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Janák V, Novák K, Kyselý R. Late History of Cattle Breeds in Central Europe in Light of Genetic and Archaeogenetic Sources-Overview, Thoughts, and Perspectives. Animals (Basel) 2024; 14:645. [PMID: 38396613 PMCID: PMC10886113 DOI: 10.3390/ani14040645] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2023] [Revised: 02/12/2024] [Accepted: 02/14/2024] [Indexed: 02/25/2024] Open
Abstract
Although Europe was not a primary centre of cattle domestication, its expansion from the Middle East and subsequent development created a complex pattern of cattle breed diversity. Many isolated populations of local historical breeds still carry the message about the physical and genetic traits of ancient populations. Since the way of life of human communities starting from the eleventh millennium BP was strongly determined by livestock husbandry, the knowledge of cattle diversity through the ages is helpful in the interpretation of many archaeological findings. Historical cattle diversity is currently at the intersection of two leading directions of genetic research. Firstly, it is archaeogenetics attempting to recover and interpret the preserved genetic information directly from archaeological finds. The advanced archaeogenetic approaches meet with the population genomics of extant cattle populations. The immense amount of genetic information collected from living cattle, due to its key economic role, allows for reconstructing the genetic profiles of the ancient populations backwards. The present paper aims to place selected archaeogenetic, genetic, and genomic findings in the picture of cattle history in Central Europe, as suggested by archaeozoological and historical records. Perspectives of the methodical connection between the genetic approaches and the approaches of traditional archaeozoology, such as osteomorphology and osteometry, are discussed. The importance, actuality, and effectiveness of combining different approaches to each archaeological find, such as morphological characterization, interpretation of the historical context, and molecular data, are stressed.
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Affiliation(s)
- Vojtěch Janák
- Institute of Archaeology of the Czech Academy of Sciences, Prague, Letenská 4, 118 00 Praha, Czech Republic
- Department of Genetics and Breeding, Institute of Animal Science, Přátelství 815, 104 00 Praha, Czech Republic;
- Department of Archaeology, Faculty of Arts, Charles University, Nám. Jana Palacha 2, 116 38 Praha, Czech Republic
| | - Karel Novák
- Department of Genetics and Breeding, Institute of Animal Science, Přátelství 815, 104 00 Praha, Czech Republic;
| | - René Kyselý
- Institute of Archaeology of the Czech Academy of Sciences, Prague, Letenská 4, 118 00 Praha, Czech Republic
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Kim K, Kim D, Hanotte O, Lee C, Kim H, Jeong C. Inference of Admixture Origins in Indigenous African Cattle. Mol Biol Evol 2023; 40:msad257. [PMID: 37995300 PMCID: PMC10701095 DOI: 10.1093/molbev/msad257] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2023] [Revised: 10/12/2023] [Accepted: 11/14/2023] [Indexed: 11/25/2023] Open
Abstract
Present-day African cattle retain a unique genetic profile composed of a mixture of the Bos taurus and Bos indicus populations introduced into the continent at different time periods. However, details of the admixture history and the exact origins of the source populations remain obscure. Here, we infer the source of admixture in the earliest domestic cattle in Africa, African taurine. We detect a significant contribution (up to ∼20%) from a basal taurine lineage, which might represent the now-extinct African aurochs. In addition, we show that the indicine ancestry of African cattle, although most closely related to so-far sampled North Indian indicine breeds, has a small amount of additional genetic affinity to Southeast Asian indicine breeds. Our findings support the hypothesis of aurochs introgression into African taurine and generate a novel hypothesis that the origin of indicine ancestry in Africa might be different indicine populations than the ones found in North India today.
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Affiliation(s)
- Kwondo Kim
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA
- Department of Agricultural Biotechnology and Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul, Republic of Korea
| | - Donghee Kim
- School of Biological Sciences, Seoul National University, Seoul, Republic of Korea
| | - Olivier Hanotte
- LiveGene, International Livestock Research Institute (ILRI), Addis Ababa, Ethiopia
- The Centre for Tropical Livestock Genetics and Health (CTLGH), The Roslin Institute, The University of Edinburgh, Midlothian, UK
- School of Life Sciences, University of Nottingham, Nottingham, UK
| | - Charles Lee
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA
| | - Heebal Kim
- Department of Agricultural Biotechnology and Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul, Republic of Korea
- Interdisciplinary Program in Bioinformatics, Seoul National University, Seoul, Republic of Korea
- eGnome, Inc., Seoul, Republic of Korea
| | - Choongwon Jeong
- School of Biological Sciences, Seoul National University, Seoul, Republic of Korea
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Kambal S, Tijjani A, Ibrahim SAE, Ahmed MKA, Mwacharo JM, Hanotte O. Candidate signatures of positive selection for environmental adaptation in indigenous African cattle: A review. Anim Genet 2023; 54:689-708. [PMID: 37697736 DOI: 10.1111/age.13353] [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: 07/28/2023] [Revised: 07/28/2023] [Accepted: 08/19/2023] [Indexed: 09/13/2023]
Abstract
Environmental adaptation traits of indigenous African cattle are increasingly being investigated to respond to the need for sustainable livestock production in the context of unpredictable climatic changes. Several studies have highlighted genomic regions under positive selection probably associated with adaptation to environmental challenges (e.g. heat stress, trypanosomiasis, tick and tick-borne diseases). However, little attention has focused on pinpointing the candidate causative variant(s) controlling the traits. This review compiled information from 22 studies on signatures of positive selection in indigenous African cattle breeds to identify regions under positive selection. We highlight some key candidate genome regions and genes of relevance to the challenges of living in extreme environments (high temperature, high altitude, high infectious disease prevalence). They include candidate genes involved in biological pathways relating to innate and adaptive immunity (e.g. BoLAs, SPAG11, IL1RL2 and GFI1B), heat stress (e.g. HSPs, SOD1 and PRLH) and hypoxia responses (e.g. BDNF and INPP4A). Notably, the highest numbers of candidate regions are found on BTA3, BTA5 and BTA7. They overlap with genes playing roles in several biological functions and pathways. These include but are not limited to growth and feed intake, cell stability, protein stability and sweat gland development. This review may further guide targeted genome studies aiming to assess the importance of candidate causative mutations, within regulatory and protein-coding genome regions, to further understand the biological mechanisms underlying African cattle's unique adaption.
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Affiliation(s)
- Sumaya Kambal
- Livestock Genetics, International Livestock Research Institute, Addis Ababa, Ethiopia
- Department of Genetics and Animal Breeding, Faculty of Animal Production, University of Khartoum, Khartoum, Sudan
- Department of Bioinformatics and Biostatistics, National University, Khartoum, Sudan
| | - Abdulfatai Tijjani
- Centre for Tropical Livestock Genetics and Health, International Livestock Research Institute, Addis Ababa, Ethiopia
- The Jackson Laboratory, Bar Harbor, Maine, USA
| | - Sabah A E Ibrahim
- Department of Bioinformatics and Biostatistics, National University, Khartoum, Sudan
| | - Mohamed-Khair A Ahmed
- Department of Genetics and Animal Breeding, Faculty of Animal Production, University of Khartoum, Khartoum, Sudan
| | - Joram M Mwacharo
- Scotland's Rural College and Centre for Tropical Livestock Genetics and Health, Edinburgh, UK
- Small Ruminant Genomics, International Centre for Agricultural Research in the Dry Areas, Addis Ababa, Ethiopia
| | - Olivier Hanotte
- Livestock Genetics, International Livestock Research Institute, Addis Ababa, Ethiopia
- Centre for Tropical Livestock Genetics and Health, International Livestock Research Institute, Addis Ababa, Ethiopia
- School of Life Sciences, University of Nottingham, Nottingham, UK
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Brunson K, Witt KE, Monge S, Williams S, Peede D, Odsuren D, Bukhchuluun D, Cameron A, Szpak P, Amartuvshin C, Honeychurch W, Wright J, Pleuger S, Erdene M, Tumen D, Rogers L, Khatanbaatar D, Batdalai B, Galdan G, Janz L. Ancient Mongolian aurochs genomes reveal sustained introgression and management in East Asia. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.08.10.552443. [PMID: 37609302 PMCID: PMC10441390 DOI: 10.1101/2023.08.10.552443] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/24/2023]
Abstract
Societies in East Asia have utilized domesticated cattle for over 5000 years, but the genetic history of cattle in East Asia remains understudied. Genome-wide analyses of 23 ancient Mongolian cattle reveal that East Asian aurochs and ancient East Asian taurine cattle are closely related, but neither are closely related to any modern East Asian breeds. We observe binary variation in aurochs diet throughout the early Neolithic, and genomic evidence shows millennia of sustained male-dominated introgression. We identify a unique connection between ancient Mongolian aurochs and the European Hereford breed. These results point to the likelihood of human management of aurochs in Northeast Asia prior to and during the initial adoption of taurine cattle pastoralism.
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Affiliation(s)
| | - Kelsey E. Witt
- Department of Genetics and Biochemistry and Center for Human Genetics, Clemson University; Clemson, South Carolina 29634, USA
- Center for Computational Molecular Biology, Brown University; Providence 02912, USA
- Department of Ecology, Evolution, and Organismal Biology, Brown University; Providence 02912, USA
| | - Susan Monge
- Department of Anthropology, University of Illinois Chicago, Chicago, IL 60607, USA
| | - Sloan Williams
- Department of Anthropology, University of Illinois Chicago, Chicago, IL 60607, USA
| | - David Peede
- Center for Computational Molecular Biology, Brown University; Providence 02912, USA
- Department of Ecology, Evolution, and Organismal Biology, Brown University; Providence 02912, USA
- Institute at Brown for Environment and Society, Brown University; Providence 02912, USA
| | - Davaakhuu Odsuren
- Department of History, Mongolian National University of Education; Ulaanbaatar, Sukhbaatar district, 210648, Mongolia
- Institute of Archaeology, Mongolian Academy of Sciences, Ulaanbaatar-51, Mongolia
| | - Dashzeveg Bukhchuluun
- Department of Anthropology, Yale University, 10 Sachem St., New Haven, CT 06511, USA
| | - Asa Cameron
- Department of Anthropology, Yale University, 10 Sachem St., New Haven, CT 06511, USA
| | - Paul Szpak
- Department of Anthropology, Trent University; Peterborough K9J 6Y1, Canada
| | - Chunag Amartuvshin
- Department of Anthropology and Archaeology, National University of Mongolia; Ulaanbaatar-51, Mongolia
| | - William Honeychurch
- Department of Anthropology, Yale University, 10 Sachem St., New Haven, CT 06511, USA
| | - Joshua Wright
- Department of Archaeology, University of Aberdeen, King’s College; Aberdeen, AB24 3FX, UK
| | - Sarah Pleuger
- School of History, Classics and Archaeology, University of Edinburgh; Edinburgh EH8 9AG, UK
| | - Myagmar Erdene
- Department of Anthropology and Archaeology, National University of Mongolia; Ulaanbaatar-51, Mongolia
| | - Dashtseveg Tumen
- Department of Anthropology and Archaeology, National University of Mongolia; Ulaanbaatar-51, Mongolia
| | - Leland Rogers
- Department of Anthropology, University of North Carolina Wilmington; Wilmington, NC 28403, USA
| | - Dorjpurev Khatanbaatar
- School of Business Administration and Humanities, The Mongolian University of Science and Technology; Mongolia
| | - Byambatseren Batdalai
- Archaeological Research Center, National University of Mongolia; Ulaanbaatar-51, Mongolia
| | - Ganbaatar Galdan
- Institute of Archaeology, Mongolian Academy of Sciences, Ulaanbaatar-51, Mongolia
| | - Lisa Janz
- Department of Anthropology, University of Toronto Scarborough; Scarborough, ON M1C 1A4, Canada
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