Publications by authors named "Ophelie Lebrasseur"

12 Publications

  • Page 1 of 1

Origins and genetic legacy of prehistoric dogs.

Science 2020 10 29;370(6516):557-564. Epub 2020 Oct 29.

Ancient Genomics Laboratory, The Francis Crick Institute, London, UK.

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.
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http://dx.doi.org/10.1126/science.aba9572DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7116352PMC
October 2020

A mitochondrial genetic divergence proxy predicts the reproductive compatibility of mammalian hybrids.

Proc Biol Sci 2020 06 3;287(1928):20200690. Epub 2020 Jun 3.

Palaeogenomics and Bio-Archaeology Research Network, Research Laboratory for Archaeology and the History of Art, University of Oxford, Oxford OX1 3QY, UK.

Numerous pairs of evolutionarily divergent mammalian species have been shown to produce hybrid offspring. In some cases, F hybrids are able to produce Fs through matings with Fs. 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 F offspring can produce Fs. 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.
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http://dx.doi.org/10.1098/rspb.2020.0690DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7341909PMC
June 2020

Specialized sledge dogs accompanied Inuit dispersal across the North American Arctic.

Proc Biol Sci 2019 12 27;286(1916):20191929. Epub 2019 Nov 27.

Institut des Sciences de l'Evolution-Montpellier, CNRS, Université de Montpellier, IRD, EPHE, Montpellier, Occitanie, France.

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.
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http://dx.doi.org/10.1098/rspb.2019.1929DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6939252PMC
December 2019

Ancient pigs reveal a near-complete genomic turnover following their introduction to Europe.

Authors:
Laurent A F Frantz James Haile Audrey T Lin Amelie Scheu Christina Geörg Norbert Benecke Michelle Alexander Anna Linderholm Victoria E Mullin Kevin G Daly Vincent M Battista Max Price Kurt J Gron Panoraia Alexandri Rose-Marie Arbogast Benjamin Arbuckle Adrian Bӑlӑşescu Ross Barnett László Bartosiewicz Gennady Baryshnikov Clive Bonsall Dušan Borić Adina Boroneanţ Jelena Bulatović Canan Çakirlar José-Miguel Carretero John Chapman Mike Church Richard Crooijmans Bea De Cupere Cleia Detry Vesna Dimitrijevic Valentin Dumitraşcu Louis du Plessis Ceiridwen J Edwards Cevdet Merih Erek Aslı Erim-Özdoğan Anton Ervynck Domenico Fulgione Mihai Gligor Anders Götherström Lionel Gourichon Martien A M Groenen Daniel Helmer Hitomi Hongo Liora K Horwitz Evan K Irving-Pease Ophélie Lebrasseur Joséphine Lesur Caroline Malone Ninna Manaseryan Arkadiusz Marciniak Holley Martlew Marjan Mashkour Roger Matthews Giedre Motuzaite Matuzeviciute Sepideh Maziar Erik Meijaard Tom McGovern Hendrik-Jan Megens Rebecca Miller Azadeh Fatemeh Mohaseb Jörg Orschiedt David Orton Anastasia Papathanasiou Mike Parker Pearson Ron Pinhasi Darko Radmanović François-Xavier Ricaut Mike Richards Richard Sabin Lucia Sarti Wolfram Schier Shiva Sheikhi Elisabeth Stephan John R Stewart Simon Stoddart Antonio Tagliacozzo Nenad Tasić Katerina Trantalidou Anne Tresset Cristina Valdiosera Youri van den Hurk Sophie Van Poucke Jean-Denis Vigne Alexander Yanevich Andrea Zeeb-Lanz Alexandros Triantafyllidis M Thomas P Gilbert Jörg Schibler Peter Rowley-Conwy Melinda Zeder Joris Peters Thomas Cucchi Daniel G Bradley Keith Dobney Joachim Burger Allowen Evin Linus Girdland-Flink Greger Larson

Proc Natl Acad Sci U S A 2019 08 12;116(35):17231-17238. Epub 2019 Aug 12.

The Palaeogenomics & Bio-Archaeology Research Network, Research Laboratory for Archaeology and History of Art, University of Oxford, Oxford OX1 3TG, United Kingdom;

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.
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http://dx.doi.org/10.1073/pnas.1901169116DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6717267PMC
August 2019

Dogs accompanied humans during the Neolithic expansion into Europe.

Biol Lett 2018 10 17;14(10). Epub 2018 Oct 17.

CNRS/MNHN/SUs - UMR 7209 AASPE, 55 rue Buffon, 75005 Paris, France.

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.
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http://dx.doi.org/10.1098/rsbl.2018.0286DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6227856PMC
October 2018

The evolutionary history of dogs in the Americas.

Science 2018 Jul;361(6397):81-85

The Palaeogenomics and Bio-Archaeology Research Network, Research Laboratory for Archaeology and History of Art, University of Oxford, Oxford, UK.

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.
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http://dx.doi.org/10.1126/science.aao4776DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7116273PMC
July 2018

Reconstructing Asian faunal introductions to eastern Africa from multi-proxy biomolecular and archaeological datasets.

PLoS One 2017 17;12(8):e0182565. Epub 2017 Aug 17.

Max Planck Institute for the Science of Human History, Jena, Germany.

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.
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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0182565PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5560628PMC
October 2017

Inferring Allele Frequency Trajectories from Ancient DNA Indicates That Selection on a Chicken Gene Coincided with Changes in Medieval Husbandry Practices.

Mol Biol Evol 2017 08;34(8):1981-1990

Department of Zoology, University of Cambridge, Cambridge, United Kingdom.

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.
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http://dx.doi.org/10.1093/molbev/msx142DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5850110PMC
August 2017

Genomic and archaeological evidence suggest a dual origin of domestic dogs.

Science 2016 06 2;352(6290):1228-31. Epub 2016 Jun 2.

The Palaeogenomics and Bio-Archaeology Research Network, Research Laboratory for Archaeology and History of Art, University of Oxford, Oxford, UK.

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.
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http://dx.doi.org/10.1126/science.aaf3161DOI Listing
June 2016

Questioning new answers regarding Holocene chicken domestication in China.

Proc Natl Acad Sci U S A 2015 May 17;112(19):E2415. Epub 2015 Apr 17.

Palaeogenomics & Bio-Archaeology Research Network, Department of Archaeology, Research Laboratory for Archaeology and the History of Art, University of Oxford, Oxford OX1 3QY, United Kingdom;

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http://dx.doi.org/10.1073/pnas.1503579112DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4434763PMC
May 2015

Using ancient DNA to study the origins and dispersal of ancestral Polynesian chickens across the Pacific.

Proc Natl Acad Sci U S A 2014 Apr 17;111(13):4826-31. Epub 2014 Mar 17.

Australian Centre for Ancient DNA, School of Earth and Environmental Sciences, University of Adelaide, Adelaide, SA 5005, Australia.

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.
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http://dx.doi.org/10.1073/pnas.1320412111DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3977275PMC
April 2014