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Rambaldi Migliore N, Bigi D, Milanesi M, Zambonelli P, Negrini R, Morabito S, Verini-Supplizi A, Liotta L, Chegdani F, Agha S, Salim B, Beja-Pereira A, Torroni A, Ajmone‐Marsan P, Achilli A, Colli L. Mitochondrial DNA control-region and coding-region data highlight geographically structured diversity and post-domestication population dynamics in worldwide donkeys. PLoS One 2024; 19:e0307511. [PMID: 39197009 PMCID: PMC11356394 DOI: 10.1371/journal.pone.0307511] [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: 01/15/2024] [Accepted: 07/05/2024] [Indexed: 08/30/2024] Open
Abstract
Donkeys (Equus asinus) have been used extensively in agriculture and transportations since their domestication, ca. 5000-7000 years ago, but the increased mechanization of the last century has largely spoiled their role as burden animals, particularly in developed countries. Consequently, donkey breeds and population sizes have been declining for decades, and the diversity contributed by autochthonous gene pools has been eroded. Here, we examined coding-region data extracted from 164 complete mitogenomes and 1392 donkey mitochondrial DNA (mtDNA) control-region sequences to (i) assess worldwide diversity, (ii) evaluate geographical patterns of variation, and (iii) provide a new nomenclature of mtDNA haplogroups. The topology of the Maximum Parsimony tree confirmed the two previously identified major clades, i.e. Clades 1 and 2, but also highlighted the occurrence of a deep-diverging lineage within Clade 2 that left a marginal trace in modern donkeys. Thanks to the identification of stable and highly diagnostic coding-region mutational motifs, the two lineages were renamed as haplogroup A and haplogroup B, respectively, to harmonize clade nomenclature with the standard currently adopted for other livestock species. Control-region diversity and population expansion metrics varied considerably between geographical areas but confirmed North-eastern Africa as the likely domestication center. The patterns of geographical distribution of variation analyzed through phylogenetic networks and AMOVA confirmed the co-occurrence of both haplogroups in all sampled populations, while differences at the regional level point to the joint effects of demography, past human migrations and trade following the spread of donkeys out of the domestication center. Despite the strong decline that donkey populations have undergone for decades in many areas of the world, the sizeable mtDNA variability we scored, and the possible identification of a new early radiating lineage further stress the need for an extensive and large-scale characterization of donkey nuclear genome diversity to identify hotspots of variation and aid the conservation of local breeds worldwide.
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Affiliation(s)
- Nicola Rambaldi Migliore
- Dipartimento di Biologia e Biotecnologie “Lazzaro Spallanzani”, University of Pavia, Via A. Ferrata, Pavia, Italy
| | - Daniele Bigi
- Dipartimento di Scienze e Tecnologie Agro-Alimentari (DISTAL), Alma Mater Studiorum Università di Bologna, Viale Giuseppe Fanin, Bologna, Italy
| | - Marco Milanesi
- Dipartimento di Scienze Animali, della Nutrizione e degli Alimenti, Università Cattolica del S. Cuore, via Emilia Parmense, Piacenza, Italy
| | - Paolo Zambonelli
- Dipartimento di Scienze e Tecnologie Agro-Alimentari (DISTAL), Alma Mater Studiorum Università di Bologna, Viale Giuseppe Fanin, Bologna, Italy
| | - Riccardo Negrini
- Dipartimento di Scienze Animali, della Nutrizione e degli Alimenti, Università Cattolica del S. Cuore, via Emilia Parmense, Piacenza, Italy
| | - Simone Morabito
- Dipartimento di Scienze Animali, della Nutrizione e degli Alimenti, Università Cattolica del S. Cuore, via Emilia Parmense, Piacenza, Italy
| | | | - Luigi Liotta
- Department of Veterinary Sciences, University of Messina, V.le Palatucci, Messina, Italy
| | - Fatima Chegdani
- Dipartimento di Scienze Animali, della Nutrizione e degli Alimenti, Università Cattolica del S. Cuore, via Emilia Parmense, Piacenza, Italy
| | - Saif Agha
- Animal Production Department, Faculty of Agriculture, Ain Shams University, Cairo, Egypt
| | - Bashir Salim
- Department of Parasitology, Faculty of Veterinary Medicine, University of Khartoum, Khartoum-North, Sudan
- Camel Research Center, King Faisal University, Al-Ahsa, Saudi Arabia
| | - Albano Beja-Pereira
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Campus de Vairão, Universidade do Porto, Vairão, Portugal
- BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vairão, Vairão, Portugal
- DGAOT, Faculty of Sciences, Universidade do Porto, Rua Campo Alegre, Porto, Portugal
| | - Antonio Torroni
- Dipartimento di Biologia e Biotecnologie “Lazzaro Spallanzani”, University of Pavia, Via A. Ferrata, Pavia, Italy
| | - Paolo Ajmone‐Marsan
- Dipartimento di Scienze Animali, della Nutrizione e degli Alimenti, Università Cattolica del S. Cuore, via Emilia Parmense, Piacenza, Italy
- CREI Romeo and Enrica Invernizzi Research Center on Sustainable Dairy Production, Università Cattolica del S. Cuore, Piacenza (PC), Italy
| | - Alessandro Achilli
- Dipartimento di Biologia e Biotecnologie “Lazzaro Spallanzani”, University of Pavia, Via A. Ferrata, Pavia, Italy
| | - Licia Colli
- Dipartimento di Scienze Animali, della Nutrizione e degli Alimenti, Università Cattolica del S. Cuore, via Emilia Parmense, Piacenza, Italy
- BioDNA Centro di Ricerca Sulla Biodiversità e sul DNA Antico, Università Cattolica del S. Cuore, Piacenza (PC), Italy
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Gmel AI, Mikko S, Ricard A, Velie BD, Gerber V, Hamilton NA, Neuditschko M. Using high-density SNP data to unravel the origin of the Franches-Montagnes horse breed. Genet Sel Evol 2024; 56:53. [PMID: 38987703 PMCID: PMC11238448 DOI: 10.1186/s12711-024-00922-6] [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: 12/22/2023] [Accepted: 07/03/2024] [Indexed: 07/12/2024] Open
Abstract
BACKGROUND The Franches-Montagnes (FM) is the last native horse breed of Switzerland, established at the end of the 19th century by cross-breeding local mares with Anglo-Norman stallions. We collected high-density SNP genotype data (Axiom™ 670 K Equine genotyping array) from 522 FM horses, including 44 old-type horses (OF), 514 European Warmblood horses (WB) from Sweden and Switzerland (including a stallion used for cross-breeding in 1990), 136 purebred Arabians (AR), 32 Shagya Arabians (SA), and 64 Thoroughbred (TB) horses, as introgressed WB stallions showed TB origin in their pedigrees. The aim of the study was to ascertain fine-scale population structures of the FM breed, including estimation of individual admixture levels and genomic inbreeding (FROH) by means of Runs of Homozygosity. RESULTS To assess fine-scale population structures within the FM breed, we applied a three-step approach, which combined admixture, genetic contribution, and FROH of individuals into a high-resolution network visualization. Based on this approach, we were able to demonstrate that population substructures, as detected by model-based clustering, can be either associated with a different genetic origin or with the progeny of most influential sires. Within the FM breed, admixed horses explained most of the genetic variance of the current breeding population, while OF horses only accounted for a small proportion of the variance. Furthermore, we illustrated that FM horses showed high TB admixture levels and we identified inconsistencies in the origin of FM horses descending from the Arabian stallion Doktryner. With the exception of WB, FM horses were less inbred compared to the other breeds. However, the relatively few but long ROH segments suggested diversity loss in both FM subpopulations. Genes located in FM- and OF-specific ROH islands had known functions involved in conformation and behaviour, two traits that are highly valued by breeders. CONCLUSIONS The FM remains the last native Swiss breed, clearly distinguishable from other historically introgressed breeds, but it suffered bottlenecks due to intensive selection of stallions, restrictive mating choices based on arbitrary definitions of pure breeding, and selection of rare coat colours. To preserve the genetic diversity of FM horses, future conservation managements strategies should involve a well-balanced selection of stallions (e.g., by integrating OF stallions in the FM breeding population) and avoid selection for rare coat colours.
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Affiliation(s)
- Annik Imogen Gmel
- Animal GenoPhenomics, Agroscope, Route de la Tioleyre 4, 1725, Posieux, Switzerland
- Equine Department, Vetsuisse Faculty, University of Zurich, Winterthurerstrasse 260, 8053, Zurich, Switzerland
| | - Sofia Mikko
- Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, Box 7023, 750 07, Uppsala, Sweden
| | - Anne Ricard
- Institut National de la Recherche Agronomique, Domaine de Vilvert, 78350, Jouy-en-Josas, France
| | - Brandon D Velie
- Equine Genetics and Genomics Group, School of Life and Environmental Sciences, University of Sydney, RMC Gunn B19-603, Sydney, NSW, 2006, Australia
| | - Vinzenz Gerber
- Institut Suisse de Médecine Equine ISME, Vetsuisse Faculty, University of Bern, Länggassstrasse 124, 3012, Bern, Switzerland
| | - Natasha Anne Hamilton
- Sydney School of Veterinary Science, University of Sydney, Sydney, NSW, 2006, Australia
| | - Markus Neuditschko
- Animal GenoPhenomics, Agroscope, Route de la Tioleyre 4, 1725, Posieux, Switzerland.
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3
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Özkan M, Gürün K, Yüncü E, Vural KB, Atağ G, Akbaba A, Fidan FR, Sağlıcan E, Altınışık EN, Koptekin D, Pawłowska K, Hodder I, Adcock SE, Arbuckle BS, Steadman SR, McMahon G, Erdal YS, Bilgin CC, Togan İ, Geigl EM, Götherström A, Grange T, Özer F, Somel M. The first complete genome of the extinct European wild ass (Equus hemionus hydruntinus). Mol Ecol 2024; 33:e17440. [PMID: 38946459 DOI: 10.1111/mec.17440] [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: 07/11/2023] [Revised: 05/17/2024] [Accepted: 06/14/2024] [Indexed: 07/02/2024]
Abstract
We present palaeogenomes of three morphologically unidentified Anatolian equids dating to the first millennium BCE, sequenced to a coverage of 0.6-6.4×. Mitochondrial DNA haplotypes of the Anatolian individuals clustered with those of Equus hydruntinus (or Equus hemionus hydruntinus), the extinct European wild ass, secular name 'hydruntine'. Further, the Anatolian wild ass whole genome profiles fell outside the genomic diversity of other extant and past Asiatic wild ass (E. hemionus) lineages. These observations suggest that the three Anatolian wild asses represent hydruntines, making them the latest recorded survivors of this lineage, about a millennium later than the latest observations in the zooarchaeological record. Our mitogenomic and genomic analyses indicate that E. h. hydruntinus was a clade belonging to ancient and present-day E. hemionus lineages that radiated possibly between 0.6 and 0.8 Mya. We also find evidence consistent with recent gene flow between hydruntines and Middle Eastern wild asses. Analyses of genome-wide heterozygosity and runs of homozygosity suggest that the Anatolian wild ass population may have lost genetic diversity by the mid-first millennium BCE, a possible sign of its eventual demise.
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Affiliation(s)
- Mustafa Özkan
- Department of Biological Sciences, Middle East Technical University, Ankara, Turkey
| | - Kanat Gürün
- Department of Biological Sciences, Middle East Technical University, Ankara, Turkey
| | - Eren Yüncü
- Department of Biological Sciences, Middle East Technical University, Ankara, Turkey
| | - Kıvılcım Başak Vural
- Department of Biological Sciences, Middle East Technical University, Ankara, Turkey
| | - Gözde Atağ
- Department of Biological Sciences, Middle East Technical University, Ankara, Turkey
| | - Ali Akbaba
- Department of Anthropology, Ankara University, Ankara, Turkey
- Alparslan University, Muş, Turkey
| | - Fatma Rabia Fidan
- Department of Biological Sciences, Middle East Technical University, Ankara, Turkey
- Cancer Dynamics Laboratory, The Francis Crick Institute, London, UK
| | - Ekin Sağlıcan
- Department of Health Informatics, Middle East Technical University, Ankara, Turkey
| | - Ezgi N Altınışık
- Department of Anthropology, Human_G Laboratory, Hacettepe University, Ankara, Turkey
| | - Dilek Koptekin
- Department of Health Informatics, Middle East Technical University, Ankara, Turkey
| | - Kamilla Pawłowska
- Department of Palaeoenvironmental Research, Adam Mickiewicz University, Poznań, Poland
| | - Ian Hodder
- Department of Anthropology, Stanford University, Stanford, California, USA
| | - Sarah E Adcock
- Institute for the Study of the Ancient World, New York University, New York, New York, USA
| | - Benjamin S Arbuckle
- Department of Anthropology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Sharon R Steadman
- Department of Sociology/Anthropology, SUNY Cortland, Cortland, New York, USA
| | - Gregory McMahon
- Classics, Humanities and Italian Studies Department, University of New Hampshire, Durham, New Hampshire, USA
| | - Yılmaz Selim Erdal
- Department of Anthropology, Human_G Laboratory, Hacettepe University, Ankara, Turkey
| | - C Can Bilgin
- Department of Biological Sciences, Middle East Technical University, Ankara, Turkey
| | - İnci Togan
- Department of Biological Sciences, Middle East Technical University, Ankara, Turkey
| | - Eva-Maria Geigl
- Institut Jacques Monod, CNRS, Université de Paris, Paris, France
| | - Anders Götherström
- Department of Archaeology and Classical Studies, Stockholm University, Stockholm, Sweden
| | - Thierry Grange
- Institut Jacques Monod, CNRS, Université de Paris, Paris, France
| | - Füsun Özer
- Department of Health Informatics, Middle East Technical University, Ankara, Turkey
| | - Mehmet Somel
- Department of Biological Sciences, Middle East Technical University, Ankara, Turkey
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4
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Librado P, Tressières G, Chauvey L, Fages A, Khan N, Schiavinato S, Calvière-Tonasso L, Kusliy MA, Gaunitz C, Liu X, Wagner S, Der Sarkissian C, Seguin-Orlando A, Perdereau A, Aury JM, Southon J, Shapiro B, Bouchez O, Donnadieu C, Collin YRH, Gregersen KM, Jessen MD, Christensen K, Claudi-Hansen L, Pruvost M, Pucher E, Vulic H, Novak M, Rimpf A, Turk P, Reiter S, Brem G, Schwall C, Barrey É, Robert C, Degueurce C, Horwitz LK, Klassen L, Rasmussen U, Kveiborg J, Johannsen NN, Makowiecki D, Makarowicz P, Szeliga M, Ilchyshyn V, Rud V, Romaniszyn J, Mullin VE, Verdugo M, Bradley DG, Cardoso JL, Valente MJ, Telles Antunes M, Ameen C, Thomas R, Ludwig A, Marzullo M, Prato O, Bagnasco Gianni G, Tecchiati U, Granado J, Schlumbaum A, Deschler-Erb S, Mráz MS, Boulbes N, Gardeisen A, Mayer C, Döhle HJ, Vicze M, Kosintsev PA, Kyselý R, Peške L, O'Connor T, Ananyevskaya E, Shevnina I, Logvin A, Kovalev AA, Iderkhangai TO, Sablin MV, Dashkovskiy PK, Graphodatsky AS, Merts I, Merts V, Kasparov AK, Pitulko VV, Onar V, Öztan A, Arbuckle BS, McColl H, Renaud G, Khaskhanov R, Demidenko S, Kadieva A, Atabiev B, Sundqvist M, Lindgren G, López-Cachero FJ, Albizuri S, Trbojević Vukičević T, Rapan Papeša A, Burić M, Rajić Šikanjić P, Weinstock J, Asensio Vilaró D, Codina F, García Dalmau C, Morer de Llorens J, Pou J, de Prado G, Sanmartí J, Kallala N, Torres JR, Maraoui-Telmini B, Belarte Franco MC, Valenzuela-Lamas S, Zazzo A, Lepetz S, Duchesne S, Alexeev A, Bayarsaikhan J, Houle JL, Bayarkhuu N, Turbat T, Crubézy É, Shingiray I, Mashkour M, Berezina NY, Korobov DS, Belinskiy A, Kalmykov A, Demoule JP, Reinhold S, Hansen S, Wallner B, Roslyakova N, Kuznetsov PF, Tishkin AA, Wincker P, Kanne K, Outram A, Orlando L. Widespread horse-based mobility arose around 2200 BCE in Eurasia. Nature 2024; 631:819-825. [PMID: 38843826 PMCID: PMC11269178 DOI: 10.1038/s41586-024-07597-5] [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: 07/17/2023] [Accepted: 05/23/2024] [Indexed: 07/19/2024]
Abstract
Horses revolutionized human history with fast mobility1. However, the timeline between their domestication and their widespread integration as a means of transport remains contentious2-4. Here we assemble a collection of 475 ancient horse genomes to assess the period when these animals were first reshaped by human agency in Eurasia. We find that reproductive control of the modern domestic lineage emerged around 2200 BCE, through close-kin mating and shortened generation times. Reproductive control emerged following a severe domestication bottleneck starting no earlier than approximately 2700 BCE, and coincided with a sudden expansion across Eurasia that ultimately resulted in the replacement of nearly every local horse lineage. This expansion marked the rise of widespread horse-based mobility in human history, which refutes the commonly held narrative of large horse herds accompanying the massive migration of steppe peoples across Europe around 3000 BCE and earlier3,5. Finally, we detect significantly shortened generation times at Botai around 3500 BCE, a settlement from central Asia associated with corrals and a subsistence economy centred on horses6,7. This supports local horse husbandry before the rise of modern domestic bloodlines.
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Affiliation(s)
- Pablo Librado
- Centre d'Anthropobiologie et de Génomique de Toulouse, CNRS UMR 5288, Université Paul Sabatier, Faculté de Médecine Purpan, Toulouse, France.
- Institut de Biologia Evolutiva (CSIC - Universitat Pompeu Fabra), Barcelona, Spain.
| | - Gaetan Tressières
- Centre d'Anthropobiologie et de Génomique de Toulouse, CNRS UMR 5288, Université Paul Sabatier, Faculté de Médecine Purpan, Toulouse, France
| | - Lorelei Chauvey
- Centre d'Anthropobiologie et de Génomique de Toulouse, CNRS UMR 5288, Université Paul Sabatier, Faculté de Médecine Purpan, Toulouse, France
| | - Antoine Fages
- Centre d'Anthropobiologie et de Génomique de Toulouse, CNRS UMR 5288, Université Paul Sabatier, Faculté de Médecine Purpan, Toulouse, France
- Zoological institute, Department of Environmental Sciences, University of Basel, Basel, Switzerland
| | - Naveed Khan
- Centre d'Anthropobiologie et de Génomique de Toulouse, CNRS UMR 5288, Université Paul Sabatier, Faculté de Médecine Purpan, Toulouse, France
- Department of Biotechnology, Abdul Wali Khan University, Mardan, Pakistan
| | - Stéphanie Schiavinato
- Centre d'Anthropobiologie et de Génomique de Toulouse, CNRS UMR 5288, Université Paul Sabatier, Faculté de Médecine Purpan, Toulouse, France
| | - Laure Calvière-Tonasso
- Centre d'Anthropobiologie et de Génomique de Toulouse, CNRS UMR 5288, Université Paul Sabatier, Faculté de Médecine Purpan, Toulouse, France
| | - Mariya A Kusliy
- Centre d'Anthropobiologie et de Génomique de Toulouse, CNRS UMR 5288, Université Paul Sabatier, Faculté de Médecine Purpan, Toulouse, France
- Department of the Diversity and Evolution of Genomes, Institute of Molecular and Cellular Biology, Novosibirsk, Russia
| | - Charleen Gaunitz
- Centre d'Anthropobiologie et de Génomique de Toulouse, CNRS UMR 5288, Université Paul Sabatier, Faculté de Médecine Purpan, Toulouse, France
- Lundbeck Foundation GeoGenetics Centre, Globe Institute, University of Copenhagen, Copenhagen, Denmark
| | - Xuexue Liu
- Centre d'Anthropobiologie et de Génomique de Toulouse, CNRS UMR 5288, Université Paul Sabatier, Faculté de Médecine Purpan, Toulouse, France
| | - Stefanie Wagner
- Centre d'Anthropobiologie et de Génomique de Toulouse, CNRS UMR 5288, Université Paul Sabatier, Faculté de Médecine Purpan, Toulouse, France
- INRAE Division Ecology and Biodiversity (ECODIV), Plant Genomic Resources Center (CNRGV), Castanet Tolosan Cedex, France
| | - Clio Der Sarkissian
- Centre d'Anthropobiologie et de Génomique de Toulouse, CNRS UMR 5288, Université Paul Sabatier, Faculté de Médecine Purpan, Toulouse, France
| | - Andaine Seguin-Orlando
- Centre d'Anthropobiologie et de Génomique de Toulouse, CNRS UMR 5288, Université Paul Sabatier, Faculté de Médecine Purpan, Toulouse, France
| | - Aude Perdereau
- Genoscope, Institut de Biologie François Jacob, CEA, CNRS, Université d'Évry, Université Paris-Saclay, Évry, France
| | - Jean-Marc Aury
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Université d'Évry, Université Paris-Saclay, Évry, France
| | - John Southon
- Department of Earth System Science, University of California, Irvine, CA, USA
| | - Beth Shapiro
- Department of Ecology and Evolutionary Biology, University of California Santa Cruz, Santa Cruz, CA, USA
| | | | | | - Yvette Running Horse Collin
- Centre d'Anthropobiologie et de Génomique de Toulouse, CNRS UMR 5288, Université Paul Sabatier, Faculté de Médecine Purpan, Toulouse, France
- Taku Skan Skan Wasakliyapi: Global Institute for Traditional Sciences, Rapid City, SD, USA
| | | | - Mads Dengsø Jessen
- Department for Prehistory Middle Ages and Renaissance, National Museum of Denmark, Copenhagen K, Denmark
| | | | | | - Mélanie Pruvost
- UMR 5199 De la Préhistoire à l'Actuel: Culture, Environnement et Anthropologie (PACEA), CNRS, Université de Bordeaux, Pessac Cédex, France
| | | | | | - Mario Novak
- Centre for Applied Bioanthropology, Institute for Anthropological Research, Zagreb, Croatia
| | | | - Peter Turk
- Narodni muzej Slovenije, Ljubljana, Slovenia
| | - Simone Reiter
- Institute of Animal Breeding and Genetics, Department of Biomedical Sciences, University of Veterinary Medicine Vienna, Vienna, Austria
| | - Gottfried Brem
- Institute of Animal Breeding and Genetics, Department of Biomedical Sciences, University of Veterinary Medicine Vienna, Vienna, Austria
| | - Christoph Schwall
- Leibniz-Zentrum für Archäologie (LEIZA), Mainz, Germany
- Department of Prehistory & Western Asian/Northeast African Archaeology, Austrian Archaeological Institute (OeAI), Austrian Academy of Sciences (OeAW), Vienna, Austria
| | - Éric Barrey
- Université Paris-Saclay, AgroParisTech, INRAE GABI UMR1313, Jouy-en-Josas, France
| | - Céline Robert
- Université Paris-Saclay, AgroParisTech, INRAE GABI UMR1313, Jouy-en-Josas, France
- Ecole Nationale Vétérinaire d'Alfort, Maisons-Alfort, France
| | | | - Liora Kolska Horwitz
- National Natural History Collections, Edmond J. Safra Campus, Givat Ram, The Hebrew University, Jerusalem, Israel
| | | | - Uffe Rasmussen
- Department of Archaeology, Moesgaard Museum, Højbjerg, Denmark
| | - Jacob Kveiborg
- Department of Archaeological Science and Conservation, Moesgaard Museum, Højbjerg, Denmark
| | | | - Daniel Makowiecki
- Institute of Archaeology, Faculty of History, Nicolaus Copernicus University, Toruń, Poland
| | | | - Marcin Szeliga
- Institute of Archaeology, Maria Curie-Skłodowska University, Lublin, Poland
| | - Vasyl Ilchyshyn
- Kremenetsko-Pochaivskii Derzhavnyi Istoriko-arkhitekturnyi Zapovidnik, Kremenets, Ukraine
| | - Vitalii Rud
- Institute of Archaeology, National Academy of Sciences of Ukraine, Kyiv, Ukraine
| | - Jan Romaniszyn
- Faculty of Archaeology, Adam Mickiewicz University, Poznań, Poland
| | - Victoria E Mullin
- Smurfit Institute of Genetics, Trinity College Dublin, Dublin, Ireland
| | - Marta Verdugo
- Smurfit Institute of Genetics, Trinity College Dublin, Dublin, Ireland
| | - Daniel G Bradley
- Smurfit Institute of Genetics, Trinity College Dublin, Dublin, Ireland
| | - João L Cardoso
- ICArEHB, Campus de Gambelas, University of Algarve, Faro, Portugal
- Universidade Aberta, Lisbon, Portugal
| | - Maria J Valente
- Faculdade de Ciências Humanas e Sociais, Centro de Estudos de Arqueologia, Artes e Ciências do Património, Universidade do Algarve, Faro, Portugal
| | - Miguel Telles Antunes
- Centre for Research on Science and Geological Engineering, Universidade Nova de Lisboa, Lisbon, Portugal
| | - Carly Ameen
- Department of Archaeology and History, University of Exeter, Exeter, UK
| | - Richard Thomas
- School of Archaeology and Ancient History, University of Leicester, Leicester, UK
| | - Arne Ludwig
- Department of Evolutionary Genetics, Leibniz-Institute for Zoo and Wildlife Research, Berlin, Germany
- Albrecht Daniel Thaer-Institute, Faculty of Life Sciences, Humboldt University Berlin, Berlin, Germany
| | - Matilde Marzullo
- Dipartimento di Beni Culturali e Ambientali, Università degli Studi di Milano, Milan, Italy
| | - Ornella Prato
- Dipartimento di Beni Culturali e Ambientali, Università degli Studi di Milano, Milan, Italy
| | | | - Umberto Tecchiati
- Dipartimento di Beni Culturali e Ambientali, Università degli Studi di Milano, Milan, Italy
| | - José Granado
- Department of Environmental Sciences, Integrative Prehistory and Archaeological Science, Basel University, Basel, Switzerland
| | - Angela Schlumbaum
- Department of Environmental Sciences, Integrative Prehistory and Archaeological Science, Basel University, Basel, Switzerland
| | - Sabine Deschler-Erb
- Department of Environmental Sciences, Integrative Prehistory and Archaeological Science, Basel University, Basel, Switzerland
| | - Monika Schernig Mráz
- Department of Environmental Sciences, Integrative Prehistory and Archaeological Science, Basel University, Basel, Switzerland
| | - Nicolas Boulbes
- Institut de Paléontologie Humaine, Fondation Albert Ier, Paris/UMR 7194 HNHP, MNHN-CNRS-UPVD/EPCC Centre Européen de Recherche Préhistorique, Tautavel, France
| | - Armelle Gardeisen
- Archéologie des Sociétés Méditeranéennes, Archimède IA-ANR-11-LABX-0032-01, CNRS UMR 5140, Université Paul Valéry, Montpellier, France
| | - Christian Mayer
- Department for Digitalization and Knowledge Transfer, Federal Monuments Authority Austria, Vienna, Austria
| | - Hans-Jürgen Döhle
- Landesamt für Denkmalpflege und Archäologie Sachsen-Anhalt - Landesmuseum für Vorgeschichte, Halle (Saale), Germany
| | - Magdolna Vicze
- National Institute of Archaeology, Hungarian National Museum, Budapest, Hungary
| | - Pavel A Kosintsev
- Paleoecology Laboratory, Institute of Plant and Animal Ecology, Ural Branch of the Russian Academy of Sciences, Ekaterinburg, Russia
- Department of History of the Institute of Humanities, Ural Federal University, Ekaterinburg, Russia
| | - René Kyselý
- Department of Natural Sciences and Archaeometry, Institute of Archaeology of the Czech Academy of Sciences, Prague, Czechia
| | | | | | - Elina Ananyevskaya
- Department of Archaeology, History Faculty, Vilnius University, Vilnius, Lithuania
| | - Irina Shevnina
- Laboratory for Archaeological Research, Akhmet Baitursynuly Kostanay Regional University, Kostanay, Kazakhstan
| | - Andrey Logvin
- Laboratory for Archaeological Research, Akhmet Baitursynuly Kostanay Regional University, Kostanay, Kazakhstan
| | - Alexey A Kovalev
- Department of Archaeological Heritage Preservation, Institute of Archaeology of the Russian Academy of Sciences, Moscow, Russia
| | - Tumur-Ochir Iderkhangai
- Department of Innovation and Technology, Ulaanbaatar Science and Technology Park, National University of Mongolia, Ulaanbaatar, Mongolia
| | - Mikhail V Sablin
- Zoological Institute, Russian Academy of Sciences, St Petersburg, Russia
| | - Petr K Dashkovskiy
- Department of Russian Regional Studies, National and State-confessional Relations, Altai State University, Barnaul, Russia
| | - Alexander S Graphodatsky
- Department of the Diversity and Evolution of Genomes, Institute of Molecular and Cellular Biology, Novosibirsk, Russia
| | - Ilia Merts
- Toraighyrov University, Joint Research Center for Archeological Studies, Pavlodar, Kazakhstan
- Department of Archaeology, Ethnography and Museology, Altai State University, Barnaul, Russia
| | - Viktor Merts
- Toraighyrov University, Joint Research Center for Archeological Studies, Pavlodar, Kazakhstan
| | - Aleksei K Kasparov
- Institute of the History of Material Culture, Russian Academy of Sciences, St. Petersburg, Russia
| | - Vladimir V Pitulko
- Institute of the History of Material Culture, Russian Academy of Sciences, St. Petersburg, Russia
- Peter the Great Museum of Anthropology and Ethnography (Kunstkamera), Russian Academy of Sciences, St Petersburg, Russia
| | - Vedat Onar
- Osteoarchaeology Practice and Research Center and Department of Anatomy, Faculty of Veterinary Medicine, Istanbul University-Cerrahpaşa, Istanbul, Türkiye
| | - Aliye Öztan
- Archaeology Department, Ankara University, Ankara, Türkiye
| | - Benjamin S Arbuckle
- Department of Anthropology, Alumni Building, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Hugh McColl
- Lundbeck Foundation GeoGenetics Centre, Globe Institute, University of Copenhagen, Copenhagen, Denmark
| | - Gabriel Renaud
- Centre d'Anthropobiologie et de Génomique de Toulouse, CNRS UMR 5288, Université Paul Sabatier, Faculté de Médecine Purpan, Toulouse, France
- Department of Health Technology, Section for Bioinformatics, Technical University of Denmark (DTU), Copenhagen, Denmark
| | - Ruslan Khaskhanov
- Kh. Ibragimov Complex Institute of the Russian Academy of Sciences (CI RAS), Grozny, Russia
| | - Sergey Demidenko
- Institute of Archaeology, Russian Academy of Sciences, Moscow, Russia
| | - Anna Kadieva
- Department of Archaeological Monuments, State Historical Museum, Moscow, Russian Federation
| | | | | | - Gabriella Lindgren
- Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, Uppsala, Sweden
- Center for Animal Breeding and Genetics, Department of Biosystems, KU Leuven, Leuven, Belgium
| | - F Javier López-Cachero
- Institut d'Arqueologia de la Universitat de Barcelona (IAUB), Seminari d'Estudis i Recerques Prehistoriques (SERP-UB), Universitat de Barcelona (UB), Barcelona, Spain
| | - Silvia Albizuri
- Institut d'Arqueologia de la Universitat de Barcelona (IAUB), Seminari d'Estudis i Recerques Prehistoriques (SERP-UB), Universitat de Barcelona (UB), Barcelona, Spain
| | - Tajana Trbojević Vukičević
- Department of Anatomy, Histology and Embryology, Faculty of Veterinary Medicine, University of Zagreb, Zagreb, Croatia
| | | | - Marcel Burić
- Department of Archaeology, Faculty of Humanities and Social Sciences, University of Zagreb, Zagreb, Croatia
| | | | - Jaco Weinstock
- Faculty of Arts and Humanities (Archaeology), University of Southampton, Southampton, UK
| | - David Asensio Vilaró
- Secció de Prehistòria i Arqueologia, IAUB Institut d'Arqueologia de la Universitat de Barcelona, Barcelona, Spain
| | - Ferran Codina
- C/Major, 20, Norfeu, Arqueologia Art i Patrimoni S.C., La Tallada d'Empordà, Spain
| | | | | | - Josep Pou
- Ajuntament de Calafell, Calafell (Tarragona), Spain
| | - Gabriel de Prado
- Museu d'Arqueologia de Catalunya (MAC-Ullastret), Ullastret, Spain
| | - Joan Sanmartí
- IEC-Institut d'Estudis Catalans (Union Académique Internationale), Barcelona, Spain
- Departament d'Història i Arqueologia, Facultat de Geografia i Història, Universitat de Barcelona, Barcelona, Spain
| | - Nabil Kallala
- Ecole Tunisienne d'Histoire et d'Anthropologie, Tunis, Tunisia
- University of Tunis, Institut National du Patrimoine, Tunis, Tunisia
| | | | | | - Maria-Carme Belarte Franco
- IEC-Institut d'Estudis Catalans (Union Académique Internationale), Barcelona, Spain
- ICREA, Catalan Institution for Research and Advanced Studies, Barcelona, Spain
- ICAC (Catalan Institute of Classical Archaeology), Tarragona, Spain
| | - Silvia Valenzuela-Lamas
- Archaeology of Social Dynamics (ASD), Institució Milà i Fontanals, Consejo Superior de Investigaciones Científicas (IMF-CSIC), Barcelona, Spain
- UNIARQ - Unidade de Arqueologia, Universidade de Lisboa, Alameda da Universidade, Lisboa, Portugal
| | - Antoine Zazzo
- Centre National de Recherche Scientifique, Muséum national d'Histoire naturelle, Archéozoologie, Archéobotanique (AASPE), CP 56, Paris, France
| | - Sébastien Lepetz
- Centre National de Recherche Scientifique, Muséum national d'Histoire naturelle, Archéozoologie, Archéobotanique (AASPE), CP 56, Paris, France
| | - Sylvie Duchesne
- Centre d'Anthropobiologie et de Génomique de Toulouse, CNRS UMR 5288, Université Paul Sabatier, Faculté de Médecine Purpan, Toulouse, France
| | - Anatoly Alexeev
- Institute for Humanities Research and Indigenous Studies of the North (IHRISN), Yakutsk, Russia
| | - Jamsranjav Bayarsaikhan
- Max Planck Institute of Geoanthropology, Jena, Germany
- Institute of Archaeology, Mongolian Academy of Science, Ulaanbaatar, Mongolia
| | - Jean-Luc Houle
- Department of Folk Studies and Anthropology, Western Kentucky University, Bowling Green, KY, USA
| | - Noost Bayarkhuu
- Archaeological Research Center and Department of Anthropology and Archaeology, National University of Mongolia, Ulaanbaatar, Mongolia
| | - Tsagaan Turbat
- Archaeological Research Center and Department of Anthropology and Archaeology, National University of Mongolia, Ulaanbaatar, Mongolia
| | - Éric Crubézy
- Centre d'Anthropobiologie et de Génomique de Toulouse, CNRS UMR 5288, Université Paul Sabatier, Faculté de Médecine Purpan, Toulouse, France
| | | | - Marjan Mashkour
- Centre National de Recherche Scientifique, Muséum national d'Histoire naturelle, Archéozoologie, Archéobotanique (AASPE), CP 56, Paris, France
- Central Laboratory, Bioarchaeology Laboratory, Archaeozoology section, University of Tehran, Tehran, Iran
| | - Natalia Ya Berezina
- Research Institute and Museum of Anthropology, Lomonosov Moscow State University, Moscow, Russia
| | - Dmitriy S Korobov
- Institute of Archaeology, Russian Academy of Sciences, Moscow, Russia
| | | | | | - Jean-Paul Demoule
- UMR du CNRS 8215 Trajectoires, Institut d'Art et Archéologie, Paris, France
| | - Sabine Reinhold
- Eurasia Department of the German Archaeological Institute, Berlin, Germany
| | - Svend Hansen
- Eurasia Department of the German Archaeological Institute, Berlin, Germany
| | - Barbara Wallner
- Institute of Animal Breeding and Genetics, Department of Biomedical Sciences, University of Veterinary Medicine Vienna, Vienna, Austria
| | - Natalia Roslyakova
- Department of Russian History and Archaeology, Samara State University of Social Sciences and Education, Samara, Russia
| | - Pavel F Kuznetsov
- Department of Russian History and Archaeology, Samara State University of Social Sciences and Education, Samara, Russia
| | - Alexey A Tishkin
- Department of Archaeology, Ethnography and Museology, Altai State University, Barnaul, Russia
| | - Patrick Wincker
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Université d'Évry, Université Paris-Saclay, Évry, France
| | - Katherine Kanne
- Department of Archaeology and History, University of Exeter, Exeter, UK
- School of Archaeology, University College Dublin, Dublin, Ireland
| | - Alan Outram
- Department of Archaeology and History, University of Exeter, Exeter, UK
| | - Ludovic Orlando
- Centre d'Anthropobiologie et de Génomique de Toulouse, CNRS UMR 5288, Université Paul Sabatier, Faculté de Médecine Purpan, Toulouse, France.
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5
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Larsson MNA, Morell Miranda P, Pan L, Başak Vural K, Kaptan D, Rodrigues Soares AE, Kivikero H, Kantanen J, Somel M, Özer F, Johansson AM, Storå J, Günther T. Ancient Sheep Genomes Reveal Four Millennia of North European Short-Tailed Sheep in the Baltic Sea Region. Genome Biol Evol 2024; 16:evae114. [PMID: 38795367 PMCID: PMC11162877 DOI: 10.1093/gbe/evae114] [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: 07/18/2023] [Revised: 04/24/2024] [Accepted: 05/21/2024] [Indexed: 05/27/2024] Open
Abstract
Sheep are among the earliest domesticated livestock species, with a wide variety of breeds present today. However, it remains unclear how far back this diversity goes, with formal documentation only dating back a few centuries. North European short-tailed (NEST) breeds are often assumed to be among the oldest domestic sheep populations, even thought to represent relicts of the earliest sheep expansions during the Neolithic period reaching Scandinavia <6,000 years ago. This study sequenced the genomes (up to 11.6X) of five sheep remains from the Baltic islands of Gotland and Åland, dating from the Late Neolithic (∼4,100 cal BP) to historical times (∼1,600 CE). Our findings indicate that these ancient sheep largely possessed the genetic characteristics of modern NEST breeds, suggesting a substantial degree of long-term continuity of this sheep type in the Baltic Sea region. Despite the wide temporal spread, population genetic analyses show high levels of affinity between the ancient genomes and they also exhibit relatively high genetic diversity when compared to modern NEST breeds, implying a loss of diversity in most breeds during the last centuries associated with breed formation and recent bottlenecks. Our results shed light on the development of breeds in Northern Europe specifically as well as the development of genetic diversity in sheep breeds, and their expansion from the domestication center in general.
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Affiliation(s)
- Martin N A Larsson
- Human Evolution, Department of Organismal Biology, Uppsala University, Uppsala, Sweden
| | - Pedro Morell Miranda
- Human Evolution, Department of Organismal Biology, Uppsala University, Uppsala, Sweden
| | - Li Pan
- Human Evolution, Department of Organismal Biology, Uppsala University, Uppsala, Sweden
| | - Kıvılcım Başak Vural
- Department of Biological Sciences, Middle East Technical University, Ankara, Turkey
| | - Damla Kaptan
- Department of Biological Sciences, Middle East Technical University, Ankara, Turkey
| | | | - Hanna Kivikero
- Department of Culture, University of Helsinki, Helsinki, Finland
| | - Juha Kantanen
- Natural Resources Institute Finland, Jokioinen, Finland
| | - Mehmet Somel
- Department of Biological Sciences, Middle East Technical University, Ankara, Turkey
| | - Füsun Özer
- Department of Anthropology, Hacettepe University, Ankara, Turkey
| | - Anna M Johansson
- Department of Animal Biosciences, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Jan Storå
- Osteoarchaeological Research Laboratory, Stockholm University, Stockholm, Sweden
| | - Torsten Günther
- Human Evolution, Department of Organismal Biology, Uppsala University, Uppsala, Sweden
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6
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Fegraeus K, Rosengren MK, Naboulsi R, Orlando L, Åbrink M, Jouni A, Velie BD, Raine A, Egner B, Mattsson CM, Lång K, Zhigulev A, Björck HM, Franco-Cereceda A, Eriksson P, Andersson G, Sahlén P, Meadows JRS, Lindgren G. An endothelial regulatory module links blood pressure regulation with elite athletic performance. PLoS Genet 2024; 20:e1011285. [PMID: 38885195 PMCID: PMC11182536 DOI: 10.1371/journal.pgen.1011285] [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: 08/10/2023] [Accepted: 05/02/2024] [Indexed: 06/20/2024] Open
Abstract
The control of transcription is crucial for homeostasis in mammals. A previous selective sweep analysis of horse racing performance revealed a 19.6 kb candidate regulatory region 50 kb downstream of the Endothelin3 (EDN3) gene. Here, the region was narrowed to a 5.5 kb span of 14 SNVs, with elite and sub-elite haplotypes analyzed for association to racing performance, blood pressure and plasma levels of EDN3 in Coldblooded trotters and Standardbreds. Comparative analysis of human HiCap data identified the span as an enhancer cluster active in endothelial cells, interacting with genes relevant to blood pressure regulation. Coldblooded trotters with the sub-elite haplotype had significantly higher blood pressure compared to horses with the elite performing haplotype during exercise. Alleles within the elite haplotype were part of the standing variation in pre-domestication horses, and have risen in frequency during the era of breed development and selection. These results advance our understanding of the molecular genetics of athletic performance and vascular traits in both horses and humans.
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Affiliation(s)
- Kim Fegraeus
- Department of Medical Sciences, Science for life laboratory, Uppsala University, Sweden
| | - Maria K. Rosengren
- Department of Animal Biosciences, Swedish University of Agricultural Sciences Uppsala, Sweden
| | - Rakan Naboulsi
- Department of Animal Biosciences, Swedish University of Agricultural Sciences Uppsala, Sweden
- Childhood Cancer Research Unit, Department of Women’s and Children’s Health, Karolinska Institute, Stockholm
| | - Ludovic Orlando
- Centre d’Anthropobiologie et de Génomique de Toulouse (CNRS UMR 5288), Université Paul Sabatier, Toulouse, France
| | - Magnus Åbrink
- Department of Biomedical Sciences and Veterinary Public Health, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Ahmad Jouni
- Department of Animal Biosciences, Swedish University of Agricultural Sciences Uppsala, Sweden
| | - Brandon D. Velie
- School of Life & Environmental Sciences, University of Sydney, Sydney, Australia
| | - Amanda Raine
- Department of Medical Sciences, Science for life laboratory, Uppsala University, Sweden
| | - Beate Egner
- Department of Cardio-Vascular Research, Veterinary Academy of Higher Learning, Babenhausen, Germany
| | - C Mikael Mattsson
- Silicon Valley Exercise Analytics (svexa), MenloPark, CA, United States of America
| | - Karin Lång
- Division of Cardiovascular Medicine, Center for Molecular Medicine, Department of Medicine, Karolinska Institutet, Stockholm, Karolinska University Hospital, Solna, Sweden
| | - Artemy Zhigulev
- KTH Royal Institute of Technology, School of Chemistry, Biotechnology and Health, Science for Life Laboratory, Stockholm, Sweden
| | - Hanna M. Björck
- Division of Cardiovascular Medicine, Center for Molecular Medicine, Department of Medicine, Karolinska Institutet, Stockholm, Karolinska University Hospital, Solna, Sweden
| | - Anders Franco-Cereceda
- Section of Cardiothoracic Surgery, Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden
| | - Per Eriksson
- Division of Cardiovascular Medicine, Center for Molecular Medicine, Department of Medicine, Karolinska Institutet, Stockholm, Karolinska University Hospital, Solna, Sweden
| | - Göran Andersson
- Department of Animal Biosciences, Swedish University of Agricultural Sciences Uppsala, Sweden
| | - Pelin Sahlén
- KTH Royal Institute of Technology, School of Chemistry, Biotechnology and Health, Science for Life Laboratory, Stockholm, Sweden
| | - Jennifer R. S. Meadows
- Department of Medical Biochemistry and Microbiology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Gabriella Lindgren
- Department of Animal Biosciences, Swedish University of Agricultural Sciences Uppsala, Sweden
- Center for Animal Breeding and Genetics, Department of Biosystems, KU Leuven, Leuven, Belgium
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7
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Arefnejad B, Zeinalabedini M, Talebi R, Mardi M, Ghaffari MR, Vahidi MF, Nekouei MK, Szmatoła T, Salekdeh GH. Unveiling the population genetic structure of Iranian horses breeds by whole-genome resequencing analysis. Mamm Genome 2024; 35:201-227. [PMID: 38520527 DOI: 10.1007/s00335-024-10035-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2023] [Accepted: 02/14/2024] [Indexed: 03/25/2024]
Abstract
Preserving genetic diversity is pivotal for enhancing genetic improvement and facilitating adaptive responses to selection. This study focuses on identifying key genetic variants, including single nucleotide polymorphisms (SNPs), insertion/deletion polymorphisms (INDELs), and copy number variants (CNVs), while exploring the genomic evolutionary connectedness among seven Iranian horses representing five indigenous breeds: Caspian, Turkemen, DareShuri, Kurdish, and Asil. Using whole-genome resequencing, we generated 2.7 Gb of sequence data, with raw reads ranging from 1.2 Gb for Caspian horses to 0.38 Gb for Turkoman horses. Post-filtering, approximately 1.9 Gb of reads remained, with ~ 1.5 Gb successfully mapped to the horse reference genome (EquCab3.0), achieving mapping rates between 76.4% (Caspian) and 98.35% (Turkoman). We identified 2,909,816 SNPs in Caspian horses, constituting around 0.1% of the genome. Notably, 71% of these SNPs were situated in intergenic regions, while 8.5 and 6.8% were located upstream and downstream, respectively. A comparative analysis of SNPs between Iranian and non-Iranian horse breeds showed that Caspian horses had the lowest number of shared SNPs with Turkoman horses. Instead, they showed a closer genetic relationship with DareShuri, Quarter, Arabian, Standardbred, and Asil breeds. Hierarchical clustering highlighted Caspian horses as a distinct cluster, underscoring their distinctive genomic signature. Caspian horses exhibit a unique genetic profile marked by an enrichment of private mutations in neurological genes, influencing sensory perception and awareness. This distinct genetic makeup shapes mating preferences and signifies a separate evolutionary trajectory. Additionally, significant non-synonymous single nucleotide polymorphisms (nsSNPs) in reproductive genes offer intervention opportunities for managing Caspian horses. These findings reveal the population genetic structure of Iranian horse breeds, contributing to the advancement of knowledge in areas such as conservation, performance traits, climate adaptation, reproduction, and resistance to diseases in equine science.
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Affiliation(s)
- Babak Arefnejad
- Department of Animal Science, University of Tehran, Karaj, Iran
| | - Mehrshad Zeinalabedini
- Department of Systems and Synthetic Biology, Agricultural Biotechnology Research Institute of Iran, Agricultural Research, Education and Extension Organization (AREEO), Karaj, Iran.
| | - Reza Talebi
- Department of Systems and Synthetic Biology, Agricultural Biotechnology Research Institute of Iran, Agricultural Research, Education and Extension Organization (AREEO), Karaj, Iran
| | - Mohsen Mardi
- Department of Systems and Synthetic Biology, Agricultural Biotechnology Research Institute of Iran, Agricultural Research, Education and Extension Organization (AREEO), Karaj, Iran
| | - Mohammad Reza Ghaffari
- Department of Systems and Synthetic Biology, Agricultural Biotechnology Research Institute of Iran, Agricultural Research, Education and Extension Organization (AREEO), Karaj, Iran
| | - Mohammad Farhad Vahidi
- Department of Systems and Synthetic Biology, Agricultural Biotechnology Research Institute of Iran, Agricultural Research, Education and Extension Organization (AREEO), Karaj, Iran
| | | | - Tomasz Szmatoła
- Centre of Experimental and Innovative Medicine, University of Agriculture in Kraków, Al. Mickiewicza 24/28, 30-059, Kraków, Poland
- Department of Animal Molecular Biology, National Research Institute of Animal Production, Krakowska 1, 32‑083, Balice, Poland
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8
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Martin-Roy R, Thyrring J, Mata X, Bangsgaard P, Bennike O, Christiansen G, Funder S, Gotfredsen AB, Gregersen KM, Hansen CH, Ilsøe PC, Klassen L, Kristensen IK, Ravnholt GB, Marin F, Der Sarkissian C. Advancing responsible genomic analyses of ancient mollusc shells. PLoS One 2024; 19:e0302646. [PMID: 38709766 PMCID: PMC11073703 DOI: 10.1371/journal.pone.0302646] [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: 01/12/2024] [Accepted: 04/09/2024] [Indexed: 05/08/2024] Open
Abstract
The analysis of the DNA entrapped in ancient shells of molluscs has the potential to shed light on the evolution and ecology of this very diverse phylum. Ancient genomics could help reconstruct the responses of molluscs to past climate change, pollution, and human subsistence practices at unprecedented temporal resolutions. Applications are however still in their infancy, partly due to our limited knowledge of DNA preservation in calcium carbonate shells and the need for optimized methods for responsible genomic data generation. To improve ancient shell genomic analyses, we applied high-throughput DNA sequencing to 27 Mytilus mussel shells dated to ~111-6500 years Before Present, and investigated the impact, on DNA recovery, of shell imaging, DNA extraction protocols and shell sub-sampling strategies. First, we detected no quantitative or qualitative deleterious effect of micro-computed tomography for recording shell 3D morphological information prior to sub-sampling. Then, we showed that double-digestion and bleach treatment of shell powder prior to silica-based DNA extraction improves shell DNA recovery, also suggesting that DNA is protected in preservation niches within ancient shells. Finally, all layers that compose Mytilus shells, i.e., the nacreous (aragonite) and prismatic (calcite) carbonate layers, with or without the outer organic layer (periostracum) proved to be valuable DNA reservoirs, with aragonite appearing as the best substrate for genomic analyses. Our work contributes to the understanding of long-term molecular preservation in biominerals and we anticipate that resulting recommendations will be helpful for future efficient and responsible genomic analyses of ancient mollusc shells.
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Affiliation(s)
- Raphaël Martin-Roy
- Centre for Anthropobiology and Genomics of Toulouse, UMR5288, CNRS, University Paul Sabatier, Toulouse, France
| | - Jakob Thyrring
- Department of Ecoscience, Aarhus University, Aarhus, Denmark
- Arctic Research Centre, Aarhus University, Aarhus, Denmark
| | - Xavier Mata
- Centre for Anthropobiology and Genomics of Toulouse, UMR5288, CNRS, University Paul Sabatier, Toulouse, France
| | - Pernille Bangsgaard
- Globe Institute, Section for GeoGenetics, University of Copenhagen, Copenhagen, Denmark
| | - Ole Bennike
- Geological Survey of Denmark and Greenland, Copenhagen, Denmark
| | | | - Svend Funder
- Globe Institute, Section for GeoGenetics, University of Copenhagen, Copenhagen, Denmark
| | | | | | | | - Peter Carsten Ilsøe
- Globe Institute, Section for GeoGenetics, University of Copenhagen, Copenhagen, Denmark
| | | | | | | | - Frédéric Marin
- Biogéosciences, UMR6282, CNRS-EPHE-uB, University of Burgundy, EPHE, Dijon, France
| | - Clio Der Sarkissian
- Centre for Anthropobiology and Genomics of Toulouse, UMR5288, CNRS, University Paul Sabatier, Toulouse, France
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9
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Askari Z, Sazmand A, Mowlavi G, Rühli F, Naddaf SR, Rezaeian M, Stöllner T, Aali A, Paknezhad N, Otranto D. Eimeria leuckarti in equid coprolites from the Sassanid Era (2nd-6th century CE) excavated in Chehrabad Salt Mine archaeological site, Iran. INTERNATIONAL JOURNAL OF PALEOPATHOLOGY 2024; 44:27-32. [PMID: 38043140 DOI: 10.1016/j.ijpp.2023.11.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/24/2023] [Revised: 10/21/2023] [Accepted: 11/24/2023] [Indexed: 12/05/2023]
Abstract
OBJECTIVE This study reports coccidian oocysts in an equid coprolite dated to the Sassanid Empire (2nd-6th century CE) recovered in Chehrabad Salt Mine archaeological site, Iran. METHODS Between 2015 and 2017, an archaeoparasitological investigation led to the discovery of an equid coprolite in the Chehrabad Salt Mine archeological site, (Douzlakh), western Iran. Samples were rehydrated using trisodium phosphate solution and were examined by light microscopy. RESULTS Seven oocysts of Eimeria leuckarti (Flesch, 1883) were identified; they were in various stages of sporulation. CONCLUSION This is the first report of ancient coccidian oocysts from equids. The importance of this observation is discussed, and current knowledge of eimeriid oocysts at archaeological sites is reviewed. SIGNIFICANCE The observations of E. leuckarti increases current knowledge of parasite biodiversity in ancient Iran when it rested along the Silk Road, a network of trade routes connecting the East and West that was central to economic, cultural, political, and religious interactions between these regions, and to livestock movement that could contribute to the transmission of the parasites from/to other regions. LIMITATIONS The contextual information about animal species present in and around the Salt Mine during its working periods, including Achaemenid dynasty (6th to 4th century BCE) and Sassanid era (2nd to 6th century CE), is very limited and does not allow secure conclusions regarding the host origin of the coprolites. SUGGESTIONS FOR FURTHER RESEARCH Application of molecular biology tools to identify the correct host origin of the coprolites and to detect more parasite species is advocated.
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Affiliation(s)
- Zeynab Askari
- Department of Parasitology and Mycology, School of Public Health, Tehran University of Medical Sciences, Tehran, Iran
| | - Alireza Sazmand
- Department of Pathobiology, Faculty of Veterinary Medicine, Bu-Ali Sina University, Hamedan, Iran.
| | - Gholamreza Mowlavi
- Department of Parasitology and Mycology, School of Public Health, Tehran University of Medical Sciences, Tehran, Iran; Center for Research of Endemic Parasites of Iran (CREPI), Tehran University of Medical Sciences, Tehran, Iran.
| | - Frank Rühli
- Institute of Evolutionary Medicine, University of Zurich, Switzerland
| | | | - Mostafa Rezaeian
- Department of Parasitology and Mycology, School of Public Health, Tehran University of Medical Sciences, Tehran, Iran
| | - Thomas Stöllner
- Ruhr-University Bochum, Institute for Archaeological Science, Bochum, Germany; German Mining Museum, Bochum, Germany
| | | | - Niloofar Paknezhad
- Department of Parasitology and Mycology, School of Public Health, Tehran University of Medical Sciences, Tehran, Iran
| | - Domenico Otranto
- Department of Pathobiology, Faculty of Veterinary Medicine, Bu-Ali Sina University, Hamedan, Iran; Department of Veterinary Medicine, University of Bari, Valenzano 70010, Bari, Italy
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10
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De Coster T, Zhao Y, Tšuiko O, Demyda-Peyrás S, Van Soom A, Vermeesch JR, Smits K. Genome-wide equine preimplantation genetic testing enabled by simultaneous haplotyping and copy number detection. Sci Rep 2024; 14:2003. [PMID: 38263320 PMCID: PMC10805710 DOI: 10.1038/s41598-023-48103-7] [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: 06/28/2023] [Accepted: 11/22/2023] [Indexed: 01/25/2024] Open
Abstract
In different species, embryonic aneuploidies and genome-wide errors are a major cause of developmental failure. The increasing number of equine embryos being produced worldwide provides the opportunity to characterize and rank or select embryos based on their genetic profile prior to transfer. Here, we explored the possibility of generic, genome-wide preimplantation genetic testing concurrently for aneuploidies (PGT-A) and monogenic (PGT-M) traits and diseases in the horse, meanwhile assessing the incidence and spectrum of chromosomal and genome-wide errors in in vitro-produced equine embryos. To this end, over 70,000 single nucleotide polymorphism (SNP) positions were genotyped in 14 trophectoderm biopsies and corresponding biopsied blastocysts, and in 26 individual blastomeres from six arrested cleavage-stage embryos. Subsequently, concurrent genome-wide copy number detection and haplotyping by haplarithmisis was performed and the presence of aneuploidies and genome-wide errors and the inherited parental haplotypes for four common disease-associated genes with high carrier frequency in different horse breeds (GBE1, PLOD1, B3GALNT2, MUTYH), and for one color coat-associated gene (STX17) were compared in biopsy-blastocyst combinations. The euploid (n = 12) or fully aneuploid (n = 2) state and the inherited parental haplotypes for 42/45 loci of interest of the biopsied blastocysts were predicted by the biopsy samples in all successfully analyzed biopsy-blastocyst combinations (n = 9). Two biopsies showed a loss of maternal chromosome 28 and 31, respectively, which were confirmed in the corresponding blastocysts. In one of those biopsies, additional complex aneuploidies not present in the blastocyst were found. Five out of six arrested embryos contained chromosomal and/or genome-wide errors in most of their blastomeres, demonstrating their contribution to equine embryonic arrest in vitro. The application of the described PGT strategy would allow to select equine embryos devoid of genetic errors and pathogenetic variants, and with the variants of interest, which will improve foaling rate and horse quality. We believe this approach will be a gamechanger in horse breeding.
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Affiliation(s)
- T De Coster
- Department of Internal Medicine, Reproduction and Population Medicine, Ghent University, Merelbeke, Belgium.
- Department of Human Genetics, KU Leuven, Leuven, Belgium.
| | - Y Zhao
- Department of Human Genetics, KU Leuven, Leuven, Belgium
| | - O Tšuiko
- Department of Human Genetics, KU Leuven, Leuven, Belgium
| | - S Demyda-Peyrás
- Department of Genetics, University of Córdoba, Córdoba, Spain
- Department of Animal Production, Veterinary School, National University of La Plata, La Plata, Argentina
| | - A Van Soom
- Department of Internal Medicine, Reproduction and Population Medicine, Ghent University, Merelbeke, Belgium
| | - J R Vermeesch
- Department of Human Genetics, KU Leuven, Leuven, Belgium
| | - K Smits
- Department of Internal Medicine, Reproduction and Population Medicine, Ghent University, Merelbeke, Belgium.
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11
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Lebrasseur O, More KD, Orlando L. Equine herpesvirus 4 infected domestic horses associated with Sintashta spoke-wheeled chariots around 4,000 years ago. Virus Evol 2024; 10:vead087. [PMID: 38465241 PMCID: PMC10924538 DOI: 10.1093/ve/vead087] [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: 06/28/2023] [Revised: 11/27/2023] [Accepted: 01/11/2024] [Indexed: 03/12/2024] Open
Abstract
Equine viral outbreaks have disrupted the socio-economic life of past human societies up until the late 19th century and continue to be of major concern to the horse industry today. With a seroprevalence of 60-80 per cent, equine herpesvirus 4 (EHV-4) is the most common horse pathogen on the planet. Yet, its evolutionary history remains understudied. Here, we screen the sequenced data of 264 archaeological horse remains to detect the presence of EHV-4. We recover the first ancient EHV-4 genome with 4.2× average depth-of-coverage from a specimen excavated in the Southeastern Urals and dated to the Early Bronze Age period, approximately 3,900 years ago. The recovery of an EHV-4 virus outside the upper respiratory tract not only points to an animal particularly infected but also highlights the importance of post-cranial bones in pathogen characterisation. Bayesian phylogenetic reconstruction provides a minimal time estimate for EHV-4 diversification to around 4,000 years ago, a time when modern domestic horses spread across the Central Asian steppes together with spoke-wheeled Sintashta chariots, or earlier. The analyses also considerably revise the diversification time of the two EHV-4 subclades from the 16th century based solely on modern data to nearly a thousand years ago. Our study paves the way for a robust reconstruction of the history of non-human pathogens and their impact on animal health.
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Affiliation(s)
- Ophélie Lebrasseur
- Centre for Anthropobiology and Genomics of Toulouse (CAGT), CNRS/Université Paul Sabatier, 37 Allées Jules Guesde, 31000, Toulouse, France
- Instituto Nacional de Antropología y Pensamiento Latinoamericano, 3 de Febrero 1370 (1426), Ciudad Autónoma de Buenos Aires, Argentina
| | - Kuldeep Dilip More
- Centre for Anthropobiology and Genomics of Toulouse (CAGT), CNRS/Université Paul Sabatier, 37 Allées Jules Guesde, 31000, Toulouse, France
| | - Ludovic Orlando
- Centre for Anthropobiology and Genomics of Toulouse (CAGT), CNRS/Université Paul Sabatier, 37 Allées Jules Guesde, 31000, Toulouse, France
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12
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Yordanov G, Palova N, Mehandjyiski I, Hristov P. Mitochondrial DNA sequencing illuminates genetic diversity and origin of Hunagrian Nonius horse breed and his relatives - Danubian horse and Serbian Nonius. Anim Biotechnol 2023; 34:3897-3907. [PMID: 37489100 DOI: 10.1080/10495398.2023.2237533] [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] [Indexed: 07/26/2023]
Abstract
From a historical perspective, horse breeding in Bulgaria has been very well developed since the time of the Thracians (early Bronze Age c. 3000 BCE). Archaeological discoveries from this era present us with an extremely rich type diversity, including wild and local primitive horses, the prototype of heavy draft horses, and fine riding horses.The objective of this study was to investigate the genetic structure of unexamined populations of three closely related horse breeds - the Danubian Nonius Hungarian Nonius and Serbian Nonius horses. A 608 bp long fragment of the mtDNA D-loop region was amplified and sequenced. The obtained results showed completely different genetic profiles between the investigated breeds. We identified nine of the 17 haplogroups described in modern horses. Most of the obtained sequences fell into M, L, G, and O'P lineages, which reflects the genetic profiles of the ancestral mares that were probably used at the initial stages of formation of the breeds. The population of the Danubian horse was characterized by a high prevalence of Central Asian specific haplogroup G (45%), followed by Western Eurasian specific haplogroups L and M (both about 21%). In contrast to the Danubian horse, in the Nonius breed the highest frequency of Western Eurasian haplogroup M (43.5%) was found, followed by Middle Eastern haplogroups O'P (26.1%) Central Asian specific E (13.0%) and G (13.1%). The Serbian Nonius horse showed a completely different genetic profile with a prevalence of the rare for Europe haplogroup D (66.7%), followed by Central Asian specific G (16.7%). The high mitochondrial haplotype diversity (Hd = 0.886) found in the investigated samples is evidence for multiple maternal origins in all populations.In conclusion, the obtained results demonstrated a high percentage of haplogroup sharing especially in the Danubian and Hungarian Nonius horse breeds, which reflects the possible common origins of the two breeds. In contrast to these breeds, the Serbian Nonius, despite the small number of investigated animals, showed a specific genetic profile, which could be explained by different and independent origins.
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Affiliation(s)
- Georgi Yordanov
- Executive Agency for Selection and Reproduction in Animal Breeding, Sofia, Bulgaria
| | - Nadezhda Palova
- Scientific Center of Agriculture, Agricultural Academy, Sredets, Bulgaria
| | - Ivan Mehandjyiski
- Research Centre of Stockbreeding and Agriculture, Agricultural Academy, Smolyan, Bulgaria
| | - Peter Hristov
- Department of Animal Diversity and Resources, Institute of Biodiversity and Ecosystem Research, Bulgarian Academy of Sciences, Sofia, Bulgaria
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13
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Manunza A, Ramirez-Diaz J, Cozzi P, Lazzari B, Tosser-Klopp G, Servin B, Johansson AM, Grøva L, Berg P, Våge DI, Stella A. Genetic diversity and historical demography of underutilised goat breeds in North-Western Europe. Sci Rep 2023; 13:20728. [PMID: 38007600 PMCID: PMC10676416 DOI: 10.1038/s41598-023-48005-8] [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: 06/22/2023] [Accepted: 11/21/2023] [Indexed: 11/27/2023] Open
Abstract
In the last decade, several studies aimed at dissecting the genetic architecture of local small ruminant breeds to discover which variations are involved in the process of adaptation to environmental conditions, a topic that has acquired priority due to climate change. Considering that traditional breeds are a reservoir of such important genetic variation, improving the current knowledge about their genetic diversity and origin is the first step forward in designing sound conservation guidelines. The genetic composition of North-Western European archetypical goat breeds is still poorly exploited. In this study we aimed to fill this gap investigating goat breeds across Ireland and Scandinavia, including also some other potential continental sources of introgression. The PCA and Admixture analyses suggest a well-defined cluster that includes Norwegian and Swedish breeds, while the crossbred Danish landrace is far apart, and there appears to be a close relationship between the Irish and Saanen goats. In addition, both graph representation of historical relationships among populations and f4-ratio statistics suggest a certain degree of gene flow between the Norse and Atlantic landraces. Furthermore, we identify signs of ancient admixture events of Scandinavian origin in the Irish and in the Icelandic goats. The time when these migrations, and consequently the introgression, of Scandinavian-like alleles occurred, can be traced back to the Viking colonisation of these two isles during the Viking Age (793-1066 CE). The demographic analysis indicates a complicated history of these traditional breeds with signatures of bottleneck, inbreeding and crossbreeding with the improved breeds. Despite these recent demographic changes and the historical genetic background shaped by centuries of human-mediated gene flow, most of them maintained their genetic identity, becoming an irreplaceable genetic resource as well as a cultural heritage.
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Affiliation(s)
- Arianna Manunza
- Institute of Agricultural Biology and Biotechnology, National Research Council, via Edoardo Bassini, 15, 20133, Milan, Italy.
| | - Johanna Ramirez-Diaz
- Institute of Agricultural Biology and Biotechnology, National Research Council, via Edoardo Bassini, 15, 20133, Milan, Italy
| | - Paolo Cozzi
- Institute of Agricultural Biology and Biotechnology, National Research Council, via Edoardo Bassini, 15, 20133, Milan, Italy
| | - Barbara Lazzari
- Institute of Agricultural Biology and Biotechnology, National Research Council, via Edoardo Bassini, 15, 20133, Milan, Italy
| | | | - Bertrand Servin
- GenPhySE, Université de Toulouse, INRAE, ENVT, 31326, Castanet-Tolosan, France
| | - Anna M Johansson
- Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, Box 7023, 75007, Uppsala, Sweden
| | - Lise Grøva
- Norwegian Institute of Bioeconomy Research, Gunnars vei 6, NO-6630, Tingvoll, Norway
| | - Peer Berg
- Faculty of Biosciences, NMBU, Norwegian University of Life Sciences, P.O. Box 5003, N-1432, ÅS, Norway
| | - Dag Inge Våge
- Faculty of Biosciences, NMBU, Norwegian University of Life Sciences, P.O. Box 5003, N-1432, ÅS, Norway
| | - Alessandra Stella
- Institute of Agricultural Biology and Biotechnology, National Research Council, via Edoardo Bassini, 15, 20133, Milan, Italy
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14
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Gu J, Li S, Zhu B, Liang Q, Chen B, Tang X, Chen C, Wu DD, Li Y. Genetic variation and domestication of horses revealed by 10 chromosome-level genomes and whole-genome resequencing. Mol Ecol Resour 2023; 23:1656-1672. [PMID: 37259205 DOI: 10.1111/1755-0998.13818] [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: 11/03/2022] [Revised: 03/07/2023] [Accepted: 05/12/2023] [Indexed: 06/02/2023]
Abstract
Understanding the genetic variations of the horse (Equus caballus) genome will improve breeding conservation and welfare. However, genetic variations in long segments, such as structural variants (SVs), remain understudied. We de novo assembled 10 chromosome-level three-dimensional horse genomes, each representing a distinct breed, and analysed horse SVs using a multi-assembly approach. Our findings suggest that SVs with the accumulation of mammalian-wide interspersed repeats related to long interspersed nuclear elements might be a horse-specific mechanism to modulate genome-wide gene regulatory networks. We found that olfactory receptors were commonly loss and accumulated deleterious mutations, but no purge of deleterious mutations occurred during horse domestication. We examined the potential effects of SVs on the spatial structure of chromatin via topologically associating domains (TADs). Breed-specific TADs were significantly enriched by breed-specific SVs. We identified 4199 unique breakpoint-resolved novel insertions across all chromosomes that account for 2.84 Mb sequences missing from the reference genome. Several novel insertions might have potential functional consequences, as 519 appeared to reside within 449 gene bodies. These genes are primarily involved in pathogen recognition, innate immune responses and drug metabolism. Moreover, 37 diverse horses were resequenced. Combining this with public data, we analysed 97 horses through a comparative population genomics approach to identify the genetic basis underlying breed characteristics using Thoroughbreds as a case study. We provide new scientific evidence for horse domestication, an understanding of the genetic mechanism underlying the phenotypic evolution of horses, and a comprehensive genetic variation resource for further genetic studies of horses.
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Affiliation(s)
- Jingjing Gu
- College of Animal Science and Technology, Hunan Agricultural University, Changsha, China
- Hunan Provincial Key Laboratory for Genetic Improvement of Domestic Animal, Changsha, China
| | - Sheng Li
- Maxun Biotechnology Institute, Changsha, China
| | - Bo Zhu
- Novogene Bioinformatics Institute, Beijing, China
| | - Qiqi Liang
- Key Laboratory of Pig Genetics and Breeding of Ministry of Agriculture & Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, Huazhong Agricultural University, Wuhan, China
| | - Bin Chen
- College of Animal Science and Technology, Hunan Agricultural University, Changsha, China
- Hunan Provincial Key Laboratory for Genetic Improvement of Domestic Animal, Changsha, China
| | - Xiangwei Tang
- College of Animal Science and Technology, Hunan Agricultural University, Changsha, China
- Hunan Provincial Key Laboratory for Genetic Improvement of Domestic Animal, Changsha, China
| | - Chujie Chen
- College of Animal Science and Technology, Hunan Agricultural University, Changsha, China
- Hunan Provincial Key Laboratory for Genetic Improvement of Domestic Animal, Changsha, China
| | - Dong-Dong Wu
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
| | - Yan Li
- State Key Laboratory for Conservation and Utilization of Bio-Resource, Yunnan University, Kunming, China
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15
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Atağ G, Vural KB, Kaptan D, Özkan M, Koptekin D, Sağlıcan E, Doğramacı S, Köz M, Yılmaz A, Söylev A, Togan İ, Somel M, Özer F. MTaxi: A comparative tool for taxon identification of ultra low coverage ancient genomes. OPEN RESEARCH EUROPE 2023; 2:100. [PMID: 37829208 PMCID: PMC10565424 DOI: 10.12688/openreseurope.14936.3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Accepted: 09/26/2023] [Indexed: 10/14/2023]
Abstract
A major challenge in zooarchaeology is to morphologically distinguish closely related species' remains, especially using small bone fragments. Shotgun sequencing aDNA from archeological remains and comparative alignment to the candidate species' reference genomes will only apply when reference nuclear genomes of comparable quality are available, and may still fail when coverages are low. Here, we propose an alternative method, MTaxi, that uses highly accessible mitochondrial DNA (mtDNA) to distinguish between pairs of closely related species from ancient DNA sequences. MTaxi utilises mtDNA transversion-type substitutions between pairs of candidate species, assigns reads to either species, and performs a binomial test to determine the sample taxon. We tested MTaxi on sheep/goat and horse/donkey data, between which zooarchaeological classification can be challenging in ways that epitomise our case. The method performed efficiently on simulated ancient genomes down to 0.3x mitochondrial coverage for both sheep/goat and horse/donkey, with no false positives. Trials on n=18 ancient sheep/goat samples and n=10 horse/donkey samples of known species identity also yielded 100% accuracy. Overall, MTaxi provides a straightforward approach to classify closely related species that are difficult to distinguish through zooarchaeological methods using low coverage aDNA data, especially when similar quality reference genomes are unavailable. MTaxi is freely available at https://github.com/goztag/MTaxi.
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Affiliation(s)
- Gözde Atağ
- Biological Sciences, Middle East Technical University, Ankara, Turkey
| | | | - Damla Kaptan
- Biological Sciences, Middle East Technical University, Ankara, Turkey
| | - Mustafa Özkan
- Biological Sciences, Middle East Technical University, Ankara, Turkey
| | - Dilek Koptekin
- Biological Sciences, Middle East Technical University, Ankara, Turkey
- Health Informatics, Middle East Technical University, Ankara, Turkey
| | - Ekin Sağlıcan
- Health Informatics, Middle East Technical University, Ankara, Turkey
| | - Sevcan Doğramacı
- Computer Engineering, Konya Food and Agriculture University, Konya, Turkey
| | - Mevlüt Köz
- Molecular Biology and Genetics, Konya Food and Agriculture University, Konya, Turkey
| | - Ardan Yılmaz
- Computer Engineering, Middle East Technical University, Ankara, Turkey
| | - Arda Söylev
- Computer Engineering, Konya Food and Agriculture University, Konya, Turkey
| | - İnci Togan
- Biological Sciences, Middle East Technical University, Ankara, Turkey
| | - Mehmet Somel
- Biological Sciences, Middle East Technical University, Ankara, Turkey
| | - Füsun Özer
- Anthropology, Hacettepe University, Ankara, Turkey
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16
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Sheikh A. Mitochondrial DNA sequencing of Kehilan and Hamdani horses from Saudi Arabia. Saudi J Biol Sci 2023; 30:103741. [PMID: 37575470 PMCID: PMC10413190 DOI: 10.1016/j.sjbs.2023.103741] [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: 05/29/2023] [Revised: 07/04/2023] [Accepted: 07/14/2023] [Indexed: 08/15/2023] Open
Abstract
The Arabian horse breed is well known for its purity and played a key role in the genetic improvement of other horses worldwide. The mitochondrial genome plays a vital role in maternal inheritance and it's helpful to evaluate its genetic diversity and conservation. It has higher mutation rates than nuclear DNA in vertebrates and therefore reveals phylogenetic relationships and haplotypes. In this study, the mitochondrial genome mutations in two Saudi horse strains, Kehilan and Hamdani demonstrated various changes in the gene and amino acid levels and included two other Saudi horses (Hadban and Seglawi) from the previous study for phylogenetic comparison. The whole mitochondrial genome sequencing resulted in intra and inter mtDNA variations between the studied horses. Interestingly, the Hamdani horse has nucleotide substitutions similar to those of the Hadban horse, which is reflected in the phylogenetic tree as a significantly close relationship. This type of study provides a better understanding of mitogenome structure and conservation of livestock species genetic data.
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Affiliation(s)
- Abdullah Sheikh
- Camel Research Center, King Faisal University, P.O. Box 400, Al-Ahsa 31982, Saudi Arabia
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17
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Vincelette A. The Characteristics, Distribution, Function, and Origin of Alternative Lateral Horse Gaits. Animals (Basel) 2023; 13:2557. [PMID: 37627349 PMCID: PMC10451235 DOI: 10.3390/ani13162557] [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: 06/15/2023] [Revised: 08/03/2023] [Accepted: 08/04/2023] [Indexed: 08/27/2023] Open
Abstract
This article traces the characteristics, origin, distribution, and function of alternative lateral horse gaits, i.e., intermediate speed lateral-sequence gaits. Such alternative lateral gaits (running walk, rack, broken pace, hard pace, and broken trot) are prized by equestrians today for their comfort and have been found in select horse breeds for hundreds of years and even exhibited in fossil equid trackways. After exploring the evolution and development of alternative lateral gaits via fossil equid trackways, human art, and historical writings, the functional and genetic factors that led to the genesis of these gaits are discussed. Such gaited breeds were particularly favored and spread by the Scythians, Celts, Turks, and Spaniards. Fast and low-swinging hard pacing gaits are common in several horse breeds of mountainous areas of East and North Asia; high-stepping rack and running walk gaits are often displayed in European and North and South American breeds; the broken pace is found in breeds of Central Asia, Southeast Asia, West Asia, Western North America, and Brazil in South America; and the broken trot occurs in breeds of North Asia, South Asia, the Southern United States, and Brazil in South America, inhabiting desert or marshy areas.
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Affiliation(s)
- Alan Vincelette
- Department of Pretheology, St. John's Seminary, 5012 Seminary Road, Camarillo, CA 93021, USA
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18
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Kusliy MA, Yurlova AA, Neumestova AI, Vorobieva NV, Gutorova NV, Molodtseva AS, Trifonov VA, Popova KO, Polosmak NV, Molodin VI, Vasiliev SK, Semibratov VP, Iderkhangai TO, Kovalev AA, Erdenebaatar D, Graphodatsky AS, Tishkin AA. Genetic History of the Altai Breed Horses: From Ancient Times to Modernity. Genes (Basel) 2023; 14:1523. [PMID: 37628575 PMCID: PMC10454587 DOI: 10.3390/genes14081523] [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: 05/20/2023] [Revised: 06/16/2023] [Accepted: 07/21/2023] [Indexed: 08/27/2023] Open
Abstract
This study focuses on expanding knowledge about the genetic diversity of the Altai horse native to Siberia. While studying modern horses from two Altai regions, where horses were subjected to less crossbreeding, we tested the hypothesis, formulated on the basis of morphological data, that the Altai horse is represented by two populations (Eastern and Southern) and that the Mongolian horse has a greater genetic proximity to Eastern Altai horses. Bone samples of ancient horses from different cultures of Altai were investigated to clarify the genetic history of this horse breed. As a genetic marker, we chose hypervariable region I of mitochondrial DNA. The results of the performed phylogenetic and population genetic analyses of our and previously published data confirmed the hypothesis stated above. As we found out, almost all the haplotypes of the ancient domesticated horses of Altai are widespread among modern Altai horses. The differences between the mitochondrial gene pools of the ancient horses of Altai and Mongolia are more significant than between those of modern horses of the respective regions, which is most likely due to an increase in migration processes between these regions after the Early Iron Age.
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Affiliation(s)
- Mariya A Kusliy
- Department of the Diversity and Evolution of Genomes, Institute of Molecular and Cellular Biology SB RAS, 630090 Novosibirsk, Russia
| | - Anna A Yurlova
- Laboratory of Genomics, Department of Regulation of Genetic Processes, Institute of Molecular and Cellular Biology SB RAS, 630090 Novosibirsk, Russia
| | - Alexandra I Neumestova
- Department of the Diversity and Evolution of Genomes, Institute of Molecular and Cellular Biology SB RAS, 630090 Novosibirsk, Russia
| | - Nadezhda V Vorobieva
- Department of the Diversity and Evolution of Genomes, Institute of Molecular and Cellular Biology SB RAS, 630090 Novosibirsk, Russia
| | - Natalya V Gutorova
- Department of Human Molecular Genetics, Institute of Cytology and Genetics SB RAS, 630090 Novosibirsk, Russia
| | - Anna S Molodtseva
- Department of the Diversity and Evolution of Genomes, Institute of Molecular and Cellular Biology SB RAS, 630090 Novosibirsk, Russia
| | - Vladimir A Trifonov
- Department of the Diversity and Evolution of Genomes, Institute of Molecular and Cellular Biology SB RAS, 630090 Novosibirsk, Russia
| | - Kseniya O Popova
- Department of the Diversity and Evolution of Genomes, Institute of Molecular and Cellular Biology SB RAS, 630090 Novosibirsk, Russia
| | - Natalia V Polosmak
- Paleometal Archeology Department, Institute of Archaeology and Ethnography SB RAS, 630090 Novosibirsk, Russia
| | - Vyacheslav I Molodin
- Paleometal Archeology Department, Institute of Archaeology and Ethnography SB RAS, 630090 Novosibirsk, Russia
| | - Sergei K Vasiliev
- Paleometal Archeology Department, Institute of Archaeology and Ethnography SB RAS, 630090 Novosibirsk, Russia
| | - Vladimir P Semibratov
- Department of Archaeology, Ethnography and Museology, Altai State University, 656049 Barnaul, Russia
| | - Tumur-O Iderkhangai
- Department of Archaeology, Ulaanbaatar School, National University of Mongolia, 13343 Ulaanbaatar, Mongolia
| | - Alexey A Kovalev
- Department of Archaeological Heritage Preservation, Institute of Archaeology of the Russian Academy of Sciences, 117292 Moscow, Russia
| | - Diimaajav Erdenebaatar
- Department of Archaeology, Ulaanbaatar School, National University of Mongolia, 13343 Ulaanbaatar, Mongolia
| | - Alexander S Graphodatsky
- Department of the Diversity and Evolution of Genomes, Institute of Molecular and Cellular Biology SB RAS, 630090 Novosibirsk, Russia
| | - Alexey A Tishkin
- Department of Archaeology, Ethnography and Museology, Altai State University, 656049 Barnaul, Russia
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19
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May-Davis S, Dzingle D, Saber E, Blades Eckelbarger P. Characterization of the Caudal Ventral Tubercle in the Sixth Cervical Vertebra in Modern Equus ferus caballus. Animals (Basel) 2023; 13:2384. [PMID: 37508161 PMCID: PMC10376820 DOI: 10.3390/ani13142384] [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: 06/01/2023] [Revised: 07/10/2023] [Accepted: 07/20/2023] [Indexed: 07/30/2023] Open
Abstract
This study examined the anomalous variations of the ventral process of C6 in modern E. ferus caballus. The aim was to provide an incremental grading protocol measuring the absence of the caudal ventral tubercle (CVT) in this ventral process. The findings revealed the most prevalent absent CVT (aCVT) was left unilateral (n = 35), with bilateral (n = 29) and right unilateral (n = 12). Grading was determined in equal increments of absence 1/4, 2/4, 3/4, with 4/4 representing a complete aCVT in 56/76, with a significance of p = 0.0013. This also applied to bilateral specimens. In those C6 osseous specimens displaying a 4/4 grade aCVT, 41/56 had a partial absence of the caudal aspect of the cranial ventral tubercle (CrVT). Here, grading absent CrVTs (aCrVT) followed similarly to aCVTs, though 4/4 was not observed. The significance between 4/4 grade aCVTs and the presentation of an aCrVT was left p = 0.00001 and right p = 0.00018. In bilateral specimens, C6 morphologically resembled C5, implying a homeotic transformation that limited the attachment sites for the cranial and thoracal longus colli muscle. This potentially diminishes function and caudal cervical stability. Therefore, it is recommended that further studies examine the morphological extent of this equine complex vertebral malformation (ECVM) as well as its interrelationships and genetic code/blueprint.
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Affiliation(s)
- Sharon May-Davis
- Canine and Equine Research Group, University of New England, Armidale, NSW 2351, Australia
| | - Diane Dzingle
- Equus Soma-Equine Osteology and Anatomy Learning Center, Aiken, SC 29805, USA
| | - Elle Saber
- Biological Data Science Institute, Australian National University, Canberra, ACT 2601, Australia
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20
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Todd ET, Fromentier A, Sutcliffe R, Running Horse Collin Y, Perdereau A, Aury JM, Èche C, Bouchez O, Donnadieu C, Wincker P, Kalbfleisch T, Petersen JL, Orlando L. Imputed genomes of historical horses provide insights into modern breeding. iScience 2023; 26:107104. [PMID: 37416458 PMCID: PMC10319840 DOI: 10.1016/j.isci.2023.107104] [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: 01/03/2023] [Revised: 04/25/2023] [Accepted: 06/08/2023] [Indexed: 07/08/2023] Open
Abstract
Historical genomes can provide important insights into recent genomic changes in horses, especially the development of modern breeds. In this study, we characterized 8.7 million genomic variants from a panel of 430 horses from 73 breeds, including newly sequenced genomes from 20 Clydesdales and 10 Shire horses. We used this modern genomic variation to impute the genomes of four historically important horses, consisting of publicly available genomes from 2 Przewalski's horses, 1 Thoroughbred, and a newly sequenced Clydesdale. Using these historical genomes, we identified modern horses with higher genetic similarity to those in the past and unveiled increased inbreeding in recent times. We genotyped variants associated with appearance and behavior to uncover previously unknown characteristics of these important historical horses. Overall, we provide insights into the history of Thoroughbred and Clydesdale breeds and highlight genomic changes in the endangered Przewalski's horse following a century of captive breeding.
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Affiliation(s)
- Evelyn T. Todd
- Centre d’Anthropobiologie et de Génomique de Toulouse (CAGT), CNRS UMR 5288, Université Paul Sabatier, 37 Allées Jules Guesde, Bâtiment A, 31000 Toulouse, France
| | - Aurore Fromentier
- Centre d’Anthropobiologie et de Génomique de Toulouse (CAGT), CNRS UMR 5288, Université Paul Sabatier, 37 Allées Jules Guesde, Bâtiment A, 31000 Toulouse, France
| | - Richard Sutcliffe
- Glasgow Museums Resource Centre, 200 Woodhead Road, Nitshill, G53 7NN Glasgow, UK
| | - Yvette Running Horse Collin
- Centre d’Anthropobiologie et de Génomique de Toulouse (CAGT), CNRS UMR 5288, Université Paul Sabatier, 37 Allées Jules Guesde, Bâtiment A, 31000 Toulouse, France
| | - Aude Perdereau
- Genoscope, Institut de biologie François Jacob, CEA, Université d’Evry, Université Paris-Saclay, 91042 Evry, France
| | - Jean-Marc Aury
- Genoscope, Institut de biologie François Jacob, CEA, Université d’Evry, Université Paris-Saclay, 91042 Evry, France
| | - Camille Èche
- GeT-PlaGe - Génome et Transcriptome - Plateforme Génomique, GET - Plateforme Génome & Transcriptome, Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement, 31326 Castanet-Tolosan Cedex, France
| | - Olivier Bouchez
- GeT-PlaGe - Génome et Transcriptome - Plateforme Génomique, GET - Plateforme Génome & Transcriptome, Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement, 31326 Castanet-Tolosan Cedex, France
| | - Cécile Donnadieu
- GeT-PlaGe - Génome et Transcriptome - Plateforme Génomique, GET - Plateforme Génome & Transcriptome, Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement, 31326 Castanet-Tolosan Cedex, France
| | - Patrick Wincker
- Genoscope, Institut de biologie François Jacob, CEA, Université d’Evry, Université Paris-Saclay, 91042 Evry, France
| | - Ted Kalbfleisch
- MH Gluck Equine Research Center, University of Kentucky, Lexington, KY 40546-0091, USA
| | - Jessica L. Petersen
- Department of Animal Science, University of Nebraska-Lincoln, 3940 Fair St, Lincoln, NE 68583-0908, USA
| | - Ludovic Orlando
- Centre d’Anthropobiologie et de Génomique de Toulouse (CAGT), CNRS UMR 5288, Université Paul Sabatier, 37 Allées Jules Guesde, Bâtiment A, 31000 Toulouse, France
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21
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Bozlak E, Radovic L, Remer V, Rigler D, Allen L, Brem G, Stalder G, Castaneda C, Cothran G, Raudsepp T, Okuda Y, Moe KK, Moe HH, Kounnavongsa B, Keonouchanh S, Van NH, Vu VH, Shah MK, Nishibori M, Kazymbet P, Bakhtin M, Zhunushov A, Paul RC, Dashnyam B, Nozawa K, Almarzook S, Brockmann GA, Reissmann M, Antczak DF, Miller DC, Sadeghi R, von Butler-Wemken I, Kostaras N, Han H, Manglai D, Abdurasulov A, Sukhbaatar B, Ropka-Molik K, Stefaniuk-Szmukier M, Lopes MS, da Câmara Machado A, Kalashnikov VV, Kalinkova L, Zaitev AM, Novoa-Bravo M, Lindgren G, Brooks S, Rosa LP, Orlando L, Juras R, Kunieda T, Wallner B. Refining the evolutionary tree of the horse Y chromosome. Sci Rep 2023; 13:8954. [PMID: 37268661 DOI: 10.1038/s41598-023-35539-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2022] [Accepted: 05/19/2023] [Indexed: 06/04/2023] Open
Abstract
The Y chromosome carries information about the demography of paternal lineages, and thus, can prove invaluable for retracing both the evolutionary trajectory of wild animals and the breeding history of domesticates. In horses, the Y chromosome shows a limited, but highly informative, sequence diversity, supporting the increasing breeding influence of Oriental lineages during the last 1500 years. Here, we augment the primary horse Y-phylogeny, which is currently mainly based on modern horse breeds of economic interest, with haplotypes (HT) segregating in remote horse populations around the world. We analyze target enriched sequencing data of 5 Mb of the Y chromosome from 76 domestic males, together with 89 whole genome sequenced domestic males and five Przewalski's horses from previous studies. The resulting phylogeny comprises 153 HTs defined by 2966 variants and offers unprecedented resolution into the history of horse paternal lineages. It reveals the presence of a remarkable number of previously unknown haplogroups in Mongolian horses and insular populations. Phylogenetic placement of HTs retrieved from 163 archaeological specimens further indicates that most of the present-day Y-chromosomal variation evolved after the domestication process that started around 4200 years ago in the Western Eurasian steppes. Our comprehensive phylogeny significantly reduces ascertainment bias and constitutes a robust evolutionary framework for analyzing horse population dynamics and diversity.
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Affiliation(s)
- Elif Bozlak
- Institute of Animal Breeding and Genetics, University of Veterinary Medicine Vienna, 1210, Vienna, Austria
- Vienna Graduate School of Population Genetics, University of Veterinary Medicine Vienna, 1210, Vienna, Austria
| | - Lara Radovic
- Institute of Animal Breeding and Genetics, University of Veterinary Medicine Vienna, 1210, Vienna, Austria
- Vienna Graduate School of Population Genetics, University of Veterinary Medicine Vienna, 1210, Vienna, Austria
| | - Viktoria Remer
- Institute of Animal Breeding and Genetics, University of Veterinary Medicine Vienna, 1210, Vienna, Austria
| | - Doris Rigler
- Institute of Animal Breeding and Genetics, University of Veterinary Medicine Vienna, 1210, Vienna, Austria
| | - Lucy Allen
- Institute of Animal Breeding and Genetics, University of Veterinary Medicine Vienna, 1210, Vienna, Austria
| | - Gottfried Brem
- Institute of Animal Breeding and Genetics, University of Veterinary Medicine Vienna, 1210, Vienna, Austria
| | - Gabrielle Stalder
- Research Institute of Wildlife Ecology, University of Veterinary Medicine Vienna, 1210, Vienna, Austria
| | - Caitlin Castaneda
- School of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, TX, 77843, USA
| | - Gus Cothran
- School of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, TX, 77843, USA
| | - Terje Raudsepp
- School of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, TX, 77843, USA
| | - Yu Okuda
- Museum of Dinosaur Research, Okayama University of Science, Okayama, Japan
| | - Kyaw Kyaw Moe
- Department of Pathology and Microbiology, University of Veterinary Science, Yezin, Nay Pyi Taw, 05282, Myanmar
| | - Hla Hla Moe
- Department of Genetics and Animal Breeding, University of Veterinary Science, Yezin, Nay Pyi Taw, 05282, Myanmar
| | - Bounthavone Kounnavongsa
- National Agriculture and Forestry Research Institute (Lao) Resources, Livestock Research Center, Xaythany District, Vientiane, Laos
| | - Soukanh Keonouchanh
- Faculty of Animal Science and Veterinary Medicine, University of Agriculture and Forestry, Hue University, Hue, Vietnam
| | - Nguyen Huu Van
- Faculty of Animal Science and Veterinary Medicine, University of Agriculture and Forestry, Hue University, Hue, Vietnam
| | - Van Hai Vu
- Faculty of Animal Science and Veterinary Medicine, University of Agriculture and Forestry, Hue University, Hue, Vietnam
| | - Manoj Kumar Shah
- Faculty of Animal Science, Veterinary Science and Fisheries, Agriculture and Forestry University, Rampur, 44209, Nepal
| | - Masahide Nishibori
- Graduate School of Integrated Sciences for Life, Hiroshima University, Higashi-Hiroshima, 739-8528, Japan
| | - Polat Kazymbet
- Radiobiological Research Institute, JSC Astana Medical University, Astana, 010000, Republic of Kazakhstan
| | - Meirat Bakhtin
- Institute of Biotechnology, National Academy of Sciences of the Kyrgyz Republic, Bishkek, 720071, Kyrgyz Republic
| | - Asankadyr Zhunushov
- Institute of Biotechnology, National Academy of Sciences of the Kyrgyz Republic, Bishkek, 720071, Kyrgyz Republic
| | - Ripon Chandra Paul
- Graduate School of Environmental and Life Science, Okayama University, Okayama, Japan
- Faculty of Animal Science and Veterinary Medicine, Patuakhali Science and Technology University, Barishal, Bangladesh
| | - Bumbein Dashnyam
- Institute of Biological Sciences, Mongolian Academy of Sciences, Ulaan Baator, Mongolia
| | - Ken Nozawa
- Primate Research Institute, Kyoto University, Aichi, Japan
| | - Saria Almarzook
- Albrecht Daniel Thaer-Institut, Humboldt-Universität zu Berlin, 10115, Berlin, Germany
| | - Gudrun A Brockmann
- Albrecht Daniel Thaer-Institut, Humboldt-Universität zu Berlin, 10115, Berlin, Germany
| | - Monika Reissmann
- Baker Institute for Animal Health, College of Veterinary Medicine, Cornell University, Ithaca, NY, 14853, USA
| | - Douglas F Antczak
- Baker Institute for Animal Health, College of Veterinary Medicine, Cornell University, Ithaca, NY, 14853, USA
| | - Donald C Miller
- Baker Institute for Animal Health, College of Veterinary Medicine, Cornell University, Ithaca, NY, 14853, USA
| | - Raheleh Sadeghi
- Baker Institute for Animal Health, College of Veterinary Medicine, Cornell University, Ithaca, NY, 14853, USA
| | - Ines von Butler-Wemken
- Barb Horse Breeding Organisation VFZB E. V., Verein der Freunde und Züchter Des Berberpferdes E.V., Kirchgasse 11, 67718, Schmalenberg, Germany
| | | | - Haige Han
- Inner Mongolia Key Laboratory of Equine Genetics, Breeding and Reproduction, College of Animal Science, Equine Research Center, Inner Mongolia Agricultural University, Hohhot, 010018, China
| | - Dugarjaviin Manglai
- Inner Mongolia Key Laboratory of Equine Genetics, Breeding and Reproduction, College of Animal Science, Equine Research Center, Inner Mongolia Agricultural University, Hohhot, 010018, China
| | - Abdugani Abdurasulov
- Department of Agriculture, Faculty of Natural Sciences and Geography, Osh State University, 723500, Osh, Kyrgyzstan
| | - Boldbaatar Sukhbaatar
- Sector of Surveillance and Diagnosis of Infectious Diseases, State Central Veterinary Laboratory, Ulaanbaatar, 17024, Mongolia
| | - Katarzyna Ropka-Molik
- National Research Institute of Animal Production, Animal Molecular Biology, 31-047, Cracow, Poland
| | | | - Maria Susana Lopes
- Biotechnology Centre of Azores, University of Azores, 9700-042, Angra do Heroísmo, Portugal
| | | | | | - Liliya Kalinkova
- All-Russian Research Institute for Horse Breeding, Ryazan, 391105, Russia
| | - Alexander M Zaitev
- All-Russian Research Institute for Horse Breeding, Ryazan, 391105, Russia
| | - Miguel Novoa-Bravo
- Genética Animal de Colombia SAS., Av. Calle 26 #69-76, 111071, Bogotá, Colombia
| | - Gabriella Lindgren
- Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, 75007, Uppsala, Sweden
- Department of Biosystems, Center for Animal Breeding and Genetics, KU Leuven, 3001, Leuven, Belgium
| | - Samantha Brooks
- Department of Animal Science, UF Genetics Institute, University of Florida, Gainesville, FL, 32610, USA
| | - Laura Patterson Rosa
- Department of Agriculture and Industry, Sul Ross State University, Alpine, TX, 79832, USA
| | - Ludovic Orlando
- Centre d'Anthropobiologie et de Génomique de Toulouse, Université Paul Sabatier, Toulouse, France
| | - Rytis Juras
- School of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, TX, 77843, USA.
| | - Tetsuo Kunieda
- Graduate School of Environmental and Life Science, Okayama University, Okayama, Japan.
- Faculty of Veterinary Medicine, Okayama University of Science, Imabari, Japan.
| | - Barbara Wallner
- Institute of Animal Breeding and Genetics, University of Veterinary Medicine Vienna, 1210, Vienna, Austria.
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22
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Clavel P, Louis L, Sarkissian CD, Thèves C, Gillet C, Chauvey L, Tressières G, Schiavinato S, Calvière-Tonasso L, Telmon N, Clavel B, Jonvel R, Tzortzis S, Bouniol L, Fémolant JM, Klunk J, Poinar H, Signoli M, Costedoat C, Spyrou MA, Seguin-Orlando A, Orlando L. Improving the extraction of ancient Yersinia pestis genomes from the dental pulp. iScience 2023; 26:106787. [PMID: 37250315 PMCID: PMC10214834 DOI: 10.1016/j.isci.2023.106787] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2022] [Revised: 02/11/2023] [Accepted: 04/26/2023] [Indexed: 05/31/2023] Open
Abstract
Ancient DNA preserved in the dental pulp offers the opportunity to characterize the genome of some of the deadliest pathogens in human history. However, while DNA capture technologies help, focus sequencing efforts, and therefore, reduce experimental costs, the recovery of ancient pathogen DNA remains challenging. Here, we tracked the kinetics of ancient Yersinia pestis DNA release in solution during a pre-digestion of the dental pulp. We found that most of the ancient Y. pestis DNA is released within 60 min at 37°C in our experimental conditions. We recommend a simple pre-digestion as an economical procedure to obtain extracts enriched in ancient pathogen DNA, as longer digestion times release other types of templates, including host DNA. Combining this procedure with DNA capture, we characterized the genome sequences of 12 ancient Y. pestis bacteria from France dating to the second pandemic outbreaks of the 17th and 18th centuries Common Era.
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Affiliation(s)
- Pierre Clavel
- Centre d’Anthropobiologie et de Génomique de Toulouse (CAGT), CNRS UMR5288, Université Paul Sabatier, 37 allées Jules Guesde, 31000 Toulouse, France
| | - Lexane Louis
- Centre d’Anthropobiologie et de Génomique de Toulouse (CAGT), CNRS UMR5288, Université Paul Sabatier, 37 allées Jules Guesde, 31000 Toulouse, France
| | - Clio Der Sarkissian
- Centre d’Anthropobiologie et de Génomique de Toulouse (CAGT), CNRS UMR5288, Université Paul Sabatier, 37 allées Jules Guesde, 31000 Toulouse, France
| | - Catherine Thèves
- Centre d’Anthropobiologie et de Génomique de Toulouse (CAGT), CNRS UMR5288, Université Paul Sabatier, 37 allées Jules Guesde, 31000 Toulouse, France
| | - Claudia Gillet
- Centre d’Anthropobiologie et de Génomique de Toulouse (CAGT), CNRS UMR5288, Université Paul Sabatier, 37 allées Jules Guesde, 31000 Toulouse, France
| | - Lorelei Chauvey
- Centre d’Anthropobiologie et de Génomique de Toulouse (CAGT), CNRS UMR5288, Université Paul Sabatier, 37 allées Jules Guesde, 31000 Toulouse, France
| | - Gaétan Tressières
- Centre d’Anthropobiologie et de Génomique de Toulouse (CAGT), CNRS UMR5288, Université Paul Sabatier, 37 allées Jules Guesde, 31000 Toulouse, France
| | - Stéphanie Schiavinato
- Centre d’Anthropobiologie et de Génomique de Toulouse (CAGT), CNRS UMR5288, Université Paul Sabatier, 37 allées Jules Guesde, 31000 Toulouse, France
| | - Laure Calvière-Tonasso
- Centre d’Anthropobiologie et de Génomique de Toulouse (CAGT), CNRS UMR5288, Université Paul Sabatier, 37 allées Jules Guesde, 31000 Toulouse, France
| | - Norbert Telmon
- Centre d’Anthropobiologie et de Génomique de Toulouse (CAGT), CNRS UMR5288, Université Paul Sabatier, 37 allées Jules Guesde, 31000 Toulouse, France
| | - Benoît Clavel
- Archéozoologie, Archéobotanique: Sociétés, Pratiques et Environnements (AASPE), CNRS-UMR7209, Muséum national d’histoire naturelle, 55 Rue Buffon, 75005 Paris, France
| | - Richard Jonvel
- Amiens Métropole Service Archéologie Préventive, 2 rue Colbert, 80000 Amiens, France
| | - Stéfan Tzortzis
- Service Régional de l’Archéologie, 21 allée Claude Forbin, 13100 Aix-en-Provence, France
| | - Laetitia Bouniol
- Service archéologique de la ville de Beauvais, 1 rue Desgroux, 60021 Beauvais, France
| | - Jean-Marc Fémolant
- Service archéologique de la ville de Beauvais, 1 rue Desgroux, 60021 Beauvais, France
| | | | - Hendrik Poinar
- McMaster Ancient DNA Centre, Departments of Anthropology, Biology and Biochemistry, McMaster University, Hamilton, ON L8S 4L9, Canada
- Michael G. DeGroote Institute of Infectious Disease Research, McMaster University, Hamilton, ON L8S, 4L9, Canada
- Humans and the Microbiome Program, Canadian Institute for Advanced Research, Toronto, ON, Canada
| | - Michel Signoli
- Aix-Marseille Université, CNRS, EFS, ADES, 13005 Marseille, France
| | | | - Maria A. Spyrou
- Institute for Archaeological Sciences, Eberhard Karls University of Tübingen, Tübingen, Germany
| | - Andaine Seguin-Orlando
- Centre d’Anthropobiologie et de Génomique de Toulouse (CAGT), CNRS UMR5288, Université Paul Sabatier, 37 allées Jules Guesde, 31000 Toulouse, France
| | - Ludovic Orlando
- Centre d’Anthropobiologie et de Génomique de Toulouse (CAGT), CNRS UMR5288, Université Paul Sabatier, 37 allées Jules Guesde, 31000 Toulouse, France
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23
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Boitard S, Liaubet L, Paris C, Fève K, Dehais P, Bouquet A, Riquet J, Mercat MJ. Whole-genome sequencing of cryopreserved resources from French Large White pigs at two distinct sampling times reveals strong signatures of convergent and divergent selection between the dam and sire lines. Genet Sel Evol 2023; 55:13. [PMID: 36864379 PMCID: PMC9979506 DOI: 10.1186/s12711-023-00789-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2022] [Accepted: 02/15/2023] [Indexed: 03/04/2023] Open
Abstract
BACKGROUND Numerous genomic scans for positive selection have been performed in livestock species within the last decade, but often a detailed characterization of the detected regions (gene or trait under selection, timing of selection events) is lacking. Cryopreserved resources stored in reproductive or DNA gene banks offer a great opportunity to improve this characterization by providing direct access to recent allele frequency dynamics, thereby differentiating between signatures from recent breeding objectives and those related to more ancient selection constraints. Improved characterization can also be achieved by using next-generation sequencing data, which helps narrowing the size of the detected regions while reducing the number of associated candidate genes. METHODS We estimated genetic diversity and detected signatures of recent selection in French Large White pigs by sequencing the genomes of 36 animals from three distinct cryopreserved samples: two recent samples from dam (LWD) and sire (LWS) lines, which had diverged from 1995 and were selected under partly different objectives, and an older sample from 1977 prior to the divergence. RESULTS French LWD and LWS lines have lost approximately 5% of the SNPs that segregated in the 1977 ancestral population. Thirty-eight genomic regions under recent selection were detected in these lines and the corresponding selection events were further classified as convergent between lines (18 regions), divergent between lines (10 regions), specific to the dam line (6 regions) or specific to the sire line (4 regions). Several biological functions were found to be significantly enriched among the genes included in these regions: body size, body weight and growth regardless of the category, early life survival and calcium metabolism more specifically in the signatures in the dam line and lipid and glycogen metabolism more specifically in the signatures in the sire line. Recent selection on IGF2 was confirmed and several other regions were linked to a single candidate gene (ARHGAP10, BMPR1B, GNA14, KATNA1, LPIN1, PKP1, PTH, SEMA3E or ZC3HAV1, among others). CONCLUSIONS These results illustrate that sequencing the genome of animals at several recent time points generates considerable insight into the traits, genes and variants under recent selection in a population. This approach could be applied to other livestock populations, e.g. by exploiting the rich biological resources stored in cryobanks.
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Affiliation(s)
- Simon Boitard
- CBGP, CIRAD, INRAE, Institut Agro, IRD, Université de Montpellier, Montferrier-sur-Lez, France. .,GenPhySE, INRAE, INP, Université de Toulouse, Castanet-Tolosan, France.
| | - Laurence Liaubet
- grid.507621.7GenPhySE, INRAE, INP, Université de Toulouse, Castanet-Tolosan, France
| | - Cyriel Paris
- grid.507621.7GenPhySE, INRAE, INP, Université de Toulouse, Castanet-Tolosan, France
| | - Katia Fève
- grid.507621.7GenPhySE, INRAE, INP, Université de Toulouse, Castanet-Tolosan, France
| | - Patrice Dehais
- grid.507621.7GenPhySE, INRAE, INP, Université de Toulouse, Castanet-Tolosan, France
| | - Alban Bouquet
- IFIP Institut du porc/Alliance R & D, Le Rheu, France
| | - Juliette Riquet
- grid.507621.7GenPhySE, INRAE, INP, Université de Toulouse, Castanet-Tolosan, France
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24
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DNA methylation-based profiling of horse archaeological remains for age-at-death and castration. iScience 2023; 26:106144. [PMID: 36843848 PMCID: PMC9950528 DOI: 10.1016/j.isci.2023.106144] [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: 09/27/2022] [Revised: 01/02/2023] [Accepted: 02/01/2023] [Indexed: 02/07/2023] Open
Abstract
Age profiling of archaeological bone assemblages can inform on past animal management practices, but is limited by the fragmentary nature of the fossil record and the lack of universal skeletal markers for age. DNA methylation clocks offer new, albeit challenging, alternatives for estimating the age-at-death of ancient individuals. Here, we take advantage of the availability of a DNA methylation clock based on 31,836 CpG sites and dental age markers in horses to assess age predictions in 84 ancient remains. We evaluate our approach using whole-genome sequencing data and develop a capture assay providing reliable estimates for only a fraction of the cost. We also leverage DNA methylation patterns to assess castration practice in the past. Our work opens for a deeper characterization of past husbandry and ritual practices and holds the potential to reveal age mortality profiles in ancient societies, once extended to human remains.
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25
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Sant J, Jenkins PA, Koskela J, Spanò D. EWF: simulating exact paths of the Wright-Fisher diffusion. Bioinformatics 2023; 39:6984715. [PMID: 36629450 PMCID: PMC9846420 DOI: 10.1093/bioinformatics/btad017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2022] [Revised: 01/06/2023] [Accepted: 01/10/2023] [Indexed: 01/12/2023] Open
Abstract
MOTIVATION The Wright-Fisher diffusion is important in population genetics in modelling the evolution of allele frequencies over time subject to the influence of biological phenomena such as selection, mutation and genetic drift. Simulating the paths of the process is challenging due to the form of the transition density. We present EWF, a robust and efficient sampler which returns exact draws for the diffusion and diffusion bridge processes, accounting for general models of selection including those with frequency dependence. RESULTS Given a configuration of selection, mutation and endpoints, EWF returns draws at the requested sampling times from the law of the corresponding Wright-Fisher process. Output was validated by comparison to approximations of the transition density via the Kolmogorov-Smirnov test and QQ plots. AVAILABILITY AND IMPLEMENTATION All softwares are available at https://github.com/JaroSant/EWF. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
| | - Paul A Jenkins
- Department of Statistics, University of Warwick, Coventry CV4 7AL, UK,Department of Computer Science, University of Warwick, Coventry CV4 7AL, UK,The Alan Turing Institute, British Library, London NW1 2DB, UK
| | - Jere Koskela
- Department of Statistics, University of Warwick, Coventry CV4 7AL, UK
| | - Dario Spanò
- Department of Statistics, University of Warwick, Coventry CV4 7AL, UK
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26
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Nishita Y, Amaike Y, Spassov N, Hristova L, Kostov D, Vladova D, Peeva S, Raichev E, Vlaeva R, Masuda R. Diversity of mitochondrial D-loop haplotypes from ancient Thracian horses in Bulgaria. Anim Sci J 2023; 94:e13810. [PMID: 36717086 DOI: 10.1111/asj.13810] [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: 08/11/2022] [Revised: 01/05/2023] [Accepted: 01/10/2023] [Indexed: 02/01/2023]
Abstract
The domestication of the horse began possibly more than 5000 years ago in the western part of the Eurasian steppe, and according to the leading hypothesis, horses first spread from the Steppe toward the region of the Thracian culture, starting in the second half of the 2nd millennium BCE and flourished from the fifth to first centuries BCE, mainly located in present-day Bulgaria. We analyzed 17 horse bone remains excavated from Thracian archaeological sites (fourth to first centuries BCE) in Bulgaria and successfully identified 17 sequences representing 14 different haplotypes of the mitochondrial D-loop. Compared with the mtDNA haplotypes of modern horses around the world, ancient Thracian horses in Bulgaria are thought to be more closely related to modern horses of Southern Europe and less related to those of Central Asia. In addition, the haplotypes we obtained represented 11 previously reported modern horse mtDNA haplogroups: A, B, D, E, G, H, I, L, N, P, and Q. All the haplogroups contain modern and regionally predominant haplotypes occurring in Europe, the Middle East, and Central Asia. Our results indicate that Thracian horses in Bulgaria have had relatively high genetic diversity and are closely related to modern horse breeds.
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Affiliation(s)
- Yoshinori Nishita
- Department of Biological Sciences, Faculty of Science, Hokkaido University, Sapporo, Japan
| | - Yosuke Amaike
- Department of Biological Sciences, Faculty of Science, Hokkaido University, Sapporo, Japan
| | - Nikolai Spassov
- National Museum of Natural History, Bulgarian Academy of Sciences, Sofia, Bulgaria
| | - Latinka Hristova
- National Museum of Natural History, Bulgarian Academy of Sciences, Sofia, Bulgaria
| | - Dimitar Kostov
- Department of Veterinary Anatomy, Histology and Embryology, Faculty of Veterinary Medicine, Trakia University, Stara Zagora, Bulgaria
| | - Diyana Vladova
- Department of Veterinary Anatomy, Histology and Embryology, Faculty of Veterinary Medicine, Trakia University, Stara Zagora, Bulgaria
| | - Stanislava Peeva
- Department of Animal Production, Faculty of Agricultural Science, Trakia University, Stara Zagora, Bulgaria
| | - Evgeniy Raichev
- Department of Animal Production, Faculty of Agricultural Science, Trakia University, Stara Zagora, Bulgaria
| | - Radka Vlaeva
- Department of Animal Production, Faculty of Agricultural Science, Trakia University, Stara Zagora, Bulgaria
| | - Ryuichi Masuda
- Department of Biological Sciences, Faculty of Science, Hokkaido University, Sapporo, Japan
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27
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Wang Y, Zhao Z, Miao X, Wang Y, Qian X, Chen L, Wang C, Li S. eSMC: a statistical model to infer admixture events from individual genomics data. BMC Genomics 2022; 23:827. [PMCID: PMC9748406 DOI: 10.1186/s12864-022-09033-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2022] [Accepted: 11/21/2022] [Indexed: 12/15/2022] Open
Abstract
Abstract
Background
Inferring historical population admixture events yield essential insights in understanding a species demographic history. Methods are available to infer admixture events in demographic history with extant genetic data from multiple sources. Due to the deficiency in ancient population genetic data, there lacks a method for admixture inference from a single source. Pairwise Sequentially Markovian Coalescent (PSMC) estimates the historical effective population size from lineage genomes of a single individual, based on the distribution of the most recent common ancestor between the diploid’s alleles. However, PSMC does not infer the admixture event.
Results
Here, we proposed eSMC, an extended PSMC model for admixture inference from a single source. We evaluated our model’s performance on both in silico data and real data. We simulated population admixture events at an admixture time range from 5 kya to 100 kya (5 years/generation) with population admix ratio at 1:1, 2:1, 3:1, and 4:1, respectively. The root means the square error is $$\pm 7.61$$
±
7.61
kya for all experiments. Then we implemented our method to infer the historical admixture events in human, donkey and goat populations. The estimated admixture time for both Han and Tibetan individuals range from 60 kya to 80 kya (25 years/generation), while the estimated admixture time for the domesticated donkeys and the goats ranged from 40 kya to 60 kya (8 years/generation) and 40 kya to 100 kya (6 years/generation), respectively. The estimated admixture times were concordance to the time that domestication occurred in human history.
Conclusion
Our eSMC effectively infers the time of the most recent admixture event in history from a single individual’s genomics data. The source code of eSMC is hosted at https://github.com/zachary-zzc/eSMC.
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Sharif MB, Fitak RR, Wallner B, Orozco-terWengel P, Frewin S, Fremaux M, Mohandesan E. Reconstruction of the Major Maternal and Paternal Lineages in the Feral New Zealand Kaimanawa Horses. Animals (Basel) 2022; 12:ani12243508. [PMID: 36552427 PMCID: PMC9774138 DOI: 10.3390/ani12243508] [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: 10/06/2022] [Revised: 11/29/2022] [Accepted: 12/08/2022] [Indexed: 12/14/2022] Open
Abstract
New Zealand has the fourth largest feral horse population in the world. The Kaimanawas (KHs) are feral horses descended from various domestic horse breeds released into the Kaimanawa ranges in the 19th and 20th centuries. Over time, the population size has fluctuated dramatically due to hunting, large-scale farming and forestry. Currently, the herd is managed by an annual round-up, limiting the number to 300 individuals to protect the native ecosystem. Here, we genotyped 96 KHs for uniparental markers (mitochondrial DNA, Y-chromosome) and assessed their genetic similarity with respect to other domestic horses. We show that at least six maternal and six paternal lineages contributed unequally to the KH gene pool, and today's KH population possibly represents two sub-populations. Our results indicate that three horse breeds, namely Welsh ponies, Thoroughbreds and Arabian horses had a major influence in the genetic-makeup of the extant KH population. We show that mitochondrial genetic diversity in KHs (π = 0.00687 ± 0.00355) is closer to that of the Sable Island horses (π = 0.0034 ± 0.00301), and less than other feral horse populations around the world. Our current findings, combined with ongoing genomic research, will provide insight into the population-specific genetic variation and inbreeding among KHs. This will largely advance equine research and improve the management of future breeding programs of these treasured New Zealand horse.
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Affiliation(s)
- Muhammad Bilal Sharif
- Department of Evolutionary Anthropology, University of Vienna, Djerassiplatz 1, A-1030 Vienna, Austria
- Human Evolution and Archaeological Sciences (HEAS), University of Vienna, Djerassiplatz 1, A-1030 Vienna, Austria
- Vienna Doctoral School of Ecology and Evolution (VDSEE), University of Vienna, Djerassiplatz 1, A-1030 Vienna, Austria
| | - Robert Rodgers Fitak
- Department of Biology, Genomics and Bioinformatics Cluster, University of Central Florida, 4110 Libra Dr, Orlando, FL 32816, USA
| | - Barbara Wallner
- Institute of Animal Breeding and Genetics, Veterinary University of Vienna, Veterinärplatz 1, A-1210 Vienna, Austria
| | - Pablo Orozco-terWengel
- Cardiff School of Biosciences, Cardiff University, The Sir Martin Evans Building, Museum Avenue, Cardiff CF10 3AX, Wales, UK
| | - Simone Frewin
- Feed2U Ltd., 19 Wairere Valley Road, Paparoa 0571, New Zealand
| | - Michelle Fremaux
- InfogeneNZ (EPAGSC), School of Agriculture and Environment, Massey University, 1 Drysdale Drive, Palmerston North 4410, New Zealand
| | - Elmira Mohandesan
- Department of Evolutionary Anthropology, University of Vienna, Djerassiplatz 1, A-1030 Vienna, Austria
- Human Evolution and Archaeological Sciences (HEAS), University of Vienna, Djerassiplatz 1, A-1030 Vienna, Austria
- Correspondence:
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29
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Cardinali I, Giontella A, Tommasi A, Silvestrelli M, Lancioni H. Unlocking Horse Y Chromosome Diversity. Genes (Basel) 2022; 13:genes13122272. [PMID: 36553539 PMCID: PMC9777570 DOI: 10.3390/genes13122272] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2022] [Revised: 11/30/2022] [Accepted: 11/30/2022] [Indexed: 12/11/2022] Open
Abstract
The present equine genetic variation mirrors the deep influence of intensive breeding programs during the last 200 years. Here, we provide a comprehensive current state of knowledge on the trends and prospects on the variation in the equine male-specific region of the Y chromosome (MSY), which was assembled for the first time in 2018. In comparison with the other 12 mammalian species, horses are now the most represented, with 56 documented MSY genes. However, in contrast to the high variability in mitochondrial DNA observed in many horse breeds from different geographic areas, modern horse populations demonstrate extremely low genetic Y-chromosome diversity. The selective pressures employed by breeders using pedigree data (which are not always error-free) as a predictive tool represent the main cause of this lack of variation in the Y-chromosome. Nevertheless, the detailed phylogenies obtained by recent fine-scaled Y-chromosomal genotyping in many horse breeds worldwide have contributed to addressing the genealogical, forensic, and population questions leading to the reappraisal of the Y-chromosome as a powerful genetic marker to avoid the loss of biodiversity as a result of selective breeding practices, and to better understand the historical development of horse breeds.
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Affiliation(s)
- Irene Cardinali
- Department of Chemistry, Biology and Biotechnology, University of Perugia, 06123 Perugia, Italy
- Correspondence: (I.C.); (A.G.)
| | - Andrea Giontella
- Department of Veterinary Medicine, University of Perugia, 06126 Perugia, Italy
- Correspondence: (I.C.); (A.G.)
| | - Anna Tommasi
- Department of Biology and Biotechnology “L. Spallanzani”, University of Pavia, 27100 Pavia, Italy
| | | | - Hovirag Lancioni
- Department of Chemistry, Biology and Biotechnology, University of Perugia, 06123 Perugia, Italy
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30
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Ropars J, Giraud T. Convergence in domesticated fungi used for cheese and dry-cured meat maturation: beneficial traits, genomic mechanisms, and degeneration. Curr Opin Microbiol 2022; 70:102236. [PMID: 36368125 DOI: 10.1016/j.mib.2022.102236] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2022] [Revised: 08/29/2022] [Accepted: 10/18/2022] [Indexed: 11/09/2022]
Abstract
Humans have domesticated genetically distant fungi for similar uses, the fermentation of lipid-rich and sugar-rich food to generate attractive aspects, odor and aroma, and to improve shelf life and product safety. Multiple independent domestication events also occurred within species. We review recent evidence of phenotypic convergence during the domestication of fungi for making cheese (Saccharomyces cerevisiae, Penicillium roqueforti, P. camemberti, and Geotrichum candidum) and for dry-cured meat making (P. nalgiovense and P. salamii). Convergence following adaptation to similar ecological niches involved colony aspect (fluffiness and color), lipolysis, proteolysis, volatile compound production, and competitive ability against food spoilers. We review evidence for convergence in genetic diversity loss in domesticated populations and in the degeneration of unused traits, such as toxin production and sexual reproduction. Phenotypic convergence sometimes occurred by similar mechanisms of genomic adaptation, in particular horizontal gene transfers and loss of genes.
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Affiliation(s)
- Jeanne Ropars
- Ecologie Systématique Evolution, IDEEV, Bâtiment 680, 12 route RD128, 91190 Gif-sur-Yvette, France
| | - Tatiana Giraud
- Ecologie Systématique Evolution, IDEEV, Bâtiment 680, 12 route RD128, 91190 Gif-sur-Yvette, France.
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31
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Leonardi M, Boschin F, Boscato P, Manica A. Following the niche: the differential impact of the last glacial maximum on four European ungulates. Commun Biol 2022; 5:1038. [PMID: 36175492 PMCID: PMC9523052 DOI: 10.1038/s42003-022-03993-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2021] [Accepted: 09/14/2022] [Indexed: 11/09/2022] Open
Abstract
Predicting the effects of future global changes on species requires a better understanding of the ecological niche dynamics in response to climate; the large climatic fluctuations of the last 50,000 years can be used as a natural experiment to that aim. Here we test whether the realized niche of horse, aurochs, red deer, and wild boar changed between 47,000 and 7500 years ago using paleoecological modelling over an extensive archaeological database. We show that they all changed their niche, with species-specific responses to climate fluctuations. We also suggest that they survived the climatic turnovers thanks to their flexibility and by expanding their niche in response to the extinction of competitors and predators. Irrespective of the mechanism behind such processes, the fact that species with long generation times can change their niche over thousands of years cautions against assuming it to stay constant both when reconstructing the past and predicting the future. European megafaunal ungulates living in open habitats over the last 50,000 years showed evidence for niche change, possibly driven by climatic change and extinction of competitors and predators
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Affiliation(s)
- Michela Leonardi
- Evolutionary Ecology Group, Department of Zoology, University of Cambridge, Downing Street, Cambridge, CB2 3EJ, UK.
| | - Francesco Boschin
- U.R. Preistoria e Antropologia, Dipartimento di Scienze Fisiche della Terra e dell'Ambiente, Università degli Studi di Siena, Via Laterina 8, 53100, Siena, Italy.
| | - Paolo Boscato
- U.R. Preistoria e Antropologia, Dipartimento di Scienze Fisiche della Terra e dell'Ambiente, Università degli Studi di Siena, Via Laterina 8, 53100, Siena, Italy
| | - Andrea Manica
- Evolutionary Ecology Group, Department of Zoology, University of Cambridge, Downing Street, Cambridge, CB2 3EJ, UK
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32
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Todd ET, Tonasso-Calvière L, Chauvey L, Schiavinato S, Fages A, Seguin-Orlando A, Clavel P, Khan N, Pérez Pardal L, Patterson Rosa L, Librado P, Ringbauer H, Verdugo M, Southon J, Aury JM, Perdereau A, Vila E, Marzullo M, Prato O, Tecchiati U, Bagnasco Gianni G, Tagliacozzo A, Tinè V, Alhaique F, Cardoso JL, Valente MJ, Telles Antunes M, Frantz L, Shapiro B, Bradley DG, Boulbes N, Gardeisen A, Horwitz LK, Öztan A, Arbuckle BS, Onar V, Clavel B, Lepetz S, Vahdati AA, Davoudi H, Mohaseb A, Mashkour M, Bouchez O, Donnadieu C, Wincker P, Brooks SA, Beja-Pereira A, Wu DD, Orlando L. The genomic history and global expansion of domestic donkeys. Science 2022; 377:1172-1180. [PMID: 36074859 DOI: 10.1126/science.abo3503] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Abstract
Donkeys transformed human history as essential beasts of burden for long-distance movement, especially across semi-arid and upland environments. They remain insufficiently studied despite globally expanding and providing key support to low- to middle-income communities. To elucidate their domestication history, we constructed a comprehensive genome panel of 207 modern and 31 ancient donkeys, as well as 15 wild equids. We found a strong phylogeographic structure in modern donkeys that supports a single domestication in Africa ~5000 BCE, followed by further expansions in this continent and Eurasia and ultimately returning to Africa. We uncover a previously unknown genetic lineage in the Levant ~200 BCE, which contributed increasing ancestry toward Asia. Donkey management involved inbreeding and the production of giant bloodlines at a time when mules were essential to the Roman economy and military.
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Affiliation(s)
- Evelyn T Todd
- Centre d'Anthropobiologie et de Génomique de Toulouse (CAGT), CNRS UMR 5288, Université Paul Sabatier, Toulouse 31000, France
| | - Laure Tonasso-Calvière
- Centre d'Anthropobiologie et de Génomique de Toulouse (CAGT), CNRS UMR 5288, Université Paul Sabatier, Toulouse 31000, France
| | - Loreleï Chauvey
- Centre d'Anthropobiologie et de Génomique de Toulouse (CAGT), CNRS UMR 5288, Université Paul Sabatier, Toulouse 31000, France
| | - Stéphanie Schiavinato
- Centre d'Anthropobiologie et de Génomique de Toulouse (CAGT), CNRS UMR 5288, Université Paul Sabatier, Toulouse 31000, France
| | - Antoine Fages
- Centre d'Anthropobiologie et de Génomique de Toulouse (CAGT), CNRS UMR 5288, Université Paul Sabatier, Toulouse 31000, France
| | - Andaine Seguin-Orlando
- Centre d'Anthropobiologie et de Génomique de Toulouse (CAGT), CNRS UMR 5288, Université Paul Sabatier, Toulouse 31000, France
| | - Pierre Clavel
- Centre d'Anthropobiologie et de Génomique de Toulouse (CAGT), CNRS UMR 5288, Université Paul Sabatier, Toulouse 31000, France
| | - Naveed Khan
- Centre d'Anthropobiologie et de Génomique de Toulouse (CAGT), CNRS UMR 5288, Université Paul Sabatier, Toulouse 31000, France.,Department of Biotechnology, Abdul Wali Khan University, Mardan 23200, Pakistan
| | - Lucía Pérez Pardal
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Campus de Vairão, Universidade do Porto, Vairão 4485-661, Portugal.,BIOPOLIS Program in Genomics, Biodiversity and Land Planning, Campus de Vairão, Universidade do Porto, Vairão 4485-661, Portugal
| | | | - Pablo Librado
- Centre d'Anthropobiologie et de Génomique de Toulouse (CAGT), CNRS UMR 5288, Université Paul Sabatier, Toulouse 31000, France
| | - Harald Ringbauer
- Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, Leipzig 04103, Germany
| | - Marta Verdugo
- Smurfit Institute of Genetics, Trinity College Dublin, Dublin D02 PN40, Ireland
| | - John Southon
- Earth System Science Department, University of California, Irvine, CA 92697, USA
| | - Jean-Marc Aury
- Genoscope, Institut de biologie François Jacob, CEA, Université d'Evry, Université Paris-Saclay, Evry 91042, France
| | - Aude Perdereau
- Genoscope, Institut de biologie François Jacob, CEA, Université d'Evry, Université Paris-Saclay, Evry 91042, France
| | - Emmanuelle Vila
- Laboratoire Archéorient, Université Lyon 2, Lyon 69007, France
| | - Matilde Marzullo
- Dipartimento di Beni Culturali e Ambientali, Università degli Studi di Milano, Milan 20122, Italy
| | - Ornella Prato
- Dipartimento di Beni Culturali e Ambientali, Università degli Studi di Milano, Milan 20122, Italy
| | - Umberto Tecchiati
- Dipartimento di Beni Culturali e Ambientali, Università degli Studi di Milano, Milan 20122, Italy
| | - Giovanna Bagnasco Gianni
- Dipartimento di Beni Culturali e Ambientali, Università degli Studi di Milano, Milan 20122, Italy
| | | | - Vincenzo Tinè
- Soprintendenza archeologia belle arti e paesaggio per le province di Verona, Rovigo e Vicenza, Verona 37121, Italy
| | | | - João Luís Cardoso
- ICArEHB, Campus de Gambelas, University of Algarve, Faro 8005-139, Portugal.,Universidade Aberta, Lisbon 1269-001, Portugal
| | - Maria João Valente
- Faculdade de Ciências Humanas e Sociais, Centro de Estudos de Arqueologia, Artes e Ciências do Património, Universidade do Algarve, Faro 8000-117, Portugal
| | - Miguel Telles Antunes
- Centre for Research on Science and Geological Engineering, Universidade NOVA de Lisboa, Lisbon 1099-085, Portugal
| | - Laurent Frantz
- Palaeogenomics Group, Department of Veterinary Sciences, Ludwig Maximilian University, Munich 80539, Germany.,School of Biological and Behavioural Sciences, Queen Mary University of London, London E1 4DQ, United Kingdom
| | - Beth Shapiro
- Department of Ecology and Evolutionary Biology, University of California, Santa Cruz, CA 95064, USA.,Howard Hughes Medical Institute, University of California, Santa Cruz, CA 95064, USA
| | - Daniel G Bradley
- Smurfit Institute of Genetics, Trinity College Dublin, Dublin D02 PN40, Ireland
| | - Nicolas Boulbes
- Institut de Paléontologie Humaine, Fondation Albert Ier, Paris / UMR 7194 HNHP, MNHN-CNRS-UPVD / EPCC Centre Européen de Recherche Préhistorique, Tautavel 66720, France
| | - Armelle Gardeisen
- Archéologie des Sociétés Méditéranéennes, Université Paul Valéry - Site Saint-Charles 2, Montpellier 34090, France
| | - Liora Kolska Horwitz
- National Natural History Collections, Edmond J. Safra Campus, Givat Ram, The Hebrew University, Jerusalem 9190401, Israel
| | - Aliye Öztan
- Archaeology Department, Ankara University, Ankara 06100, Turkey
| | - Benjamin S Arbuckle
- Department of Anthropology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Vedat Onar
- Osteoarchaeology Practice and Research Center and Department of Anatomy, Faculty of Veterinary Medicine, Istanbul University-Cerrahpaşa, Istanbul 34320, Turkey
| | - Benoît Clavel
- Archéozoologie, Archéobotanique, Sociétés, Pratiques et Environnements, Muséum National d'Histoire Naturelle, Paris 75005, France
| | - Sébastien Lepetz
- Archéozoologie, Archéobotanique, Sociétés, Pratiques et Environnements, Muséum National d'Histoire Naturelle, Paris 75005, France
| | - Ali Akbar Vahdati
- Provincial Office of the Iranian Center for Cultural Heritage, Handicrafts and Tourism Organisation, North Khorassan, Bojnord 9416745775, Iran
| | - Hossein Davoudi
- Archaezoology section, Bioarchaeology Laboratory of the Central Laboratory, University of Tehran, Tehran CP1417634934, Iran
| | - Azadeh Mohaseb
- Archéozoologie, Archéobotanique, Sociétés, Pratiques et Environnements, Muséum National d'Histoire Naturelle, Paris 75005, France.,Archaezoology section, Bioarchaeology Laboratory of the Central Laboratory, University of Tehran, Tehran CP1417634934, Iran
| | - Marjan Mashkour
- Archéozoologie, Archéobotanique, Sociétés, Pratiques et Environnements, Muséum National d'Histoire Naturelle, Paris 75005, France.,Archaezoology section, Bioarchaeology Laboratory of the Central Laboratory, University of Tehran, Tehran CP1417634934, Iran.,Department of Osteology, National Museum of Iran, Tehran 1136918111, Iran
| | - Olivier Bouchez
- GeT-PlaGe - Génome et Transcriptome - Plateforme Génomique, GET - Plateforme Génome & Transcriptome, Institut National de Recherche pour l'Agriculture, l'Alimentation et l'Environnement, Castaneet-Tolosan Cedex 31326, France
| | - Cécile Donnadieu
- GeT-PlaGe - Génome et Transcriptome - Plateforme Génomique, GET - Plateforme Génome & Transcriptome, Institut National de Recherche pour l'Agriculture, l'Alimentation et l'Environnement, Castaneet-Tolosan Cedex 31326, France
| | - Patrick Wincker
- Genoscope, Institut de biologie François Jacob, CEA, Université d'Evry, Université Paris-Saclay, Evry 91042, France
| | - Samantha A Brooks
- Department of Animal Science, UF Genetics Institute, University of Florida, Gainesville, FL 32610, USA
| | - Albano Beja-Pereira
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Campus de Vairão, Universidade do Porto, Vairão 4485-661, Portugal.,BIOPOLIS Program in Genomics, Biodiversity and Land Planning, Campus de Vairão, Universidade do Porto, Vairão 4485-661, Portugal.,DGAOT, Faculty of Sciences, Universidade do Porto, Porto 4169-007, Portugal.,Sustainable Agrifood Production Research Centre (GreenUPorto), Universidade do Porto, Vairão 4485-646, Portugal
| | - Dong-Dong Wu
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650201, China.,Kunming Natural History Museum of Zoology, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650223, China
| | - Ludovic Orlando
- Centre d'Anthropobiologie et de Génomique de Toulouse (CAGT), CNRS UMR 5288, Université Paul Sabatier, Toulouse 31000, France
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33
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Chak STC, Harris SE, Hultgren KM, Duffy JE, Rubenstein DR. Demographic inference provides insights into the extirpation and ecological dominance of eusocial snapping shrimps. J Hered 2022; 113:552-562. [PMID: 35921239 DOI: 10.1093/jhered/esac035] [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: 11/08/2021] [Accepted: 07/27/2022] [Indexed: 11/14/2022] Open
Abstract
Although eusocial animals often achieve ecological dominance in the ecosystems where they occur, many populations are unstable, resulting in local extinction. Both patterns may be linked to the characteristic demography of eusocial species-high reproductive skew and reproductive division of labor support stable effective population sizes that make eusocial groups more competitive in some species, but also lower effective population sizes that increase susceptibility to population collapse in others. Here, we examine the relationship between demography and social organization in Synalpheus snapping shrimps, a group in which eusociality has evolved recently and repeatedly. We show using coalescent demographic modelling that eusocial species have had lower but more stable effective population sizes across 100,000 generations. Our results are consistent with the idea that stable population sizes may enable competitive dominance in eusocial shrimps, but they also suggest that recent population declines are likely caused by eusocial shrimps' heightened sensitivity to environmental changes, perhaps as a result of their low effective population sizes and localized dispersal. Thus, although the unique life histories and demography of eusocial shrimps have likely contributed to their persistence and ecological dominance over evolutionary timescales, these social traits may also make them vulnerable to contemporary environmental change.
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Affiliation(s)
- Solomon T C Chak
- Department of Ecology, Evolution and Environmental Biology, Columbia University, New York, NY, USA.,Department of Biological Sciences, New Jersey Institute of Technology, Newark, NJ, USA.,Department of Biological Sciences, SUNY College at Old Westbury, Old Westbury, NY, USA
| | - Stephen E Harris
- Department of Ecology, Evolution and Environmental Biology, Columbia University, New York, NY, USA.,Biology Department, SUNY Purchase College, Purchase, NY, USA
| | | | - J Emmett Duffy
- Tennenbaum Marine Observatories Network, Smithsonian Institution, Edgewater, MD, USA
| | - Dustin R Rubenstein
- Department of Ecology, Evolution and Environmental Biology, Columbia University, New York, NY, USA
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34
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Salek Ardestani S, Zandi MB, Vahedi SM, Janssens S. Population structure and genomic footprints of selection in five major Iranian horse breeds. Anim Genet 2022; 53:627-639. [PMID: 35919961 DOI: 10.1111/age.13243] [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: 03/03/2022] [Revised: 06/08/2022] [Accepted: 07/04/2022] [Indexed: 11/28/2022]
Abstract
The genetic structure and characteristics of Iranian native breeds are yet to be comprehensibly investigated and studied. Therefore, we employed genomic information of 364 Iranian native horses representing the Asil (n = 109), Caspian (n = 40), Dareshuri (n = 44), Kurdish (n = 95), and Turkoman (n = 76) breeds to reveal the genetic structure and characteristics. For these and 19 other horse breeds, principal component analysis, Bayesian model-based, Neighbor-Net, and bootstrap-based TreeMix approaches were applied to investigate and compare their genetic structure. Additionally, three haplotype-based methods including haplotype homozygosity pooled, integrated haplotype score, and number of segregating sites by length were applied to trace genomic footprints of selection of Asil, Caspian, Dareshuri, Kurdish, and Turkoman groups. Then, the Mahalanobis distance based on the negative-log10 rank-based P-values was estimated based on the haplotype homozygosity pooled, integrated haplotype score, and number of segregating sites by length values. Asil, Caspian, Dareshuri, Kurdish, and Turkoman can be categorized into five different genetic clusters. Based on the top 1% of Mahalanobis distance based on the negative-log10 rank-based P-values of SNPs, we identified 24 SNPs formerly reported to be associated with different traits and >100 genes undergoing selection pressures in Asil, Caspian, Dareshuri, Kurdish, and Turkoman. The detected QTL undergoing selection pressures were associated with withers height, equine metabolic syndrome, overall body size, insect bite hypersensitivity, guttural pouch tympany, white markings, Rhodococcus equi infection, jumping test score, alternate gaits, and body weight traits. Our findings will aid to have a better perspective of the genetic characteristics and population structure of Asil, Caspian, Dareshuri, Kurdish, and Turkoman horses as Iranian native horse breeds.
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Affiliation(s)
| | | | - Seyed Milad Vahedi
- Department of Animal Science and Aquaculture, Dalhousie University, Truro, Nova Scotia, Canada
| | - Steven Janssens
- Department Biosystems, Center Animal Breeding and Genetics, KU Leuven, Leuven, Belgium
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35
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Beckman AK, Richey BMS, Rosenthal GG. Behavioral responses of wild animals to anthropogenic change: insights from domestication. Behav Ecol Sociobiol 2022. [DOI: 10.1007/s00265-022-03205-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
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36
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Liu X, Orlando L. mapDATAge: a ShinyR package to chart ancient DNA data through space and time. Bioinformatics 2022; 38:3992-3994. [PMID: 35771611 PMCID: PMC9364369 DOI: 10.1093/bioinformatics/btac425] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2022] [Revised: 05/25/2022] [Accepted: 06/28/2022] [Indexed: 12/24/2022] Open
Abstract
SUMMARY Ancient DNA datasets are increasingly difficult to visualize for users lacking computational experience. Here, we describe mapDATAge, which aims to provide user-friendly automated modules for the interactive mapping of allele, haplogroup and/or ancestry distributions through space and time. mapDATAge enhances collaborative data sharing while assisting the assessment and reporting of spatiotemporal patterns of genetic changes. AVAILABILITY AND IMPLEMENTATION mapDATAge is a Shiny R application designed for exploring spatiotemporal patterns in ancient DNA data through a graphical user interface. It is freely available under GNU Public License in Github: https://github.com/xuefenfei712/mapDATAge. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Xuexue Liu
- Centre for Anthropobiology and Genomics of Toulouse, CNRS UMR 5288, Université de Toulouse, Université Paul Sabatier, Toulouse 31000, France
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37
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Srigyan M, Bolívar H, Ureña I, Santana J, Petersen A, Iriarte E, Kırdök E, Bergfeldt N, Mora A, Jakobsson M, Abdo K, Braemer F, Smith C, Ibañez JJ, Götherström A, Günther T, Valdiosera C. Bioarchaeological evidence of one of the earliest Islamic burials in the Levant. Commun Biol 2022; 5:554. [PMID: 35672445 PMCID: PMC9174286 DOI: 10.1038/s42003-022-03508-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2021] [Accepted: 05/20/2022] [Indexed: 11/27/2022] Open
Abstract
The Middle East plays a central role in human history harbouring a vast diversity of ethnic, cultural and religious groups. However, much remains to be understood about past and present genomic diversity in this region. Here we present a multidisciplinary bioarchaeological analysis of two individuals dated to the late 7th and early 8th centuries, the Umayyad Era, from Tell Qarassa, an open-air site in modern-day Syria. Radiocarbon dates and burial type are consistent with one of the earliest Islamic Arab burials in the Levant. Interestingly, we found genomic similarity to a genotyped group of modern-day Bedouins and Saudi rather than to most neighbouring Levantine groups. This study represents the genomic analysis of a secondary use site with characteristics consistent with an early Islamic burial in the Levant. We discuss our findings and possible historic scenarios in the light of forces such as genetic drift and their possible interaction with religious and cultural processes (including diet and subsistence practices). Ancient genomic and archaeological data combine to identify a surprisingly early Islamic burial in modern day Syria.
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Affiliation(s)
- Megha Srigyan
- Human Evolution, Department of Organismal Biology, Uppsala University, Uppsala, Sweden.,Department of Ecology and Evolutionary Biology, University of California Santa Cruz, Santa Cruz, CA, 95064, USA
| | - Héctor Bolívar
- Centre for Palaeogenetics, 10691, Stockholm, Sweden.,Instituto del Patrimonio Cultural de España, 28040, Madrid, Spain
| | - Irene Ureña
- Centre for Palaeogenetics, 10691, Stockholm, Sweden
| | - Jonathan Santana
- Department of Historical Sciences, Universidad de Las Palmas de Gran Canaria, Las Palmas de G.C., E35001, Spain
| | | | - Eneko Iriarte
- Laboratorio de Evolución Humana, Departamento de Historia, Geografía y Comunicación, Universidad de Burgos, 09001, Burgos, Spain
| | - Emrah Kırdök
- Department of Biotechnology, Mersin University, 33343, Mersin, Turkey
| | | | - Alice Mora
- Dept. Archaeology and History, La Trobe University, Melbourne, VIC, 3086, Australia
| | - Mattias Jakobsson
- Human Evolution, Department of Organismal Biology, Uppsala University, Uppsala, Sweden
| | - Khaled Abdo
- General Directorate of Antiquities and Museums, Damascus, Syrian Arab Republic
| | - Frank Braemer
- Université Côte d'Azur, CNRS, Culture et Environment, Préhistoire Antiquité Moyen Age, Nice, France
| | - Colin Smith
- Laboratorio de Evolución Humana, Departamento de Historia, Geografía y Comunicación, Universidad de Burgos, 09001, Burgos, Spain.,Dept. Archaeology and History, La Trobe University, Melbourne, VIC, 3086, Australia
| | - Juan José Ibañez
- Archaeology of Social Dynamics, Milà i Fontanals Institution, Spanish National Research Council (CSIC), Barcelona, Spain
| | | | - Torsten Günther
- Human Evolution, Department of Organismal Biology, Uppsala University, Uppsala, Sweden.
| | - Cristina Valdiosera
- Laboratorio de Evolución Humana, Departamento de Historia, Geografía y Comunicación, Universidad de Burgos, 09001, Burgos, Spain. .,Dept. Archaeology and History, La Trobe University, Melbourne, VIC, 3086, Australia.
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Kanne K. Riding, Ruling, and Resistance: Equestrianism and Political Authority in the Hungarian Bronze Age. CURRENT ANTHROPOLOGY 2022. [DOI: 10.1086/720271] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
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Cai D, Zhu S, Gong M, Zhang N, Wen J, Liang Q, Sun W, Shao X, Guo Y, Cai Y, Zheng Z, Zhang W, Hu S, Wang X, Tian H, Li Y, Liu W, Yang M, Yang J, Wu D, Orlando L, Jiang Y. Radiocarbon and genomic evidence for the survival of Equus Sussemionus until the late Holocene. eLife 2022; 11:73346. [PMID: 35543411 PMCID: PMC9142152 DOI: 10.7554/elife.73346] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2021] [Accepted: 05/11/2022] [Indexed: 12/02/2022] Open
Abstract
The exceptionally rich fossil record available for the equid family has provided textbook examples of macroevolutionary changes. Horses, asses, and zebras represent three extant subgenera of Equus lineage, while the Sussemionus subgenus is another remarkable Equus lineage ranging from North America to Ethiopia in the Pleistocene. We sequenced 26 archaeological specimens from Northern China in the Holocene that could be assigned morphologically and genetically to Equus ovodovi, a species representative of Sussemionus. We present the first high-quality complete genome of the Sussemionus lineage, which was sequenced to 13.4× depth of coverage. Radiocarbon dating demonstrates that this lineage survived until ~3500 years ago, despite continued demographic collapse during the Last Glacial Maximum and the great human expansion in East Asia. We also confirmed the Equus phylogenetic tree and found that Sussemionus diverged from the ancestor of non-caballine equids ~2.3–2.7 million years ago and possibly remained affected by secondary gene flow post-divergence. We found that the small genetic diversity, rather than enhanced inbreeding, limited the species’ chances of survival. Our work adds to the growing literature illustrating how ancient DNA can inform on extinction dynamics and the long-term resilience of species surviving in cryptic population pockets.
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Affiliation(s)
- Dawei Cai
- Bioarchaeology Laboratory, Jilin University, Changchun, China
| | - Siqi Zhu
- Bioarchaeology Laboratory, Jilin University, Changchun, China
| | - Mian Gong
- College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Naifan Zhang
- Bioarchaeology Laboratory, Jilin University, Changchuin, China
| | - Jia Wen
- College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Qiyao Liang
- Bioarchaeology Laboratory, Jilin University, Changchun, China
| | - Weilu Sun
- Bioarchaeology Laboratory, Jilin University, Changchun, China
| | - Xinyue Shao
- Bioarchaeology Laboratory, Jilin University, Changchun, China
| | - Yaqi Guo
- Bioarchaeology Laboratory, Jilin University, Changchun, China
| | - Yudong Cai
- College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Zhuqing Zheng
- College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Wei Zhang
- Heilongjiang Provincial Institute of Cultural Relics and Archaeology, Harbin, China
| | - Songmei Hu
- Shaanxi Provincial Institute of Archaeology, Xi'an, China
| | - Xiaoyang Wang
- Ningxia Institute of Cultural Relics and Archaeology, Yinchuan, China
| | - He Tian
- Heilongjiang Provincial Institute of Cultural Relics and Archaeology, Harbin, China
| | - Youqian Li
- Heilongjiang Provincial Institute of Cultural Relics and Archaeology, Harbin, China
| | - Wei Liu
- Heilongjiang Provincial Institute of Cultural Relics and Archaeology, Harbin, China
| | - Miaomiao Yang
- Shaanxi Provincial Institute of Archaeology, Xi'an, China
| | - Jian Yang
- Ningxia Institute of Cultural Relics and Archaeology, Yinchuan, China
| | - Duo Wu
- College of Earth and Environmental Sciences, Lanzhou University, Lanzhou, China
| | - Ludovic Orlando
- 7Centre d'Anthropobiologie et de Génomique de Toulouse, Université Paul Sabatier, CNRS UMR 5288, Toulouse, France
| | - Yu Jiang
- College of Animal Science and Technology, Northwest A&F University, Yangling, China
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Iriarte J, Ziegler MJ, Outram AK, Robinson M, Roberts P, Aceituno FJ, Morcote-Ríos G, Keesey TM. Ice Age megafauna rock art in the Colombian Amazon? Philos Trans R Soc Lond B Biol Sci 2022; 377:20200496. [PMID: 35249392 PMCID: PMC8899627 DOI: 10.1098/rstb.2020.0496] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
Megafauna paintings have accompanied the earliest archaeological contexts across the continents, revealing a fundamental inter-relationship between early humans and megafauna during the global human expansion as unfamiliar landscapes were humanized and identities built into new territories. However, the identification of extinct megafauna from rock art is controversial. Here, we examine potential megafauna depictions in the rock art of Serranía de la Lindosa, Colombian Amazon, that includes a giant sloth, a gomphothere, a camelid, horses and three-toed ungulates with trunks. We argue that they are Ice Age rock art based on the (i) naturalistic appearance and diagnostic morphological features of the animal images, (ii) late Pleistocene archaeological dates from La Lindosa confirming the contemporaneity of humans and megafauna, (iii) recovery of ochre pigments in late Pleistocene archaeological strata, (iv) the presence of most megafauna identified in the region during the late Pleistocene as attested by archaeological and palaeontological records, and (v) widespread depiction of extinct megafauna in rock art across the Americas. Our findings contribute to the emerging picture of considerable geographical and stylistic variation of geometric and figurative rock art from early human occupations across South America. Lastly, we discuss the implications of our findings for understanding the early human history of tropical South America. This article is part of the theme issue ‘Tropical forests in the deep human past’.
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Affiliation(s)
- José Iriarte
- Department of Archaeology, University of Exeter, Exeter, UK
| | - Michael J Ziegler
- Max Planck Institute for the Science of Human History, Jena, Germany
| | - Alan K Outram
- Department of Archaeology, University of Exeter, Exeter, UK
| | - Mark Robinson
- Department of Archaeology, University of Exeter, Exeter, UK
| | - Patrick Roberts
- Max Planck Institute for the Science of Human History, Jena, Germany
| | | | - Gaspar Morcote-Ríos
- Instituto de Ciencias Naturales, Universidad Nacional de Colombia, Bogotá, Colombia
| | - T Michael Keesey
- Max Planck Institute for the Science of Human History, Jena, Germany
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Suchan T, Chauvey L, Poullet M, Tonasso‐Calvière L, Schiavinato S, Clavel P, Clavel B, Lepetz S, Seguin‐Orlando A, Orlando L. Assessing the impact of USER‐treatment on hyRAD capture applied to ancient DNA. Mol Ecol Resour 2022; 22:2262-2274. [DOI: 10.1111/1755-0998.13619] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2021] [Revised: 03/09/2022] [Accepted: 03/23/2022] [Indexed: 12/01/2022]
Affiliation(s)
- Tomasz Suchan
- Centre d’Anthropobiologie et de Génomique de Toulouse (CAGT) Université Paul Sabatier Faculté de Santé 37 allées Jules Guesde, Bâtiment A 31000 Toulouse France
- W. Szafer Institute of Botany Polish Academy of Sciences Lubicz 46 31‐512 Kraków Poland
| | - Lorelei Chauvey
- Centre d’Anthropobiologie et de Génomique de Toulouse (CAGT) Université Paul Sabatier Faculté de Santé 37 allées Jules Guesde, Bâtiment A 31000 Toulouse France
| | - Marine Poullet
- Centre d’Anthropobiologie et de Génomique de Toulouse (CAGT) Université Paul Sabatier Faculté de Santé 37 allées Jules Guesde, Bâtiment A 31000 Toulouse France
| | - Laure Tonasso‐Calvière
- Centre d’Anthropobiologie et de Génomique de Toulouse (CAGT) Université Paul Sabatier Faculté de Santé 37 allées Jules Guesde, Bâtiment A 31000 Toulouse France
| | - Stéphanie Schiavinato
- Centre d’Anthropobiologie et de Génomique de Toulouse (CAGT) Université Paul Sabatier Faculté de Santé 37 allées Jules Guesde, Bâtiment A 31000 Toulouse France
| | - Pierre Clavel
- Centre d’Anthropobiologie et de Génomique de Toulouse (CAGT) Université Paul Sabatier Faculté de Santé 37 allées Jules Guesde, Bâtiment A 31000 Toulouse France
| | - Benoit Clavel
- Archéozoologie, Archéobotanique: sociétés, pratiques et environnements (AASPE) Muséum National d’Histoire Naturelle CNRS CP 55 rue Buffon Paris France
| | - Sébastien Lepetz
- Archéozoologie, Archéobotanique: sociétés, pratiques et environnements (AASPE) Muséum National d’Histoire Naturelle CNRS CP 55 rue Buffon Paris France
| | - Andaine Seguin‐Orlando
- Centre d’Anthropobiologie et de Génomique de Toulouse (CAGT) Université Paul Sabatier Faculté de Santé 37 allées Jules Guesde, Bâtiment A 31000 Toulouse France
| | - Ludovic Orlando
- Centre d’Anthropobiologie et de Génomique de Toulouse (CAGT) Université Paul Sabatier Faculté de Santé 37 allées Jules Guesde, Bâtiment A 31000 Toulouse France
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Gilroy R, Leng J, Ravi A, Adriaenssens EM, Oren A, Baker D, La Ragione RM, Proudman C, Pallen MJ. Metagenomic investigation of the equine faecal microbiome reveals extensive taxonomic diversity. PeerJ 2022; 10:e13084. [PMID: 35345588 PMCID: PMC8957277 DOI: 10.7717/peerj.13084] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2021] [Accepted: 02/17/2022] [Indexed: 01/12/2023] Open
Abstract
Background The horse plays crucial roles across the globe, including in horseracing, as a working and companion animal and as a food animal. The horse hindgut microbiome makes a key contribution in turning a high fibre diet into body mass and horsepower. However, despite its importance, the horse hindgut microbiome remains largely undefined. Here, we applied culture-independent shotgun metagenomics to thoroughbred equine faecal samples to deliver novel insights into this complex microbial community. Results We performed metagenomic sequencing on five equine faecal samples to construct 123 high- or medium-quality metagenome-assembled genomes from Bacteria and Archaea. In addition, we recovered nearly 200 bacteriophage genomes. We document surprising taxonomic diversity, encompassing dozens of novel or unnamed bacterial genera and species, to which we have assigned new Candidatus names. Many of these genera are conserved across a range of mammalian gut microbiomes. Conclusions Our metagenomic analyses provide new insights into the bacterial, archaeal and bacteriophage components of the horse gut microbiome. The resulting datasets provide a key resource for future high-resolution taxonomic and functional studies on the equine gut microbiome.
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Affiliation(s)
- Rachel Gilroy
- Quadram Institute Bioscience, Norwich, United Kingdom
| | - Joy Leng
- School of Veterinary Medicine, University of Surrey, Guildford, United Kingdom
| | - Anuradha Ravi
- Quadram Institute Bioscience, Norwich, United Kingdom
| | | | - Aharon Oren
- The Institute of Life Sciences, Hebrew University of Jerusalem, Jerusalem, Israel
| | - Dave Baker
- Quadram Institute Bioscience, Norwich, United Kingdom
| | | | | | - Mark J. Pallen
- Quadram Institute Bioscience, Norwich, United Kingdom
- School of Veterinary Medicine, University of Surrey, Guildford, United Kingdom
- University of East Anglia, Norwich, United Kingdom
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Panziera D, Requier F, Chantawannakul P, Pirk CWW, Blacquière T. The Diversity Decline in Wild and Managed Honey Bee Populations Urges for an Integrated Conservation Approach. Front Ecol Evol 2022. [DOI: 10.3389/fevo.2022.767950] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023] Open
Abstract
Many parts of the globe experience severe losses and fragmentation of habitats, affecting the self-sustainability of pollinator populations. A number of bee species coexist as wild and managed populations. Using honey bees as an example, we argue that several management practices in beekeeping threaten genetic diversity in both wild and managed populations, and drive population decline. Large-scale movement of hive stocks, introductions into new areas, breeding programs and trading of queens contribute to reducing genetic diversity, as recent research demonstrated for wild and managed honey bees within a few decades. Examples of the effects of domestication in other organisms show losses of both genetic diversity and fitness functions. Cases of natural selection and feralization resulted in maintenance of a higher genetic diversity, including in a Varroa destructor surviving population of honey bees. To protect the genetic diversity of honey bee populations, exchange between regions should be avoided. The proposed solution to selectively breed all local subspecies for a use in beekeeping would reduce the genetic diversity of each, and not address the value of the genetic diversity present in hybridized populations. The protection of Apis mellifera’s, Apis cerana’s and Apis koschevnikovi’s genetic diversities could be based on natural selection. In beekeeping, it implies to not selectively breed but to leave the choice of the next generation of queens to the colonies, as in nature. Wild populations surrounded by beekeeping activity could be preserved by allowing Darwinian beekeeping in a buffer zone between the wild and regular beekeeping area.
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Gudea A, Martonos C, Cosma C, Stan F. Morphological Characteristics of a Horse Discovered in an Avar-Period Grave from Sâncraiu de Mureș (Alba County, Romania). Animals (Basel) 2022; 12:ani12040478. [PMID: 35203187 PMCID: PMC8868351 DOI: 10.3390/ani12040478] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2022] [Revised: 02/10/2022] [Accepted: 02/11/2022] [Indexed: 11/30/2022] Open
Abstract
Simple Summary The present study deals with the morphological description of the animal remains in an Avar grave that contained the remnants of a horse burial, along with its owner, in a cemetery situated in Sâncraiu de Mures, Alba County, Romania, located geographically in the Transylvanian Plateau. The investigation of the grave and the data about the remains were published by archaeologists from the Institute of Archaeology of Cluj Napoca, Romania. For analysis and study, the animal bone remains were sent to the Faculty of Veterinary Medicine Cluj-Napoca. After a careful analysis of the morphological characteristics of the bones, the conclusions showed that the bones belonged to one young horse of 2–2.5 years, with an average recalculated shoulder height as being situated in the 1300–1400 mm interval. The study provides a set of morphological data regarding the characteristics of the horses from this scantily represented history in Romania, and the results show that the data obtained are consistent with the similar Avar horse burials in the region. Abstract Archeozoological studies provide an insight into human–environment relations, bringing important information on the morphology of the animal and the role of the animal and its functions. The purpose of this study was to reveal the morphological characteristics of the horse identified in an 8th century BC Avar cemetery dated, as it resulted from the investigation carried out on the materials presented to the Anatomy Lab of Department of Comparative Anatomy. The cleaning and conditioning of the materials were performed in the lab, followed by anatomical and osteometrical study. The identification of the species, the osteometrical interpretation and the assessment of age at death constituted the basis of the main conclusions. Based on the morphological and metrical data, we concluded that the fragments originated from a single young horse individual (Equus caballus) no older than 2.5 (2–2.5 years age span) included into class 5 of height (Vitt scale) with slender extremities. An overview of the available data (horse morphology) from similar sites in Romania and neighboring territories (Hungary and Croatia) is presented, with the intention of a general framing for the characteristics of the horses used by the Avar populations.
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Affiliation(s)
- Alexandru Gudea
- Department of Anatomy, Faculty of Veterinary Medicine, 3–5 Manastrur Street, 400372 Cluj-Napoca, Romania; (A.G.); (F.S.)
| | - Cristian Martonos
- Department of Anatomy, Faculty of Veterinary Medicine, 3–5 Manastrur Street, 400372 Cluj-Napoca, Romania; (A.G.); (F.S.)
- Correspondence: ; Tel.: +40-786-606-379
| | - Călin Cosma
- Institute of Archaeology and Art History Cluj-Napoca, 12–14 M. Kogalniceanu Street, 400084 Cluj-Napoca, Romania;
| | - Florin Stan
- Department of Anatomy, Faculty of Veterinary Medicine, 3–5 Manastrur Street, 400372 Cluj-Napoca, Romania; (A.G.); (F.S.)
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Marín Navas C, Delgado Bermejo JV, McLean AK, León Jurado JM, de Torres ARDLBYR, Navas González FJ. One Hundred Years of Coat Colour Influences on Genetic Diversity in the Process of Development of a Composite Horse Breed. Vet Sci 2022; 9:vetsci9020068. [PMID: 35202321 PMCID: PMC8879117 DOI: 10.3390/vetsci9020068] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2021] [Revised: 01/27/2022] [Accepted: 02/04/2022] [Indexed: 02/04/2023] Open
Abstract
Genetic diversity and demographic parameters were computed to evaluate the historic effects of coat colour segregation in the process of configuration of the Hispano-Arabian horse (Há). Pedigree records from 207,100 individuals born between 1884 and 2019 were used. Although coat colour is not a determinant for the admission of Hispano-Arabian individuals as apt for breeding, it may provide a representative visual insight into the gene contribution of Spanish Purebred horses (PRE), given many of the dilution genes described in Há are not present in the Arabian Purebred breed (PRá). The lack of consideration of coat colour inheritance patterns by the entities in charge of individual registration and the dodging behaviour of breeders towards the historic banning policies, may have acted as a buffer for diversity loss (lower than 8%). Inbreeding levels ranged from 1.81% in smokey cream horses to 8.80 for white horses. Contextually, crossbred breeding may increase the likelihood for double dilute combinations to occur as denoted by the increased number of Há horses displaying Pearl coats (53 Há against 3 PRE and 0 PRá). Bans against certain coat colours and patterns may have prevented an appropriate registration of genealogical information from the 4th generation onwards for decades. This may have brought about the elongation of generation intervals. Breeder tastes may have returned to the formerly officially-recognised coat colours (Grey and Bay) and Chestnut/Sorrel. However, coat colour conditioning effects must be evaluated timely for relatively short specific periods, as these may describe cyclic patterns already described in owners’ and breeders’ tastes over the centuries.
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Affiliation(s)
- Carmen Marín Navas
- Department of Genetics, Faculty of Veterinary Sciences, University of Córdoba, 14071 Córdoba, Spain; (C.M.N.); (J.V.D.B.)
| | - Juan Vicente Delgado Bermejo
- Department of Genetics, Faculty of Veterinary Sciences, University of Córdoba, 14071 Córdoba, Spain; (C.M.N.); (J.V.D.B.)
| | - Amy Katherine McLean
- Department of Animal Science, University of California Davis, Davis, CA 95617, USA;
| | - José Manuel León Jurado
- Centro Agropecuario Provincial de Córdoba, Diputación Provincial de Córdoba, 14071 Córdoba, Spain;
| | | | - Francisco Javier Navas González
- Department of Genetics, Faculty of Veterinary Sciences, University of Córdoba, 14071 Córdoba, Spain; (C.M.N.); (J.V.D.B.)
- Correspondence: ; Tel.: +34-651-679-262
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Demystifying the genetic origins of the Mangalarga Horse through the influential stallion Turbante J.O. J Equine Vet Sci 2022; 113:103910. [DOI: 10.1016/j.jevs.2022.103910] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2022] [Revised: 02/15/2022] [Accepted: 02/17/2022] [Indexed: 11/20/2022]
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Y-Chromosomal Insights into Breeding History and Sire Line Genealogies of Arabian Horses. Genes (Basel) 2022; 13:genes13020229. [PMID: 35205275 PMCID: PMC8871751 DOI: 10.3390/genes13020229] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2021] [Revised: 01/13/2022] [Accepted: 01/21/2022] [Indexed: 12/24/2022] Open
Abstract
The Y chromosome is a valuable genetic marker for studying the origin and influence of paternal lineages in populations. In this study, we conducted Y-chromosomal lineage-tracing in Arabian horses. First, we resolved a Y haplotype phylogeny based on the next generation sequencing data of 157 males from several breeds. Y-chromosomal haplotypes specific for Arabian horses were inferred by genotyping a collection of 145 males representing most Arabian sire lines that are active around the globe. These lines formed three discrete haplogroups, and the same haplogroups were detected in Arabian populations native to the Middle East. The Arabian haplotypes were clearly distinct from the ones detected in Akhal Tekes, Turkoman horses, and the progeny of two Thoroughbred foundation sires. However, a haplotype introduced into the English Thoroughbred by the stallion Byerley Turk (1680), was shared among Arabians, Turkomans, and Akhal Tekes, which opens a discussion about the historic connections between Oriental horse types. Furthermore, we genetically traced Arabian sire line breeding in the Western World over the past 200 years. This confirmed a strong selection for relatively few male lineages and uncovered incongruences to written pedigree records. Overall, we demonstrate how fine-scaled Y-analysis contributes to a better understanding of the historical development of horse breeds.
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Librado P, Orlando L. OUP accepted manuscript. Bioinformatics 2022; 38:2070-2071. [PMID: 35080599 PMCID: PMC8963280 DOI: 10.1093/bioinformatics/btac046] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2021] [Revised: 01/14/2022] [Indexed: 11/13/2022] Open
Affiliation(s)
| | - Ludovic Orlando
- Centre for Anthropobiology and Genomics of Toulouse, CNRS UMR 5288, Université de Toulouse, Université Paul Sabatier, 31000 Toulouse, France
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Liu X, Zhang Y, Liu W, Li Y, Pan J, Pu Y, Han J, Orlando L, Ma Y, Jiang L. A single-nucleotide mutation within the TBX3 enhancer increased body size in Chinese horses. Curr Biol 2021; 32:480-487.e6. [PMID: 34906355 PMCID: PMC8796118 DOI: 10.1016/j.cub.2021.11.052] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2021] [Revised: 09/23/2021] [Accepted: 11/22/2021] [Indexed: 01/15/2023]
Abstract
Chinese ponies are endemic to the mountainous areas of southwestern China and were first reported in the archaeological record at the Royal Tomb of Zhongshan King, Mancheng, dated to approximately ∼2,100 YBP.1 Previous work has started uncovering the genetic basis of size variation in western ponies and horses, revealing a limited number of loci, including HMGA2,2LCORL/NCAPG,3ZFAT, and LASP1.4,5 Whether the same genetic pathways also drive the small body size of Chinese ponies, which show striking anatomical differences to Shetland ponies,6 remains unclear.2,7 To test this, we combined whole-genome sequences of 187 horses across China. Statistical analyses revealed top association between genetic variation at the T-box transcription factor 3 (TBX3) and the body size. Fine-scale analysis across an extended population of 189 ponies and 574 horses narrowed down the association to one A/G SNP at an enhancer region upstream of the TBX3 (ECA8:20,644,555, p = 2.34e−39). Luciferase assays confirmed the single-nucleotide G mutation upregulating TBX3 expression, and enhancer-knockout mice exhibited shorter limbs than wild-type littermates (p < 0.01). Re-analysis of ancient DNA data showed that the G allele, which is most frequent in modern horses, first occurred some ∼2,300 years ago and rose in frequency since. This supports selection for larger size in Asia from approximately the beginning of the Chinese Empire. Overall, this study characterized the causal regulatory mutation underlying small body size in Chinese ponies and revealed size as one of the main selection targets of past Chinese breeders. One single A/G SNP in TBX3 enhancer region drives size variation in Chinese horses The frequency of the G variant correlates positively with size in 763 horses Cellular and mice models confirm it affects TBX3 transcription and the limb length The G variant first occurred ∼2,300 years ago and rose in frequency since
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Affiliation(s)
- Xuexue Liu
- Laboratory of Animal (Poultry) Genetics Breeding and Reproduction, Ministry of Agriculture, Institute of Animal Science, Chinese Academy of Agricultural Sciences (CAAS), Beijing 100193, P.R. China; Centre d'Anthropobiologie et de Génomique de Toulouse, Université Paul Sabatier, 37 allées Jules Guesde, 31000 Toulouse, France; CAAS-ILRI Joint Laboratory on Livestock and Forage Genetic Resources, Institute of Animal Science, Chinese Academy of Agricultural Sciences (CAAS), Beijing 100193, P.R. China
| | - Yanli Zhang
- Laboratory of Animal (Poultry) Genetics Breeding and Reproduction, Ministry of Agriculture, Institute of Animal Science, Chinese Academy of Agricultural Sciences (CAAS), Beijing 100193, P.R. China; CAAS-ILRI Joint Laboratory on Livestock and Forage Genetic Resources, Institute of Animal Science, Chinese Academy of Agricultural Sciences (CAAS), Beijing 100193, P.R. China
| | - Wujun Liu
- College of Animal Science, Xinjiang Agriculture University, Urumqi, Xinjiang, China
| | - Yefang Li
- Laboratory of Animal (Poultry) Genetics Breeding and Reproduction, Ministry of Agriculture, Institute of Animal Science, Chinese Academy of Agricultural Sciences (CAAS), Beijing 100193, P.R. China; CAAS-ILRI Joint Laboratory on Livestock and Forage Genetic Resources, Institute of Animal Science, Chinese Academy of Agricultural Sciences (CAAS), Beijing 100193, P.R. China
| | - Jianfei Pan
- Laboratory of Animal (Poultry) Genetics Breeding and Reproduction, Ministry of Agriculture, Institute of Animal Science, Chinese Academy of Agricultural Sciences (CAAS), Beijing 100193, P.R. China; CAAS-ILRI Joint Laboratory on Livestock and Forage Genetic Resources, Institute of Animal Science, Chinese Academy of Agricultural Sciences (CAAS), Beijing 100193, P.R. China
| | - Yabin Pu
- Laboratory of Animal (Poultry) Genetics Breeding and Reproduction, Ministry of Agriculture, Institute of Animal Science, Chinese Academy of Agricultural Sciences (CAAS), Beijing 100193, P.R. China; CAAS-ILRI Joint Laboratory on Livestock and Forage Genetic Resources, Institute of Animal Science, Chinese Academy of Agricultural Sciences (CAAS), Beijing 100193, P.R. China
| | - Jianlin Han
- CAAS-ILRI Joint Laboratory on Livestock and Forage Genetic Resources, Institute of Animal Science, Chinese Academy of Agricultural Sciences (CAAS), Beijing 100193, P.R. China; International Livestock Research Institute (ILRI), Nairobi 00100, Kenya
| | - Ludovic Orlando
- Centre d'Anthropobiologie et de Génomique de Toulouse, Université Paul Sabatier, 37 allées Jules Guesde, 31000 Toulouse, France.
| | - Yuehui Ma
- Laboratory of Animal (Poultry) Genetics Breeding and Reproduction, Ministry of Agriculture, Institute of Animal Science, Chinese Academy of Agricultural Sciences (CAAS), Beijing 100193, P.R. China; CAAS-ILRI Joint Laboratory on Livestock and Forage Genetic Resources, Institute of Animal Science, Chinese Academy of Agricultural Sciences (CAAS), Beijing 100193, P.R. China.
| | - Lin Jiang
- Laboratory of Animal (Poultry) Genetics Breeding and Reproduction, Ministry of Agriculture, Institute of Animal Science, Chinese Academy of Agricultural Sciences (CAAS), Beijing 100193, P.R. China; CAAS-ILRI Joint Laboratory on Livestock and Forage Genetic Resources, Institute of Animal Science, Chinese Academy of Agricultural Sciences (CAAS), Beijing 100193, P.R. China.
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The Sequence Analysis of Mitochondrial DNA Revealed Some Major Centers of Horse Domestications: The Archaeologist's Cut. J Equine Vet Sci 2021; 109:103830. [PMID: 34871751 DOI: 10.1016/j.jevs.2021.103830] [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: 09/24/2021] [Revised: 11/28/2021] [Accepted: 11/29/2021] [Indexed: 11/22/2022]
Abstract
The question about the time and the place of horse domestication, a process which had a profound impact on the progress of mankind, is disputable. According to the most widely accepted hypothesis, the earliest domestication of the horse happened in the western parts of the Eurasian steppes, between the Northern Black Sea region and present-day Kazakhstan and Turkmenistan. It seems that it occurred not earlier than the first half and most probably during the middle (even the last third) of the fourth millennium BC (from ∼ 5.5 kya). The next steps of large-scale horse breeding occurred almost simultaneously in Eurasia and North Africa due to the development of the social structure of human communities. On the other hand, the morphological differences between wild and domestic animals are rather vague and the genetic introgression between them is speculative. In this review, we have tried to gather all available scientific data on the existing possible hypotheses for the earliest domestication of the horse, as well as to highlight some data on the most plausible ones. This is due to the frequency of some significant data on the frequency of strictly defined mitotypes in different historical periods of human civilizations existing in the same periods.
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