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Mullan S, Nogueira SSC, Nogueira-Filho S, Zanella A, Rooney N, Held SDE, Mendl M. Farming non-typical sentient species: ethical framework requires passing a high bar. JOURNAL OF AGRICULTURAL & ENVIRONMENTAL ETHICS 2024; 37:10. [PMID: 38803823 PMCID: PMC11127879 DOI: 10.1007/s10806-024-09928-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Accepted: 05/07/2024] [Indexed: 05/29/2024]
Abstract
More widespread farming of species not typically used as livestock may be part of a sustainable approach for promoting human health and economic prosperity in a world with an increasing population; a current example is peccary farming in the Neotropics. Others have argued that species that are local to a region and which are usually not farmed should be considered for use as livestock. They may have a more desirable nutrient profile than species that are presently used as livestock. It may also reduce the pressure from hunting on other wild species, and cause less environmental damage than exotic species. We propose a sentiocentric utilitarian framework that could be used to decide whether species that are local, but generally not used as livestock, should be farmed. To illustrate the use of our decision-making framework, we employ two contrasting neotropical case studies: the Spotted Paca (Cuniculus paca) and the Capybara (Hydrochoerus hydrochaeris). We argue that it may be acceptable to use non-sentient species that are typically not farmed as livestock. However, research should determine whether farming them offers human, environmental or sustainability benefits. In addition, we recommend that if invertebrate species are considered for farming, research should be conducted to determine the likelihood that they are sentient. Finally, given the ethical failings of current livestock farming practices, we argue that a high bar must be met if 'new' species that are sentient are to be farmed.
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Affiliation(s)
- Siobhan Mullan
- School of Veterinary Medicine, University College Dublin, Belfield, Dublin 4, Ireland
| | - Selene S. C. Nogueira
- Departamento de Ciências Biológicas, Universidade Estadual de Santa Cruz, Rod. Jorge Amado, Km 16 - Salobrinho, Ilhéus, BA 45662-900 Brazil
| | - Sérgio Nogueira-Filho
- Departamento de Ciências Agrárias E Ambientais, Universidade Estadual de Santa Cruz, Rod. Jorge Amado, Km 16, Salobrinho, Ilhéus, BA 45662-900 Brazil
| | - Adroaldo Zanella
- Department of Preventive Veterinary Medicine and Animal Health, University of São Paulo, R. Duque de Caxias, 225, Caixa Postal 23, Pirassununga, SP 13635-900 Brazil
| | - Nicola Rooney
- Bristol Vet School, University of Bristol, Langford, Avon, BS40 5DU UK
| | | | - Michael Mendl
- Bristol Vet School, University of Bristol, Langford, Avon, BS40 5DU UK
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Flack N, Hughes L, Cassens J, Enriquez M, Gebeyehu S, Alshagawi M, Hatfield J, Kauffman A, Brown B, Klaeui C, Mabrouk IF, Walls C, Yeater T, Rivas A, Faulk C. The genome of Przewalski's horse ( Equus ferus przewalskii). BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.02.20.581252. [PMID: 38464182 PMCID: PMC10925127 DOI: 10.1101/2024.02.20.581252] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/12/2024]
Abstract
The Przewalski's horse (Equus ferus przewalskii) is an endangered equid native to the steppes of central Asia. After becoming extinct in the wild, multiple conservation efforts convened to preserve the species including captive breeding programs, reintroduction and monitoring systems, protected lands, and cloning. Availability of a highly contiguous reference genome is essential to support these continued efforts. We used Oxford Nanopore sequencing to produce a scaffold-level 2.5 Gb nuclear assembly and 16,002 bp mitogenome from a captive Przewalski's mare. All assembly drafts were generated from 111 Gb of sequence from a single PromethION R10.4.1 flow cell. The mitogenome contained 37 genes in the standard mammalian configuration and was 99.63% identical to the domestic horse (Equus caballus). The nuclear assembly, EquPr2, contained 2,146 scaffolds with an N50 of 85.1 Mb, 43X mean depth, and BUSCO quality score of 98.92%. EquPr2 successfully improves upon the existing Przewalski's horse reference genome (Burgud), with 25-fold fewer scaffolds, a 166-fold larger N50, and phased pseudohaplotypes. Modified basecalls revealed 79.5% DNA methylation and 2.1% hydroxymethylation globally. Allele-specific methylation analysis between pseudohaplotypes revealed 226 differentially methylated regions (DMRs) in known imprinted genes and loci not previously reported as imprinted. The heterozygosity rate of 0.165% matches previous estimates for the species and compares favorably to other endangered animals. This improved Przewalski's horse assembly will serve as a valuable resource for conservation efforts and comparative genomics investigations.
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Affiliation(s)
- Nicole Flack
- Department of Veterinary and Biomedical Sciences, College of Veterinary Medicine, University of Minnesota Saint Paul, MN, USA
| | - Lauren Hughes
- Department of Veterinary Population Medicine, College of Veterinary Medicine, University of Minnesota Saint Paul, MN, USA
| | - Jacob Cassens
- Division of Environmental Health Sciences, School of Public Health, University of Minnesota Minneapolis, MN, USA
| | - Maya Enriquez
- ANSC 8520 Students, University of Minnesota Minneapolis, MN, USA
| | - Samrawit Gebeyehu
- Department of Animal Science, College of Food, Agricultural and Natural Resource Sciences, University of Minnesota Saint Paul, MN, USA
| | | | - Jason Hatfield
- ANSC 8520 Students, University of Minnesota Minneapolis, MN, USA
| | - Anna Kauffman
- ANSC 8520 Students, University of Minnesota Minneapolis, MN, USA
| | - Baylor Brown
- ANSC 8520 Students, University of Minnesota Minneapolis, MN, USA
| | - Caitlin Klaeui
- ANSC 8520 Students, University of Minnesota Minneapolis, MN, USA
| | - Islam F. Mabrouk
- ANSC 8520 Students, University of Minnesota Minneapolis, MN, USA
| | - Carrie Walls
- Department of Animal Science, College of Food, Agricultural and Natural Resource Sciences, University of Minnesota Saint Paul, MN, USA
| | - Taylor Yeater
- ANSC 8520 Students, University of Minnesota Minneapolis, MN, USA
| | | | - Christopher Faulk
- Department of Animal Science, College of Food, Agricultural and Natural Resource Sciences, University of Minnesota Saint Paul, MN, USA
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MacPhillamy C, Ren Y, Chen T, Hiendleder S, Low WY. MicroRNA breed and parent-of-origin effects provide insights into biological pathways differentiating cattle subspecies in fetal liver. Front Genet 2023; 14:1329939. [PMID: 38162682 PMCID: PMC10757722 DOI: 10.3389/fgene.2023.1329939] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2023] [Accepted: 12/01/2023] [Indexed: 01/03/2024] Open
Abstract
Introduction: MicroRNAs (miRNAs) play a crucial role in regulating gene expression during key developmental processes, including fetal development. Brahman (Bos taurus indicus) and Angus (Bos taurus taurus) cattle breeds represent two major cattle subspecies with strikingly different phenotypes. Methods: We analyzed miRNA expression in liver samples of purebred and reciprocal crosses of Angus and Brahman to investigate breed and parent-of-origin effects at the onset of accelerated fetal growth. Results: We identified eight novel miRNAs in fetal liver samples and 14 differentially expressed miRNAs (DEMs) between purebred samples. Correlation of gene expression modules and miRNAs by breed and parent-of-origin effects revealed an enrichment of genes associated with breed-specific differences in traits such as heat tolerance (Brahman) and fat deposition (Angus). We demonstrate that genes predicted to be targets of DEMs were more likely to be differentially expressed than non-targets (p-value < 0.05). We identified several miRNAs (bta-miR-187, bta-miR-216b, bta-miR-2284c, bta-miR-2285c, bta-miR-2285cp, bta-miR-2419-3p, bta-miR-2419-5p, and bta-miR-11984) that showed similar correlation patterns as bta-miR-2355-3p, which has been associated with the glutamatergic synapse pathway, a key facilitator of heat tolerance. Furthermore, we report Angus-breed-specific miRNAs (bta-miR-2313-5p, btamiR-490, bta-miR-2316, and bta-miR-11990) that may be involved in fat deposition. Finally, we showed that the DEMs identified in fetal liver are involved in Rap1, MAPK, and Ras signalling pathways, which are important for fetal development, muscle development and metabolic traits such as fat metabolism. Conclusion: Our work sheds light on the miRNA expression patterns that contribute to gene expression differences driving phenotypic differences in indicine and taurine cattle.
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Affiliation(s)
- Callum MacPhillamy
- The Davies Research Centre, School of Animal and Veterinary Sciences, University of Adelaide, Roseworthy, SA, Australia
| | - Yan Ren
- The Davies Research Centre, School of Animal and Veterinary Sciences, University of Adelaide, Roseworthy, SA, Australia
| | - Tong Chen
- The Davies Research Centre, School of Animal and Veterinary Sciences, University of Adelaide, Roseworthy, SA, Australia
| | - Stefan Hiendleder
- The Davies Research Centre, School of Animal and Veterinary Sciences, University of Adelaide, Roseworthy, SA, Australia
- Robinson Research Institute, The University of Adelaide, North Adelaide, SA, Australia
| | - Wai Yee Low
- The Davies Research Centre, School of Animal and Veterinary Sciences, University of Adelaide, Roseworthy, SA, Australia
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Le Meillour L, Zazzo A, Zirah S, Tombret O, Barriel V, Arthur KW, Arthur JW, Cauliez J, Chaix L, Curtis MC, Gifford-Gonzalez D, Gunn I, Gutherz X, Hildebrand E, Khalidi L, Millet M, Mitchell P, Studer J, Vila E, Welker F, Pleurdeau D, Lesur J. The name of the game: palaeoproteomics and radiocarbon dates further refine the presence and dispersal of caprines in eastern and southern Africa. ROYAL SOCIETY OPEN SCIENCE 2023; 10:231002. [PMID: 38026023 PMCID: PMC10663795 DOI: 10.1098/rsos.231002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/13/2023] [Accepted: 11/03/2023] [Indexed: 12/01/2023]
Abstract
We report the first large-scale palaeoproteomics research on eastern and southern African zooarchaeological samples, thereby refining our understanding of early caprine (sheep and goat) pastoralism in Africa. Assessing caprine introductions is a complicated task because of their skeletal similarity to endemic wild bovid species and the sparse and fragmentary state of relevant archaeological remains. Palaeoproteomics has previously proved effective in clarifying species attributions in African zooarchaeological materials, but few comparative protein sequences of wild bovid species have been available. Using newly generated type I collagen sequences for wild species, as well as previously published sequences, we assess species attributions for elements originally identified as caprine or 'unidentifiable bovid' from 17 eastern and southern African sites that span seven millennia. We identified over 70% of the archaeological remains and the direct radiocarbon dating of domesticate specimens allows refinement of the chronology of caprine presence in both African regions. These results thus confirm earlier occurrences in eastern Africa and the systematic association of domesticated caprines with wild bovids at all archaeological sites. The combined biomolecular approach highlights repeatability and accuracy of the methods for conclusive contribution in species attribution of archaeological remains in dry African environments.
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Affiliation(s)
- Louise Le Meillour
- Unité Archéozoologie, Archéobotanique: Sociétés, Pratiques, Environnements (AASPE), Muséum national d'Histoire naturelle, CNRS, CP 56, 55 rue Buffon, 75005 Paris, France
- Unité Molécules de Communication et Adaptations des Micro-organismes (MCAM), Muséum national d'Histoire naturelle, CNRS, CP 54, 57 rue Cuvier, 75005 Paris, France
- Section for Molecular Ecology and Evolution, Globe Institute, Faculty of Health and Medical Sciences, University of Copenhagen, Øster Farimagsgade 5, 1353 København, Denmark
| | - Antoine Zazzo
- Unité Archéozoologie, Archéobotanique: Sociétés, Pratiques, Environnements (AASPE), Muséum national d'Histoire naturelle, CNRS, CP 56, 55 rue Buffon, 75005 Paris, France
| | - Séverine Zirah
- Unité Molécules de Communication et Adaptations des Micro-organismes (MCAM), Muséum national d'Histoire naturelle, CNRS, CP 54, 57 rue Cuvier, 75005 Paris, France
| | - Olivier Tombret
- Unité Archéozoologie, Archéobotanique: Sociétés, Pratiques, Environnements (AASPE), Muséum national d'Histoire naturelle, CNRS, CP 56, 55 rue Buffon, 75005 Paris, France
- Unité Histoire naturelle de l'Homme Préhistorique (HNHP), Muséum national d'Histoire naturelle, CNRS, UPVD, 1 rue René Panhard, 75013 Paris, France
| | - Véronique Barriel
- Centre de Recherche en Paléontologie – Paris (CR2P), Muséum national d'Histoire naturelle, CNRS, Sorbonne Université, CP 38, 8 rue Buffon, 75005 Paris, France
| | - Kathryn W. Arthur
- Department of Anthropology, University of South Florida St. Petersburg, 140 7th Avenue South, St. Petersburg, FL 33713, USA
| | - John W. Arthur
- Department of Anthropology, University of South Florida St. Petersburg, 140 7th Avenue South, St. Petersburg, FL 33713, USA
| | - Jessie Cauliez
- Unité Travaux et Recherches Archéologiques sur les Cultures, les Espaces et les Sociétés (TRACES), CNRS, Université Toulouse Jean Jaurès, 5 allées Antonio Machado, 31058 Toulouse, France
| | - Louis Chaix
- Département d'archéozoologie, Muséum d'histoire naturelle (MHNG), 1 route de Malagnou, 1208 Genève, Switzerland
| | - Matthew C. Curtis
- Anthropology Program, California State University Channel Islands, 1 University Drive, Camarillo, CA 93012, USA
| | - Diane Gifford-Gonzalez
- Department of Anthropology, University of California, Santa Cruz, Social Sciences 1 Faculty Svcs, 1156 High Street, Santa Cruz, CA 95064-1077, USA
| | - Imogen Gunn
- Museum of Archaeology and Anthropology, University of Cambridge, Downing Street, Cambridge CB2 3DZ, UK
| | - Xavier Gutherz
- Unité Archéologie des Sociétés Méditerranéennes (ASM), CNRS, Université Montpellier III, Ministère de la Culture, INRAP, Montpellier, France
| | | | - Lamya Khalidi
- Unité Cultures et Environnements. Préhistoire, Antiquité, Moyen Age (CEPAM), Université Côte d'Azur, CNRS, 24 avenue des Diables Bleus, 06300 Nice, France
| | - Marie Millet
- Département des Antiquités Égyptiennes, Musée du Louvre, Paris, France
| | - Peter Mitchell
- School of Archaeology, University of Oxford, Oxford, OX1 3TG, United Kingdom and Rock Art Research Institute, University of the Witwatersrand, PO Wits 2050, Johannesburg, South Africa
| | - Jacqueline Studer
- Département d'archéozoologie, Muséum d'histoire naturelle (MHNG), 1 route de Malagnou, 1208 Genève, Switzerland
| | - Emmanuelle Vila
- Unité Archéorient, Environnements et sociétés de l'Orient ancien, CNRS, Université de Lyon 2, Maison de l'Orient et de la Méditerranée, 7 rue Raulin, 69007 Lyon, France
| | - Frido Welker
- Section for Molecular Ecology and Evolution, Globe Institute, Faculty of Health and Medical Sciences, University of Copenhagen, Øster Farimagsgade 5, 1353 København, Denmark
| | - David Pleurdeau
- Unité Histoire naturelle de l'Homme Préhistorique (HNHP), Muséum national d'Histoire naturelle, CNRS, UPVD, 1 rue René Panhard, 75013 Paris, France
| | - Joséphine Lesur
- Unité Archéozoologie, Archéobotanique: Sociétés, Pratiques, Environnements (AASPE), Muséum national d'Histoire naturelle, CNRS, CP 56, 55 rue Buffon, 75005 Paris, France
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5
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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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Sun Y, Ma L, Li S, Wang Y, Xiao R, Yang J, Dijkstra JM, Xia C. Crystal Structure of a Classical MHC Class I Molecule in Dogs; Comparison of DLA-88*0 and DLA-88*5 Category Molecules. Cells 2023; 12:cells12071097. [PMID: 37048169 PMCID: PMC10093629 DOI: 10.3390/cells12071097] [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: 02/20/2023] [Revised: 03/31/2023] [Accepted: 03/31/2023] [Indexed: 04/14/2023] Open
Abstract
DLA-88 is a classical major histocompatibility complex (MHC) class I gene in dogs, and allelic DLA-88 molecules have been divided into two categories named "DLA-88*0" and "DLA-88*5." The defining difference between the two categories concerns an LQW motif in the α2 domain helical region of the DLA-88*5 molecules that includes the insertion of an extra amino acid compared to MHC class I consensus length. We here show that this motif has been exchanged by recombination between different DLA-88 evolutionary lineages. Previously, with pDLA-88*508:01, the structure of a molecule of the DLA-88*5 category was elucidated. The present study is the first to elucidate a structure, using X-ray crystallography, of the DLA-88*0 category, namely DLA-88*001:04 complexed with β2m and a nonamer peptide derived from canine distemper virus (CDV). The LQW motif that distinguishes DLA-88*5 from DLA-88*0 causes a shallower peptide binding groove (PBG) and a leucine exposed at the top of the α2 domain helix expected to affect T cell selection. Peptide ligand amino acid substitution and pMHC-I complex formation and stability analyses revealed that P2 and P3 are the major anchor residue positions for binding to DLA-88*001:04. We speculate that the distribution pattern of the LQW motif among canine classical MHC class I alleles represents a strategy to enhance allogeneic rejection by T cells of transmissible cancers such as canine transmissible venereal tumor (CTVT).
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Affiliation(s)
- Yujiao Sun
- Yantai Institute of China Agricultural University, No. 2006, Binhai Mid-Rd, High-Tech Zone, Yantai City 264003, China
| | - Lizhen Ma
- Department of Microbiology and Immunology, College of Veterinary Medicine, China Agricultural University, Beijing 100193, China
- Beijing Institute of Radiation Medicine, 27 Taiping Road, Beijing 100850, China
| | - Shen Li
- Department of Microbiology and Immunology, College of Veterinary Medicine, China Agricultural University, Beijing 100193, China
| | - Yawen Wang
- Department of Microbiology and Immunology, College of Veterinary Medicine, China Agricultural University, Beijing 100193, China
| | - Ruiqi Xiao
- Department of Microbiology and Immunology, College of Veterinary Medicine, China Agricultural University, Beijing 100193, China
| | - Junqi Yang
- Department of Microbiology and Immunology, College of Veterinary Medicine, China Agricultural University, Beijing 100193, China
| | - Johannes M Dijkstra
- Center for Medical Science, Fujita Health University, Toyoake, Aichi 470-1192, Japan
| | - Chun Xia
- Yantai Institute of China Agricultural University, No. 2006, Binhai Mid-Rd, High-Tech Zone, Yantai City 264003, China
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Guarino-Vignon P, Lefeuvre M, Chimènes A, Monnereau A, Guliyev F, Pecqueur L, Jovenet E, Lyonnet B, Bon C. Genome-wide analysis of a collective grave from Mentesh Tepe provides insight into the population structure of early neolithic population in the South Caucasus. Commun Biol 2023; 6:319. [PMID: 36966245 PMCID: PMC10039893 DOI: 10.1038/s42003-023-04681-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2022] [Accepted: 03/08/2023] [Indexed: 03/27/2023] Open
Abstract
Despite the localisation of the southern Caucasus at the outskirt of the Fertile Crescent, the Neolithisation process started there only at the beginning of the sixth millennium with the Shomutepe-Shulaveri culture of yet unclear origins. We present here genomic data for three new individuals from Mentesh Tepe in Azerbaijan, dating back to the beginnings of the Shomutepe-Shulaveri culture. We evidence that two juveniles, buried embracing each other, were brothers. We show that the Mentesh Tepe Neolithic population is the product of a recent gene flow between the Anatolian farmer-related population and the Caucasus/Iranian population, demonstrating that population admixture was at the core of the development of agriculture in the South Caucasus. By comparing Bronze Age individuals from the South Caucasus with Neolithic individuals from the same region, including Mentesh Tepe, we evidence that gene flows between Pontic Steppe populations and Mentesh Tepe-related groups contributed to the makeup of the Late Bronze Age and modern Caucasian populations. Our results show that the high cultural diversity during the Neolithic period of the South Caucasus deserves close genetic analysis.
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Affiliation(s)
- Perle Guarino-Vignon
- UMR7206 Éco-Anthropologie (EA), CNRS, Muséum National d'Histoire Naturelle, Université Paris-Cité, Paris, France.
- UMR5288 CAGT, CNRS, Université Paul Sabatier, Toulouse, France.
| | - Maël Lefeuvre
- UMR7206 Éco-Anthropologie (EA), CNRS, Muséum National d'Histoire Naturelle, Université Paris-Cité, Paris, France
| | - Amélie Chimènes
- UMR7206 Éco-Anthropologie (EA), CNRS, Muséum National d'Histoire Naturelle, Université Paris-Cité, Paris, France
| | - Aurore Monnereau
- Department of Archaeology, University of York, BioArCh, Environment Building Wentworth Way Heslington, York, YO10 5NG, UK
| | - Farhad Guliyev
- Head of the Science Fund and the Museum Department of the Institute of Archeology, Ethnography and Anthropology, Azerbaijan National Academy of Science, Baku, Azerbaijan
| | - Laure Pecqueur
- UMR7206 Éco-Anthropologie (EA), CNRS, Muséum National d'Histoire Naturelle, Université Paris-Cité, Paris, France
- Institut National de Recherches Archéologiques Préventives, Centre-île de France, Paris, France
| | - Elsa Jovenet
- Institut National de Recherches Archéologiques Préventives, Centre-île de France, Paris, France
| | - Bertille Lyonnet
- UMR7192 PROCLAC « Proche-Orient - Caucase: langues, archéologie, cultures », CNRS, Paris, France
| | - Céline Bon
- UMR7206 Éco-Anthropologie (EA), CNRS, Muséum National d'Histoire Naturelle, Université Paris-Cité, Paris, France.
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Origins, timing and introgression of domestic geese revealed by whole genome data. J Anim Sci Biotechnol 2023; 14:26. [PMID: 36782272 PMCID: PMC9926862 DOI: 10.1186/s40104-022-00826-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2022] [Accepted: 12/14/2022] [Indexed: 02/15/2023] Open
Abstract
BACKGROUND Geese are among the most important poultry species in the world. The current generally accepted hypothesis is that the European domestic geese originated from greylag geese (Anser anser), and Chinese domestic geese have two origins, most of which originated from swan geese (Anser cygnoides), and the Yili goose originated from greylag geese. To explain the origin and demographic history of geese, we selected 14 goose breeds from Europe and China and wild populations of swan and greylag geese, and whole genome sequencing data were obtained for 74 samples. RESULTS Population structure analysis and phylogenetic trees showed that the wild ancestor of Chinese domestic geese, except for Yili, is the swan geese, and the wild ancestor of Chinese Yili and European domestic geese is greylag geese. Analysis of the demographic history suggests that the domestication of Chinese geese occurred ~ 3499 years ago and that of the European geese occurred ~ 7552 years ago. Furthermore, gene flow was observed between domestic geese and their wild ancestors. Analysis of introgression showed that Yili geese had been introgressed by Chinese domestic geese, and the body size of Yili geese may be influenced by introgression events of some growth-related genes, including IGF-1. CONCLUSIONS Our study provides evidence for the origin of geese at the genome-wide level and advances the understanding of the history of goose domestication and the traits affected by introgression events.
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Snead AA, Alda F. Time-Series Sequences for Evolutionary Inferences. Integr Comp Biol 2022; 62:1771-1783. [PMID: 36104153 DOI: 10.1093/icb/icac146] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2022] [Revised: 07/28/2022] [Accepted: 07/29/2022] [Indexed: 01/05/2023] Open
Affiliation(s)
- Anthony A Snead
- Department of Biological Sciences, University of Alabama, 300 Hackberry Lane, Tuscaloosa, AL 35487, USA
| | - Fernando Alda
- Department of Biology, Geology and Environmental Science, University of Tennessee at Chattanooga, 615 McCallie Ave, Chattanooga, TN 37403, USA
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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: 1] [Impact Index Per Article: 0.5] [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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Balcarcel AM, Geiger M, Clauss M, Sánchez‐Villagra MR. The mammalian brain under domestication: Discovering patterns after a century of old and new analyses. JOURNAL OF EXPERIMENTAL ZOOLOGY. PART B, MOLECULAR AND DEVELOPMENTAL EVOLUTION 2022; 338:460-483. [PMID: 34813150 PMCID: PMC9787656 DOI: 10.1002/jez.b.23105] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/19/2021] [Revised: 09/24/2021] [Accepted: 10/27/2021] [Indexed: 12/30/2022]
Abstract
Comparisons of wild and domestic populations have established brain reduction as one of the most consistent patterns correlated with domestication. Over a century of scholarly work has been devoted to this subject, and yet, new data continue to foster its debate. Current arguments, both for and against the validity of brain reduction occurring in domestic taxa, have repeatedly cited a small set of reviews on this subject. The original works, their sampling, methodological details, and nuances of results that would be key to establishing validity, particularly in light of new data, have not been investigated. To facilitate and encourage a more informed discussion, we present a comprehensive review of original brain reduction literature for four mammalian clades: Artiodactyla, Perissodactyla, Carnivora, and Glires. Among these are studies that generated the most cited brain reduction values in modern domestication literature. In doing so, we provide a fairer stage for the critique of traits associated with domestication. We conclude that while brain reduction magnitudes may contain error, empirical data collectively support the reduction in brain size and cranial capacity for domestic forms.
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Affiliation(s)
- A. M. Balcarcel
- Palaeontological Institute and MuseumUniversity of ZurichZurichSwitzerland
| | - M. Geiger
- Palaeontological Institute and MuseumUniversity of ZurichZurichSwitzerland
| | - M. Clauss
- Vetsuisse Faculty, Clinic for Zoo Animals, Exotic Pets and WildlifeUniversity of ZurichZurichSwitzerland
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12
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Nilson SM, Gandolfi B, Grahn RA, Kurushima JD, Lipinski MJ, Randi E, Waly NE, Driscoll C, Murua Escobar H, Schuster RK, Maruyama S, Labarthe N, Chomel BB, Ghosh SK, Ozpinar H, Rah HC, Millán J, Mendes-de-Almeida F, Levy JK, Heitz E, Scherk MA, Alves PC, Decker JE, Lyons LA. Genetics of randomly bred cats support the cradle of cat domestication being in the Near East. Heredity (Edinb) 2022; 129:346-355. [PMID: 36319737 PMCID: PMC9708682 DOI: 10.1038/s41437-022-00568-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2021] [Revised: 09/29/2022] [Accepted: 09/30/2022] [Indexed: 11/04/2022] Open
Abstract
Cat domestication likely initiated as a symbiotic relationship between wildcats (Felis silvestris subspecies) and the peoples of developing agrarian societies in the Fertile Crescent. As humans transitioned from hunter-gatherers to farmers ~12,000 years ago, bold wildcats likely capitalized on increased prey density (i.e., rodents). Humans benefited from the cats' predation on these vermin. To refine the site(s) of cat domestication, over 1000 random-bred cats of primarily Eurasian descent were genotyped for single-nucleotide variants and short tandem repeats. The overall cat population structure suggested a single worldwide population with significant isolation by the distance of peripheral subpopulations. The cat population heterozygosity decreased as genetic distance from the proposed cat progenitor's (F.s. lybica) natural habitat increased. Domestic cat origins are focused in the eastern Mediterranean Basin, spreading to nearby islands, and southernly via the Levantine coast into the Nile Valley. Cat population diversity supports the migration patterns of humans and other symbiotic species.
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Affiliation(s)
- Sara M Nilson
- Division of Animal Sciences, University of Missouri, Columbia, MO, 65211, USA
| | - Barbara Gandolfi
- Department of Population Health and Reproduction, School of Veterinary Medicine, University of California, Davis, CA, 95616, USA
| | - Robert A Grahn
- Department of Population Health and Reproduction, School of Veterinary Medicine, University of California, Davis, CA, 95616, USA
| | - Jennifer D Kurushima
- Department of Population Health and Reproduction, School of Veterinary Medicine, University of California, Davis, CA, 95616, USA
| | - Monika J Lipinski
- Department of Population Health and Reproduction, School of Veterinary Medicine, University of California, Davis, CA, 95616, USA
| | - Ettore Randi
- Department of Chemistry and Bioscience, Aalborg University, Fredrik Bajers Vej 7H, 9220, Aalborg Øst, Denmark
| | - Nashwa E Waly
- Department of Animal Medicine, Faculty of Veterinary Medicine, Assuit University, 71526, Assiut, Egypt
| | | | - Hugo Murua Escobar
- Clinic for Hematology, Oncology and Palliative Care, University Medical Center Rostock, 18055, Rostock, Germany
| | - Rolf K Schuster
- Central Veterinary Research Laboratory, Dubai, United Arab Emirates
| | - Soichi Maruyama
- Laboratory of Veterinary Public Health, Nihon University, 1866 Kameino, Fujisawa, Kanagawa, 252-0880, Japan
| | - Norma Labarthe
- Programa de Bioética, Ética Aplicada e Saúde Coletiva, Fundação Oswaldo Cruz, Rio de Janeiro, RJ, 21040-360, Brazil
- Programa de Pós-Graduação em Medicina Veterinária - Clínica e Reprodução Animal, Faculdade de Veterinária, Universidade Federal Fluminense, Rua Vital Brazil Filho 64, Niterói, RJ, 24230-340, Brazil
| | - Bruno B Chomel
- Department of Population Health and Reproduction, School of Veterinary Medicine, University of California, Davis, CA, 95616, USA
| | | | - Haydar Ozpinar
- Graduate School of Health Sciences, Istanbul Gedik University, 34876, İstanbul, Turkey
| | - Hyung-Chul Rah
- Research Institute of Veterinary Medicine, College of Veterinary Medicine, Chungbuk National University, Cheongju, 28644, South Korea
| | - Javier Millán
- Instituto Agroalimentario de Aragón-IA2 (Universidad de Zaragoza-CITA), Miguel Servet 177, 50013, Zaragoza, Spain
- Fundación ARAID, Avda. de Ranillas, 50018, Zaragoza, Spain
- Facultad de Ciencias de la Vida, Universidad Andres Bello, Santiago, Chile
| | - Flavya Mendes-de-Almeida
- Programa de Pós-Graduação em Medicina Veterinária - Clínica e Reprodução Animal, Faculdade de Veterinária, Universidade Federal Fluminense, Rua Vital Brazil Filho 64, Niterói, RJ, 24230-340, Brazil
| | - Julie K Levy
- Maddie's Shelter Medicine Program, College of Veterinary Medicine, University of Florida, Gainesville, FL, 32608, USA
| | | | | | - Paulo C Alves
- CIBIO/InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos/InBIO Associate Lab & Faculdade de Ciências, Universidade do Porto, Campus e Vairão, 4485-661, Vila do Conde, Portugal
- Wildlife Biology Program, University of Montana, Missoula, MT, 59812, USA
| | - Jared E Decker
- Division of Animal Sciences, University of Missouri, Columbia, MO, 65211, USA.
- Institute for Data Science and Informatics, University of Missouri, Columbia, MO, 65211, USA.
| | - Leslie A Lyons
- Department of Population Health and Reproduction, School of Veterinary Medicine, University of California, Davis, CA, 95616, USA.
- Department of Veterinary Medicine & Surgery, College of Veterinary Medicine, University of Missouri, Columbia, MO, 65211, USA.
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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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Hekkala ER, Colten R, Cunningham SW, Smith O, Ikram S. Using Mitogenomes to Explore the Social and Ecological Contexts of Crocodile Mummification in Ancient Egypt. BULLETIN OF THE PEABODY MUSEUM OF NATURAL HISTORY 2022. [DOI: 10.3374/014.063.0101] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Evon R. Hekkala
- Department of Biological Sciences, Fordham University, Bronx, NY 10458 USA —
| | - Roger Colten
- Division of Anthropology, Peabody Museum of Natural History, Yale University, New Haven, CT 06520–8118 USA
| | - Seth W. Cunningham
- Department of Biological Sciences, Fordham University, Bronx, NY 10458 USA
| | - Oliver Smith
- Micropathology, Ltd., University of Warwick Science Park, Coventry, CV4 7EZ, United Kingdom
| | - Salima Ikram
- Department of Sociology, Egyptology, and Anthropology, The American University in Cairo, Cairo, Egypt
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15
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Li T, Qin P, Chen B, Niu X, Wang Y, Niu Y, Wei C, Hou D, Ma H, Han R, Li H, Liu X, Kang X, Li Z. A novel 27-bp indel in the intron region of the YBX3 gene is associated with growth traits in chickens. Br Poult Sci 2022; 63:590-596. [PMID: 35382648 DOI: 10.1080/00071668.2022.2059340] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Abstract
1. The DNA/RNA binding protein YBX3 is associated with gene transcription, DNA repair, and the progression of various diseases and is highly conserved from bacteria to humans.2. The following experiment found a 27-bp insertion/deletion polymorphism in the intron region of the YBX3 gene through resequencing. In cross-designed, F2 resource groups, the indel was significantly associated with broiler weight and body size at 0, 2, 4, 6, 8, 10 and 12 weeks of age and several other traits (semi evisceration weight (SEW), evisceration weight (EW), semi evisceration rate (SER), evisceration rate (ER), head weight (HW), claw weight (CLW), wing weight (DWW), gizzard weight (GW), pancreas weight (PW), chest muscle weight (CMW), leg weight (LW), leg muscle weight (LMW), shedding weight (SW), carcass weight (CW) and pectoral area (PA)) (P<0.05).3. The insertion-insertion (II) genotype was significantly associated with the greatest growth traits and carcass traits, whereas the values associated with the insertion-deletion (ID) genotype were the lowest in the F2 reciprocal cross chickens.4. The mutation sites were genotyped in 3611 individuals from 13 different chicken breeds and cross-designed F2 resource groups. The II genotype is the most important in commercial broilers, and the I allele frequency observed in these breeds was relatively high. However, there is still considerable potential in breeding dual-purpose chickens and commercial laying hens.5. The mRNA expression of the YBX3 gene in tissues from different breeds and developmental stages demonstrated that the 27-bp indel may affect the entire development process of poultry by affecting muscle development. These findings are beneficial for elucidating the function of the YBX3 gene and facilitating enhanced reproduction in the chicken industry.
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Affiliation(s)
- Tong Li
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou 450002, China
| | - Panpan Qin
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou 450002, China
| | - Bingjie Chen
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou 450002, China
| | - Xinran Niu
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou 450002, China
| | - Yanxing Wang
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou 450002, China
| | - Yufang Niu
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou 450002, China
| | - Chengjie Wei
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou 450002, China
| | - Dan Hou
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou 450002, China
| | - Haoxiang Ma
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou 450002, China
| | - Ruili Han
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou 450002, China
| | - Hong Li
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou 450002, China
| | - Xiaojun Liu
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou 450002, China.,Henan Innovative Engineering Research Centre of Poultry Germplasm Resource, Henan Agricultural University, Zhengzhou 450002, China
| | - Xiangtao Kang
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou 450002, China.,Henan Innovative Engineering Research Centre of Poultry Germplasm Resource, Henan Agricultural University, Zhengzhou 450002, China
| | - Zhuanjian Li
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou 450002, China.,Henan Innovative Engineering Research Centre of Poultry Germplasm Resource, Henan Agricultural University, Zhengzhou 450002, China
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16
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Abstract
Archaeological and paleontological records offer tremendous yet often untapped potential for examining long-term biodiversity trends and the impact of climate change and human activity on ecosystems. Yet, zooarchaeological and fossil remains suffer various limitations, including that they are often highly fragmented and morphologically unidentifiable, preventing them from being optimally leveraged for addressing fundamental research questions in archaeology, paleontology, and conservation paleobiology. Here, we explore the potential of palaeoproteomics—the study of ancient proteins—to serve as a critical tool for creating richer, more informative datasets about biodiversity change that can be leveraged to generate more realistic, constructive, and effective conservation and restoration strategies into the future.
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17
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Peng Y, Cai X, Wang Y, Liu Z, Zhao Y. Genome‐wide analysis suggests multiple domestication events of Chinese local pigs. Anim Genet 2022; 53:293-306. [DOI: 10.1111/age.13183] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2022] [Revised: 02/12/2022] [Accepted: 02/12/2022] [Indexed: 01/02/2023]
Affiliation(s)
- Yebo Peng
- State Key Laboratory of Agrobiotechnology College of Biological Sciences China Agricultural University Beijing China
| | - Xinyu Cai
- State Key Laboratory of Agrobiotechnology College of Biological Sciences China Agricultural University Beijing China
| | - Yuzhan Wang
- State Key Laboratory of Agrobiotechnology College of Biological Sciences China Agricultural University Beijing China
| | - Zexuan Liu
- State Key Laboratory of Agrobiotechnology College of Biological Sciences China Agricultural University Beijing China
| | - Yiqiang Zhao
- State Key Laboratory of Agrobiotechnology College of Biological Sciences China Agricultural University Beijing China
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18
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Hecht EE, Kukekova AV, Gutman DA, Acland GM, Preuss TM, Trut LN. Neuromorphological Changes following Selection for Tameness and Aggression in the Russian Farm-Fox experiment. J Neurosci 2021; 41:6144-6156. [PMID: 34127519 PMCID: PMC8276742 DOI: 10.1523/jneurosci.3114-20.2021] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2020] [Revised: 05/11/2021] [Accepted: 05/17/2021] [Indexed: 01/13/2023] Open
Abstract
The Russian farm-fox experiment is an unusually long-running and well-controlled study designed to replicate wolf-to-dog domestication. As such, it offers an unprecedented window onto the neural mechanisms governing the evolution of behavior. Here we report evolved changes to gray matter morphology resulting from selection for tameness versus aggressive responses toward humans in a sample of 30 male fox brains. Contrasting with standing ideas on the effects of domestication on brain size, tame foxes did not show reduced brain volume. Rather, gray matter volume in both the tame and aggressive strains was increased relative to conventional farm foxes bred without deliberate selection on behavior. Furthermore, tame- and aggressive-enlarged regions overlapped substantially, including portions of motor, somatosensory, and prefrontal cortex, amygdala, hippocampus, and cerebellum. We also observed differential morphologic covariation across distributed gray matter networks. In one prefrontal-cerebellum network, this covariation differentiated the three populations along the tame-aggressive behavioral axis. Surprisingly, a prefrontal-hypothalamic network differentiated the tame and aggressive foxes together from the conventional strain. These findings indicate that selection for opposite behaviors can influence brain morphology in a similar way.SIGNIFICANCE STATEMENT Domestication represents one of the largest and most rapid evolutionary shifts of life on earth. However, its neural correlates are largely unknown. Here we report the neuroanatomical consequences of selective breeding for tameness or aggression in the seminal Russian farm-fox experiment. Compared with a population of conventional farm-bred control foxes, tame foxes show neuroanatomical changes in the PFC and hypothalamus, paralleling wolf-to-dog shifts. Surprisingly, though, aggressive foxes also show similar changes. Moreover, both strains show increased gray matter volume relative to controls. These results indicate that similar brain adaptations can result from selection for opposite behavior, that existing ideas of brain changes in domestication may need revision, and that significant neuroanatomical change can evolve very quickly, within the span of <100 generations.
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Affiliation(s)
- Erin E Hecht
- Department of Human Evolutionary Biology, Harvard University, Cambridge, MA 02138
| | - Anna V Kukekova
- Department of Animal Sciences, College of Agriculture, Consumer, and Environmental Sciences, University of IL Urbana-Champaign, Urbana, IL 61801
| | | | - Gregory M Acland
- Baker Institute for Animal Health, College of Veterinary Medicine, Cornell University, Ithaca, New York, 14853
| | - Todd M Preuss
- Yerkes National Primate Research Center, Emory University, Atlanta, GA 30322
| | - Lyudmila N Trut
- Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia, 630090
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19
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Balcarcel AM, Veitschegger K, Clauss M, Sánchez-Villagra MR. Intensive human contact correlates with smaller brains: differential brain size reduction in cattle types. Proc Biol Sci 2021; 288:20210813. [PMID: 34102890 PMCID: PMC8188006 DOI: 10.1098/rspb.2021.0813] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2021] [Accepted: 05/17/2021] [Indexed: 12/30/2022] Open
Abstract
Cattle are one of the most intensively bred domestic animals, providing humans with a multitude of products and uses. Using data from the fossil record, we test if their domestication, as for other taxa, has resulted in a reduction of their brain size. We not only conclude that Bos taurus (domestic cattle) have smaller brains than their wild ancestor, Bos primigenius (aurochs), but that brain size varies significantly by breed, with some having much smaller brains than others. Differences in husbandry practices between several breed categories align with a range of human engagement, which also aligns with the degree of selection for docility. Sampling 317 domestics from 71 breeds, we investigate if differences in brain size correlate with the intensity of human contact. A clear pattern emerges whereby a brain reduction gradient parallels a gradient in behavioural selection. Bullfighting cattle, which are bred for fighting and aggressive temperament, have much larger brains than dairy breeds, which are intensively selected for docility. Our results add to a fundamental aspect of animal domestication theory: the interplay between basic features of the domestic environment-selection for docility, absence of predators and human provision of resources-seems to explain differences in brain size.
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Affiliation(s)
- A. M. Balcarcel
- Palaeontological Institute and Museum, University of Zurich, Karl-Schmid-Strasse 4, 8006 Zurich, Switzerland
| | - K. Veitschegger
- Palaeontological Institute and Museum, University of Zurich, Karl-Schmid-Strasse 4, 8006 Zurich, Switzerland
| | - M. Clauss
- Clinic for Zoo Animals, Exotic Pets and Wildlife, University of Zurich, Winterthurerstrasse 260, 8057 Zurich, Switzerland
| | - M. R. Sánchez-Villagra
- Palaeontological Institute and Museum, University of Zurich, Karl-Schmid-Strasse 4, 8006 Zurich, Switzerland
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20
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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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21
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Farm Animals Are Long Away from Natural Behavior: Open Questions and Operative Consequences on Animal Welfare. Animals (Basel) 2021; 11:ani11030724. [PMID: 33800925 PMCID: PMC8001272 DOI: 10.3390/ani11030724] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2021] [Revised: 03/03/2021] [Accepted: 03/05/2021] [Indexed: 01/05/2023] Open
Abstract
Simple Summary Animal welfare is a very important issue. One of the tasks of researchers is to provide explanations and possible solutions to questions arising from non-experts. This work analyzes part of the extensive literature on relationships between selection and domestic, mainly farm, animals’ behavior and deals with some very important themes, such as the role of regulations, domestication, and selection. Abstract The concept of welfare applied to farm animals has undergone a remarkable evolution. The growing awareness of citizens pushes farmers to guarantee the highest possible level of welfare to their animals. New perspectives could be opened for animal welfare reasoning around the concept of domestic, especially farm, animals as partial human artifacts. Therefore, it is important to understand how much a particular behavior of a farm animal is far from the natural one of its ancestors. This paper is a contribution to better understand the role of genetics of the farm animals on their behavior. This means that the naïve approach to animal welfare regarding returning animals to their natural state should be challenged and that welfare assessment should be considered.
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22
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Baumann C, Pfrengle S, Münzel SC, Molak M, Feuerborn TR, Breidenstein A, Reiter E, Albrecht G, Kind CJ, Verjux C, Leduc C, Conard NJ, Drucker DG, Giemsch L, Thalmann O, Bocherens H, Schuenemann VJ. A refined proposal for the origin of dogs: the case study of Gnirshöhle, a Magdalenian cave site. Sci Rep 2021; 11:5137. [PMID: 33664287 PMCID: PMC7933181 DOI: 10.1038/s41598-021-83719-7] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2020] [Accepted: 02/08/2021] [Indexed: 02/08/2023] Open
Abstract
Dogs are known to be the oldest animals domesticated by humans. Although many studies have examined wolf domestication, the geographic and temporal origin of this process is still being debated. To address this issue, our study sheds new light on the early stages of wolf domestication during the Magdalenian period (16–14 ka cal BP) in the Hegau Jura region (Southwestern Germany and Switzerland). By combining morphology, genetics, and isotopes, our multidisciplinary approach helps to evaluate alternate processes driving the early phases of domestication. The isotope analysis uncovered a restricted, low δ15N protein diet for all analyzed Gnirshöhle specimens, while morphological examinations and phylogenetic relationships did not unequivocally assign them to one or the other canid lineage. Intriguingly, the newly generated mitochondrial canid genomes span the entire genetic diversity of modern dogs and wolves. Such high mitochondrial diversity could imply that Magdalenian people tamed and reared animals originating from different wolf lineages. We discuss our results in light of three ecological hypotheses and conclude that both domestication and the existence of a specialized wolf ecomorph are highly probable. However, due to their proximity to humans and a restricted diet, we propose domestication as the most likely scenario explaining the patterns observed herein.
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Affiliation(s)
- Chris Baumann
- Biogeology, Department of Geosciences, University of Tübingen, Hölderlinstraße 12, 72074, Tübingen, Germany. .,Institute for Archaeological Sciences, University of Tübingen, Rümelinstraße 23, 72070, Tübingen, Germany.
| | - Saskia Pfrengle
- Institute for Archaeological Sciences, University of Tübingen, Rümelinstraße 23, 72070, Tübingen, Germany. .,Institute of Evolutionary Medicine, University of Zurich, Winterthurerstrasse 190, 8057, Zurich, Switzerland.
| | - Susanne C Münzel
- Institute for Archaeological Sciences, University of Tübingen, Rümelinstraße 23, 72070, Tübingen, Germany
| | - Martyna Molak
- Centre of New Technologies, University of Warsaw, S. Banacha 2c, 02-097, Warsaw, Poland
| | - Tatiana R Feuerborn
- Institute for Archaeological Sciences, University of Tübingen, Rümelinstraße 23, 72070, Tübingen, Germany.,Section for Evolutionary Genomics, GLOBE Institute, Øster Farimagsgade 5, Bygning 7, 1353, København K, Denmark
| | - Abagail Breidenstein
- Institute of Evolutionary Medicine, University of Zurich, Winterthurerstrasse 190, 8057, Zurich, Switzerland
| | - Ella Reiter
- Institute for Archaeological Sciences, University of Tübingen, Rümelinstraße 23, 72070, Tübingen, Germany
| | - Gerd Albrecht
- Department of Archaeology, Markgräflerland-Museum Society, Wilhelmstraße 7, 79379, Müllheim, Germany
| | - Claus-Joachim Kind
- State Office for Cultural Heritage Baden-Württemberg, Berliner Str. 12, 73728, Esslingen, Germany
| | - Christian Verjux
- Service Régional de l'Archéologie (UMR 7041 ArScAn-Équipe Ethnologie Préhistorique), DRAC Centre, Val de Loire, 6 Rue de la Manufacture, 45000, Orléans, France
| | - Charlotte Leduc
- INRAP, 12 Rue de Méric, 57000, Metz, France.,UMR8215-Trajectoires, CNRS, 21 Allée de l'Université, 92023, Nanterre Cedex, France
| | - Nicholas J Conard
- Institute for Archaeological Sciences, University of Tübingen, Rümelinstraße 23, 72070, Tübingen, Germany.,Department for Early Prehistory and Quaternary Ecology, University of Tübingen, Burgsteige 11, 72070, Tübingen, Germany.,Senckenberg Centre for Human Evolution and Paleoenvironment, Schloss Hohentübingen, University of Tübingen, 72070, Tübingen, Germany
| | - Dorothée G Drucker
- Senckenberg Centre for Human Evolution and Palaeoenvironment, University of Tübingen, Sigwartstraße 10, 72076, Tübingen, Germany
| | - Liane Giemsch
- Archäologisches Museum Frankfurt, Karmelitergasse 1, 60311, Frankfurt am Main, Germany
| | - Olaf Thalmann
- Department of Pediatric Gastroenterology and Metabolic Diseases, Poznan University of Medical Sciences, Szpitalna 27/33, 60-572, Poznan, Poland
| | - Hervé Bocherens
- Biogeology, Department of Geosciences, University of Tübingen, Hölderlinstraße 12, 72074, Tübingen, Germany.,Senckenberg Centre for Human Evolution and Palaeoenvironment, University of Tübingen, Sigwartstraße 10, 72076, Tübingen, Germany
| | - Verena J Schuenemann
- Institute for Archaeological Sciences, University of Tübingen, Rümelinstraße 23, 72070, Tübingen, Germany. .,Institute of Evolutionary Medicine, University of Zurich, Winterthurerstrasse 190, 8057, Zurich, Switzerland. .,Senckenberg Centre for Human Evolution and Palaeoenvironment, University of Tübingen, Rümelinstraße 23, 72070, Tübingen, Germany.
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23
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Xu W, Lin Y, Zhao K, Li H, Tian Y, Ngatia JN, Ma Y, Sahu SK, Guo H, Guo X, Xu YC, Liu H, Kristiansen K, Lan T, Zhou X. An efficient pipeline for ancient DNA mapping and recovery of endogenous ancient DNA from whole-genome sequencing data. Ecol Evol 2021; 11:390-401. [PMID: 33437437 PMCID: PMC7790629 DOI: 10.1002/ece3.7056] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2020] [Revised: 10/10/2020] [Accepted: 10/29/2020] [Indexed: 12/20/2022] Open
Abstract
Ancient DNA research has developed rapidly over the past few decades due to improvements in PCR and next-generation sequencing (NGS) technologies, but challenges still exist. One major challenge in relation to ancient DNA research is to recover genuine endogenous ancient DNA sequences from raw sequencing data. This is often difficult due to degradation of ancient DNA and high levels of contamination, especially homologous contamination that has extremely similar genetic background with that of the real ancient DNA. In this study, we collected whole-genome sequencing (WGS) data from 6 ancient samples to compare different mapping algorithms. To further explore more effective methods to separate endogenous DNA from homologous contaminations, we attempted to recover reads based on ancient DNA specific characteristics of deamination, depurination, and DNA fragmentation with different parameters. We propose a quick and improved pipeline for separating endogenous ancient DNA while simultaneously decreasing homologous contaminations to very low proportions. Our goal in this research was to develop useful recommendations for ancient DNA mapping and for separation of endogenous DNA to facilitate future studies of ancient DNA.
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Affiliation(s)
- Wenhao Xu
- Institute of Vertebrate Paleontology and PaleoanthropologyChinese Academy of SciencesBeijingChina
- College of InformaticsHuazhong Agricultural UniversityWuhanChina
| | - Yu Lin
- State Key Laboratory of Agricultural GenomicsBGI‐ShenzhenShenzhenChina
- Guangdong Provincial Key Laboratory of Genome Read and WriteBGI‐ShenzhenShenzhenChina
| | - Keliang Zhao
- Institute of Vertebrate Paleontology and PaleoanthropologyChinese Academy of SciencesBeijingChina
- CAS Center for Excellence in Life and PaleoenvironmentBeijingChina
| | - Haimeng Li
- State Key Laboratory of Agricultural GenomicsBGI‐ShenzhenShenzhenChina
- School of Future TechnologyUniversity of Chinese Academy of SciencesBeijingChina
| | - Yinping Tian
- State Key Laboratory of Agricultural GenomicsBGI‐ShenzhenShenzhenChina
| | | | - Yue Ma
- College of Wildlife ResourcesNortheast Forestry UniversityHarbinChina
| | - Sunil Kumar Sahu
- State Key Laboratory of Agricultural GenomicsBGI‐ShenzhenShenzhenChina
| | - Huabing Guo
- Forest Inventory and Planning Institute of Jilin ProvinceChangchunChina
| | - Xiaosen Guo
- State Key Laboratory of Agricultural GenomicsBGI‐ShenzhenShenzhenChina
- Guangdong Provincial Academician Workstation of BGI Synthetic GenomicsBGI‐ShenzhenShenzhenChina
| | - Yan Chun Xu
- College of Wildlife ResourcesNortheast Forestry UniversityHarbinChina
| | - Huan Liu
- State Key Laboratory of Agricultural GenomicsBGI‐ShenzhenShenzhenChina
- Department of BiologyLaboratory of Genomics and Molecular BiomedicineUniversity of CopenhagenCopenhagenDenmark
| | - Karsten Kristiansen
- State Key Laboratory of Agricultural GenomicsBGI‐ShenzhenShenzhenChina
- Department of BiologyLaboratory of Genomics and Molecular BiomedicineUniversity of CopenhagenCopenhagenDenmark
| | - Tianming Lan
- State Key Laboratory of Agricultural GenomicsBGI‐ShenzhenShenzhenChina
- Department of BiologyLaboratory of Genomics and Molecular BiomedicineUniversity of CopenhagenCopenhagenDenmark
| | - Xinying Zhou
- Institute of Vertebrate Paleontology and PaleoanthropologyChinese Academy of SciencesBeijingChina
- CAS Center for Excellence in Life and PaleoenvironmentBeijingChina
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24
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Šimić G, Vukić V, Kopić J, Krsnik Ž, Hof PR. Molecules, Mechanisms, and Disorders of Self-Domestication: Keys for Understanding Emotional and Social Communication from an Evolutionary Perspective. Biomolecules 2020; 11:E2. [PMID: 33375093 PMCID: PMC7822183 DOI: 10.3390/biom11010002] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2020] [Revised: 12/18/2020] [Accepted: 12/20/2020] [Indexed: 12/16/2022] Open
Abstract
The neural crest hypothesis states that the phenotypic features of the domestication syndrome are due to a reduced number or disruption of neural crest cells (NCCs) migration, as these cells differentiate at their final destinations and proliferate into different tissues whose activity is reduced by domestication. Comparing the phenotypic characteristics of modern and prehistoric man, it is clear that during their recent evolutionary past, humans also went through a process of self-domestication with a simultaneous prolongation of the period of socialization. This has led to the development of social abilities and skills, especially language, as well as neoteny. Disorders of neural crest cell development and migration lead to many different conditions such as Waardenburg syndrome, Hirschsprung disease, fetal alcohol syndrome, DiGeorge and Treacher-Collins syndrome, for which the mechanisms are already relatively well-known. However, for others, such as Williams-Beuren syndrome and schizophrenia that have the characteristics of hyperdomestication, and autism spectrum disorders, and 7dupASD syndrome that have the characteristics of hypodomestication, much less is known. Thus, deciphering the biological determinants of disordered self-domestication has great potential for elucidating the normal and disturbed ontogenesis of humans, as well as for the understanding of evolution of mammals in general.
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Affiliation(s)
- Goran Šimić
- Department of Neuroscience, Croatian Institute for Brain Research, University of Zagreb Medical School, 10000 Zagreb, Croatia; (V.V.); (J.K.); (Ž.K.)
| | - Vana Vukić
- Department of Neuroscience, Croatian Institute for Brain Research, University of Zagreb Medical School, 10000 Zagreb, Croatia; (V.V.); (J.K.); (Ž.K.)
| | - Janja Kopić
- Department of Neuroscience, Croatian Institute for Brain Research, University of Zagreb Medical School, 10000 Zagreb, Croatia; (V.V.); (J.K.); (Ž.K.)
| | - Željka Krsnik
- Department of Neuroscience, Croatian Institute for Brain Research, University of Zagreb Medical School, 10000 Zagreb, Croatia; (V.V.); (J.K.); (Ž.K.)
| | - Patrick R. Hof
- Nash Family Department of Neuroscience, Friedman Brain Institute, and Ronald M. Loeb Center for Alzheimer’s disease, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA;
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25
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Garrett Vieira F, Samaniego Castruita JA, Gilbert MTP. Using in silico predicted ancestral genomes to improve the efficiency of paleogenome reconstruction. Ecol Evol 2020; 10:12700-12709. [PMID: 33304488 PMCID: PMC7713980 DOI: 10.1002/ece3.6925] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2020] [Revised: 09/23/2020] [Accepted: 09/28/2020] [Indexed: 01/20/2023] Open
Abstract
Paleogenomics is the nascent discipline concerned with sequencing and analysis of genome-scale information from historic, ancient, and even extinct samples. While once inconceivable due to the challenges of DNA damage, contamination, and the technical limitations of PCR-based Sanger sequencing, following the dawn of the second-generation sequencing revolution, it has rapidly become a reality. However, a significant challenge facing ancient DNA studies on extinct species is the lack of closely related reference genomes against which to map the sequencing reads from ancient samples. Although bioinformatic efforts to improve the assemblies have focused mainly in mapping algorithms, in this article we explore the potential of an alternative approach, namely using reconstructed ancestral genome as reference for mapping DNA sequences of ancient samples. Specifically, we present a preliminary proof of concept for a general framework and demonstrate how under certain evolutionary divergence thresholds, considerable mapping improvements can be easily obtained.
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Affiliation(s)
- Filipe Garrett Vieira
- Section for Evolutionary GenomicsThe GLOBE InstituteFaculty of Health and Medical SciencesUniversity of CopenhagenCopenhagenDenmark
| | - José Alfredo Samaniego Castruita
- Section for Evolutionary GenomicsThe GLOBE InstituteFaculty of Health and Medical SciencesUniversity of CopenhagenCopenhagenDenmark
| | - M. Thomas P. Gilbert
- Section for Evolutionary GenomicsThe GLOBE InstituteFaculty of Health and Medical SciencesUniversity of CopenhagenCopenhagenDenmark
- University MuseumNorwegian University of Science and TechnologyTrondheimNorway
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26
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He Z, Dai X, Beaumont M, Yu F. Detecting and Quantifying Natural Selection at Two Linked Loci from Time Series Data of Allele Frequencies with Forward-in-Time Simulations. Genetics 2020; 216:521-541. [PMID: 32826299 PMCID: PMC7536848 DOI: 10.1534/genetics.120.303463] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2019] [Accepted: 08/15/2020] [Indexed: 12/16/2022] Open
Abstract
Recent advances in DNA sequencing techniques have made it possible to monitor genomes in great detail over time. This improvement provides an opportunity for us to study natural selection based on time serial samples of genomes while accounting for genetic recombination effect and local linkage information. Such time series genomic data allow for more accurate estimation of population genetic parameters and hypothesis testing on the recent action of natural selection. In this work, we develop a novel Bayesian statistical framework for inferring natural selection at a pair of linked loci by capitalising on the temporal aspect of DNA data with the additional flexibility of modeling the sampled chromosomes that contain unknown alleles. Our approach is built on a hidden Markov model where the underlying process is a two-locus Wright-Fisher diffusion with selection, which enables us to explicitly model genetic recombination and local linkage. The posterior probability distribution for selection coefficients is computed by applying the particle marginal Metropolis-Hastings algorithm, which allows us to efficiently calculate the likelihood. We evaluate the performance of our Bayesian inference procedure through extensive simulations, showing that our approach can deliver accurate estimates of selection coefficients, and the addition of genetic recombination and local linkage brings about significant improvement in the inference of natural selection. We also illustrate the utility of our method on real data with an application to ancient DNA data associated with white spotting patterns in horses.
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Affiliation(s)
- Zhangyi He
- School of Mathematics, University of Bristol, BS8 1UG, United Kingdom
| | - Xiaoyang Dai
- School of Biological Sciences, University of Bristol, BS8 1TQ, United Kingdom
| | - Mark Beaumont
- School of Biological Sciences, University of Bristol, BS8 1TQ, United Kingdom
| | - Feng Yu
- School of Mathematics, University of Bristol, BS8 1UG, United Kingdom
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27
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Wu MY, Low GW, Forcina G, van Grouw H, Lee BPYH, Oh RRY, Rheindt FE. Historic and modern genomes unveil a domestic introgression gradient in a wild red junglefowl population. Evol Appl 2020; 13:2300-2315. [PMID: 33005225 PMCID: PMC7513718 DOI: 10.1111/eva.13023] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2019] [Revised: 04/27/2020] [Accepted: 04/29/2020] [Indexed: 01/08/2023] Open
Abstract
The red junglefowl Gallus gallus is the ancestor of the domestic chicken and arguably the most important bird species on Earth. Continual gene flow between domestic and wild populations has compromised its gene pool, especially since the last century when human encroachment and habitat loss would have led to increased contact opportunities. We present the first combined genomic and morphological admixture assessment of a native population of red junglefowl, sampled from recolonized parts of its former range in Singapore, partly using whole genomes resequenced from dozens of individuals. Crucially, this population was genomically anchored to museum samples from adjacent Peninsular Malaysia collected ~110-150 years ago to infer the magnitude of modern domestic introgression across individuals. We detected a strong feral-wild genomic continuum with varying levels of domestic introgression in different subpopulations across Singapore. Using a trait scoring scheme, we determined morphological thresholds that can be used by conservation managers to successfully identify individuals with low levels of domestic introgression, and selected traits that were particularly useful for predicting domesticity in genomic profiles. Our study underscores the utility of combined genomic and morphological approaches in population management and suggests a way forward to safeguard the allelic integrity of wild red junglefowl in perpetuity.
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Affiliation(s)
- Meng Yue Wu
- Department of Biological Sciences National University of Singapore Singapore Singapore
| | - Gabriel Weijie Low
- Department of Biological Sciences National University of Singapore Singapore Singapore
- School of Biological Sciences Monash University Clayton Victoria Australia
| | - Giovanni Forcina
- Department of Biological Sciences National University of Singapore Singapore Singapore
- CIBIO/InBIO Centro de Investigação em Biodiversidade e Recursos Genéticos Universidade do Porto Vairão Portugal
| | - Hein van Grouw
- Bird Group Department of Life Sciences Natural History Museum Herts UK
| | - Benjamin P Y-H Lee
- Wildlife Management Research Wildlife Management Division National Parks Board Singapore Singapore
| | - Rachel Rui Ying Oh
- Centre of Urban Greenery and Ecology National Parks Board Singapore Singapore
- School of Biological Sciences Centre for Biodiversity and Conservation Sciences University of Queensland Brisbane Queensland Australia
| | - Frank E Rheindt
- Department of Biological Sciences National University of Singapore Singapore Singapore
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28
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Le Meillour L, Zirah S, Zazzo A, Cersoy S, Détroit F, Imalwa E, Lebon M, Nankela A, Tombret O, Pleurdeau D, Lesur J. Palaeoproteomics gives new insight into early southern African pastoralism. Sci Rep 2020; 10:14427. [PMID: 32879376 PMCID: PMC7468255 DOI: 10.1038/s41598-020-71374-3] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2020] [Accepted: 08/03/2020] [Indexed: 01/22/2023] Open
Abstract
The advent of domestication is a major step that transformed the subsistence strategies of past human societies. In Africa, domestic caprines (sheep and goat) were introduced in the north-eastern part of the continent from the Near East more than 9000 years ago. However, their diffusion southwards was slow. They are thought to have made their first appearance in the southern part of the continent ca. 2000 years ago, at a few Later Stone Age sites, including Leopard Cave (Erongo region, Namibia), which provided the oldest directly dated remains assigned to sheep or goat on the basis of morphology of bones and teeth. However, similarities in morphology, not only between these two domesticated caprine species, but also between them and the small wild antelopes, raised questions about the morphological species attribution of these remains. Additionally, the high fragmentation of the site's osteological remains makes it difficult to achieve species-level taxonomic identification by comparative anatomy. In this paper, we report molecular species identification of the Leopard Cave remains using palaeoproteomics, a method that uses protein markers in bone and tooth collagen to achieve taxonomic identification of archaeological remains. We also report new direct radiocarbon dates. Wild antelope remains from museum collections were used to enrich the available protein record and propose de novo type I collagen sequences. Our results demonstrate that the remains morphologically described as domesticates actually belong to a wild antelope species and that domestic caprines first appeared at Leopard Cave 1500 years later than previously thought. This study illustrates that the use of palaeoproteomics coupled with direct radiocarbon dates is particularly suited to complement classic zooarchaeological studies, in this case concerning the arrival of the first herding practices in arid environments.
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Affiliation(s)
- Louise Le Meillour
- UMR 7209 Archéozoologie, Archéobotanique: Sociétés, Pratiques et Environnements (AASPE), Muséum national d'Histoire naturelle, CNRS, 55 rue Buffon, 75005, Paris, France.
- UMR 7245 Molécules de Communication et Adaptations des Microorganismes (MCAM), Muséum national d'Histoire naturelle, CNRS, 63 rue Buffon, 75005, Paris, France.
| | - Séverine Zirah
- UMR 7245 Molécules de Communication et Adaptations des Microorganismes (MCAM), Muséum national d'Histoire naturelle, CNRS, 63 rue Buffon, 75005, Paris, France
| | - Antoine Zazzo
- UMR 7209 Archéozoologie, Archéobotanique: Sociétés, Pratiques et Environnements (AASPE), Muséum national d'Histoire naturelle, CNRS, 55 rue Buffon, 75005, Paris, France
| | - Sophie Cersoy
- USR 3224 Centre de Recherche sur la Conservation (CRCC), Muséum national d'Histoire naturelle, CNRS, Ministère de la Culture, 36 rue Geoffroy Saint Hilaire, 75005, Paris, France
| | - Florent Détroit
- UMR 7194 Histoire naturelle de l'Homme Préhistorique (HNHP), Muséum national d'Histoire naturelle, CNRS, UPVD, 1 rue René Panhard, 75013, Paris, France
| | | | - Matthieu Lebon
- UMR 7194 Histoire naturelle de l'Homme Préhistorique (HNHP), Muséum national d'Histoire naturelle, CNRS, UPVD, 1 rue René Panhard, 75013, Paris, France
| | - Alma Nankela
- National Heritage Council of Namibia, 153 Dr. AB May and Rev. Michael Scott streets, Ausspannplatz, Windhoek, Namibia
| | - Olivier Tombret
- UMR 7209 Archéozoologie, Archéobotanique: Sociétés, Pratiques et Environnements (AASPE), Muséum national d'Histoire naturelle, CNRS, 55 rue Buffon, 75005, Paris, France
- UMR 7194 Histoire naturelle de l'Homme Préhistorique (HNHP), Muséum national d'Histoire naturelle, CNRS, UPVD, 1 rue René Panhard, 75013, Paris, France
| | - David Pleurdeau
- UMR 7194 Histoire naturelle de l'Homme Préhistorique (HNHP), Muséum national d'Histoire naturelle, CNRS, UPVD, 1 rue René Panhard, 75013, Paris, France
| | - Joséphine Lesur
- UMR 7209 Archéozoologie, Archéobotanique: Sociétés, Pratiques et Environnements (AASPE), Muséum national d'Histoire naturelle, CNRS, 55 rue Buffon, 75005, Paris, France.
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29
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Biodeteriogens Characterization and Molecular Analyses of Diverse Funeral Accessories from XVII Century. APPLIED SCIENCES-BASEL 2020. [DOI: 10.3390/app10165451] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
A historical crypt offers us a particular view of the conditions of some buried materials (in this case textiles) and the various biogenic phenomena to which they were subjected over the centuries. In addition, significant knowledge can come by studying the DNA of buried objects which allows the recognition of materials, but also to reveal some practice of the funeral ceremony. In this study, the deteriorating microbial communities colonizing various funeral textile items were identified and characterized using microscopic observation, cultivation, polymerase chain reaction (PCR) and sequencing, hydrolytic tests; and culture-independent analysis (high-throughput sequencing, MinION platform). Different PCR assays and consequent sequencing of amplicons were employed to recognize the animal origin of bodice reinforcements and the type of plant used to embellish the young girl. The analysis of ancient DNA (aDNA from animal and plant) was also completed by the application of high-throughput sequencing through Illumina platform. The combination of all these techniques permitted the identification of a complex microbiota composed by dangerous degradative microorganisms able to hydrolyze various organic substrates such as fibroin, keratin, and cellulose. Bacteria responsible for metal corrosion and bio-mineralization, and entomopathogenic and phytopathogenic fungi. The analysis of aDNA identified the animal component used in bodice manufacturing, the plant utilized as ornament and probably the season of this fatal event.
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30
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Wagner JK, Colwell C, Claw KG, Stone AC, Bolnick DA, Hawks J, Brothers KB, Garrison NA. Fostering Responsible Research on Ancient DNA. Am J Hum Genet 2020; 107:183-195. [PMID: 32763189 PMCID: PMC7413888 DOI: 10.1016/j.ajhg.2020.06.017] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Anticipating and addressing the social implications of scientific work is a fundamental responsibility of all scientists. However, expectations for ethically sound practices can evolve over time as the implications of science come to be better understood. Contemporary researchers who work with ancient human remains, including those who conduct ancient DNA research, face precisely this challenge as it becomes clear that practices such as community engagement are needed to address the important social implications of this work. To foster and promote ethical engagement between researchers and communities, we offer five practical recommendations for ancient DNA researchers: (1) formally consult with communities; (2) address cultural and ethical considerations; (3) engage communities and support capacity building; (4) develop plans to report results and manage data; and (5) develop plans for long-term responsibility and stewardship. Ultimately, every member of a research team has an important role in fostering ethical research on ancient DNA.
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Affiliation(s)
- Jennifer K Wagner
- Professional Practice and Social Implications Committee (formerly the Social Issues Committee), American Society of Human Genetics, Bethesda, MD 20814, USA; Responsible Ancient DNA Research Working Group, American Society of Human Genetics, Bethesda, MD 20814, USA; Center for Translational Bioethics and Health Care Policy, Geisinger, Danville, PA 17822, USA.
| | - Chip Colwell
- Responsible Ancient DNA Research Working Group, American Society of Human Genetics, Bethesda, MD 20814, USA; Department of Anthropology, Denver Museum of Nature and Science, Denver, CO 80205, USA
| | - Katrina G Claw
- Responsible Ancient DNA Research Working Group, American Society of Human Genetics, Bethesda, MD 20814, USA; Division of Biomedical Informatics and Personalized Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Anne C Stone
- Responsible Ancient DNA Research Working Group, American Society of Human Genetics, Bethesda, MD 20814, USA; School of Human Evolution and Social Change, Arizona State University, Tempe, AZ 85287, USA
| | - Deborah A Bolnick
- Responsible Ancient DNA Research Working Group, American Society of Human Genetics, Bethesda, MD 20814, USA; Department of Anthropology, University of Connecticut, Storrs, CT 06269, USA; Institute for Systems Genomics, University of Connecticut, Storrs, CT 06269, USA
| | - John Hawks
- Responsible Ancient DNA Research Working Group, American Society of Human Genetics, Bethesda, MD 20814, USA; Department of Anthropology, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Kyle B Brothers
- Professional Practice and Social Implications Committee (formerly the Social Issues Committee), American Society of Human Genetics, Bethesda, MD 20814, USA; Responsible Ancient DNA Research Working Group, American Society of Human Genetics, Bethesda, MD 20814, USA; Department of Pediatrics, University of Louisville, Louisville, KY 40202, USA
| | - Nanibaa' A Garrison
- Professional Practice and Social Implications Committee (formerly the Social Issues Committee), American Society of Human Genetics, Bethesda, MD 20814, USA; Responsible Ancient DNA Research Working Group, American Society of Human Genetics, Bethesda, MD 20814, USA; Institute for Society and Genetics, University of California, Los Angeles, Los Angeles, CA 90095, USA; Institute for Precision Health, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA; Division of General Internal Medicine and Health Services Research, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA
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31
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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: 15] [Impact Index Per Article: 3.8] [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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Machine learning-based analyses support the existence of species complexes for Strongyloides fuelleborni and Strongyloides stercoralis. Parasitology 2020; 147:1184-1195. [PMID: 32539880 PMCID: PMC7443747 DOI: 10.1017/s0031182020000979] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
Human strongyloidiasis is a serious disease mostly attributable to Strongyloides stercoralis and to a lesser extent Strongyloides fuelleborni, a parasite mainly of non-human primates. The role of animals as reservoirs of human-infecting Strongyloides is ill-defined, and whether dogs are a source of human infection is debated. Published multi-locus sequence typing (MLST) studies attempt to elucidate relationships between Strongyloides genotypes, hosts, and distributions, but typically examine relatively few worms, making it difficult to identify population-level trends. Combining MLST data from multiple studies is often impractical because they examine different combinations of loci, eliminating phylogeny as a means of examining these data collectively unless hundreds of specimens are excluded. A recently-described machine learning approach that facilitates clustering of MLST data may offer a solution, even for datasets that include specimens sequenced at different combinations of loci. By clustering various MLST datasets as one using this procedure, we sought to uncover associations among genotype, geography, and hosts that remained elusive when examining datasets individually. Multiple datasets comprising hundreds of S. stercoralis and S. fuelleborni individuals were combined and clustered. Our results suggest that the commonly proposed 'two lineage' population structure of S. stercoralis (where lineage A infects humans and dogs, lineage B only dogs) is an over-simplification. Instead, S. stercoralis seemingly represents a species complex, including two distinct populations over-represented in dogs, and other populations vastly more common in humans. A distinction between African and Asian S. fuelleborni is also supported here, emphasizing the need for further resolving these taxonomic relationships through modern investigations.
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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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34
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Ahmad HI, Ahmad MJ, Jabbir F, Ahmar S, Ahmad N, Elokil AA, Chen J. The Domestication Makeup: Evolution, Survival, and Challenges. Front Ecol Evol 2020. [DOI: 10.3389/fevo.2020.00103] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
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35
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Williams AC, Hill LJ. The 4 D's of Pellagra and Progress. Int J Tryptophan Res 2020; 13:1178646920910159. [PMID: 32327922 PMCID: PMC7163231 DOI: 10.1177/1178646920910159] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2019] [Accepted: 02/06/2020] [Indexed: 12/12/2022] Open
Abstract
Nicotinamide homeostasis is a candidate common denominator to explain smooth transitions, whether demographic, epidemiological or economic. This 'NAD world', dependent on hydrogen-based energy, is not widely recognised as it is neither measured nor viewed from a sufficiently multi-genomic or historical perspective. Reviewing the importance of meat and nicotinamide balances during our co-evolution, recent history suggests that populations only modernise and age well with low fertility on a suitably balanced diet. Imbalances on the low meat side lead to an excess of infectious disease, short lives and boom-bust demographics. On the high side, meat has led to an excess of degenerative, allergic and metabolic disease and low fertility. A 'Goldilocks' diet derived from mixed and sustainable farming (preserving the topsoil) allows for high intellectual capital, height and good health with controlled population growth resulting in economic growth and prosperity. Implementing meat equity worldwide could lead to progress for future generations on 'spaceship' earth by establishing control over population quality, thermostat and biodiversity, if it is not already too late.
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Affiliation(s)
- Adrian C Williams
- Department of Neurology, University
Hospitals Birmingham NHS Foundation Trust, Birmingham, UK
| | - Lisa J Hill
- School of Biomedical Sciences, Institute
of Clinical Sciences, University of Birmingham, Birmingham, UK
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36
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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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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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38
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Sazmand A, Joachim A, Otranto D. Zoonotic parasites of dromedary camels: so important, so ignored. Parasit Vectors 2019; 12:610. [PMID: 31881926 PMCID: PMC6935189 DOI: 10.1186/s13071-019-3863-3] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2019] [Accepted: 12/19/2019] [Indexed: 01/14/2023] Open
Abstract
With a global population of about 35 million in 47 countries, dromedary camels play a crucial role in the economy of many marginal, desert areas of the world where they survive under harsh conditions. Nonetheless, there is scarce knowledge regarding camels' parasite fauna which can reduce their milk and meat productions. In addition, only scattered information is available about zoonotic parasites transmitted to humans via contamination (e.g. Cryptosporidium spp., Giardia duodenalis, Balantidium coli, Blastocystis spp. and Enterocytozoon bieneusi), as foodborne infections (e.g. Toxoplasma gondii, Trichinella spp. and Linguatula serrata) or by arthropod vectors (Trypanosoma spp.). Herein, we draw attention of the scientific community and health policy-making organizations to the role camels play in the epidemiology of parasitic zoonotic diseases also in the view of an increase in their farming in desert areas worldwide.
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Affiliation(s)
- Alireza Sazmand
- Department of Pathobiology, Faculty of Veterinary Science, Bu-Ali Sina University, Hamedan, 6517658978 Iran
| | - Anja Joachim
- Institute of Parasitology, Department of Pathobiology, University of Veterinary Medicine Vienna, Veterinaerplatz 1, 1210 Vienna, Austria
| | - Domenico Otranto
- Department of Pathobiology, Faculty of Veterinary Science, Bu-Ali Sina University, Hamedan, 6517658978 Iran
- Department of Veterinary Medicine, University of Bari, Str. prov. per Casamassima km 3, 70010 Valenzano, Bari, Italy
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39
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McHugo GP, Dover MJ, MacHugh DE. Unlocking the origins and biology of domestic animals using ancient DNA and paleogenomics. BMC Biol 2019; 17:98. [PMID: 31791340 PMCID: PMC6889691 DOI: 10.1186/s12915-019-0724-7] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2019] [Accepted: 11/13/2019] [Indexed: 12/13/2022] Open
Abstract
Animal domestication has fascinated biologists since Charles Darwin first drew the parallel between evolution via natural selection and human-mediated breeding of livestock and companion animals. In this review we show how studies of ancient DNA from domestic animals and their wild progenitors and congeners have shed new light on the genetic origins of domesticates, and on the process of domestication itself. High-resolution paleogenomic data sets now provide unprecedented opportunities to explore the development of animal agriculture across the world. In addition, functional population genomics studies of domestic and wild animals can deliver comparative information useful for understanding recent human evolution.
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Affiliation(s)
- Gillian P McHugo
- Animal Genomics Laboratory, UCD School of Agriculture and Food Science, University College Dublin, Dublin, D04 V1W8, Ireland
| | - Michael J Dover
- Animal Genomics Laboratory, UCD School of Agriculture and Food Science, University College Dublin, Dublin, D04 V1W8, Ireland
| | - David E MacHugh
- Animal Genomics Laboratory, UCD School of Agriculture and Food Science, University College Dublin, Dublin, D04 V1W8, Ireland. .,UCD Conway Institute of Biomolecular and Biomedical Research, University College Dublin, Dublin, D04 V1W8, Ireland.
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40
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Gering E, Incorvaia D, Henriksen R, Conner J, Getty T, Wright D. Getting Back to Nature: Feralization in Animals and Plants. Trends Ecol Evol 2019; 34:1137-1151. [PMID: 31488326 PMCID: PMC7479514 DOI: 10.1016/j.tree.2019.07.018] [Citation(s) in RCA: 40] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2019] [Revised: 07/23/2019] [Accepted: 07/25/2019] [Indexed: 11/24/2022]
Abstract
Formerly domesticated organisms and artificially selected genes often escape controlled cultivation, but their subsequent evolution is not well studied. In this review, we examine plant and animal feralization through an evolutionary lens, including how natural selection, artificial selection, and gene flow shape feral genomes, traits, and fitness. Available evidence shows that feralization is not a mere reversal of domestication. Instead, it is shaped by the varied and complex histories of feral populations, and by novel selection pressures. To stimulate further insight we outline several future directions. These include testing how 'domestication genes' act in wild settings, studying the brains and behaviors of feral animals, and comparative analyses of feral populations and taxa. This work offers feasible and exciting research opportunities with both theoretical and practical applications.
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Affiliation(s)
- Eben Gering
- Department of Integrative Biology and Ecology, Evolutionary Biology, and Behavior Program, Michigan State University, East Lansing, MI, USA; Department of Biological Sciences, Halmos College of Natural Sciences and Oceanography, Nova Southeastern University, Davie, FL, USA.
| | - Darren Incorvaia
- Department of Integrative Biology and Ecology, Evolutionary Biology, and Behavior Program, Michigan State University, East Lansing, MI, USA
| | - Rie Henriksen
- IIFM Biology and AVIAN Behavioural Genomics and Physiology Group, Linköping University, Linköping, Sweden
| | - Jeffrey Conner
- Department of Integrative Biology and Ecology, Evolutionary Biology, and Behavior Program, Michigan State University, East Lansing, MI, USA; Kellogg Biological Station and Dept. of Plant Biology, Michigan State University, Hickory Corners, MI, USA
| | - Thomas Getty
- Department of Integrative Biology and Ecology, Evolutionary Biology, and Behavior Program, Michigan State University, East Lansing, MI, USA
| | - Dominic Wright
- IIFM Biology and AVIAN Behavioural Genomics and Physiology Group, Linköping University, Linköping, Sweden
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41
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Trumble BC, Finch CE. THE EXPOSOME IN HUMAN EVOLUTION: FROM DUST TO DIESEL. THE QUARTERLY REVIEW OF BIOLOGY 2019; 94:333-394. [PMID: 32269391 PMCID: PMC7141577 DOI: 10.1086/706768] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
Global exposures to air pollution and cigarette smoke are novel in human evolutionary history and are associated with about 16 million premature deaths per year. We investigate the history of the human exposome for relationships between novel environmental toxins and genetic changes during human evolution in six phases. Phase I: With increased walking on savannas, early human ancestors inhaled crustal dust, fecal aerosols, and spores; carrion scavenging introduced new infectious pathogens. Phase II: Domestic fire exposed early Homo to novel toxins from smoke and cooking. Phases III and IV: Neolithic to preindustrial Homo sapiens incurred infectious pathogens from domestic animals and dense communities with limited sanitation. Phase V: Industrialization introduced novel toxins from fossil fuels, industrial chemicals, and tobacco at the same time infectious pathogens were diminishing. Thereby, pathogen-driven causes of mortality were replaced by chronic diseases driven by sterile inflammogens, exogenous and endogenous. Phase VI: Considers future health during global warming with increased air pollution and infections. We hypothesize that adaptation to some ancient toxins persists in genetic variations associated with inflammation and longevity.
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Affiliation(s)
- Benjamin C Trumble
- School of Human Evolution & Social Change and Center for Evolution and Medicine, Arizona State University Tempe, Arizona 85287 USA
| | - Caleb E Finch
- Leonard Davis School of Gerontology and Dornsife College, University of Southern California Los Angeles, California 90089-0191 USA
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42
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McHugo GP, Browett S, Randhawa IAS, Howard DJ, Mullen MP, Richardson IW, Park SDE, Magee DA, Scraggs E, Dover MJ, Correia CN, Hanrahan JP, MacHugh DE. A Population Genomics Analysis of the Native Irish Galway Sheep Breed. Front Genet 2019; 10:927. [PMID: 31649720 PMCID: PMC6792165 DOI: 10.3389/fgene.2019.00927] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2019] [Accepted: 09/05/2019] [Indexed: 12/24/2022] Open
Abstract
The Galway sheep population is the only native Irish sheep breed and this livestock genetic resource is currently categorised as 'at-risk'. In the present study, comparative population genomics analyses of Galway sheep and other sheep populations of European origin were used to investigate the microevolution and recent genetic history of the breed. These analyses support the hypothesis that British Leicester sheep were used in the formation of the Galway. When compared to conventional and endangered breeds, the Galway breed was intermediate in effective population size, genomic inbreeding and runs of homozygosity. This indicates that, although the Galway breed is declining, it is still relatively genetically diverse and that conservation and management plans informed by genomic information may aid its recovery. The Galway breed also exhibited distinct genomic signatures of artificial or natural selection when compared to other breeds, which highlighted candidate genes that may be involved in production and health traits.
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Affiliation(s)
- Gillian P McHugo
- Animal Genomics Laboratory, UCD School of Agriculture and Food Science, University College Dublin, Dublin, Ireland
| | - Sam Browett
- Animal Genomics Laboratory, UCD School of Agriculture and Food Science, University College Dublin, Dublin, Ireland
| | - Imtiaz A S Randhawa
- Sydney School of Veterinary Science, University of Sydney, Camden, NSW, Australia
| | - Dawn J Howard
- Animal and Grassland Research and Innovation Centre, Athenry, Ireland
| | - Michael P Mullen
- Animal and Grassland Research and Innovation Centre, Athenry, Ireland
| | | | | | - David A Magee
- Animal Genomics Laboratory, UCD School of Agriculture and Food Science, University College Dublin, Dublin, Ireland
| | - Erik Scraggs
- Animal Genomics Laboratory, UCD School of Agriculture and Food Science, University College Dublin, Dublin, Ireland
| | - Michael J Dover
- Animal Genomics Laboratory, UCD School of Agriculture and Food Science, University College Dublin, Dublin, Ireland
| | - Carolina N Correia
- Animal Genomics Laboratory, UCD School of Agriculture and Food Science, University College Dublin, Dublin, Ireland
| | - James P Hanrahan
- Animal and Grassland Research and Innovation Centre, Athenry, Ireland
| | - David E MacHugh
- Animal Genomics Laboratory, UCD School of Agriculture and Food Science, University College Dublin, Dublin, Ireland.,UCD Conway Institute of Biomolecular and Biomedical Research, University College Dublin, Dublin, Ireland
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43
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Pálsdóttir AH, Bläuer A, Rannamäe E, Boessenkool S, Hallsson JH. Not a limitless resource: ethics and guidelines for destructive sampling of archaeofaunal remains. ROYAL SOCIETY OPEN SCIENCE 2019; 6:191059. [PMID: 31824712 PMCID: PMC6837180 DOI: 10.1098/rsos.191059] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/19/2019] [Accepted: 09/09/2019] [Indexed: 05/04/2023]
Abstract
With the advent of ancient DNA, as well as other methods such as isotope analysis, destructive sampling of archaeofaunal remains has increased much faster than the effort to collect and curate them. While there has been considerable discussion regarding the ethics of destructive sampling and analysis of human remains, this dialogue has not extended to archaeofaunal material. Here we address this gap and discuss the ethical challenges surrounding destructive sampling of materials from archaeofaunal collections. We suggest ways of mitigating the negative aspects of destructive sampling and present step-by-step guidelines aimed at relevant stakeholders, including scientists, holding institutions and scientific journals. Our suggestions are in most cases easily implemented without significant increases in project costs, but with clear long-term benefits in the preservation and use of zooarchaeological material.
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Affiliation(s)
- Albína Hulda Pálsdóttir
- Centre for Ecological and Evolutionary Synthesis (CEES), Department of Biosciences, University of Oslo, Postbox 1066, Blindern, 0316 Oslo, Norway
- Faculty of Agricultural and Environmental Sciences, The Agricultural University of Iceland, Keldnaholti - Árleyni 22, 112 Reykjavík, Iceland
- Author for correspondence: Albína Hulda Pálsdóttir e-mail:
| | - Auli Bläuer
- Natural Resources Institute Finland (Luke), Itäinen Pitkäkatu 4 A, 20520 Turku, Finland
- University of Turku, Archaeology, Akatemiankatu 1, FI-20500 Turku, Finland
| | - Eve Rannamäe
- Natural Resources Institute Finland (Luke), Itäinen Pitkäkatu 4 A, 20520 Turku, Finland
- Institute of History and Archaeology, University of Tartu, Jakobi 2, 51005 Tartu, Estonia
| | - Sanne Boessenkool
- Centre for Ecological and Evolutionary Synthesis (CEES), Department of Biosciences, University of Oslo, Postbox 1066, Blindern, 0316 Oslo, Norway
| | - Jón Hallsteinn Hallsson
- Faculty of Agricultural and Environmental Sciences, The Agricultural University of Iceland, Keldnaholti - Árleyni 22, 112 Reykjavík, Iceland
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44
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Cornille A, Antolín F, Garcia E, Vernesi C, Fietta A, Brinkkemper O, Kirleis W, Schlumbaum A, Roldán-Ruiz I. A Multifaceted Overview of Apple Tree Domestication. TRENDS IN PLANT SCIENCE 2019; 24:770-782. [PMID: 31296442 DOI: 10.1016/j.tplants.2019.05.007] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/03/2019] [Revised: 05/15/2019] [Accepted: 05/20/2019] [Indexed: 05/19/2023]
Abstract
The apple is an iconic tree and a major fruit crop worldwide. It is also a model species for the study of the evolutionary processes and genomic basis underlying the domestication of clonally propagated perennial crops. Multidisciplinary approaches from across Eurasia have documented the pace and process of cultivation of this remarkable crop. While population genetics and genomics have revealed the overall domestication history of apple across Eurasia, untangling the evolutionary processes involved, archeobotany has helped to document the transition from gathering and using apples to the practice of cultivation. Further studies integrating archeogenetic and archeogenomic approaches will bring new insights about key traits involved in apple domestication. Such knowledge has potential to boost innovation in present-day apple breeding.
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Affiliation(s)
- Amandine Cornille
- Génétique Quantitative et Evolution- Le Moulon, INRA, Univ. Paris-Sud, CNRS, AgroParisTech, Université Paris-Saclay, Gif-sur-Yvette, France.
| | - Ferran Antolín
- Integrative Prehistory and Archeological Science (IPNA/IPAS), Department of Environmental Sciences, University of Basel, Spalenring 145, 4055 Basel, Switzerland
| | - Elena Garcia
- Department of Horticulture, University of Arkansas, Fayetteville, AR, USA
| | - Cristiano Vernesi
- Department of Biodiversity and Molecular Ecology, Research and Innovation Centre - Fondazione Edmund Mach, via Edmund Mach 1, 38010 San Michele all'Adige, TN, Italy
| | - Alice Fietta
- Department of Biodiversity and Molecular Ecology, Research and Innovation Centre - Fondazione Edmund Mach, via Edmund Mach 1, 38010 San Michele all'Adige, TN, Italy
| | - Otto Brinkkemper
- Cultural Heritage Agency, PO Box 1600, 3800 BP Amersfoort, The Netherlands
| | - Wiebke Kirleis
- Institute for Prehistoric and Protohistoric Archeology/Graduate School Human Development in Landscapes, Christian-Albrechts-University Kiel, Kiel, Germany
| | - Angela Schlumbaum
- Integrative Prehistory and Archeological Science (IPNA/IPAS), Department of Environmental Sciences, University of Basel, Spalenring 145, 4055 Basel, Switzerland
| | - Isabel Roldán-Ruiz
- Flanders Research Institute for Agriculture, Fisheries, and Food (ILVO), Plant Sciences Unit, Caritasstraat 39, 9090 Melle, Belgium; Ghent University, Faculty of Sciences, Department of Plant Biotechnology and Bioinformatics, Technologiepark 71, 9052 Ghent, Belgium
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45
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Cesarani A, Sechi T, Gaspa G, Usai MG, Sorbolini S, Macciotta NPP, Carta A. Investigation of genetic diversity and selection signatures between Sarda and Sardinian Ancestral black, two related sheep breeds with evident morphological differences. Small Rumin Res 2019. [DOI: 10.1016/j.smallrumres.2019.06.014] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
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46
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Lan TM, Lin Y, Njaramba-Ngatia J, Guo XS, Li RG, Li HM, Kumar-Sahu S, Wang X, Yang XJ, Guo HB, Xu WH, Kristiansen K, Liu H, Xu YC. Improving Species Identification of Ancient Mammals Based on Next-Generation Sequencing Data. Genes (Basel) 2019; 10:E509. [PMID: 31284503 PMCID: PMC6679096 DOI: 10.3390/genes10070509] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2019] [Revised: 06/26/2019] [Accepted: 07/03/2019] [Indexed: 11/16/2022] Open
Abstract
The taxonomical identification merely based on morphology is often difficult for ancient remains. Therefore, universal or specific PCR amplification followed by sequencing and BLAST (basic local alignment search tool) search has become the most frequently used genetic-based method for the species identification of biological samples, including ancient remains. However, it is challenging for these methods to process extremely ancient samples with severe DNA fragmentation and contamination. Here, we applied whole-genome sequencing data from 12 ancient samples with ages ranging from 2.7 to 700 kya to compare different mapping algorithms, and tested different reference databases, mapping similarities and query coverage to explore the best method and mapping parameters that can improve the accuracy of ancient mammal species identification. The selected method and parameters were tested using 152 ancient samples, and 150 of the samples were successfully identified. We further screened the BLAST-based mapping results according to the deamination characteristics of ancient DNA to improve the ability of ancient species identification. Our findings demonstrate a marked improvement to the normal procedures used for ancient species identification, which was achieved through defining the mapping and filtering guidelines to identify true ancient DNA sequences. The guidelines summarized in this study could be valuable in archaeology, paleontology, evolution, and forensic science. For the convenience of the scientific community, we wrote a software script with Perl, called AncSid, which is made available on GitHub.
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Affiliation(s)
- Tian Ming Lan
- Laboratory of Genomics and Molecular Biomedicine, Department of Biology, University of Copenhagen, DK-2100 Copenhagen, Denmark
- BGI-Shenzhen, Shenzhen 518083, China
| | - Yu Lin
- BGI-Shenzhen, Shenzhen 518083, China
- China National GeneBank, BGI-Shenzhen, Shenzhen 518083, China
| | | | | | - Ren Gui Li
- Key Laboratory of State Forestry and Grassland Administration (State Park Administration) on Conservation Biology of Rare Animals in The Giant Panda National Park, China Conservation and Research Center of Giant Panda, Dujiangyan 611830, China
| | - Hai Meng Li
- BGI-Shenzhen, Shenzhen 518083, China
- School of Future Technology, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Sunil Kumar-Sahu
- BGI-Shenzhen, Shenzhen 518083, China
- China National GeneBank, BGI-Shenzhen, Shenzhen 518083, China
| | - Xie Wang
- China National GeneBank, BGI-Shenzhen, Shenzhen 518083, China
| | - Xiu Juan Yang
- Heilongjiang Provincial Museum, Harbin 150001, China
| | - Hua Bing Guo
- Forest Inventory and Planning Institute of Jilin Province, Changchun 130022, China
| | - Wen Hao Xu
- College of Informatics, Huazhong Agricultural University, Wuhan 430070, China
| | - Karsten Kristiansen
- Laboratory of Genomics and Molecular Biomedicine, Department of Biology, University of Copenhagen, DK-2100 Copenhagen, Denmark
- BGI-Shenzhen, Shenzhen 518083, China
| | - Huan Liu
- BGI-Shenzhen, Shenzhen 518083, China.
- State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen 518083, China.
| | - Yan Chun Xu
- Key Laboratory of State Forestry and Grassland Administration (State Park Administration) on Conservation Biology of Rare Animals in The Giant Panda National Park, China Conservation and Research Center of Giant Panda, Dujiangyan 611830, China.
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Rexroad C, Vallet J, Matukumalli LK, Reecy J, Bickhart D, Blackburn H, Boggess M, Cheng H, Clutter A, Cockett N, Ernst C, Fulton JE, Liu J, Lunney J, Neibergs H, Purcell C, Smith TPL, Sonstegard T, Taylor J, Telugu B, Eenennaam AV, Tassell CPV, Wells K. Genome to Phenome: Improving Animal Health, Production, and Well-Being - A New USDA Blueprint for Animal Genome Research 2018-2027. Front Genet 2019; 10:327. [PMID: 31156693 PMCID: PMC6532451 DOI: 10.3389/fgene.2019.00327] [Citation(s) in RCA: 73] [Impact Index Per Article: 14.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2018] [Accepted: 03/26/2019] [Indexed: 11/15/2022] Open
Abstract
In 2008, a consortium led by the Agricultural Research Service (ARS) and the National Institute for Food and Agriculture (NIFA) published the "Blueprint for USDA Efforts in Agricultural Animal Genomics 2008-2017," which served as a guiding document for research and funding in animal genomics. In the decade that followed, many of the goals set forth in the blueprint were accomplished. However, several other goals require further research. In addition, new topics not covered in the original blueprint, which are the result of emerging technologies, require exploration. To develop a new, updated blueprint, ARS and NIFA, along with scientists in the animal genomics field, convened a workshop titled "Genome to Phenome: A USDA Blueprint for Improving Animal Production" in November 2017, and these discussions were used to develop new goals for the next decade. Like the previous blueprint, these goals are grouped into the broad categories "Science to Practice," "Discovery Science," and "Infrastructure." New goals for characterizing the microbiome, enhancing the use of gene editing and other biotechnologies, and preserving genetic diversity are included in the new blueprint, along with updated goals within many genome research topics described in the previous blueprint. The updated blueprint that follows describes the vision, current state of the art, the research needed to advance the field, expected deliverables, and partnerships needed for each animal genomics research topic. Accomplishment of the goals described in the blueprint will significantly increase the ability to meet the demands for animal products by an increasing world population within the next decade.
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Affiliation(s)
- Caird Rexroad
- Office of National Programs, Agricultural Research Service, United States Department of Agriculture, Beltsville, MD, United States
| | - Jeffrey Vallet
- Office of National Programs, Agricultural Research Service, United States Department of Agriculture, Beltsville, MD, United States
| | - Lakshmi Kumar Matukumalli
- National Institute of Food and Agriculture, United States Department of Agriculture, Washington, DC, United States
| | - James Reecy
- Department of Animal Science, Iowa State University, Ames, IA, United States
| | - Derek Bickhart
- Dairy Forage Research Center, Agricultural Research Service, United States Department of Agriculture, Madison, WI, United States
| | - Harvey Blackburn
- National Animal Germplasm Program, Agricultural Research Service, United States Department of Agriculture, Fort Collins, CO, United States
| | - Mark Boggess
- Meat Animal Research Center, Agricultural Research Service, United States Department of Agriculture, Clay Center, NE, United States
| | - Hans Cheng
- Avian Disease and Oncology Laboratory, Agricultural Research Service, United States Department of Agriculture, East Lansing, MI, United States
| | - Archie Clutter
- Agricultural Research Division, University of Nebraska-Lincoln, Lincoln, NE, United States
| | - Noelle Cockett
- President’s Office, Utah State University, Logan, UT, United States
| | - Catherine Ernst
- Department of Animal Science, Michigan State University, East Lansing, MI, United States
| | | | - John Liu
- Department of Biology, College of Arts and Sciences, Syracuse University, Syracuse, NY, United States
| | - Joan Lunney
- Animal Parasitic Diseases Laboratory, Agricultural Research Service, United States Department of Agriculture, Beltsville, MD, United States
| | - Holly Neibergs
- Department of Animal Sciences, Washington State University, Pullman, WA, United States
| | - Catherine Purcell
- Department of Commerce, National Oceanic and Atmospheric Administration, La Jolla, CA, United States
| | - Timothy P. L. Smith
- Meat Animal Research Center, Agricultural Research Service, United States Department of Agriculture, Clay Center, NE, United States
| | - Tad Sonstegard
- Acceligen, A Recombinetics Company, St. Paul, MN, United States
| | - Jerry Taylor
- Division of Animal Science, University of Missouri, Columbia, MO, United States
| | - Bhanu Telugu
- Department of Animal and Avian Sciences, University of Maryland, College Park, MD, United States
| | - Alison Van Eenennaam
- Department of Animal Science, University of California, Davis, Davis, CA, United States
| | - Curtis P. Van Tassell
- Animal Genomics and Improvement Laboratory, Agricultural Research Service, United States Department of Agriculture, Beltsville, MD, United States
| | - Kevin Wells
- Animal Genomics and Improvement Laboratory, Agricultural Research Service, United States Department of Agriculture, Beltsville, MD, United States
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48
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The Promise of Paleogenomics Beyond Our Own Species. Trends Genet 2019; 35:319-329. [PMID: 30954285 DOI: 10.1016/j.tig.2019.02.006] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2019] [Revised: 02/18/2019] [Accepted: 02/25/2019] [Indexed: 02/06/2023]
Abstract
Paleogenomics, also known as genome-wide ancient DNA analysis, is transforming our understanding of the human past, but has been much less intensively used to understand the history of other species. However, paleogenomic studies of non-human animals and plants have the potential to address an equally rich range of evolutionary, paleoecological, paleoenvironmental, and archaeological research questions. Three recent case studies of cave bears, horses, and maize provide examples of the ways that paleogenomics can be used to examine potential causes of extinctions and dynamic processes of domestication. Much more research in these areas is needed, and we conclude by highlighting key future directions.
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49
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Pongrácz P. The future of biology from a canine perspective. Biol Futur 2019; 70:89-92. [PMID: 34554423 DOI: 10.1556/019.70.2019.11] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Affiliation(s)
- Péter Pongrácz
- Department of Ethology, Eötvös Loránd University, Budapest, Hungary.
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50
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Pitt D, Sevane N, Nicolazzi EL, MacHugh DE, Park SDE, Colli L, Martinez R, Bruford MW, Orozco‐terWengel P. Domestication of cattle: Two or three events? Evol Appl 2019; 12:123-136. [PMID: 30622640 PMCID: PMC6304694 DOI: 10.1111/eva.12674] [Citation(s) in RCA: 49] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2017] [Revised: 03/19/2018] [Accepted: 06/10/2018] [Indexed: 02/06/2023] Open
Abstract
Cattle have been invaluable for the transition of human society from nomadic hunter-gatherers to sedentary farming communities throughout much of Europe, Asia and Africa since the earliest domestication of cattle more than 10,000 years ago. Although current understanding of relationships among ancestral populations remains limited, domestication of cattle is thought to have occurred on two or three occasions, giving rise to the taurine (Bos taurus) and indicine (Bos indicus) species that share the aurochs (Bos primigenius) as common ancestor ~250,000 years ago. Indicine and taurine cattle were domesticated in the Indus Valley and Fertile Crescent, respectively; however, an additional domestication event for taurine in the Western Desert of Egypt has also been proposed. We analysed medium density Illumina Bovine SNP array (~54,000 loci) data across 3,196 individuals, representing 180 taurine and indicine populations to investigate population structure within and between populations, and domestication and demographic dynamics using approximate Bayesian computation (ABC). Comparative analyses between scenarios modelling two and three domestication events consistently favour a model with only two episodes and suggest that the additional genetic variation component usually detected in African taurine cattle may be explained by hybridization with local aurochs in Africa after the domestication of taurine cattle in the Fertile Crescent. African indicine cattle exhibit high levels of shared genetic variation with Asian indicine cattle due to their recent divergence and with African taurine cattle through relatively recent gene flow. Scenarios with unidirectional or bidirectional migratory events between European taurine and Asian indicine cattle are also plausible, although further studies are needed to disentangle the complex human-mediated dispersion patterns of domestic cattle. This study therefore helps to clarify the effect of past demographic history on the genetic variation of modern cattle, providing a basis for further analyses exploring alternative migratory routes for early domestic populations.
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Affiliation(s)
- Daniel Pitt
- School of BiosciencesCardiff UniversityCardiffUK
| | | | | | - David E. MacHugh
- Animal Genomics LaboratoryUCD School of Agriculture and Food Science, UCD College of Health and Agricultural SciencesUniversity College DublinDublinIreland
- UCD Conway Institute of Biomolecular and Biomedical ResearchUniversity College DublinDublinIreland
| | | | - Licia Colli
- Istituto di Zootecnica e BioDNA Centro di Ricerca sulla Biodiversità e sul DNA AnticoUniversità Cattolica del S. Cuore di PiacenzaPiacenzaItaly
| | - Rodrigo Martinez
- Corporación Colombiana De Investigación Agropecuaria (Corpoica)Centro de investigaciones TibaitatáBogotáColombia
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