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Desvars-Larrive A, Vogl AE, Puspitarani GA, Yang L, Joachim A, Käsbohrer A. A One Health framework for exploring zoonotic interactions demonstrated through a case study. Nat Commun 2024; 15:5650. [PMID: 39009576 PMCID: PMC11250852 DOI: 10.1038/s41467-024-49967-7] [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: 02/26/2024] [Accepted: 06/24/2024] [Indexed: 07/17/2024] Open
Abstract
The eco-epidemiology of zoonoses is often oversimplified to host-pathogen interactions while findings derived from global datasets are rarely directly transferable to smaller-scale contexts. Through a systematic literature search, we compiled a dataset of naturally occurring zoonotic interactions in Austria, spanning 1975-2022. We introduce the concept of zoonotic web to describe the complex relationships between zoonotic agents, their hosts, vectors, food, and environmental sources. The zoonotic web was explored through network analysis. After controlling for research effort, we demonstrate that, within the projected unipartite source-source network of zoonotic agent sharing, the most influential zoonotic sources are human, cattle, chicken, and some meat products. Analysis of the One Health 3-cliques (triangular sets of nodes representing human, animal, and environment) confirms the increased probability of zoonotic spillover at human-cattle and human-food interfaces. We characterise six communities of zoonotic agent sharing, which assembly patterns are likely driven by highly connected infectious agents in the zoonotic web, proximity to human, and anthropogenic activities. Additionally, we report a frequency of emerging zoonotic diseases in Austria of one every six years. Here, we present a flexible network-based approach that offers insights into zoonotic transmission chains, facilitating the development of locally-relevant One Health strategies against zoonoses.
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Affiliation(s)
- Amélie Desvars-Larrive
- Centre for Food Science and Veterinary Public Health, Clinical Department for Farm Animals and Food System Science, University of Veterinary Medicine Vienna, Vienna, Austria.
- Complexity Science Hub, Vienna, Austria.
| | - Anna Elisabeth Vogl
- Centre for Food Science and Veterinary Public Health, Clinical Department for Farm Animals and Food System Science, University of Veterinary Medicine Vienna, Vienna, Austria
| | - Gavrila Amadea Puspitarani
- Centre for Food Science and Veterinary Public Health, Clinical Department for Farm Animals and Food System Science, University of Veterinary Medicine Vienna, Vienna, Austria
- Complexity Science Hub, Vienna, Austria
| | | | - Anja Joachim
- Centre of Pathobiology, Department of Biological Sciences and Pathobiology, University of Veterinary Medicine Vienna, Vienna, Austria
| | - Annemarie Käsbohrer
- Centre for Food Science and Veterinary Public Health, Clinical Department for Farm Animals and Food System Science, University of Veterinary Medicine Vienna, Vienna, Austria
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Abdelmanova AA, Deniskova TE, Kharzinova VR, Chinarov RY, Boronetskaya OI, Sölkner J, Brem G, Ai H, Huang L, Trukhachev VI, Zinovieva NA. Tracing the Dynamical Genetic Diversity Changes of Russian Livni Pigs during the Last 50 Years with the Museum, Old, and Modern Samples. Animals (Basel) 2024; 14:1629. [PMID: 38891676 PMCID: PMC11171240 DOI: 10.3390/ani14111629] [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: 04/24/2024] [Revised: 05/27/2024] [Accepted: 05/27/2024] [Indexed: 06/21/2024] Open
Abstract
The pig industry is usually considered an intensive livestock industry, mainly supported by hybrid breeding between commercial pig breeds. However, people's pursuit of a more natural environment and higher meat quality has led to an increasing demand for eco-friendly and diverse pig feeding systems. Therefore, the importance of rearing and conserving local pig breeds is increasing. The Livni pig is a local breed with good adaptability to the environmental and fodder conditions in central Russia. In this study, we aimed to analyze the genetic diversity and population structure of Livni pigs using whole-genome single nucleotide polymorphism (SNP) data. We utilized the Porcine GGP HD BeadChip on genotype samples from old (n = 32, 2004) and modern (n = 32, 2019) populations of Livni pigs. For the museum samples of Livni pigs (n = 3), we extracted DNA from their teeth, performed genomic sequencing, and obtained SNP genotypes from the whole-genome sequences. SNP genotypes of Landrace (n = 32) and Large White (n = 32) pigs were included for comparative analysis. We observed that the allelic richness of Livni pigs was higher than those of Landrace and Large White pigs (AR = 1.775-1.798 vs. 1.703 and 1.668, respectively). The effective population size estimates (NE5 = 108 for Livni pigs, NE5 = 59 for Landrace and Large White pigs) confirmed their genetic diversity tendency. This was further supported by the length and number of runs of homozygosity, as well as the genomic inbreeding coefficient (almost twofold lower in Livni pigs compared to Landrace and Large White pigs). These findings suggest that the Livni pig population exhibits higher genetic diversity and experiences lower selection pressure compared to commercial pig populations. Furthermore, both principal component and network tree analyses demonstrated a clear differentiation between Livni pigs and transboundary commercial pigs. The TreeMix results indicated gene flow from Landrace ancestors to Livni pigs (2019) and from Large White ancestors to Livni pigs (2004), which was consistent with their respective historical breeding backgrounds. The comparative analysis of museum, old, and modern Livni pigs indicated that the modern Livni pig populations have preserved their historical genomic components, suggesting their potential suitability for future design selection programs.
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Affiliation(s)
- Alexandra A. Abdelmanova
- L.K. Ernst Federal Research Center for Animal Husbandry, Dubrovitsy, Podolsk Municipal District, Moscow Region, Podolsk 142132, Russia; (A.A.A.); (V.R.K.); (R.Y.C.)
| | - Tatiana E. Deniskova
- L.K. Ernst Federal Research Center for Animal Husbandry, Dubrovitsy, Podolsk Municipal District, Moscow Region, Podolsk 142132, Russia; (A.A.A.); (V.R.K.); (R.Y.C.)
| | - Veronika R. Kharzinova
- L.K. Ernst Federal Research Center for Animal Husbandry, Dubrovitsy, Podolsk Municipal District, Moscow Region, Podolsk 142132, Russia; (A.A.A.); (V.R.K.); (R.Y.C.)
| | - Roman Yu Chinarov
- L.K. Ernst Federal Research Center for Animal Husbandry, Dubrovitsy, Podolsk Municipal District, Moscow Region, Podolsk 142132, Russia; (A.A.A.); (V.R.K.); (R.Y.C.)
| | - Oksana I. Boronetskaya
- Museum of Livestock, Timiryazev Russian State Agrarian University—Moscow Agrarian Academy, 49, ul. Timiryazevskaya, Moscow 127550, Russia; (O.I.B.); (V.I.T.)
| | - Johann Sölkner
- Division of Livestock Sciences, University of Natural Resources and Life Sciences, 1180 Vienna, Austria;
| | - Gottfried Brem
- Institute of Animal Breeding and Genetics, University of Veterinary Medicine (VMU), Veterinärplatz, 1210 Vienna, Austria;
| | - Huashui Ai
- National Key Laboratory for Swine Genetic Improvement and Germplasm Innovation, Ministry of Science and Technology of China, Jiangxi Agricultural University, Nanchang 330045, China; (H.A.); (L.H.)
| | - Lusheng Huang
- National Key Laboratory for Swine Genetic Improvement and Germplasm Innovation, Ministry of Science and Technology of China, Jiangxi Agricultural University, Nanchang 330045, China; (H.A.); (L.H.)
| | - Vladimir I. Trukhachev
- Museum of Livestock, Timiryazev Russian State Agrarian University—Moscow Agrarian Academy, 49, ul. Timiryazevskaya, Moscow 127550, Russia; (O.I.B.); (V.I.T.)
| | - Natalia A. Zinovieva
- L.K. Ernst Federal Research Center for Animal Husbandry, Dubrovitsy, Podolsk Municipal District, Moscow Region, Podolsk 142132, Russia; (A.A.A.); (V.R.K.); (R.Y.C.)
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Cartuche Macas LF, Camacho Vallejo ME, González Ariza A, León Jurado JM, Delgado Bermejo JV, Marín Navas C, Navas González FJ. Analysis of Endangered Andalusian Black Cattle (Negra Andaluza) Reveals Genetic Reservoir for Bovine Black Trunk. Animals (Basel) 2024; 14:1131. [PMID: 38612370 PMCID: PMC11010997 DOI: 10.3390/ani14071131] [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: 02/03/2024] [Revised: 03/21/2024] [Accepted: 04/07/2024] [Indexed: 04/14/2024] Open
Abstract
This comprehensive study on the Andalusian Black cattle breed reveals a substantial population decline, with the average herd size decreasing significantly from 305.54 to 88.28 animals per herd. This decline is primarily attributed to agricultural changes and the introduction of foreign meat-focused breeds. The male-to-female ratio shift is noteworthy, with more cows than bulls, impacting selection intensity for both genders. Inbreeding levels, though relatively low historically (5.94%) and currently (7.23%), raise concerns as 37.08% historically and 48.82% currently of the animals exhibit inbreeding. Positive assortative mating is evident, reflected by the increasing non-random mating coefficient (α). Key ancestors play a crucial role in shaping genetic diversity, with one ancestor significantly influencing the current genetic pool and the top 10 ancestors contributing substantially. Breed maintains a conservation index of 2.75, indicating relatively high genetic diversity. Recent conservation efforts have led to an increase in registered animals. The Cañadas Reales, historical transhumance routes, may have contributed to genetic connections among provinces. Challenges include the historical bottleneck, demographic changes, and potential impacts from reproductive practices. The Andalusian Black breed's conservation necessitates ongoing efforts in genealogical registration, targeted breeding programs, and collaborative initiatives to address the observed demographic shifts and ensure sustainable genetic diversity.
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Affiliation(s)
- Luis Favian Cartuche Macas
- Faculty of Biology, Amazonian State University, Lago Agrio Headquarters, Nueva Loja 210203, Ecuador;
- Department of Genetics, Faculty of Veterinary Sciences, University of Córdoba, 14014 Córdoba, Spain; (J.V.D.B.); (C.M.N.)
| | | | - Antonio González Ariza
- Centro Agropecuario Provincial de Córdoba, Diputación Provincial de Córdoba, 14014 Córdoba, Spain; (A.G.A.); (J.M.L.J.)
| | - José Manuel León Jurado
- Centro Agropecuario Provincial de Córdoba, Diputación Provincial de Córdoba, 14014 Córdoba, Spain; (A.G.A.); (J.M.L.J.)
| | - Juan Vicente Delgado Bermejo
- Department of Genetics, Faculty of Veterinary Sciences, University of Córdoba, 14014 Córdoba, Spain; (J.V.D.B.); (C.M.N.)
| | - Carmen Marín Navas
- Department of Genetics, Faculty of Veterinary Sciences, University of Córdoba, 14014 Córdoba, Spain; (J.V.D.B.); (C.M.N.)
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Soto I, Balzani P, Oficialdegui FJ, Molinero C, Kouba A, Ahmed DA, Turbelin AJ, Hudgins EJ, Bodey TW, Gojery SA, Courchamp F, Cuthbert RN, Haubrock PJ. The wild cost of invasive feral animals worldwide. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 912:169281. [PMID: 38101642 DOI: 10.1016/j.scitotenv.2023.169281] [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: 10/27/2023] [Revised: 12/04/2023] [Accepted: 12/09/2023] [Indexed: 12/17/2023]
Abstract
Invasive non-native species are a growing burden to economies worldwide. While domesticated animals (i.e. livestock, beasts of burden or pets) have enabled our ways of life and provide sustenance for countless individuals, they may cause substantial impacts when they escape or are released (i.e. become feral) and then become invasive with impacts. We used the InvaCost database to evaluate monetary impacts from species in the Domestic Animal Diversity Information System database. We found a total cost of $141.95 billion from only 18 invasive feral species. Invasive feral livestock incurred the highest costs at $90.03 billion, with pets contributing $50.93 billion and beasts of burden having much lower costs at $0.98 billion. Agriculture was the most affected sector at $80.79 billion, followed by the Environment ($43.44 billion), and Authorities-Stakeholders sectors ($5.52 billion). Damage costs comprised the majority ($124.94 billion), with management and mixed damage-management costs making up the rest ($9.62 and $7.38 billion, respectively). These economic impacts were observed globally, where Oceania, North America and Europe were the most impacted regions. Islands recorded a higher economic burden than continental areas, with livestock species dominating costs more on islands than mainlands compared to other feral species. The costs of invasive feral animals were on average twice higher than those of wild species. The management of invasive feral populations requires higher investment, updated regulations, and comprehensive risk assessments. These are especially complex when considering the potential conflicts arising from interventions with species that have close ties to humans. Effective communication to raise public awareness of the impacts of feral populations and appropriate legislation to prevent or control such invasive feral populations will substantially contribute to minimizing their socioeconomic and environmental impacts.
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Affiliation(s)
- Ismael Soto
- University of South Bohemia in České Budějovice, Faculty of Fisheries and Protection of Waters, South Bohemian Research Centre of Aquaculture and Biodiversity of Hydrocenoses, Zátiší 728/II, 389 25 Vodňany, Czech Republic.
| | - Paride Balzani
- University of South Bohemia in České Budějovice, Faculty of Fisheries and Protection of Waters, South Bohemian Research Centre of Aquaculture and Biodiversity of Hydrocenoses, Zátiší 728/II, 389 25 Vodňany, Czech Republic
| | - Francisco J Oficialdegui
- University of South Bohemia in České Budějovice, Faculty of Fisheries and Protection of Waters, South Bohemian Research Centre of Aquaculture and Biodiversity of Hydrocenoses, Zátiší 728/II, 389 25 Vodňany, Czech Republic
| | | | - Antonín Kouba
- University of South Bohemia in České Budějovice, Faculty of Fisheries and Protection of Waters, South Bohemian Research Centre of Aquaculture and Biodiversity of Hydrocenoses, Zátiší 728/II, 389 25 Vodňany, Czech Republic
| | - Danish A Ahmed
- Center for Applied Mathematics and Bioinformatics, Department of Mathematics and Natural Sciences, Gulf University for Science and Technology, Hawally, Kuwait
| | - Anna J Turbelin
- Université Paris-Saclay, CNRS, AgroParisTech, Ecologie Systématique Evolution, 91190, Gif-sur-Yvette, France
| | - Emma J Hudgins
- Department of Biology, Carleton University, Ottawa K1S 5B6, Canada; School of Agriculture, Food, and Ecosystem Sciences, University of Melbourne, Parkville 3010, Australia
| | - Thomas W Bodey
- School of Biological Sciences, King's College, University of Aberdeen, Aberdeen AB24 3FX, UK
| | | | - Franck Courchamp
- Université Paris-Saclay, CNRS, AgroParisTech, Ecologie Systématique Evolution, 91190, Gif-sur-Yvette, France
| | - Ross N Cuthbert
- Institute for Global Food Security, School of Biological Sciences, Queen's University Belfast, Belfast BT9 5DL, United Kingdom
| | - Phillip J Haubrock
- University of South Bohemia in České Budějovice, Faculty of Fisheries and Protection of Waters, South Bohemian Research Centre of Aquaculture and Biodiversity of Hydrocenoses, Zátiší 728/II, 389 25 Vodňany, Czech Republic; Center for Applied Mathematics and Bioinformatics, Department of Mathematics and Natural Sciences, Gulf University for Science and Technology, Hawally, Kuwait; Senckenberg Research Institute and Natural History Museum Frankfurt, Department of River Ecology and Conservation, Gelnhausen, Germany
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Friedrich J, Bailey RI, Talenti A, Chaudhry U, Ali Q, Obishakin EF, Ezeasor C, Powell J, Hanotte O, Tijjani A, Marshall K, Prendergast J, Wiener P. Mapping restricted introgression across the genomes of admixed indigenous African cattle breeds. Genet Sel Evol 2023; 55:91. [PMID: 38097935 PMCID: PMC10722721 DOI: 10.1186/s12711-023-00861-8] [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: 06/16/2023] [Accepted: 11/24/2023] [Indexed: 12/17/2023] Open
Abstract
BACKGROUND The genomes of indigenous African cattle are composed of components with Middle Eastern (taurine) and South Asian (indicine) origins, providing a valuable model to study hybridization and to identify genetic barriers to gene flow. In this study, we analysed indigenous African cattle breeds as models of hybrid zones, considering taurine and indicine samples as ancestors. In a genomic cline analysis of whole-genome sequence data, we considered over 8 million variants from 144 animals, which allows for fine-mapping of potential genomic incompatibilities at high resolution across the genome. RESULTS We identified several thousand variants that had significantly steep clines ('SCV') across the whole genome, indicating restricted introgression. Some of the SCV were clustered into extended regions, with the longest on chromosome 7, spanning 725 kb and including 27 genes. We found that variants with a high phenotypic impact (e.g. indels, intra-genic and missense variants) likely represent greater genetic barriers to gene flow. Furthermore, our findings provide evidence that a large proportion of breed differentiation in African cattle could be linked to genomic incompatibilities and reproductive isolation. Functional evaluation of genes with SCV suggest that mitonuclear incompatibilities and genes associated with fitness (e.g. resistance to paratuberculosis) could account for restricted gene flow in indigenous African cattle. CONCLUSIONS To our knowledge, this is the first time genomic cline analysis has been applied to identify restricted introgression in the genomes of indigenous African cattle and the results provide extended insights into mechanisms (e.g. genomic incompatibilities) contributing to hybrid differentiation. These results have important implications for our understanding of genetic incompatibilities and reproductive isolation and provide important insights into the impact of cross-breeding cattle with the aim of producing offspring that are both hardy and productive.
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Affiliation(s)
- Juliane Friedrich
- Division of Genetics and Genomics, The Roslin Institute and Royal (Dick), School of Veterinary Studies, University of Edinburgh, Midlothian, UK.
| | - Richard I Bailey
- Department of Ecology and Vertebrate Zoology, University of Łódź, Łódź, Poland
| | - Andrea Talenti
- Division of Genetics and Genomics, The Roslin Institute and Royal (Dick), School of Veterinary Studies, University of Edinburgh, Midlothian, UK
| | - Umer Chaudhry
- School of Veterinary Medicine, St. George's University, St. George's, Caribbean, Grenada
| | - Qasim Ali
- Department of Parasitology, The University of Agriculture Dera Ismail Khan, Khyber Pakhtunkhwa, Pakistan
| | - Emmanuel F Obishakin
- Biotechnology Division, National Veterinary Research Institute, Vom, Plateau State, Nigeria
| | - Chukwunonso Ezeasor
- Department of Veterinary Pathology and Microbiology, University of Nigeria, Nsukka, Enugu State, Nigeria
| | - Jessica Powell
- Division of Infection and Immunity, The Roslin Institute and Royal (Dick), School of Veterinary Studies, University of Edinburgh, Midlothian, UK
| | - Olivier Hanotte
- International Livestock Research Institute (ILRI), Addis Ababa, Ethiopia
- School of Life Sciences, University of Nottingham, Nottingham, UK
- Centre for Tropical Livestock Genetics and Health (CTLGH), The Roslin Institute, University of Edinburgh, Midlothian, UK
| | | | - Karen Marshall
- Centre for Tropical Livestock Genetics and Health (CTLGH), ILRI Kenya, Nairobi, Kenya
| | - James Prendergast
- Division of Genetics and Genomics, The Roslin Institute and Royal (Dick), School of Veterinary Studies, University of Edinburgh, Midlothian, UK
| | - Pamela Wiener
- Division of Genetics and Genomics, The Roslin Institute and Royal (Dick), School of Veterinary Studies, University of Edinburgh, Midlothian, UK.
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Ginja C, Guimarães S, da Fonseca RR, Rasteiro R, Rodríguez-Varela R, Simões LG, Sarmento C, Belarte MC, Kallala N, Torres JR, Sanmartí J, Arruda AM, Detry C, Davis S, Matos J, Götherström A, Pires AE, Valenzuela-Lamas S. Iron age genomic data from Althiburos - Tunisia renew the debate on the origins of African taurine cattle. iScience 2023; 26:107196. [PMID: 37485357 PMCID: PMC10359934 DOI: 10.1016/j.isci.2023.107196] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2022] [Revised: 12/22/2022] [Accepted: 06/20/2023] [Indexed: 07/25/2023] Open
Abstract
The Maghreb is a key region for understanding the dynamics of cattle dispersal and admixture with local aurochs following their earliest domestication in the Fertile Crescent more than 10,000 years ago. Here, we present data on autosomal genomes and mitogenomes obtained for four archaeological specimens of Iron Age (∼2,800 cal BP-2,000 cal BP) domestic cattle from the Eastern Maghreb, i.e. Althiburos (El Kef, Tunisia). D-loop sequences were obtained for an additional eight cattle specimens from this site. Maternal lineages were assigned to the elusive R and ubiquitous African-T1 haplogroups found in two and ten Althiburos specimens, respectively. Our results can be explained by post-domestication hybridization of Althiburos cattle with local aurochs. However, we cannot rule out an independent domestication in North Africa considering the shared ancestry of Althiburos cattle with the pre-domestic Moroccan aurochs and present-day African taurine cattle.
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Affiliation(s)
- Catarina Ginja
- BIOPOLIS-CIBIO-InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos - ArchGen group, Universidade do Porto, Vairão, Portugal
| | - Silvia Guimarães
- BIOPOLIS-CIBIO-InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos - ArchGen group, Universidade do Porto, Vairão, Portugal
| | - Rute R. da Fonseca
- Center for Global Mountain Biodiversity, GLOBE Institute, University of Copenhagen, Copenhagen, Denmark
| | - Rita Rasteiro
- MRC Integrative Epidemiology Unit, University of Bristol, Bristol, UK
| | | | - Luciana G. Simões
- Human Evolution, Department of Organismal Biology, Uppsala University, Uppsala, Sweden
| | - Cindy Sarmento
- BIOPOLIS-CIBIO-InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos - ArchGen group, Universidade do Porto, Vairão, Portugal
| | - Maria Carme Belarte
- ICREA, Institut Català de Recerca i Estudis Avançats, Barcelona, Spain
- ICAC, Institut Català d'Arqueologia Clàssica, Tarragona, Spain
| | - Nabil Kallala
- INP, Institut National du Patrimoine, Tunis, Tunisia
- Faculté des Sciences Humaines et Sociales, Université de Tunis, Tunis, Tunisia
| | | | - Joan Sanmartí
- In memoriam, Departament de Prehistòria, Història Antiga i Arqueologia, Universitat de Barcelona, Barcelona, Spain
| | - Ana Margarida Arruda
- UNIARQ, Centro de Arqueologia da Universidade de Lisboa, Faculdade de Letras da Universidade de Lisboa, Lisboa, Portugal
| | - Cleia Detry
- UNIARQ, Centro de Arqueologia da Universidade de Lisboa, Faculdade de Letras da Universidade de Lisboa, Lisboa, Portugal
| | - Simon Davis
- BIOPOLIS-CIBIO-InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos - ArchGen group, Universidade do Porto, Vairão, Portugal
- LARC/DGPC, Laboratório de Arqueociências, Direcção Geral do Património Cultural, Lisboa, Portugal
| | - José Matos
- Unidade Estratégica de Investigação e Serviços de Biotecnologia e Recursos Genéticos, Instituto Nacional de Investigação Agrária e Veterinária, I.P, Oeiras, Portugal
- CE3C, Centro de Ecologia, Evolução e Alterações Ambientais, Universidade de Lisboa, Lisboa, Portugal
| | | | - Ana Elisabete Pires
- BIOPOLIS-CIBIO-InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos - ArchGen group, Universidade do Porto, Vairão, Portugal
- Faculdade de Medicina Veterinária, Universidade Lusófona, Lisboa, Portugal
| | - Silvia Valenzuela-Lamas
- UNIARQ, Centro de Arqueologia da Universidade de Lisboa, Faculdade de Letras da Universidade de Lisboa, Lisboa, Portugal
- Archaeology of Social Dynamics, Consejo Superior de Investigaciones Científicas-Institució Milà i Fontanals d'Humanitats (CSIC-IMF), Barcelona, Spain
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de Sousa AA, Rigby Dames BA, Graff EC, Mohamedelhassan R, Vassilopoulos T, Charvet CJ. Going beyond established model systems of Alzheimer's disease: companion animals provide novel insights into the neurobiology of aging. Commun Biol 2023; 6:655. [PMID: 37344566 DOI: 10.1038/s42003-023-05034-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2022] [Accepted: 06/12/2023] [Indexed: 06/23/2023] Open
Abstract
Alzheimer's disease (AD) is characterized by brain plaques, tangles, and cognitive impairment. AD is one of the most common age-related dementias in humans. Progress in characterizing AD and other age-related disorders is hindered by a perceived dearth of animal models that naturally reproduce diseases observed in humans. Mice and nonhuman primates are model systems used to understand human diseases. Still, these model systems lack many of the biological characteristics of Alzheimer-like diseases (e.g., plaques, tangles) as they grow older. In contrast, companion animal models (cats and dogs) age in ways that resemble humans. Both companion animal models and humans show evidence of brain atrophy, plaques, and tangles, as well as cognitive decline with age. We embrace a One Health perspective, which recognizes that the health of humans is connected to those of animals, and we illustrate how such a perspective can work synergistically to enhance human and animal health. A comparative biology perspective is ideally suited to integrate insights across veterinary and human medical disciplines and solve long-standing problems in aging.
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Affiliation(s)
- Alexandra A de Sousa
- Centre for Health and Cognition, Bath Spa University, Bath, UK
- Department of Psychology, University of Bath, Bath, UK
| | - Brier A Rigby Dames
- Department of Psychology, University of Bath, Bath, UK
- Department of Computer Science, University of Bath, Bath, UK
- Department of Biology and Biochemistry, Milner Centre for Evolution, University of Bath, Bath, UK
| | - Emily C Graff
- Department of Pathobiology, College of Veterinary Medicine, Auburn University, Auburn, AL, USA
| | - Rania Mohamedelhassan
- Department of Anatomy, Physiology and Pharmacology, College of Veterinary Medicine, Auburn University, Auburn, AL, USA
| | - Tatianna Vassilopoulos
- Department of Anatomy, Physiology and Pharmacology, College of Veterinary Medicine, Auburn University, Auburn, AL, USA
| | - Christine J Charvet
- Department of Anatomy, Physiology and Pharmacology, College of Veterinary Medicine, Auburn University, Auburn, AL, USA.
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8
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Tancredi D, Cardinali I. Being a Dog: A Review of the Domestication Process. Genes (Basel) 2023; 14:genes14050992. [PMID: 37239352 DOI: 10.3390/genes14050992] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2023] [Revised: 04/19/2023] [Accepted: 04/26/2023] [Indexed: 05/28/2023] Open
Abstract
The process of canine domestication represents certainly one of the most interesting questions that evolutionary biology aims to address. A "multiphase" view of this process is now accepted, with a first phase during which different groups of wolves were attracted by the anthropogenic niche and a second phase characterized by the gradual establishment of mutual relationships between wolves and humans. Here, we provide a review of dog (Canis familiaris) domestication, highlighting the ecological differences between dogs and wolves, analyzing the molecular mechanisms which seem to have influenced the affiliative behaviors first observed in Belyaev's foxes, and describing the genetics of ancient European dogs. Then, we focus on three Mediterranean peninsulas (Balkan, Iberian and Italian), which together represent the main geographic area for studying canine domestication dynamics, as it has shaped the current genetic variability of dog populations, and where a well-defined European genetic structure was pinpointed through the analysis of uniparental genetic markers and their phylogeny.
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Affiliation(s)
- Domenico Tancredi
- Department of Chemistry, Biology and Biotechnology, Università degli Studi di Perugia, 06123 Perugia, Italy
| | - Irene Cardinali
- Department of Chemistry, Biology and Biotechnology, Università degli Studi di Perugia, 06123 Perugia, Italy
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Begou P, Kassomenos P. The ecosyndemic framework of the global environmental change and the COVID-19 pandemic. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 857:159327. [PMID: 36220476 PMCID: PMC9547397 DOI: 10.1016/j.scitotenv.2022.159327] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/19/2022] [Revised: 09/03/2022] [Accepted: 10/05/2022] [Indexed: 06/16/2023]
Abstract
The ecosyndemic theory combines the concept of 'synergy' with 'epidemic' and the term "eco" implies the role of the environmental changes. Each of the conditions enhances the negative impacts of the other in an additive way making our society more vulnerable and heightening individual risk factors. In this study, we analyze the mutually reinforcing links between the environment and health from the complexity angle of the ecosyndemic theory and propose the characterization of the COVID-19 pandemic as ecosyndemic. We use the term 'ecosyndemic' because the global environmental change contributes to local-scale, regional-scale and global-scale alterations of the Earth's systems. These changes have their root causes in the way that people interact with the physical, chemical, and biotic factors of the environment. These interactions disturb nature and the consequences have feedbacks in every living organism.
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Affiliation(s)
- Paraskevi Begou
- Laboratory of Meteorology and Climatology, Department of Physics, University of Ioannina, GR-45110 Ioannina, Greece.
| | - Pavlos Kassomenos
- Laboratory of Meteorology and Climatology, Department of Physics, University of Ioannina, GR-45110 Ioannina, Greece
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10
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Snead AA, Clark RD. The Biological Hierarchy, Time, and Temporal 'Omics in Evolutionary Biology: A Perspective. Integr Comp Biol 2022; 62:1872-1886. [PMID: 36057775 DOI: 10.1093/icb/icac138] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2022] [Revised: 08/28/2022] [Accepted: 08/29/2022] [Indexed: 01/05/2023] Open
Abstract
Sequencing data-genomics, transcriptomics, epigenomics, proteomics, and metabolomics-have revolutionized biological research, enabling a more detailed study of processes, ranging from subcellular to evolutionary, that drive biological organization. These processes, collectively, are responsible for generating patterns of phenotypic variation and can operate over dramatically different timescales (milliseconds to billions of years). While researchers often study phenotypic variation at specific levels of biological organization to isolate processes operating at that particular scale, the varying types of sequence data, or 'omics, can also provide complementary inferences to link molecular and phenotypic variation to produce an integrated view of evolutionary biology, ranging from molecular pathways to speciation. We briefly describe how 'omics has been used across biological levels and then demonstrate the utility of integrating different types of sequencing data across multiple biological levels within the same study to better understand biological phenomena. However, single-time-point studies cannot evaluate the temporal dynamics of these biological processes. Therefore, we put forward temporal 'omics as a framework that can better enable researchers to study the temporal dynamics of target processes. Temporal 'omics is not infallible, as the temporal sampling regime directly impacts inferential ability. Thus, we also discuss the role the temporal sampling regime plays in deriving inferences about the environmental conditions driving biological processes and provide examples that demonstrate the impact of the sampling regime on biological inference. Finally, we forecast the future of temporal 'omics by highlighting current methodological advancements that will enable temporal 'omics to be extended across species and timescales. We extend this discussion to using temporal multi-omics to integrate across the biological hierarchy to evaluate and link the temporal dynamics of processes that generate phenotypic variation.
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Affiliation(s)
- Anthony A Snead
- Department of Biological Sciences, University of Alabama, 300 Hackberry Lane, Tuscaloosa, AL 35487, USA
| | - René D Clark
- Department of Ecology, Evolution and Natural Resources, Rutgers University, 14 College Farm Road, New Brunswick, NJ 08901, USA
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11
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Solberg SØ, Loskutov IG, Breian L, Diederichsen A. The Impact of N.I. Vavilov on the Conservation and Use of Plant Genetic Resources in Scandinavia: A Review. PLANTS (BASEL, SWITZERLAND) 2022; 12:143. [PMID: 36616272 PMCID: PMC9823609 DOI: 10.3390/plants12010143] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/15/2022] [Revised: 11/29/2022] [Accepted: 12/20/2022] [Indexed: 06/17/2023]
Abstract
In this review we examine Nikolai Ivanovich Vavilov's relationship to Scandinavia and the impact he and his ideas have had on Scandinavia. We trace the historical connections from Vavilov back to 18th century scientists, such as Carl Von Linneaus (Sweden) and 19th century European scientists such as Alphonse de Candolle (Switzerland), Henry de Vilmorin (France), and William Bateson (England). Vavilov has influenced the conservation work in Scandinavia resulting amongst other in the establishment of the Nordic Gene Bank in 1979 and the Svalbard Global Seed Vault which started operating in 2008. Vavilov travelled to Scandinavia in 1921 and in 1931 to give lectures and exchange ideas, especially with the breeders at the Swedish Seed Association (Svalöf) in Scania, Sweden, but also at the Copenhagen University in Denmark. Vavilov did not recognize Scandinavia as part of a center of origin of cultivated plants. It was only after World War II, when P.M. Zhukovsky, a scholar of N.I Vavilov, developed the concept of mega-centers of diversity of cultivated plants, that Scandinavia became part of what he termed the European-Siberian Region of Diversity. We list species domesticated in Scandinavia or Northern Europe, and we further discuss concepts related to crop evolution and highlight the great impact Vavilov has had by inspiring scientists across disciplines and over many decades.
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Affiliation(s)
- Svein Ø. Solberg
- Department of Agriculture, Faculty of Applied Ecology, Agricultural Sciences and Biotechnology, Inland Norway University of Applied Sciences, P.O. Box 400, 2418 Elverum, Norway
| | - Igor G. Loskutov
- N.I. Vavilov Institute of Plant Genetic Resources (VIR), 42-44, B. Morskaya Street, 190000 St. Petersburg, Russia
- Faculty of Biology, St. Petersburg State University, 7-9, Universitetskaya Emb., 199034 St. Petersburg, Russia
| | - Line Breian
- Linguistics and Theory of Science, Department of Philosophy, University of Gothenburg, Box 100, 405 30 Gothenburg, Sweden
| | - Axel Diederichsen
- Plant Gene Resources of Canada, Agriculture and Agri-Food Canada, Saskatoon Research Centre, 107 Science Place, Saskatoon, SK S7N 0X2, Canada
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12
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Legacies of domestication, Neolithic diffusion and trade between Indian subcontinent and Island Southeast Asia shape maternal genetic diversity of Andaman cattle. PLoS One 2022; 17:e0278681. [PMID: 36490290 PMCID: PMC9733863 DOI: 10.1371/journal.pone.0278681] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2022] [Accepted: 11/22/2022] [Indexed: 12/13/2022] Open
Abstract
Andaman cattle is a precious indigenous livestock species endemic to Andaman and Nicobar Islands, India. Till date, origin and genetic makeup of the breed which is warranted for breed conservation is not known. Moreover, the spread of zebu cattle from Indus valley to different parts of Island Southeast Asia (ISEA) is not properly understood. Here, we report the genetic diversity, population structure of Andaman cattle and their evolution in the context of epicentre of zebu domestication and ISEA. High genetic diversity in complete mitochondrial D-loop sequences indicated the ability of the breed to withstand impending climate change. Total 81 haplotypes were detected and all of them except three belonged to Bos indicus. The presence of taurine haplotypes in Andaman cattle indicate introgression by European-derived cattle. A poor phylogenetic signal of Andaman cattle with genetic affinities with cattle of Indian subcontinent and ISEA was observed. The poor phylogenetic structure may be due to multidirectional gene flow from Indian subcontinent and ISEA, with which Andaman shares a close cultural and trade relationship from Neolithic age. We hypothesize that Andaman cattle is the outcome of Neolithic diffusion from centre of zebu domestication along with multidirectional commercial exchange between Indian subcontinent and ISEA.
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13
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Erven JAM, Çakirlar C, Bradley DG, Raemaekers DCM, Madsen O. Imputation of Ancient Whole Genome Sus scrofa DNA Introduces Biases Toward Main Population Components in the Reference Panel. Front Genet 2022; 13:872486. [PMID: 35903348 PMCID: PMC9315352 DOI: 10.3389/fgene.2022.872486] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2022] [Accepted: 05/20/2022] [Indexed: 11/13/2022] Open
Abstract
Sequencing ancient DNA to high coverage is often limited by sample quality and cost. Imputing missing genotypes can potentially increase information content and quality of ancient data, but requires different computational approaches than modern DNA imputation. Ancient imputation beyond humans has not been investigated. In this study we report results of a systematic evaluation of imputation of three whole genome ancient Sus scrofa samples from the Early and Late Neolithic (∼7,100–4,500 BP), to test the utility of imputation. We show how issues like genetic architecture and, reference panel divergence, composition and size affect imputation accuracy. We evaluate a variety of imputation methods, including Beagle5, GLIMPSE, and Impute5 with varying filters, pipelines, and variant calling methods. We achieved genotype concordance in most cases reaching above 90%; with the highest being 98% with ∼2,000,000 variants recovered using GLIMPSE. Despite this high concordance the sources of diversity present in the genotypes called in the original high coverage genomes were not equally imputed leading to biases in downstream analyses; a trend toward genotypes most common in the reference panel is observed. This demonstrates that the current reference panel does not possess the full diversity needed for accurate imputation of ancient Sus, due to missing variations from Near Eastern and Mesolithic wild boar. Imputation of ancient Sus scrofa holds potential but should be approached with caution due to these biases, and suggests that there is no universal approach for imputation of non-human ancient species.
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Affiliation(s)
- J. A. M. Erven
- Groningen Institute of Archaeology, University of Groningen, Groningen, Netherlands
- *Correspondence: J. A. M. Erven,
| | - C. Çakirlar
- Groningen Institute of Archaeology, University of Groningen, Groningen, Netherlands
| | - D. G. Bradley
- Smurfit Institute of Genetics, Trinity College Dublin, Dublin, Ireland
| | - D. C. M. Raemaekers
- Groningen Institute of Archaeology, University of Groningen, Groningen, Netherlands
| | - O. Madsen
- Animal Breeding and Genomics, Wageningen University and Research, Wageningen, Netherlands
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14
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Genome-wide local ancestry and evidence for mitonuclear coadaptation in African hybrid cattle populations (Bos taurus/indicus). iScience 2022; 25:104672. [PMID: 35832892 PMCID: PMC9272374 DOI: 10.1016/j.isci.2022.104672] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2022] [Revised: 05/11/2022] [Accepted: 06/21/2022] [Indexed: 11/21/2022] Open
Abstract
The phenotypic diversity of African cattle reflects adaptation to a wide range of agroecological conditions, human-mediated selection preferences, and complex patterns of admixture between the humpless Bos taurus (taurine) and humped Bos indicus (zebu) subspecies, which diverged 150-500 thousand years ago. Despite extensive admixture, all African cattle possess taurine mitochondrial haplotypes, even populations with significant zebu biparental and male uniparental nuclear ancestry. This has been interpreted as the result of human-mediated dispersal ultimately stemming from zebu bulls imported from South Asia during the last three millennia. Here, we assess whether ancestry at mitochondrially targeted nuclear genes in African admixed cattle is impacted by mitonuclear functional interactions. Using high-density SNP data, we find evidence for mitonuclear coevolution across hybrid African cattle populations with a significant increase of taurine ancestry at mitochondrially targeted nuclear genes. Our results, therefore, support the hypothesis of incompatibility between the taurine mitochondrial genome and the zebu nuclear genome.
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15
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Smith WJ, Quilodrán CS, Jezierski MT, Sendell-Price AT, Clegg SM. The wild ancestors of domestic animals as a neglected and threatened component of biodiversity. CONSERVATION BIOLOGY : THE JOURNAL OF THE SOCIETY FOR CONSERVATION BIOLOGY 2022; 36:e13867. [PMID: 34811819 DOI: 10.1111/cobi.13867] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/28/2021] [Revised: 09/27/2021] [Accepted: 11/12/2021] [Indexed: 06/13/2023]
Abstract
Domestic animals have immense economic, cultural, and practical value and have played pivotal roles in the development of human civilization. Many domesticates have, among their wild relatives, undomesticated forms representative of their ancestors. Resurgent interest in these ancestral forms has highlighted the unclear genetic status of many, and some are threatened with extinction by hybridization with domestic conspecifics. We considered the contemporary status of these ancestral forms relative to their scientific, practical, and ecological importance; the varied impacts of wild-domestic hybridization; and the challenges and potential resolutions involved in conservation efforts. Identifying and conserving ancestral forms, particularly with respect to disentangling patterns of gene flow from domesticates, is complex because of the lack of available genomic and phenotypic baselines. Comparative behavioral, ecological, and genetic studies of ancestral-type, feral, and domestic animals should be prioritized to establish the contemporary status of the former. Such baseline information will be fundamental in ensuring successful conservation efforts.
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Affiliation(s)
- William J Smith
- Edward Grey Institute of Field Ornithology, Department of Zoology, University of Oxford, Oxford, UK
| | - Claudio S Quilodrán
- Edward Grey Institute of Field Ornithology, Department of Zoology, University of Oxford, Oxford, UK
- Department of Biology and Biochemistry, University of Fribourg, Fribourg, Switzerland
| | - Michał T Jezierski
- Edward Grey Institute of Field Ornithology, Department of Zoology, University of Oxford, Oxford, UK
| | - Ashley T Sendell-Price
- Edward Grey Institute of Field Ornithology, Department of Zoology, University of Oxford, Oxford, UK
- Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
| | - Sonya M Clegg
- Edward Grey Institute of Field Ornithology, Department of Zoology, University of Oxford, Oxford, UK
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16
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Changes in Neuropeptide Prohormone Genes among Cetartiodactyla Livestock and Wild Species Associated with Evolution and Domestication. Vet Sci 2022; 9:vetsci9050247. [PMID: 35622775 PMCID: PMC9144646 DOI: 10.3390/vetsci9050247] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2022] [Revised: 05/18/2022] [Accepted: 05/19/2022] [Indexed: 12/10/2022] Open
Abstract
The impact of evolution and domestication processes on the sequences of neuropeptide prohormone genes that participate in cell–cell signaling influences multiple biological process that involve neuropeptide signaling. This information is important to understand the physiological differences between Cetartiodactyla domesticated species such as cow, pig, and llama and wild species such as hippopotamus, giraffes, and whales. Systematic analysis of changes associated with evolutionary and domestication forces in neuropeptide prohormone protein sequences that are processed into neuropeptides was undertaken. The genomes from 118 Cetartiodactyla genomes representing 22 families were mined for 98 neuropeptide prohormone genes. Compared to other Cetartiodactyla suborders, Ruminantia preserved PYY2 and lost RLN1. Changes in GNRH2, IAPP, INSL6, POMC, PRLH, and TAC4 protein sequences could result in the loss of some bioactive neuropeptides in some families. An evolutionary model suggested that most neuropeptide prohormone genes disfavor sequence changes that incorporate large and hydrophobic amino acids. A compelling finding was that differences between domestic and wild species are associated with the molecular system underlying ‘fight or flight’ responses. Overall, the results demonstrate the importance of simultaneously comparing the neuropeptide prohormone gene complement from close and distant-related species. These findings broaden the foundation for empirical studies about the function of the neuropeptidome associated with health, behavior, and food production.
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17
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Eda M, Itahashi Y, Kikuchi H, Sun G, Hsu KH, Gakuhari T, Yoneda M, Jiang L, Yang G, Nakamura S. Multiple lines of evidence of early goose domestication in a 7,000-y-old rice cultivation village in the lower Yangtze River, China. Proc Natl Acad Sci U S A 2022; 119:e2117064119. [PMID: 35254874 PMCID: PMC8944903 DOI: 10.1073/pnas.2117064119] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2021] [Accepted: 01/10/2022] [Indexed: 11/25/2022] Open
Abstract
Poultry are farmed globally, with chicken (Gallus gallus domesticus) being the leading domesticated species. Although domestic chicken bones have been reported from some Early Holocene sites, their origin is controversial and there is no reliable domestic chicken bone older than the Middle Holocene. Here, we studied goose bones from Tianluoshan—a 7,000-y-old rice cultivation village in the lower Yangtze River valley, China—using histological, geochemical, biochemical, and morphological approaches. Histological analysis revealed that one of the bones was derived from a locally bred chick, although no wild goose species breed in southern China. The analysis of oxygen-stable isotope composition supported this observation and further revealed that some of the mature bones were also derived from locally bred individuals. The nitrogen-stable isotope composition showed that locally bred mature birds fed on foods different from those eaten by migrant individuals. Morphological analysis revealed that the locally bred mature birds were homogenous in size, whereas radiocarbon dating clearly demonstrated that the samples from locally bred individuals were ∼7,000 y old. The histological, geochemical, biochemical, morphological, and contextual evidence suggest that geese at Tianluoshan village were at an early stage of domestication. The goose population appears to have been maintained for several generations without the introduction of individuals from other populations and may have been fed cultivated paddy rice. These findings indicate that goose domestication dates back 7,000 y, making geese the oldest domesticated poultry species in history.
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Affiliation(s)
- Masaki Eda
- Hokkaido University Museum, Hokkaido University, Hokkaido 060-0810, Japan
| | - Yu Itahashi
- Faculty of Humanities and Social Sciences, University of Tsukuba, Ibaraki 305-8571, Japan
- The University Museum, The University of Tokyo, Tokyo 113-0033, Japan
| | - Hiroki Kikuchi
- Department of Archaeology and Museology, Lanzhou University, Gansu 730020, China
| | - Guoping Sun
- Zhejiang Provincial Institute of Cultural Relics and Archaeology, Zhejiang 310012, China
| | - Kai-hsuan Hsu
- Graduate School of Humanities and Human Sciences, Hokkaido University, Hokkaido 060-0810, Japan
| | - Takashi Gakuhari
- Center for the Study of Ancient Civilizations and Cultural Resources, Kanazawa University, Ishikawa 920-1192, Japan
| | - Minoru Yoneda
- The University Museum, The University of Tokyo, Tokyo 113-0033, Japan
| | - Leping Jiang
- Zhejiang Provincial Institute of Cultural Relics and Archaeology, Zhejiang 310012, China
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18
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Cubric‐Curik V, Novosel D, Brajkovic V, Rota Stabelli O, Krebs S, Sölkner J, Šalamon D, Ristov S, Berger B, Trivizaki S, Bizelis I, Ferenčaković M, Rothammer S, Kunz E, Simčič M, Dovč P, Bunevski G, Bytyqi H, Marković B, Brka M, Kume K, Stojanović S, Nikolov V, Zinovieva N, Schönherz AA, Guldbrandtsen B, Čačić M, Radović S, Miracle P, Vernesi C, Curik I, Medugorac I. Large‐scale mitogenome sequencing reveals consecutive expansions of domestic taurine cattle and supports sporadic aurochs introgression. Evol Appl 2021; 15:663-678. [PMID: 35505892 PMCID: PMC9046920 DOI: 10.1111/eva.13315] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Revised: 10/01/2021] [Accepted: 10/11/2021] [Indexed: 11/29/2022] Open
Affiliation(s)
- Vlatka Cubric‐Curik
- Department of Animal Science University of Zagreb Faculty of Agriculture Zagreb Croatia
| | - Dinko Novosel
- Department of Animal Science University of Zagreb Faculty of Agriculture Zagreb Croatia
- Department of Pathology Croatian Veterinary Institute Zagreb Croatia
| | - Vladimir Brajkovic
- Department of Animal Science University of Zagreb Faculty of Agriculture Zagreb Croatia
| | - Omar Rota Stabelli
- Department of Sustainable Agro‐Ecosystems and Bioresources, Research and Innovation Centre Fondazione Edmund Mach S. Michele all' Adige Italy
| | - Stefan Krebs
- Laboratory for Functional Genome Analysis Gene Center Ludwig Maximilians University Munich Munich Germany
| | - Johann Sölkner
- Division of Livestock Sciences Department of Sustainable Agricultural Systems BOKU‐University of Natural Resources and Life Sciences Vienna Vienna Austria
| | - Dragica Šalamon
- Department of Animal Science University of Zagreb Faculty of Agriculture Zagreb Croatia
| | | | - Beate Berger
- AREC Raumberg‐Gumpenstein Institute of Organic Farming and Biodiversity of Farm Animals Thalheim Austria
| | | | - Iosif Bizelis
- Faculty of Animal Science and Aquaculture Department of Animal Breeding & Husbandry Agricultural University of Athens Athens Greece
| | - Maja Ferenčaković
- Department of Animal Science University of Zagreb Faculty of Agriculture Zagreb Croatia
| | - Sophie Rothammer
- Population Genomics Group Faculty of Veterinary Medicine Department of Veterinary Sciences LMU Munich Munich Germany
| | - Elisabeth Kunz
- Population Genomics Group Faculty of Veterinary Medicine Department of Veterinary Sciences LMU Munich Munich Germany
| | - Mojca Simčič
- Biotechnical Faculty Department of Animal Science University of Ljubljana Ljubljana Slovenia
| | - Peter Dovč
- Biotechnical Faculty Department of Animal Science University of Ljubljana Ljubljana Slovenia
| | - Gojko Bunevski
- Faculty of Agricultural Sciences and Food University Ss. Cyril and Methodius Skopje Macedonia
| | - Hysen Bytyqi
- Faculty of Agriculture and Veterinary Department of Animal Science University of Prishtina Prishtina Kosovo
| | - Božidarka Marković
- Biotechnical Faculty Department of Livestock Science University of Montenegro Podgorica Montenegro
| | - Muhamed Brka
- Faculty of Agriculture and Food Science Institute of Animal Sciences University of Sarajevo Sarajevo Bosnia and Herzegovina
| | | | - Srđan Stojanović
- Ministry of Agriculture, Forestry and Water Management Beograd Serbia
| | - Vasil Nikolov
- Executive Agency for Selection and Reproduction in Animal Breeding Sofia Bulgaria
| | - Natalia Zinovieva
- Center of Biotechnology and Molecular Diagnostics of the L.K. Ernst Institute of Animal Husbandry Moscow Region Russia
| | | | - Bernt Guldbrandtsen
- Department of Animal Sciences Rheinische Friedrich‐Wilhelms‐Universität Bonn Bonn Germany
| | - Mato Čačić
- Croatian Agricultural Agency Zagreb Croatia
| | - Siniša Radović
- Institute for Quaternary Palaeontology and Geology Croatian Academy of Sciences and Arts Zagreb Croatia
| | - Preston Miracle
- Department of Archaeology University of Cambridge Cambridge UK
| | - Cristiano Vernesi
- Department of Sustainable Agro‐Ecosystems and Bioresources, Research and Innovation Centre Fondazione Edmund Mach S. Michele all' Adige Italy
| | - Ino Curik
- Department of Animal Science University of Zagreb Faculty of Agriculture Zagreb Croatia
| | - Ivica Medugorac
- Population Genomics Group Faculty of Veterinary Medicine Department of Veterinary Sciences LMU Munich Munich Germany
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19
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Passamonti MM, Somenzi E, Barbato M, Chillemi G, Colli L, Joost S, Milanesi M, Negrini R, Santini M, Vajana E, Williams JL, Ajmone-Marsan P. The Quest for Genes Involved in Adaptation to Climate Change in Ruminant Livestock. Animals (Basel) 2021; 11:2833. [PMID: 34679854 PMCID: PMC8532622 DOI: 10.3390/ani11102833] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2021] [Revised: 09/21/2021] [Accepted: 09/23/2021] [Indexed: 12/14/2022] Open
Abstract
Livestock radiated out from domestication centres to most regions of the world, gradually adapting to diverse environments, from very hot to sub-zero temperatures and from wet and humid conditions to deserts. The climate is changing; generally global temperature is increasing, although there are also more extreme cold periods, storms, and higher solar radiation. These changes impact livestock welfare and productivity. This review describes advances in the methodology for studying livestock genomes and the impact of the environment on animal production, giving examples of discoveries made. Sequencing livestock genomes has facilitated genome-wide association studies to localize genes controlling many traits, and population genetics has identified genomic regions under selection or introgressed from one breed into another to improve production or facilitate adaptation. Landscape genomics, which combines global positioning and genomics, has identified genomic features that enable animals to adapt to local environments. Combining the advances in genomics and methods for predicting changes in climate is generating an explosion of data which calls for innovations in the way big data sets are treated. Artificial intelligence and machine learning are now being used to study the interactions between the genome and the environment to identify historic effects on the genome and to model future scenarios.
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Affiliation(s)
- Matilde Maria Passamonti
- Department of Animal Science, Food and Nutrition—DIANA, Università Cattolica del Sacro Cuore, Via Emilia Parmense, 84, 29122 Piacenza, Italy; (M.M.P.); (E.S.); (M.B.); (L.C.); (R.N.); (J.L.W.)
| | - Elisa Somenzi
- Department of Animal Science, Food and Nutrition—DIANA, Università Cattolica del Sacro Cuore, Via Emilia Parmense, 84, 29122 Piacenza, Italy; (M.M.P.); (E.S.); (M.B.); (L.C.); (R.N.); (J.L.W.)
| | - Mario Barbato
- Department of Animal Science, Food and Nutrition—DIANA, Università Cattolica del Sacro Cuore, Via Emilia Parmense, 84, 29122 Piacenza, Italy; (M.M.P.); (E.S.); (M.B.); (L.C.); (R.N.); (J.L.W.)
| | - Giovanni Chillemi
- Department for Innovation in Biological, Agro-Food and Forest Systems–DIBAF, Università Della Tuscia, Via S. Camillo de Lellis snc, 01100 Viterbo, Italy; (G.C.); (M.M.)
| | - Licia Colli
- Department of Animal Science, Food and Nutrition—DIANA, Università Cattolica del Sacro Cuore, Via Emilia Parmense, 84, 29122 Piacenza, Italy; (M.M.P.); (E.S.); (M.B.); (L.C.); (R.N.); (J.L.W.)
- Research Center on Biodiversity and Ancient DNA—BioDNA, Università Cattolica del Sacro Cuore, Via Emilia Parmense, 84, 29122 Piacenza, Italy
| | - Stéphane Joost
- Laboratory of Geographic Information Systems (LASIG), School of Architecture, Civil and Environmental Engineering (ENAC), Ecole Polytechnique Fédérale de Lausanne (EPFL), 1015 Lausanne, Switzerland; (S.J.); (E.V.)
| | - Marco Milanesi
- Department for Innovation in Biological, Agro-Food and Forest Systems–DIBAF, Università Della Tuscia, Via S. Camillo de Lellis snc, 01100 Viterbo, Italy; (G.C.); (M.M.)
| | - Riccardo Negrini
- Department of Animal Science, Food and Nutrition—DIANA, Università Cattolica del Sacro Cuore, Via Emilia Parmense, 84, 29122 Piacenza, Italy; (M.M.P.); (E.S.); (M.B.); (L.C.); (R.N.); (J.L.W.)
| | - Monia Santini
- Impacts on Agriculture, Forests and Ecosystem Services (IAFES) Division, Fondazione Centro Euro-Mediterraneo Sui Cambiamenti Climatici (CMCC), Viale Trieste 127, 01100 Viterbo, Italy;
| | - Elia Vajana
- Laboratory of Geographic Information Systems (LASIG), School of Architecture, Civil and Environmental Engineering (ENAC), Ecole Polytechnique Fédérale de Lausanne (EPFL), 1015 Lausanne, Switzerland; (S.J.); (E.V.)
| | - John Lewis Williams
- Department of Animal Science, Food and Nutrition—DIANA, Università Cattolica del Sacro Cuore, Via Emilia Parmense, 84, 29122 Piacenza, Italy; (M.M.P.); (E.S.); (M.B.); (L.C.); (R.N.); (J.L.W.)
| | - Paolo Ajmone-Marsan
- Department of Animal Science, Food and Nutrition—DIANA, Università Cattolica del Sacro Cuore, Via Emilia Parmense, 84, 29122 Piacenza, Italy; (M.M.P.); (E.S.); (M.B.); (L.C.); (R.N.); (J.L.W.)
- Nutrigenomics and Proteomics Research Center—PRONUTRIGEN, Università Cattolica del Sacro Cuore, Via Emilia Parmense, 84, 29122 Piacenza, Italy
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20
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Hall SJG, Brenig B, Ashdown RA, Curry MR. Conservation of rare wild‐living cattle
Bos taurus
(L.): coat colour gene illuminates breed history, and associated reproductive anomalies have not reduced herd fertility. J Zool (1987) 2021. [DOI: 10.1111/jzo.12929] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Affiliation(s)
| | - B. Brenig
- Institute of Veterinary Medicine University of Göttingen Göttingen Germany
| | | | - M. R. Curry
- School of Life Sciences University of Lincoln Lincoln UK
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21
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Ancient Faunal History Revealed by Interdisciplinary Biomolecular Approaches. DIVERSITY 2021. [DOI: 10.3390/d13080370] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Starting four decades ago, studies have examined the ecology and evolutionary dynamics of populations and species using short mitochondrial DNA fragments and stable isotopes. Through technological and analytical advances, the methods and biomolecules at our disposal have increased significantly to now include lipids, whole genomes, proteomes, and even epigenomes. At an unprecedented resolution, the study of ancient biomolecules has made it possible for us to disentangle the complex processes that shaped the ancient faunal diversity across millennia, with the potential to aid in implicating probable causes of species extinction and how humans impacted the genetics and ecology of wild and domestic species. However, even now, few studies explore interdisciplinary biomolecular approaches to reveal ancient faunal diversity dynamics in relation to environmental and anthropogenic impact. This review will approach how biomolecules have been implemented in a broad variety of topics and species, from the extinct Pleistocene megafauna to ancient wild and domestic stocks, as well as how their future use has the potential to offer an enhanced understanding of drivers of past faunal diversity on Earth.
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22
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Campbell MC, Ranciaro A. Human adaptation, demography and cattle domestication: an overview of the complexity of lactase persistence in Africa. Hum Mol Genet 2021; 30:R98-R109. [PMID: 33847744 DOI: 10.1093/hmg/ddab027] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2020] [Revised: 01/13/2021] [Accepted: 01/13/2021] [Indexed: 01/30/2023] Open
Abstract
Lactase persistence (LP) is a genetically-determined trait that is prevalent in African, European and Arab populations with a tradition of animal herding and milk consumption. To date, genetic analyses have identified several common variants that are associated with LP. Furthermore, data have indicated that these functional alleles likely have been maintained in pastoralist populations due to the action of recent selection, exemplifying the ongoing evolution of anatomically modern humans. Additionally, demographic history has also played a role in the geographic distribution of LP and associated alleles in Africa. In particular, the migration of ancestral herders and their subsequent admixture with local populations were integral to the spread of LP alleles and the culture of pastoralism across the continent. The timing of these demographic events was often correlated with known major environmental changes and/or the ability of domesticated cattle to resist/avoid infectious diseases. This review summarizes recent advances in our understanding of the genetic basis and evolutionary history of LP, as well as the factors that influenced the origin and spread of pastoralism in Africa.
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Affiliation(s)
- Michael C Campbell
- Department of Biology, Howard University, EE Just Hall Biology Building, 415 College Street NW, Washington, DC 20059, USA
| | - Alessia Ranciaro
- Department of Genetics, Perelman School of Medicine at the University of Pennsylvania, 415 Curie Boulevard, Philadelphia, PA 19104, USA
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23
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Phillips MJ, Shazwani Zakaria S. Enhancing mitogenomic phylogeny and resolving the relationships of extinct megafaunal placental mammals. Mol Phylogenet Evol 2021; 158:107082. [PMID: 33482383 DOI: 10.1016/j.ympev.2021.107082] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2020] [Revised: 12/21/2020] [Accepted: 01/11/2021] [Indexed: 10/22/2022]
Abstract
Mitochondrial genomes provided the first widely used sequences that were sufficiently informative to resolve relationships among animals across a wide taxonomic domain, from within species to between phyla. However, mitogenome studies supported several anomalous relationships and fell partly out of favour as sequencing multiple, independent nuclear loci proved to be highly effective. A tendency to blame mitochondrial DNA (mtDNA) has overshadowed efforts to understand and ameliorate underlying model misspecification. Here we find that influential assessments of the infidelity of mitogenome phylogenies have often been overstated, but nevertheless, substitution saturation and compositional non-stationarity substantially mislead reconstruction. We show that RY coding the mtDNA, excluding protein-coding 3rd codon sites, partitioning models based on amino acid hydrophobicity and enhanced taxon sampling improve the accuracy of mitogenomic phylogeny reconstruction for placental mammals, almost to the level of multi-gene nuclear datasets. Indeed, combined analysis of mtDNA with 3-fold longer nuclear sequence data either maintained or improved upon the nuclear support for all generally accepted clades, even those that mtDNA alone did not favour, thus indicating "hidden support". Confident mtDNA phylogeny reconstruction is especially important for understanding the evolutionary dynamics of mitochondria themselves, and for merging extinct taxa into the tree of life, with ancient DNA often only accessible as mtDNA. Our ancient mtDNA analyses lend confidence to the relationships of three extinct megafaunal taxa: glyptodonts are nested within armadillos, the South American ungulate, Macrauchenia is sister to horses and rhinoceroses, and sabre-toothed and scimitar cats are the monophyletic sister-group of modern cats.
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Affiliation(s)
- Matthew J Phillips
- School of Biology and Environmental Science, Queensland University of Technology, 2 George Street, Brisbane 4000, QLD, Australia.
| | - Sarah Shazwani Zakaria
- School of Biology and Environmental Science, Queensland University of Technology, 2 George Street, Brisbane 4000, QLD, Australia; School of Biology, Faculty of Applied Sciences, Universiti Teknologi MARA (UiTM) Caw. Negeri Sembilan, Kuala Pilah 72000, Malaysia
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24
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Miklósi Á, Abdai J, Temesi A. Searching where the treasure is: on the emergence of human companion animal partnership (HCAP). Anim Cogn 2021; 24:387-394. [PMID: 33433824 PMCID: PMC8035090 DOI: 10.1007/s10071-020-01467-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2020] [Revised: 12/14/2020] [Accepted: 12/21/2020] [Indexed: 10/26/2022]
Abstract
In our view, the discipline, often referred to as human-animal interaction (HAI), lacks a well-defined conceptual framework. It is too narrow both with respect to the animal species investigated and the nature of human-animal interactions studied. So instead, we introduce the term human-companion animal partnership (HCAP) that is not only a better descriptor for most research efforts within HAI but also helps to direct research efforts on an ethological basis. In our approach, 'companion' is a function and not a feature of some species. This means that many species had and could have a potential to form mixed social groups with humans if they evolve some capacity of social competence. This view may initiate new comparative research involving a range of species to find out how complex social engagement could be maintained in such hetero-specific social groups based on evolutionary heritage, recent selection and individual experience (socialisation). Our approach emphasises the role of human caring behaviour and social competence in the emergence of a partnership with several species, and thus could also help in setting expectations for welfare and aid in designing artificial companions for specific purposes.
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Affiliation(s)
- Ádám Miklósi
- Department of Ethology, Eötvös Loránd University, Budapest, Hungary. .,MTA-ELTE Comparative Ethology Research Group, Budapest, Hungary.
| | - Judit Abdai
- MTA-ELTE Comparative Ethology Research Group, Budapest, Hungary
| | - Andrea Temesi
- Department of Ethology, Eötvös Loránd University, Budapest, Hungary
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25
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Abstract
The equid family contains only one single extant genus, Equus, including seven living species grouped into horses on the one hand and zebras and asses on the other. In contrast, the equine fossil record shows that an extraordinarily richer diversity existed in the past and provides multiple examples of a highly dynamic evolution punctuated by several waves of explosive radiations and extinctions, cross-continental migrations, and local adaptations. In recent years, genomic technologies have provided new analytical solutions that have enhanced our understanding of equine evolution, including the species radiation within Equus; the extinction dynamics of several lineages; and the domestication history of two individual species, the horse and the donkey. Here, we provide an overview of these recent developments and suggest areas for further research.
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Affiliation(s)
- Pablo Librado
- Laboratoire d'Anthropobiologie Moléculaire et d'Imagerie de Synthèse, CNRS UMR 5288, Université Paul Sabatier, Toulouse 31000, France;
| | - Ludovic Orlando
- Laboratoire d'Anthropobiologie Moléculaire et d'Imagerie de Synthèse, CNRS UMR 5288, Université Paul Sabatier, Toulouse 31000, France;
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26
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Genetic Diversity of Historical and Modern Populations of Russian Cattle Breeds Revealed by Microsatellite Analysis. Genes (Basel) 2020; 11:genes11080940. [PMID: 32824045 PMCID: PMC7463645 DOI: 10.3390/genes11080940] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2020] [Revised: 08/10/2020] [Accepted: 08/12/2020] [Indexed: 01/24/2023] Open
Abstract
Analysis of ancient and historical DNA has great potential to trace the genetic diversity of local cattle populations during their centuries-long development. Forty-nine specimens representing five cattle breeds (Kholmogor, Yaroslavl, Great Russian, Novgorod, and Holland), dated from the end of the 19th century to the first half of the 20th century, were genotyped for nine polymorphic microsatellite loci. Using a multiple-tube approach, we determined the consensus genotypes of all samples/loci analysed. Amplification errors, including allelic drop-out (ADO) and false alleles (FA), occurred with an average frequency of 2.35% and 0.79%, respectively. A significant effect of allelic length on ADO rate (r2 = 0.620, p = 0.05) was shown. We did not observe significant differences in genetic diversity among historical samples and modern representatives of Kholmogor and Yaroslavl breeds. The unbiased expected heterozygosity values were 0.726–0.774 and 0.708–0.739; the allelic richness values were 2.716–2.893 and 2.661–2.758 for the historical and modern samples, respectively. Analyses of FST and Jost’s D genetic distances, and the results of STRUCTURE clustering, showed the maintenance of a part of historical components in the modern populations of Kholmogor and Yaroslavl cattle. Our study contributes to the conservation of biodiversity in the local Russian genetic resources of cattle.
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27
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Peyrégne S, Prüfer K. Present-Day DNA Contamination in Ancient DNA Datasets. Bioessays 2020; 42:e2000081. [PMID: 32648350 DOI: 10.1002/bies.202000081] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2020] [Revised: 05/20/2020] [Indexed: 01/06/2023]
Abstract
Present-day contamination can lead to false conclusions in ancient DNA studies. A number of methods are available to estimate contamination, which use a variety of signals and are appropriate for different types of data. Here an overview of currently available methods highlighting their strengths and weaknesses is provided, and a classification based on the signals used to estimate contamination is proposed. This overview aims at enabling researchers to choose the most appropriate methods for their dataset. Based on this classification, potential avenues for the further development of methods are discussed.
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Affiliation(s)
- Stéphane Peyrégne
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, 04103, Germany
| | - Kay Prüfer
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, 04103, Germany.,Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Jena, 07745, Germany
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28
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Schweizer RM, Wayne RK. Illuminating the mysteries of wolf history. Mol Ecol 2020; 29:1589-1591. [PMID: 32286714 DOI: 10.1111/mec.15438] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2020] [Revised: 03/12/2020] [Accepted: 03/26/2020] [Indexed: 11/29/2022]
Abstract
One of the most enduring surprises about the genetic history of Late Pleistocene populations is that continuity is often disturbed by upheaval. In fact, studies that support population continuity are increasingly rare in humans, a variety of vertebrate taxa, and vascular plants (Hofreiter & Stewart 2009; Burbrink et al. 2016). Perhaps such continuity should not be expected as the Pleistocene is marked by episodes of climate change, glaciation and the invasions of humans into previously isolated areas. Although fossils are one of the primary sources for inferring population continuity, a problem with fossil material is that, even if similar morphological forms might exist in a place over time, they may not be from the same genetic lineage. There are now readily available methods to assess genetic continuity solely from DNA found in fossil material, provided the record is fairly continuous. In a From the Cover article in this issue of Molecular Ecology, Loog et al. (2020) apply some of these readily available methods to analyse mitochondrial genomes and model the demography of wolves over the last 50,000 years.
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Affiliation(s)
- Rena M Schweizer
- Division of Biological Sciences, University of Montana, Missoula, MT, USA
| | - Robert K Wayne
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, CA, USA
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29
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Abstract
The domestication of animals led to a major shift in human subsistence patterns, from a hunter-gatherer to a sedentary agricultural lifestyle, which ultimately resulted in the development of complex societies. Over the past 15,000 years, the phenotype and genotype of multiple animal species, such as dogs, pigs, sheep, goats, cattle and horses, have been substantially altered during their adaptation to the human niche. Recent methodological innovations, such as improved ancient DNA extraction methods and next-generation sequencing, have enabled the sequencing of whole ancient genomes. These genomes have helped reconstruct the process by which animals entered into domestic relationships with humans and were subjected to novel selection pressures. Here, we discuss and update key concepts in animal domestication in light of recent contributions from ancient genomics.
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30
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Beyond broad strokes: sociocultural insights from the study of ancient genomes. Nat Rev Genet 2020; 21:355-366. [DOI: 10.1038/s41576-020-0218-z] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/04/2020] [Indexed: 01/01/2023]
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31
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Gabbianelli F, Alhaique F, Romagnoli G, Brancazi L, Piermartini L, Ottoni C, Valentini A, Chillemi G. Was the Cinta Senese Pig Already a Luxury Food in the Late Middle Ages? Ancient DNA and Archaeozoological Evidence from Central Italy. Genes (Basel) 2020; 11:genes11010085. [PMID: 31940807 PMCID: PMC7017058 DOI: 10.3390/genes11010085] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2019] [Revised: 01/08/2020] [Accepted: 01/08/2020] [Indexed: 11/16/2022] Open
Abstract
The Cinta senese is a pig breed, highly esteemed for its meat and derived products, characterized by a black coat with a typical white “belt” and documented by scant iconography, since the 13th–14th century in Italy. A piece of pottery showing a Cinta pig was found in the Graffignano castle (Northern Latium, Italy) dated 15th–16th centuries, spurring us to investigate the diet of the inhabitants. Ancient DNA analysis was carried out on 21 pig specimens on three nuclear SNPs: (1) g.43597545C>T, on the KIT gene, informative for the identification of the Cinta senese breed; (2) rs81460129, on an intergenic region in chr. 16, which discriminates between domestic pigs and wild boars, and; (3) a SNP on the ZFY/ZFX homologous genes, to determine the sex of the individuals. Our results indicate that the Cinta senese was present in Northern Latium in Late Medieval time, although it was not the only breed, and that pigs, including Cinta, interbred with wild boars, suggesting free-range breeding for all types of pigs. Moreover, the unexpected high proportion of young females may be considered as evidence for the wealth of the family inhabiting the castle.
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Affiliation(s)
- Federica Gabbianelli
- DIBAF, University of Tuscia, 01100 Viterbo, Italy;
- Correspondence: (F.G.); (G.C.)
| | | | | | - Luca Brancazi
- PhD School of Archaeology, Post-Classical Archaeology, Sapienza University, 00118 Rome, Italy;
| | | | - Claudio Ottoni
- Department of Oral and Maxillofacial Sciences, Diet and Ancient Technology Laboratory (DANTE), Sapienza University, 00118 Rome, Italy;
| | | | - Giovanni Chillemi
- DIBAF, University of Tuscia, 01100 Viterbo, Italy;
- Institute of Biomembranes, Bioenergetics and Molecular Biotechnologies, IBIOM, CNR, 70121 Bari, Italy
- Correspondence: (F.G.); (G.C.)
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32
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Hofreiter M, Hartmann S. Reconstructing protein-coding sequences from ancient DNA. Methods Enzymol 2020; 642:21-33. [DOI: 10.1016/bs.mie.2020.05.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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