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Konopiński MK, Fijarczyk AM, Biedrzycka A. Complex patterns shape immune genes diversity during invasion of common raccoon in Europe - Selection in action despite genetic drift. Evol Appl 2022; 16:134-151. [PMID: 36699132 PMCID: PMC9850017 DOI: 10.1111/eva.13517] [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: 06/23/2022] [Revised: 11/24/2022] [Accepted: 11/28/2022] [Indexed: 12/14/2022] Open
Abstract
Rapid adaptation is common in invasive populations and is crucial to their long-term success. The primary target of selection in the invasive species' new range is standing genetic variation. Therefore, genetic drift and natural selection acting on existing variation are key evolutionary processes through which invaders will evolve over a short timescale. In this study, we used the case of the raccoon Procyon lotor invasion in Europe to identify the forces shaping the diversity of immune genes during invasion. The genes involved in the defence against infection should be under intense selection pressure in the invasive range where novel pathogens are expected to occur. To disentangle the selective and demographic processes shaping the adaptive immune diversity of its invasive and expanding populations, we have developed species-specific single-nucleotide polymorphism markers located in the coding regions of targeted immune-related genes. We characterised the genetic diversity of 110 functionally important immune genes in two invasive and one native raccoon genetic clusters, each presenting a different demographic history. Despite the strong effect of demographic processes in the invasive clusters, we detected a subset of genes exhibiting the diversity pattern suggestive of selection. The most likely process shaping the variation in those genes was balancing selection. The selected genes belong to toll-like receptors and cytokine-related genes. Our results suggest that the prevalence of selection depends on the level of diversity, that is - less genetically diverse invasive population from the Czech Republic displayed fewer signs of selection. Our results highlight the role of standing genetic variation in adapting to new environment. Understanding the evolutionary mechanisms behind invasion success would enable predicting how populations may respond to environmental change.
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Affiliation(s)
| | - Anna M. Fijarczyk
- Laval University Département de BiologieUniversité LavalQuébecQuébecCanada
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2
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Waineina RW, Okeno TO, Ilatsia ED, Ngeno K. Selection Signature Analyses Revealed Genes Associated With Adaptation, Production, and Reproduction in Selected Goat Breeds in Kenya. Front Genet 2022; 13:858923. [PMID: 35528543 PMCID: PMC9068939 DOI: 10.3389/fgene.2022.858923] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2022] [Accepted: 03/22/2022] [Indexed: 11/13/2022] Open
Abstract
Artificial and natural selection in livestock is expected to leave unique footprints on their genomes. Goat breeds in Kenya have evolved for survival, breeding, and production in various harsh ecological areas, and their genomes are likely to have acquired unique alleles for adaptation to such diverse production environments and other traits of economic importance. To investigate signals of selection for some selected goat breeds in Kenya, Alpine (n = 29), Galla (n = 12), Saanen (n = 24), and Toggenburg (n = 31) were considered. A total of 53,347 single-nucleotide polymorphisms (SNPs) generated using the Illumina GoatSNP50 BeadChip were analyzed. After quality control, 47,663 autosomal single-nucleotide polymorphisms remained for downstream analyses. Several complementary approaches were applied for the following analyses: integrated Haplotype Score (iHS), cross-population-extended haplotype homozygosity (XP-EHH), hapFLK, and FLK. A total of 404 top genomic regions were identified across all the four breeds, based on the four complementary analyses. Out of the 16 identified putative selection signature regions by the intersection of multiple-selective signal analyses, most of the putative regions were found to overlap significantly with the iHS and XP-EHH analyses on chromosomes 3, 4, 10, 15, 22, and 26. These regions were enriched with some genes involved in pathways associated directly or indirectly with environmental adaptation regulating immune responses (e.g., HYAL1 and HYAL3), milk production (e.g., LEPR and PDE4B), and adaptability (e.g., MST1 and PCK). The results revealed few intersect between breeds in genomic selection signature regions. In general, this did not present the typical classic selection signatures as predicted due to the complex nature of the traits. The results support that some various selection pressures (e.g., environmental challenges, artificial selection, and genome admixture challenges) have molded the genome of goat breeds in Kenya. Therefore, the research provides new knowledge on the conservation and utilization of these goat genetic resources in Kenya. In-depth research is needed to detect precise genes connected with adaptation and production in goat breeds in Kenya.
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Affiliation(s)
- Ruth W Waineina
- Department of Animal Sciences, Animal Breeding and Genomics Group, Egerton University, Egerton, Kenya.,Dairy Research Institute, Kenya Agricultural and Livestock Organization, Naivasha, Kenya
| | - Tobias O Okeno
- Department of Animal Sciences, Animal Breeding and Genomics Group, Egerton University, Egerton, Kenya
| | - Evans D Ilatsia
- Dairy Research Institute, Kenya Agricultural and Livestock Organization, Naivasha, Kenya
| | - Kiplangat Ngeno
- Department of Animal Sciences, Animal Breeding and Genomics Group, Egerton University, Egerton, Kenya
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3
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Selection signatures in melanocortin-1 receptor gene of turkeys (Meleagris gallopavo) raised in hot humid tropics. Trop Anim Health Prod 2022; 54:183. [PMID: 35525911 DOI: 10.1007/s11250-022-03185-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2021] [Accepted: 04/28/2022] [Indexed: 10/18/2022]
Abstract
Feather colours are used by avian species for defense, adaptation and signaling. Melanocortin-1 receptor (MC1R) gene is one of the genes responsible for feather colour. This study identified selection signatures in MC1R gene of Nigerian indigenous turkeys (NIT) using British United turkeys (BUT) as control breed to investigate the evolutionary processes that have shaped NIT with various feather colours. Complete MC1R gene of 146 NIT (76 males and 70 females) and 32 BUT (18 males and 14 females) were sequenced. Transition/transversion and codon usage biases were predicted using MEGA v6 software. The selective force acting on the gene was predicted using HyPhy software. The FST values were estimated using Arlequin v3.5. The highest transition/transversion bias was predicted for white BUT (1.00) while the lowest was predicted for black NIT (0.50). Negative dN-dS values, indicative of purifying selection, were observed in MC1R gene of all the turkeys. The highest pairwise FST was observed between the MC1R gene of white BUT and black NIT while the least was observed between lavender NIT and white NIT. No recombination event was observed in black NIT and white BUT. The relative synonymous codon usage was the same among different colours for some codons. Presence of purifying selection in MC1R gene of all the turkeys with different feather colours confirms that the gene plays role in many biological processes such as feather colouration, behaviour, pain perception, immunity, growth and adaptation. The results also suggested that the genetic mechanisms generating different feather colours in turkeys are conserved.
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4
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Alves-Pereira A, Zucchi MI, Clement CR, Viana JPG, Pinheiro JB, Veasey EA, de Souza AP. Selective signatures and high genome-wide diversity in traditional Brazilian manioc (Manihot esculenta Crantz) varieties. Sci Rep 2022; 12:1268. [PMID: 35075210 PMCID: PMC8786832 DOI: 10.1038/s41598-022-05160-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2021] [Accepted: 01/05/2022] [Indexed: 11/09/2022] Open
Abstract
Knowledge about genetic diversity is essential to promote effective use and conservation of crops, because it enables farmers to adapt their crops to specific needs and is the raw material for breeding. Manioc (Manihot esculenta ssp. esculenta) is one of the world's major food crops and has the potential to help achieve food security in the context of on-going climate changes. We evaluated single nucleotide polymorphisms in traditional Brazilian manioc varieties conserved in the gene bank of the Luiz de Queiroz College of Agriculture, University of São Paulo. We assessed genome-wide diversity and identified selective signatures contrasting varieties from different biomes with samples of manioc's wild ancestor M. esculenta ssp. flabellifolia. We identified signatures of selection putatively associated with resistance genes, plant development and response to abiotic stresses that might have been important for the crop's domestication and diversification resulting from cultivation in different environments. Additionally, high neutral genetic diversity within groups of varieties from different biomes and low genetic divergence among biomes reflect the complexity of manioc's evolutionary dynamics under traditional cultivation. Our results exemplify how smallholder practices contribute to conserve manioc's genetic resources, maintaining variation of potential adaptive significance and high levels of neutral genetic diversity.
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Affiliation(s)
- Alessandro Alves-Pereira
- Departamento de Biologia Vegetal, Instituto de Biologia, Universidade Estadual de Campinas (UNICAMP), Av. Cândido Rondon, 400, Cidade Universitária, CP: 6010, Campinas, SP, 13083-875, Brazil.,Centro de Biologia Molecular e Engenharia Genética, Universidade Estadual de Campinas (UNICAMP), Av. Cândido Rondon, 400, Cidade Universitária, CP: 6010, Campinas, SP, 13083-875, Brazil
| | - Maria Imaculada Zucchi
- Agência Paulista de Tecnologia Dos Agronegócios (APTA), Pólo Centro-Sul. Rodovia SP 127, km 30, Piracicaba, SP, 13400-970, Brazil
| | - Charles R Clement
- Instituto Nacional de Pesquisas da Amazônia (INPA), Av. André Araújo, 2936, Petrópolis, Manaus, AM, 69067-375, Brazil
| | - João Paulo Gomes Viana
- Department of Crop Sciences, University of Illinois at Urbana-Champaign (UIUC), AW-101 Turner Hall, 1102 South Goodwin Avenue, Urbana, IL, 61801-4798, USA
| | - José Baldin Pinheiro
- Departamento de Genética, Escola Superior de Agricultura "Luiz de Queiróz", Universidade de São Paulo (ESALQ/USP), Av. Pádua Dias, 11, Piracicaba, SP, 13400-970, Brazil
| | - Elizabeth Ann Veasey
- Departamento de Genética, Escola Superior de Agricultura "Luiz de Queiróz", Universidade de São Paulo (ESALQ/USP), Av. Pádua Dias, 11, Piracicaba, SP, 13400-970, Brazil
| | - Anete Pereira de Souza
- Departamento de Biologia Vegetal, Instituto de Biologia, Universidade Estadual de Campinas (UNICAMP), Av. Cândido Rondon, 400, Cidade Universitária, CP: 6010, Campinas, SP, 13083-875, Brazil. .,Centro de Biologia Molecular e Engenharia Genética, Universidade Estadual de Campinas (UNICAMP), Av. Cândido Rondon, 400, Cidade Universitária, CP: 6010, Campinas, SP, 13083-875, Brazil.
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5
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Ouhrouch A, Boitard S, Boyer F, Servin B, Da Silva A, Pompanon F, Haddioui A, Benjelloun B. Genomic Uniqueness of Local Sheep Breeds From Morocco. Front Genet 2021; 12:723599. [PMID: 34925440 PMCID: PMC8675355 DOI: 10.3389/fgene.2021.723599] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2021] [Accepted: 11/09/2021] [Indexed: 01/17/2023] Open
Abstract
Sheep farming is a major source of meat in Morocco and plays a key role in the country's agriculture. This study aims at characterizing the whole-genome diversity and demographic history of the main Moroccan sheep breeds, as well as to identify selection signatures within and between breeds. Whole genome data from 87 individuals representing the five predominant local breeds were used to estimate their level of neutral genetic diversity and to infer the variation of their effective population size over time. In addition, we used two methods to detect selection signatures: either for detecting selective sweeps within each breed separately or by detecting differentially selected regions by contrasting different breeds. We identified hundreds of genomic regions putatively under selection, which related to several biological terms involved in local adaptation or the expression of zootechnical performances such as Growth, UV protection, Cell maturation or Feeding behavior. The results of this study revealed selection signatures in genes that have an important role in traits of interest and increased our understanding of how genetic diversity is distributed in these local breeds. Thus, Moroccan local sheep breeds exhibit both a high genetic diversity and a large set of adaptive variations, and therefore, represent a valuable genetic resource for the conservation of sheep in the context of climate change.
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Affiliation(s)
- Abdessamad Ouhrouch
- Livestock Genomics Laboratory, Regional Center of Agricultural Research Tadla, National Institute of Agricultural Research INRA, Rabat, Morocco.,Biotechnologies and Valorization of Plant-Genetic Resources Laboratory, Sultan Moulay Slimane University, Beni Mellal, Morocco
| | - Simon Boitard
- CBGP, Université de Montpellier, CIRAD, INRAE, Institut Agro, IRD, Montpellier, France
| | - Frédéric Boyer
- Université Grenoble Alpes, Université Savoie MT-Blanc, CNRS, LECA, Grenoble, France
| | - Bertrand Servin
- GenPhySE, Université de Toulouse, INRA, INPT, INP-ENVT, Castanet-Tolosan, France
| | - Anne Da Silva
- PEREINE/E2LIM, Faculty of Science and Technics, Limoges, France
| | - François Pompanon
- Université Grenoble Alpes, Université Savoie MT-Blanc, CNRS, LECA, Grenoble, France
| | - Abdelmajid Haddioui
- Biotechnologies and Valorization of Plant-Genetic Resources Laboratory, Sultan Moulay Slimane University, Beni Mellal, Morocco
| | - Badr Benjelloun
- Livestock Genomics Laboratory, Regional Center of Agricultural Research Tadla, National Institute of Agricultural Research INRA, Rabat, Morocco
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6
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Alshwairikh YA, Kroeze SL, Olsson J, Stephens‐Cardenas SA, Swain WL, Waits LP, Horn RL, Narum SR, Seaborn T. Influence of environmental conditions at spawning sites and migration routes on adaptive variation and population connectivity in Chinook salmon. Ecol Evol 2021; 11:16890-16908. [PMID: 34938480 PMCID: PMC8668735 DOI: 10.1002/ece3.8324] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2021] [Revised: 10/05/2021] [Accepted: 10/18/2021] [Indexed: 11/25/2022] Open
Abstract
Many species that undergo long breeding migrations, such as anadromous fishes, face highly heterogeneous environments along their migration corridors and at their spawning sites. These environmental challenges encountered at different life stages may act as strong selective pressures and drive local adaptation. However, the relative influence of environmental conditions along the migration corridor compared with the conditions at spawning sites on driving selection is still unknown. In this study, we performed genome-environment associations (GEA) to understand the relationship between landscape and environmental conditions driving selection in seven populations of the anadromous Chinook salmon (Oncorhynchus tshawytscha)-a species of important economic, social, cultural, and ecological value-in the Columbia River basin. We extracted environmental variables for the shared migration corridors and at distinct spawning sites for each population, and used a Pool-seq approach to perform whole genome resequencing. Bayesian and univariate GEA tests with migration-specific and spawning site-specific environmental variables indicated many more candidate SNPs associated with environmental conditions at the migration corridor compared with spawning sites. Specifically, temperature, precipitation, terrain roughness, and elevation variables of the migration corridor were the most significant drivers of environmental selection. Additional analyses of neutral loci revealed two distinct clusters representing populations from different geographic regions of the drainage that also exhibit differences in adult migration timing (summer vs. fall). Tests for genomic regions under selection revealed a strong peak on chromosome 28, corresponding to the GREB1L/ROCK1 region that has been identified previously in salmonids as a region associated with adult migration timing. Our results show that environmental variation experienced throughout migration corridors imposed a greater selective pressure on Chinook salmon than environmental conditions at spawning sites.
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Affiliation(s)
| | | | - Jenny Olsson
- Department of Ecology and Environmental ScienceUmeå UniversityUmeåSweden
| | | | - William L. Swain
- Wildlife Genomics and Disease LaboratoryProgram in EcologyDepartment of Veterinary SciencesUniversity of WyomingLaramieWyomingUSA
| | - Lisette P. Waits
- Department of Fish and Wildlife SciencesUniversity of IdahoMoscowIdahoUSA
| | | | - Shawn R. Narum
- Columbia River Inter‐Tribal Fish CommissionHagermanIdahoUSA
| | - Travis Seaborn
- Department of Fish and Wildlife SciencesUniversity of IdahoMoscowIdahoUSA
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7
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Denoyelle L, Talouarn E, Bardou P, Colli L, Alberti A, Danchin C, Del Corvo M, Engelen S, Orvain C, Palhière I, Rupp R, Sarry J, Salavati M, Amills M, Clark E, Crepaldi P, Faraut T, Masiga CW, Pompanon F, Rosen BD, Stella A, Van Tassell CP, Tosser-Klopp G. VarGoats project: a dataset of 1159 whole-genome sequences to dissect Capra hircus global diversity. Genet Sel Evol 2021; 53:86. [PMID: 34749642 PMCID: PMC8573910 DOI: 10.1186/s12711-021-00659-6] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2020] [Accepted: 07/22/2021] [Indexed: 11/10/2022] Open
Abstract
Background Since their domestication 10,500 years ago, goat populations with distinctive genetic backgrounds have adapted to a broad variety of environments and breeding conditions. The VarGoats project is an international 1000-genome resequencing program designed to understand the consequences of domestication and breeding on the genetic diversity of domestic goats and to elucidate how speciation and hybridization have modeled the genomes of a set of species representative of the genus Capra. Findings A dataset comprising 652 sequenced goats and 507 public goat sequences, including 35 animals representing eight wild species, has been collected worldwide. We identified 74,274,427 single nucleotide polymorphisms (SNPs) and 13,607,850 insertion-deletions (InDels) by aligning these sequences to the latest version of the goat reference genome (ARS1). A Neighbor-joining tree based on Reynolds genetic distances showed that goats from Africa, Asia and Europe tend to group into independent clusters. Because goat breeds from Oceania and Caribbean (Creole) all derive from imported animals, they are distributed along the tree according to their ancestral geographic origin. Conclusions We report on an unprecedented international effort to characterize the genome-wide diversity of domestic goats. This large range of sequenced individuals represents a unique opportunity to ascertain how the demographic and selection processes associated with post-domestication history have shaped the diversity of this species. Data generated for the project will also be extremely useful to identify deleterious mutations and polymorphisms with causal effects on complex traits, and thus will contribute to new knowledge that could be used in genomic prediction and genome-wide association studies. Supplementary Information The online version contains supplementary material available at 10.1186/s12711-021-00659-6.
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Affiliation(s)
- Laure Denoyelle
- GenPhySE, Université de Toulouse, INRAE, ENVT, 31326, Castanet-Tolosan, France.,Université Grenoble Alpes, Université Savoie Mont Blanc, CNRS, LECA, 38000, Grenoble, France
| | - Estelle Talouarn
- GenPhySE, Université de Toulouse, INRAE, ENVT, 31326, Castanet-Tolosan, France
| | - Philippe Bardou
- GenPhySE, Université de Toulouse, INRAE, ENVT, 31326, Castanet-Tolosan, France.,Sigenae, INRAE, 31326, Castanet-Tolosan, France
| | - Licia Colli
- Dipartimento Di Scienze Animali, Della Nutrizione E Degli Alimenti, BioDNA Centro Di Ricerca Sulla Biodiversità E Sul DNA Antico, Facoltà Di Scienze Agrarie, Alimentari E Ambientali, Università Cattolica del Sacro Cuore, Milan, Italy
| | - Adriana Alberti
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, 91057, Evry, France
| | - Coralie Danchin
- Institut de L'Elevage, Maison Nationale Des Eleveurs, 149 Rue de Bercy, 75595, Paris cedex 12, France
| | - Marcello Del Corvo
- Dipartimento Di Scienze Animali, Della Nutrizione E Degli Alimenti, BioDNA Centro Di Ricerca Sulla Biodiversità E Sul DNA Antico, Facoltà Di Scienze Agrarie, Alimentari E Ambientali, Università Cattolica del Sacro Cuore, Milan, Italy
| | - Stéfan Engelen
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, 91057, Evry, France
| | - Céline Orvain
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, 91057, Evry, France
| | - Isabelle Palhière
- GenPhySE, Université de Toulouse, INRAE, ENVT, 31326, Castanet-Tolosan, France
| | - Rachel Rupp
- GenPhySE, Université de Toulouse, INRAE, ENVT, 31326, Castanet-Tolosan, France
| | - Julien Sarry
- GenPhySE, Université de Toulouse, INRAE, ENVT, 31326, Castanet-Tolosan, France
| | - Mazdak Salavati
- The Roslin Institute and R(D)SVS, University of Edinburgh, Easter Bush Campus, Edinburgh, EH25 9RG, UK.,Centre for Tropical Livestock Genetics and Health (CTLGH), Easter Bush Campus, Edinburgh, EH25 9RG, UK
| | - Marcel Amills
- Centre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB, Universitat Autònoma de Barcelona, 08193, Bellaterra, Spain
| | - Emily Clark
- The Roslin Institute and R(D)SVS, University of Edinburgh, Easter Bush Campus, Edinburgh, EH25 9RG, UK.,Centre for Tropical Livestock Genetics and Health (CTLGH), Easter Bush Campus, Edinburgh, EH25 9RG, UK
| | - Paola Crepaldi
- Depth. Agricultural and Environmental Sciences-Production, Landscape, Agroenergy, University of Milan, Milan, Italy
| | - Thomas Faraut
- GenPhySE, Université de Toulouse, INRAE, ENVT, 31326, Castanet-Tolosan, France
| | - Clet Wandui Masiga
- Tropical Institute of Development Innovations (TRIDI), P O Box 23158, Kampala, Uganda
| | - François Pompanon
- Université Grenoble Alpes, Université Savoie Mont Blanc, CNRS, LECA, 38000, Grenoble, France
| | - Benjamin D Rosen
- Animal Genomics and Improvement Laboratory, BARC, USDA-ARS, Beltsville, MD, 20705, USA
| | - Alessandra Stella
- Istituto Di Biologia E Biotecnologia Agraria, Consiglio Nazionale Delle Ricerche, Milan, Italy
| | - Curtis P Van Tassell
- Animal Genomics and Improvement Laboratory, BARC, USDA-ARS, Beltsville, MD, 20705, USA
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Kidner J, Theodorou P, Engler JO, Taubert M, Husemann M. A brief history and popularity of methods and tools used to estimate micro-evolutionary forces. Ecol Evol 2021; 11:13723-13743. [PMID: 34707813 PMCID: PMC8525119 DOI: 10.1002/ece3.8076] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2020] [Revised: 07/12/2021] [Accepted: 08/12/2021] [Indexed: 11/30/2022] Open
Abstract
Population genetics is a field of research that predates the current generations of sequencing technology. Those approaches, that were established before massively parallel sequencing methods, have been adapted to these new marker systems (in some cases involving the development of new methods) that allow genome-wide estimates of the four major micro-evolutionary forces-mutation, gene flow, genetic drift, and selection. Nevertheless, classic population genetic markers are still commonly used and a plethora of analysis methods and programs is available for these and high-throughput sequencing (HTS) data. These methods employ various and diverse theoretical and statistical frameworks, to varying degrees of success, to estimate similar evolutionary parameters making it difficult to get a concise overview across the available approaches. Presently, reviews on this topic generally focus on a particular class of methods to estimate one or two evolutionary parameters. Here, we provide a brief history of methods and a comprehensive list of available programs for estimating micro-evolutionary forces. We furthermore analyzed their usage within the research community based on popularity (citation bias) and discuss the implications of this bias for the software community. We found that a few programs received the majority of citations, with program success being independent of both the parameters estimated and the computing platform. The only deviation from a model of exponential growth in the number of citations was found for the presence of a graphical user interface (GUI). Interestingly, no relationship was found for the impact factor of the journals, when the tools were published, suggesting accessibility might be more important than visibility.
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Affiliation(s)
- Jonathan Kidner
- General Zoology Institute for Biology Martin Luther University Halle-Wittenberg Halle (Saale) Germany
| | - Panagiotis Theodorou
- General Zoology Institute for Biology Martin Luther University Halle-Wittenberg Halle (Saale) Germany
| | - Jan O Engler
- Terrestrial Ecology Unit Department of Biology Ghent University Ghent Belgium
| | - Martin Taubert
- Aquatic Geomicrobiology Institute for Biodiversity Friedrich Schiller University Jena Jena Germany
| | - Martin Husemann
- General Zoology Institute for Biology Martin Luther University Halle-Wittenberg Halle (Saale) Germany
- Centrum für Naturkunde University of Hamburg Hamburg Germany
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9
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Kominakis A, Tarsani E, Hager-Theodorides AL, Mastranestasis I, Gkelia D, Hadjigeorgiou I. Genetic differentiation of mainland-island sheep of Greece: Implications for identifying candidate genes for long-term local adaptation. PLoS One 2021; 16:e0257461. [PMID: 34529728 PMCID: PMC8445479 DOI: 10.1371/journal.pone.0257461] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2021] [Accepted: 09/01/2021] [Indexed: 11/23/2022] Open
Abstract
In Greece, a number of local sheep breeds are raised in a wide range of ecological niches across the country. These breeds can be used for the identification of genetic variants that contribute to local adaptation. To this end, 50k genotypes of 90 local sheep from mainland Greece (Epirus, n = 35 and Peloponnesus, n = 55) were used, as well as 147 genotypes of sheep from insular Greece (Skyros, n = 21), Lemnos, n = 36 and Lesvos, n = 90). Principal components and phylogenetic analysis along with admixture and spatial point patterns analyses suggested genetic differentiation of 'mainland-island' populations. Genome scans for signatures of selection and genome-wide association analysis (GWAS) pointed to one highly differentiating marker on OAR4 (FST = 0.39, FLK = 21.93, FDR p-value = 0.10) that also displayed genome wide significance (FDR p-value = 0.002) during GWAS. A total number of 6 positional candidate genes (LOC106990429, ZNF804B, TEX47, STEAP4, SRI and ADAM22) were identified within 500 kb flanking regions around the significant marker. In addition, two QTLs related to fat tail deposition are reported in genomic regions 800 kb downstream the significant marker. Based on gene ontology analysis and literature evidence, the identified candidate genes possess biological functions relevant to local adaptation that worth further investigation.
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Affiliation(s)
- Antonios Kominakis
- Department of Animal Science, Agricultural University of Athens, Athens, Greece
| | - Eirini Tarsani
- Department of Animal Science, Agricultural University of Athens, Athens, Greece
| | | | | | - Dimitra Gkelia
- Association of Pastoral Farmers of Epirus, Ioannina, Greece
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10
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Rostamzadeh Mahdabi E, Esmailizadeh A, Ayatollahi Mehrgardi A, Asadi Fozi M. A genome-wide scan to identify signatures of selection in two Iranian indigenous chicken ecotypes. Genet Sel Evol 2021; 53:72. [PMID: 34503452 PMCID: PMC8428137 DOI: 10.1186/s12711-021-00664-9] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2021] [Accepted: 08/25/2021] [Indexed: 11/10/2022] Open
Abstract
Background Various regions of the chicken genome have been under natural and artificial selection for thousands of years. The substantial diversity that exits among chickens from different geographic regions provides an excellent opportunity to investigate the genomic regions under selection which, in turn, will increase our knowledge about the mechanisms that underlie chicken diversity and adaptation. Several statistics have been developed to detect genomic regions that are under selection. In this study, we applied approaches based on differences in allele or haplotype frequencies (FST and hapFLK, respectively) between populations, differences in long stretches of consecutive homozygous sequences (ROH), and differences in allele frequencies within populations (composite likelihood ratio (CLR)) to identify inter- and intra-populations traces of selection in two Iranian indigenous chicken ecotypes, the Lari fighting chicken and the Khazak or creeper (short-leg) chicken. Results Using whole-genome resequencing data of 32 individuals from the two chicken ecotypes, approximately 11.9 million single nucleotide polymorphisms (SNPs) were detected and used in genomic analyses after quality processing. Examination of the distribution of ROH in the two populations indicated short to long ROH, ranging from 0.3 to 5.4 Mb. We found 90 genes that were detected by at least two of the four applied methods. Gene annotation of the detected putative regions under selection revealed candidate genes associated with growth (DCN, MEOX2 and CACNB1), reproduction (ESR1 and CALCR), disease resistance (S1PR1, ALPK1 and MHC-B), behavior pattern (AGMO, GNAO1 and PSEN1), and morphological traits (IHH and NHEJ1). Conclusions Our findings show that these two phenotypically different indigenous chicken populations have been under selection for reproduction, immune, behavioral, and morphology traits. The results illustrate that selection can play an important role in shaping signatures of differentiation across the genomic landscape of two chicken populations. Supplementary Information The online version contains supplementary material available at 10.1186/s12711-021-00664-9.
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Affiliation(s)
- Elaheh Rostamzadeh Mahdabi
- Department of Animal Science, Faculty of Agriculture, Shahid Bahonar University of Kerman, 22 Bahman Blvd, Kerman, Iran
| | - Ali Esmailizadeh
- Department of Animal Science, Faculty of Agriculture, Shahid Bahonar University of Kerman, 22 Bahman Blvd, Kerman, Iran
| | - Ahmad Ayatollahi Mehrgardi
- Department of Animal Science, Faculty of Agriculture, Shahid Bahonar University of Kerman, 22 Bahman Blvd, Kerman, Iran
| | - Masood Asadi Fozi
- Department of Animal Science, Faculty of Agriculture, Shahid Bahonar University of Kerman, 22 Bahman Blvd, Kerman, Iran.
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11
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Abdelmanova AS, Dotsev AV, Romanov MN, Stanishevskaya OI, Gladyr EA, Rodionov AN, Vetokh AN, Volkova NA, Fedorova ES, Gusev IV, Griffin DK, Brem G, Zinovieva NA. Unveiling Comparative Genomic Trajectories of Selection and Key Candidate Genes in Egg-Type Russian White and Meat-Type White Cornish Chickens. BIOLOGY 2021; 10:biology10090876. [PMID: 34571753 PMCID: PMC8469556 DOI: 10.3390/biology10090876] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/04/2021] [Revised: 08/20/2021] [Accepted: 08/30/2021] [Indexed: 01/14/2023]
Abstract
Comparison of genomic footprints in chicken breeds with different selection history is a powerful tool in elucidating genomic regions that have been targeted by recent and more ancient selection. In the present work, we aimed at examining and comparing the trajectories of artificial selection in the genomes of the native egg-type Russian White (RW) and meat-type White Cornish (WC) breeds. Combining three different statistics (top 0.1% SNP by FST value at pairwise breed comparison, hapFLK analysis, and identification of ROH island shared by more than 50% of individuals), we detected 45 genomic regions under putative selection including 11 selective sweep regions, which were detected by at least two different methods. Four of such regions were breed-specific for each of RW breed (on GGA1, GGA5, GGA8, and GGA9) and WC breed (on GGA1, GGA5, GGA8, and GGA28), while three remaining regions on GGA2 (two sweeps) and GGA3 were common for both breeds. Most of identified genomic regions overlapped with known QTLs and/or candidate genes including those for body temperatures, egg productivity, and feed intake in RW chickens and those for growth, meat and carcass traits, and feed efficiency in WC chickens. These findings were concordant with the breed origin and history of their artificial selection. We determined a set of 188 prioritized candidate genes retrieved from the 11 overlapped regions of putative selection and reviewed their functions relative to phenotypic traits of interest in the two breeds. One of the RW-specific sweep regions harbored the known domestication gene, TSHR. Gene ontology and functional annotation analysis provided additional insight into a functional coherence of genes in the sweep regions. We also showed a greater candidate gene richness on microchromosomes relative to macrochromosomes in these genomic areas. Our results on the selection history of RW and WC chickens and their key candidate genes under selection serve as a profound information for further conservation of their genomic diversity and efficient breeding.
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Affiliation(s)
- Alexandra S. Abdelmanova
- L.K. Ernst Federal Research Center for Animal Husbandry, 142132 Podolsk, Russia; (A.S.A.); (A.V.D.); (E.A.G.); (A.N.R.); (A.N.V.); (N.A.V.); (I.V.G.)
| | - Arsen V. Dotsev
- L.K. Ernst Federal Research Center for Animal Husbandry, 142132 Podolsk, Russia; (A.S.A.); (A.V.D.); (E.A.G.); (A.N.R.); (A.N.V.); (N.A.V.); (I.V.G.)
| | - Michael N. Romanov
- School of Biosciences, University of Kent, Canterbury, Kent CT2 7NJ, UK;
- K.I. Skryabin Moscow State Academy of Veterinary Medicine and Biotechnology, 23 Akademika Skryabina St., 109472 Moscow, Russia
- Correspondence: (M.N.R.); (N.A.Z.); Tel.: +798-57154351 (M.N.R.); +749-67651163 (N.A.Z.)
| | - Olga I. Stanishevskaya
- Russian Research Institute of Farm Animal Genetics and Breeding—Branch of the L.K. Ernst Federal Research Center for Animal Husbandry, Pushkin, 196601 St. Petersburg, Russia; (O.I.S.); (E.S.F.)
| | - Elena A. Gladyr
- L.K. Ernst Federal Research Center for Animal Husbandry, 142132 Podolsk, Russia; (A.S.A.); (A.V.D.); (E.A.G.); (A.N.R.); (A.N.V.); (N.A.V.); (I.V.G.)
| | - Andrey N. Rodionov
- L.K. Ernst Federal Research Center for Animal Husbandry, 142132 Podolsk, Russia; (A.S.A.); (A.V.D.); (E.A.G.); (A.N.R.); (A.N.V.); (N.A.V.); (I.V.G.)
| | - Anastasia N. Vetokh
- L.K. Ernst Federal Research Center for Animal Husbandry, 142132 Podolsk, Russia; (A.S.A.); (A.V.D.); (E.A.G.); (A.N.R.); (A.N.V.); (N.A.V.); (I.V.G.)
| | - Natalia A. Volkova
- L.K. Ernst Federal Research Center for Animal Husbandry, 142132 Podolsk, Russia; (A.S.A.); (A.V.D.); (E.A.G.); (A.N.R.); (A.N.V.); (N.A.V.); (I.V.G.)
| | - Elena S. Fedorova
- Russian Research Institute of Farm Animal Genetics and Breeding—Branch of the L.K. Ernst Federal Research Center for Animal Husbandry, Pushkin, 196601 St. Petersburg, Russia; (O.I.S.); (E.S.F.)
| | - Igor V. Gusev
- L.K. Ernst Federal Research Center for Animal Husbandry, 142132 Podolsk, Russia; (A.S.A.); (A.V.D.); (E.A.G.); (A.N.R.); (A.N.V.); (N.A.V.); (I.V.G.)
| | - Darren K. Griffin
- School of Biosciences, University of Kent, Canterbury, Kent CT2 7NJ, UK;
| | - Gottfried Brem
- Institute of Animal Breeding and Genetics, University of Veterinary Medicine, 1210 Vienna, Austria;
| | - Natalia A. Zinovieva
- L.K. Ernst Federal Research Center for Animal Husbandry, 142132 Podolsk, Russia; (A.S.A.); (A.V.D.); (E.A.G.); (A.N.R.); (A.N.V.); (N.A.V.); (I.V.G.)
- Correspondence: (M.N.R.); (N.A.Z.); Tel.: +798-57154351 (M.N.R.); +749-67651163 (N.A.Z.)
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12
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Serranito B, Taurisson-Mouret D, Harkat S, Laoun A, Ouchene-Khelifi NA, Pompanon F, Benjelloun B, Cecchi G, Thevenon S, Lenstra JA, Da Silva A. Search for Selection Signatures Related to Trypanosomosis Tolerance in African Goats. Front Genet 2021; 12:715732. [PMID: 34413881 PMCID: PMC8369930 DOI: 10.3389/fgene.2021.715732] [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: 05/27/2021] [Accepted: 06/28/2021] [Indexed: 12/13/2022] Open
Abstract
Livestock is heavily affected by trypanosomosis in Africa. Through strong selective pressure, several African indigenous breeds of cattle and small ruminants have acquired varying degrees of tolerance against this disease. In this study, we combined LFMM and PCAdapt for analyzing two datasets of goats from West-Central Africa and East Africa, respectively, both comprising breeds with different assumed levels of trypanotolerance. The objectives were (i) to identify molecular signatures of selection related to trypanotolerance; and (ii) to guide an optimal sampling for subsequent studies. From 33 identified signatures, 18 had been detected previously in the literature as being mainly associated with climatic adaptations. The most plausible signatures of trypanotolerance indicate the genes DIS3L2, COPS7B, PD5A, UBE2K, and UBR1. The last gene is of particular interest since previous literature has already identified E3-ubiquitin ligases as playing a decisive role in the immune response. For following-up on these findings, the West-Central African area appears particularly relevant because of (i) a clear parasitic load gradient related to a humidity gradient, and (ii) still restricted admixture levels between goat breeds. This study illustrates the importance of protecting local breeds, which have retained unique allelic combinations conferring their remarkable adaptations.
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Affiliation(s)
- Bruno Serranito
- Museum National d’Histoire Naturelle, CRESCO, Dinard, France
- University of Limoges, PEREINE, E2LIM, Limoges, France
| | | | - Sahraoui Harkat
- Science Veterinary Institute, University of Blida, Blida, Algeria
| | | | | | - François Pompanon
- Univ. Grenoble Alpes, Univ. Savoie Mont Blanc, CNRS, LECA, Grenoble, France
| | - Badr Benjelloun
- National Institute of Agronomic Research, Regional Centre of Agronomic Research, Beni-Mellal, Morocco
| | - Giuliano Cecchi
- Food and Agriculture Organization of the United Nations, Animal Production and Health Division, Rome, Italy
| | - Sophie Thevenon
- CIRAD, UMR INTERTRYP, Montpellier, France
- INTERTRYP, University of Montpellier, CIRAD, IRD, Montpellier, France
| | | | - Anne Da Silva
- University of Limoges, PEREINE, E2LIM, Limoges, France
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13
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Bakoev S, Getmantseva L, Kostyunina O, Bakoev N, Prytkov Y, Usatov A, Tatarinova TV. Genome-wide analysis of genetic diversity and artificial selection in Large White pigs in Russia. PeerJ 2021; 9:e11595. [PMID: 34249494 PMCID: PMC8256806 DOI: 10.7717/peerj.11595] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2021] [Accepted: 05/21/2021] [Indexed: 11/20/2022] Open
Abstract
Breeding practices adopted at different farms are aimed at maximizing the profitability of pig farming. In this work, we have analyzed the genetic diversity of Large White pigs in Russia. We compared genomes of historic and modern Large White Russian breeds using 271 pig samples. We have identified 120 candidate regions associated with the differentiation of modern and historic pigs and analyzed genomic differences between the modern farms. The identified genes were associated with height, fitness, conformation, reproductive performance, and meat quality.
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Affiliation(s)
- Siroj Bakoev
- Federal Research Center for Animal Husbandry named after Academy Member LK. Ernst, Dubrovitsy, Russia.,Centre for Strategic Planning and Management of Biomedical Health Risks, Moscow, Russia
| | - Lyubov Getmantseva
- Federal Research Center for Animal Husbandry named after Academy Member LK. Ernst, Dubrovitsy, Russia
| | - Olga Kostyunina
- Federal Research Center for Animal Husbandry named after Academy Member LK. Ernst, Dubrovitsy, Russia
| | - Nekruz Bakoev
- Federal Research Center for Animal Husbandry named after Academy Member LK. Ernst, Dubrovitsy, Russia
| | - Yuri Prytkov
- Federal Research Center for Animal Husbandry named after Academy Member LK. Ernst, Dubrovitsy, Russia
| | | | - Tatiana V Tatarinova
- Department of Biology, University of La Verne, La Verne, CA, United States of America.,Department of Genomics and Bioinformatics, Institute of Fundamental Biology and Biotechnology, Siberian Federal University, Krasnoyarsk, Russia.,Institute for Information Transmission Problems, Moscow, Russia.,Vavilov Institute for General Genetics, Moscow, Russia
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14
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Rowan TN, Durbin HJ, Seabury CM, Schnabel RD, Decker JE. Powerful detection of polygenic selection and evidence of environmental adaptation in US beef cattle. PLoS Genet 2021; 17:e1009652. [PMID: 34292938 PMCID: PMC8297814 DOI: 10.1371/journal.pgen.1009652] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2020] [Accepted: 06/09/2021] [Indexed: 12/19/2022] Open
Abstract
Selection on complex traits can rapidly drive evolution, especially in stressful environments. This polygenic selection does not leave intense sweep signatures on the genome, rather many loci experience small allele frequency shifts, resulting in large cumulative phenotypic changes. Directional selection and local adaptation are changing populations; but, identifying loci underlying polygenic or environmental selection has been difficult. We use genomic data on tens of thousands of cattle from three populations, distributed over time and landscapes, in linear mixed models with novel dependent variables to map signatures of selection on complex traits and local adaptation. We identify 207 genomic loci associated with an animal's birth date, representing ongoing selection for monogenic and polygenic traits. Additionally, hundreds of additional loci are associated with continuous and discrete environments, providing evidence for historical local adaptation. These candidate loci highlight the nervous system's possible role in local adaptation. While advanced technologies have increased the rate of directional selection in cattle, it has likely been at the expense of historically generated local adaptation, which is especially problematic in changing climates. When applied to large, diverse cattle datasets, these selection mapping methods provide an insight into how selection on complex traits continually shapes the genome. Further, understanding the genomic loci implicated in adaptation may help us breed more adapted and efficient cattle, and begin to understand the basis for mammalian adaptation, especially in changing climates. These selection mapping approaches help clarify selective forces and loci in evolutionary, model, and agricultural contexts.
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Affiliation(s)
- Troy N. Rowan
- Division of Animal Sciences, University of Missouri, Columbia, Missouri, United States of America
- Genetics Area Program, University of Missouri, Columbia, Missouri, United States of America
- Department of Animal Science, University of Tennessee, Knoxville, Tennessee, United States of America
- College of Veterinary Medicine, Large Animal Clinical Science, University of Tennessee, Knoxville, Tennessee, United States of America
| | - Harly J. Durbin
- Division of Animal Sciences, University of Missouri, Columbia, Missouri, United States of America
- Genetics Area Program, University of Missouri, Columbia, Missouri, United States of America
| | - Christopher M. Seabury
- Department of Veterinary Pathobiology, Texas A&M University, College Station, Texas, United States of America
| | - Robert D. Schnabel
- Division of Animal Sciences, University of Missouri, Columbia, Missouri, United States of America
- Genetics Area Program, University of Missouri, Columbia, Missouri, United States of America
- Institute for Data Science and Informatics, University of Missouri, Columbia, Missouri, United States of America
| | - Jared E. Decker
- Division of Animal Sciences, University of Missouri, Columbia, Missouri, United States of America
- Genetics Area Program, University of Missouri, Columbia, Missouri, United States of America
- Institute for Data Science and Informatics, University of Missouri, Columbia, Missouri, United States of America
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15
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Sweet-Jones J, Lenis VP, Yurchenko AA, Yudin NS, Swain M, Larkin DM. Genotyping and Whole-Genome Resequencing of Welsh Sheep Breeds Reveal Candidate Genes and Variants for Adaptation to Local Environment and Socioeconomic Traits. Front Genet 2021; 12:612492. [PMID: 34220925 PMCID: PMC8253514 DOI: 10.3389/fgene.2021.612492] [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: 09/30/2020] [Accepted: 05/10/2021] [Indexed: 12/25/2022] Open
Abstract
Background Advances in genetic tools applied to livestock breeding has prompted research into the previously neglected breeds adapted to harsh local environments. One such group is the Welsh mountain sheep breeds, which can be farmed at altitudes of 300 m above sea level but are considered to have a low productive value because of their poor wool quality and small carcass size. This is contrary to the lowland breeds which are more suited to wool and meat production qualities, but do not fare well on upland pasture. Herein, medium-density genotyping data from 317 individuals representing 15 Welsh sheep breeds were used alongside the whole-genome resequencing data of 14 breeds from the same set to scan for the signatures of selection and candidate genetic variants using haplotype- and SNP-based approaches. Results Haplotype-based selection scan performed on the genotyping data pointed to a strong selection in the regions of GBA3, PPARGC1A, APOB, and PPP1R16B genes in the upland breeds, and RNF24, PANK2, and MUC15 in the lowland breeds. SNP-based selection scan performed on the resequencing data pointed to the missense mutations under putative selection relating to a local adaptation in the upland breeds with functions such as angiogenesis (VASH1), anti-oxidation (RWDD1), cell stress (HSPA5), membrane transport (ABCA13 and SLC22A7), and insulin signaling (PTPN1 and GIGFY1). By contrast, genes containing candidate missense mutations in the lowland breeds are related to cell cycle (CDK5RAP2), cell adhesion (CDHR3), and coat color (MC1R). Conclusion We found new variants in genes with potentially functional consequences to the adaptation of local sheep to their environments in Wales. Knowledge of these variations is important for improving the adaptative qualities of UK and world sheep breeds through a marker-assisted selection.
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Affiliation(s)
- James Sweet-Jones
- Royal Veterinary College, University of London, London, United Kingdom
| | - Vasileios Panagiotis Lenis
- Institute of Biological, Environmental and Rural Sciences, University of Aberystwyth, Aberystwyth, United Kingdom.,School of Health and Life Sciences, Teesside University, Middlesbrough, United Kingdom
| | - Andrey A Yurchenko
- The Federal Research Center Institute of Cytology and Genetics, The Siberian Branch of the Russian Academy of Sciences (ICG SB RAS), Novosibirsk, Russia
| | - Nikolay S Yudin
- The Federal Research Center Institute of Cytology and Genetics, The Siberian Branch of the Russian Academy of Sciences (ICG SB RAS), Novosibirsk, Russia
| | - Martin Swain
- Institute of Biological, Environmental and Rural Sciences, University of Aberystwyth, Aberystwyth, United Kingdom
| | - Denis M Larkin
- Royal Veterinary College, University of London, London, United Kingdom.,The Federal Research Center Institute of Cytology and Genetics, The Siberian Branch of the Russian Academy of Sciences (ICG SB RAS), Novosibirsk, Russia
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16
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Grummer JA, Whitlock MC, Schulte PM, Taylor EB. Growth genes are implicated in the evolutionary divergence of sympatric piscivorous and insectivorous rainbow trout (Oncorhynchus mykiss). BMC Ecol Evol 2021; 21:63. [PMID: 33888062 PMCID: PMC8063319 DOI: 10.1186/s12862-021-01795-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2021] [Accepted: 04/12/2021] [Indexed: 12/26/2022] Open
Abstract
Background Identifying ecologically significant phenotypic traits and the genomic mechanisms that underly them are crucial steps in understanding traits associated with population divergence. We used genome-wide data to identify genomic regions associated with key traits that distinguish two ecomorphs of rainbow trout (Oncorhynchus mykiss)—insectivores and piscivores—that coexist for the non-breeding portion of the year in Kootenay Lake, southeastern British Columbia. “Gerrards” are large-bodied, rapidly growing piscivores with high metabolic rates that spawn north of Kootenay Lake in the Lardeau River, in contrast to the insectivorous populations that are on average smaller in body size, with lower growth and metabolic rates, mainly forage on aquatic insects, and spawn in tributaries immediately surrounding Kootenay Lake. We used pool-seq data representing ~ 60% of the genome and 80 fish per population to assess the level of genomic divergence between ecomorphs and to identify and interrogate loci that may play functional or selective roles in their divergence. Results Genomic divergence was high between sympatric insectivores and piscivores (\documentclass[12pt]{minimal}
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\begin{document}$$F_{\text{ST}}$$\end{document}FST = 0.188), and in fact higher than between insectivorous populations from Kootenay Lake and the Blackwater River (\documentclass[12pt]{minimal}
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\begin{document}$$F_{\text{ST}}$$\end{document}FST = 0.159) that are > 500 km apart. A window-based \documentclass[12pt]{minimal}
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\begin{document}$$F_{\text{ST}}$$\end{document}FST analysis did not reveal “islands” of genomic differentiation; however, the window with highest \documentclass[12pt]{minimal}
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\begin{document}$$F_{\text{ST}}$$\end{document}FST estimate did include a gene associated with insulin secretion. Although we explored the use of the “Local score” approach to identify genomic outlier regions, this method was ultimately not used because simulations revealed a high false discovery rate (~ 20%). Gene ontology (GO) analysis identified several growth processes as enriched in genes occurring in the ~ 200 most divergent genomic windows, indicating many loci of small effect involved in growth and growth-related metabolic processes are associated with the divergence of these ecomorphs. Conclusion Our results reveal a high degree of genomic differentiation between piscivorous and insectivorous populations and indicate that the large body piscivorous phenotype is likely not due to one or a few loci of large effect. Rather, the piscivore phenotype may be controlled by several loci of small effect, thus highlighting the power of whole-genome resequencing in identifying genomic regions underlying population-level phenotypic divergences. Supplementary Information The online version contains supplementary material available at 10.1186/s12862-021-01795-9.
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Affiliation(s)
- Jared A Grummer
- Department of Zoology and Biodiversity Research Centre, University of British Columbia, 6270 University Blvd., Vancouver, BC, V6T 1Z4, Canada.
| | - Michael C Whitlock
- Department of Zoology and Biodiversity Research Centre, University of British Columbia, 6270 University Blvd., Vancouver, BC, V6T 1Z4, Canada
| | - Patricia M Schulte
- Department of Zoology and Biodiversity Research Centre, University of British Columbia, 6270 University Blvd., Vancouver, BC, V6T 1Z4, Canada
| | - Eric B Taylor
- Department of Zoology and Biodiversity Research Centre, University of British Columbia, 6270 University Blvd., Vancouver, BC, V6T 1Z4, Canada.,Beaty Biodiversity Museum, University of British Columbia, 6270 University Blvd., Vancouver, BC, V6T 1Z4, Canada
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17
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Olazcuaga L, Loiseau A, Parrinello H, Paris M, Fraimout A, Guedot C, Diepenbrock LM, Kenis M, Zhang J, Chen X, Borowiec N, Facon B, Vogt H, Price DK, Vogel H, Prud'homme B, Estoup A, Gautier M. A Whole-Genome Scan for Association with Invasion Success in the Fruit Fly Drosophila suzukii Using Contrasts of Allele Frequencies Corrected for Population Structure. Mol Biol Evol 2021; 37:2369-2385. [PMID: 32302396 PMCID: PMC7403613 DOI: 10.1093/molbev/msaa098] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Evidence is accumulating that evolutionary changes are not only common during biological invasions but may also contribute directly to invasion success. The genomic basis of such changes is still largely unexplored. Yet, understanding the genomic response to invasion may help to predict the conditions under which invasiveness can be enhanced or suppressed. Here, we characterized the genome response of the spotted wing drosophila Drosophila suzukii during the worldwide invasion of this pest insect species, by conducting a genome-wide association study to identify genes involved in adaptive processes during invasion. Genomic data from 22 population samples were analyzed to detect genetic variants associated with the status (invasive versus native) of the sampled populations based on a newly developed statistic, we called C2, that contrasts allele frequencies corrected for population structure. We evaluated this new statistical framework using simulated data sets and implemented it in an upgraded version of the program BayPass. We identified a relatively small set of single-nucleotide polymorphisms that show a highly significant association with the invasive status of D. suzukii populations. In particular, two genes, RhoGEF64C and cpo, contained single-nucleotide polymorphisms significantly associated with the invasive status in the two separate main invasion routes of D. suzukii. Our methodological approaches can be applied to any other invasive species, and more generally to any evolutionary model for species characterized by nonequilibrium demographic conditions for which binary covariables of interest can be defined at the population level.
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Affiliation(s)
- Laure Olazcuaga
- INRAE, UMR CBGP (INRAE-IRD-Cirad - Montpellier SupAgro), Montferrier-sur-Lez, France
| | - Anne Loiseau
- INRAE, UMR CBGP (INRAE-IRD-Cirad - Montpellier SupAgro), Montferrier-sur-Lez, France
| | - Hugues Parrinello
- MGX, Biocampus Montpellier, CNRS, INSERM, Universite de Montpellier, Montpellier, France
| | | | - Antoine Fraimout
- INRAE, UMR CBGP (INRAE-IRD-Cirad - Montpellier SupAgro), Montferrier-sur-Lez, France
| | | | | | | | - Jinping Zhang
- MoA-CABI Joint Laboratory for Bio-Safety, Chinese Academy of Agricultural Sciences, BeiXiaGuan, Haidian Qu, China
| | - Xiao Chen
- College of Plant Protection, Yunnan Agricultural University, Kunming, Yunnan Province, China
| | - Nicolas Borowiec
- UMR INRAE-CNRS-Université Côte d'Azur Sophia Agrobiotech Institute, Sophia Antipolis, France
| | - Benoit Facon
- UMR Peuplements Végétaux et Bioagresseurs en Milieu Tropical, INRAE, Saint-Pierre, La Réunion, France
| | - Heidrun Vogt
- Julius Kühn-Institut (JKI), Federal Research Centre for Cultivated Plants, Institute for Plant Protection in Fruit Crops and Viticulture, Dossenheim, Germany
| | - Donald K Price
- School of Life Sciences, University of Nevada, Las Vegas, Las Vegas, NV
| | - Heiko Vogel
- Department of Entomology, Max Planck Institute for Chemical Ecology, Jena, Germany
| | | | - Arnaud Estoup
- INRAE, UMR CBGP (INRAE-IRD-Cirad - Montpellier SupAgro), Montferrier-sur-Lez, France
| | - Mathieu Gautier
- INRAE, UMR CBGP (INRAE-IRD-Cirad - Montpellier SupAgro), Montferrier-sur-Lez, France
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18
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Hussain I, Raza RZ, Ali S, Abrar M, Abbasi AA. Molecular signatures of selection on the human GLI3 associated central nervous system specific enhancers. Dev Genes Evol 2021; 231:21-32. [PMID: 33655411 DOI: 10.1007/s00427-021-00672-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2020] [Accepted: 02/09/2021] [Indexed: 11/25/2022]
Abstract
The zinc finger-containing transcription factor Gli3 is a key mediator of Hedgehog (Hh) signaling pathway. In vertebrates, Gli3 has widespread expression pattern during early embryonic development. Along the anteroposterior axes of the central nervous system (CNS), dorsoventral neural pattern elaboration is achieved through Hh mediated spatio-temporal deployment of Gli3 transcripts. Previously, we and others uncovered a set of enhancers that mediate many of the known aspects of Gli3 expression during neurogenesis. However, the potential role of Gli3 associated enhancers in trait evolution has not yet received any significant attention. Here, we investigate the evolutionary patterns of Gli3 associated CNS-specific enhancers that have been reported so far. A subset of these enhancers has undergone an accelerated rate of molecular evolution in the human lineage in comparison to other primates/mammals. These fast-evolving enhancers have acquired human-specific changes in transcription factor binding sites (TFBSs). These human-unique changes within subset of Gli3 associated CNS-specific enhancers were further validated as single nucleotide polymorphisms through 1000 Genome Project Phase 3 data. This work not only infers the molecular evolutionary patterns of Gli3 associated enhancers but also provides clues for putative genetic basis of the population-specificity of gene expression regulation.
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Affiliation(s)
- Irfan Hussain
- National Center for Bioinformatics, Program of Comparative and Evolutionary Genomics, Faculty of Biological Sciences, Quaid-i-Azam University, Islamabad, 45320, Pakistan
| | - Rabail Zehra Raza
- Department of Biological Sciences, National University of Medical Sciences, The Mall, Rawalpindi, Pakistan
| | - Shahid Ali
- National Center for Bioinformatics, Program of Comparative and Evolutionary Genomics, Faculty of Biological Sciences, Quaid-i-Azam University, Islamabad, 45320, Pakistan
| | - Muhammad Abrar
- National Center for Bioinformatics, Program of Comparative and Evolutionary Genomics, Faculty of Biological Sciences, Quaid-i-Azam University, Islamabad, 45320, Pakistan
| | - Amir Ali Abbasi
- National Center for Bioinformatics, Program of Comparative and Evolutionary Genomics, Faculty of Biological Sciences, Quaid-i-Azam University, Islamabad, 45320, Pakistan.
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19
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Lindo J, DeGiorgio M. Understanding the Adaptive Evolutionary Histories of South American Ancient and Present-Day Populations via Genomics. Genes (Basel) 2021; 12:360. [PMID: 33801556 PMCID: PMC8001801 DOI: 10.3390/genes12030360] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2021] [Revised: 02/18/2021] [Accepted: 02/22/2021] [Indexed: 12/03/2022] Open
Abstract
The South American continent is remarkably diverse in its ecological zones, spanning the Amazon rainforest, the high-altitude Andes, and Tierra del Fuego. Yet the original human populations of the continent successfully inhabited all these zones, well before the buffering effects of modern technology. Therefore, it is likely that the various cultures were successful, in part, due to positive natural selection that allowed them to successfully establish populations for thousands of years. Detecting positive selection in these populations is still in its infancy, as the ongoing effects of European contact have decimated many of these populations and introduced gene flow from outside of the continent. In this review, we explore hypotheses of possible human biological adaptation, methods to identify positive selection, the utilization of ancient DNA, and the integration of modern genomes through the identification of genomic tracts that reflect the ancestry of the first populations of the Americas.
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Affiliation(s)
- John Lindo
- Department of Anthropology, Emory University, Atlanta, GA 30322, USA
| | - Michael DeGiorgio
- Department of Computer and Electrical Engineering and Computer Science, Florida Atlantic University, Boca Raton, FL 33431, USA
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20
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Gu Z, Pan S, Lin Z, Hu L, Dai X, Chang J, Xue Y, Su H, Long J, Sun M, Ganusevich S, Sokolov V, Sokolov A, Pokrovsky I, Ji F, Bruford MW, Dixon A, Zhan X. Climate-driven flyway changes and memory-based long-distance migration. Nature 2021; 591:259-264. [PMID: 33658718 DOI: 10.1038/s41586-021-03265-0] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2020] [Accepted: 01/20/2021] [Indexed: 01/31/2023]
Abstract
Millions of migratory birds occupy seasonally favourable breeding grounds in the Arctic1, but we know little about the formation, maintenance and future of the migration routes of Arctic birds and the genetic determinants of migratory distance. Here we established a continental-scale migration system that used satellite tracking to follow 56 peregrine falcons (Falco peregrinus) from 6 populations that breed in the Eurasian Arctic, and resequenced 35 genomes from 4 of these populations. The breeding populations used five migration routes across Eurasia, which were probably formed by longitudinal and latitudinal shifts in their breeding grounds during the transition from the Last Glacial Maximum to the Holocene epoch. Contemporary environmental divergence between the routes appears to maintain their distinctiveness. We found that the gene ADCY8 is associated with population-level differences in migratory distance. We investigated the regulatory mechanism of this gene, and found that long-term memory was the most likely selective agent for divergence in ADCY8 among the peregrine populations. Global warming is predicted to influence migration strategies and diminish the breeding ranges of peregrine populations of the Eurasian Arctic. Harnessing ecological interactions and evolutionary processes to study climate-driven changes in migration can facilitate the conservation of migratory birds.
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Affiliation(s)
- Zhongru Gu
- Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China.,Cardiff University-Institute of Zoology Joint Laboratory for Biocomplexity Research, Chinese Academy of Sciences, Beijing, China.,University of the Chinese Academy of Sciences, Beijing, China
| | - Shengkai Pan
- Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China.,Cardiff University-Institute of Zoology Joint Laboratory for Biocomplexity Research, Chinese Academy of Sciences, Beijing, China
| | - Zhenzhen Lin
- Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China.,Cardiff University-Institute of Zoology Joint Laboratory for Biocomplexity Research, Chinese Academy of Sciences, Beijing, China
| | - Li Hu
- Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China.,Cardiff University-Institute of Zoology Joint Laboratory for Biocomplexity Research, Chinese Academy of Sciences, Beijing, China.,University of the Chinese Academy of Sciences, Beijing, China
| | - Xiaoyang Dai
- School of Biological Sciences, University of Bristol, Bristol, UK
| | - Jiang Chang
- State Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Sciences, Beijing, China
| | - Yuanchao Xue
- Key Laboratory of RNA Biology, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
| | - Han Su
- Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China.,Cardiff University-Institute of Zoology Joint Laboratory for Biocomplexity Research, Chinese Academy of Sciences, Beijing, China.,University of the Chinese Academy of Sciences, Beijing, China
| | - Juan Long
- Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China.,Cardiff University-Institute of Zoology Joint Laboratory for Biocomplexity Research, Chinese Academy of Sciences, Beijing, China.,University of the Chinese Academy of Sciences, Beijing, China
| | - Mengru Sun
- University of the Chinese Academy of Sciences, Beijing, China.,Key Laboratory of RNA Biology, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
| | | | - Vasiliy Sokolov
- Institute of Plant and Animal Ecology, Ural Division Russian Academy of Sciences, Ekaterinburg, Russia
| | - Aleksandr Sokolov
- Arctic Research Station of the Institute of Plant and Animal Ecology, Ural Division Russian Academy of Sciences, Labytnangi, Russia
| | - Ivan Pokrovsky
- Arctic Research Station of the Institute of Plant and Animal Ecology, Ural Division Russian Academy of Sciences, Labytnangi, Russia.,Department of Migration, Max Planck Institute of Animal Behavior, Radolfzell, Germany.,Laboratory of Ornithology, Institute of Biological Problems of the North FEB RAS, Magadan, Russia
| | - Fen Ji
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Michael W Bruford
- Cardiff University-Institute of Zoology Joint Laboratory for Biocomplexity Research, Chinese Academy of Sciences, Beijing, China.,School of Biosciences and Sustainable Places Institute, Cardiff University, Cardiff, UK
| | - Andrew Dixon
- Cardiff University-Institute of Zoology Joint Laboratory for Biocomplexity Research, Chinese Academy of Sciences, Beijing, China.,Emirates Falconers' Club, Abu Dhabi, United Arab Emirates.,Reneco International Wildlife Consultants, Abu Dhabi, United Arab Emirates.,International Wildlife Consultants, Carmarthen, UK
| | - Xiangjiang Zhan
- Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China. .,Cardiff University-Institute of Zoology Joint Laboratory for Biocomplexity Research, Chinese Academy of Sciences, Beijing, China. .,University of the Chinese Academy of Sciences, Beijing, China. .,Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming, China.
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21
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Eydivandi S, Roudbar MA, Karimi MO, Sahana G. Genomic scans for selective sweeps through haplotype homozygosity and allelic fixation in 14 indigenous sheep breeds from Middle East and South Asia. Sci Rep 2021; 11:2834. [PMID: 33531649 PMCID: PMC7854752 DOI: 10.1038/s41598-021-82625-2] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2020] [Accepted: 01/22/2021] [Indexed: 01/30/2023] Open
Abstract
The performance and productivity of livestock have consistently improved by natural and artificial selection over the centuries. Both these selections are expected to leave patterns on the genome and lead to changes in allele frequencies, but natural selection has played the major role among indigenous populations. Detecting selective sweeps in livestock may assist in understanding the processes involved in domestication, genome evolution and discovery of genomic regions associated with economically important traits. We investigated population genetic diversity and selection signals in this study using SNP genotype data of 14 indigenous sheep breeds from Middle East and South Asia, including six breeds from Iran, namely Iranian Balochi, Afshari, Moghani, Qezel, Zel, and Lori-Bakhtiari, three breeds from Afghanistan, namely Afghan Balochi, Arabi, and Gadik, three breeds from India, namely Indian Garole, Changthangi, and Deccani, and two breeds from Bangladesh, namely Bangladeshi Garole and Bangladesh East. The SNP genotype data were generated by the Illumina OvineSNP50 Genotyping BeadChip array. To detect genetic diversity and population structure, we used principal component analysis (PCA), admixture, phylogenetic analyses, and Runs of homozygosity. We applied four complementary statistical tests, FST (fixation index), xp-EHH (cross-population extended haplotype homozygosity), Rsb (extended haplotype homozygosity between-populations), and FLK (the extension of the Lewontin and Krakauer) to detect selective sweeps. Our results not only confirm the previous studies but also provide a suite of novel candidate genes involved in different traits in sheep. On average, FST, xp-EHH, Rsb, and FLK detected 128, 207, 222, and 252 genomic regions as candidates for selective sweeps, respectively. Furthermore, nine overlapping candidate genes were detected by these four tests, especially TNIK, DOCK1, USH2A, and TYW1B which associate with resistance to diseases and climate adaptation. Knowledge of candidate genomic regions in sheep populations may facilitate the identification and potential exploitation of the underlying genes in sheep breeding.
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Affiliation(s)
- Sirous Eydivandi
- Department of Animal Science, Behbahan Branch, Islamic Azad University, Behbahan, Iran.
- Center for Quantitative Genetics and Genomics, Faculty of Technical Sciences, Aarhus University, 8830, Tjele, Denmark.
| | - Mahmoud Amiri Roudbar
- Department of Animal Science, Safiabad-Dezful Agricultural and Natural Resources Research and Education Center, Agricultural Research, Education and Extension Organization (AREEO), Dezful, Iran
| | - Mohammad Osman Karimi
- Department of Animal Science, Faculty of Agriculture, Herat University, Herat, Afghanistan
| | - Goutam Sahana
- Center for Quantitative Genetics and Genomics, Faculty of Technical Sciences, Aarhus University, 8830, Tjele, Denmark
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22
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Esoh KK, Apinjoh TO, Nyanjom SG, Wonkam A, Chimusa ER, Amenga-Etego L, Amambua-Ngwa A, Achidi EA. Fine scale human genetic structure in three regions of Cameroon reveals episodic diversifying selection. Sci Rep 2021; 11:1039. [PMID: 33441574 PMCID: PMC7807043 DOI: 10.1038/s41598-020-79124-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2020] [Accepted: 10/28/2020] [Indexed: 01/29/2023] Open
Abstract
Inferences from genetic association studies rely largely on the definition and description of the underlying populations that highlight their genetic similarities and differences. The clustering of human populations into subgroups (population structure) can significantly confound disease associations. This study investigated the fine-scale genetic structure within Cameroon that may underlie disparities observed with Cameroonian ethnicities in malaria genome-wide association studies in sub-Saharan Africa. Genotype data of 1073 individuals from three regions and three ethnic groups in Cameroon were analyzed using measures of genetic proximity to ascertain fine-scale genetic structure. Model-based clustering revealed distinct ancestral proportions among the Bantu, Semi-Bantu and Foulbe ethnic groups, while haplotype-based coancestry estimation revealed possible longstanding and ongoing sympatric differentiation among individuals of the Foulbe ethnic group, and their Bantu and Semi-Bantu counterparts. A genome scan found strong selection signatures in the HLA gene region, confirming longstanding knowledge of natural selection on this genomic region in African populations following immense disease pressure. Signatures of selection were also observed in the HBB gene cluster, a genomic region known to be under strong balancing selection in sub-Saharan Africa due to its co-evolution with malaria. This study further supports the role of evolution in shaping genomes of Cameroonian populations and reveals fine-scale hierarchical structure among and within Cameroonian ethnicities that may impact genetic association studies in the country.
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Affiliation(s)
- Kevin K Esoh
- Department of Biochemistry, Jomo Kenyatta University of Agriculture and Technology, P.O. Box 62000, Nairobi, City Square, Kenya
| | - Tobias O Apinjoh
- Department of Biochemistry and Molecular Biology, University of Buea, P.O. Box 63, Buea, South West Region, Cameroon.
| | - Steven G Nyanjom
- Department of Biochemistry, Jomo Kenyatta University of Agriculture and Technology, P.O. Box 62000, Nairobi, City Square, Kenya
| | - Ambroise Wonkam
- Division of Human Genetics, Department of Pathology, Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Health Sciences Campus, Anzio Rd, Observatory, 7925, South Africa
| | - Emile R Chimusa
- Division of Human Genetics, Department of Pathology, Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Health Sciences Campus, Anzio Rd, Observatory, 7925, South Africa
| | - Lucas Amenga-Etego
- West African Centre for Cell Biology of Infectious Pathogens, University of Ghana, Legon, Accra, Ghana
| | | | - Eric A Achidi
- Department of Biochemistry and Molecular Biology, University of Buea, P.O. Box 63, Buea, South West Region, Cameroon
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23
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Pfeifer B, Alachiotis N, Pavlidis P, Schimek MG. Genome scans for selection and introgression based on k-nearest neighbour techniques. Mol Ecol Resour 2020; 20:1597-1609. [PMID: 32639602 PMCID: PMC7689739 DOI: 10.1111/1755-0998.13221] [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: 10/24/2019] [Revised: 06/22/2020] [Accepted: 06/29/2020] [Indexed: 12/27/2022]
Abstract
In recent years, genome-scan methods have been extensively used to detect local signatures of selection and introgression. Most of these methods are either designed for one or the other case, which may impair the study of combined cases. Here, we introduce a series of versatile genome-scan methods applicable for both cases, the detection of selection and introgression. The proposed approaches are based on nonparametric k-nearest neighbour (kNN) techniques, while incorporating pairwise Fixation Index (FST ) and pairwise nucleotide differences (dxy ) as features. We benchmark our methods using a wide range of simulation scenarios, with varying parameters, such as recombination rates, population background histories, selection strengths, the proportion of introgression and the time of gene flow. We find that kNN-based methods perform remarkably well compared with the state-of-the-art. Finally, we demonstrate how to perform kNN-based genome scans on real-world genomic data using the population genomics R-package popgenome.
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Affiliation(s)
- Bastian Pfeifer
- Research Unit of Statistical Bioinformatics, Institute for Medical Informatics, Statistics and Documentation, Medical University of Graz, Graz, Austria
| | | | - Pavlos Pavlidis
- Institute of Computer Science, Foundation for Research and Technology-Hellas, Crete, Greece
| | - Michael G Schimek
- Research Unit of Statistical Bioinformatics, Institute for Medical Informatics, Statistics and Documentation, Medical University of Graz, Graz, Austria
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24
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Barrera-Redondo J, Piñero D, Eguiarte LE. Genomic, Transcriptomic and Epigenomic Tools to Study the Domestication of Plants and Animals: A Field Guide for Beginners. Front Genet 2020; 11:742. [PMID: 32760427 PMCID: PMC7373799 DOI: 10.3389/fgene.2020.00742] [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: 04/25/2020] [Accepted: 06/22/2020] [Indexed: 01/07/2023] Open
Abstract
In the last decade, genomics and the related fields of transcriptomics and epigenomics have revolutionized the study of the domestication process in plants and animals, leading to new discoveries and new unresolved questions. Given that some domesticated taxa have been more studied than others, the extent of genomic data can range from vast to nonexistent, depending on the domesticated taxon of interest. This review is meant as a rough guide for students and academics that want to start a domestication research project using modern genomic tools, as well as for researchers already conducting domestication studies that are interested in following a genomic approach and looking for alternate strategies (cheaper or more efficient) and future directions. We summarize the theoretical and technical background needed to carry out domestication genomics, starting from the acquisition of a reference genome and genome assembly, to the sampling design for population genomics, paleogenomics, transcriptomics, epigenomics and experimental validation of domestication-related genes. We also describe some examples of the aforementioned approaches and the relevant discoveries they made to understand the domestication of the studied taxa.
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Affiliation(s)
| | | | - Luis E. Eguiarte
- Departamento de Ecología Evolutiva, Instituto de Ecología, Universidad Nacional Autónoma de México, Mexico City, Mexico
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25
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Harris AM, DeGiorgio M. Identifying and Classifying Shared Selective Sweeps from Multilocus Data. Genetics 2020; 215:143-171. [PMID: 32152048 PMCID: PMC7198270 DOI: 10.1534/genetics.120.303137] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2019] [Accepted: 02/29/2020] [Indexed: 11/18/2022] Open
Abstract
Positive selection causes beneficial alleles to rise to high frequency, resulting in a selective sweep of the diversity surrounding the selected sites. Accordingly, the signature of a selective sweep in an ancestral population may still remain in its descendants. Identifying signatures of selection in the ancestor that are shared among its descendants is important to contextualize the timing of a sweep, but few methods exist for this purpose. We introduce the statistic SS-H12, which can identify genomic regions under shared positive selection across populations and is based on the theory of the expected haplotype homozygosity statistic H12, which detects recent hard and soft sweeps from the presence of high-frequency haplotypes. SS-H12 is distinct from comparable statistics because it requires a minimum of only two populations, and properly identifies and differentiates between independent convergent sweeps and true ancestral sweeps, with high power and robustness to a variety of demographic models. Furthermore, we can apply SS-H12 in conjunction with the ratio of statistics we term [Formula: see text] and [Formula: see text] to further classify identified shared sweeps as hard or soft. Finally, we identified both previously reported and novel shared sweep candidates from human whole-genome sequences. Previously reported candidates include the well-characterized ancestral sweeps at LCT and SLC24A5 in Indo-Europeans, as well as GPHN worldwide. Novel candidates include an ancestral sweep at RGS18 in sub-Saharan Africans involved in regulating the platelet response and implicated in sudden cardiac death, and a convergent sweep at C2CD5 between European and East Asian populations that may explain their different insulin responses.
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Affiliation(s)
- Alexandre M Harris
- Department of Biology, Pennsylvania State University, University Park, Pennsylvania 16802
- Molecular, Cellular, and Integrative Biosciences at the Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, Pennsylvania 16802
| | - Michael DeGiorgio
- Department of Computer and Electrical Engineering and Computer Science, Florida Atlantic University, Boca Raton, Florida 33431
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26
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Scossa F, Fernie AR. The evolution of metabolism: How to test evolutionary hypotheses at the genomic level. Comput Struct Biotechnol J 2020; 18:482-500. [PMID: 32180906 PMCID: PMC7063335 DOI: 10.1016/j.csbj.2020.02.009] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2019] [Revised: 02/12/2020] [Accepted: 02/13/2020] [Indexed: 01/21/2023] Open
Abstract
The origin of primordial metabolism and its expansion to form the metabolic networks extant today represent excellent systems to study the impact of natural selection and the potential adaptive role of novel compounds. Here we present the current hypotheses made on the origin of life and ancestral metabolism and present the theories and mechanisms by which the large chemical diversity of plants might have emerged along evolution. In particular, we provide a survey of statistical methods that can be used to detect signatures of selection at the gene and population level, and discuss potential and limits of these methods for investigating patterns of molecular adaptation in plant metabolism.
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Affiliation(s)
- Federico Scossa
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, 14476 Potsdam-Golm, Germany
- Council for Agricultural Research and Economics (CREA), Research Centre for Genomics and Bioinformatics (CREA-GB), Via Ardeatina 546, 00178 Rome, Italy
| | - Alisdair R. Fernie
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, 14476 Potsdam-Golm, Germany
- Center of Plant Systems Biology and Biotechnology (CPSBB), Plovdiv, Bulgaria
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27
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Morris KM, Hindle MM, Boitard S, Burt DW, Danner AF, Eory L, Forrest HL, Gourichon D, Gros J, Hillier LW, Jaffredo T, Khoury H, Lansford R, Leterrier C, Loudon A, Mason AS, Meddle SL, Minvielle F, Minx P, Pitel F, Seiler JP, Shimmura T, Tomlinson C, Vignal A, Webster RG, Yoshimura T, Warren WC, Smith J. The quail genome: insights into social behaviour, seasonal biology and infectious disease response. BMC Biol 2020; 18:14. [PMID: 32050986 PMCID: PMC7017630 DOI: 10.1186/s12915-020-0743-4] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2019] [Accepted: 01/24/2020] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND The Japanese quail (Coturnix japonica) is a popular domestic poultry species and an increasingly significant model species in avian developmental, behavioural and disease research. RESULTS We have produced a high-quality quail genome sequence, spanning 0.93 Gb assigned to 33 chromosomes. In terms of contiguity, assembly statistics, gene content and chromosomal organisation, the quail genome shows high similarity to the chicken genome. We demonstrate the utility of this genome through three diverse applications. First, we identify selection signatures and candidate genes associated with social behaviour in the quail genome, an important agricultural and domestication trait. Second, we investigate the effects and interaction of photoperiod and temperature on the transcriptome of the quail medial basal hypothalamus, revealing key mechanisms of photoperiodism. Finally, we investigate the response of quail to H5N1 influenza infection. In quail lung, many critical immune genes and pathways were downregulated after H5N1 infection, and this may be key to the susceptibility of quail to H5N1. CONCLUSIONS We have produced a high-quality genome of the quail which will facilitate further studies into diverse research questions using the quail as a model avian species.
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Affiliation(s)
- Katrina M Morris
- The Roslin Institute and R(D)SVS, University of Edinburgh, Easter Bush, Midlothian, EH25 9RG, UK.
| | - Matthew M Hindle
- The Roslin Institute and R(D)SVS, University of Edinburgh, Easter Bush, Midlothian, EH25 9RG, UK
| | - Simon Boitard
- GenPhySE, Université de Toulouse, INRAE, ENVT, 31326, Castanet Tolosan, France
| | - David W Burt
- The John Hay Building, Queensland Biosciences Precinct, 306 Carmody Road, The University of Queensland, QLD, St Lucia, 4072, Australia
| | - Angela F Danner
- Virology Division, Department of Infectious Diseases, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN, 38105, USA
| | - Lel Eory
- The Roslin Institute and R(D)SVS, University of Edinburgh, Easter Bush, Midlothian, EH25 9RG, UK
| | - Heather L Forrest
- Virology Division, Department of Infectious Diseases, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN, 38105, USA
| | - David Gourichon
- PEAT Pôle d'Expérimentation Avicole de Tours, Centre de recherche Val de Loire, INRAE, 1295, Nouzilly, UE, France
| | - Jerome Gros
- Department of Developmental and Stem Cell Biology, Institut Pasteur, 25 rue du Docteur Roux, 75724, Cedex 15, Paris, France
- CNRS URA3738, 25 rue du Dr Roux, 75015, Paris, France
| | - LaDeana W Hillier
- McDonnell Genome Institute, Washington University School of Medicine, 4444 Forest Park Blvd, St Louis, MO, 63108, USA
| | - Thierry Jaffredo
- CNRS UMR7622, Inserm U 1156, Laboratoire de Biologie du Développement, Sorbonne Université, IBPS, 75005, Paris, France
| | - Hanane Khoury
- CNRS UMR7622, Inserm U 1156, Laboratoire de Biologie du Développement, Sorbonne Université, IBPS, 75005, Paris, France
| | - Rusty Lansford
- Department of Radiology and Developmental Neuroscience Program, Saban Research Institute, Children's Hospital Los Angeles and Keck School of Medicine of the University of Southern California, Los Angeles, CA, 90027, USA
| | - Christine Leterrier
- UMR85 Physiologie de la Reproduction et des Comportements, INRAE, CNRS, Université François Rabelais, IFCE, INRAE, Val de Loire, 37380, Nouzilly, Centre, France
| | - Andrew Loudon
- Centre for Biological Timing, Faculty of Biology, Medicine and Health, School of Medical Sciences, University of Manchester, 3.001, A.V. Hill Building, Oxford Road, Manchester, M13 9PT, UK
| | - Andrew S Mason
- The Roslin Institute and R(D)SVS, University of Edinburgh, Easter Bush, Midlothian, EH25 9RG, UK
| | - Simone L Meddle
- The Roslin Institute and R(D)SVS, University of Edinburgh, Easter Bush, Midlothian, EH25 9RG, UK
| | - Francis Minvielle
- GABI, INRAE, AgroParisTech, Université Paris-Saclay, 78350, Jouy-en-Josas, France
| | - Patrick Minx
- McDonnell Genome Institute, Washington University School of Medicine, 4444 Forest Park Blvd, St Louis, MO, 63108, USA
| | - Frédérique Pitel
- GenPhySE, Université de Toulouse, INRAE, ENVT, 31326, Castanet Tolosan, France
| | - J Patrick Seiler
- Virology Division, Department of Infectious Diseases, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN, 38105, USA
| | - Tsuyoshi Shimmura
- Department of Biological Production, Tokyo University of Agriculture and Technology, 3-8-1 Harumi-cho, Fuchu, Tokyo, 183-8538, Japan
| | - Chad Tomlinson
- McDonnell Genome Institute, Washington University School of Medicine, 4444 Forest Park Blvd, St Louis, MO, 63108, USA
| | - Alain Vignal
- GenPhySE, Université de Toulouse, INRAE, ENVT, 31326, Castanet Tolosan, France
| | - Robert G Webster
- Virology Division, Department of Infectious Diseases, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN, 38105, USA
| | - Takashi Yoshimura
- Institute of Transformative Bio-Molecules (WPI-ITbM), Nagoya University, Furo-cho, Chikusa-ku, Nagoya, 464-8601, Japan
| | - Wesley C Warren
- Department of Animal Sciences, Department of Surgery, Institute for Data Science and Informatics, University of Missouri, Bond Life Sciences Center, 1201 Rollins Street, Columbia, MO, 65211, USA
| | - Jacqueline Smith
- The Roslin Institute and R(D)SVS, University of Edinburgh, Easter Bush, Midlothian, EH25 9RG, UK
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28
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Price N, Lopez L, Platts AE, Lasky JR. In the presence of population structure: From genomics to candidate genes underlying local adaptation. Ecol Evol 2020; 10:1889-1904. [PMID: 32128123 PMCID: PMC7042746 DOI: 10.1002/ece3.6002] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2019] [Revised: 12/19/2019] [Accepted: 12/23/2019] [Indexed: 12/25/2022] Open
Abstract
Understanding the genomic signatures, genes, and traits underlying local adaptation of organisms to heterogeneous environments is of central importance to the field evolutionary biology. To identify loci underlying local adaptation, models that combine allelic and environmental variation while controlling for the effects of population structure have emerged as the method of choice. Despite being evaluated in simulation studies, there has not been a thorough investigation of empirical evidence supporting local adaptation across these alleles. To evaluate these methods, we use 875 Arabidopsis thaliana Eurasian accessions and two mixed models (GEMMA and LFMM) to identify candidate SNPs underlying local adaptation to climate. Subsequently, to assess evidence of local adaptation and function among significant SNPs, we examine allele frequency differentiation and recent selection across Eurasian populations, in addition to their distribution along quantitative trait loci (QTL) explaining fitness variation between Italy and Sweden populations and cis-regulatory/nonsynonymous sites showing significant selective constraint. Our results indicate that significant LFMM/GEMMA SNPs show low allele frequency differentiation and linkage disequilibrium across locally adapted Italy and Sweden populations, in addition to a poor association with fitness QTL peaks (highest logarithm of odds score). Furthermore, when examining derived allele frequencies across the Eurasian range, we find that these SNPs are enriched in low-frequency variants that show very large climatic differentiation but low levels of linkage disequilibrium. These results suggest that their enrichment along putative functional sites most likely represents deleterious variation that is independent of local adaptation. Among all the genomic signatures examined, only SNPs showing high absolute allele frequency differentiation (AFD) and linkage disequilibrium (LD) between Italy and Sweden populations showed a strong association with fitness QTL peaks and were enriched along selectively constrained cis-regulatory/nonsynonymous sites. Using these SNPs, we find strong evidence linking flowering time, freezing tolerance, and the abscisic-acid pathway to local adaptation.
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Affiliation(s)
- Nicholas Price
- Department of Bioagricultural Sciences & Pest ManagementColorado State UniversityFort CollinsCOUSA
- Department of Biological SciencesUniversity of CyprusNicosiaCyprus
| | - Lua Lopez
- Department of BiologyBinghamton University (State University of New York)BinghamtonNYUSA
| | - Adrian E. Platts
- Simons Center for Quantitative BiologyCold Spring Harbor LaboratoryCold Spring HarborNYUSA
- Department of BiologyCenter for Genomics and Systems BiologyNew York UniversityNew YorkNYUSA
| | - Jesse R. Lasky
- Department of BiologyPennsylvania State UniversityUniversity ParkPAUSA
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29
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Inference of Selection from Genetic Time Series Using Various Parametric Approximations to the Wright-Fisher Model. G3-GENES GENOMES GENETICS 2019; 9:4073-4086. [PMID: 31597676 PMCID: PMC6893182 DOI: 10.1534/g3.119.400778] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
Detecting genomic regions under selection is an important objective of population genetics. Typical analyses for this goal are based on exploiting genetic diversity patterns in present time data but rapid advances in DNA sequencing have increased the availability of time series genomic data. A common approach to analyze such data is to model the temporal evolution of an allele frequency as a Markov chain. Based on this principle, several methods have been proposed to infer selection intensity. One of their differences lies in how they model the transition probabilities of the Markov chain. Using the Wright-Fisher model is a natural choice but its computational cost is prohibitive for large population sizes so approximations to this model based on parametric distributions have been proposed. Here, we compared the performance of some of these approximations with respect to their power to detect selection and their estimation of the selection coefficient. We developped a new generic Hidden Markov Model likelihood calculator and applied it on genetic time series simulated under various evolutionary scenarios. The Beta with spikes approximation, which combines discrete fixation probabilities with a continuous Beta distribution, was found to perform consistently better than the others. This distribution provides an almost perfect fit to the Wright-Fisher model in terms of selection inference, for a computational cost that does not increase with population size. We further evaluated this model for population sizes not accessible to the Wright-Fisher model and illustrated its performance on a dataset of two divergently selected chicken populations.
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30
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Dolebo AT, Khayatzadeh N, Melesse A, Wragg D, Rekik M, Haile A, Rischkowsky B, Rothschild MF, Mwacharo JM. Genome-wide scans identify known and novel regions associated with prolificacy and reproduction traits in a sub-Saharan African indigenous sheep (Ovis aries). Mamm Genome 2019; 30:339-352. [PMID: 31758253 PMCID: PMC6884434 DOI: 10.1007/s00335-019-09820-5] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2019] [Accepted: 11/12/2019] [Indexed: 02/05/2023]
Abstract
Maximizing the number of offspring born per female is a key functionality trait in commercial- and/or subsistence-oriented livestock enterprises. Although the number of offspring born is closely associated with female fertility and reproductive success, the genetic control of these traits remains poorly understood in sub-Saharan Africa livestock. Using selection signature analysis performed on Ovine HD BeadChip data from the prolific Bonga sheep in Ethiopia, 41 candidate regions under selection were identified. The analysis revealed one strong selection signature on a candidate region on chromosome X spanning BMP15, suggesting this to be the primary candidate prolificacy gene in the breed. The analysis also identified several candidate regions spanning genes not reported before in prolific sheep but underlying fertility and reproduction in other species. The genes associated with female reproduction traits included SPOCK1 (age at first oestrus), GPR173 (mediator of ovarian cyclicity), HB-EGF (signalling early pregnancy success) and SMARCAL1 and HMGN3a (regulate gene expression during embryogenesis). The genes involved in male reproduction were FOXJ1 (sperm function and successful fertilization) and NME5 (spermatogenesis). We also observed genes such as PKD2L2, MAGED1 and KDM3B, which have been associated with diverse fertility traits in both sexes of other species. The results confirm the complexity of the genetic mechanisms underlying reproduction while suggesting that prolificacy in the Bonga sheep, and possibly African indigenous sheep is partly under the control of BMP15 while other genes that enhance male and female fertility are essential for reproductive fitness.
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Affiliation(s)
- Asrat Tera Dolebo
- Southern Agricultural Research Institute (SARI), P.O. Box 06, Hawassa, Ethiopia
- Department of Animal and Range Sciences, Hawassa University, P.O Box 5, Hawassa, Ethiopia
| | - Negar Khayatzadeh
- Department of Sustainable Agricultural Systems, Division of Livestock Sciences, University of Natural Resources and Life Sciences (BOKU), Gregor-Mendel-Strasse, 1180, Vienna, Austria
| | - Aberra Melesse
- Department of Animal and Range Sciences, Hawassa University, P.O Box 5, Hawassa, Ethiopia
| | - David Wragg
- Centre for Tropical Livestock Genetics and Health, The Roslin Institute, Edinburgh, UK
| | - Mourad Rekik
- Small Ruminant Genomics, International Centre for Agricultural Research in the Dry Areas (ICARDA), P.O. Box 5689, Addis Ababa, Ethiopia
| | - Aynalem Haile
- Small Ruminant Genomics, International Centre for Agricultural Research in the Dry Areas (ICARDA), P.O. Box 5689, Addis Ababa, Ethiopia
| | - Barbara Rischkowsky
- Small Ruminant Genomics, International Centre for Agricultural Research in the Dry Areas (ICARDA), P.O. Box 5689, Addis Ababa, Ethiopia
| | - Max F Rothschild
- Department of Animal Science, Iowa State University, 2255 Kildee Hall, Ames, IA, 50011-3150, USA
| | - Joram M Mwacharo
- Small Ruminant Genomics, International Centre for Agricultural Research in the Dry Areas (ICARDA), P.O. Box 5689, Addis Ababa, Ethiopia.
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31
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Llanos‐Garrido A, Pérez‐Tris J, Díaz JA. The combined use of raw and phylogenetically independent methods of outlier detection uncovers genome-wide dynamics of local adaptation in a lizard. Ecol Evol 2019; 9:14356-14367. [PMID: 31938524 PMCID: PMC6953648 DOI: 10.1002/ece3.5872] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2019] [Revised: 10/04/2019] [Accepted: 10/10/2019] [Indexed: 02/06/2023] Open
Abstract
Local adaptation is a dynamic process by which different allele combinations are selected in different populations at different times, and whose genetic signature can be inferred by genome-wide outlier analyses. We combined gene flow estimates with two methods of outlier detection, one of them independent of population coancestry (CIOA) and the other one not (ROA), to identify genetic variants favored when ecology promotes phenotypic convergence. We analyzed genotyping-by-sequencing data from five populations of a lizard distributed over an environmentally heterogeneous range that has been changing since the split of eastern and western lineages ca. 3 mya. Overall, western lizards inhabit forest habitat and are unstriped, whereas eastern ones inhabit shrublands and are striped. However, one population (Lerma) has unstriped phenotype despite its eastern ancestry. The analysis of 73,291 SNPs confirmed the east-west division and identified nonoverlapping sets of outliers (12 identified by ROA and 9 by CIOA). ROA revealed ancestral adaptive variation in the uncovered outliers that were subject to divergent selection and differently fixed for eastern and western populations at the extremes of the environmental gradient. Interestingly, such variation was maintained in Lerma, where we found high levels of heterozygosity for ROA outliers, whereas CIOA uncovered innovative variants that were selected only there. Overall, it seems that both the maintenance of ancestral variation and asymmetric migration have counterbalanced adaptive lineage splitting in our model species. This scenario, which is likely promoted by a changing and heterogeneous environment, could hamper ecological speciation of locally adapted populations despite strong genetic structure between lineages.
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Affiliation(s)
- Alejandro Llanos‐Garrido
- Informatics GroupFaculty of Arts and SciencesHarvard UniversityCambridgeMAUSA
- Departamento de BiodiversidadUniversidad Complutense de MadridMadridSpain
| | - Javier Pérez‐Tris
- Departamento de BiodiversidadUniversidad Complutense de MadridMadridSpain
| | - José A. Díaz
- Departamento de BiodiversidadUniversidad Complutense de MadridMadridSpain
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32
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Fustier MA, Martínez-Ainsworth NE, Aguirre-Liguori JA, Venon A, Corti H, Rousselet A, Dumas F, Dittberner H, Camarena MG, Grimanelli D, Ovaskainen O, Falque M, Moreau L, de Meaux J, Montes-Hernández S, Eguiarte LE, Vigouroux Y, Manicacci D, Tenaillon MI. Common gardens in teosintes reveal the establishment of a syndrome of adaptation to altitude. PLoS Genet 2019; 15:e1008512. [PMID: 31860672 PMCID: PMC6944379 DOI: 10.1371/journal.pgen.1008512] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2019] [Revised: 01/06/2020] [Accepted: 11/07/2019] [Indexed: 12/14/2022] Open
Abstract
In plants, local adaptation across species range is frequent. Yet, much has to be discovered on its environmental drivers, the underlying functional traits and their molecular determinants. Genome scans are popular to uncover outlier loci potentially involved in the genetic architecture of local adaptation, however links between outliers and phenotypic variation are rarely addressed. Here we focused on adaptation of teosinte populations along two elevation gradients in Mexico that display continuous environmental changes at a short geographical scale. We used two common gardens, and phenotyped 18 traits in 1664 plants from 11 populations of annual teosintes. In parallel, we genotyped these plants for 38 microsatellite markers as well as for 171 outlier single nucleotide polymorphisms (SNPs) that displayed excess of allele differentiation between pairs of lowland and highland populations and/or correlation with environmental variables. Our results revealed that phenotypic differentiation at 10 out of the 18 traits was driven by local selection. Trait covariation along the elevation gradient indicated that adaptation to altitude results from the assembly of multiple co-adapted traits into a complex syndrome: as elevation increases, plants flower earlier, produce less tillers, display lower stomata density and carry larger, longer and heavier grains. The proportion of outlier SNPs associating with phenotypic variation, however, largely depended on whether we considered a neutral structure with 5 genetic groups (73.7%) or 11 populations (13.5%), indicating that population stratification greatly affected our results. Finally, chromosomal inversions were enriched for both SNPs whose allele frequencies shifted along elevation as well as phenotypically-associated SNPs. Altogether, our results are consistent with the establishment of an altitudinal syndrome promoted by local selective forces in teosinte populations in spite of detectable gene flow. Because elevation mimics climate change through space, SNPs that we found underlying phenotypic variation at adaptive traits may be relevant for future maize breeding.
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Affiliation(s)
- Margaux-Alison Fustier
- Génétique Quantitative et Evolution – Le Moulon, Université Paris-Saclay, Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement, Centre National de la Recherche Scientifique, AgroParisTech, Gif-sur-Yvette, France
| | - Natalia E. Martínez-Ainsworth
- Génétique Quantitative et Evolution – Le Moulon, Université Paris-Saclay, Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement, Centre National de la Recherche Scientifique, AgroParisTech, Gif-sur-Yvette, France
| | - Jonás A. Aguirre-Liguori
- Departamento de Ecología Evolutiva, Instituto de Ecología, Universidad Nacional Autónoma de México, Ciudad de México, Mexico
| | - Anthony Venon
- Génétique Quantitative et Evolution – Le Moulon, Université Paris-Saclay, Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement, Centre National de la Recherche Scientifique, AgroParisTech, Gif-sur-Yvette, France
| | - Hélène Corti
- Génétique Quantitative et Evolution – Le Moulon, Université Paris-Saclay, Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement, Centre National de la Recherche Scientifique, AgroParisTech, Gif-sur-Yvette, France
| | - Agnès Rousselet
- Génétique Quantitative et Evolution – Le Moulon, Université Paris-Saclay, Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement, Centre National de la Recherche Scientifique, AgroParisTech, Gif-sur-Yvette, France
| | - Fabrice Dumas
- Génétique Quantitative et Evolution – Le Moulon, Université Paris-Saclay, Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement, Centre National de la Recherche Scientifique, AgroParisTech, Gif-sur-Yvette, France
| | - Hannes Dittberner
- Institute of Botany, University of Cologne Biocenter, Cologne, Germany
| | - María G. Camarena
- Campo Experimental Bajío, InstitutoNacional de Investigaciones Forestales, Agrícolas y Pecuarias, Celaya, Mexico
| | - Daniel Grimanelli
- UMR Diversité, Adaptation et Développement des plantes, Université de Montpellier, Institut de Recherche pour le développement, Montpellier, France
| | - Otso Ovaskainen
- Organismal and Evolutionary Biology Research Programme, University of Helsinki, Helsinki, Finland
- Centre for Biodiversity Dynamics, Department of Biology, Norwegian University of Science and Technology, Trondheim, Norway
| | - Matthieu Falque
- Génétique Quantitative et Evolution – Le Moulon, Université Paris-Saclay, Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement, Centre National de la Recherche Scientifique, AgroParisTech, Gif-sur-Yvette, France
| | - Laurence Moreau
- Génétique Quantitative et Evolution – Le Moulon, Université Paris-Saclay, Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement, Centre National de la Recherche Scientifique, AgroParisTech, Gif-sur-Yvette, France
| | - Juliette de Meaux
- Institute of Botany, University of Cologne Biocenter, Cologne, Germany
| | - Salvador Montes-Hernández
- Campo Experimental Bajío, InstitutoNacional de Investigaciones Forestales, Agrícolas y Pecuarias, Celaya, Mexico
| | - Luis E. Eguiarte
- Departamento de Ecología Evolutiva, Instituto de Ecología, Universidad Nacional Autónoma de México, Ciudad de México, Mexico
| | - Yves Vigouroux
- UMR Diversité, Adaptation et Développement des plantes, Université de Montpellier, Institut de Recherche pour le développement, Montpellier, France
| | - Domenica Manicacci
- Génétique Quantitative et Evolution – Le Moulon, Université Paris-Saclay, Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement, Centre National de la Recherche Scientifique, AgroParisTech, Gif-sur-Yvette, France
| | - Maud I. Tenaillon
- Génétique Quantitative et Evolution – Le Moulon, Université Paris-Saclay, Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement, Centre National de la Recherche Scientifique, AgroParisTech, Gif-sur-Yvette, France
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33
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Refoyo-Martínez A, da Fonseca RR, Halldórsdóttir K, Árnason E, Mailund T, Racimo F. Identifying loci under positive selection in complex population histories. Genome Res 2019; 29:1506-1520. [PMID: 31362936 PMCID: PMC6724678 DOI: 10.1101/gr.246777.118] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2018] [Accepted: 07/23/2019] [Indexed: 12/24/2022]
Abstract
Detailed modeling of a species’ history is of prime importance for understanding how natural selection operates over time. Most methods designed to detect positive selection along sequenced genomes, however, use simplified representations of past histories as null models of genetic drift. Here, we present the first method that can detect signatures of strong local adaptation across the genome using arbitrarily complex admixture graphs, which are typically used to describe the history of past divergence and admixture events among any number of populations. The method—called graph-aware retrieval of selective sweeps (GRoSS)—has good power to detect loci in the genome with strong evidence for past selective sweeps and can also identify which branch of the graph was most affected by the sweep. As evidence of its utility, we apply the method to bovine, codfish, and human population genomic data containing panels of multiple populations related in complex ways. We find new candidate genes for important adaptive functions, including immunity and metabolism in understudied human populations, as well as muscle mass, milk production, and tameness in specific bovine breeds. We are also able to pinpoint the emergence of large regions of differentiation owing to inversions in the history of Atlantic codfish.
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Affiliation(s)
- Alba Refoyo-Martínez
- Lundbeck GeoGenetics Centre, The Globe Institute, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen 1350, Denmark
| | - Rute R da Fonseca
- Centre for Macroecology, Evolution and Climate, The Globe Institute, Faculty of Health and Medical Sciences, University of Copenhagen, Copehnagen 2100, Denmark
| | - Katrín Halldórsdóttir
- Faculty of Life and Environmental Sciences, University of Iceland, Reykjavík 107, Iceland
| | - Einar Árnason
- Faculty of Life and Environmental Sciences, University of Iceland, Reykjavík 107, Iceland.,Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, Massachusetts 02138, USA
| | - Thomas Mailund
- Bioinformatics Research Centre, Aarhus University, Aarhus 8000, Denmark
| | - Fernando Racimo
- Lundbeck GeoGenetics Centre, The Globe Institute, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen 1350, Denmark
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34
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Preite V, Sailer C, Syllwasschy L, Bray S, Ahmadi H, Krämer U, Yant L. Convergent evolution in Arabidopsis halleri and Arabidopsis arenosa on calamine metalliferous soils. Philos Trans R Soc Lond B Biol Sci 2019; 374:20180243. [PMID: 31154972 PMCID: PMC6560266 DOI: 10.1098/rstb.2018.0243] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/25/2019] [Indexed: 01/09/2023] Open
Abstract
It is a plausible hypothesis that parallel adaptation events to the same environmental challenge should result in genetic changes of similar or identical effects, depending on the underlying fitness landscapes. However, systematic testing of this is scarce. Here we examine this hypothesis in two closely related plant species, Arabidopsis halleri and Arabidopsis arenosa, which co-occur at two calamine metalliferous (M) sites harbouring toxic levels of the heavy metals zinc and cadmium. We conduct individual genome resequencing alongside soil elemental analysis for 64 plants from eight populations on M and non-metalliferous (NM) soils, and identify genomic footprints of selection and local adaptation. Selective sweep and environmental association analyses indicate a modest degree of gene as well as functional network convergence, whereby the proximal molecular factors mediating this convergence mostly differ between site pairs and species. Notably, we observe repeated selection on identical single nucleotide polymorphisms in several A. halleri genes at two independently colonized M sites. Our data suggest that species-specific metal handling and other biological features could explain a low degree of convergence between species. The parallel establishment of plant populations on calamine M soils involves convergent evolution, which will probably be more pervasive across sites purposely chosen for maximal similarity in soil composition. This article is part of the theme issue 'Convergent evolution in the genomics era: new insights and directions'.
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Affiliation(s)
- Veronica Preite
- Molecular Genetics and Physiology of Plants, Faculty of Biology and Biotechnology, Ruhr University Bochum, 44801 Bochum, Germany
| | - Christian Sailer
- Cell and Developmental Biology, John Innes Centre, Norwich NR4 7UH, UK
| | - Lara Syllwasschy
- Molecular Genetics and Physiology of Plants, Faculty of Biology and Biotechnology, Ruhr University Bochum, 44801 Bochum, Germany
| | - Sian Bray
- Cell and Developmental Biology, John Innes Centre, Norwich NR4 7UH, UK
| | - Hassan Ahmadi
- Molecular Genetics and Physiology of Plants, Faculty of Biology and Biotechnology, Ruhr University Bochum, 44801 Bochum, Germany
| | - Ute Krämer
- Molecular Genetics and Physiology of Plants, Faculty of Biology and Biotechnology, Ruhr University Bochum, 44801 Bochum, Germany
| | - Levi Yant
- Cell and Developmental Biology, John Innes Centre, Norwich NR4 7UH, UK
- School of Life Sciences, University of Nottingham, Nottingham NG7 2RD, UK
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35
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Lee KM, Coop G. Population genomics perspectives on convergent adaptation. Philos Trans R Soc Lond B Biol Sci 2019; 374:20180236. [PMID: 31154979 PMCID: PMC6560269 DOI: 10.1098/rstb.2018.0236] [Citation(s) in RCA: 40] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/21/2018] [Indexed: 01/12/2023] Open
Abstract
Convergent adaptation is the independent evolution of similar traits conferring a fitness advantage in two or more lineages. Cases of convergent adaptation inform our ideas about the ecological and molecular basis of adaptation. In judging the degree to which putative cases of convergent adaptation provide an independent replication of the process of adaptation, it is necessary to establish the degree to which the evolutionary change is unexpected under null models and to show that selection has repeatedly, independently driven these changes. Here, we discuss the issues that arise from these questions particularly for closely related populations, where gene flow and standing variation add additional layers of complexity. We outline a conceptual framework to guide intuition as to the extent to which evolutionary change represents the independent gain of information owing to selection and show that this is a measure of how surprised we should be by convergence. Additionally, we summarize the ways population and quantitative genetics and genomics may help us address questions related to convergent adaptation, as well as open new questions and avenues of research. This article is part of the theme issue 'Convergent evolution in the genomics era: new insights and directions'.
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Affiliation(s)
- Kristin M. Lee
- Center for Population Biology, University of California, Davis, CA 95616, USA
- Department of Evolution and Ecology, University of California, Davis, CA 95616, USA
| | - Graham Coop
- Center for Population Biology, University of California, Davis, CA 95616, USA
- Department of Evolution and Ecology, University of California, Davis, CA 95616, USA
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36
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Harpur BA, Guarna MM, Huxter E, Higo H, Moon KM, Hoover SE, Ibrahim A, Melathopoulos AP, Desai S, Currie RW, Pernal SF, Foster LJ, Zayed A. Integrative Genomics Reveals the Genetics and Evolution of the Honey Bee's Social Immune System. Genome Biol Evol 2019; 11:937-948. [PMID: 30768172 PMCID: PMC6447389 DOI: 10.1093/gbe/evz018] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/24/2019] [Indexed: 12/13/2022] Open
Abstract
Social organisms combat pathogens through individual innate immune responses or through social immunity—behaviors among individuals that limit pathogen transmission within groups. Although we have a relatively detailed understanding of the genetics and evolution of the innate immune system of animals, we know little about social immunity. Addressing this knowledge gap is crucial for understanding how life-history traits influence immunity, and identifying if trade-offs exist between innate and social immunity. Hygienic behavior in the Western honey bee, Apis mellifera, provides an excellent model for investigating the genetics and evolution of social immunity in animals. This heritable, colony-level behavior is performed by nurse bees when they detect and remove infected or dead brood from the colony. We sequenced 125 haploid genomes from two artificially selected highly hygienic populations and a baseline unselected population. Genomic contrasts allowed us to identify a minimum of 73 genes tentatively associated with hygienic behavior. Many genes were within previously discovered QTLs associated with hygienic behavior and were predictive of hygienic behavior within the unselected population. These genes were often involved in neuronal development and sensory perception in solitary insects. We found that genes associated with hygienic behavior have evidence of positive selection within honey bees (Apis), supporting the hypothesis that social immunity contributes to fitness. Our results indicate that genes influencing developmental neurobiology and behavior in solitary insects may have been co-opted to give rise to a novel and adaptive social immune phenotype in honey bees.
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Affiliation(s)
- Brock A Harpur
- Department of Entomology, Purdue University.,Department of Biology, York University, Toronto, Ontario, Canada
| | - Maria Marta Guarna
- Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, British Columbia, Canada.,Agriculture and Agri-Food Canada, Beaverlodge Research Farm, Beaverlodge, Alberta, Canada
| | | | - Heather Higo
- Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, British Columbia, Canada
| | - Kyung-Mee Moon
- Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, British Columbia, Canada
| | - Shelley E Hoover
- Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, British Columbia, Canada.,Agriculture and Agri-Food Canada, Beaverlodge Research Farm, Beaverlodge, Alberta, Canada.,Alberta Agriculture and Forestry, Agriculture Centre, Lethbridge, Alberta, Canada
| | - Abdullah Ibrahim
- Agriculture and Agri-Food Canada, Beaverlodge Research Farm, Beaverlodge, Alberta, Canada
| | - Andony P Melathopoulos
- Agriculture and Agri-Food Canada, Beaverlodge Research Farm, Beaverlodge, Alberta, Canada.,Department of Horticulture, College of Agricultural Sciences, Oregon State University
| | - Suresh Desai
- Department of Entomology, University of Manitoba, Winnipeg, Manitoba, Canada
| | - Robert W Currie
- Department of Entomology, University of Manitoba, Winnipeg, Manitoba, Canada
| | - Stephen F Pernal
- Agriculture and Agri-Food Canada, Beaverlodge Research Farm, Beaverlodge, Alberta, Canada
| | - Leonard J Foster
- Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, British Columbia, Canada
| | - Amro Zayed
- Department of Biology, York University, Toronto, Ontario, Canada
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37
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The Effect of Neutral Recombination Variation on Genome Scans for Selection. G3-GENES GENOMES GENETICS 2019; 9:1851-1867. [PMID: 30971391 PMCID: PMC6553532 DOI: 10.1534/g3.119.400088] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Recently, there has been an increasing interest in identifying the role that regions of low recombination or inversion play in adaptation of species to local environments. Many examples of groups of adapted genes located within inversions are arising in the literature, in part inspired by theory that predicts the evolution of these so-called “supergenes.” We still, however, have a poor understanding of how genomic heterogeneity, such as varying rates of recombination, may confound signals of selection. Here, I evaluate the effect of neutral inversions and recombination variation on genome scans for selection, including tests for selective sweeps, differentiation outlier tests, and association tests. There is considerable variation among methods in their performance, with some methods being unaffected and some showing elevated false positive signals within a neutral inversion or region of low recombination. In some cases the false positive signal can be dampened or removed, if it is possible to use a quasi-independent set of SNPs to parameterize the model before performing the test. These results will be helpful to those seeking to understand the importance of regions of low recombination in adaptation.
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38
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Vignal A, Boitard S, Thébault N, Dayo GK, Yapi-Gnaore V, Youssao Abdou Karim I, Berthouly-Salazar C, Pálinkás-Bodzsár N, Guémené D, Thibaud-Nissen F, Warren WC, Tixier-Boichard M, Rognon X. A guinea fowl genome assembly provides new evidence on evolution following domestication and selection in galliformes. Mol Ecol Resour 2019; 19:997-1014. [PMID: 30945415 PMCID: PMC6579635 DOI: 10.1111/1755-0998.13017] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2018] [Revised: 03/19/2019] [Accepted: 03/25/2019] [Indexed: 01/25/2023]
Abstract
The helmeted guinea fowl Numida meleagris belongs to the order Galliformes. Its natural range includes a large part of sub‐Saharan Africa, from Senegal to Eritrea and from Chad to South Africa. Archaeozoological and artistic evidence suggest domestication of this species may have occurred about 2,000 years BP in Mali and Sudan primarily as a food resource, although villagers also benefit from its capacity to give loud alarm calls in case of danger, of its ability to consume parasites such as ticks and to hunt snakes, thus suggesting its domestication may have resulted from a commensal association process. Today, it is still farmed in Africa, mainly as a traditional village poultry, and is also bred more intensively in other countries, mainly France and Italy. The lack of available molecular genetic markers has limited the genetic studies conducted to date on guinea fowl. We present here a first‐generation whole‐genome sequence draft assembly used as a reference for a study by a Pool‐seq approach of wild and domestic populations from Europe and Africa. We show that the domestic populations share a higher genetic similarity between each other than they do to wild populations living in the same geographical area. Several genomic regions showing selection signatures putatively related to domestication or importation to Europe were detected, containing candidate genes, most notably EDNRB2, possibly explaining losses in plumage coloration phenotypes in domesticated populations.
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Affiliation(s)
- Alain Vignal
- GenPhySE, INRA, INPT, INP-ENVT, Université de Toulouse, Castanet Tolosan, France
| | - Simon Boitard
- GenPhySE, INRA, INPT, INP-ENVT, Université de Toulouse, Castanet Tolosan, France
| | - Noémie Thébault
- GenPhySE, INRA, INPT, INP-ENVT, Université de Toulouse, Castanet Tolosan, France
| | | | | | | | | | | | | | - Francoise Thibaud-Nissen
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland
| | - Wesley C Warren
- McDonnell Genome Institute, Washington University School of Medicine, St. Louis, Missouri.,Bond Life Sciences Center, University of Missouri, Columbia, Missouri
| | | | - Xavier Rognon
- GABI, INRA, AgroParisTech, Université Paris-Saclay, Jouy-en-Josas, France
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39
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Librado P, Orlando L. Detecting Signatures of Positive Selection along Defined Branches of a Population Tree Using LSD. Mol Biol Evol 2019; 35:1520-1535. [PMID: 29617830 PMCID: PMC5967574 DOI: 10.1093/molbev/msy053] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Identifying the genomic basis underlying local adaptation is paramount to evolutionary biology, and bears many applications in the fields of conservation biology, crop, and animal breeding, as well as personalized medicine. Although many approaches have been developed to detect signatures of positive selection within single populations and population pairs, the increasing wealth of high-throughput sequencing data requires improved methods capable of handling multiple, and ideally large number of, populations in a single analysis. In this study, we introduce LSD (levels of exclusively shared differences), a fast and flexible framework to perform genome-wide selection scans, along the internal and external branches of a given population tree. We use forward simulations to demonstrate that LSD can identify branches targeted by positive selection with remarkable sensitivity and specificity. We illustrate a range of potential applications by analyzing data from the 1000 Genomes Project and uncover a list of adaptive candidates accompanying the expansion of anatomically modern humans out of Africa and their spread to Europe.
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Affiliation(s)
- Pablo Librado
- Centre for GeoGenetics, Natural History Museum of Denmark, Copenhagen, Denmark
- Laboratoire d’Anthropobiologie Moléculaire et d’Imagerie de Synthèse, CNRS UMR 5288, Université de Toulouse, Université Paul Sabatier, Toulouse, France
- Corresponding author: E-mail:
| | - Ludovic Orlando
- Centre for GeoGenetics, Natural History Museum of Denmark, Copenhagen, Denmark
- Laboratoire d’Anthropobiologie Moléculaire et d’Imagerie de Synthèse, CNRS UMR 5288, Université de Toulouse, Université Paul Sabatier, Toulouse, France
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40
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The Effects of Demography and Genetics on the Neutral Distribution of Quantitative Traits. Genetics 2019; 211:1371-1394. [PMID: 30782599 DOI: 10.1534/genetics.118.301839] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2018] [Accepted: 02/15/2019] [Indexed: 11/18/2022] Open
Abstract
Neutral models for quantitative trait evolution are useful for identifying phenotypes under selection. These models often assume normally distributed phenotypes. This assumption may be violated when a trait is affected by relatively few variants or when the effects of those variants arise from skewed or heavy tailed distributions. Molecular phenotypes such as gene expression levels may have these properties. To accommodate deviations from normality, models making fewer assumptions about the underlying genetics and patterns of variation are needed. Here, we develop a general neutral model for quantitative trait variation using a coalescent approach. This model allows interpretation of trait distributions in terms of familiar population genetic parameters because it is based on the coalescent. We show how the normal distribution resulting from the infinitesimal limit, where the number of loci grows large as the effect size per mutation becomes small, depends only on expected pairwise coalescent times. We then demonstrate how deviations from normality depend on demography through the distribution of coalescence times as well as through genetic parameters. In particular, population growth events exacerbate deviations while bottlenecks reduce them. We demonstrate the practical applications of this model by showing how to sample from the neutral distribution of [Formula: see text], the ratio of the variance between subpopulations to that in the overall population. We further show it is likely impossible to distinguish sparsity from skewed or heavy tailed mutational effects using only sampled trait values. The model analyzed here greatly expands the parameter space for neutral trait models.
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41
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Sun S, Miao Z, Ratcliffe B, Campbell P, Pasch B, El-Kassaby YA, Balasundaram B, Chen C. SNP variable selection by generalized graph domination. PLoS One 2019; 14:e0203242. [PMID: 30677030 PMCID: PMC6345469 DOI: 10.1371/journal.pone.0203242] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2018] [Accepted: 01/08/2019] [Indexed: 11/19/2022] Open
Abstract
BACKGROUND High-throughput sequencing technology has revolutionized both medical and biological research by generating exceedingly large numbers of genetic variants. The resulting datasets share a number of common characteristics that might lead to poor generalization capacity. Concerns include noise accumulated due to the large number of predictors, sparse information regarding the p≫n problem, and overfitting and model mis-identification resulting from spurious collinearity. Additionally, complex correlation patterns are present among variables. As a consequence, reliable variable selection techniques play a pivotal role in predictive analysis, generalization capability, and robustness in clustering, as well as interpretability of the derived models. METHODS AND FINDINGS K-dominating set, a parameterized graph-theoretic generalization model, was used to model SNP (single nucleotide polymorphism) data as a similarity network and searched for representative SNP variables. In particular, each SNP was represented as a vertex in the graph, (dis)similarity measures such as correlation coefficients or pairwise linkage disequilibrium were estimated to describe the relationship between each pair of SNPs; a pair of vertices are adjacent, i.e. joined by an edge, if the pairwise similarity measure exceeds a user-specified threshold. A minimum k-dominating set in the SNP graph was then made as the smallest subset such that every SNP that is excluded from the subset has at least k neighbors in the selected ones. The strength of k-dominating set selection in identifying independent variables, and in culling representative variables that are highly correlated with others, was demonstrated by a simulated dataset. The advantages of k-dominating set variable selection were also illustrated in two applications: pedigree reconstruction using SNP profiles of 1,372 Douglas-fir trees, and species delineation for 226 grasshopper mouse samples. A C++ source code that implements SNP-SELECT and uses Gurobi optimization solver for the k-dominating set variable selection is available (https://github.com/transgenomicsosu/SNP-SELECT).
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Affiliation(s)
- Shuzhen Sun
- Department of Biochemistry and Molecular Biology, Oklahoma State University, Stillwater, United States of America
- Department of Forest and Conservation Sciences, Faculty of Forestry, The University of British Columbia, Vancouver, B.C. Canada
| | - Zhuqi Miao
- Center for Health Systems Innovation, Oklahoma State University, Stillwater, United States of America
| | - Blaise Ratcliffe
- Department of Forest and Conservation Sciences, Faculty of Forestry, The University of British Columbia, Vancouver, B.C. Canada
| | - Polly Campbell
- Department of Integrative Biology, Oklahoma State University, Stillwater, United States of America
- Department of Evolution, Ecology and Organismal Biology, University of California, Riverside, Riverside, United States of America
| | - Bret Pasch
- Department of Biological Sciences, Northern Arizona University, Flagstaff, United States of America
| | - Yousry A. El-Kassaby
- Department of Forest and Conservation Sciences, Faculty of Forestry, The University of British Columbia, Vancouver, B.C. Canada
| | - Balabhaskar Balasundaram
- School of Industrial Engineering and Management, Oklahoma State University, Stillwater, United States of America
| | - Charles Chen
- Department of Biochemistry and Molecular Biology, Oklahoma State University, Stillwater, United States of America
- * E-mail:
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42
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Walugembe M, Bertolini F, Dematawewa CMB, Reis MP, Elbeltagy AR, Schmidt CJ, Lamont SJ, Rothschild MF. Detection of Selection Signatures Among Brazilian, Sri Lankan, and Egyptian Chicken Populations Under Different Environmental Conditions. Front Genet 2019; 9:737. [PMID: 30693019 PMCID: PMC6339939 DOI: 10.3389/fgene.2018.00737] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2018] [Accepted: 12/22/2018] [Indexed: 12/12/2022] Open
Abstract
Extreme environmental conditions are a major challenge in livestock production. Changes in climate, particularly those that contribute to weather extremes like drought or excessive humidity, may result in reduced performance and reproduction and could compromise the animal's immune function. Animal survival within extreme environmental conditions could be in response to natural selection and to artificial selection for production traits that over time together may leave selection signatures in the genome. The aim of this study was to identify selection signatures that may be involved in the adaptation of indigenous chickens from two different climatic regions (Sri Lanka = Tropical; Egypt = Arid) and in non-indigenous chickens that derived from human migration events to the generally tropical State of São Paulo, Brazil. To do so, analyses were conducted using fixation index (Fst) and hapFLK analyses. Chickens from Brazil (n = 156), Sri Lanka (n = 92), and Egypt (n = 96) were genotyped using the Affymetrix Axiom®600k Chicken Genotyping Array. Pairwise Fst analyses among countries did not detect major regions of divergence between chickens from Sri Lanka and Brazil, with ecotypes/breeds from Brazil appearing to be genetically related to Asian-Indian (Sri Lanka) ecotypes. However, several differences were detected in comparisons of Egyptian with either Sri Lankan or Brazilian populations, and common regions of difference on chromosomes 2, 3 and 8 were detected. The hapFLK analyses for the three separate countries suggested unique regions that are potentially under selection on chromosome 1 for all three countries, on chromosome 4 for Sri Lankan, and on chromosomes 3, 5, and 11 for the Egyptian populations. Some of identified regions under selection with hapFLK analyses contained genes such as TLR3, SOCS2, EOMES, and NFAT5 whose biological functions could provide insights in understanding adaptation mechanisms in response to arid and tropical environments.
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Affiliation(s)
- Muhammed Walugembe
- Department of Animal Science, Iowa State University, Ames, IA, United States
| | - Francesca Bertolini
- Department of Animal Science, Iowa State University, Ames, IA, United States
| | | | - Matheus P Reis
- Department of Animal Science, College of Agricultural and Veterinary Sciences, São Paulo State University, Jaboticabal, Brazil
| | - Ahmed R Elbeltagy
- Department of Animal Biotechnology, Animal Production Research Institute, Giza, Egypt
| | - Carl J Schmidt
- Animal and Food Sciences, University of Delaware, Newark, DE, United States
| | - Susan J Lamont
- Department of Animal Science, Iowa State University, Ames, IA, United States
| | - Max F Rothschild
- Department of Animal Science, Iowa State University, Ames, IA, United States
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43
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Cheruiyot EK, Bett RC, Amimo JO, Zhang Y, Mrode R, Mujibi FDN. Signatures of Selection in Admixed Dairy Cattle in Tanzania. Front Genet 2018; 9:607. [PMID: 30619449 PMCID: PMC6305962 DOI: 10.3389/fgene.2018.00607] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2018] [Accepted: 11/19/2018] [Indexed: 01/07/2023] Open
Abstract
Multiple studies have investigated selection signatures in domestic cattle and other species. However, there is a dearth of information about the response to selection in genomes of highly admixed crossbred cattle in relation to production and adaptation to tropical environments. In this study, we evaluated 839 admixed crossbred cows sampled from two major dairy regions in Tanzania namely Rungwe and Lushoto districts, in order to understand their genetic architecture and detect genomic regions showing preferential selection. Animals were genotyped at 150,000 SNP loci using the Geneseek Genomic Profiler (GGP) High Density (HD) SNP array. Population structure analysis showed a large within-population genetic diversity in the study animals with a high degree of variation in admixture ranging between 7 and 100% taurine genes (dairyness) of mostly Holstein and Friesian ancestry. We explored evidence of selection signatures using three statistical methods (iHS, XP-EHH, and pcadapt). Selection signature analysis identified 108 candidate selection regions in the study population. Annotation of these regions yielded interesting genes potentially under strong positive selection including ABCG2, ABCC2, XKR4, LYN, TGS1, TOX, HERC6, KIT, PLAG1, CHCHD7, NCAPG, and LCORL that are involved in multiple biological pathways underlying production and adaptation processes. Several candidate selection regions showed an excess of African taurine ancestral allele dosage. Our results provide further useful insight into potential selective sweeps in the genome of admixed cattle with possible adaptive and productive importance. Further investigations will be necessary to better characterize these candidate regions with respect to their functional significance to tropical adaptations for dairy cattle.
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Affiliation(s)
- Evans Kiptoo Cheruiyot
- Department of Animal Production, College of Agriculture and Veterinary Sciences, University of Nairobi, Nairobi, Kenya.,USOMI Limited, Nairobi, Kenya
| | - Rawlynce Cheruiyot Bett
- Department of Animal Production, College of Agriculture and Veterinary Sciences, University of Nairobi, Nairobi, Kenya
| | - Joshua Oluoch Amimo
- Department of Animal Production, College of Agriculture and Veterinary Sciences, University of Nairobi, Nairobi, Kenya
| | - Yi Zhang
- College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Raphael Mrode
- International Livestock Research Institute, Nairobi, Kenya.,Scotland's Rural College, Edinburgh, United Kingdom
| | - Fidalis D N Mujibi
- USOMI Limited, Nairobi, Kenya.,Nelson Mandela African Institute of Science and Technology, Arusha, Tanzania
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44
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Oget C, Servin B, Palhière I. Genetic diversity analysis of French goat populations reveals selective sweeps involved in their differentiation. Anim Genet 2018; 50:54-63. [PMID: 30549070 PMCID: PMC6590323 DOI: 10.1111/age.12752] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/19/2018] [Indexed: 12/31/2022]
Abstract
After domestication 11 000 years ago in Asia Minor, the goat followed human migration to Europe and Asia. It was then introduced in Africa and is now raised all over the world. In this study, we exploited a dataset composed of 54 000 SNPs (Illumina goat DNA chip) to analyze the genetic diversity of 223 individuals belonging to eight French breeds (Alpine, Angora, Corse, Fossés, Poitevine, Provençale, Pyrénées and Saanen). Analyses carried out included individual-based approaches (principal component analysis and population structure) and population-based approaches (phylogenetic tree constructions). The results of the genetic diversity analyses revealed that French breeds are clearly differentiated, in particular, the Angora breed that originates from south west Asia. The Provençale breed shows a very original genetic pattern that could be the result of ancient admixture. Then, selection signatures were detected by identifying regions of outlying genetic differentiation between populations. Five genomic regions were detected under selection on chromosomes 5, 6, 11, 13 and 20, revealing mainly soft selective sweeps and a few hard selective sweeps and highlighting candidate genes that had been selected for during the evolutionary history of these breeds. Among them, two coat coloration genes (ADAMTS20 and ASIP) and one gene related to milk composition (CSN1S1) were involved.
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Affiliation(s)
- C Oget
- GenPhySE, INRA, Université de Toulouse, INPT, ENVT, 31326, Castanet Tolosan, France
| | - B Servin
- GenPhySE, INRA, Université de Toulouse, INPT, ENVT, 31326, Castanet Tolosan, France
| | - I Palhière
- GenPhySE, INRA, Université de Toulouse, INPT, ENVT, 31326, Castanet Tolosan, France
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Bertolini F, Servin B, Talenti A, Rochat E, Kim ES, Oget C, Palhière I, Crisà A, Catillo G, Steri R, Amills M, Colli L, Marras G, Milanesi M, Nicolazzi E, Rosen BD, Van Tassell CP, Guldbrandtsen B, Sonstegard TS, Tosser-Klopp G, Stella A, Rothschild MF, Joost S, Crepaldi P. Signatures of selection and environmental adaptation across the goat genome post-domestication. Genet Sel Evol 2018; 50:57. [PMID: 30449276 PMCID: PMC6240954 DOI: 10.1186/s12711-018-0421-y] [Citation(s) in RCA: 88] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2017] [Accepted: 10/15/2018] [Indexed: 01/03/2023] Open
Abstract
BACKGROUND Since goat was domesticated 10,000 years ago, many factors have contributed to the differentiation of goat breeds and these are classified mainly into two types: (i) adaptation to different breeding systems and/or purposes and (ii) adaptation to different environments. As a result, approximately 600 goat breeds have developed worldwide; they differ considerably from one another in terms of phenotypic characteristics and are adapted to a wide range of climatic conditions. In this work, we analyzed the AdaptMap goat dataset, which is composed of data from more than 3000 animals collected worldwide and genotyped with the CaprineSNP50 BeadChip. These animals were partitioned into groups based on geographical area, production uses, available records on solid coat color and environmental variables including the sampling geographical coordinates, to investigate the role of natural and/or artificial selection in shaping the genome of goat breeds. RESULTS Several signatures of selection on different chromosomal regions were detected across the different breeds, sub-geographical clusters, phenotypic and climatic groups. These regions contain genes that are involved in important biological processes, such as milk-, meat- or fiber-related production, coat color, glucose pathway, oxidative stress response, size, and circadian clock differences. Our results confirm previous findings in other species on adaptation to extreme environments and human purposes and provide new genes that could explain some of the differences between goat breeds according to their geographical distribution and adaptation to different environments. CONCLUSIONS These analyses of signatures of selection provide a comprehensive first picture of the global domestication process and adaptation of goat breeds and highlight possible genes that may have contributed to the differentiation of this species worldwide.
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Affiliation(s)
- Francesca Bertolini
- Department of Animal Science, Iowa State University, Ames, IA 50011 USA
- National Institute of Aquatic Resources, Technical University of Denmark (DTU), 2800 Lyngby, Denmark
| | - Bertrand Servin
- GenPhySE, INRA, Université de Toulouse, INPT, ENVT, 31326 Castanet Tolosan, France
| | - Andrea Talenti
- Dipartimento di Medicina Veterinaria, Università degli Studi di Milano, 20133 Milan, Italy
| | - Estelle Rochat
- Laboratory of Geographic Information Systems (LASIG), School of Architecture, Civil and Environmental Engineering (ENAC), Ecole Polytechnique Fédérale de Lausanne (EPFL), 1015 Lausanne, Switzerland
| | | | - Claire Oget
- GenPhySE, INRA, Université de Toulouse, INPT, ENVT, 31326 Castanet Tolosan, France
| | - Isabelle Palhière
- GenPhySE, INRA, Université de Toulouse, INPT, ENVT, 31326 Castanet Tolosan, France
| | - Alessandra Crisà
- Consiglio per la ricerca in agricoltura e l’analisi dell’economia agraria (CREA) - Research Centre for Animal Production and Acquaculture, 00015 Monterotondo, Roma, Italy
| | - Gennaro Catillo
- Consiglio per la ricerca in agricoltura e l’analisi dell’economia agraria (CREA) - Research Centre for Animal Production and Acquaculture, 00015 Monterotondo, Roma, Italy
| | - Roberto Steri
- Consiglio per la ricerca in agricoltura e l’analisi dell’economia agraria (CREA) - Research Centre for Animal Production and Acquaculture, 00015 Monterotondo, Roma, Italy
| | - Marcel Amills
- Centre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB, Campus Universitat Autonoma de Barcelona, Bellaterra, 08193 Barcelona, Spain
| | - Licia Colli
- DIANA Dipartimento di Scienze Animali, della Nutrizione e degli Alimenti, Università Cattolica del S. Cuore, 29100 Piacenza, Italy
- BioDNA Centro di Ricerca sulla Biodiversità e sul DNA Antico, Università Cattolica del S. Cuore, 29100 Piacenza, Italy
| | - Gabriele Marras
- Fondazione Parco Tecnologico Padano (PTP), 26900 Lodi, Italy
| | - Marco Milanesi
- DIANA Dipartimento di Scienze Animali, della Nutrizione e degli Alimenti, Università Cattolica del S. Cuore, 29100 Piacenza, Italy
- Department of Support, Production and Animal Health, School of Veterinary Medicine, São Paulo State University (UNESP), Araçatuba, Brazil
| | | | - Benjamin D. Rosen
- Animal Genomics and Improvement Laboratory, ARS USDA, Beltsville, MD 20705 USA
| | | | - Bernt Guldbrandtsen
- Center for Quantitative Genetics and Genomics, Aarhus University, 8830 Tjele, Denmark
| | | | - Gwenola Tosser-Klopp
- GenPhySE, INRA, Université de Toulouse, INPT, ENVT, 31326 Castanet Tolosan, France
| | - Alessandra Stella
- BioDNA Centro di Ricerca sulla Biodiversità e sul DNA Antico, Università Cattolica del S. Cuore, 29100 Piacenza, Italy
| | - Max F. Rothschild
- Department of Animal Science, Iowa State University, Ames, IA 50011 USA
| | - Stéphane Joost
- Laboratory of Geographic Information Systems (LASIG), School of Architecture, Civil and Environmental Engineering (ENAC), Ecole Polytechnique Fédérale de Lausanne (EPFL), 1015 Lausanne, Switzerland
| | - Paola Crepaldi
- Dipartimento di Medicina Veterinaria, Università degli Studi di Milano, 20133 Milan, Italy
| | - the AdaptMap consortium
- Department of Animal Science, Iowa State University, Ames, IA 50011 USA
- National Institute of Aquatic Resources, Technical University of Denmark (DTU), 2800 Lyngby, Denmark
- GenPhySE, INRA, Université de Toulouse, INPT, ENVT, 31326 Castanet Tolosan, France
- Dipartimento di Medicina Veterinaria, Università degli Studi di Milano, 20133 Milan, Italy
- Laboratory of Geographic Information Systems (LASIG), School of Architecture, Civil and Environmental Engineering (ENAC), Ecole Polytechnique Fédérale de Lausanne (EPFL), 1015 Lausanne, Switzerland
- Recombinetics Inc, St Paul, 55104 MN USA
- Consiglio per la ricerca in agricoltura e l’analisi dell’economia agraria (CREA) - Research Centre for Animal Production and Acquaculture, 00015 Monterotondo, Roma, Italy
- Centre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB, Campus Universitat Autonoma de Barcelona, Bellaterra, 08193 Barcelona, Spain
- DIANA Dipartimento di Scienze Animali, della Nutrizione e degli Alimenti, Università Cattolica del S. Cuore, 29100 Piacenza, Italy
- BioDNA Centro di Ricerca sulla Biodiversità e sul DNA Antico, Università Cattolica del S. Cuore, 29100 Piacenza, Italy
- Fondazione Parco Tecnologico Padano (PTP), 26900 Lodi, Italy
- Department of Support, Production and Animal Health, School of Veterinary Medicine, São Paulo State University (UNESP), Araçatuba, Brazil
- Animal Genomics and Improvement Laboratory, ARS USDA, Beltsville, MD 20705 USA
- Center for Quantitative Genetics and Genomics, Aarhus University, 8830 Tjele, Denmark
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Rajpurohit S, Gefen E, Bergland AO, Petrov DA, Gibbs AG, Schmidt P. Spatiotemporal dynamics and genome-wide association genome-wide association analysis of desiccation tolerance in Drosophila melanogaster. Mol Ecol 2018; 27:3525-3540. [PMID: 30051644 PMCID: PMC6129450 DOI: 10.1111/mec.14814] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2016] [Revised: 06/11/2018] [Accepted: 06/20/2018] [Indexed: 12/13/2022]
Abstract
Water availability is a major environmental challenge to a variety of terrestrial organisms. In insects, desiccation tolerance varies predictably over spatial and temporal scales and is an important physiological determinant of fitness in natural populations. Here, we examine the dynamics of desiccation tolerance in North American populations of Drosophila melanogaster using: (a) natural populations sampled across latitudes and seasons; (b) experimental evolution in field mesocosms over seasonal time; (c) genome-wide associations to identify SNPs/genes associated with variation for desiccation tolerance; and (d) subsequent analysis of patterns of clinal/seasonal enrichment in existing pooled sequencing data of populations sampled in both North America and Australia. A cline in desiccation tolerance was observed, for which tolerance exhibited a positive association with latitude; tolerance also varied predictably with culture temperature, demonstrating a significant degree of thermal plasticity. Desiccation tolerance evolved rapidly in field mesocosms, although only males showed differences in desiccation tolerance between spring and autumn collections from natural populations. Water loss rates did not vary significantly among latitudinal or seasonal populations; however, changes in metabolic rates during prolonged exposure to dry conditions are consistent with increased tolerance in higher latitude populations. Genome-wide associations in a panel of inbred lines identified twenty-five SNPs in twenty-one loci associated with sex-averaged desiccation tolerance, but there is no robust signal of spatially varying selection on genes associated with desiccation tolerance. Together, our results suggest that desiccation tolerance is a complex and important fitness component that evolves rapidly and predictably in natural populations.
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Affiliation(s)
- Subhash Rajpurohit
- Department of Biology, University of Pennsylvania, 433 S. University Ave, Philadelphia, PA 19104, USA
| | - Eran Gefen
- Department of Biology, University of Haifa-Oranim, Tivon 36006, Israel
| | - Alan O. Bergland
- Department of Biology, University of Virginia, Charlottesville, VA 22903
| | - Dmitri A. Petrov
- Department of Biology, Stanford University, Stanford, CA 94305, USA
| | - Allen G. Gibbs
- School of Life Sciences, University of Nevada, Las Vegas, NV 89154, USA
| | - Paul Schmidt
- Department of Biology, University of Pennsylvania, 433 S. University Ave, Philadelphia, PA 19104, USA
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Consistent signatures of selection from genomic analysis of pairs of temporal and spatial Plasmodium falciparum populations from The Gambia. Sci Rep 2018; 8:9687. [PMID: 29946063 PMCID: PMC6018809 DOI: 10.1038/s41598-018-28017-5] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2018] [Accepted: 06/14/2018] [Indexed: 11/16/2022] Open
Abstract
Genome sequences of 247 Plasmodium falciparum isolates collected in The Gambia in 2008 and 2014 were analysed to identify changes possibly related to the scale-up of antimalarial interventions that occurred during this period. Overall, there were 15 regions across the genomes with signatures of positive selection. Five of these were sweeps around known drug resistance and antigenic loci. Signatures at antigenic loci such as thrombospodin related adhesive protein (Pftrap) were most frequent in eastern Gambia, where parasite prevalence and transmission remain high. There was a strong temporal differentiation at a non-synonymous SNP in a cysteine desulfarase (Pfnfs) involved in iron-sulphur complex biogenesis. During the 7-year period, the frequency of the lysine variant at codon 65 (Pfnfs-Q65K) increased by 22% (10% to 32%) in the Greater Banjul area. Between 2014 and 2015, the frequency of this variant increased by 6% (20% to 26%) in eastern Gambia. IC50 for lumefantrine was significantly higher in Pfnfs-65K isolates. This is probably the first evidence of directional selection on Pfnfs or linked loci by lumefantrine. Given the declining malaria transmission, the consequent loss of population immunity, and sustained drug pressure, it is important to monitor Gambian P. falciparum populations for further signs of adaptation.
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Bihan-Duval EL, Hennequet-Antier C, Berri C, Beauclercq SA, Bourin MC, Boulay M, Demeure O, Boitard S. Identification of genomic regions and candidate genes for chicken meat ultimate pH by combined detection of selection signatures and QTL. BMC Genomics 2018; 19:294. [PMID: 29695245 PMCID: PMC5918591 DOI: 10.1186/s12864-018-4690-1] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2017] [Accepted: 04/17/2018] [Indexed: 02/02/2023] Open
Abstract
BACKGROUND The understanding of the biological determinism of meat ultimate pH, which is strongly related to muscle glycogen content, is a key point for the control of muscle integrity and meat quality in poultry. In the present study, we took advantage of a unique model of two broiler lines divergently selected for the ultimate pH of the pectoralis major muscle (PM-pHu) in order to decipher the genetic control of this trait. Two complementary approaches were used: detection of selection signatures generated during the first five generations and genome-wide association study for PM-pHu and Sartorius muscle pHu (SART-pHu) at the sixth generation of selection. RESULTS Sixty-three genomic regions showed significant signatures of positive selection. Out of the 10 most significant regions (detected by HapFLK or FLK method with a p-value below 1e-6), 4 were detected as soon as the first generation (G1) and were recovered at each of the four following ones (G2-G5). Another four corresponded to a later onset of selection as they were detected only at G5. In total, 33 SNPs, located in 24 QTL regions, were significantly associated with PM-pHu. For SART-pHu, we detected 18 SNPs located in 10 different regions. These results confirmed a polygenic determinism for these traits and highlighted two major QTL: one for PM-pHu on GGA1 (with a Bayes Factor (BF) of 300) and one for SART-pHu on GGA4 (with a BF of 257). Although selection signatures were enriched in QTL for PM-pHu, several QTL with strong effect haven't yet responded to selection, suggesting that the divergence between lines might be further increased. CONCLUSIONS A few regions of major interest with significant selection signatures and/or strong association with PM-pHu or SART-pHu were evidenced for the first time in chicken. Their gene content suggests several candidates associated with diseases of glycogen storage in humans. The impact of these candidate genes on meat quality and muscle integrity should be further investigated in chicken.
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Affiliation(s)
| | | | - Cécile Berri
- BOA, INRA, Université de Tours, 37380, Nouzilly, France
| | | | - Marie Christine Bourin
- Institut Technique de l'Aviculture (ITAVI), Centre INRA Val de Loire, F-37380, Nouzilly, France
| | - Maryse Boulay
- Syndicat des Sélectionneurs Avicoles et Aquacoles Français (SYSAAF), Centre INRA Val de Loire, Unité de Recherches Avicoles, F-37380, Nouzilly, France
| | - Olivier Demeure
- PEGASE, Agrocampus Ouest, INRA, 35590,, Saint-Gilles, France.,Groupe Grimaud, La Corbière, 49450, Roussay, France
| | - Simon Boitard
- GenPhySE, Université de Toulouse, INRA, ENVT, 31320, Castanet Tolosan, France
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49
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Storfer A, Patton A, Fraik AK. Navigating the Interface Between Landscape Genetics and Landscape Genomics. Front Genet 2018; 9:68. [PMID: 29593776 PMCID: PMC5859105 DOI: 10.3389/fgene.2018.00068] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2017] [Accepted: 02/15/2018] [Indexed: 11/13/2022] Open
Abstract
As next-generation sequencing data become increasingly available for non-model organisms, a shift has occurred in the focus of studies of the geographic distribution of genetic variation. Whereas landscape genetics studies primarily focus on testing the effects of landscape variables on gene flow and genetic population structure, landscape genomics studies focus on detecting candidate genes under selection that indicate possible local adaptation. Navigating the transition between landscape genomics and landscape genetics can be challenging. The number of molecular markers analyzed has shifted from what used to be a few dozen loci to thousands of loci and even full genomes. Although genome scale data can be separated into sets of neutral loci for analyses of gene flow and population structure and putative loci under selection for inference of local adaptation, there are inherent differences in the questions that are addressed in the two study frameworks. We discuss these differences and their implications for study design, marker choice and downstream analysis methods. Similar to the rapid proliferation of analysis methods in the early development of landscape genetics, new analytical methods for detection of selection in landscape genomics studies are burgeoning. We focus on genome scan methods for detection of selection, and in particular, outlier differentiation methods and genetic-environment association tests because they are the most widely used. Use of genome scan methods requires an understanding of the potential mismatches between the biology of a species and assumptions inherent in analytical methods used, which can lead to high false positive rates of detected loci under selection. Key to choosing appropriate genome scan methods is an understanding of the underlying demographic structure of study populations, and such data can be obtained using neutral loci from the generated genome-wide data or prior knowledge of a species' phylogeographic history. To this end, we summarize recent simulation studies that test the power and accuracy of genome scan methods under a variety of demographic scenarios and sampling designs. We conclude with a discussion of additional considerations for future method development, and a summary of methods that show promise for landscape genomics studies but are not yet widely used.
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Affiliation(s)
- Andrew Storfer
- School of Biological Sciences, Washington State University, Pullman, WA, United States
| | - Austin Patton
- School of Biological Sciences, Washington State University, Pullman, WA, United States
| | - Alexandra K Fraik
- School of Biological Sciences, Washington State University, Pullman, WA, United States
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50
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Convergent genomic signatures of domestication in sheep and goats. Nat Commun 2018; 9:813. [PMID: 29511174 PMCID: PMC5840369 DOI: 10.1038/s41467-018-03206-y] [Citation(s) in RCA: 157] [Impact Index Per Article: 26.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2017] [Accepted: 01/29/2018] [Indexed: 12/15/2022] Open
Abstract
The evolutionary basis of domestication has been a longstanding question and its genetic architecture is becoming more tractable as more domestic species become genome-enabled. Before becoming established worldwide, sheep and goats were domesticated in the fertile crescent 10,500 years before present (YBP) where their wild relatives remain. Here we sequence the genomes of wild Asiatic mouflon and Bezoar ibex in the sheep and goat domestication center and compare their genomes with that of domestics from local, traditional, and improved breeds. Among the genomic regions carrying selective sweeps differentiating domestic breeds from wild populations, which are associated among others to genes involved in nervous system, immunity and productivity traits, 20 are common to Capra and Ovis. The patterns of selection vary between species, suggesting that while common targets of selection related to domestication and improvement exist, different solutions have arisen to achieve similar phenotypic end-points within these closely related livestock species. The sheep and goat were domesticated ~10,500 years ago in the same region of the Middle-East. Here, Alberto et al compare the genomes of wild Asiatic mouflon and Bezoar ibex with that of domestics from local, traditional and improved breeds and find common targets of selection related to domestication and improvement in sheep and goats.
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