X per individual, and estimated an average rate of 0.77 x 10-8 de novo mutations per site per generation (95 % CI: 0.69 x 10-8 - 0.85 x 10-8). By phasing 50 % of the mutations to parental origins, we found that the mutation rate is positively correlated with the paternal age. The paternal lineage contributed an average of 81 % of the de novo mutations, with a trend of an increasing male contribution for older fathers. About 3.5 % of de novo mutations were shared between siblings, with no parental bias, suggesting that they arose from early development (postzygotic) stages. Finally, the divergence times between closely related primates calculated based on the yearly mutation rate of rhesus macaque generally reconcile with divergence estimated with molecular clock methods, except for the Cercopithecidae/Hominoidea molecular divergence dated at 52 Mya using our new estimate of the yearly mutation rate.

evolutionary biology↗

bioRxiv2019

Ancient RNA from Late Pleistocene permafrost and historical canids shows tissue-specific transcriptome survival

While sequencing ancient DNA from archaeological material is now commonplace, very few attempts to sequence ancient transcriptomes have been made, even from typically stable deposition environments such as permafrost. This is presumably due to assumptions that RNA completely degrades relatively quickly, particularly when dealing with autolytic, nuclease-rich mammalian tissues. However, given the recent successes in sequencing ancient RNA (aRNA) from various sources including plants and animals, we suspect that these assumptions may be incorrect or exaggerated. To challenge the underlying dogma, we generated shotgun RNA data from sources that might normally be dismissed for such study. Here we present aRNA data generated from two historical wolf skins, and permafrost-preserved liver tissue of a 14,300-year-old Pleistocene canid. Not only is the latter the oldest RNA ever to be sequenced, but also shows evidence of biologically relevant tissue-specificity and close similarity to equivalent data derived from modern-day control tissue. Other hallmarks of RNA-seq data such as exon-exon junction presence and high endogenous ribosomal RNA content confirms our datas authenticity. By performing independent technical replicates using two high-throughput sequencing platforms, we show not only that aRNA can survive for extended periods in mammalian tissues, but also that it has potential for tissue identification, and possibly further uses such as in vivo genome activity and adaptation, when sequenced using this technology.

genomics↗

bioRxiv2018

Early Pleistocene enamel proteome sequences from Dmanisi resolve Stephanorhinus phylogeny.

Ancient DNA (aDNA) sequencing has enabled unprecedented reconstruction of speciation, migration, and admixture events for extinct taxa1. Outside the permafrost, however, irreversible aDNA post-mortem degradation2 has so far limited aDNA recovery within the {small tilde}0.5 million years (Ma) time range3. Tandem mass spectrometry (MS)-based collagen type I (COL1) sequencing provides direct access to older biomolecular information4, though with limited phylogenetic use. In the absence of molecular evidence, the speciation of several Early and Middle Pleistocene extinct species remain contentious. In this study, we address the phylogenetic relationships of the Eurasian Pleistocene Rhinocerotidae5-7 using {small tilde}1.77 million years (Ma) old dental enamel proteome sequences of a Stephanorhinus specimen from the Dmanisi archaeological site in Georgia (South Caucasus)8. Molecular phylogenetic analyses place the Dmanisi Stephanorhinus as a sister group to the woolly (Coelodonta antiquitatis) and Mercks rhinoceros (S. kirchbergensis) clade. We show that Coelodonta evolved from an early Stephanorhinus lineage and that this genus includes at least two distinct evolutionary lines. As such, the genus Stephanorhinus is currently paraphyletic and its systematic revision is therefore needed. We demonstrate that Early Pleistocene dental enamel proteome sequencing overcomes the limits of ancient collagen- and aDNA-based phylogenetic inference, and also provides additional information about the sex and taxonomic assignment of the specimens analysed. Dental enamel, the hardest tissue in vertebrates, is highly abundant in the fossil record. Our findings reveal that palaeoproteomic investigation of this material can push biomolecular investigation further back into the Early Pleistocene.

evolutionary biology↗

bioRxiv2018

Abundance of whales in West and East Greenland in summer 2015

An aerial line transect survey of whales in West and East Greenland was conducted in August-September 2015. The survey covered the area between the coast of West Greenland and offshore (up to 100 km) to the shelf break. In East Greenland, the survey lines covered the area from the coast up to 50 km offshore crossing the shelf break. A total of 423 sightings of 12 cetacean species were obtained and abundance estimates were developed for common minke whale, from now on called minke whale, (Balaenoptera acutorostrata) (32 sightings), fin whale (Balaenoptera physalus) (129 sightings), humpback whale (Megaptera novaeangliae) (84 sightings), harbour porpoise (Phocoena phocoena) (55 sightings), long-finned pilot whale, from now on called pilot whale, (Globicephala melas) (42 sightings) and white-beaked dolphins (Lagenorhynchus albirostri) (50 sightings). The developed at-surface abundance estimates were corrected for both perception bias and availability bias if possible. Data on surface corrections for minke whales and harbour porpoises were collected from whales instrumented with satellite-linked time-depth-recorders. Options for estimation methods are presented and the preferred estimates are: Minke whales: 5,095 (95% CI: 2,171-11,961) in West Greenland and 2,762 (95% CI: 1,160-6,574) in East Greenland, fin whales: 2,215 (95% CI: 1,017-4,823) in West Greenland and 6,440 (95% CI: 3,901-10,632) in East Greenland, humpback whales: 993 (95% CI: 434-2,272) in West Greenland and 4,223 (95%CI: 1,845-9,666) in East Greenland, harbour porpoise: 83,321 (95% CI: 43,377-160,047) in West Greenland and 1,642 (95% CI: 319-8,464) in East Greenland, pilot whales: 9,190 (95% CI: 3,635-23,234) in West Greenland and 258 (95% CI: 50-1,354) in East Greenland, white-beaked dolphins 15,261 (95% CI: 7,048-33,046) in West Greenland and 11,889 (95% CI: 4,710-30,008) in East Greenland. The abundance of cetaceans in coastal areas of East Greenland has not been estimated before, but the limited historical information from the area indicate that the achieved abundance estimates were remarkably high. When comparing the abundance estimates from 2015 in West Greenland with a similar survey conducted in 2007 there is a clear trend towards lower densities in 2015 for the three baleen whale species and white-beaked dolphins. Harbour porpoises and pilot whales however, did not show a similar decline. The decline in baleen whale and white-beaked dolphin abundance is likely due to emigration to the East Greenland shelf areas where recent climate driven changes in pelagic productivity may have accelerated favourable conditions for these species.

ecology↗

bioRxiv2018

Modern wolves trace their origin to a late Pleistocene expansion from Beringia

Grey wolves (Canis lupus) are one of the few large terrestrial carnivores that maintained a wide geographic distribution across the Northern Hemisphere throughout the Pleistocene and Holocene. Recent genetic studies have suggested that, despite this continuous presence, major demographic changes occurred in wolf populations between the late Pleistocene and early Holocene, and that extant wolves trace their ancestry to a single late Pleistocene population. Both the geographic origin of this ancestral population and how it became widespread remain a mystery. Here we analyzed a large dataset of novel modern and ancient mitochondrial wolf genomes, spanning the last 50,000 years, using a spatially and temporally explicit modeling framework to show that contemporary wolf populations across the globe trace their ancestry to an expansion from Beringia at the end of the Last Glacial Maximum - a process most likely driven by the significant ecological changes that occurred across the Northern Hemisphere during this period. This study provides direct ancient genetic evidence that long-range migration has played an important role in the population history of a large carnivore and provides an insight into how wolves survived the wave of megafaunal extinctions at the end of the last glaciation. Moreover, because late Pleistocene grey wolves were the likely source from which all modern dogs trace their origins, the demographic history described in this study has fundamental implications for understanding the geographical origin of the dog.

evolutionary biology↗