1
|
Susat J, Haller-Caskie M, Bonczarowska JH, da Silva NA, Schierhold K, Rind MM, Schmölcke U, Kirleis W, Sondermann H, Rinne C, Müller J, Nebel A, Krause-Kyora B. Neolithic Yersinia pestis infections in humans and a dog. Commun Biol 2024; 7:1013. [PMID: 39155318 PMCID: PMC11330967 DOI: 10.1038/s42003-024-06676-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2023] [Accepted: 08/02/2024] [Indexed: 08/20/2024] Open
Abstract
Yersinia pestis has been infecting humans since the Late Neolithic (LN). Whether those early infections were isolated zoonoses or initiators of a pandemic remains unclear. We report Y. pestis infections in two individuals (of 133) from the LN necropolis at Warburg (Germany, 5300-4900 cal BP). Our analyses show that the two genomes belong to distinct strains and reflect independent infection events. All LN genomes known today (n = 4) are basal in the phylogeny and represent separate lineages that probably originated in different animal hosts. In the LN, an opening of the landscape resulted in the introduction of new rodent species, which may have acted as Y. pestis reservoirs. Coincidentally, the number of dogs increased, possibly leading to Y. pestis infections in canines. Indeed, we detect Y. pestis in an LN dog. Collectively, our data suggest that Y. pestis frequently entered human settlements at the time without causing significant outbreaks.
Collapse
Affiliation(s)
- Julian Susat
- Institute of Clinical Molecular Biology, Kiel University, Kiel, Germany
| | | | - Joanna H Bonczarowska
- Institute of Clinical Molecular Biology, Kiel University, Kiel, Germany
- Department of Genetics, Yale School of Medicine, New Haven, CT, USA
| | | | | | | | - Ulrich Schmölcke
- Centre for Baltic and Scandinavian Archaeology (ZBSA), Schloss Gottorf, Schleswig, Germany
| | - Wiebke Kirleis
- Institute of Pre- and Protohistoric Archaeology, Kiel University, Kiel, Germany
| | - Holger Sondermann
- Centre for Structural Systems Biology (CSSB), Deutsches Elektronen-Synchrotron DESY, Hamburg, Germany
- Kiel University, Kiel, Germany
| | - Christoph Rinne
- Institute of Pre- and Protohistoric Archaeology, Kiel University, Kiel, Germany
| | - Johannes Müller
- Institute of Pre- and Protohistoric Archaeology, Kiel University, Kiel, Germany
| | - Almut Nebel
- Institute of Clinical Molecular Biology, Kiel University, Kiel, Germany
| | - Ben Krause-Kyora
- Institute of Clinical Molecular Biology, Kiel University, Kiel, Germany.
| |
Collapse
|
2
|
Coutinho-Lima D, Dreger DL, Doadrio I, Parker HG, Ghanavi HR, Frantz L, Larson G, Ostrander EA, Godinho R. Multiple ancestries and shared gene flow among modern livestock guarding dogs. iScience 2024; 27:110396. [PMID: 39156647 PMCID: PMC11326944 DOI: 10.1016/j.isci.2024.110396] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2024] [Revised: 05/24/2024] [Accepted: 06/25/2024] [Indexed: 08/20/2024] Open
Abstract
Livestock guarding dogs (LGDs) have been used to protect livestock for millennia. While previous works suggested a single origin of modern LGDs, the degree and source of shared ancestry have not been tested. To address this, we generated genome-wide SNP data from 304 LGDs and combined it with public genomic data from 2,183 modern and 22 ancient dogs. Our findings reveal shared ancestry and extensive gene flow among modern LGD breeds which we attribute to historical livestock migrations. Additionally, admixture between LGDs and free-ranging dogs argues against reproductive isolation as a core mechanism for maintaining the specialized skills of LGDs. Finally, we identify two lineages within modern LGDs and uncover multiple ancestries tracing back to distinct Eurasian ancient dogs, concordant with the absence of a single ancestor. Overall, our work explores the complex evolutionary history of LGDs, offering valuable insights into how human and livestock co-migrations shaped this functional group.
Collapse
Affiliation(s)
- Diogo Coutinho-Lima
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO, Laboratório Associado, Campus de Vairão, Universidade do Porto, Vairão, Portugal
- Departamento de Biologia, Faculdade de Ciências da Universidade do Porto, Porto, Portugal
- BIOPOLIS - Program in Genomics, Biodiversity and Land Planning, CIBIO, Vairão, Portugal
| | - Dayna L. Dreger
- Cancer Genetics and Comparative Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - Ignacio Doadrio
- Museo Nacional de Ciencias Naturales, Consejo Superior de Investigaciones Científicas, Madrid, Spain
| | - Heidi G. Parker
- Cancer Genetics and Comparative Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | | | - Laurent Frantz
- School of Biological and Behavioural Sciences, Queen Mary University of London, London, UK
- Palaeogenomics Group, Faculty of Veterinary Sciences, Ludwig-Maximilians-University of Munich, Munich, Germany
| | - Greger Larson
- Palaeogenomics & Bio-Archaeology Research Network, Research Laboratory for Archaeology and History of Art, University of Oxford, Oxford, UK
| | - Elaine A. Ostrander
- Cancer Genetics and Comparative Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - Raquel Godinho
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO, Laboratório Associado, Campus de Vairão, Universidade do Porto, Vairão, Portugal
- Departamento de Biologia, Faculdade de Ciências da Universidade do Porto, Porto, Portugal
- BIOPOLIS - Program in Genomics, Biodiversity and Land Planning, CIBIO, Vairão, Portugal
| |
Collapse
|
3
|
Nguyen AK, Schall PZ, Kidd JM. A map of canine sequence variation relative to a Greenland wolf outgroup. Mamm Genome 2024:10.1007/s00335-024-10056-1. [PMID: 39088040 DOI: 10.1007/s00335-024-10056-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2024] [Accepted: 07/25/2024] [Indexed: 08/02/2024]
Abstract
For over 15 years, canine genetics research relied on a reference assembly from a Boxer breed dog named Tasha (i.e., canFam3.1). Recent advances in long-read sequencing and genome assembly have led to the development of numerous high-quality assemblies from diverse canines. These assemblies represent notable improvements in completeness, contiguity, and the representation of gene promoters and gene models. Although genome graph and pan-genome approaches have promise, most genetic analyses in canines rely upon the mapping of Illumina sequencing reads to a single reference. The Dog10K consortium, and others, have generated deep catalogs of genetic variation through an alignment of Illumina sequencing reads to a reference genome obtained from a German Shepherd Dog named Mischka (i.e., canFam4, UU_Cfam_GSD_1.0). However, alignment to a breed-derived genome may introduce bias in genotype calling across samples. Since the use of an outgroup reference genome may remove this effect, we have reprocessed 1929 samples analyzed by the Dog10K consortium using a Greenland wolf (mCanLor1.2) as the reference. We efficiently performed remapping and variant calling using a GPU-implementation of common analysis tools. The resulting call set removes the variability in genetic differences seen across samples and breed relationships revealed by principal component analysis are not affected by the choice of reference genome. Using this sequence data, we inferred the history of population sizes and found that village dog populations experienced a 9-13 fold reduction in historic effective population size relative to wolves.
Collapse
Affiliation(s)
- Anthony K Nguyen
- Department of Human Genetics, University of Michigan, Ann Arbor, MI, USA
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, USA
| | - Peter Z Schall
- Department of Human Genetics, University of Michigan, Ann Arbor, MI, USA
| | - Jeffrey M Kidd
- Department of Human Genetics, University of Michigan, Ann Arbor, MI, USA.
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, USA.
| |
Collapse
|
4
|
Souilmi Y, Wasef S, Williams MP, Conroy G, Bar I, Bover P, Dann J, Heiniger H, Llamas B, Ogbourne S, Archer M, Ballard JWO, Reed E, Tobler R, Koungoulos L, Walshe K, Wright JL, Balme J, O’Connor S, Cooper A, Mitchell KJ. Ancient genomes reveal over two thousand years of dingo population structure. Proc Natl Acad Sci U S A 2024; 121:e2407584121. [PMID: 38976766 PMCID: PMC11287250 DOI: 10.1073/pnas.2407584121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2024] [Accepted: 06/04/2024] [Indexed: 07/10/2024] Open
Abstract
Dingoes are culturally and ecologically important free-living canids whose ancestors arrived in Australia over 3,000 B.P., likely transported by seafaring people. However, the early history of dingoes in Australia-including the number of founding populations and their routes of introduction-remains uncertain. This uncertainty arises partly from the complex and poorly understood relationship between modern dingoes and New Guinea singing dogs, and suspicions that post-Colonial hybridization has introduced recent domestic dog ancestry into the genomes of many wild dingo populations. In this study, we analyzed genome-wide data from nine ancient dingo specimens ranging in age from 400 to 2,746 y old, predating the introduction of domestic dogs to Australia by European colonists. We uncovered evidence that the continent-wide population structure observed in modern dingo populations had already emerged several thousand years ago. We also detected excess allele sharing between New Guinea singing dogs and ancient dingoes from coastal New South Wales (NSW) compared to ancient dingoes from southern Australia, irrespective of any post-Colonial hybrid ancestry in the genomes of modern individuals. Our results are consistent with several demographic scenarios, including a scenario where the ancestry of dingoes from the east coast of Australia results from at least two waves of migration from source populations with varying affinities to New Guinea singing dogs. We also contribute to the growing body of evidence that modern dingoes derive little genomic ancestry from post-Colonial hybridization with other domestic dog lineages, instead descending primarily from ancient canids introduced to Sahul thousands of years ago.
Collapse
Affiliation(s)
- Yassine Souilmi
- Australian Centre for Ancient DNA, School of Biological Sciences, The University of Adelaide, Adelaide, SA5005, Australia
- The Environment Institute, School of Biological Sciences, The University of Adelaide, Adelaide, SA5005, Australia
| | - Sally Wasef
- Ancient DNA Facility, Defence Genomics, Genomics Research Centre, Queensland University of Technology, Kelvin Grove, QLD4059, Australia
- Innovation Division, Forensic Science Queensland, Queensland Health, Coopers Plains, QLD4108, Australia
| | - Matthew P. Williams
- Australian Centre for Ancient DNA, School of Biological Sciences, The University of Adelaide, Adelaide, SA5005, Australia
- Department of Biology, The Pennsylvania State University, State College, PA16802
| | - Gabriel Conroy
- School of Science, Technology and Engineering, University of the Sunshine Coast, Maroochydore, QLD4556, Australia
- Centre for Bioinnovation, University of the Sunshine Coast, Maroochydore, QLD4556, Australia
| | - Ido Bar
- Centre for Planetary Health and Food Security, School of Environment and Science, Griffith University, Nathan, QLD4111, Australia
| | - Pere Bover
- Fundación Agencia Aragonesa para la Investigacióny el Desarrollo (ARAID), Zaragoza50018, Spain
- Instituto Universitario de Investigación en Ciencias Ambientales de Aragón (IUCA)-Grupo Aragosaurus, Universidad de Zaragoza, Zaragoza50009, Spain
| | - Jackson Dann
- Grützner Laboratory of Comparative Genomics, School of Biological Sciences, The University of Adelaide, Adelaide, SA5005, Australia
| | - Holly Heiniger
- Australian Research Council Centre of Excellence for Australian Biodiversity and Heritage (CABAH), AdelaideSA5005, Australia
| | - Bastien Llamas
- Australian Centre for Ancient DNA, School of Biological Sciences, The University of Adelaide, Adelaide, SA5005, Australia
- Australian Research Council Centre of Excellence for Australian Biodiversity and Heritage (CABAH), AdelaideSA5005, Australia
- National Centre for Indigenous Genomics, John Curtin School of Medical Research, Australian National University, ActonACT2601, Australia
- Indigenous Genomics, Telethon Kids Institute, Adelaide, SA5000, Australia
| | - Steven Ogbourne
- Centre for Bioinnovation, University of the Sunshine Coast, Maroochydore, QLD4556, Australia
| | - Michael Archer
- Earth and Sustainability Science Research Centre, School of Biological, Earth & Environmental Sciences, University of New South Wales Sydney, SydneyNSW2052, Australia
| | - J. William O. Ballard
- School of Biosciences, University of Melbourne, Royal Parade, Parkville, VIC3052, Australia
| | - Elizabeth Reed
- Ecology and Evolutionary Biology, School of Biological Sciences, The University of Adelaide, AdelaideSA5005, Australia
| | - Raymond Tobler
- Australian Centre for Ancient DNA, School of Biological Sciences, The University of Adelaide, Adelaide, SA5005, Australia
- Evolution of Cultural Diversity Initiative, School of Culture, History and Language, College of Asia and the Pacific, The Australian National University, Acton, ACT2601, Australia
| | - Loukas Koungoulos
- Archaeology and Natural History, School of Culture, History and Language, College of Asia and the Pacific, Australian National University, Acton, ACT2601, Australia
- Australian Museum Research Institute, Australian Museum, Sydney, NSW2010, Australia
- Australian Research Council Centre of Excellence for Australian Biodiversity and Heritage, The Australian National University, Acton, ACT2601, Australia
| | - Keryn Walshe
- School of Anthropology and Archaeology, University of Auckland, Auckland1010, New Zealand
| | - Joanne L. Wright
- Queensland Department of Education, Kelvin Grove State College, Kelvin Grove, QLD4059, Australia
| | - Jane Balme
- School of Social Sciences, University of Western Australia, Crawley, WA6009, Australia
| | - Sue O’Connor
- Archaeology and Natural History, School of Culture, History and Language, College of Asia and the Pacific, Australian National University, Acton, ACT2601, Australia
- Australian Research Council Centre of Excellence for Australian Biodiversity and Heritage, The Australian National University, Acton, ACT2601, Australia
| | - Alan Cooper
- Gulbali Institute, Charles Sturt University, Albury, NSW2640, Australia
| | - Kieren J. Mitchell
- Australian Centre for Ancient DNA, School of Biological Sciences, The University of Adelaide, Adelaide, SA5005, Australia
- Australian Research Council Centre of Excellence for Australian Biodiversity and Heritage (CABAH), AdelaideSA5005, Australia
- Manaaki Whenua—Landcare Research, Lincoln, Canterbury7608, New Zealand
| |
Collapse
|
5
|
Leon-Apodaca AV, Kumar M, del Castillo A, Conroy GC, Lamont RW, Ogbourne S, Cairns KM, Borburgh L, Behrendorff L, Subramanian S, Szpiech ZA. Genomic Consequences of Isolation and Inbreeding in an Island Dingo Population. Genome Biol Evol 2024; 16:evae130. [PMID: 38913571 PMCID: PMC11221432 DOI: 10.1093/gbe/evae130] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2023] [Revised: 05/29/2024] [Accepted: 06/03/2024] [Indexed: 06/26/2024] Open
Abstract
Dingoes come from an ancient canid lineage that originated in East Asia around 8,000 to 11,000 years BP. As Australia's largest terrestrial predator, dingoes play an important ecological role. A small, protected population exists on a world heritage listed offshore island, K'gari (formerly Fraser Island). Concern regarding the persistence of dingoes on K'gari has risen due to their low genetic diversity and elevated inbreeding levels. However, whole-genome sequence data is lacking from this population. Here, we include five new whole-genome sequences of K'gari dingoes. We analyze a total of 18 whole-genome sequences of dingoes sampled from mainland Australia and K'gari to assess the genomic consequences of their demographic histories. Long (>1 Mb) runs of homozygosity (ROHs)-indicators of inbreeding-are elevated in all sampled dingoes. However, K'gari dingoes showed significantly higher levels of very long ROH (>5 Mb), providing genomic evidence for small population size, isolation, inbreeding, and a strong founder effect. Our results suggest that, despite current levels of inbreeding, the K'gari population is purging strongly deleterious mutations, which, in the absence of further reductions in population size, may facilitate the persistence of small populations despite low genetic diversity and isolation. However, there may be little to no purging of mildly deleterious alleles, which may have important long-term consequences, and should be considered by conservation and management programs.
Collapse
Affiliation(s)
- Ana V Leon-Apodaca
- Department of Biology, Pennsylvania State University, University Park, PA, USA
| | - Manoharan Kumar
- School of Science, Technology & Engineering, University of the Sunshine Coast, 1 Moreton Parade, Petrie, Queensland, Australia
| | - Andres del Castillo
- Department of Biology, Pennsylvania State University, University Park, PA, USA
| | - Gabriel C Conroy
- School of Science, Technology & Engineering, University of the Sunshine Coast, 90 Sippy Downs Drive, Sippy Downs, Queensland, Australia
- Centre for Bioinnovation, University of the Sunshine Coast, 90 Sippy Downs Drive, Sippy Downs, Queensland, Australia
| | - Robert W Lamont
- School of Science, Technology & Engineering, University of the Sunshine Coast, 90 Sippy Downs Drive, Sippy Downs, Queensland, Australia
- Centre for Bioinnovation, University of the Sunshine Coast, 90 Sippy Downs Drive, Sippy Downs, Queensland, Australia
| | - Steven Ogbourne
- Centre for Bioinnovation, University of the Sunshine Coast, 90 Sippy Downs Drive, Sippy Downs, Queensland, Australia
| | - Kylie M Cairns
- Evolution & Ecology Research Centre, School of Biological, Earth and Environmental Sciences, UNSW Australia, Sydney, NSW 2052, Australia
- Centre for Ecosystem Science, School of Biological, Earth and Environmental Sciences, UNSW Australia, Sydney, NSW 2052, Australia
| | - Liz Borburgh
- School of Science, Technology & Engineering, University of the Sunshine Coast, 90 Sippy Downs Drive, Sippy Downs, Queensland, Australia
| | - Linda Behrendorff
- Queensland Parks and Wildlife Service, Department of Environment & Science, K’gari, Australia
| | - Sankar Subramanian
- School of Science, Technology & Engineering, University of the Sunshine Coast, 1 Moreton Parade, Petrie, Queensland, Australia
- Centre for Bioinnovation, University of the Sunshine Coast, 90 Sippy Downs Drive, Sippy Downs, Queensland, Australia
| | - Zachary A Szpiech
- Department of Biology, Pennsylvania State University, University Park, PA, USA
- Institute for Computational and Data Sciences, Pennsylvania State University, University Park, PA, USA
| |
Collapse
|
6
|
Bougiouri K, Aninta SG, Charlton S, Harris A, Carmagnini A, Piličiauskienė G, Feuerborn TR, Scarsbrook L, Tabadda K, Blaževičius P, Parker HG, Gopalakrishnan S, Larson G, Ostrander EA, Irving-Pease EK, Frantz LA, Racimo F. Imputation of ancient canid genomes reveals inbreeding history over the past 10,000 years. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.15.585179. [PMID: 38903121 PMCID: PMC11188068 DOI: 10.1101/2024.03.15.585179] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/22/2024]
Abstract
The multi-millenia long history between dogs and humans has placed them at the forefront of archeological and genomic research. Despite ongoing efforts including the analysis of ancient dog and wolf genomes, many questions remain regarding their geographic and temporal origins, and the microevolutionary processes that led to the diversity of breeds today. Although ancient genomes provide valuable information, their use is hindered by low depth of coverage and post-mortem damage, which inhibits confident genotype calling. In the present study, we assess how genotype imputation of ancient dog and wolf genomes, utilising a large reference panel, can improve the resolution provided by ancient datasets. Imputation accuracy was evaluated by down-sampling high coverage dog and wolf genomes to 0.05-2x coverage and comparing concordance between imputed and high coverage genotypes. We measured the impact of imputation on principal component analyses and runs of homozygosity. Our findings show high (R2>0.9) imputation accuracy for dogs with coverage as low as 0.5x and for wolves as low as 1.0x. We then imputed a dataset of 90 ancient dog and wolf genomes, to assess changes in inbreeding during the last 10,000 years of dog evolution. Ancient dog and wolf populations generally exhibited lower inbreeding levels than present-day individuals. Interestingly, regions with low ROH density maintained across ancient and present-day samples were significantly associated with genes related to olfaction and immune response. Our study indicates that imputing ancient canine genomes is a viable strategy that allows for the use of analytical methods previously limited to high-quality genetic data.
Collapse
Affiliation(s)
- Katia Bougiouri
- Section for Molecular Ecology and Evolution, Globe Institute, University of Copenhagen, Copenhagen, Denmark
| | - Sabhrina Gita Aninta
- School of Biological and Behavioural Sciences, Queen Mary University of London, London, UK
- Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Sophy Charlton
- BioArCh, Department of Archaeology, University of York, York, UK
| | - Alex Harris
- National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Alberto Carmagnini
- School of Biological and Behavioural Sciences, Queen Mary University of London, London, UK
- Palaeogenomics Group, Department of Veterinary Sciences, Ludwig Maximilian University, Munich, Germany
| | - Giedrė Piličiauskienė
- Department of Archeology, Faculty of History, Vilnius University, Vilnius, Lithuania
| | - Tatiana R. Feuerborn
- National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Lachie Scarsbrook
- The Palaeogenomics and Bio-archaeology Research Network, Research Laboratory for Archaeology and History of Art, University of Oxford, Oxford, UK
| | - Kristina Tabadda
- The Palaeogenomics and Bio-archaeology Research Network, Research Laboratory for Archaeology and History of Art, University of Oxford, Oxford, UK
| | - Povilas Blaževičius
- Department of Archeology, Faculty of History, Vilnius University, Vilnius, Lithuania
- National Museum of Lithuania, Vilnius, Lithuania
| | - Heidi G. Parker
- National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Shyam Gopalakrishnan
- Center for Evolutionary Hologenomics, Globe Institute, University of Copenhagen, Copenhagen, Denmark
| | - Greger Larson
- The Palaeogenomics and Bio-archaeology Research Network, Research Laboratory for Archaeology and History of Art, University of Oxford, Oxford, UK
| | - Elaine A. Ostrander
- National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Evan K. Irving-Pease
- Section for Molecular Ecology and Evolution, Globe Institute, University of Copenhagen, Copenhagen, Denmark
| | - Laurent A.F. Frantz
- School of Biological and Behavioural Sciences, Queen Mary University of London, London, UK
- Palaeogenomics Group, Department of Veterinary Sciences, Ludwig Maximilian University, Munich, Germany
| | - Fernando Racimo
- Section for Molecular Ecology and Evolution, Globe Institute, University of Copenhagen, Copenhagen, Denmark
| |
Collapse
|
7
|
Wang SZ, Yan Y, Widlund M, Qian CC, Zhang LL, Zhang SJ, Li ZM, Cao P, Dai QY, Feng XT, Liu F, Wang L, Gao C, Fu QM, Hytönen MK, Lohi H, Savolainen P, Wang GD. Historic dog Furs Unravel the Origin and Artificial Selection of Modern Nordic Lapphund and Elkhound dog Breeds. Mol Biol Evol 2024; 41:msae108. [PMID: 38842255 PMCID: PMC11226788 DOI: 10.1093/molbev/msae108] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2024] [Revised: 05/28/2024] [Accepted: 05/31/2024] [Indexed: 06/07/2024] Open
Abstract
The origins and extreme morphological evolution of the modern dog breeds are poorly studied because the founder populations are extinct. Here, we analyse eight 100 to 200 years old dog fur samples obtained from traditional North Swedish clothing, to explore the origin and artificial selection of the modern Nordic Lapphund and Elkhound dog breeds. Population genomic analysis confirmed the Lapphund and Elkhound breeds to originate from the local dog population, and showed a distinct decrease in genetic diversity in agreement with intense breeding. We identified eleven genes under positive selection during the breed development. In particular, the MSRB3 gene, associated with breed-related ear morphology, was selected in all Lapphund and Elkhound breeds, and functional assays showed that a SNP mutation in the 3'UTR region suppresses its expression through miRNA regulation. Our findings demonstrate analysis of near-modern dog artifacts as an effective tool for interpreting the origin and artificial selection of the modern dog breeds.
Collapse
Affiliation(s)
- Shi-Zhi Wang
- Key Laboratory of Genetic Evolution & Animal Models, Yunnan Key Laboratory of Molecular Biology of Domestic Animals, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
- Yunnan Animal Science and Veterinary Institute, Kunming, China
| | - Yu Yan
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan University, Kunming, China
| | - Malin Widlund
- Department of Gene Technology, KTH Royal Institute of Technology, Science for Life Laboratory, Stockholm, Sweden
| | - Chen-Chang Qian
- Key Laboratory of Genetic Evolution & Animal Models, Yunnan Key Laboratory of Molecular Biology of Domestic Animals, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
- Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, China
| | | | - Shao-Jie Zhang
- Key Laboratory of Genetic Evolution & Animal Models, Yunnan Key Laboratory of Molecular Biology of Domestic Animals, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
- Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, China
| | - Zi-Mai Li
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China
| | - Peng Cao
- Key Laboratory of Vertebrate Evolution and Human Origins, Institute of Vertebrate Paleontology and Paleoanthropology, Chinese Academy of Sciences, Beijing, China
| | - Qing-Yan Dai
- Key Laboratory of Vertebrate Evolution and Human Origins, Institute of Vertebrate Paleontology and Paleoanthropology, Chinese Academy of Sciences, Beijing, China
| | - Xiao-Tian Feng
- Key Laboratory of Vertebrate Evolution and Human Origins, Institute of Vertebrate Paleontology and Paleoanthropology, Chinese Academy of Sciences, Beijing, China
| | - Feng Liu
- Key Laboratory of Vertebrate Evolution and Human Origins, Institute of Vertebrate Paleontology and Paleoanthropology, Chinese Academy of Sciences, Beijing, China
| | - Lu Wang
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan University, Kunming, China
| | - Chao Gao
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China
| | - Qiao-Mei Fu
- Key Laboratory of Vertebrate Evolution and Human Origins, Institute of Vertebrate Paleontology and Paleoanthropology, Chinese Academy of Sciences, Beijing, China
| | - Marjo K Hytönen
- Department of Medical and Clinical Genetics, Department of Veterinary Biosciences, University of Helsinki, Helsinki, Finland
- Folkhälsan Research Center, Helsinki, Finland
| | - Hannes Lohi
- Department of Medical and Clinical Genetics, Department of Veterinary Biosciences, University of Helsinki, Helsinki, Finland
- Folkhälsan Research Center, Helsinki, Finland
| | - Peter Savolainen
- Department of Gene Technology, KTH Royal Institute of Technology, Science for Life Laboratory, Stockholm, Sweden
| | - Guo-Dong Wang
- Key Laboratory of Genetic Evolution & Animal Models, Yunnan Key Laboratory of Molecular Biology of Domestic Animals, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
- Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, China
| |
Collapse
|
8
|
Nguyen AK, Blacksmith MS, Kidd JM. Duplications and Retrogenes Are Numerous and Widespread in Modern Canine Genomic Assemblies. Genome Biol Evol 2024; 16:evae142. [PMID: 38946312 PMCID: PMC11259980 DOI: 10.1093/gbe/evae142] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2023] [Revised: 05/08/2024] [Accepted: 06/24/2024] [Indexed: 07/02/2024] Open
Abstract
Recent years have seen a dramatic increase in the number of canine genome assemblies available. Duplications are an important source of evolutionary novelty and are also prone to misassembly. We explored the duplication content of nine canine genome assemblies using both genome self-alignment and read-depth approaches. We find that 8.58% of the genome is duplicated in the canFam4 assembly, derived from the German Shepherd Dog Mischka, including 90.15% of unplaced contigs. Highlighting the continued difficulty in properly assembling duplications, less than half of read-depth and assembly alignment duplications overlap, but the mCanLor1.2 Greenland wolf assembly shows greater concordance. Further study shows the presence of multiple segments that have alignments to four or more duplicate copies. These high-recurrence duplications correspond to gene retrocopies. We identified 3,892 candidate retrocopies from 1,316 parental genes in the canFam4 assembly and find that ∼8.82% of duplicated base pairs involve a retrocopy, confirming this mechanism as a major driver of gene duplication in canines. Similar patterns are found across eight other recent canine genome assemblies, with metrics supporting a greater quality of the PacBio HiFi mCanLor1.2 assembly. Comparison between the wolf and other canine assemblies found that 92% of retrocopy insertions are shared between assemblies. By calculating the number of generations since genome divergence, we estimate that new retrocopy insertions appear, on average, in 1 out of 3,514 births. Our analyses illustrate the impact of retrogene formation on canine genomes and highlight the variable representation of duplicated sequences among recently completed canine assemblies.
Collapse
Affiliation(s)
- Anthony K Nguyen
- Department of Human Genetics, University of Michigan, Ann Arbor, MI, USA
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, USA
| | - Matthew S Blacksmith
- Department of Human Genetics, University of Michigan, Ann Arbor, MI, USA
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, USA
| | - Jeffrey M Kidd
- Department of Human Genetics, University of Michigan, Ann Arbor, MI, USA
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, USA
| |
Collapse
|
9
|
Boch M, Huber L, Lamm C. Domestic dogs as a comparative model for social neuroscience: Advances and challenges. Neurosci Biobehav Rev 2024; 162:105700. [PMID: 38710423 PMCID: PMC7616343 DOI: 10.1016/j.neubiorev.2024.105700] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2023] [Revised: 03/19/2024] [Accepted: 04/30/2024] [Indexed: 05/08/2024]
Abstract
Dogs and humans have lived together for thousands of years and share many analogous socio-cognitive skills. Dog neuroimaging now provides insight into the neural bases of these shared social abilities. Here, we summarize key findings from dog fMRI identifying neocortical brain areas implicated in visual social cognition, such as face, body, and emotion perception, as well as action observation in dogs. These findings provide converging evidence that the temporal cortex plays a significant role in visual social cognition in dogs. We further briefly review investigations into the neural base of the dog-human relationship, mainly involving limbic brain regions. We then discuss current challenges in the field, such as statistical power and lack of common template spaces, and how to overcome them. Finally, we argue that the foundation has now been built to investigate and compare the neural bases of more complex socio-cognitive phenomena shared by dogs and humans. This will strengthen and expand the role of the domestic dog as a powerful comparative model species and provide novel insights into the evolutionary roots of social cognition.
Collapse
Affiliation(s)
- Magdalena Boch
- Social, Cognitive and Affective Neuroscience Unit, Department of Cognition, Emotion, and Methods in Psychology, Faculty of Psychology, University of Vienna, Vienna 1010, Austria; Department of Cognitive Biology, Faculty of Life Sciences, University of Vienna, Vienna 1090, Austria.
| | - Ludwig Huber
- Comparative Cognition, Messerli Research Institute, University of Veterinary Medicine Vienna, Medical University of Vienna and University of Vienna, Vienna 1210, Austria
| | - Claus Lamm
- Social, Cognitive and Affective Neuroscience Unit, Department of Cognition, Emotion, and Methods in Psychology, Faculty of Psychology, University of Vienna, Vienna 1010, Austria; Vienna Cognitive Science Hub, University of Vienna, Vienna 1010, Austria
| |
Collapse
|
10
|
Zhang M, Song Y, Wang C, Sun G, Zhuang L, Guo M, Ren L, Wangdue S, Dong G, Dai Q, Cao P, Yang R, Liu F, Feng X, Bennett EA, Zhang X, Chen X, Wang F, Luan F, Dong W, Lu G, Hao D, Hou H, Wang H, Qiao H, Wang Z, Hu X, He W, Xi L, Wang W, Shao J, Sun Z, Yue L, Ding Y, Tashi N, Tsho Y, Tong Y, Yang Y, Zhu S, Miao B, Wang W, Zhang L, Hu S, Ni X, Fu Q. Ancient Mitogenomes Reveal the Maternal Genetic History of East Asian Dogs. Mol Biol Evol 2024; 41:msae062. [PMID: 38507661 PMCID: PMC11003542 DOI: 10.1093/molbev/msae062] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2023] [Revised: 02/27/2024] [Accepted: 03/11/2024] [Indexed: 03/22/2024] Open
Abstract
Recent studies have suggested that dogs were domesticated during the Last Glacial Maximum (LGM) in Siberia, which contrasts with previous proposed domestication centers (e.g. Europe, the Middle East, and East Asia). Ancient DNA provides a powerful resource for the study of mammalian evolution and has been widely used to understand the genetic history of domestic animals. To understand the maternal genetic history of East Asian dogs, we have made a complete mitogenome dataset of 120 East Asian canids from 38 archaeological sites, including 102 newly sequenced from 12.9 to 1 ka BP (1,000 years before present). The majority (112/119, 94.12%) belonged to haplogroup A, and half of these (55/112, 49.11%) belonged to sub-haplogroup A1b. Most existing mitochondrial haplogroups were present in ancient East Asian dogs. However, mitochondrial lineages in ancient northern dogs (northeastern Eurasia and northern East Asia) were deeper and older than those in southern East Asian dogs. Results suggests that East Asian dogs originated from northeastern Eurasian populations after the LGM, dispersing in two possible directions after domestication. Western Eurasian (Europe and the Middle East) dog maternal ancestries genetically influenced East Asian dogs from approximately 4 ka BP, dramatically increasing after 3 ka BP, and afterwards largely replaced most primary maternal lineages in northern East Asia. Additionally, at least three major mitogenome sub-haplogroups of haplogroup A (A1a, A1b, and A3) reveal at least two major dispersal waves onto the Qinghai-Tibet Plateau in ancient times, indicating eastern (A1b and A3) and western (A1a) Eurasian origins.
Collapse
Affiliation(s)
- Ming Zhang
- China-Central Asia “the Belt and Road” Joint Laboratory on Human and Environment Research, Key Laboratory of Cultural Heritage Research and Conservation, School of Culture Heritage, Northwest University, Xi’an, China
- Key Laboratory of Vertebrate Evolution and Human Origins, Institute of Vertebrate Paleontology and Paleoanthropology, Center for Excellence in Life and Paleoenvironment, Chinese Academy of Sciences, Beijing, China
| | - Yanbo Song
- School of Archaeology, Shandong University, Jinan, China
| | - Caihui Wang
- China-Central Asia “the Belt and Road” Joint Laboratory on Human and Environment Research, Key Laboratory of Cultural Heritage Research and Conservation, School of Culture Heritage, Northwest University, Xi’an, China
| | - Guoping Sun
- Zhejiang Provincial Institute of Cultural Relics and Archaeology, Hangzhou, China
| | | | | | - Lele Ren
- School of History and Culture, Lanzhou University, Lanzhou, China
| | - Shargan Wangdue
- Tibet Institute for Conservation and Research of Cultural Relics, Lhasa, China
| | - Guanghui Dong
- Key Laboratory of Western China's Environmental Systems (Ministry of Education), College of Earth and Environmental Sciences, Lanzhou University, Lanzhou, China
| | - Qingyan Dai
- Key Laboratory of Vertebrate Evolution and Human Origins, Institute of Vertebrate Paleontology and Paleoanthropology, Center for Excellence in Life and Paleoenvironment, Chinese Academy of Sciences, Beijing, China
| | - Peng Cao
- Key Laboratory of Vertebrate Evolution and Human Origins, Institute of Vertebrate Paleontology and Paleoanthropology, Center for Excellence in Life and Paleoenvironment, Chinese Academy of Sciences, Beijing, China
| | - Ruowei Yang
- Key Laboratory of Vertebrate Evolution and Human Origins, Institute of Vertebrate Paleontology and Paleoanthropology, Center for Excellence in Life and Paleoenvironment, Chinese Academy of Sciences, Beijing, China
| | - Feng Liu
- Key Laboratory of Vertebrate Evolution and Human Origins, Institute of Vertebrate Paleontology and Paleoanthropology, Center for Excellence in Life and Paleoenvironment, Chinese Academy of Sciences, Beijing, China
| | - Xiaotian Feng
- Key Laboratory of Vertebrate Evolution and Human Origins, Institute of Vertebrate Paleontology and Paleoanthropology, Center for Excellence in Life and Paleoenvironment, Chinese Academy of Sciences, Beijing, China
| | - E Andrew Bennett
- Key Laboratory of Vertebrate Evolution and Human Origins, Institute of Vertebrate Paleontology and Paleoanthropology, Center for Excellence in Life and Paleoenvironment, Chinese Academy of Sciences, Beijing, China
| | - Xiaoling Zhang
- Key Laboratory of Vertebrate Evolution and Human Origins, Institute of Vertebrate Paleontology and Paleoanthropology, Center for Excellence in Life and Paleoenvironment, Chinese Academy of Sciences, Beijing, China
| | - Xi Chen
- Department of Cultural Heritage and Museology, Nanjing Normal University, Nanjing, China
| | - Fen Wang
- School of Archaeology, Shandong University, Jinan, China
| | - Fengshi Luan
- School of Archaeology, Shandong University, Jinan, China
| | - Wenbin Dong
- Shandong Provincial Institute of Cultural Relics and Archaeology, Jinan, China
| | - Guoquan Lu
- School of Archaeology, Shandong University, Jinan, China
| | - Daohua Hao
- Shandong Provincial Institute of Cultural Relics and Archaeology, Jinan, China
| | - Hongwei Hou
- Gansu Provincial Institute of Cultural Relics and Archaeology, Lanzhou, China
| | - Hui Wang
- Gansu Provincial Institute of Cultural Relics and Archaeology, Lanzhou, China
- Fudan Archaeological Science Institute, Fudan University, Shanghai, China
| | - Hong Qiao
- Qinghai Provincial Cultural Relics and Archaeology Institute, Xining, China
| | - Zhongxin Wang
- Qinghai Provincial Cultural Relics and Archaeology Institute, Xining, China
| | - Xiaojun Hu
- Qinghai Provincial Cultural Relics and Archaeology Institute, Xining, China
| | - Wei He
- Tibet Institute for Conservation and Research of Cultural Relics, Lhasa, China
| | - Lin Xi
- Shaanxi Academy of Archaeology, Xi’an, China
| | - Weilin Wang
- School of Archaeology and Museology, Shanxi University, Taiyuan, China
| | - Jing Shao
- Shaanxi Academy of Archaeology, Xi’an, China
| | | | | | - Yan Ding
- Shaanxi Academy of Archaeology, Xi’an, China
| | - Norbu Tashi
- Tibet Institute for Conservation and Research of Cultural Relics, Lhasa, China
| | - Yang Tsho
- Tibet Institute for Conservation and Research of Cultural Relics, Lhasa, China
| | - Yan Tong
- Tibet Institute for Conservation and Research of Cultural Relics, Lhasa, China
| | - Yangheshan Yang
- School of Ecological and Environmental Sciences, East China Normal University, Shanghai, China
| | - Shilun Zhu
- Key Laboratory of Vertebrate Evolution and Human Origins, Institute of Vertebrate Paleontology and Paleoanthropology, Center for Excellence in Life and Paleoenvironment, Chinese Academy of Sciences, Beijing, China
- University of the Chinese Academy of Sciences, Beijing, China
| | - Bo Miao
- Key Laboratory of Vertebrate Evolution and Human Origins, Institute of Vertebrate Paleontology and Paleoanthropology, Center for Excellence in Life and Paleoenvironment, Chinese Academy of Sciences, Beijing, China
| | - Wenjun Wang
- Key Laboratory of Vertebrate Evolution and Human Origins, Institute of Vertebrate Paleontology and Paleoanthropology, Center for Excellence in Life and Paleoenvironment, Chinese Academy of Sciences, Beijing, China
- Science and Technology Archaeology, National Centre for Archaeology, Beijing, China
| | - Lizhao Zhang
- Key Laboratory of Vertebrate Evolution and Human Origins, Institute of Vertebrate Paleontology and Paleoanthropology, Center for Excellence in Life and Paleoenvironment, Chinese Academy of Sciences, Beijing, China
| | - Songmei Hu
- Joint International Research Laboratory of Environmental and Social Archaeology, Shandong University, Qingdao, China
- Shaanxi Academy of Archaeology, Xi’an, China
| | - Xijun Ni
- Key Laboratory of Vertebrate Evolution and Human Origins, Institute of Vertebrate Paleontology and Paleoanthropology, Center for Excellence in Life and Paleoenvironment, Chinese Academy of Sciences, Beijing, China
- University of the Chinese Academy of Sciences, Beijing, China
| | - Qiaomei Fu
- Key Laboratory of Vertebrate Evolution and Human Origins, Institute of Vertebrate Paleontology and Paleoanthropology, Center for Excellence in Life and Paleoenvironment, Chinese Academy of Sciences, Beijing, China
- University of the Chinese Academy of Sciences, Beijing, China
| |
Collapse
|
11
|
Abbona CC, Lebrasseur O, Prevosti FJ, Peralta E, González Venanzi L, Frantz L, Larson G, Gil AF, Neme GA. Patagonian partnerships: the extinct Dusicyon avus and its interaction with prehistoric human communities. ROYAL SOCIETY OPEN SCIENCE 2024; 11:231835. [PMID: 38601034 PMCID: PMC11004678 DOI: 10.1098/rsos.231835] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/29/2023] [Revised: 02/19/2024] [Accepted: 02/21/2024] [Indexed: 04/12/2024]
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 (δ13Ccol and δ15N) 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.
Collapse
Affiliation(s)
- Cinthia C. Abbona
- Instituto de Evolución, Ecología Histórica y Ambiente (IDEVEA), UTN-CONICET, Avenue Gral. Urquiza 314, CP5600, San Rafael, Mendoza, Argentina
| | - Ophélie Lebrasseur
- Palaeogenomics and Bio-Archaeology Research Network, School of Archaeology, University of Oxford, OxfordOX1 3TG, UK
| | - Francisco J. Prevosti
- Museo de Ciencias Antropológicas y Naturales, Universidad Nacional de La Rioja (UNLaR), Avenue Luis M. de la Fuente S/N, La Rioja5300, Argentina
| | - Eva Peralta
- Instituto de Evolución, Ecología Histórica y Ambiente (IDEVEA), UTN-CONICET, Avenue Gral. Urquiza 314, CP5600, San Rafael, Mendoza, Argentina
| | - Lucio González Venanzi
- Div. Arqueología, Anexo Museo, Laboratory 128 (FCNyM-UNLP), La Plata, Argentina, FHumyAr (UNR), Rosario, Argentina
| | - Laurent Frantz
- Graduate School Life Science Munich, Faculty of Biology/Biocenter, Grosshadernerstr, 2-4, 82152 Planegg-Martinsried, Munich, Germany
| | - Greger Larson
- Palaeogenomics and Bio-Archaeology Research Network, School of Archaeology, University of Oxford, OxfordOX1 3TG, UK
| | - Adolfo F. Gil
- Instituto de Evolución, Ecología Histórica y Ambiente (IDEVEA), UTN-CONICET, Avenue Gral. Urquiza 314, CP5600, San Rafael, Mendoza, Argentina
| | - Gustavo A. Neme
- Instituto de Evolución, Ecología Histórica y Ambiente (IDEVEA), UTN-CONICET, Avenue Gral. Urquiza 314, CP5600, San Rafael, Mendoza, Argentina
| |
Collapse
|
12
|
Leon-Apodaca AV, Kumar M, del Castillo A, Conroy GC, Lamont RW, Ogbourne S, Cairns KM, Borburgh L, Behrendorff L, Subramanian S, Szpiech ZA. Genomic consequences of isolation and inbreeding in an island dingo population. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.09.15.557950. [PMID: 37745583 PMCID: PMC10516007 DOI: 10.1101/2023.09.15.557950] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/26/2023]
Abstract
Dingoes come from an ancient canid lineage that originated in East Asia around 8000-11,000 years BP. As Australia's largest terrestrial predator, dingoes play an important ecological role. A small, protected population exists on a world heritage listed offshore island, K'gari (formerly Fraser Island). Concern regarding the persistence of dingoes on K'gari has risen due to their low genetic diversity and elevated inbreeding levels. However, whole-genome sequencing data is lacking from this population. Here, we include five new whole-genome sequences of K'gari dingoes. We analyze a total of 18 whole genome sequences of dingoes sampled from mainland Australia and K'gari to assess the genomic consequences of their demographic histories. Long (>1 Mb) runs of homozygosity (ROH) - indicators of inbreeding - are elevated in all sampled dingoes. However, K'gari dingoes showed significantly higher levels of very long ROH (>5 Mb), providing genomic evidence for small population size, isolation, inbreeding, and a strong founder effect. Our results suggest that, despite current levels of inbreeding, the K'gari population is purging strongly deleterious mutations, which, in the absence of further reductions in population size, may facilitate the persistence of small populations despite low genetic diversity and isolation. However, there may be little to no purging of mildly deleterious alleles, which may have important long-term consequences, and should be considered by conservation and management programs.
Collapse
Affiliation(s)
| | - Manoharan Kumar
- School of Science, Technology & Engineering, University of the Sunshine Coast, 1 Moreton Parade, Petrie, Queensland, Australia
| | | | - Gabriel C. Conroy
- School of Science, Technology & Engineering, University of the Sunshine Coast, 90 Sippy Downs Drive, Sippy Downs, Queensland, Australia
- Centre for Bioinnovation, University of the Sunshine Coast, 90 Sippy Downs Drive, Sippy Downs, Queensland, Australia
| | - Robert W Lamont
- School of Science, Technology & Engineering, University of the Sunshine Coast, 90 Sippy Downs Drive, Sippy Downs, Queensland, Australia
- Centre for Bioinnovation, University of the Sunshine Coast, 90 Sippy Downs Drive, Sippy Downs, Queensland, Australia
| | - Steven Ogbourne
- Centre for Bioinnovation, University of the Sunshine Coast, 90 Sippy Downs Drive, Sippy Downs, Queensland, Australia
| | - Kylie M. Cairns
- Evolution & Ecology Research Centre, School of Biological, Earth and Environmental Sciences, UNSW Australia, Sydney NSW 2052, Australia
- Centre for Ecosystem Science, School of Biological, Earth and Environmental Sciences, UNSW Australia, Sydney NSW 2052, Australia
| | - Liz Borburgh
- School of Science, Technology & Engineering, University of the Sunshine Coast, 90 Sippy Downs Drive, Sippy Downs, Queensland, Australia
| | - Linda Behrendorff
- Queensland Parks and Wildlife Service, Department of Environment & Science, K’gari, Australia
| | - Sankar Subramanian
- School of Science, Technology & Engineering, University of the Sunshine Coast, 1 Moreton Parade, Petrie, Queensland, Australia
- Centre for Bioinnovation, University of the Sunshine Coast, 90 Sippy Downs Drive, Sippy Downs, Queensland, Australia
| | - Zachary A. Szpiech
- Department of Biology, Pennsylvania State University, PA, USA
- Institute for Computational and Data Sciences, Pennsylvania State University, PA, USA
| |
Collapse
|
13
|
Amici F, Meacci S, Caray E, Oña L, Liebal K, Ciucci P. A first exploratory comparison of the behaviour of wolves (Canis lupus) and wolf-dog hybrids in captivity. Anim Cogn 2024; 27:9. [PMID: 38429445 PMCID: PMC10907477 DOI: 10.1007/s10071-024-01849-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2023] [Revised: 10/31/2023] [Accepted: 11/07/2023] [Indexed: 03/03/2024]
Abstract
Extensive introgression of genes from domesticated taxa may be a serious threat for the genomic integrity and adaptability of wild populations. Grey wolves (Canis lupus) are especially vulnerable to this phenomenon, but there are no studies yet assessing the potential behavioural effects of dog-introgression in wolves. In this study, we conducted a first systematic comparison of admixed (N = 11) and non-admixed (N = 14) wolves in captivity, focusing on their reaction to unfamiliar humans and novel objects, and the cohesiveness of their social groups. When exposed to unfamiliar humans in the experimental task, wolves were more vigilant, fearful and aggressive than admixed wolves, and less likely to approach humans, but also more likely to spend time in human proximity. When exposed to novel objects, wolves were more aggressive than admixed wolves, less likely to spend time in object proximity, and more likely to interact with objects, but also less vigilant and as fearful as admixed wolves. Finally, social networks were more cohesive in wolves than in admixed wolves. Although caution is needed when comparing groups of captive individuals with different life experiences, our study suggests that dog admixture may lead to important behavioural changes in wolves, with possible implications for conservation strategies.
Collapse
Affiliation(s)
- Federica Amici
- Life Sciences, Institute for Biology, Human Biology and Primate Cognition, Leipzig University, Leipzig, Germany.
- Department of Comparative Cultural Psychology, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany.
| | - Simone Meacci
- Department of Biology and Biotechnology "Charles Darwin", Sapienza University of Rome, Rome, Italy
| | - Emmeline Caray
- Department of Life Sciences, University of Strasbourg, Strasbourg, France
| | - Linda Oña
- Life Sciences, Institute for Biology, Human Biology and Primate Cognition, Leipzig University, Leipzig, Germany
| | - Katja Liebal
- Life Sciences, Institute for Biology, Human Biology and Primate Cognition, Leipzig University, Leipzig, Germany
- Department of Comparative Cultural Psychology, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Paolo Ciucci
- Department of Biology and Biotechnology "Charles Darwin", Sapienza University of Rome, Rome, Italy
| |
Collapse
|
14
|
Simon A, Coop G. The contribution of gene flow, selection, and genetic drift to five thousand years of human allele frequency change. Proc Natl Acad Sci U S A 2024; 121:e2312377121. [PMID: 38363870 PMCID: PMC10907250 DOI: 10.1073/pnas.2312377121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2023] [Accepted: 01/09/2024] [Indexed: 02/18/2024] Open
Abstract
Genomic time series from experimental evolution studies and ancient DNA datasets offer us a chance to directly observe the interplay of various evolutionary forces. We show how the genome-wide variance in allele frequency change between two time points can be decomposed into the contributions of gene flow, genetic drift, and linked selection. In closed populations, the contribution of linked selection is identifiable because it creates covariances between time intervals, and genetic drift does not. However, repeated gene flow between populations can also produce directionality in allele frequency change, creating covariances. We show how to accurately separate the fraction of variance in allele frequency change due to admixture and linked selection in a population receiving gene flow. We use two human ancient DNA datasets, spanning around 5,000 y, as time transects to quantify the contributions to the genome-wide variance in allele frequency change. We find that a large fraction of genome-wide change is due to gene flow. In both cases, after correcting for known major gene flow events, we do not observe a signal of genome-wide linked selection. Thus despite the known role of selection in shaping long-term polymorphism levels, and an increasing number of examples of strong selection on single loci and polygenic scores from ancient DNA, it appears to be gene flow and drift, and not selection, that are the main determinants of recent genome-wide allele frequency change. Our approach should be applicable to the growing number of contemporary and ancient temporal population genomics datasets.
Collapse
Affiliation(s)
- Alexis Simon
- Center for Population Biology, University of California, Davis, CA95616
- Department of Evolution and Ecology, University of California, Davis, CA95616
| | - Graham Coop
- Center for Population Biology, University of California, Davis, CA95616
- Department of Evolution and Ecology, University of California, Davis, CA95616
| |
Collapse
|
15
|
Gojobori J, Arakawa N, Xiaokaiti X, Matsumoto Y, Matsumura S, Hongo H, Ishiguro N, Terai Y. Japanese wolves are most closely related to dogs and share DNA with East Eurasian dogs. Nat Commun 2024; 15:1680. [PMID: 38396028 PMCID: PMC10891106 DOI: 10.1038/s41467-024-46124-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2022] [Accepted: 02/14/2024] [Indexed: 02/25/2024] Open
Abstract
Although the domestic dog's origin is still unclear, this lineage is believed to have been domesticated from an extinct population of gray wolves, which is expected to be more closely related to dogs than to other populations of gray wolves. Here, we sequence the whole genomes of nine Japanese wolves (7.5-100x: Edo to Meiji periods) and 11 modern Japanese dogs and analyze them together with those from other populations of dogs and wolves. A phylogenomic tree shows that, among the gray wolves, Japanese wolves are closest to the dog, suggesting that the ancestor of dogs is closely related to the ancestor of the Japanese wolf. Based on phylogenetic and geographic relationships, the dog lineage has most likely originated in East Asia, where it diverged from a common ancestor with the Japanese wolf. Since East Eurasian dogs possess Japanese wolf ancestry, we estimate an introgression event from the ancestor of the Japanese wolf to the ancestor of the East Eurasian dog that occurred before the dog's arrival in the Japanese archipelago.
Collapse
Affiliation(s)
- Jun Gojobori
- SOKENDAI (The Graduate University for Advanced Studies), Research Center for Integrative Evolutionary Science, Shonan Village, Hayama, Kanagawa, 240-0193, Japan
| | - Nami Arakawa
- SOKENDAI (The Graduate University for Advanced Studies), Research Center for Integrative Evolutionary Science, Shonan Village, Hayama, Kanagawa, 240-0193, Japan
| | - Xiayire Xiaokaiti
- SOKENDAI (The Graduate University for Advanced Studies), Research Center for Integrative Evolutionary Science, Shonan Village, Hayama, Kanagawa, 240-0193, Japan
| | - Yuki Matsumoto
- Research and Development Section, Anicom Specialty Medical Institute, Naka-ku, Chojamachi, Yokohama, 231-0033, Japan
| | - Shuichi Matsumura
- Faculty of Applied Biological Sciences, Gifu University, Yanagido 1-1, Gifu, 501-1193, Japan
| | - Hitomi Hongo
- SOKENDAI (The Graduate University for Advanced Studies), Research Center for Integrative Evolutionary Science, Shonan Village, Hayama, Kanagawa, 240-0193, Japan
| | - Naotaka Ishiguro
- SOKENDAI (The Graduate University for Advanced Studies), Research Center for Integrative Evolutionary Science, Shonan Village, Hayama, Kanagawa, 240-0193, Japan.
- Faculty of Applied Biological Sciences, Gifu University, Yanagido 1-1, Gifu, 501-1193, Japan.
| | - Yohey Terai
- SOKENDAI (The Graduate University for Advanced Studies), Research Center for Integrative Evolutionary Science, Shonan Village, Hayama, Kanagawa, 240-0193, Japan.
| |
Collapse
|
16
|
Janák V, Novák K, Kyselý R. Late History of Cattle Breeds in Central Europe in Light of Genetic and Archaeogenetic Sources-Overview, Thoughts, and Perspectives. Animals (Basel) 2024; 14:645. [PMID: 38396613 PMCID: PMC10886113 DOI: 10.3390/ani14040645] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2023] [Revised: 02/12/2024] [Accepted: 02/14/2024] [Indexed: 02/25/2024] Open
Abstract
Although Europe was not a primary centre of cattle domestication, its expansion from the Middle East and subsequent development created a complex pattern of cattle breed diversity. Many isolated populations of local historical breeds still carry the message about the physical and genetic traits of ancient populations. Since the way of life of human communities starting from the eleventh millennium BP was strongly determined by livestock husbandry, the knowledge of cattle diversity through the ages is helpful in the interpretation of many archaeological findings. Historical cattle diversity is currently at the intersection of two leading directions of genetic research. Firstly, it is archaeogenetics attempting to recover and interpret the preserved genetic information directly from archaeological finds. The advanced archaeogenetic approaches meet with the population genomics of extant cattle populations. The immense amount of genetic information collected from living cattle, due to its key economic role, allows for reconstructing the genetic profiles of the ancient populations backwards. The present paper aims to place selected archaeogenetic, genetic, and genomic findings in the picture of cattle history in Central Europe, as suggested by archaeozoological and historical records. Perspectives of the methodical connection between the genetic approaches and the approaches of traditional archaeozoology, such as osteomorphology and osteometry, are discussed. The importance, actuality, and effectiveness of combining different approaches to each archaeological find, such as morphological characterization, interpretation of the historical context, and molecular data, are stressed.
Collapse
Affiliation(s)
- Vojtěch Janák
- Institute of Archaeology of the Czech Academy of Sciences, Prague, Letenská 4, 118 00 Praha, Czech Republic
- Department of Genetics and Breeding, Institute of Animal Science, Přátelství 815, 104 00 Praha, Czech Republic;
- Department of Archaeology, Faculty of Arts, Charles University, Nám. Jana Palacha 2, 116 38 Praha, Czech Republic
| | - Karel Novák
- Department of Genetics and Breeding, Institute of Animal Science, Přátelství 815, 104 00 Praha, Czech Republic;
| | - René Kyselý
- Institute of Archaeology of the Czech Academy of Sciences, Prague, Letenská 4, 118 00 Praha, Czech Republic
| |
Collapse
|
17
|
McCartney JM, Leavens DA. The Role of Life History and Familiarity in Performance of Working and Non-Working Dogs ( Canis lupus familiaris) in a Point-Following Task. Animals (Basel) 2024; 14:573. [PMID: 38396541 PMCID: PMC10885941 DOI: 10.3390/ani14040573] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2024] [Revised: 02/04/2024] [Accepted: 02/07/2024] [Indexed: 02/25/2024] Open
Abstract
Domestic dogs are very successful at following human communicative gestures in paradigms such as the object-choice task. Pet dogs also prefer responding to cues given by a familiar cue-giver and this had not been found in working dogs. Therefore, we tested three groups of dogs in the object-choice task (n = 54): the groups were "Actively working" dogs from working dog breeds, pet dogs from "Non-working breeds" and pet dogs from "Working breeds". We found that "Actively working" and "Working breeds" dog groups outperformed "Non-working breeds" in following a point in the object-choice task. We also found that both "Actively working" and "Working breeds" preferred a familiar cue-giver over an unfamiliar one, in contrast to previous findings. Therefore, we conclude that dogs' abilities to perform well in the object-choice task is influenced by the selective history of the breed, and this is then increased by life experience and training.
Collapse
|
18
|
Lamontagne A, Gaunet F. Behavioural Synchronisation between Dogs and Humans: Unveiling Interspecific Motor Resonance? Animals (Basel) 2024; 14:548. [PMID: 38396516 PMCID: PMC10886274 DOI: 10.3390/ani14040548] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2023] [Revised: 02/05/2024] [Accepted: 02/06/2024] [Indexed: 02/25/2024] Open
Abstract
Dogs' behavioural synchronisation with humans is of growing scientific interest. However, studies lack a comprehensive exploration of the neurocognitive foundations of this social cognitive ability. Drawing parallels from the mechanisms underlying behavioural synchronisation in humans, specifically motor resonance and the recruitment of mirror neurons, we hypothesise that dogs' behavioural synchronisation with humans is underpinned by a similar mechanism, namely interspecific motor resonance. Based on a literature review, we argue that dogs possess the prerequisites for motor resonance, and we suggest that interspecific behavioural synchronisation relies on the activation of both human and canine mirror neurons. Furthermore, interspecific behavioural studies highlight certain characteristics of motor resonance, including motor contagion and its social modulators. While these findings strongly suggest the potential existence of interspecific motor resonance, direct proof remains to be established. Our analysis thus paves the way for future research to confirm the existence of interspecific motor resonance as the neurocognitive foundation for interspecific behavioural synchronisation. Unravelling the neurocognitive mechanisms underlying this behavioural adjustment holds profound implications for understanding the evolutionary dynamics of dogs alongside humans and improving the day-to-day management of dog-human interactions.
Collapse
Affiliation(s)
- Angélique Lamontagne
- Centre de Recherche en Psychologie et Neuroscience (UMR 7077), Aix-Marseille University, Centre National de la Recherche Scientifique, 3 Place Victor Hugo, 13331 Marseille, Cedex 03, France
- Association Agir pour la Vie Animale (AVA), 76220 Cuy-Saint-Fiacre, France
| | - Florence Gaunet
- Centre de Recherche en Psychologie et Neuroscience (UMR 7077), Aix-Marseille University, Centre National de la Recherche Scientifique, 3 Place Victor Hugo, 13331 Marseille, Cedex 03, France
| |
Collapse
|
19
|
McKeague B, Finlay C, Rooney N. Conservation detection dogs: A critical review of efficacy and methodology. Ecol Evol 2024; 14:e10866. [PMID: 38371867 PMCID: PMC10869951 DOI: 10.1002/ece3.10866] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2023] [Revised: 11/09/2023] [Accepted: 12/02/2023] [Indexed: 02/20/2024] Open
Abstract
Conservation detection dogs (CDD) use their exceptional olfactory abilities to assist a wide range of conservation projects through the detection of target specimens or species. CDD are generally quicker, can cover wider areas and find more samples than humans and other analytical tools. However, their efficacy varies between studies; methodological and procedural standardisation in the field is lacking. Considering the cost of deploying a CDD team and the limited financial resources within conservation, it is vital that their performance is quantified and reliable. This review aims to summarise what is currently known about the use of scent detection dogs in conservation and elucidate which factors affect efficacy. We describe the efficacy of CDD across species and situational contexts like training and fieldwork. Reported sensitivities (i.e. the proportion of target samples found out of total available) ranged from 23.8% to 100% and precision rates (i.e. proportion of alerts that are true positives) from 27% to 100%. CDD are consistently shown to be better than other techniques, but performance varies substantially across the literature. There is no consistent difference in efficacy between training, testing and fieldwork, hence we need to understand the factors affecting this. We highlight the key variables that can alter CDD performance. External effects include target odour, training methods, sample management, search methodology, environment and the CDD handler. Internal effects include dog breed, personality, diet, age and health. Unfortunately, much of the research fails to provide adequate information on the dogs, handlers, training, experience and samples. This results in an inability to determine precisely why an individual study has high or low efficacy. It is clear that CDDs can be effective and applied to possibly limitless conservation scenarios, but moving forward researchers must provide more consistent and detailed methodologies so that comparisons can be conducted, results are more easily replicated and progress can be made in standardising CDD work.
Collapse
Affiliation(s)
- Beth McKeague
- School of Biological SciencesQueen's University BelfastBelfastUK
| | | | - Nicola Rooney
- Bristol Veterinary SchoolUniversity of BristolBristolUK
| |
Collapse
|
20
|
Simon A, Coop G. The contribution of gene flow, selection, and genetic drift to five thousand years of human allele frequency change. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.07.11.548607. [PMID: 37503227 PMCID: PMC10370008 DOI: 10.1101/2023.07.11.548607] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/29/2023]
Abstract
Genomic time series from experimental evolution studies and ancient DNA datasets offer us a chance to directly observe the interplay of various evolutionary forces. We show how the genome-wide variance in allele frequency change between two time points can be decomposed into the contributions of gene flow, genetic drift, and linked selection. In closed populations, the contribution of linked selection is identifiable because it creates covariances between time intervals, and genetic drift does not. However, repeated gene flow between populations can also produce directionality in allele frequency change, creating covariances. We show how to accurately separate the fraction of variance in allele frequency change due to admixture and linked selection in a population receiving gene flow. We use two human ancient DNA datasets, spanning around 5,000 years, as time transects to quantify the contributions to the genome-wide variance in allele frequency change. We find that a large fraction of genome-wide change is due to gene flow. In both cases, after correcting for known major gene flow events, we do not observe a signal of genome-wide linked selection. Thus despite the known role of selection in shaping long-term polymorphism levels, and an increasing number of examples of strong selection on single loci and polygenic scores from ancient DNA, it appears to be gene flow and drift, and not selection, that are the main determinants of recent genome-wide allele frequency change. Our approach should be applicable to the growing number of contemporary and ancient temporal population genomics datasets.
Collapse
Affiliation(s)
- Alexis Simon
- Center for Population Biology, University of California, Davis, CA 95616
- Department of Evolution and Ecology, University of California, Davis, CA 95616
| | - Graham Coop
- Center for Population Biology, University of California, Davis, CA 95616
- Department of Evolution and Ecology, University of California, Davis, CA 95616
| |
Collapse
|
21
|
Wu G. Recent Advances in the Nutrition and Metabolism of Dogs and Cats. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2024; 1446:1-14. [PMID: 38625522 DOI: 10.1007/978-3-031-54192-6_1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/17/2024]
Abstract
Domestic dogs (facultative carnivores) and cats (obligate carnivores) have been human companions for at least 12,000 and 9000 years, respectively. These animal species have a relatively short digestive tract but a large stomach volume and share many common features of physiological processes, intestinal microbes, and nutrient metabolism. The taste buds of the canine and feline tongues can distinguish sour, umami, bitter, and salty substances. Dogs, but not cats, possess sweet receptors. α-Amylase activity is either absent or very low in canine and feline saliva, and is present at low or substantial levels in the pancreatic secretions of cats or dogs, respectively. Thus, unlike cats, dogs have adapted to high-starch rations while also consuming animal-sourced foods. At metabolic levels, both dogs and cats synthesize de novo vitamin C and many amino acids (AAs, such as Ala, Asn, Asp, Glu, Gln, Gly, Pro, and Ser) but have a very limited ability to form vitamin D3. Compared with dogs, cats have higher requirements for AAs, some B-complex vitamins, and choline; greater rates of gluconeogenesis; a higher capacity to tolerate AA imbalances and antagonism; a more limited ability to synthesize arginine and taurine from glutamine/proline and cysteine, respectively; and a very limited ability to generate polyunsaturated fatty acids (PUFAs) from respective substrates. Unlike dogs, cats cannot convert either β-carotene into vitamin A or tryptophan into niacin. Dogs can thrive on one large meal daily and select high-fat over low-fat diets, whereas cats eat more frequently during light and dark periods and select high-protein over low-protein diets. There are increasing concerns over the health of skin, hair, bone, and joints (specialized connective tissues containing large amounts of collagen and/or keratin); sarcopenia (age-related losses of skeletal-muscle mass and function); and cognitive function in dogs and cats. Sufficient intakes of proteinogenic AAs and taurine along with vitamins, minerals, and PUFAs are crucial for the normal structures of the skin, hair, bone, and joints, while mitigating sarcopenia and cognitive dysfunction. Although pet owners may have different perceptions about the feeding and management practice of their dogs and cats, the health and well-being of the companion animals critically depend on safe, balanced, and nutritive foods. The new knowledge covered in this volume of Adv Exp Med Biol is essential to guide the formulation of pet foods to improve the growth, development, brain function, reproduction, lactation, and health of the companion animals.
Collapse
Affiliation(s)
- Guoyao Wu
- Department of Animal Science, Texas A&M University, College Station, TX, 77843, USA.
| |
Collapse
|
22
|
Petr M, Haller BC, Ralph PL, Racimo F. slendr: a framework for spatio-temporal population genomic simulations on geographic landscapes. PEER COMMUNITY JOURNAL 2023; 3:e121. [PMID: 38984034 PMCID: PMC11233137 DOI: 10.24072/pcjournal.354] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 07/11/2024]
Abstract
One of the goals of population genetics is to understand how evolutionary forces shape patterns of genetic variation over time. However, because populations evolve across both time and space, most evolutionary processes also have an important spatial component, acting through phenomena such as isolation by distance, local mate choice, or uneven distribution of resources. This spatial dimension is often neglected, partly due to the lack of tools specifically designed for building and evaluating complex spatio-temporal population genetic models. To address this methodological gap, we present a new framework for simulating spatially-explicit genomic data, implemented in a new R package called slendr (www.slendr.net), which leverages a SLiM simulation back-end script bundled with the package. With this framework, the users can programmatically and visually encode spatial population ranges and their temporal dynamics (i.e., population displacements, expansions, and contractions) either on real Earth landscapes or on abstract custom maps, and schedule splits and gene-flow events between populations using a straightforward declarative language. Additionally, slendr can simulate data from traditional, non-spatial models, either with SLiM or using an alternative built-in coalescent msprime back end. Together with its R-idiomatic interface to the tskit library for tree-sequence processing and analysis, slendr opens up the possibility of performing efficient, reproducible simulations of spatio-temporal genomic data entirely within the R environment, leveraging its wealth of libraries for geospatial data analysis, statistics, and visualization. Here, we present the design of the slendr R package and demonstrate its features on several practical example workflows.
Collapse
Affiliation(s)
- Martin Petr
- Lundbeck Foundation GeoGenetics Centre, Globe Institute, University of Copenhagen, Denmark
- Section for Molecular Ecology and Evolution, Globe Institute, University of Copenhagen, Denmark
| | - Benjamin C Haller
- Department of Computational Biology, Cornell University, Ithaca, NY, USA
| | - Peter L Ralph
- Institute of Ecology and Evolution, University of Oregon, Eugene, OR, USA
| | - Fernando Racimo
- Lundbeck Foundation GeoGenetics Centre, Globe Institute, University of Copenhagen, Denmark
- Section for Molecular Ecology and Evolution, Globe Institute, University of Copenhagen, Denmark
| |
Collapse
|
23
|
Lin AT, Hammond-Kaarremaa L, Liu HL, Stantis C, McKechnie I, Pavel M, Pavel SSM, Wyss SSÁ, Sparrow DQ, Carr K, Aninta SG, Perri A, Hartt J, Bergström A, Carmagnini A, Charlton S, Dalén L, Feuerborn TR, France CAM, Gopalakrishnan S, Grimes V, Harris A, Kavich G, Sacks BN, Sinding MHS, Skoglund P, Stanton DWG, Ostrander EA, Larson G, Armstrong CG, Frantz LAF, Hawkins MTR, Kistler L. The history of Coast Salish "woolly dogs" revealed by ancient genomics and Indigenous Knowledge. Science 2023; 382:1303-1308. [PMID: 38096292 PMCID: PMC7615573 DOI: 10.1126/science.adi6549] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2023] [Accepted: 10/25/2023] [Indexed: 12/18/2023]
Abstract
Ancestral Coast Salish societies in the Pacific Northwest kept long-haired "woolly dogs" that were bred and cared for over millennia. However, the dog wool-weaving tradition declined during the 19th century, and the population was lost. In this study, we analyzed genomic and isotopic data from a preserved woolly dog pelt from "Mutton," collected in 1859. Mutton is the only known example of an Indigenous North American dog with dominant precolonial ancestry postdating the onset of settler colonialism. We identified candidate genetic variants potentially linked with their distinct woolly phenotype. We integrated these data with interviews from Coast Salish Elders, Knowledge Keepers, and weavers about shared traditional knowledge and memories surrounding woolly dogs, their importance within Coast Salish societies, and how colonial policies led directly to their disappearance.
Collapse
Affiliation(s)
- Audrey T Lin
- Department of Anthropology, National Museum of Natural History, Smithsonian Institution, Washington, DC, USA
- Richard Gilder Graduate School, American Museum of Natural History, New York, NY, USA
| | - Liz Hammond-Kaarremaa
- Department of Anthropology, National Museum of Natural History, Smithsonian Institution, Washington, DC, USA
- Vancouver Island University, Nanaimo, BC, Canada
| | - Hsiao-Lei Liu
- Department of Anthropology, National Museum of Natural History, Smithsonian Institution, Washington, DC, USA
| | - Chris Stantis
- Department of Anthropology, National Museum of Natural History, Smithsonian Institution, Washington, DC, USA
- Department of Geology and Geophysics, University of Utah, Salt Lake City, UT, USA
| | - Iain McKechnie
- Department of Anthropology, University of Victoria, Victoria, BC, Canada
| | - Michael Pavel
- Twana/Skokomish Indian Tribe, Skokomish Nation, WA, USA
| | - Susan sa'hLa mitSa Pavel
- Twana/Skokomish Indian Tribe, Skokomish Nation, WA, USA
- Coast Salish Wool Weaving Center, Skokomish Nation, WA, USA
- The Evergreen State College, Olympia, WA, USA
| | | | | | | | - Sabhrina Gita Aninta
- School of Biological and Behavioural Sciences, Queen Mary University of London, London, UK
| | - Angela Perri
- Department of Anthropology, Texas A&M University, College Station, TX, USA
- Chronicle Heritage, Phoenix, AZ, USA
| | - Jonathan Hartt
- Department of Indigenous Studies, Simon Fraser University, Burnaby, BC, Canada
| | - Anders Bergström
- Ancient Genomics Laboratory, The Francis Crick Institute, London, UK
- School of Biological Sciences, University of East Anglia, Norwich, UK
| | - Alberto Carmagnini
- Palaeogenomics Group, Institute of Palaeoanatomy, Domestication Research and the History of Veterinary Medicine, Ludwig-Maximilians-Universität, Munich, Germany
| | - Sophy Charlton
- PalaeoBARN, School of Archaeology, University of Oxford, Oxford, UK
- BioArCh, Department of Archaeology, University of York, York, UK
| | - Love Dalén
- Centre for Palaeogenetics, Stockholm, Sweden
- Department of Zoology, Stockholm University, Stockholm, Sweden
- Department of Bioinformatics and Genetics, Swedish Museum of Natural History, Stockholm, Sweden
| | - Tatiana R Feuerborn
- Center for Evolutionary Hologenomics, The Globe Institute, University of Copenhagen, Copenhagen, Denmark
- National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | | | - Shyam Gopalakrishnan
- Center for Evolutionary Hologenomics, The Globe Institute, University of Copenhagen, Copenhagen, Denmark
| | - Vaughan Grimes
- Department of Archaeology, Memorial University of Newfoundland, St. Johns, NL, Canada
| | - Alex Harris
- National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - Gwénaëlle Kavich
- Museum Conservation Institute, Smithsonian Institution, Suitland, MD, USA
| | - Benjamin N Sacks
- Mammalian Ecology and Conservation Unit, Veterinary Genetics Laboratory, School of Veterinary Medicine, University of California, Davis, Davis, CA, USA
- Department of Population Health and Reproduction, School of Veterinary Medicine, University of California, Davis, Davis, CA, USA
| | | | - Pontus Skoglund
- Ancient Genomics Laboratory, The Francis Crick Institute, London, UK
| | - David W G Stanton
- Palaeogenomics Group, Institute of Palaeoanatomy, Domestication Research and the History of Veterinary Medicine, Ludwig-Maximilians-Universität, Munich, Germany
- Cardiff School of Biosciences, Cardiff University, Cardiff, UK
| | - Elaine A Ostrander
- National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - Greger Larson
- PalaeoBARN, School of Archaeology, University of Oxford, Oxford, UK
| | - Chelsey G Armstrong
- Department of Indigenous Studies, Simon Fraser University, Burnaby, BC, Canada
| | - Laurent A F Frantz
- School of Biological and Behavioural Sciences, Queen Mary University of London, London, UK
- Palaeogenomics Group, Institute of Palaeoanatomy, Domestication Research and the History of Veterinary Medicine, Ludwig-Maximilians-Universität, Munich, Germany
| | - Melissa T R Hawkins
- Department of Vertebrate Zoology, National Museum of Natural History, Smithsonian Institution, Washington, DC, USA
| | - Logan Kistler
- Department of Anthropology, National Museum of Natural History, Smithsonian Institution, Washington, DC, USA
| |
Collapse
|
24
|
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 IRM, Ryan H, Sheridan A, Sinding MHS, 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, Frantz L. Limited historical admixture between European wildcats and domestic cats. Curr Biol 2023; 33:4751-4760.e14. [PMID: 37935117 DOI: 10.1016/j.cub.2023.08.031] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2023] [Revised: 06/07/2023] [Accepted: 08/09/2023] [Indexed: 11/09/2023]
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.
Collapse
Affiliation(s)
- Alexandra Jamieson
- The Palaeogenomics & Bio-Archaeology Research Network, Research Laboratory for Archaeology and History of Art, The University of Oxford, OX1 3TG Oxford, UK; Palaeogenomics Group, Institute of Palaeoanatomy, Domestication Research and the History of Veterinary Medicine, Ludwig-Maximilians-Universität, 80539 Munich, Germany
| | - Alberto Carmagnini
- Palaeogenomics Group, Institute of Palaeoanatomy, Domestication Research and the History of Veterinary Medicine, Ludwig-Maximilians-Universität, 80539 Munich, Germany; School of Biological and Chemical Sciences, Queen Mary University of London, E1 4NS London, UK
| | - Jo Howard-McCombe
- School of Biological Sciences, University of Bristol, BS8 1TQ Bristol, UK; RZSS WildGenes Laboratory, Royal Zoological Society of Scotland, EH12 6TS Edinburgh, UK
| | - Sean Doherty
- Department of Archaeology, University of Exeter, EX4 4QE Exeter, UK
| | - Alexandra Hirons
- The Palaeogenomics & Bio-Archaeology Research Network, Research Laboratory for Archaeology and History of Art, The University of Oxford, OX1 3TG Oxford, UK
| | - Evangelos Dimopoulos
- The Palaeogenomics & Bio-Archaeology Research Network, Research Laboratory for Archaeology and History of Art, The University of Oxford, OX1 3TG Oxford, UK; Department of Veterinary Medicine, University of Cambridge, CB3 0ES Cambridge, UK
| | - Audrey T Lin
- Department of Anthropology, National Museum of Natural History, Smithsonian Institution, Washington, DC 20560, USA
| | - Richard Allen
- The Palaeogenomics & Bio-Archaeology Research Network, Research Laboratory for Archaeology and History of Art, The University of Oxford, OX1 3TG Oxford, UK
| | - Hugo Anderson-Whymark
- Department of Scottish History and Archaeology, National Museums Scotland, EH1 1JF Edinburgh, UK
| | - Ross Barnett
- Center for Evolutionary Hologenomics, The GLOBE Institute, University of Copenhagen, 2100 Copenhagen, Denmark
| | - Colleen Batey
- Institute for Northern Studies, University of the Highlands and Islands, KW15 1FL Kirkwall, UK; Department of Archaeology, University of Durham, DH1 3LE Durham, UK
| | - Fiona Beglane
- CERIS, School of Science, Atlantic Technological University, F91 YW50 Sligo, Ireland
| | - Will Bowden
- Department of Classics and Archaeology, University of Nottingham, NG7 2RD Nottingham, UK
| | - John Bratten
- Department of Anthropology, University of West Florida, Pensacola, FL 32514, USA
| | - Bea De Cupere
- Royal Belgian Institute of Natural Sciences, 1000 Brussels, Belgium
| | - Ellie Drew
- York Archaeological Trust, YO1 7BX York, UK
| | - Nicole M Foley
- Veterinary Integrative Biosciences, Texas A&M University, College Station, TX 77843, USA
| | - Tom Fowler
- Department of Classics and Archaeology, University of Nottingham, NG7 2RD Nottingham, UK
| | - Allison Fox
- Manx National Heritage, Manx Museum, IM1 3LY Douglas, Isle of Man
| | - Eva-Maria Geigl
- Université Paris-Cité, CNRS, Institut Jacques Monod, 75013 Paris, France
| | | | - Thierry Grange
- Université Paris-Cité, CNRS, Institut Jacques Monod, 75013 Paris, France
| | - David Griffiths
- Department for Continuing Education, University of Oxford, OX1 2JA Oxford, UK
| | - Daniel Groß
- Museum Lolland-Falster, 4800 Nykøbing Falster, Denmark
| | - Ashleigh Haruda
- The Palaeogenomics & Bio-Archaeology Research Network, Research Laboratory for Archaeology and History of Art, The University of Oxford, OX1 3TG Oxford, UK
| | | | - Zoe Knapp
- Department of Archaeology, University of Reading, RG6 6AB Reading, UK
| | - Ophélie Lebrasseur
- Centre for Anthropobiology and Genomics of Toulouse, CNRS UMR 5288, Universite de Toulouse, Universite Paul Sabatier, 31000 Toulouse, France; The Palaeogenomics & Bio-Archaeology Research Network, Research Laboratory for Archaeology and History of Art, The University of Oxford, OX1 3TG Oxford, UK
| | - Pablo Librado
- Centre for Anthropobiology and Genomics of Toulouse, CNRS UMR 5288, Universite de Toulouse, Universite Paul Sabatier, 31000 Toulouse, France
| | - Leslie A Lyons
- Department of Veterinary Medicine & Surgery, College of Veterinary Medicine, University of Missouri, Columbia, MO 65211, USA
| | - Ingrid Mainland
- UHI Archaeology Institute, University of the Highlands and Islands, Orkney, Scotland
| | | | - Violeta Muñoz-Fuentes
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, CB10 1SD Cambridge, UK
| | - Carsten Nowak
- Centre for Wildlife Genetics & LOEWE Centre for Translational Biodiversity Genomics (TBG), Senckenberg Research Institute, 60325 Frankfurt, Germany
| | - Terry O'Connor
- BioArCh, Department of Archaeology, University of York, YO10 5DD York, UK
| | - Joris Peters
- SNSB, State Collection of Palaeoanatomy Munich, 85586 Poing, Germany; Institute of Palaeoanatomy, Domestication Research and the History of Veterinary Medicine, Ludwig-Maximilians-Universität, 80539 Munich, Germany
| | | | - Hannah Ryan
- The Palaeogenomics & Bio-Archaeology Research Network, Research Laboratory for Archaeology and History of Art, The University of Oxford, OX1 3TG Oxford, UK
| | - Alison Sheridan
- Department of Scottish History and Archaeology, National Museums Scotland, EH1 1JF Edinburgh, UK
| | | | | | - Pooja Swali
- The Francis Crick Institute, NW1 1AT London, UK
| | | | - Gabor Thomas
- Department of Archaeology, University of Reading, RG6 6AB Reading, UK
| | - Theis Zetner Trolle Jensen
- Section for Molecular Ecology and Evolution, GLOBE Institute, University of Copenhagen, 2100 Copenhagen, Denmark
| | - Andrew C Kitchener
- Department of Natural Sciences, National Museums Scotland, EH1 1JF Edinburgh, UK; School of Geosciences, University of Edinburgh, EH8 9XP Edinburgh, UK
| | - Helen Senn
- RZSS WildGenes Laboratory, Royal Zoological Society of Scotland, EH12 6TS Edinburgh, UK
| | - Daniel Lawson
- School of Mathematics, University of Bristol, BS8 1UG Bristol, UK
| | | | - William J Murphy
- Veterinary Integrative Biosciences, Texas A&M University, College Station, TX 77843, USA
| | - Mark Beaumont
- School of Biological Sciences, University of Bristol, BS8 1TQ Bristol, UK
| | - Claudio Ottoni
- Centre of Molecular Anthropology for Ancient DNA Studies, Department of Biology, University of Rome Tor Vergata, 00133 Roma, Italy
| | - Naomi Sykes
- Department of Archaeology, University of Exeter, EX4 4QE Exeter, UK
| | - Greger Larson
- The Palaeogenomics & Bio-Archaeology Research Network, Research Laboratory for Archaeology and History of Art, The University of Oxford, OX1 3TG Oxford, UK.
| | - Laurent Frantz
- Palaeogenomics Group, Institute of Palaeoanatomy, Domestication Research and the History of Veterinary Medicine, Ludwig-Maximilians-Universität, 80539 Munich, Germany; School of Biological and Chemical Sciences, Queen Mary University of London, E1 4NS London, UK.
| |
Collapse
|
25
|
Granado J, Susat J, Gerling C, Schernig-Mráz M, Schlumbaum A, Deschler-Erb S, Krause-Kyora B. A melting pot of Roman dogs north of the Alps with high phenotypic and genetic diversity and similar diets. Sci Rep 2023; 13:17389. [PMID: 37833364 PMCID: PMC10575936 DOI: 10.1038/s41598-023-44060-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2023] [Accepted: 10/03/2023] [Indexed: 10/15/2023] Open
Abstract
Several dog skeletons were excavated at the Roman town of Augusta Raurica and at the military camp of Vindonissa, located in the northern Alpine region of Switzerland (Germania Superior). The relationships between them and the people, the nature of their lives, and the circumstances of their deaths are unclear. In order to gain insight into this dog population, we collected 31 dogs deposited almost simultaneously in two wells (second half of the third century CE), three dogs from burial contexts (70-200 CE and third to fifth century CE) at Augusta Raurica, and two dogs from burial contexts at Vindonissa (ca. first century CE). We detected a mixed population of young and adult dogs including small, medium and large sized individuals. Three small dogs had conspicuous phenotypes: abnormally short legs, and one with a brachycephalic skull. Stable isotope analysis of a subset of the dogs showed that their diets were omnivorous with a substantial input of animal proteins and little variation, except one with a particularly low δ15N value, indicating a diet low in animal proteins. Partial mitochondrial DNA sequences from 25 dogs revealed eight haplotypes within canine haplogroup A (11 dogs; 44%; 5 haplotypes), C (8 dogs; 32%; 1 haplotype), D (4 dogs, 16%; 1 haplotype) and B (2 dogs, 8%; 1 haplotype). Based on shotgun sequencing, four Roman mitogenomes were assembled, representing sub-haplogroups A1b3, A1b2 and C2. No canine pathogens were identified, weakening the assumption of infectious disease as a cause for dog disposal. The genetic and morphological diversity observed in dogs of Augusta Raurica and Vindonissa is similar to modern dog diversity.
Collapse
Affiliation(s)
- José Granado
- Department Environmental Science, Integrative Prehistory and Archaeological Science (IPAS), University of Basel, Spalenring 145, 4055, Basel, Switzerland
| | - Julian Susat
- Institute of Clinical Molecular Biology (IKMB), Christian-Albrechts-University Kiel, Rosalind-Franklin-Strasse 12, 24105, Kiel, Germany
| | - Claudia Gerling
- Department Environmental Science, Integrative Prehistory and Archaeological Science (IPAS), University of Basel, Spalenring 145, 4055, Basel, Switzerland
| | - Monika Schernig-Mráz
- Department Environmental Science, Integrative Prehistory and Archaeological Science (IPAS), University of Basel, Spalenring 145, 4055, Basel, Switzerland
| | - Angela Schlumbaum
- Department Environmental Science, Integrative Prehistory and Archaeological Science (IPAS), University of Basel, Spalenring 145, 4055, Basel, Switzerland
| | - Sabine Deschler-Erb
- Department Environmental Science, Integrative Prehistory and Archaeological Science (IPAS), University of Basel, Spalenring 145, 4055, Basel, Switzerland.
| | - Ben Krause-Kyora
- Institute of Clinical Molecular Biology (IKMB), Christian-Albrechts-University Kiel, Rosalind-Franklin-Strasse 12, 24105, Kiel, Germany
| |
Collapse
|
26
|
Peng MS, Liu YH, Shen QK, Zhang XH, Dong J, Li JX, Zhao H, Zhang H, Zhang X, He Y, Shi H, Cui C, Ouzhuluobu, Wu TY, Liu SM, Gonggalanzi, Baimakangzhuo, Bai C, Duojizhuoma, Liu T, Dai SS, Murphy RW, Qi XB, Dong G, Su B, Zhang YP. Genetic and cultural adaptations underlie the establishment of dairy pastoralism in the Tibetan Plateau. BMC Biol 2023; 21:208. [PMID: 37798721 PMCID: PMC10557253 DOI: 10.1186/s12915-023-01707-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2023] [Accepted: 09/20/2023] [Indexed: 10/07/2023] Open
Abstract
BACKGROUND Domestication and introduction of dairy animals facilitated the permanent human occupation of the Tibetan Plateau. Yet the history of dairy pastoralism in the Tibetan Plateau remains poorly understood. Little is known how Tibetans adapted to milk and dairy products. RESULTS We integrated archeological evidence and genetic analysis to show the picture that the dairy ruminants, together with dogs, were introduced from West Eurasia into the Tibetan Plateau since ~ 3600 years ago. The genetic admixture between the exotic and indigenous dogs enriched the candidate lactase persistence (LP) allele 10974A > G of West Eurasian origin in Tibetan dogs. In vitro experiments demonstrate that - 13838G > A functions as a LP allele in Tibetans. Unlike multiple LP alleles presenting selective signatures in West Eurasians and South Asians, the de novo origin of Tibetan-specific LP allele - 13838G > A with low frequency (~ 6-7%) and absence of selection corresponds - 13910C > T in pastoralists across eastern Eurasia steppe. CONCLUSIONS Results depict a novel scenario of genetic and cultural adaptations to diet and expand current understanding of the establishment of dairy pastoralism in the Tibetan Plateau.
Collapse
Affiliation(s)
- Min-Sheng Peng
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, China
- Yunnan Key Laboratory of Molecular Biology of Domestic Animals, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, China
- KIZ-CUHK Joint Laboratory of Bioresources and Molecular Research in Common Diseases, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yan-Hu Liu
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, China
- Yunnan Key Laboratory of Molecular Biology of Domestic Animals, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, China
- KIZ-CUHK Joint Laboratory of Bioresources and Molecular Research in Common Diseases, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Quan-Kuan Shen
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, China
- Yunnan Key Laboratory of Molecular Biology of Domestic Animals, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, China
- KIZ-CUHK Joint Laboratory of Bioresources and Molecular Research in Common Diseases, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Xiao-Hua Zhang
- State Key Laboratory for Conservation and Utilization of Bio-Resources, Yunnan University, Kunming, 650091, China
- Institute of Medical Biology, Chinese Academy of Medical Science, Peking Union Medical College, Kunming, 650118, China
| | - Jiajia Dong
- Key Laboratory of Western China's Environmental Systems (Ministry of Education), College of Earth and Environmental Sciences, Lanzhou University, Lanzhou, 730000, China
| | - Jin-Xiu Li
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, China
- Yunnan Key Laboratory of Molecular Biology of Domestic Animals, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, China
| | - Hui Zhao
- State Key Laboratory for Conservation and Utilization of Bio-Resources, Yunnan University, Kunming, 650091, China
| | - Hui Zhang
- State Key Laboratory of Primate Biomedical Research (LPBR), School of Primate Translational Medicine, Kunming University of Science and Technology (KUST), Kunming, 650000, China
| | - Xiaoming Zhang
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yaoxi He
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Hong Shi
- State Key Laboratory of Primate Biomedical Research (LPBR), School of Primate Translational Medicine, Kunming University of Science and Technology (KUST), Kunming, 650000, China
| | - Chaoying Cui
- High Altitude Medical Research Center, School of Medicine, Tibetan University, Lhasa, 850000, China
| | - Ouzhuluobu
- High Altitude Medical Research Center, School of Medicine, Tibetan University, Lhasa, 850000, China
| | - Tian-Yi Wu
- National Key Laboratory of High Altitude Medicine, High Altitude Medical Research Institute, Xining, 810000, China
| | - Shi-Ming Liu
- National Key Laboratory of High Altitude Medicine, High Altitude Medical Research Institute, Xining, 810000, China
| | - Gonggalanzi
- High Altitude Medical Research Center, School of Medicine, Tibetan University, Lhasa, 850000, China
| | - Baimakangzhuo
- High Altitude Medical Research Center, School of Medicine, Tibetan University, Lhasa, 850000, China
| | - Caijuan Bai
- The First People's Hospital of Gansu Province, Lanzhou, 730000, China
| | - Duojizhuoma
- High Altitude Medical Research Center, School of Medicine, Tibetan University, Lhasa, 850000, China
| | - Ti Liu
- State Key Laboratory for Conservation and Utilization of Bio-Resources, Yunnan University, Kunming, 650091, China
| | - Shan-Shan Dai
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, China
- Yunnan Key Laboratory of Molecular Biology of Domestic Animals, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, China
- KIZ-CUHK Joint Laboratory of Bioresources and Molecular Research in Common Diseases, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Robert W Murphy
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, China
- Centre for Biodiversity and Conservation Biology, Royal Ontario Museum, Toronto, ON, M5S 2C6, Canada
| | - Xue-Bin Qi
- State Key Laboratory of Primate Biomedical Research (LPBR), School of Primate Translational Medicine, Kunming University of Science and Technology (KUST), Kunming, 650000, China.
- Tibetan Fukang Hospital, Lhasa, 850000, China.
| | - Guanghui Dong
- Key Laboratory of Western China's Environmental Systems (Ministry of Education), College of Earth and Environmental Sciences, Lanzhou University, Lanzhou, 730000, China.
| | - Bing Su
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, China.
- University of Chinese Academy of Sciences, Beijing, 100049, China.
| | - Ya-Ping Zhang
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, China.
- Yunnan Key Laboratory of Molecular Biology of Domestic Animals, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, China.
- KIZ-CUHK Joint Laboratory of Bioresources and Molecular Research in Common Diseases, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, China.
- University of Chinese Academy of Sciences, Beijing, 100049, China.
- State Key Laboratory for Conservation and Utilization of Bio-Resources, Yunnan University, Kunming, 650091, China.
| |
Collapse
|
27
|
Flegontov P, Işıldak U, Maier R, Yüncü E, Changmai P, Reich D. Modeling of African population history using f-statistics is biased when applying all previously proposed SNP ascertainment schemes. PLoS Genet 2023; 19:e1010931. [PMID: 37676865 PMCID: PMC10508636 DOI: 10.1371/journal.pgen.1010931] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2023] [Revised: 09/19/2023] [Accepted: 08/21/2023] [Indexed: 09/09/2023] Open
Abstract
f-statistics have emerged as a first line of analysis for making inferences about demographic history from genome-wide data. Not only are they guaranteed to allow robust tests of the fits of proposed models of population history to data when analyzing full genome sequencing data-that is, all single nucleotide polymorphisms (SNPs) in the individuals being analyzed-but they are also guaranteed to allow robust tests of models for SNPs ascertained as polymorphic in a population that is an outgroup in a phylogenetic sense to all groups being analyzed. True "outgroup ascertainment" is in practice impossible in humans because our species has arisen from a substructured ancestral population that does not descend from a homogeneous ancestral population going back many hundreds of thousands of years into the past. However, initial studies suggested that non-outgroup-ascertainment schemes might produce robust enough results using f-statistics, and that motivated widespread fitting of models to data using non-outgroup-ascertained SNP panels such as the "Affymetrix Human Origins array" which has been genotyped on thousands of modern individuals from hundreds of populations, or the "1240k" in-solution enrichment reagent which has been the source of about 70% of published genome-wide data for ancient humans. In this study, we show that while analyses of population history using such panels work well for studies of relationships among non-African populations and one African outgroup, when co-modeling more than one sub-Saharan African and/or archaic human groups (Neanderthals and Denisovans), fitting of f-statistics to such SNP sets is expected to frequently lead to false rejection of true demographic histories, and failure to reject incorrect models. Analyzing panels of SNPs polymorphic in archaic humans, which has been suggested as a solution for the ascertainment problem, has limited statistical power and retains important biases. However, by carrying out simulations of diverse demographic histories, we show that bias in inferences based on f-statistics can be minimized by ascertaining on variants common in a union of diverse African groups; such ascertainment retains high statistical power while allowing co-analysis of archaic and modern groups.
Collapse
Affiliation(s)
- Pavel Flegontov
- Department of Human Evolutionary Biology, Harvard University, Cambridge, Massachusetts, United States of America
- Department of Biology and Ecology, Faculty of Science, University of Ostrava, Ostrava, Czechia
- Kalmyk Research Center of the Russian Academy of Sciences, Elista, Russia
| | - Ulaş Işıldak
- Department of Biology and Ecology, Faculty of Science, University of Ostrava, Ostrava, Czechia
| | - Robert Maier
- Department of Human Evolutionary Biology, Harvard University, Cambridge, Massachusetts, United States of America
| | - Eren Yüncü
- Department of Biology and Ecology, Faculty of Science, University of Ostrava, Ostrava, Czechia
| | - Piya Changmai
- Department of Biology and Ecology, Faculty of Science, University of Ostrava, Ostrava, Czechia
| | - David Reich
- Department of Human Evolutionary Biology, Harvard University, Cambridge, Massachusetts, United States of America
- Department of Genetics, Harvard Medical School, Boston, Massachusetts, United States of America
- Howard Hughes Medical Institute, Harvard Medical School, Boston, Massachusetts, United States of America
- Broad Institute of Harvard and MIT, Cambridge, Massachusetts, United States of America
| |
Collapse
|
28
|
Ciucani MM, Ramos-Madrigal J, Hernández-Alonso G, Carmagnini A, Aninta SG, Sun X, Scharff-Olsen CH, Lanigan LT, Fracasso I, Clausen CG, Aspi J, Kojola I, Baltrūnaitė L, Balčiauskas L, Moore J, Åkesson M, Saarma U, Hindrikson M, Hulva P, Bolfíková BČ, Nowak C, Godinho R, Smith S, Paule L, Nowak S, Mysłajek RW, Lo Brutto S, Ciucci P, Boitani L, Vernesi C, Stenøien HK, Smith O, Frantz L, Rossi L, Angelici FM, Cilli E, Sinding MHS, Gilbert MTP, Gopalakrishnan S. The extinct Sicilian wolf shows a complex history of isolation and admixture with ancient dogs. iScience 2023; 26:107307. [PMID: 37559898 PMCID: PMC10407145 DOI: 10.1016/j.isci.2023.107307] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2022] [Revised: 11/04/2022] [Accepted: 07/04/2023] [Indexed: 08/11/2023] Open
Abstract
The Sicilian wolf remained isolated in Sicily from the end of the Pleistocene until its extermination in the 1930s-1960s. Given its long-term isolation on the island and distinctive morphology, the genetic origin of the Sicilian wolf remains debated. We sequenced four nuclear genomes and five mitogenomes from the seven existing museum specimens to investigate the Sicilian wolf ancestry, relationships with extant and extinct wolves and dogs, and diversity. Our results show that the Sicilian wolf is most closely related to the Italian wolf but carries ancestry from a lineage related to European Eneolithic and Bronze Age dogs. The average nucleotide diversity of the Sicilian wolf was half of the Italian wolf, with 37-50% of its genome contained in runs of homozygosity. Overall, we show that, by the time it went extinct, the Sicilian wolf had high inbreeding and low-genetic diversity, consistent with a population in an insular environment.
Collapse
Affiliation(s)
- Marta Maria Ciucani
- Section for Evolutionary Genomics, the Globe Institute, University of Copenhagen, Copenhagen, Denmark
| | - Jazmín Ramos-Madrigal
- Section for Evolutionary Genomics, the Globe Institute, University of Copenhagen, Copenhagen, Denmark
- Center for Evolutionary Hologenomics, the Globe Institute, University of Copenhagen, Copenhagen, Denmark
| | - Germán Hernández-Alonso
- Section for Evolutionary Genomics, the Globe Institute, University of Copenhagen, Copenhagen, Denmark
- Center for Evolutionary Hologenomics, the Globe Institute, University of Copenhagen, Copenhagen, Denmark
| | - Alberto Carmagnini
- Palaeogenomics Group, Department of Veterinary Sciences, Ludwig Maximilian University, Munich, Germany
- School of Biological and Behavioural Sciences, Queen Mary University of London, London, UK
| | - Sabhrina Gita Aninta
- Palaeogenomics Group, Department of Veterinary Sciences, Ludwig Maximilian University, Munich, Germany
- School of Biological and Behavioural Sciences, Queen Mary University of London, London, UK
| | - Xin Sun
- Center for Evolutionary Hologenomics, the Globe Institute, University of Copenhagen, Copenhagen, Denmark
| | | | - Liam Thomas Lanigan
- Section for Evolutionary Genomics, the Globe Institute, University of Copenhagen, Copenhagen, Denmark
| | - Ilaria Fracasso
- Forest Ecology Unit, Research and Innovation Centre, Fondazione Edmund Mach, San Michele all'Adige (TN), Italy
| | - Cecilie G. Clausen
- Section for Evolutionary Genomics, the Globe Institute, University of Copenhagen, Copenhagen, Denmark
- Center for Evolutionary Hologenomics, the Globe Institute, University of Copenhagen, Copenhagen, Denmark
| | - Jouni Aspi
- Ecology and Genetics Research Unit, University of Oulu, Finland
| | - Ilpo Kojola
- Natural Resources Institute Finland, Rovaniemi, Finland
| | | | | | - Jane Moore
- Società Amatori Cirneco dell’Etna, Modica (RG), Italy
| | - Mikael Åkesson
- Swedish University of Agricultural Sciences, Grimsö Wildlife Research Station, Department of Ecology, Riddarhyttan, Sweden
| | - Urmas Saarma
- Department of Zoology, Institute of Ecology and Earth Sciences, University of Tartu, Tartu, Estonia
| | - Maris Hindrikson
- Department of Zoology, Institute of Ecology and Earth Sciences, University of Tartu, Tartu, Estonia
| | - Pavel Hulva
- Charles University, Department of Zoology, Faculty of Science, Prague 2, Czech Republic
| | | | - Carsten Nowak
- Center for Wildlife Genetics, Senckenberg Research Institute and Natural History Museum Frankfurt, Gelnhausen, Germany
| | - Raquel Godinho
- CIBIO/InBIO, University of Porto, Vairão, Portugal
- BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Vairão, Portugal
| | - Steve Smith
- Konrad Lorenz Institute of Ethology, University of Veterinary Medicine, Vienna, Austria
| | - Ladislav Paule
- Faculty of Forestry, Technical University, Zvolen, Slovakia
| | - Sabina Nowak
- Department of Ecology, Institute of Functional Biology and Ecology, Faculty of Biology, University of Warsaw, Biological and Chemical Research Centre, Warszawa, Poland
| | - Robert W. Mysłajek
- Department of Ecology, Institute of Functional Biology and Ecology, Faculty of Biology, University of Warsaw, Biological and Chemical Research Centre, Warszawa, Poland
| | - Sabrina Lo Brutto
- Department of Biological, Chemical, and Pharmaceutical Sciences and Technology (STEBICEF), University of Palermo, Palermo, Italy
- Museum of Zoology "P. Doderlein", SIMUA, University of Palermo, Palermo, Italy
| | - Paolo Ciucci
- Università di Roma La Sapienza, Department Biology and Biotechnologies "Charles Darwin", Roma, Italy
| | - Luigi Boitani
- Università di Roma La Sapienza, Department Biology and Biotechnologies "Charles Darwin", Roma, Italy
| | - Cristiano Vernesi
- Forest Ecology Unit, Research and Innovation Centre, Fondazione Edmund Mach, San Michele all'Adige (TN), Italy
| | - Hans K. Stenøien
- NTNU University Museum, Norwegian University of Science and Technology, Trondheim, Norway
| | - Oliver Smith
- Section for Evolutionary Genomics, the Globe Institute, University of Copenhagen, Copenhagen, Denmark
| | - Laurent Frantz
- Palaeogenomics Group, Department of Veterinary Sciences, Ludwig Maximilian University, Munich, Germany
- School of Biological and Behavioural Sciences, Queen Mary University of London, London, UK
| | | | - Francesco Maria Angelici
- FIZV, Via Marco Aurelio 2, Roma, Italy
- National Center for Wildlife, Al Imam Faisal Ibn Turki Ibn Abdullah, Ulaishah, Saudi Arabia
| | - Elisabetta Cilli
- Laboratory of Ancient DNA, Department of Cultural Heritage (DBC), University of Bologna, Bologna, Italy
| | - Mikkel-Holger S. Sinding
- Section for Evolutionary Genomics, the Globe Institute, University of Copenhagen, Copenhagen, Denmark
- Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - M. Thomas P. Gilbert
- Section for Evolutionary Genomics, the Globe Institute, University of Copenhagen, Copenhagen, Denmark
- Center for Evolutionary Hologenomics, the Globe Institute, University of Copenhagen, Copenhagen, Denmark
- University Museum, Norwegian University of Science and Technology, Trondheim, Norway
| | - Shyam Gopalakrishnan
- Section for Evolutionary Genomics, the Globe Institute, University of Copenhagen, Copenhagen, Denmark
- Center for Evolutionary Hologenomics, the Globe Institute, University of Copenhagen, Copenhagen, Denmark
| |
Collapse
|
29
|
Meadows JRS, Kidd JM, Wang GD, Parker HG, Schall PZ, Bianchi M, Christmas MJ, Bougiouri K, Buckley RM, Hitte C, Nguyen AK, Wang C, Jagannathan V, Niskanen JE, Frantz LAF, Arumilli M, Hundi S, Lindblad-Toh K, Ginja C, Agustina KK, André C, Boyko AR, Davis BW, Drögemüller M, Feng XY, Gkagkavouzis K, Iliopoulos G, Harris AC, Hytönen MK, Kalthoff DC, Liu YH, Lymberakis P, Poulakakis N, Pires AE, Racimo F, Ramos-Almodovar F, Savolainen P, Venetsani S, Tammen I, Triantafyllidis A, vonHoldt B, Wayne RK, Larson G, Nicholas FW, Lohi H, Leeb T, Zhang YP, Ostrander EA. Genome sequencing of 2000 canids by the Dog10K consortium advances the understanding of demography, genome function and architecture. Genome Biol 2023; 24:187. [PMID: 37582787 PMCID: PMC10426128 DOI: 10.1186/s13059-023-03023-7] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2022] [Accepted: 07/25/2023] [Indexed: 08/17/2023] Open
Abstract
BACKGROUND The international Dog10K project aims to sequence and analyze several thousand canine genomes. Incorporating 20 × data from 1987 individuals, including 1611 dogs (321 breeds), 309 village dogs, 63 wolves, and four coyotes, we identify genomic variation across the canid family, setting the stage for detailed studies of domestication, behavior, morphology, disease susceptibility, and genome architecture and function. RESULTS We report the analysis of > 48 M single-nucleotide, indel, and structural variants spanning the autosomes, X chromosome, and mitochondria. We discover more than 75% of variation for 239 sampled breeds. Allele sharing analysis indicates that 94.9% of breeds form monophyletic clusters and 25 major clades. German Shepherd Dogs and related breeds show the highest allele sharing with independent breeds from multiple clades. On average, each breed dog differs from the UU_Cfam_GSD_1.0 reference at 26,960 deletions and 14,034 insertions greater than 50 bp, with wolves having 14% more variants. Discovered variants include retrogene insertions from 926 parent genes. To aid functional prioritization, single-nucleotide variants were annotated with SnpEff and Zoonomia phyloP constraint scores. Constrained positions were negatively correlated with allele frequency. Finally, the utility of the Dog10K data as an imputation reference panel is assessed, generating high-confidence calls across varied genotyping platform densities including for breeds not included in the Dog10K collection. CONCLUSIONS We have developed a dense dataset of 1987 sequenced canids that reveals patterns of allele sharing, identifies likely functional variants, informs breed structure, and enables accurate imputation. Dog10K data are publicly available.
Collapse
Affiliation(s)
- Jennifer R S Meadows
- Science for Life Laboratory, Department of Medical Biochemistry and Microbiology, Uppsala University, 75132, Uppsala, Sweden.
| | - Jeffrey M Kidd
- Department of Human Genetics, University of Michigan, Ann Arbor, MI, 48107, USA.
| | - Guo-Dong Wang
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, China
| | - Heidi G Parker
- National Human Genome Research Institute, National Institutes of Health, 50 South Drive, Building 50 Room 5351, Bethesda, MD, 20892, USA
| | - Peter Z Schall
- Department of Human Genetics, University of Michigan, Ann Arbor, MI, 48107, USA
| | - Matteo Bianchi
- Science for Life Laboratory, Department of Medical Biochemistry and Microbiology, Uppsala University, 75132, Uppsala, Sweden
| | - Matthew J Christmas
- Science for Life Laboratory, Department of Medical Biochemistry and Microbiology, Uppsala University, 75132, Uppsala, Sweden
| | - Katia Bougiouri
- Section for Molecular Ecology and Evolution, Globe Institute, University of Copenhagen, Øster Voldgade 5-7, 1350, Copenhagen, Denmark
| | - Reuben M Buckley
- National Human Genome Research Institute, National Institutes of Health, 50 South Drive, Building 50 Room 5351, Bethesda, MD, 20892, USA
| | - Christophe Hitte
- University of Rennes, CNRS, Institute Genetics and Development Rennes - UMR6290, 35000, Rennes, France
| | - Anthony K Nguyen
- Department of Human Genetics, University of Michigan, Ann Arbor, MI, 48107, USA
| | - Chao Wang
- Science for Life Laboratory, Department of Medical Biochemistry and Microbiology, Uppsala University, 75132, Uppsala, Sweden
| | - Vidhya Jagannathan
- Institute of Genetics, Vetsuisse Faculty, University of Bern, 3001, Bern, Switzerland
| | - Julia E Niskanen
- Department of Medical and Clinical Genetics, Department of Veterinary Biosciences, University of Helsinki and Folkhälsan Research Center, 02900, Helsinki, Finland
| | - Laurent A F Frantz
- School of Biological and Behavioural Sciences, Queen Mary University of London, London E14NS, UK and Palaeogenomics Group, Department of Veterinary Sciences, Ludwig Maximilian University, D-80539, Munich, Germany
| | - Meharji Arumilli
- Department of Medical and Clinical Genetics, Department of Veterinary Biosciences, University of Helsinki and Folkhälsan Research Center, 02900, Helsinki, Finland
| | - Sruthi Hundi
- Department of Medical and Clinical Genetics, Department of Veterinary Biosciences, University of Helsinki and Folkhälsan Research Center, 02900, Helsinki, Finland
| | - Kerstin Lindblad-Toh
- Science for Life Laboratory, Department of Medical Biochemistry and Microbiology, Uppsala University, 75132, Uppsala, Sweden
- Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
| | - Catarina Ginja
- BIOPOLIS-CIBIO-InBIO-Centro de Investigação Em Biodiversidade E Recursos Genéticos - ArchGen Group, Universidade Do Porto, 4485-661, Vairão, Portugal
| | | | - Catherine André
- University of Rennes, CNRS, Institute Genetics and Development Rennes - UMR6290, 35000, Rennes, France
| | - Adam R Boyko
- Department of Biomedical Sciences, Cornell University, 930 Campus Road, Ithaca, NY, 14853, USA
| | - Brian W Davis
- Department of Veterinary Integrative Biosciences, School of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, TX, 77843, USA
| | - Michaela Drögemüller
- Institute of Genetics, Vetsuisse Faculty, University of Bern, 3001, Bern, Switzerland
| | - Xin-Yao Feng
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, China
| | - Konstantinos Gkagkavouzis
- Department of Genetics, School of Biology, ), Aristotle University of Thessaloniki, Thessaloniki, Macedonia 54124, Greece and Genomics and Epigenomics Translational Research (GENeTres), Center for Interdisciplinary Research and Innovation (CIRI-AUTH, Balkan Center, Thessaloniki, Greece
| | - Giorgos Iliopoulos
- NGO "Callisto", Wildlife and Nature Conservation Society, 54621, Thessaloniki, Greece
| | - Alexander C Harris
- National Human Genome Research Institute, National Institutes of Health, 50 South Drive, Building 50 Room 5351, Bethesda, MD, 20892, USA
| | - Marjo K Hytönen
- Department of Medical and Clinical Genetics, Department of Veterinary Biosciences, University of Helsinki and Folkhälsan Research Center, 02900, Helsinki, Finland
| | - Daniela C Kalthoff
- NGO "Callisto", Wildlife and Nature Conservation Society, 54621, Thessaloniki, Greece
| | - Yan-Hu Liu
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, China
| | - Petros Lymberakis
- Natural History Museum of Crete & Department of Biology, University of Crete, 71202, Irakleio, Greece
- Biology Department, School of Sciences and Engineering, University of Crete, Heraklion, Greece
- Palaeogenomics and Evolutionary Genetics Lab, Institute of Molecular Biology and Biotechnology (IMBB), Foundation for Research and Technology - Hellas (FORTH), Heraklion, Greece
| | - Nikolaos Poulakakis
- Natural History Museum of Crete & Department of Biology, University of Crete, 71202, Irakleio, Greece
- Biology Department, School of Sciences and Engineering, University of Crete, Heraklion, Greece
- Palaeogenomics and Evolutionary Genetics Lab, Institute of Molecular Biology and Biotechnology (IMBB), Foundation for Research and Technology - Hellas (FORTH), Heraklion, Greece
| | - Ana Elisabete Pires
- BIOPOLIS-CIBIO-InBIO-Centro de Investigação Em Biodiversidade E Recursos Genéticos - ArchGen Group, Universidade Do Porto, 4485-661, Vairão, Portugal
| | - Fernando Racimo
- Section for Molecular Ecology and Evolution, Globe Institute, University of Copenhagen, Øster Voldgade 5-7, 1350, Copenhagen, Denmark
| | | | - Peter Savolainen
- Department of Gene Technology, Science for Life Laboratory, KTH - Royal Institute of Technology, 17121, Solna, Sweden
| | - Semina Venetsani
- Department of Genetics, School of Biology, Aristotle University of Thessaloniki, 54124, Thessaloniki, Macedonia, Greece
| | - Imke Tammen
- Sydney School of Veterinary Science, The University of Sydney, Sydney, NSW, 2570, Australia
| | - Alexandros Triantafyllidis
- Department of Genetics, School of Biology, ), Aristotle University of Thessaloniki, Thessaloniki, Macedonia 54124, Greece and Genomics and Epigenomics Translational Research (GENeTres), Center for Interdisciplinary Research and Innovation (CIRI-AUTH, Balkan Center, Thessaloniki, Greece
| | - Bridgett vonHoldt
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ, 08544, USA
| | - Robert K Wayne
- Department of Ecology and Evolutionary Biology, Ecology and Evolutionary Biology, University of California, Los Angeles, CA, 90095-7246, USA
| | - Greger Larson
- Palaeogenomics and Bio-Archaeology Research Network, School of Archaeology, University of Oxford, Oxford, OX1 3TG, UK
| | - Frank W Nicholas
- Sydney School of Veterinary Science, The University of Sydney, Sydney, NSW, 2570, Australia
| | - Hannes Lohi
- Department of Medical and Clinical Genetics, Department of Veterinary Biosciences, University of Helsinki and Folkhälsan Research Center, 02900, Helsinki, Finland
| | - Tosso Leeb
- Institute of Genetics, Vetsuisse Faculty, University of Bern, 3001, Bern, Switzerland
| | - Ya-Ping Zhang
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, China
| | - Elaine A Ostrander
- National Human Genome Research Institute, National Institutes of Health, 50 South Drive, Building 50 Room 5351, Bethesda, MD, 20892, USA.
| |
Collapse
|
30
|
Li WL, Liu YH, Li JX, Ding MT, Adeola AC, Isakova J, Aldashev AA, Peng MS, Huang X, Xie G, Chen X, Yang WK, Zhou WW, Ghanatsaman ZA, Olaogun SC, Sanke OJ, Dawuda PM, Hytönen MK, Lohi H, Esmailizadeh A, Poyarkov AD, Savolainen P, Wang GD, Zhang YP. Multiple Origins and Genomic Basis of Complex Traits in Sighthounds. Mol Biol Evol 2023; 40:msad158. [PMID: 37433053 PMCID: PMC10401622 DOI: 10.1093/molbev/msad158] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2023] [Revised: 06/24/2023] [Accepted: 06/27/2023] [Indexed: 07/13/2023] Open
Abstract
Sighthounds, a distinctive group of hounds comprising numerous breeds, have their origins rooted in ancient artificial selection of dogs. In this study, we performed genome sequencing for 123 sighthounds, including one breed from Africa, six breeds from Europe, two breeds from Russia, and four breeds and 12 village dogs from the Middle East. We gathered public genome data of five sighthounds and 98 other dogs as well as 31 gray wolves to pinpoint the origin and genes influencing the morphology of the sighthound genome. Population genomic analysis suggested that sighthounds originated from native dogs independently and were comprehensively admixed among breeds, supporting the multiple origins hypothesis of sighthounds. An additional 67 published ancient wolf genomes were added for gene flow detection. Results showed dramatic admixture of ancient wolves in African sighthounds, even more than with modern wolves. Whole-genome scan analysis identified 17 positively selected genes (PSGs) in the African population, 27 PSGs in the European population, and 54 PSGs in the Middle Eastern population. None of the PSGs overlapped in the three populations. Pooled PSGs of the three populations were significantly enriched in "regulation of release of sequestered calcium ion into cytosol" (gene ontology: 0051279), which is related to blood circulation and heart contraction. In addition, ESR1, JAK2, ADRB1, PRKCE, and CAMK2D were under positive selection in all three selected groups. This suggests that different PSGs in the same pathway contributed to the similar phenotype of sighthounds. We identified an ESR1 mutation (chr1: g.42,177,149 T > C) in the transcription factor (TF) binding site of Stat5a and a JAK2 mutation (chr1: g.93,277,007 T > A) in the TF binding site of Sox5. Functional experiments confirmed that the ESR1 and JAK2 mutation reduced their expression. Our results provide new insights into the domestication history and genomic basis of sighthounds.
Collapse
Affiliation(s)
- Wu-Lue Li
- State Key Laboratory of Genetic Resources and Evolution, Yunnan Laboratory of Molecular Biology of Domestic Animals, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
- Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, China
| | - Yan-Hu Liu
- State Key Laboratory of Genetic Resources and Evolution, Yunnan Laboratory of Molecular Biology of Domestic Animals, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
| | - Jin-Xiu Li
- State Key Laboratory of Genetic Resources and Evolution, Yunnan Laboratory of Molecular Biology of Domestic Animals, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
| | - Meng-Ting Ding
- State Key Laboratory of Genetic Resources and Evolution, Yunnan Laboratory of Molecular Biology of Domestic Animals, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
- Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, China
| | - Adeniyi C Adeola
- State Key Laboratory of Genetic Resources and Evolution, Yunnan Laboratory of Molecular Biology of Domestic Animals, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
- Sino-Africa Joint Research Center, Chinese Academy of Sciences, Kunming, China
| | - Jainagul Isakova
- Laboratory of Molecular and Cell Biology, Institute of Molecular Biology and Medicine, Bishkek, Kyrgyzstan
| | - Almaz A Aldashev
- Laboratory of Molecular and Cell Biology, Institute of Molecular Biology and Medicine, Bishkek, Kyrgyzstan
| | - Min-Sheng Peng
- State Key Laboratory of Genetic Resources and Evolution, Yunnan Laboratory of Molecular Biology of Domestic Animals, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
- Sino-Africa Joint Research Center, Chinese Academy of Sciences, Kunming, China
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, School of Life Sciences, Yunnan University, Kunming, China
| | - Xuezhen Huang
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, School of Life Sciences, Yunnan University, Kunming, China
| | - Guoli Xie
- State Key Laboratory of Genetic Resources and Evolution, Yunnan Laboratory of Molecular Biology of Domestic Animals, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
| | - Xi Chen
- Research Center for Ecology and Environment of Central Asia, Chinese Academy of Sciences, Urumqi, China
- Key Laboratory of Biogeography and Bioresource in Arid Land, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi, China
| | - Wei-Kang Yang
- Key Laboratory of Biogeography and Bioresource in Arid Land, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi, China
| | - Wei-Wei Zhou
- State Key Laboratory of Genetic Resources and Evolution, Yunnan Laboratory of Molecular Biology of Domestic Animals, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
| | - Zeinab Amiri Ghanatsaman
- Animal Science Research Department, Fars Agricultural and Natural Resources research and Education Center, Agricultural Research, Education and Extension Organization (AREEO), Shiraz, Iran
| | - Sunday C Olaogun
- Department of Veterinary Medicine, Faculty of Veterinary Medicine, University of Ibadan, Ibadan, Nigeria
| | - Oscar J Sanke
- Ministry of Agriculture and Natural Resources, Taraba State Government, Jalingo, Nigeria
| | - Philip M Dawuda
- Department of Animal Science, Faculty of Agriculture, National University of Lesotho, Roma, Southern Africa
| | - Marjo K Hytönen
- Department of Medical and Clinical Genetics, University of Helsinki, Helsinki, Finland
- Folkhälsan Research Center, Helsinki, Finland
- Department of Veterinary Biosciences, University of Helsinki, Helsinki, Finland
| | - Hannes Lohi
- Department of Medical and Clinical Genetics, University of Helsinki, Helsinki, Finland
- Folkhälsan Research Center, Helsinki, Finland
- Department of Veterinary Biosciences, University of Helsinki, Helsinki, Finland
| | - Ali Esmailizadeh
- State Key Laboratory of Genetic Resources and Evolution, Yunnan Laboratory of Molecular Biology of Domestic Animals, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
- Department of Animal Science, Faculty of Agriculture, Shahid Bahonar University of Kerman, Kerman, Iran
| | - Andrey D Poyarkov
- Severtsov Institute of Ecology and Evolution, Russian Academy of Science, Moscow, Russia
| | - Peter Savolainen
- KTH Royal Institute of Technology, School of Engineering Sciences in Chemistry, Biotechnology and Health, Department of Gene Technology, Science for Life Laboratory, Solna, Sweden
| | - Guo-Dong Wang
- State Key Laboratory of Genetic Resources and Evolution, Yunnan Laboratory of Molecular Biology of Domestic Animals, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
- Sino-Africa Joint Research Center, Chinese Academy of Sciences, Kunming, China
| | - Ya-Ping Zhang
- State Key Laboratory of Genetic Resources and Evolution, Yunnan Laboratory of Molecular Biology of Domestic Animals, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
- Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, China
- Sino-Africa Joint Research Center, Chinese Academy of Sciences, Kunming, China
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, School of Life Sciences, Yunnan University, Kunming, China
| |
Collapse
|
31
|
Cairns KM, Crowther MS, Parker HG, Ostrander EA, Letnic M. Genome-wide variant analyses reveal new patterns of admixture and population structure in Australian dingoes. Mol Ecol 2023; 32:4133-4150. [PMID: 37246949 PMCID: PMC10524503 DOI: 10.1111/mec.16998] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2022] [Revised: 04/29/2023] [Accepted: 05/05/2023] [Indexed: 05/30/2023]
Abstract
Admixture between species is a cause for concern in wildlife management. Canids are particularly vulnerable to interspecific hybridisation, and genetic admixture has shaped their evolutionary history. Microsatellite DNA testing, relying on a small number of genetic markers and geographically restricted reference populations, has identified extensive domestic dog admixture in Australian dingoes and driven conservation management policy. But there exists a concern that geographic variation in dingo genotypes could confound ancestry analyses that use a small number of genetic markers. Here, we apply genome-wide single-nucleotide polymorphism (SNP) genotyping to a set of 402 wild and captive dingoes collected from across Australia and then carry out comparisons to domestic dogs. We then perform ancestry modelling and biogeographic analyses to characterise population structure in dingoes and investigate the extent of admixture between dingoes and dogs in different regions of the continent. We show that there are at least five distinct dingo populations across Australia. We observed limited evidence of dog admixture in wild dingoes. Our work challenges previous reports regarding the occurrence and extent of dog admixture in dingoes, as our ancestry analyses show that previous assessments severely overestimate the degree of domestic dog admixture in dingo populations, particularly in south-eastern Australia. These findings strongly support the use of genome-wide SNP genotyping as a refined method for wildlife managers and policymakers to assess and inform dingo management policy and legislation moving forwards.
Collapse
Affiliation(s)
- Kylie M. Cairns
- Evolution & Ecology Research Centre, School of Biological, Earth and Environmental Sciences, University of New South Wales, Sydney, NSW, Australia
- Centre for Ecosystem Science, School of Biological, Earth and Environmental Sciences, University of New South Wales, Sydney, NSW, Australia
| | - Mathew S. Crowther
- School of Life and Environmental Sciences, University of Sydney, New South Wales 2006, Australia
| | - Heidi G. Parker
- National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, United States
| | - Elaine A. Ostrander
- National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, United States
| | - Mike Letnic
- Evolution & Ecology Research Centre, School of Biological, Earth and Environmental Sciences, University of New South Wales, Sydney, NSW, Australia
- Centre for Ecosystem Science, School of Biological, Earth and Environmental Sciences, University of New South Wales, Sydney, NSW, Australia
| |
Collapse
|
32
|
Doan K, Schnitzler A, Preston F, Griggo C, Lang G, Belhaoues F, Blaise E, Crégut-Bonnoure E, Frère S, Foucras S, Gardeisen A, Laurent A, Müller W, Picavet R, Puissant S, Yvinec JH, Pilot M. Evolutionary history of the extinct wolf population from France in the context of global phylogeographic changes throughout the Holocene. Mol Ecol 2023; 32:4627-4647. [PMID: 37337956 DOI: 10.1111/mec.17054] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2022] [Revised: 05/20/2023] [Accepted: 06/05/2023] [Indexed: 06/21/2023]
Abstract
Phylogeographic patterns in large mammals result from natural environmental factors and anthropogenic effects, which in some cases include domestication. The grey wolf was once widely distributed across the Holarctic, but experienced phylogeographic shifts and demographic declines during the Holocene. In the 19th-20th centuries, the species became extirpated from large parts of Europe due to direct extermination and habitat loss. We reconstructed the evolutionary history of the extinct Western European wolves based on the mitogenomic composition of 78 samples from France (Neolithic-20th century) in the context of other populations of wolves and dogs worldwide. We found a close genetic similarity of French wolves from ancient, medieval and recent populations, which suggests the long-term continuity of maternal lineages. MtDNA haplotypes of the French wolves showed large diversity and fell into two main haplogroups of modern Holarctic wolves. Our worldwide phylogeographic analysis indicated that haplogroup W1, which includes wolves from Eurasia and North America, originated in Northern Siberia. Haplogroup W2, which includes only European wolves, originated in Europe ~35 kya and its frequency was reduced during the Holocene due to an expansion of haplogroup W1 from the east. Moreover, we found that dog haplogroup D, currently restricted to Europe and the Middle East, was nested within the wolf haplogroup W2. This suggests European origin of haplogroup D, probably as a result of an ancient introgression from European wolves. Our results highlight the dynamic evolutionary history of European wolves during the Holocene, with a partial lineage replacement and introgressive hybridization with local dog populations.
Collapse
Affiliation(s)
- Karolina Doan
- Museum and Institute of Zoology, Polish Academy of Sciences, Warsaw, Poland
| | - Annik Schnitzler
- UMR 7194 HNHP CNRS/MNHN/UPVD, Equipe NOMADE, Muséum national d'histoire naturelle, Paris, France
| | | | - Christophe Griggo
- Université Grenoble Alpes, Laboratoire EDYTEM, URM 5204 Bâtiment "Pôle Montagne", 5 bd de la mer Caspienne, France
| | - Gérard Lang
- Espace Chasse et Nature Chemin de Strasbourg, France
| | - Fabien Belhaoues
- ASM - Archéologie des Sociétés Méditerranéennes, UMR 5140, Université Paul-Valéry, CNRS, MCC, Montpellier, France
- Labex ARCHIMEDE programme IA-ANR-11-LABX-0032-01, Montpellier, France
| | - Emilie Blaise
- ASM - Archéologie des Sociétés Méditerranéennes, UMR 5140, Université Paul-Valéry, CNRS, MCC, Montpellier, France
- Labex ARCHIMEDE programme IA-ANR-11-LABX-0032-01, Montpellier, France
| | - Evelyne Crégut-Bonnoure
- Muséum Requien, Avignon; Laboratoire TRACES-UMR 5608, Université Toulouse-Jean Jaurès, Toulouse, France
| | - Stéphane Frère
- Inrap, UMR 7209 AASPE, Muséum National d'Histoire Naturelle, La Courneuve, France
| | | | - Armelle Gardeisen
- ASM - Archéologie des Sociétés Méditerranéennes, UMR 5140, Université Paul-Valéry, CNRS, MCC, Montpellier, France
- Labex ARCHIMEDE programme IA-ANR-11-LABX-0032-01, Montpellier, France
| | | | - Werner Müller
- Laboratoire d'archéozoologie, Université de Neuchâtel, Avenue de Bellevaux 51, Neuchâtel, Switzerland
| | | | - Stéphane Puissant
- Muséum d'Histoire naturelle - Jardin de l'Arquebuse CS 73310 F-21033 Dijon Cedex, France
| | - Jean-Hervé Yvinec
- INRAP, UMR 7209 AASPE, Laboratoire d'archéozoologie de Compiègne, CRAVO, Compiègne, France
| | - Małgorzata Pilot
- Museum and Institute of Zoology, Polish Academy of Sciences, Warsaw, Poland
- School of Life Sciences, University of Lincoln, Lincoln, UK
- Faculty of Biology, University of Gdańsk, Gdańsk, Poland
| |
Collapse
|
33
|
Morrill K, Chen F, Karlsson E. Comparative neurogenetics of dog behavior complements efforts towards human neuropsychiatric genetics. Hum Genet 2023; 142:1231-1246. [PMID: 37578529 DOI: 10.1007/s00439-023-02580-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2023] [Accepted: 06/02/2023] [Indexed: 08/15/2023]
Abstract
Domestic dogs display a wide array of heritable behaviors that have intermediate genetic complexity thanks to a long history of human-influenced selection. Comparative genetics in dogs could address the scarcity of non-human neurogenetic systems relevant to human neuropsychiatric disorders, which are characterized by mental, emotional, and behavioral symptoms and involve vastly complex genetic and non-genetic risk factors. Our review describes the diverse behavioral "phenome" of domestic dogs, past and ongoing sources of behavioral selection, and the state of canine behavioral genetics. We highlight two naturally disordered behavioral domains that illustrate how dogs may prove useful as a comparative, forward neurogenetic system: canine age-related cognitive dysfunction, which can be examined more rapidly given the attenuated lifespan of dogs, and compulsive disorders, which may have genetic roots in purpose-bred behaviors. Growing community science initiatives aimed at the companion dog population will be well suited to investigating such complex behavioral phenotypes and offer a comparative resource that parallels human genomic initiatives in scale and dimensionality.
Collapse
Affiliation(s)
- Kathleen Morrill
- Bioinformatics and Integrative Biology, University of Massachusetts Chan Medical School, Worcester, MA, USA.
- Vertebrate Genome Biology, Broad Institute of MIT and Harvard, Cambridge, MA, USA.
- Morningside Graduate School of Biomedical Sciences UMass Chan Medical School, Worcester, MA, USA.
| | - Frances Chen
- Bioinformatics and Integrative Biology, University of Massachusetts Chan Medical School, Worcester, MA, USA
- Vertebrate Genome Biology, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Elinor Karlsson
- Bioinformatics and Integrative Biology, University of Massachusetts Chan Medical School, Worcester, MA, USA
- Vertebrate Genome Biology, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| |
Collapse
|
34
|
O'Neill DG, McMillan KM, Church DB, Brodbelt DC. Dog breeds and conformations in the UK in 2019: VetCompass canine demography and some consequent welfare implications. PLoS One 2023; 18:e0288081. [PMID: 37494312 PMCID: PMC10370710 DOI: 10.1371/journal.pone.0288081] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2023] [Accepted: 06/19/2023] [Indexed: 07/28/2023] Open
Abstract
INTRODUCTION Growing concerns over health and welfare impacts from extreme phenotypes in dogs have created an urgent need for reliable demographic information on the national breed structures of dogs. METHODS This study included all dogs under primary veterinary care in the UK during 2019 at practices participating in VetCompass. Demographic data on these dogs were analysed to report on the frequency of common breeds and also to report on conformation, bodyweight, sex and neuter associations with these breeds. RESULTS The study included 2,237,105 dogs under UK veterinary care in 2019. Overall, 69.4% (n = 1,551,462) were classified as purebred, 6.7% (149,308) as designer-crossbred and 24.0% (536,335) as nondesigner-crossbred. Across 800 unique breed names, the most frequent breeds at any age were nondesigner-crossbred (n = 536,335, 24.0%), Labrador Retriever (154,222, 6.9%) and Jack Russell Terrier (101,294, 4.5%). Among 229,624 (10.3%) dogs aged under one year, the most frequent breeds were nondesigner-crossbred (n = 45,995, 20.0%), French Bulldog (16,036, 7.0%) and Cockapoo (14,321, 6.2%). Overall, based on breed characteristics, 17.6% (395,739) were classified as brachycephalic, 43.1% (969,403) as mesaticephalic and 8.3% (186,320) as dolichocephalic. Of 1,551,336 dogs that were classifiable based on breed, 52.6% (815,673) were chondrodystrophic. Of 1,462,925 dogs that were classifiable, there were 54.6% (n = 798,426) short haired, 32.6% (476,883) medium haired and 12.8% (186,934) long haired. Of 1,547,653 dogs that were classifiable for ear carriage, 24.5% (n = 379,581) were erect, 28.1% (434,273) were semi-erect, 19.7% (305,475) were v-shaped drop and 27.7% (428,324) were pendulous. Overall, there was a 1.09:1.00 ratio of male (n = 1,163,512; 52.2%) to female dogs (n = 1,067,552; 47.8%). CONCLUSIONS Health and welfare issues linked to popular breeds with extreme phenotypes suggest that there is much work to do to help owners to make more welfare-friendly decisions when choosing which type of dog to own.
Collapse
Affiliation(s)
- Dan G O'Neill
- Pathobiology and Population Sciences, The Royal Veterinary College, Hatfield, United Kingdom
| | - Kirsten M McMillan
- DataSEA (Science, Engineering & Analytics), Research Team, Strategy & Transformation, Dogs Trust, London, United Kingdom
| | - David B Church
- Clinical Science and Services, The Royal Veterinary College, Hatfield, United Kingdom
| | - Dave C Brodbelt
- Pathobiology and Population Sciences, The Royal Veterinary College, Hatfield, United Kingdom
| |
Collapse
|
35
|
Son KH, Aldonza MBD, Nam AR, Lee KH, Lee JW, Shin KJ, Kang K, Cho JY. Integrative mapping of the dog epigenome: Reference annotation for comparative intertissue and cross-species studies. SCIENCE ADVANCES 2023; 9:eade3399. [PMID: 37406108 DOI: 10.1126/sciadv.ade3399] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/09/2022] [Accepted: 06/02/2023] [Indexed: 07/07/2023]
Abstract
Dogs have become a valuable model in exploring multifaceted diseases and biology relevant to human health. Despite large-scale dog genome projects producing high-quality draft references, a comprehensive annotation of functional elements is still lacking. We addressed this through integrative next-generation sequencing of transcriptomes paired with five histone marks and DNA methylome profiling across 11 tissue types, deciphering the dog's epigenetic code by defining distinct chromatin states, super-enhancer, and methylome landscapes, and thus showed that these regions are associated with a wide range of biological functions and cell/tissue identity. In addition, we confirmed that the phenotype-associated variants are enriched in tissue-specific regulatory regions and, therefore, the tissue of origin of the variants can be traced. Ultimately, we delineated conserved and dynamic epigenomic changes at the tissue- and species-specific resolutions. Our study provides an epigenomic blueprint of the dog that can be used for comparative biology and medical research.
Collapse
Affiliation(s)
- Keun Hong Son
- Department of Biochemistry, College of Veterinary Medicine, Seoul National University, Seoul, Korea
- Comparative Medicine and Disease Research Center (CDRC), Science Research Center (SRC), Seoul National University, Seoul, Korea
- BK21 PLUS Program for Creative Veterinary Science Research and Research Institute for Veterinary Science, Seoul National University, Seoul, Korea
| | - Mark Borris D Aldonza
- Department of Biochemistry, College of Veterinary Medicine, Seoul National University, Seoul, Korea
- Comparative Medicine and Disease Research Center (CDRC), Science Research Center (SRC), Seoul National University, Seoul, Korea
- BK21 PLUS Program for Creative Veterinary Science Research and Research Institute for Veterinary Science, Seoul National University, Seoul, Korea
| | - A-Reum Nam
- Department of Biochemistry, College of Veterinary Medicine, Seoul National University, Seoul, Korea
- Comparative Medicine and Disease Research Center (CDRC), Science Research Center (SRC), Seoul National University, Seoul, Korea
- BK21 PLUS Program for Creative Veterinary Science Research and Research Institute for Veterinary Science, Seoul National University, Seoul, Korea
| | - Kang-Hoon Lee
- Department of Biochemistry, College of Veterinary Medicine, Seoul National University, Seoul, Korea
- BK21 PLUS Program for Creative Veterinary Science Research and Research Institute for Veterinary Science, Seoul National University, Seoul, Korea
| | - Jeong-Woon Lee
- Department of Biochemistry, College of Veterinary Medicine, Seoul National University, Seoul, Korea
- Comparative Medicine and Disease Research Center (CDRC), Science Research Center (SRC), Seoul National University, Seoul, Korea
- BK21 PLUS Program for Creative Veterinary Science Research and Research Institute for Veterinary Science, Seoul National University, Seoul, Korea
| | - Kyung-Ju Shin
- Department of Biochemistry, College of Veterinary Medicine, Seoul National University, Seoul, Korea
- BK21 PLUS Program for Creative Veterinary Science Research and Research Institute for Veterinary Science, Seoul National University, Seoul, Korea
| | - Keunsoo Kang
- Department of Microbiology, College of Natural Sciences, Dankook University, Cheonan, Korea
| | - Je-Yoel Cho
- Department of Biochemistry, College of Veterinary Medicine, Seoul National University, Seoul, Korea
- Comparative Medicine and Disease Research Center (CDRC), Science Research Center (SRC), Seoul National University, Seoul, Korea
- BK21 PLUS Program for Creative Veterinary Science Research and Research Institute for Veterinary Science, Seoul National University, Seoul, Korea
| |
Collapse
|
36
|
Boch M, Wagner IC, Karl S, Huber L, Lamm C. Functionally analogous body- and animacy-responsive areas are present in the dog (Canis familiaris) and human occipito-temporal lobe. Commun Biol 2023; 6:645. [PMID: 37369804 PMCID: PMC10300132 DOI: 10.1038/s42003-023-05014-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2022] [Accepted: 06/05/2023] [Indexed: 06/29/2023] Open
Abstract
Comparing the neural correlates of socio-cognitive skills across species provides insights into the evolution of the social brain and has revealed face- and body-sensitive regions in the primate temporal lobe. Although from a different lineage, dogs share convergent visuo-cognitive skills with humans and a temporal lobe which evolved independently in carnivorans. We investigated the neural correlates of face and body perception in dogs (N = 15) and humans (N = 40) using functional MRI. Combining univariate and multivariate analysis approaches, we found functionally analogous occipito-temporal regions involved in the perception of animate entities and bodies in both species and face-sensitive regions in humans. Though unpredicted, we also observed neural representations of faces compared to inanimate objects, and dog compared to human bodies in dog olfactory regions. These findings shed light on the evolutionary foundations of human and dog social cognition and the predominant role of the temporal lobe.
Collapse
Affiliation(s)
- Magdalena Boch
- Social, Cognitive and Affective Neuroscience Unit, Department of Cognition, Emotion, and Methods in Psychology, Faculty of Psychology, University of Vienna, Vienna, Austria.
- Department of Cognitive Biology, Faculty of Life Sciences, University of Vienna, Vienna, Austria.
| | - Isabella C Wagner
- Social, Cognitive and Affective Neuroscience Unit, Department of Cognition, Emotion, and Methods in Psychology, Faculty of Psychology, University of Vienna, Vienna, Austria
- Vienna Cognitive Science Hub, University of Vienna, Vienna, Austria
- Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna, Austria
| | - Sabrina Karl
- Comparative Cognition, Messerli Research Institute, University of Veterinary Medicine Vienna, Medical University of Vienna and University of Vienna, Vienna, Austria
| | - Ludwig Huber
- Comparative Cognition, Messerli Research Institute, University of Veterinary Medicine Vienna, Medical University of Vienna and University of Vienna, Vienna, Austria
| | - Claus Lamm
- Social, Cognitive and Affective Neuroscience Unit, Department of Cognition, Emotion, and Methods in Psychology, Faculty of Psychology, University of Vienna, Vienna, Austria
- Vienna Cognitive Science Hub, University of Vienna, Vienna, Austria
| |
Collapse
|
37
|
Ahn B, Kang M, Jeon H, Kim JS, Jiang H, Ha J, Park C. Origin and population structure of native dog breeds in the Korean peninsula and East Asia. iScience 2023; 26:106982. [PMID: 37378348 PMCID: PMC10291505 DOI: 10.1016/j.isci.2023.106982] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2022] [Revised: 01/13/2023] [Accepted: 05/24/2023] [Indexed: 06/29/2023] Open
Abstract
To study the ancestry and phylogenetic relationships of native Korean dog breeds to other Asian dog populations, we analyzed nucleotide variations in whole-genome sequences of 205 canid individuals. Sapsaree, Northern Chinese indigenous dog, and Tibetan Mastiff were largely related to West Eurasian ancestry. Jindo, Donggyeongi, Shiba, Southern Chinese indigenous (SCHI), Vietnamese indigenous dogs (VIET), and Indonesian indigenous dogs were related to Southeast and East Asian ancestry. Among East Asian dog breeds, Sapsaree presented the highest haplotype sharing with German Shepherds, indicating ancient admixture of European ancestry to modern East Asian dog breeds. SCHI showed greater haplotype sharing with New Guinea singing dogs, VIET, and Jindo than with other Asian breeds. The predicted divergence time of East Asian populations from their common ancestor was approximately 2,000 to 11,000 years ago. Our results expand understanding of the genetic history of dogs in the Korean peninsula to the Asian continent and Oceanic region.
Collapse
Affiliation(s)
- Byeongyong Ahn
- Department of Stem Cell and Regenerative Biotechnology, Konkuk University, Gwangjin-gu, Seoul 05029, Republic of Korea
| | - Mingue Kang
- Department of Stem Cell and Regenerative Biotechnology, Konkuk University, Gwangjin-gu, Seoul 05029, Republic of Korea
| | - Hyoim Jeon
- Department of Stem Cell and Regenerative Biotechnology, Konkuk University, Gwangjin-gu, Seoul 05029, Republic of Korea
| | - Jong-Seok Kim
- Department of Korean Jindo and Domestic Animal, Jindo 58927, Republic of Korea
| | - Hao Jiang
- College of Animal Science, Jilin University, Changchun, Jilin 130119, China
| | - Jihong Ha
- Korean Sapsaree Foundation, Gyeongsan 38412, Republic of Korea
| | - Chankyu Park
- Department of Stem Cell and Regenerative Biotechnology, Konkuk University, Gwangjin-gu, Seoul 05029, Republic of Korea
| |
Collapse
|
38
|
Barash A, Preiss-Bloom S, Machluf Y, Fabbri E, Malkinson D, Velli E, Mucci N, Barash A, Caniglia R, Dayan T, Dekel Y. Possible origins and implications of atypical morphologies and domestication-like traits in wild golden jackals (Canis aureus). Sci Rep 2023; 13:7388. [PMID: 37149712 PMCID: PMC10164184 DOI: 10.1038/s41598-023-34533-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2022] [Accepted: 05/03/2023] [Indexed: 05/08/2023] Open
Abstract
Deciphering the origins of phenotypic variations in natural animal populations is a challenging topic for evolutionary and conservation biologists. Atypical morphologies in mammals are usually attributed to interspecific hybridisation or de-novo mutations. Here we report the case of four golden jackals (Canis aureus), that were observed during a camera-trapping wildlife survey in Northern Israel, displaying anomalous morphological traits, such as white patches, an upturned tail, and long thick fur which resemble features of domesticated mammals. Another individual was culled under permit and was genetically and morphologically examined. Paternal and nuclear genetic profiles, as well as geometric morphometric data, identified this individual as a golden jackal rather than a recent dog/wolf-jackal hybrid. Its maternal haplotype suggested past introgression of African wolf (Canis lupaster) mitochondrial DNA, as previously documented in other jackals from Israel. When viewed in the context of the jackal as an overabundant species in Israel, the rural nature of the surveyed area, the abundance of anthropogenic waste, and molecular and morphological findings, the possibility of an individual presenting incipient stages of domestication should also be considered.
Collapse
Affiliation(s)
- Ayelet Barash
- School of Zoology and The Steinhardt Museum of Natural History, Tel Aviv University, Tel Aviv, Israel
- Unit of Agrigenomics, Shamir Research Institute, University of Haifa, 1290000, Kazerin, Israel
| | - Shlomo Preiss-Bloom
- School of Zoology and The Steinhardt Museum of Natural History, Tel Aviv University, Tel Aviv, Israel
| | - Yossy Machluf
- Unit of Agrigenomics, Shamir Research Institute, University of Haifa, 1290000, Kazerin, Israel
| | - Elena Fabbri
- Unit for Conservation Genetics (BIO‑CGE), Italian Institute for Environmental Protection and Research (ISPRA), Via Cà Fornacetta 9, Ozzano dell'Emilia, 40064, Bologna, Italy
| | - Dan Malkinson
- Department of Geography and Environmental Studies, University of Haifa, 3498838, Haifa, Israel
| | - Edoardo Velli
- Unit for Conservation Genetics (BIO‑CGE), Italian Institute for Environmental Protection and Research (ISPRA), Via Cà Fornacetta 9, Ozzano dell'Emilia, 40064, Bologna, Italy
| | - Nadia Mucci
- Unit for Conservation Genetics (BIO‑CGE), Italian Institute for Environmental Protection and Research (ISPRA), Via Cà Fornacetta 9, Ozzano dell'Emilia, 40064, Bologna, Italy
| | - Alon Barash
- The Azrieli Faculty of Medicine, Bar Ilan University, 8 Henrietta Szold St, Safed, Israel
| | - Romolo Caniglia
- Unit for Conservation Genetics (BIO‑CGE), Italian Institute for Environmental Protection and Research (ISPRA), Via Cà Fornacetta 9, Ozzano dell'Emilia, 40064, Bologna, Italy.
| | - Tamar Dayan
- School of Zoology and The Steinhardt Museum of Natural History, Tel Aviv University, Tel Aviv, Israel.
| | - Yaron Dekel
- Unit of Agrigenomics, Shamir Research Institute, University of Haifa, 1290000, Kazerin, Israel.
- The Cheryl Spencer Department of Nursing and The Cheryl Spencer Institute of Nursing Research, University of Haifa, 3498838, Haifa, Israel.
| |
Collapse
|
39
|
Moon KL, Huson HJ, Morrill K, Wang MS, Li X, Srikanth K, Lindblad-Toh K, Svenson GJ, Karlsson EK, Shapiro B. Comparative genomics of Balto, a famous historic dog, captures lost diversity of 1920s sled dogs. Science 2023; 380:eabn5887. [PMID: 37104591 PMCID: PMC10184777 DOI: 10.1126/science.abn5887] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2021] [Accepted: 11/23/2022] [Indexed: 04/29/2023]
Abstract
We reconstruct the phenotype of Balto, the heroic sled dog renowned for transporting diphtheria antitoxin to Nome, Alaska, in 1925, using evolutionary constraint estimates from the Zoonomia alignment of 240 mammals and 682 genomes from dogs and wolves of the 21st century. Balto shares just part of his diverse ancestry with the eponymous Siberian husky breed. Balto's genotype predicts a combination of coat features atypical for modern sled dog breeds, and a slightly smaller stature. He had enhanced starch digestion compared with Greenland sled dogs and a compendium of derived homozygous coding variants at constrained positions in genes connected to bone and skin development. We propose that Balto's population of origin, which was less inbred and genetically healthier than that of modern breeds, was adapted to the extreme environment of 1920s Alaska.
Collapse
Affiliation(s)
- Katherine L. Moon
- Department of Ecology and Evolutionary Biology, University of California Santa Cruz, Santa Cruz, CA, USA
- Howard Hughes Medical Institute, University of California Santa Cruz, Santa Cruz, CA, USA
| | - Heather J. Huson
- Department of Animal Sciences, Cornell University College of Agriculture and Life Sciences, Ithaca, NY, 14853, USA
| | - Kathleen Morrill
- Bioinformatics and Integrative Biology, UMass Chan Medical School, Worcester, MA 01655, USA
- Morningside Graduate School of Biomedical Sciences, UMass Chan Medical School, Worcester, MA 01655, USA
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Ming-Shan Wang
- Department of Ecology and Evolutionary Biology, University of California Santa Cruz, Santa Cruz, CA, USA
- Howard Hughes Medical Institute, University of California Santa Cruz, Santa Cruz, CA, USA
| | - Xue Li
- Bioinformatics and Integrative Biology, UMass Chan Medical School, Worcester, MA 01655, USA
- Morningside Graduate School of Biomedical Sciences, UMass Chan Medical School, Worcester, MA 01655, USA
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Krishnamoorthy Srikanth
- Department of Animal Sciences, Cornell University College of Agriculture and Life Sciences, Ithaca, NY, 14853, USA
| | | | - Kerstin Lindblad-Toh
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Department of Medical Biochemistry and Microbiology, Science for Life Laboratory, Uppsala University; Uppsala, 751 32, Sweden
| | | | - Elinor K. Karlsson
- Bioinformatics and Integrative Biology, UMass Chan Medical School, Worcester, MA 01655, USA
- Morningside Graduate School of Biomedical Sciences, UMass Chan Medical School, Worcester, MA 01655, USA
| | - Beth Shapiro
- Department of Ecology and Evolutionary Biology, University of California Santa Cruz, Santa Cruz, CA, USA
- Howard Hughes Medical Institute, University of California Santa Cruz, Santa Cruz, CA, USA
| |
Collapse
|
40
|
Tancredi D, Cardinali I. Being a Dog: A Review of the Domestication Process. Genes (Basel) 2023; 14:genes14050992. [PMID: 37239352 DOI: 10.3390/genes14050992] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2023] [Revised: 04/19/2023] [Accepted: 04/26/2023] [Indexed: 05/28/2023] Open
Abstract
The process of canine domestication represents certainly one of the most interesting questions that evolutionary biology aims to address. A "multiphase" view of this process is now accepted, with a first phase during which different groups of wolves were attracted by the anthropogenic niche and a second phase characterized by the gradual establishment of mutual relationships between wolves and humans. Here, we provide a review of dog (Canis familiaris) domestication, highlighting the ecological differences between dogs and wolves, analyzing the molecular mechanisms which seem to have influenced the affiliative behaviors first observed in Belyaev's foxes, and describing the genetics of ancient European dogs. Then, we focus on three Mediterranean peninsulas (Balkan, Iberian and Italian), which together represent the main geographic area for studying canine domestication dynamics, as it has shaped the current genetic variability of dog populations, and where a well-defined European genetic structure was pinpointed through the analysis of uniparental genetic markers and their phylogeny.
Collapse
Affiliation(s)
- Domenico Tancredi
- Department of Chemistry, Biology and Biotechnology, Università degli Studi di Perugia, 06123 Perugia, Italy
| | - Irene Cardinali
- Department of Chemistry, Biology and Biotechnology, Università degli Studi di Perugia, 06123 Perugia, Italy
| |
Collapse
|
41
|
Rangel-Negrín A, Gómez-Espinosa EE, Chavira-Ramírez DR, Dias PAD. Dog barks influence the physiological stress and behavior of a wild primate. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 882:163585. [PMID: 37088396 DOI: 10.1016/j.scitotenv.2023.163585] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/03/2022] [Revised: 04/10/2023] [Accepted: 04/15/2023] [Indexed: 05/03/2023]
Abstract
Non-lethal impacts of dogs on primates have seldom been assessed. We used an experimental approach to determine if mantled howler monkeys (Alouatta palliata) perceive dog barks as an aversive stimulus and thus display physiological and behavioral responses toward simulated barks. For one year (1754 h of observations) we studied 16 adult males belonging to five groups in Los Tuxtlas (Mexico), and recorded the occurrence of naturally occurring dog barks, their sound pressure level (SPL), and the behavioral responses of howler monkeys to barks. We then exposed males to bark playbacks at two SPL treatments, 40 and 80 dB in a total of 50 experiments. We assayed glucocorticoid metabolite concentrations in fecal samples (fGCM) as a marker of the physiological stress response of males. We also recorded the duration of vigilance, vocalizations, and flight in relation to playbacks. Naturally occurring barks were frequent and usually elicited behavioral responses by males. fGCM concentrations increased after bark playbacks and with stimuli intensity. Time spent vigilant increased following playbacks independently of stimuli intensity but both vocalizations and flight were linked to stimuli intensity: vocalizations were the longest after barks played-back at 80 dB, but males spent more time fleeing in response to 40 dB bark playbacks. These results provide evidence that dog barks are pervasive in the habitat of mantled howler monkeys living at Los Tuxtlas and disturb males, both physiologically and behaviorally. Although the potential costs of physiological and behavioral responses could not be determined, there is sufficient evidence to assume that they do have negative impacts on individuals. Therefore, our study provides avenues for future research on dog-wildlife interactions and valuable information for the design of conservation actions aimed at mitigating the impact of dogs on mantled howler monkeys.
Collapse
Affiliation(s)
- Ariadna Rangel-Negrín
- Primate Behavioral Ecology Lab, Instituto de Neuro-etología, Universidad Veracruzana, Xalapa, Mexico.
| | | | - David Roberto Chavira-Ramírez
- Departamento de Biología de la Reproducción, Instituto Nacional de Ciencias Médicas y Nutrición Salvador Zubirán, Ciudad de México, Mexico
| | - Pedro A D Dias
- Primate Behavioral Ecology Lab, Instituto de Neuro-etología, Universidad Veracruzana, Xalapa, Mexico.
| |
Collapse
|
42
|
Amino acid nutrition and metabolism in domestic cats and dogs. J Anim Sci Biotechnol 2023; 14:19. [PMID: 36803865 PMCID: PMC9942351 DOI: 10.1186/s40104-022-00827-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2022] [Accepted: 12/21/2022] [Indexed: 02/22/2023] Open
Abstract
Domestic cats and dogs are carnivores that have evolved differentially in the nutrition and metabolism of amino acids. This article highlights both proteinogenic and nonproteinogenic amino acids. Dogs inadequately synthesize citrulline (the precursor of arginine) from glutamine, glutamate, and proline in the small intestine. Although most breeds of dogs have potential for adequately converting cysteine into taurine in the liver, a small proportion (1.3%-2.5%) of the Newfoundland dogs fed commercially available balanced diets exhibit a deficiency of taurine possibly due to gene mutations. Certain breeds of dogs (e.g., golden retrievers) are more prone to taurine deficiency possibly due to lower hepatic activities of cysteine dioxygenase and cysteine sulfinate decarboxylase. De novo synthesis of arginine and taurine is very limited in cats. Thus, concentrations of both taurine and arginine in feline milk are the greatest among domestic mammals. Compared with dogs, cats have greater endogenous nitrogen losses and higher dietary requirements for many amino acids (e.g., arginine, taurine, cysteine, and tyrosine), and are less sensitive to amino acid imbalances and antagonisms. Throughout adulthood, cats and dogs may lose 34% and 21% of their lean body mass, respectively. Adequate intakes of high-quality protein (i.e., 32% and 40% animal protein in diets of aging dogs and cats, respectively; dry matter basis) are recommended to alleviate aging-associated reductions in the mass and function of skeletal muscles and bones. Pet-food grade animal-sourced foodstuffs are excellent sources of both proteinogenic amino acids and taurine for cats and dogs, and can help to optimize their growth, development, and health.
Collapse
|
43
|
Bargas-Galarraga I, Vilà C, Gonzalez-Voyer A. High Investment in Reproduction Is Associated with Reduced Life Span in Dogs. Am Nat 2023; 201:163-174. [PMID: 36724469 DOI: 10.1086/722531] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
AbstractProminent differences in aging among and within species present an evolutionary puzzle. The theories proposed to explain evolutionary differences in aging are based on the axiom that selection maximizes fitness, not necessarily life span. This implies trade-offs between investment in self-maintenance and investment in reproduction, where high investments in growth and current reproduction are associated with short life spans. Fast growth and large adult size are related to shorter life spans in the domestic dog, a bourgeoning model in aging research; however, whether reproduction influences life span in this system remains unknown. Here we test the relationship between reproduction and differences in life span among dog breeds, simultaneously controlling for shared ancestry and recent gene flow. We found that shared ancestry explains a higher proportion of the among-breed variation in life history traits, in comparison with recent gene flow. Our results also show that reproductive investment negatively impacts life span, and more strongly so in large breeds, an effect that is not merely a correlated response of adult size. These results suggest that basic life history trade-offs are apparent in a domestic animal whose diversity is the result of artificial selection and that among-breed differences in life span are due to a combination of size and reproduction.
Collapse
|
44
|
Flegontov P, Işıldak U, Maier R, Yüncü E, Changmai P, Reich D. Modeling of African population history using f -statistics can be highly biased and is not addressed by previously suggested SNP ascertainment schemes. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.01.22.525077. [PMID: 36711923 PMCID: PMC9882349 DOI: 10.1101/2023.01.22.525077] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
f -statistics have emerged as a first line of analysis for making inferences about demographic history from genome-wide data. These statistics can provide strong evidence for either admixture or cladality, which can be robust to substantial rates of errors or missing data. f -statistics are guaranteed to be unbiased under "SNP ascertainment" (analyzing non-randomly chosen subsets of single nucleotide polymorphisms) only if it relies on a population that is an outgroup for all groups analyzed. However, ascertainment on a true outgroup that is not co-analyzed with other populations is often impractical and uncommon in the literature. In this study focused on practical rather than theoretical aspects of SNP ascertainment, we show that many non-outgroup ascertainment schemes lead to false rejection of true demographic histories, as well as to failure to reject incorrect models. But the bias introduced by common ascertainments such as the 1240K panel is mostly limited to situations when more than one sub-Saharan African and/or archaic human groups (Neanderthals and Denisovans) or non-human outgroups are co-modelled, for example, f 4 -statistics involving one non-African group, two African groups, and one archaic group. Analyzing panels of SNPs polymorphic in archaic humans, which has been suggested as a solution for the ascertainment problem, cannot fix all these problems since for some classes of f -statistics it is not a clean outgroup ascertainment, and in other cases it demonstrates relatively low power to reject incorrect demographic models since it provides a relatively small number of variants common in anatomically modern humans. And due to the paucity of high-coverage archaic genomes, archaic individuals used for ascertainment often act as sole representatives of the respective groups in an analysis, and we show that this approach is highly problematic. By carrying out large numbers of simulations of diverse demographic histories, we find that bias in inferences based on f -statistics introduced by non-outgroup ascertainment can be minimized if the derived allele frequency spectrum in the population used for ascertainment approaches the spectrum that existed at the root of all groups being co-analyzed. Ascertaining on sites with variants common in a diverse group of African individuals provides a good approximation to such a set of SNPs, addressing the great majority of biases and also retaining high statistical power for studying population history. Such a "pan-African" ascertainment, although not completely problem-free, allows unbiased exploration of demographic models for the widest set of archaic and modern human populations, as compared to the other ascertainment schemes we explored.
Collapse
Affiliation(s)
- Pavel Flegontov
- Department of Human Evolutionary Biology, Harvard University, Cambridge, MA, USA
- Department of Biology and Ecology, Faculty of Science, University of Ostrava, Ostrava, Czechia
- Kalmyk Research Center of the Russian Academy of Sciences, Elista, Russia
| | - Ulaş Işıldak
- Department of Biology and Ecology, Faculty of Science, University of Ostrava, Ostrava, Czechia
| | - Robert Maier
- Department of Human Evolutionary Biology, Harvard University, Cambridge, MA, USA
| | - Eren Yüncü
- Department of Biology and Ecology, Faculty of Science, University of Ostrava, Ostrava, Czechia
| | - Piya Changmai
- Department of Biology and Ecology, Faculty of Science, University of Ostrava, Ostrava, Czechia
| | - David Reich
- Department of Human Evolutionary Biology, Harvard University, Cambridge, MA, USA
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
- Howard Hughes Medical Institute, Harvard Medical School, Boston, MA, USA
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
| |
Collapse
|
45
|
Herwijnen IRV, van der Borg JAM, Kapteijn CM, Arndt SS, Vinke CM. Factors regarding the dog owner's household situation, antisocial behaviours, animal views and animal treatment in a population of dogs confiscated after biting humans and/ or other animals. PLoS One 2023; 18:e0282574. [PMID: 36947497 PMCID: PMC10032511 DOI: 10.1371/journal.pone.0282574] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2022] [Accepted: 02/21/2023] [Indexed: 03/23/2023] Open
Abstract
To examine the dog ownership factors characteristic to a population of dogs confiscated after a human and/ or animal-directed biting incident, we compared bite risk assessment reports of 159 confiscated dogs in the time frame 2008, 2009, 2010 (tf1) and of 215 confiscated dogs in the time frame 2020, 2021, 2022 (until mid-May; tf2). The reports were compiled by the same institute in a standardized format. We studied frequencies and chi-square pairwise comparisons (P<0.05) for 30 identified ownership factors. Overall (tf1 and tf2), 1,308 ownership factors were mentioned in the reports and reports mentioning ≥5 factors were twice as frequent in tf2 (38%) than tf1 (16%). Our data suggest that nine factors may in particular serve as a warning signal for biting incidents, as these factors were most frequently (≥15%) prevalent in the total of reported cases: having a multiple dog household, a dog reportedly roaming a neighbourhood without an owner, a dog's care tasks being transferred, a short leash and muzzle obligation served to the owner for a dog, an isolated and/ or confined keeping of a dog, a dog owner's (suspected) substance abuse, a dog owner's (suspected) animal abuse, a dog owner aggressing at confiscation of the dog and a dog owner being reported on for antisocial behaviours such as intimidation. Particularly, a dog owner's aggressive or antisocial behaviours and previous obligations to muzzle and short leash a dog (in our dataset often inappropriately adhered to by owners), may indicate that a proportion of owners of confiscated dogs, may not always be willing and/ or capable to guarantee societal safety. The results show that identification of dog ownership factors, might be useful for establishing biting incident policies and further studies should be done on preventive measures and controls.
Collapse
Affiliation(s)
- Ineke R van Herwijnen
- Division of Animals in Science and Society, Faculty of Veterinary Medicine, Department of Population Health Sciences, Utrecht University, Utrecht, The Netherlands
| | - Joanne A M van der Borg
- Division of Animals in Science and Society, Faculty of Veterinary Medicine, Department of Population Health Sciences, Utrecht University, Utrecht, The Netherlands
| | - Chantal M Kapteijn
- Division of Animals in Science and Society, Faculty of Veterinary Medicine, Department of Population Health Sciences, Utrecht University, Utrecht, The Netherlands
| | - Saskia S Arndt
- Division of Animals in Science and Society, Faculty of Veterinary Medicine, Department of Population Health Sciences, Utrecht University, Utrecht, The Netherlands
| | - Claudia M Vinke
- Division of Animals in Science and Society, Faculty of Veterinary Medicine, Department of Population Health Sciences, Utrecht University, Utrecht, The Netherlands
| |
Collapse
|
46
|
Brumm A, Germonpré M, Koungoulos L. The human-initiated model of wolf domestication - An expansion based on human-dingo relations in Aboriginal Australia. Front Psychol 2023; 14:1082338. [PMID: 37205085 PMCID: PMC10187142 DOI: 10.3389/fpsyg.2023.1082338] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2022] [Accepted: 02/15/2023] [Indexed: 05/21/2023] Open
Abstract
The historically known relationship of interspecies companionship between Aboriginal foraging communities in Australia and free-ranging dingoes provides a model for understanding the human-canid relations that gave rise to the first domesticated dogs. Here, we propose that a broadly similar relationship might have developed early in time between wild-living wolves and mobile groups of foragers in Late Pleistocene Eurasia, with hunter-gatherers routinely raiding wild wolf dens for pre-weaned pups, which were socialized to humans and kept in camp as tamed companions ("pets"). We outline a model in which captive wolf pups that reverted to the wild to breed when they were sexually mature established their territories in the vicinity of foraging communities - in a "liminal" ecological zone between humans and truly wild-living wolves. Many (or most) of the wolf pups humans took from the wilderness to rear in camp may have derived from these liminal dens where the breeding pairs had been under indirect human selection for tameness over many generations. This highlights the importance of the large seasonal hunting/aggregation camps associated with mammoth kill-sites in Gravettian/Epigravettian central Europe. Large numbers of foragers gathered regularly at these locations during the wild wolf birthing season. We infer that if a pattern of this kind occurred over long periods of time then there might have been a pronounced effect on genetic variation in free-ranging wolves that denned and whelped in the liminal zones in the vicinity of these human seasonal aggregation sites. The argument is not that wolves were domesticated in central Europe. Rather, it is this pattern of hunter-gatherers who caught and reared wild wolf pups gathering seasonally in large numbers that might have been the catalyst for the early changes leading to the first domesticated dogs - whether in western Eurasia or further afield.
Collapse
Affiliation(s)
- Adam Brumm
- Australian Research Centre for Human Evolution, Griffith University, Brisbane, QLD, Australia
- *Correspondence: Adam Brumm,
| | | | - Loukas Koungoulos
- School of Humanities, The University of Sydney, Sydney, NSW, Australia
- College of Asia and the Pacific, The Australian National University, Canberra, NSW, Australia
| |
Collapse
|
47
|
Pigs as Pets: Early Human Relations with the Sulawesi Warty Pig ( Sus celebensis). Animals (Basel) 2022; 13:ani13010048. [PMID: 36611658 PMCID: PMC9817959 DOI: 10.3390/ani13010048] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2022] [Revised: 12/15/2022] [Accepted: 12/15/2022] [Indexed: 12/25/2022] Open
Abstract
The Sulawesi warty pig (S. celebensis) is a wild and still-extant suid that is endemic to the Indonesian island of Sulawesi. It has long been theorised that S. celebensis was domesticated and/or deliberately introduced to other islands in Indonesia prior to the advent of the Neolithic farming transition in the region. Thus far, however, there has been no empirical support for this idea, nor have scientists critiqued the argument that S. celebensis was a pre-Neolithic domesticate in detail. Here, it is proposed that early foragers could have formed a relationship with S. celebensis that was similar in essence to the close association between Late Pleistocene foragers in Eurasia and the wild wolf ancestors of domestic dogs. That is, a longstanding practice of hunter-gatherers intensively socialising wild-caught S. celebensis piglets for adoption into human society as companion animals ('pets') may have altered the predator-prey dynamic, brought aspects of wild pig behaviour and reproduction under indirect human selection and control, and caused changes that differentiated human-associated pigs from their solely wild-living counterparts.
Collapse
|
48
|
Seeing Things: A Community Science Investigation into Motion Illusion Susceptibility in Domestic Cats ( Felis silvestris catus) and Dogs ( Canis lupus familiaris). Animals (Basel) 2022; 12:ani12243562. [PMID: 36552482 PMCID: PMC9774501 DOI: 10.3390/ani12243562] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2022] [Revised: 11/25/2022] [Accepted: 12/14/2022] [Indexed: 12/23/2022] Open
Abstract
Illusions-visual fields that distort perception-can inform the understanding of visual perception and its evolution. An example of one such illusion, the Rotating Snakes illusion, causes the perception of motion in a series of static concentric circles. The current study investigated pet dogs' and cats' perception of the Rotating Snakes illusion in a community science paradigm. The results reveal that neither species spent significantly more time at the illusion than at either of the controls, failing to indicate susceptibility to the illusion. Specific behavioral data at each stimulus reveal that the most common behaviors of both species were Inactive and Stationary, while Locomotion and Pawing were the least common, supporting the finding that susceptibility may not be present. This study is the first to examine susceptibility to the Rotating Snakes illusion in dogs, as well as to directly compare the phenomenon between dogs and cats. We suggest future studies might consider exploring alternative methods in testing susceptibility to motion illusions in non-human animals.
Collapse
|
49
|
Söylev A, Çokoglu SS, Koptekin D, Alkan C, Somel M. CONGA: Copy number variation genotyping in ancient genomes and low-coverage sequencing data. PLoS Comput Biol 2022; 18:e1010788. [PMID: 36516232 PMCID: PMC9873172 DOI: 10.1371/journal.pcbi.1010788] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2022] [Revised: 01/24/2023] [Accepted: 12/03/2022] [Indexed: 12/15/2022] Open
Abstract
To date, ancient genome analyses have been largely confined to the study of single nucleotide polymorphisms (SNPs). Copy number variants (CNVs) are a major contributor of disease and of evolutionary adaptation, but identifying CNVs in ancient shotgun-sequenced genomes is hampered by typical low genome coverage (<1×) and short fragments (<80 bps), precluding standard CNV detection software to be effectively applied to ancient genomes. Here we present CONGA, tailored for genotyping CNVs at low coverage. Simulations and down-sampling experiments suggest that CONGA can genotype deletions >1 kbps with F-scores >0.75 at ≥1×, and distinguish between heterozygous and homozygous states. We used CONGA to genotype 10,002 outgroup-ascertained deletions across a heterogenous set of 71 ancient human genomes spanning the last 50,000 years, produced using variable experimental protocols. A fraction of these (21/71) display divergent deletion profiles unrelated to their population origin, but attributable to technical factors such as coverage and read length. The majority of the sample (50/71), despite originating from nine different laboratories and having coverages ranging from 0.44×-26× (median 4×) and average read lengths 52-121 bps (median 69), exhibit coherent deletion frequencies. Across these 50 genomes, inter-individual genetic diversity measured using SNPs and CONGA-genotyped deletions are highly correlated. CONGA-genotyped deletions also display purifying selection signatures, as expected. CONGA thus paves the way for systematic CNV analyses in ancient genomes, despite the technical challenges posed by low and variable genome coverage.
Collapse
Affiliation(s)
- Arda Söylev
- Department of Computer Engineering, Konya Food and Agriculture University, Konya, Turkey
- Institute for Medical Biometry and Bioinformatics, Medical Faculty, Heinrich Heine University, Düsseldorf, Germany
- * E-mail: (AS); (MS)
| | | | - Dilek Koptekin
- Department of Health Informatics, Graduate School of Informatics, Middle East Technical University, Ankara, Turkey
| | - Can Alkan
- Department of Computer Engineering, Bilkent University, Ankara, Turkey
| | - Mehmet Somel
- Department of Biology, Middle East Technical University, Ankara, Turkey
- * E-mail: (AS); (MS)
| |
Collapse
|
50
|
Balcarcel AM, Geiger M, Clauss M, Sánchez‐Villagra MR. The mammalian brain under domestication: Discovering patterns after a century of old and new analyses. JOURNAL OF EXPERIMENTAL ZOOLOGY. PART B, MOLECULAR AND DEVELOPMENTAL EVOLUTION 2022; 338:460-483. [PMID: 34813150 PMCID: PMC9787656 DOI: 10.1002/jez.b.23105] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/19/2021] [Revised: 09/24/2021] [Accepted: 10/27/2021] [Indexed: 12/30/2022]
Abstract
Comparisons of wild and domestic populations have established brain reduction as one of the most consistent patterns correlated with domestication. Over a century of scholarly work has been devoted to this subject, and yet, new data continue to foster its debate. Current arguments, both for and against the validity of brain reduction occurring in domestic taxa, have repeatedly cited a small set of reviews on this subject. The original works, their sampling, methodological details, and nuances of results that would be key to establishing validity, particularly in light of new data, have not been investigated. To facilitate and encourage a more informed discussion, we present a comprehensive review of original brain reduction literature for four mammalian clades: Artiodactyla, Perissodactyla, Carnivora, and Glires. Among these are studies that generated the most cited brain reduction values in modern domestication literature. In doing so, we provide a fairer stage for the critique of traits associated with domestication. We conclude that while brain reduction magnitudes may contain error, empirical data collectively support the reduction in brain size and cranial capacity for domestic forms.
Collapse
Affiliation(s)
- A. M. Balcarcel
- Palaeontological Institute and MuseumUniversity of ZurichZurichSwitzerland
| | - M. Geiger
- Palaeontological Institute and MuseumUniversity of ZurichZurichSwitzerland
| | - M. Clauss
- Vetsuisse Faculty, Clinic for Zoo Animals, Exotic Pets and WildlifeUniversity of ZurichZurichSwitzerland
| | | |
Collapse
|