32 results on '"Lebrasseur O"'
Search Results
2. Grey wolf genomic history reveals a dual ancestry of dogs
- Author
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Bergström, A., Stanton, D. W. G., Taron, U. H., Frantz, L., Sinding, M. -H. S., Ersmark, E., Pfrengle, S., Cassatt-Johnstone, M., Lebrasseur, O., Girdland-Flink, L., Fernandes, D. M., Ollivier, M., Speidel, L., Gopalakrishnan, S., Westbury, M. V., Ramos-Madrigal, J., Feuerborn, T. R., Reiter, E., Gretzinger, J., Münzel, S. C., Swali, P., Conard, N. J., Carøe, C., Haile, J., Linderholm, A., Androsov, S., Barnes, I., Baumann, C., Benecke, N., Bocherens, H., Brace, S., Carden, R. F., Drucker, D. G., Fedorov, S., Gasparik, M., Germonpré, M., Grigoriev, S., Groves, P., Hertwig, S. T., Ivanova, V. V., Janssens, L., Jennings, R. P., Kasparov, A. K., Kirillova, I. V., Kurmaniyazov, I., Kuzmin, Y. V., Kosintsev, P. A., Lázničková-Galetová, M., Leduc, C., Nikolskiy, P., Nussbaumer, M., O’Drisceoil, C., Orlando, L., Outram, A., Pavlova, E. Y., Perri, A. R., Pilot, M., Pitulko, V. V., Plotnikov, V. V., Protopopov, A. V., Rehazek, A., Sablin, M., Seguin-Orlando, A., Storå, J., Verjux, C., Zaibert, V. F., Zazula, G., Crombé, P., Hansen, A. J., Willerslev, E., Leonard, J. A., Götherström, A., Pinhasi, R., Schuenemann, V. J., Hofreiter, M., Gilbert, M. T. P., Shapiro, B., Larson, G., Krause, J., Dalén, L., Skoglund, P., Bergström, A., Stanton, D. W. G., Taron, U. H., Frantz, L., Sinding, M. -H. S., Ersmark, E., Pfrengle, S., Cassatt-Johnstone, M., Lebrasseur, O., Girdland-Flink, L., Fernandes, D. M., Ollivier, M., Speidel, L., Gopalakrishnan, S., Westbury, M. V., Ramos-Madrigal, J., Feuerborn, T. R., Reiter, E., Gretzinger, J., Münzel, S. C., Swali, P., Conard, N. J., Carøe, C., Haile, J., Linderholm, A., Androsov, S., Barnes, I., Baumann, C., Benecke, N., Bocherens, H., Brace, S., Carden, R. F., Drucker, D. G., Fedorov, S., Gasparik, M., Germonpré, M., Grigoriev, S., Groves, P., Hertwig, S. T., Ivanova, V. V., Janssens, L., Jennings, R. P., Kasparov, A. K., Kirillova, I. V., Kurmaniyazov, I., Kuzmin, Y. V., Kosintsev, P. A., Lázničková-Galetová, M., Leduc, C., Nikolskiy, P., Nussbaumer, M., O’Drisceoil, C., Orlando, L., Outram, A., Pavlova, E. Y., Perri, A. R., Pilot, M., Pitulko, V. V., Plotnikov, V. V., Protopopov, A. V., Rehazek, A., Sablin, M., Seguin-Orlando, A., Storå, J., Verjux, C., Zaibert, V. F., Zazula, G., Crombé, P., Hansen, A. J., Willerslev, E., Leonard, J. A., Götherström, A., Pinhasi, R., Schuenemann, V. J., Hofreiter, M., Gilbert, M. T. P., Shapiro, B., Larson, G., Krause, J., Dalén, L., and Skoglund, P.
- Abstract
The grey wolf (Canis lupus) was the first species to give rise to a domestic population, and they remained widespread throughout the last Ice Age when many other large mammal species went extinct. Little is known, however, about the history and possible extinction of past wolf populations or when and where the wolf progenitors of the present-day dog lineage (Canis familiaris) lived1–8. Here we analysed 72 ancient wolf genomes spanning the last 100,000 years from Europe, Siberia and North America. We found that wolf populations were highly connected throughout the Late Pleistocene, with levels of differentiation an order of magnitude lower than they are today. This population connectivity allowed us to detect natural selection across the time series, including rapid fixation of mutations in the gene IFT88 40,000–30,000 years ago. We show that dogs are overall more closely related to ancient wolves from eastern Eurasia than to those from western Eurasia, suggesting a domestication process in the east. However, we also found that dogs in the Near East and Africa derive up to half of their ancestry from a distinct population related to modern southwest Eurasian wolves, reflecting either an independent domestication process or admixture from local wolves. None of the analysed ancient wolf genomes is a direct match for either of these dog ancestries, meaning that the exact progenitor populations remain to be located. © 2022, The Author(s).
- Published
- 2022
3. Holocene cultural history of Red jungle fowl (Gallus gallus) and its domestic descendant in East Asia
- Author
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Larson, G, Peters, J, Lebrasseur, O, and Deng, H
- Subjects
Ancient DNA analysis ,Global and Planetary Change ,Red jungle fowl (Gallus gallus) ,Holocene ,Domestic chicken ,Geology ,Zooarchaeology ,Palaeozoogeography ,Shang Dynasty ,East Asia ,Palaeoclimate ,Ecology, Evolution, Behavior and Systematics - Abstract
Nearly three decades ago, zooarchaeologists postulated that chicken husbandry was practiced in Northern China by ∼8.0 ka calBP. Recently, ancient mitogenome analyses of galliform remains suggested that Red jungle fowl (Gallus gallus) was already present in the Yellow River basin several millennia earlier, shortly after the onset of the Holocene. If these conclusions are correct, the origins of chicken domestication and husbandry in the region may have been spurred by agricultural innovations in the lower Yellow River basin including millet cultivation, pig husbandry, and dog breeding. In addition, the dispersal of poultry farming from East Asia to Asia Minor and Europe could therefore date to the Neolithic along ancient trade routes across Central Asia rather than via South Asia and Mesopotamia. For this scenario to be plausible, the post-Pleistocene climatic conditions must have been favourable to allow for a northward extension of the native distribution of tropical Red jungle fowl currently not found north of ∼25°N. This study combines Holocene palaeoclimate and archaeofaunal archives with new zooarchaeological insights alongside a discussion of methodological issues and cultural aspects in order to revisit the hypothesis of an early Holocene Gallus domestication and Neolithic poultry husbandry in Northern China. Our results regarding the natural and cultural history of Red jungle fowl and domestic chickens in East Asia, and the timing of chicken dispersal across the Old World suggest that an early Holocene domestication of chickens is problematic at best. We conclude by postulating an alternative model for the early exploitation of a key domestic species in present-day East Asia.
- Published
- 2016
4. Reply to Beavan, Bryant, and Storey and Matisoo-Smith: Ancestral Polynesian "D" haplotypes reflect authentic Pacific chicken lineages
- Author
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Thomson, V. A., primary, Lebrasseur, O., additional, Austin, J. J., additional, Hunt, T. L., additional, Burney, D. A., additional, Denham, T., additional, Rawlence, N. J., additional, Wood, J. R., additional, Gongora, J., additional, Flink, L. G., additional, Linderholm, A., additional, Dobney, K., additional, Larson, G., additional, and Cooper, A., additional
- Published
- 2014
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5. Isotopic Investigation of Animal Husbandry in the Welsh and English Periods at Dryslwyn Castle, Carmarthenshire, Wales
- Author
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Millard, A. R., primary, Jimenez‐Cano, N. G., additional, Lebrasseur, O., additional, and Sakai, Y., additional
- Published
- 2011
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6. Isotopic Investigation of Animal Husbandry in the Welsh and English Periods at Dryslwyn Castle, Carmarthenshire, Wales.
- Author
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Millard, A. R., Jimenez‐Cano, N. G., Lebrasseur, O., and Sakai, Y.
- Subjects
ISOTOPIC analysis ,DOMESTIC animals ,ANCIENT agriculture ,CARBON isotope spectra ,NITROGEN isotopes ,MEDIEVAL civilization ,WELSH history, 1063-1284 ,HISTORICAL archaeology ,THIRTEENTH century - Abstract
ABSTRACT Dryslwyn Castle in southwest Wales was founded by a Welsh lord in the AD 1220s, captured by the English in 1287, and declined from c.1407 until it was abandoned c.1450. In contrast to historical evidence for changes in procurement of meat, previous zooarchaeological work has suggested that throughout these three periods, there was no change in the supply of animals. We have analysed the stable carbon and nitrogen isotope values of 20 cattle and 25 pigs from the Castle to further test this hypothesis. Our results show that there was no detectable change in the source of supply of cattle to the Castle when it passed from Welsh to English control, though differences in isotope ratios compared to cattle from York suggest that such changes might well be detectable. For pigs, there was an increase in carbon isotope ratios in the English period and a reversion to the previous values in the decline period, which is interpreted as reflecting a change in diet of the pigs from woodland to more open environments. Such a change is anticipated locally due to human population pressure in the English period, but could also reflect a change in the region of supply. This paper shows that there is potential for developing isotope analyses as part of the study of medieval husbandry. Copyright © 2011 John Wiley & Sons, Ltd. [ABSTRACT FROM AUTHOR]
- Published
- 2013
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7. Genomic and archaeological evidence suggest a dual origin of domestic dogs
- Author
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Laurent Frantz, Ve, Mullin, Pionnier-Capitan M, Lebrasseur O, Ollivier M, Perri A, Linderholm A, Mattiangeli V, Md, Teasdale, Ea, Dimopoulos, Tresset A, Duffraisse M, McCormick F, Bartosiewicz L, Gál E, Éa, Nyerges, Mv, Sablin, Bréhard S, Mashkour M, and Bălăşescu A
8. Ancient genomes reveal structural shifts after the arrival of Steppe-related ancestry in the Italian Peninsula
- Author
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Stefano Benazzi, Andrea Dolfini, Ophélie Lebrasseur, Eugenia D’Atanasio, Mait Metspalu, Cinzia Scaggion, Monica Miari, Mario Federico Rolfo, Greger Larson, Jessica Beckett, Tina Saupe, Francesco Montinaro, Cristian Capelli, Flavio De Angelis, Luca Pagani, Luca Alessandri, Ruoyun Hui, Letizia Silvestri, Robin Skeates, Anu Solnik, Christiana L. Scheib, Sahra Talamo, Toomas Kivisild, Ilenia Arienzo, Nicola Carrara, Classical and Mediterranean Archaeology, Saupe T., Montinaro F., Scaggion C., Carrara N., Kivisild T., D'Atanasio E., Hui R., Solnik A., Lebrasseur O., Larson G., Alessandri L., Arienzo I., De Angelis F., Rolfo M.F., Skeates R., Silvestri L., Beckett J., Talamo S., Dolfini A., Miari M., Metspalu M., Benazzi S., Capelli C., Pagani L., and Scheib C.L.
- Subjects
0301 basic medicine ,Human Migration ,Settore L-ANT/01 ,Datasets as Topic ,genome-wide shotgun data ,Biology ,General Biochemistry, Genetics and Molecular Biology ,03 medical and health sciences ,0302 clinical medicine ,Cave ,Peninsula ,Bronze Age ,Leprosy ,Human population genetics ,Kinship ,Humans ,DNA, Ancient ,isotope ,ancient DNA ,History, Ancient ,isotopes ,kinship ,geography ,geography.geographical_feature_category ,human population genetic ,Genome, Human ,Genomics ,Chalcolithic ,immunity ,Archaeology ,Genetics, Population ,Phenotype ,030104 developmental biology ,Ancient DNA ,Italy ,human population genetics ,Genetic structure ,later prehistory ,gene flow ,General Agricultural and Biological Sciences ,030217 neurology & neurosurgery - Abstract
Across Europe, the genetics of the Chalcolithic/Bronze Age transition is increasingly characterized in terms of an influx of Steppe-related ancestry. The effect of this major shift on the genetic structure of populations in the Italian Peninsula remains underexplored. Here, genome-wide shotgun data for 22 individuals from commingled cave and single burials in Northeastern and Central Italy dated between 3200 and 1500 BCE provide the first genomic characterization of Bronze Age individuals (n = 8; 0.001-1.2× coverage) from the central Italian Peninsula, filling a gap in the literature between 1950 and 1500 BCE. Our study confirms a diversity of ancestry components during the Chalcolithic and the arrival of Steppe-related ancestry in the central Italian Peninsula as early as 1600 BCE, with this ancestry component increasing through time. We detect close patrilineal kinship in the burial patterns of Chalcolithic commingled cave burials and a shift away from this in the Bronze Age (2200-900 BCE) along with lowered runs of homozygosity, which may reflect larger changes in population structure. Finally, we find no evidence that the arrival of Steppe-related ancestry in Central Italy directly led to changes in frequency of 115 phenotypes present in the dataset, rather that the post-Roman Imperial period had a stronger influence, particularly on the frequency of variants associated with protection against Hansen's disease (leprosy). Our study provides a closer look at local dynamics of demography and phenotypic shifts as they occurred as part of a broader phenomenon of widespread admixture during the Chalcolithic/Bronze Age transition. ispartof: CURRENT BIOLOGY vol:31 issue:12 pages:2576-+ ispartof: location:England status: published
- Published
- 2021
9. Anthropogenic events and responses to environmental stress are shaping the genomes of Ethiopian indigenous goats.
- Author
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Belay S, Belay G, Nigussie H, Ahbara AM, Tijjani A, Dessie T, Tarekegn GM, Jian-Lin H, Mor S, Woldekiros HS, Dobney K, Lebrasseur O, Hanotte O, and Mwacharo JM
- Subjects
- Animals, Ethiopia, Stress, Physiological genetics, Genetic Variation, Goats genetics, Genome, Phylogeny
- Abstract
Anthropological and biophysical processes have shaped livestock genomes over Millenia and can explain their current geographic distribution and genetic divergence. We analyzed 57 Ethiopian indigenous domestic goat genomes alongside 67 equivalents of east, west, and north-west African, European, South Asian, Middle East, and wild Bezoar goats. Cluster, ADMIXTURE (K = 4) and phylogenetic analysis revealed four genetic groups comprising African, European, South Asian, and wild Bezoar goats. The Middle Eastern goats had an admixed genome of these four genetic groups. At K = 5, the West African Dwarf and Moroccan goats were separated from East African goats demonstrating a likely historical legacy of goat arrival and dispersal into Africa via the coastal Mediterranean Sea and the Horn of Africa. F
ST , XP-EHH, and Hp analysis revealed signatures of selection in Ethiopian goats overlaying genes for thermo-sensitivity, oxidative stress response, high-altitude hypoxic adaptation, reproductive fitness, pathogen defence, immunity, pigmentation, DNA repair, modulation of renal function and integrated fluid and electrolyte homeostasis. Notable examples include TRPV1 (a nociception gene); PTPMT1 (a critical hypoxia survival gene); RETREG (a regulator of reticulophagy during starvation), and WNK4 (a molecular switch for osmoregulation). These results suggest that human-mediated translocations and adaptation to contrasting environments are shaping indigenous African goat genomes., (© 2024. The Author(s).)- Published
- 2024
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10. Facilitating accessible, rapid, and appropriate processing of ancient metagenomic data with AMDirT.
- Author
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Borry M, Forsythe A, Andrades Valtueña A, Hübner A, Ibrahim A, Quagliariello A, White AE, Kocher A, Vågene ÅJ, Bartholdy BP, Spurīte D, Ponce-Soto GY, Neumann G, Huang IT, Light I, Velsko IM, Jackson I, Frangenberg J, Serrano JG, Fumey J, Özdoğan KT, Blevins KE, Daly KG, Lopopolo M, Moraitou M, Michel M, van Os M, Bravo-Lopez MJ, Sarhan MS, Dagtas ND, Oskolkov N, Smith OS, Lebrasseur O, Rozwalak P, Eisenhofer R, Wasef S, Ramachandran SL, Vanghi V, Warinner C, and Fellows Yates JA
- Subjects
- Humans, High-Throughput Nucleotide Sequencing methods, Software, Metagenome, Computational Biology methods, DNA, Ancient analysis, Metagenomics methods, Metadata
- Abstract
Background: Access to sample-level metadata is important when selecting public metagenomic sequencing datasets for reuse in new biological analyses. The Standards, Precautions, and Advances in Ancient Metagenomics community (SPAAM, https://spaam-community.org) has previously published AncientMetagenomeDir, a collection of curated and standardised sample metadata tables for metagenomic and microbial genome datasets generated from ancient samples. However, while sample-level information is useful for identifying relevant samples for inclusion in new projects, Next Generation Sequencing (NGS) library construction and sequencing metadata are also essential for appropriately reprocessing ancient metagenomic data. Currently, recovering information for downloading and preparing such data is difficult when laboratory and bioinformatic metadata is heterogeneously recorded in prose-based publications., Methods: Through a series of community-based hackathon events, AncientMetagenomeDir was updated to provide standardised library-level metadata of existing and new ancient metagenomic samples. In tandem, the companion tool 'AMDirT' was developed to facilitate rapid data filtering and downloading of ancient metagenomic data, as well as improving automated metadata curation and validation for AncientMetagenomeDir., Results: AncientMetagenomeDir was extended to include standardised metadata of over 6000 ancient metagenomic libraries. The companion tool 'AMDirT' provides both graphical- and command-line interface based access to such metadata for users from a wide range of computational backgrounds. We also report on errors with metadata reporting that appear to commonly occur during data upload and provide suggestions on how to improve the quality of data sharing by the community., Conclusions: Together, both standardised metadata reporting and tooling will help towards easier incorporation and reuse of public ancient metagenomic datasets into future analyses., Competing Interests: No competing interests were disclosed., (Copyright: © 2024 Borry M et al.)
- Published
- 2024
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11. Patagonian partnerships: the extinct Dusicyon avus and its interaction with prehistoric human communities.
- Author
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Abbona CC, Lebrasseur O, Prevosti FJ, Peralta E, González Venanzi L, Frantz L, Larson G, Gil AF, and Neme GA
- Abstract
The southern Mendoza province, located in the northern region of Patagonia, was inhabited by hunter-gatherer groups until historic times. Previous archaeological studies have reported canid remains among faunal assemblages, which were assumed to be part of the human diet. However, the taxonomic identification and significance of these canids within human groups have raised questions. In this study, we used ancient DNA analysis, morphological examination and stable isotope analysis (δ
13 Ccol and δ15 N) to re-evaluate the taxonomic assignment of a canid discovered at the Late Holocene burial site of Cañada Seca. Previous morphological identifications suggested that it belonged to the genus Lycalopex , but our results conclusively demonstrate that the individual belongs to the extinct fox species Dusicyon avus . This finding expands Dusicyon avus' known geographical distribution to Patagonia's northern extremity. Furthermore, statistical predictions based on genetic divergence undermine the hypothesis that hybridization between Canis and Dusicyon , facilitated by the introduction of domestic dogs, played a role in the extinction of Dusicyon species. On the other hand, our findings indicate that a Dusicyon avus individual shared a similar diet and was probably buried alongside humans, suggesting a close relationship between the two species during their lives and deaths., Competing Interests: We declare we have no competing interests, (© 2024 The Authors.)- Published
- 2024
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12. Whole-genome resource sequences of 57 indigenous Ethiopian goats.
- Author
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Belay S, Belay G, Nigussie H, Jian-Lin H, Tijjani A, Ahbara AM, Tarekegn GM, Woldekiros HS, Mor S, Dobney K, Lebrasseur O, Hanotte O, and Mwacharo JM
- Subjects
- Animals, Biological Evolution, DNA, Ethiopia, Genome, Goats genetics
- Abstract
Domestic goats are distributed worldwide, with approximately 35% of the one billion world goat population occurring in Africa. Ethiopia has 52.5 million goats, ~99.9% of which are considered indigenous landraces deriving from animals introduced to the Horn of Africa in the distant past by nomadic herders. They have continued to be managed by smallholder farmers and semi-mobile pastoralists throughout the region. We report here 57 goat genomes from 12 Ethiopian goat populations sampled from different agro-climates. The data were generated through sequencing DNA samples on the Illumina NovaSeq 6000 platform at a mean depth of 9.71x and 150 bp pair-end reads. In total, ~2 terabytes of raw data were generated, and 99.8% of the clean reads mapped successfully against the goat reference genome assembly at a coverage of 99.6%. About 24.76 million SNPs were generated. These SNPs can be used to study the population structure and genome dynamics of goats at the country, regional, and global levels to shed light on the species' evolutionary trajectory., (© 2024. The Author(s).)
- Published
- 2024
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13. Equine herpesvirus 4 infected domestic horses associated with Sintashta spoke-wheeled chariots around 4,000 years ago.
- Author
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Lebrasseur O, More KD, and Orlando L
- Abstract
Equine viral outbreaks have disrupted the socio-economic life of past human societies up until the late 19th century and continue to be of major concern to the horse industry today. With a seroprevalence of 60-80 per cent, equine herpesvirus 4 (EHV-4) is the most common horse pathogen on the planet. Yet, its evolutionary history remains understudied. Here, we screen the sequenced data of 264 archaeological horse remains to detect the presence of EHV-4. We recover the first ancient EHV-4 genome with 4.2× average depth-of-coverage from a specimen excavated in the Southeastern Urals and dated to the Early Bronze Age period, approximately 3,900 years ago. The recovery of an EHV-4 virus outside the upper respiratory tract not only points to an animal particularly infected but also highlights the importance of post-cranial bones in pathogen characterisation. Bayesian phylogenetic reconstruction provides a minimal time estimate for EHV-4 diversification to around 4,000 years ago, a time when modern domestic horses spread across the Central Asian steppes together with spoke-wheeled Sintashta chariots, or earlier. The analyses also considerably revise the diversification time of the two EHV-4 subclades from the 16th century based solely on modern data to nearly a thousand years ago. Our study paves the way for a robust reconstruction of the history of non-human pathogens and their impact on animal health., Competing Interests: None declared., (© The Author(s) 2024. Published by Oxford University Press.)
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- 2024
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14. Ancient chicken remains reveal the origins of virulence in Marek's disease virus.
- Author
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Fiddaman SR, Dimopoulos EA, Lebrasseur O, du Plessis L, Vrancken B, Charlton S, Haruda AF, Tabbada K, Flammer PG, Dascalu S, Marković N, Li H, Franklin G, Symmons R, Baron H, Daróczi-Szabó L, Shaymuratova DN, Askeyev IV, Putelat O, Sana M, Davoudi H, Fathi H, Mucheshi AS, Vahdati AA, Zhang L, Foster A, Sykes N, Baumberg GC, Bulatović J, Askeyev AO, Askeyev OV, Mashkour M, Pybus OG, Nair V, Larson G, Smith AL, and Frantz LAF
- Subjects
- Animals, Lymphoma virology, Virulence genetics, Phylogeny, Chickens virology, Herpesvirus 2, Gallid classification, Herpesvirus 2, Gallid genetics, Herpesvirus 2, Gallid pathogenicity, Marek Disease history, Marek Disease virology
- Abstract
The pronounced growth in livestock populations since the 1950s has altered the epidemiological and evolutionary trajectory of their associated pathogens. For example, Marek's disease virus (MDV), which causes lymphoid tumors in chickens, has experienced a marked increase in virulence over the past century. Today, MDV infections kill >90% of unvaccinated birds, and controlling it costs more than US$1 billion annually. By sequencing MDV genomes derived from archeological chickens, we demonstrate that it has been circulating for at least 1000 years. We functionally tested the Meq oncogene, one of 49 viral genes positively selected in modern strains, demonstrating that ancient MDV was likely incapable of driving tumor formation. Our results demonstrate the power of ancient DNA approaches to trace the molecular basis of virulence in economically relevant pathogens.
- Published
- 2023
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15. Limited historical admixture between European wildcats and domestic cats.
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Jamieson A, Carmagnini A, Howard-McCombe J, Doherty S, Hirons A, Dimopoulos E, Lin AT, Allen R, Anderson-Whymark H, Barnett R, Batey C, Beglane F, Bowden W, Bratten J, De Cupere B, Drew E, Foley NM, Fowler T, Fox A, Geigl EM, Gotfredsen AB, Grange T, Griffiths D, Groß D, Haruda A, Hjermind J, Knapp Z, Lebrasseur O, Librado P, Lyons LA, Mainland I, McDonnell C, Muñoz-Fuentes V, Nowak C, O'Connor T, Peters J, Russo IM, Ryan H, Sheridan A, Sinding MS, Skoglund P, Swali P, Symmons R, Thomas G, Trolle Jensen TZ, Kitchener AC, Senn H, Lawson D, Driscoll C, Murphy WJ, Beaumont M, Ottoni C, Sykes N, Larson G, and Frantz L
- Subjects
- Humans, Cats genetics, Animals, Cattle, Bees, Sheep, Swine, Chickens, Europe, Gene Flow, Hybridization, Genetic, Felis genetics
- Abstract
Domestic cats were derived from the Near Eastern wildcat (Felis lybica), after which they dispersed with people into Europe. As they did so, it is possible that they interbred with the indigenous population of European wildcats (Felis silvestris). Gene flow between incoming domestic animals and closely related indigenous wild species has been previously demonstrated in other taxa, including pigs, sheep, goats, bees, chickens, and cattle. In the case of cats, a lack of nuclear, genome-wide data, particularly from Near Eastern wildcats, has made it difficult to either detect or quantify this possibility. To address these issues, we generated 75 ancient mitochondrial genomes, 14 ancient nuclear genomes, and 31 modern nuclear genomes from European and Near Eastern wildcats. Our results demonstrate that despite cohabitating for at least 2,000 years on the European mainland and in Britain, most modern domestic cats possessed less than 10% of their ancestry from European wildcats, and ancient European wildcats possessed little to no ancestry from domestic cats. The antiquity and strength of this reproductive isolation between introduced domestic cats and local wildcats was likely the result of behavioral and ecological differences. Intriguingly, this long-lasting reproductive isolation is currently being eroded in parts of the species' distribution as a result of anthropogenic activities., Competing Interests: Declaration of interests The authors declare no competing interests., (Copyright © 2023 The Authors. Published by Elsevier Inc. All rights reserved.)
- Published
- 2023
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16. Reply to Peng et al.: Chicken tessellation requires more pieces.
- Author
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Peters J, Fuller DQ, Irving-Pease EK, Lebrasseur O, Best J, Smallman R, and Larson G
- Subjects
- Animals, Chickens
- Published
- 2022
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17. Grey wolf genomic history reveals a dual ancestry of dogs.
- Author
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Bergström A, Stanton DWG, Taron UH, Frantz L, Sinding MS, Ersmark E, Pfrengle S, Cassatt-Johnstone M, Lebrasseur O, Girdland-Flink L, Fernandes DM, Ollivier M, Speidel L, Gopalakrishnan S, Westbury MV, Ramos-Madrigal J, Feuerborn TR, Reiter E, Gretzinger J, Münzel SC, Swali P, Conard NJ, Carøe C, Haile J, Linderholm A, Androsov S, Barnes I, Baumann C, Benecke N, Bocherens H, Brace S, Carden RF, Drucker DG, Fedorov S, Gasparik M, Germonpré M, Grigoriev S, Groves P, Hertwig ST, Ivanova VV, Janssens L, Jennings RP, Kasparov AK, Kirillova IV, Kurmaniyazov I, Kuzmin YV, Kosintsev PA, Lázničková-Galetová M, Leduc C, Nikolskiy P, Nussbaumer M, O'Drisceoil C, Orlando L, Outram A, Pavlova EY, Perri AR, Pilot M, Pitulko VV, Plotnikov VV, Protopopov AV, Rehazek A, Sablin M, Seguin-Orlando A, Storå J, Verjux C, Zaibert VF, Zazula G, Crombé P, Hansen AJ, Willerslev E, Leonard JA, Götherström A, Pinhasi R, Schuenemann VJ, Hofreiter M, Gilbert MTP, Shapiro B, Larson G, Krause J, Dalén L, and Skoglund P
- Subjects
- Africa, Animals, DNA, Ancient analysis, Domestication, Europe, History, Ancient, Middle East, Mutation, North America, Selection, Genetic, Siberia, Tumor Suppressor Proteins genetics, Dogs genetics, Genome genetics, Genomics, Phylogeny, Wolves classification, Wolves genetics
- Abstract
The grey wolf (Canis lupus) was the first species to give rise to a domestic population, and they remained widespread throughout the last Ice Age when many other large mammal species went extinct. Little is known, however, about the history and possible extinction of past wolf populations or when and where the wolf progenitors of the present-day dog lineage (Canis familiaris) lived
1-8 . Here we analysed 72 ancient wolf genomes spanning the last 100,000 years from Europe, Siberia and North America. We found that wolf populations were highly connected throughout the Late Pleistocene, with levels of differentiation an order of magnitude lower than they are today. This population connectivity allowed us to detect natural selection across the time series, including rapid fixation of mutations in the gene IFT88 40,000-30,000 years ago. We show that dogs are overall more closely related to ancient wolves from eastern Eurasia than to those from western Eurasia, suggesting a domestication process in the east. However, we also found that dogs in the Near East and Africa derive up to half of their ancestry from a distinct population related to modern southwest Eurasian wolves, reflecting either an independent domestication process or admixture from local wolves. None of the analysed ancient wolf genomes is a direct match for either of these dog ancestries, meaning that the exact progenitor populations remain to be located., (© 2022. The Author(s).)- Published
- 2022
- Full Text
- View/download PDF
18. The biocultural origins and dispersal of domestic chickens.
- Author
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Peters J, Lebrasseur O, Irving-Pease EK, Paxinos PD, Best J, Smallman R, Callou C, Gardeisen A, Trixl S, Frantz L, Sykes N, Fuller DQ, and Larson G
- Subjects
- Animals, Animals, Domestic, Branchial Region, Cultural Characteristics, Millets, Thailand, Chickens, Domestication
- Abstract
Though chickens are the most numerous and ubiquitous domestic bird, their origins, the circumstances of their initial association with people, and the routes along which they dispersed across the world remain controversial. In order to establish a robust spatial and temporal framework for their origins and dispersal, we assessed archaeological occurrences and the domestic status of chickens from ∼600 sites in 89 countries by combining zoogeographic, morphological, osteometric, stratigraphic, contextual, iconographic, and textual data. Our results suggest that the first unambiguous domestic chicken bones are found at Neolithic Ban Non Wat in central Thailand dated to ∼1650 to 1250 BCE, and that chickens were not domesticated in the Indian Subcontinent. Chickens did not arrive in Central China, South Asia, or Mesopotamia until the late second millennium BCE, and in Ethiopia and Mediterranean Europe by ∼800 BCE. To investigate the circumstances of their initial domestication, we correlated the temporal spread of rice and millet cultivation with the first appearance of chickens within the range of red junglefowl species. Our results suggest that agricultural practices focused on the production and storage of cereal staples served to draw arboreal red junglefowl into the human niche. Thus, the arrival of rice agriculture may have first facilitated the initiation of the chicken domestication process, and then, following their integration within human communities, allowed for their dispersal across the globe.
- Published
- 2022
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19. Fourth Report on Chicken Genes and Chromosomes 2022.
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Smith J, Alfieri JM, Anthony N, Arensburger P, Athrey GN, Balacco J, Balic A, Bardou P, Barela P, Bigot Y, Blackmon H, Borodin PM, Carroll R, Casono MC, Charles M, Cheng H, Chiodi M, Cigan L, Coghill LM, Crooijmans R, Das N, Davey S, Davidian A, Degalez F, Dekkers JM, Derks M, Diack AB, Djikeng A, Drechsler Y, Dyomin A, Fedrigo O, Fiddaman SR, Formenti G, Frantz LAF, Fulton JE, Gaginskaya E, Galkina S, Gallardo RA, Geibel J, Gheyas AA, Godinez CJP, Goodell A, Graves JAM, Griffin DK, Haase B, Han JL, Hanotte O, Henderson LJ, Hou ZC, Howe K, Huynh L, Ilatsia E, Jarvis ED, Johnson SM, Kaufman J, Kelly T, Kemp S, Kern C, Keroack JH, Klopp C, Lagarrigue S, Lamont SJ, Lange M, Lanke A, Larkin DM, Larson G, Layos JKN, Lebrasseur O, Malinovskaya LP, Martin RJ, Martin Cerezo ML, Mason AS, McCarthy FM, McGrew MJ, Mountcastle J, Muhonja CK, Muir W, Muret K, Murphy TD, Ng'ang'a I, Nishibori M, O'Connor RE, Ogugo M, Okimoto R, Ouko O, Patel HR, Perini F, Pigozzi MI, Potter KC, Price PD, Reimer C, Rice ES, Rocos N, Rogers TF, Saelao P, Schauer J, Schnabel RD, Schneider VA, Simianer H, Smith A, Stevens MP, Stiers K, Tiambo CK, Tixier-Boichard M, Torgasheva AA, Tracey A, Tregaskes CA, Vervelde L, Wang Y, Warren WC, Waters PD, Webb D, Weigend S, Wolc A, Wright AE, Wright D, Wu Z, Yamagata M, Yang C, Yin ZT, Young MC, Zhang G, Zhao B, and Zhou H
- Published
- 2022
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20. One hundred years of zoonoses research in the Horn of Africa: A scoping review.
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Cavalerie L, Wardeh M, Lebrasseur O, Nanyingi M, McIntyre KM, Kaba M, Asrat D, Christley R, Pinchbeck G, Baylis M, and Mor SM
- Subjects
- Africa South of the Sahara epidemiology, Animals, History, 20th Century, History, 21st Century, Humans, Research history, Zoonoses epidemiology
- Abstract
Background: One Health is particularly relevant to the Horn of Africa where many people's livelihoods are highly dependent on livestock and their shared environment. In this context, zoonoses may have a dramatic impact on both human and animal health, but also on country economies. This scoping review aimed to characterise and evaluate the nature of zoonotic disease research in the Horn region. Specifically, it addressed the following questions: (i) what specific zoonotic diseases have been prioritised for research, (ii) what data have been reported (human, animal or environment), (iii) what methods have been applied, and (iv) who has been doing the research?, Methodology/principal Findings: We used keyword combinations to search online databases for peer-reviewed papers and theses. Screening and data extraction (disease, country, domain and method) was performed using DistillerSR. A total of 2055 studies focusing on seven countries and over 60 zoonoses were included. Brucellosis attracted the highest attention in terms of research while anthrax, Q fever and leptospirosis have been comparatively under-studied. Research efforts did not always align with zoonoses priorities identified at national levels. Despite zoonoses being a clear target for 'One Health' research, a very limited proportion of studies report data on the three domains of human, animal and environment. Descriptive and observational epidemiological studies were dominant and only a low proportion of publications were multidisciplinary. Finally, we found that a minority of international collaborations were between Global South countries with a high proportion of authors having affiliations from outside the Horn of Africa., Conclusions/significance: There is a growing interest in zoonoses research in the Horn of Africa. Recommendations arising from this scoping review include: (i) ensuring zoonoses research aligns with national and global research agendas; (ii) encouraging researchers to adopt a holistic, transdisciplinary One Health approach following high quality reporting standards (COHERE, PRISMA, etc.); and (iii) empowering local researchers supported by regional and international partnerships to engage in zoonoses research., Competing Interests: The authors have declared that no competing interests exist.
- Published
- 2021
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21. Ancient genomes reveal structural shifts after the arrival of Steppe-related ancestry in the Italian Peninsula.
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Saupe T, Montinaro F, Scaggion C, Carrara N, Kivisild T, D'Atanasio E, Hui R, Solnik A, Lebrasseur O, Larson G, Alessandri L, Arienzo I, De Angelis F, Rolfo MF, Skeates R, Silvestri L, Beckett J, Talamo S, Dolfini A, Miari M, Metspalu M, Benazzi S, Capelli C, Pagani L, and Scheib CL
- Subjects
- Datasets as Topic, Genetics, Population, Genomics, History, Ancient, Humans, Italy, Leprosy genetics, Phenotype, DNA, Ancient, Genome, Human genetics, Human Migration history
- Abstract
Across Europe, the genetics of the Chalcolithic/Bronze Age transition is increasingly characterized in terms of an influx of Steppe-related ancestry. The effect of this major shift on the genetic structure of populations in the Italian Peninsula remains underexplored. Here, genome-wide shotgun data for 22 individuals from commingled cave and single burials in Northeastern and Central Italy dated between 3200 and 1500 BCE provide the first genomic characterization of Bronze Age individuals (n = 8; 0.001-1.2× coverage) from the central Italian Peninsula, filling a gap in the literature between 1950 and 1500 BCE. Our study confirms a diversity of ancestry components during the Chalcolithic and the arrival of Steppe-related ancestry in the central Italian Peninsula as early as 1600 BCE, with this ancestry component increasing through time. We detect close patrilineal kinship in the burial patterns of Chalcolithic commingled cave burials and a shift away from this in the Bronze Age (2200-900 BCE) along with lowered runs of homozygosity, which may reflect larger changes in population structure. Finally, we find no evidence that the arrival of Steppe-related ancestry in Central Italy directly led to changes in frequency of 115 phenotypes present in the dataset, rather that the post-Roman Imperial period had a stronger influence, particularly on the frequency of variants associated with protection against Hansen's disease (leprosy). Our study provides a closer look at local dynamics of demography and phenotypic shifts as they occurred as part of a broader phenomenon of widespread admixture during the Chalcolithic/Bronze Age transition., Competing Interests: Declaration of interests The authors declare no competing interests., (Copyright © 2021 The Authors. Published by Elsevier Inc. All rights reserved.)
- Published
- 2021
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22. Origins and genetic legacy of prehistoric dogs.
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Bergström A, Frantz L, Schmidt R, Ersmark E, Lebrasseur O, Girdland-Flink L, Lin AT, Storå J, Sjögren KG, Anthony D, Antipina E, Amiri S, Bar-Oz G, Bazaliiskii VI, Bulatović J, Brown D, Carmagnini A, Davy T, Fedorov S, Fiore I, Fulton D, Germonpré M, Haile J, Irving-Pease EK, Jamieson A, Janssens L, Kirillova I, Horwitz LK, Kuzmanovic-Cvetković J, Kuzmin Y, Losey RJ, Dizdar DL, Mashkour M, Novak M, Onar V, Orton D, Pasarić M, Radivojević M, Rajković D, Roberts B, Ryan H, Sablin M, Shidlovskiy F, Stojanović I, Tagliacozzo A, Trantalidou K, Ullén I, Villaluenga A, Wapnish P, Dobney K, Götherström A, Linderholm A, Dalén L, Pinhasi R, Larson G, and Skoglund P
- Subjects
- Africa, Animals, Domestication, Europe, Genomics, Population, Animals, Domestic genetics, Dogs genetics, Wolves genetics
- Abstract
Dogs were the first domestic animal, but little is known about their population history and to what extent it was linked to humans. We sequenced 27 ancient dog genomes and found that all dogs share a common ancestry distinct from present-day wolves, with limited gene flow from wolves since domestication but substantial dog-to-wolf gene flow. By 11,000 years ago, at least five major ancestry lineages had diversified, demonstrating a deep genetic history of dogs during the Paleolithic. Coanalysis with human genomes reveals aspects of dog population history that mirror humans, including Levant-related ancestry in Africa and early agricultural Europe. Other aspects differ, including the impacts of steppe pastoralist expansions in West and East Eurasia and a near-complete turnover of Neolithic European dog ancestry., (Copyright © 2020 The Authors, some rights reserved; exclusive licensee American Association for the Advancement of Science. No claim to original U.S. Government Works.)
- Published
- 2020
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23. A mitochondrial genetic divergence proxy predicts the reproductive compatibility of mammalian hybrids.
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Allen R, Ryan H, Davis BW, King C, Frantz L, Irving-Pease E, Barnett R, Linderholm A, Loog L, Haile J, Lebrasseur O, White M, Kitchener AC, Murphy WJ, and Larson G
- Subjects
- Animals, Fertility, Genetic Drift, Infertility, Mitochondria genetics, Reproduction, Biological Evolution, Hybridization, Genetic, Mammals
- Abstract
Numerous pairs of evolutionarily divergent mammalian species have been shown to produce hybrid offspring. In some cases, F
1 hybrids are able to produce F2 s through matings with F1 s. In other instances, the hybrids are only able to produce offspring themselves through backcrosses with a parent species owing to unisexual sterility (Haldane's Rule). Here, we explicitly tested whether genetic distance, computed from mitochondrial and nuclear genes, can be used as a proxy to predict the relative fertility of the hybrid offspring resulting from matings between species of terrestrial mammals. We assessed the proxy's predictive power using a well-characterized felid hybrid system, and applied it to modern and ancient hominins. Our results revealed a small overlap in mitochondrial genetic distance values that distinguish species pairs whose calculated distances fall within two categories: those whose hybrid offspring follow Haldane's Rule, and those whose hybrid F1 offspring can produce F2 s. The strong correlation between genetic distance and hybrid fertility demonstrated here suggests that this proxy can be employed to predict whether the hybrid offspring of two mammalian species will follow Haldane's Rule.- Published
- 2020
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- View/download PDF
24. Specialized sledge dogs accompanied Inuit dispersal across the North American Arctic.
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Ameen C, Feuerborn TR, Brown SK, Linderholm A, Hulme-Beaman A, Lebrasseur O, Sinding MS, Lounsberry ZT, Lin AT, Appelt M, Bachmann L, Betts M, Britton K, Darwent J, Dietz R, Fredholm M, Gopalakrishnan S, Goriunova OI, Grønnow B, Haile J, Hallsson JH, Harrison R, Heide-Jørgensen MP, Knecht R, Losey RJ, Masson-MacLean E, McGovern TH, McManus-Fry E, Meldgaard M, Midtdal Å, Moss ML, Nikitin IG, Nomokonova T, Pálsdóttir AH, Perri A, Popov AN, Rankin L, Reuther JD, Sablin M, Schmidt AL, Shirar S, Smiarowski K, Sonne C, Stiner MC, Vasyukov M, West CF, Ween GB, Wennerberg SE, Wiig Ø, Woollett J, Dalén L, Hansen AJ, P Gilbert MT, Sacks BN, Frantz L, Larson G, Dobney K, Darwent CM, and Evin A
- Subjects
- Alaska, Animals, Archaeology, Arctic Regions, Canada, DNA, Ancient analysis, DNA, Mitochondrial analysis, Greenland, Human Migration, Animal Distribution, Dogs anatomy & histology, Dogs genetics, Genome, Mitochondrial, Phenotype
- Abstract
Domestic dogs have been central to life in the North American Arctic for millennia. The ancestors of the Inuit were the first to introduce the widespread usage of dog sledge transportation technology to the Americas, but whether the Inuit adopted local Palaeo-Inuit dogs or introduced a new dog population to the region remains unknown. To test these hypotheses, we generated mitochondrial DNA and geometric morphometric data of skull and dental elements from a total of 922 North American Arctic dogs and wolves spanning over 4500 years. Our analyses revealed that dogs from Inuit sites dating from 2000 BP possess morphological and genetic signatures that distinguish them from earlier Palaeo-Inuit dogs, and identified a novel mitochondrial clade in eastern Siberia and Alaska. The genetic legacy of these Inuit dogs survives today in modern Arctic sledge dogs despite phenotypic differences between archaeological and modern Arctic dogs. Together, our data reveal that Inuit dogs derive from a secondary pre-contact migration of dogs distinct from Palaeo-Inuit dogs, and probably aided the Inuit expansion across the North American Arctic beginning around 1000 BP.
- Published
- 2019
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25. Ancient pigs reveal a near-complete genomic turnover following their introduction to Europe.
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Frantz LAF, Haile J, Lin AT, Scheu A, Geörg C, Benecke N, Alexander M, Linderholm A, Mullin VE, Daly KG, Battista VM, Price M, Gron KJ, Alexandri P, Arbogast RM, Arbuckle B, Bӑlӑşescu A, Barnett R, Bartosiewicz L, Baryshnikov G, Bonsall C, Borić D, Boroneanţ A, Bulatović J, Çakirlar C, Carretero JM, Chapman J, Church M, Crooijmans R, De Cupere B, Detry C, Dimitrijevic V, Dumitraşcu V, du Plessis L, Edwards CJ, Erek CM, Erim-Özdoğan A, Ervynck A, Fulgione D, Gligor M, Götherström A, Gourichon L, Groenen MAM, Helmer D, Hongo H, Horwitz LK, Irving-Pease EK, Lebrasseur O, Lesur J, Malone C, Manaseryan N, Marciniak A, Martlew H, Mashkour M, Matthews R, Matuzeviciute GM, Maziar S, Meijaard E, McGovern T, Megens HJ, Miller R, Mohaseb AF, Orschiedt J, Orton D, Papathanasiou A, Pearson MP, Pinhasi R, Radmanović D, Ricaut FX, Richards M, Sabin R, Sarti L, Schier W, Sheikhi S, Stephan E, Stewart JR, Stoddart S, Tagliacozzo A, Tasić N, Trantalidou K, Tresset A, Valdiosera C, van den Hurk Y, Van Poucke S, Vigne JD, Yanevich A, Zeeb-Lanz A, Triantafyllidis A, Gilbert MTP, Schibler J, Rowley-Conwy P, Zeder M, Peters J, Cucchi T, Bradley DG, Dobney K, Burger J, Evin A, Girdland-Flink L, and Larson G
- Subjects
- Animals, Europe, History, Ancient, Middle East, Skin Pigmentation genetics, DNA, Ancient, DNA, Mitochondrial genetics, Domestication, Gene Flow, Phylogeny, Swine genetics
- Abstract
Archaeological evidence indicates that pig domestication had begun by ∼10,500 y before the present (BP) in the Near East, and mitochondrial DNA (mtDNA) suggests that pigs arrived in Europe alongside farmers ∼8,500 y BP. A few thousand years after the introduction of Near Eastern pigs into Europe, however, their characteristic mtDNA signature disappeared and was replaced by haplotypes associated with European wild boars. This turnover could be accounted for by substantial gene flow from local European wild boars, although it is also possible that European wild boars were domesticated independently without any genetic contribution from the Near East. To test these hypotheses, we obtained mtDNA sequences from 2,099 modern and ancient pig samples and 63 nuclear ancient genomes from Near Eastern and European pigs. Our analyses revealed that European domestic pigs dating from 7,100 to 6,000 y BP possessed both Near Eastern and European nuclear ancestry, while later pigs possessed no more than 4% Near Eastern ancestry, indicating that gene flow from European wild boars resulted in a near-complete disappearance of Near East ancestry. In addition, we demonstrate that a variant at a locus encoding black coat color likely originated in the Near East and persisted in European pigs. Altogether, our results indicate that while pigs were not independently domesticated in Europe, the vast majority of human-mediated selection over the past 5,000 y focused on the genomic fraction derived from the European wild boars, and not on the fraction that was selected by early Neolithic farmers over the first 2,500 y of the domestication process., Competing Interests: The authors declare no conflict of interest., (Copyright © 2019 the Author(s). Published by PNAS.)
- Published
- 2019
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26. Dogs accompanied humans during the Neolithic expansion into Europe.
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Ollivier M, Tresset A, Frantz LAF, Bréhard S, Bălăşescu A, Mashkour M, Boroneanţ A, Pionnier-Capitan M, Lebrasseur O, Arbogast RM, Bartosiewicz L, Debue K, Rabinovich R, Sablin MV, Larson G, Hänni C, Hitte C, and Vigne JD
- Subjects
- Agriculture, Animals, Dogs classification, Europe, Fossils, Haplotypes, Humans, Sequence Analysis, DNA, Archaeology, DNA, Mitochondrial, Dogs genetics
- Abstract
Near Eastern Neolithic farmers introduced several species of domestic plants and animals as they dispersed into Europe. Dogs were the only domestic species present in both Europe and the Near East prior to the Neolithic. Here, we assessed whether early Near Eastern dogs possessed a unique mitochondrial lineage that differentiated them from Mesolithic European populations. We then analysed mitochondrial DNA sequences from 99 ancient European and Near Eastern dogs spanning the Upper Palaeolithic to the Bronze Age to assess if incoming farmers brought Near Eastern dogs with them, or instead primarily adopted indigenous European dogs after they arrived. Our results show that European pre-Neolithic dogs all possessed the mitochondrial haplogroup C, and that the Neolithic and Post-Neolithic dogs associated with farmers from Southeastern Europe mainly possessed haplogroup D. Thus, the appearance of haplogroup D most probably resulted from the dissemination of dogs from the Near East into Europe. In Western and Northern Europe, the turnover is incomplete and haplogroup C persists well into the Chalcolithic at least. These results suggest that dogs were an integral component of the Neolithic farming package and a mitochondrial lineage associated with the Near East was introduced into Europe alongside pigs, cows, sheep and goats. It got diluted into the native dog population when reaching the Western and Northern margins of Europe., (© 2018 The Author(s).)
- Published
- 2018
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27. The evolutionary history of dogs in the Americas.
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Ní Leathlobhair M, Perri AR, Irving-Pease EK, Witt KE, Linderholm A, Haile J, Lebrasseur O, Ameen C, Blick J, Boyko AR, Brace S, Cortes YN, Crockford SJ, Devault A, Dimopoulos EA, Eldridge M, Enk J, Gopalakrishnan S, Gori K, Grimes V, Guiry E, Hansen AJ, Hulme-Beaman A, Johnson J, Kitchen A, Kasparov AK, Kwon YM, Nikolskiy PA, Lope CP, Manin A, Martin T, Meyer M, Myers KN, Omura M, Rouillard JM, Pavlova EY, Sciulli P, Sinding MS, Strakova A, Ivanova VV, Widga C, Willerslev E, Pitulko VV, Barnes I, Gilbert MTP, Dobney KM, Malhi RS, Murchison EP, Larson G, and Frantz LAF
- Subjects
- Americas, Animals, Cell Nucleus genetics, Dog Diseases genetics, Genome, Mitochondrial, Human Migration, Humans, Phylogeny, Sexually Transmitted Diseases transmission, Siberia, Wolves classification, Wolves genetics, Biological Evolution, Dog Diseases transmission, Dogs classification, Dogs genetics, Domestication, Neoplasms veterinary, Sexually Transmitted Diseases veterinary
- Abstract
Dogs were present in the Americas before the arrival of European colonists, but the origin and fate of these precontact dogs are largely unknown. We sequenced 71 mitochondrial and 7 nuclear genomes from ancient North American and Siberian dogs from time frames spanning ~9000 years. Our analysis indicates that American dogs were not derived from North American wolves. Instead, American dogs form a monophyletic lineage that likely originated in Siberia and dispersed into the Americas alongside people. After the arrival of Europeans, native American dogs almost completely disappeared, leaving a minimal genetic legacy in modern dog populations. The closest detectable extant lineage to precontact American dogs is the canine transmissible venereal tumor, a contagious cancer clone derived from an individual dog that lived up to 8000 years ago., (Copyright © 2018 The Authors, some rights reserved; exclusive licensee American Association for the Advancement of Science. No claim to original U.S. Government Works.)
- Published
- 2018
- Full Text
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28. Reconstructing Asian faunal introductions to eastern Africa from multi-proxy biomolecular and archaeological datasets.
- Author
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Prendergast ME, Buckley M, Crowther A, Frantz L, Eager H, Lebrasseur O, Hutterer R, Hulme-Beaman A, Van Neer W, Douka K, Veall MA, Quintana Morales EM, Schuenemann VJ, Reiter E, Allen R, Dimopoulos EA, Helm RM, Shipton C, Mwebi O, Denys C, Horton M, Wynne-Jones S, Fleisher J, Radimilahy C, Wright H, Searle JB, Krause J, Larson G, and Boivin NL
- Subjects
- Africa, Animals, Animals, Domestic genetics, Archaeology, Asia, Chickens, Collagen analysis, Collagen genetics, DNA Fingerprinting, History, Ancient, Radiometric Dating, Rats, Introduced Species history
- Abstract
Human-mediated biological exchange has had global social and ecological impacts. In sub-Saharan Africa, several domestic and commensal animals were introduced from Asia in the pre-modern period; however, the timing and nature of these introductions remain contentious. One model supports introduction to the eastern African coast after the mid-first millennium CE, while another posits introduction dating back to 3000 BCE. These distinct scenarios have implications for understanding the emergence of long-distance maritime connectivity, and the ecological and economic impacts of introduced species. Resolution of this longstanding debate requires new efforts, given the lack of well-dated fauna from high-precision excavations, and ambiguous osteomorphological identifications. We analysed faunal remains from 22 eastern African sites spanning a wide geographic and chronological range, and applied biomolecular techniques to confirm identifications of two Asian taxa: domestic chicken (Gallus gallus) and black rat (Rattus rattus). Our approach included ancient DNA (aDNA) analysis aided by BLAST-based bioinformatics, Zooarchaeology by Mass Spectrometry (ZooMS) collagen fingerprinting, and direct AMS (accelerator mass spectrometry) radiocarbon dating. Our results support a late, mid-first millennium CE introduction of these species. We discuss the implications of our findings for models of biological exchange, and emphasize the applicability of our approach to tropical areas with poor bone preservation.
- Published
- 2017
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29. Inferring Allele Frequency Trajectories from Ancient DNA Indicates That Selection on a Chicken Gene Coincided with Changes in Medieval Husbandry Practices.
- Author
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Loog L, Thomas MG, Barnett R, Allen R, Sykes N, Paxinos PD, Lebrasseur O, Dobney K, Peters J, Manica A, Larson G, and Eriksson A
- Subjects
- Alleles, Animal Husbandry, Animals, Animals, Domestic genetics, Bayes Theorem, Breeding, DNA, Ancient analysis, DNA, Mitochondrial genetics, Dioxygenases genetics, Gene Frequency genetics, Poultry genetics, Receptors, Thyrotropin genetics, Chickens genetics, Selection, Genetic genetics, Sequence Analysis, DNA methods
- Abstract
Ancient DNA provides an opportunity to infer the drivers of natural selection by linking allele frequency changes to temporal shifts in environment or cultural practices. However, analyses have often been hampered by uneven sampling and uncertainties in sample dating, as well as being confounded by demographic processes. Here, we present a Bayesian statistical framework for quantifying the timing and strength of selection using ancient DNA that explicitly addresses these challenges. We applied this method to time series data for two loci: TSHR and BCDO2, both hypothesised to have undergone strong and recent selection in domestic chickens. The derived variant in TSHR, associated with reduced aggression to conspecifics and faster onset of egg laying, shows strong selection beginning around 1,100 years ago, coincident with archaeological evidence for intensified chicken production and documented changes in egg and chicken consumption. To our knowledge, this is the first example of preindustrial domesticate trait selection in response to a historically attested cultural shift in food preference. For BCDO2, we find support for selection, but demonstrate that the recent rise in allele frequency could also have been driven by gene flow from imported Asian chickens during more recent breed formations. Our findings highlight that traits found ubiquitously in modern domestic species may not necessarily have originated during the early stages of domestication. In addition, our results demonstrate the importance of precise estimation of allele frequency trajectories through time for understanding the drivers of selection., (© The Author 2017. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.)
- Published
- 2017
- Full Text
- View/download PDF
30. Genomic and archaeological evidence suggest a dual origin of domestic dogs.
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Frantz LA, Mullin VE, Pionnier-Capitan M, Lebrasseur O, Ollivier M, Perri A, Linderholm A, Mattiangeli V, Teasdale MD, Dimopoulos EA, Tresset A, Duffraisse M, McCormick F, Bartosiewicz L, Gál E, Nyerges ÉA, Sablin MV, Bréhard S, Mashkour M, Bălăşescu A, Gillet B, Hughes S, Chassaing O, Hitte C, Vigne JD, Dobney K, Hänni C, Bradley DG, and Larson G
- Subjects
- Animals, Archaeology, DNA, Mitochondrial genetics, Dogs classification, Europe, Asia, Eastern, Genomics, Haplotypes, Human Migration, Phylogeny, Animals, Domestic genetics, Dogs genetics, Wolves genetics
- Abstract
The geographic and temporal origins of dogs remain controversial. We generated genetic sequences from 59 ancient dogs and a complete (28x) genome of a late Neolithic dog (dated to ~4800 calendar years before the present) from Ireland. Our analyses revealed a deep split separating modern East Asian and Western Eurasian dogs. Surprisingly, the date of this divergence (~14,000 to 6400 years ago) occurs commensurate with, or several millennia after, the first appearance of dogs in Europe and East Asia. Additional analyses of ancient and modern mitochondrial DNA revealed a sharp discontinuity in haplotype frequencies in Europe. Combined, these results suggest that dogs may have been domesticated independently in Eastern and Western Eurasia from distinct wolf populations. East Eurasian dogs were then possibly transported to Europe with people, where they partially replaced European Paleolithic dogs., (Copyright © 2016, American Association for the Advancement of Science.)
- Published
- 2016
- Full Text
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31. Questioning new answers regarding Holocene chicken domestication in China.
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Peters J, Lebrasseur O, Best J, Miller H, Fothergill T, Dobney K, Thomas RM, Maltby M, Sykes N, Hanotte O, O'Connor T, Collins MJ, and Larson G
- Subjects
- Animals, Animal Husbandry history, Biological Evolution, Chickens genetics, DNA, Mitochondrial analysis
- Published
- 2015
- Full Text
- View/download PDF
32. Using ancient DNA to study the origins and dispersal of ancestral Polynesian chickens across the Pacific.
- Author
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Thomson VA, Lebrasseur O, Austin JJ, Hunt TL, Burney DA, Denham T, Rawlence NJ, Wood JR, Gongora J, Girdland Flink L, Linderholm A, Dobney K, Larson G, and Cooper A
- Subjects
- Animals, Base Pairing genetics, Bayes Theorem, Genome, Mitochondrial genetics, Geography, Haplotypes genetics, Humans, Locus Control Region genetics, Molecular Sequence Data, Pacific Ocean, Phylogeny, Polynesia, Time Factors, Animal Migration, Chickens genetics, DNA genetics
- Abstract
The human colonization of Remote Oceania remains one of the great feats of exploration in history, proceeding east from Asia across the vast expanse of the Pacific Ocean. Human commensal and domesticated species were widely transported as part of this diaspora, possibly as far as South America. We sequenced mitochondrial control region DNA from 122 modern and 22 ancient chicken specimens from Polynesia and Island Southeast Asia and used these together with Bayesian modeling methods to examine the human dispersal of chickens across this area. We show that specific techniques are essential to remove contaminating modern DNA from experiments, which appear to have impacted previous studies of Pacific chickens. In contrast to previous reports, we find that all ancient specimens and a high proportion of the modern chickens possess a group of unique, closely related haplotypes found only in the Pacific. This group of haplotypes appears to represent the authentic founding mitochondrial DNA chicken lineages transported across the Pacific, and allows the early dispersal of chickens across Micronesia and Polynesia to be modeled. Importantly, chickens carrying this genetic signature persist on several Pacific islands at high frequencies, suggesting that the original Polynesian chicken lineages may still survive. No early South American chicken samples have been detected with the diagnostic Polynesian mtDNA haplotypes, arguing against reports that chickens provide evidence of Polynesian contact with pre-European South America. Two modern specimens from the Philippines carry haplotypes similar to the ancient Pacific samples, providing clues about a potential homeland for the Polynesian chicken.
- Published
- 2014
- Full Text
- View/download PDF
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