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      Whole genome structural analysis of Caribbean hair sheep reveals quantitative link to West African ancestry

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          Abstract

          Hair sheep of Caribbean origin have become an important part of the U.S. sheep industry. Their lack of wool eliminates a number of health concerns and drastically reduces the cost of production. More importantly, Caribbean hair sheep demonstrate robust production performance even in the presence of drug-resistant gastrointestinal nematodes, a rising concern to the industry. Despite the growing importance of hair sheep in the Americas their genetic origins have remained speculative. Prior to this report no genetic studies were able to identify a unique geographical origin of hair sheep in the New World. Our study clarifies the African and European ancestry of Caribbean hair sheep. Whole-genome structural analysis was conducted on four established breeds of hair sheep from the Caribbean region. Using breeds representing Africa and Europe we establish an objective measure indicating Caribbean hair sheep are derived from Iberian and West African origins. Caribbean hair sheep result from West African introgression into established ecotypes of Iberian descent. Genotypes from 47,750 autosomal single nucleotide polymorphism markers scored in 290 animals were used to characterize the population structure of the St. Croix, Barbados Blackbelly, Morada Nova, and Santa Ines. Principal components, admixture, and phylogenetic analyses results correlate with historical patterns of colonization and trade. These patterns support co-migration of these sheep with humans.

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          SNPhylo: a pipeline to construct a phylogenetic tree from huge SNP data

          Background Phylogenetic trees are widely used for genetic and evolutionary studies in various organisms. Advanced sequencing technology has dramatically enriched data available for constructing phylogenetic trees based on single nucleotide polymorphisms (SNPs). However, massive SNP data makes it difficult to perform reliable analysis, and there has been no ready-to-use pipeline to generate phylogenetic trees from these data. Results We developed a new pipeline, SNPhylo, to construct phylogenetic trees based on large SNP datasets. The pipeline may enable users to construct a phylogenetic tree from three representative SNP data file formats. In addition, in order to increase reliability of a tree, the pipeline has steps such as removing low quality data and considering linkage disequilibrium. A maximum likelihood method for the inference of phylogeny is also adopted in generation of a tree in our pipeline. Conclusions Using SNPhylo, users can easily produce a reliable phylogenetic tree from a large SNP data file. Thus, this pipeline can help a researcher focus more on interpretation of the results of analysis of voluminous data sets, rather than manipulations necessary to accomplish the analysis.
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            Selection Signatures in Worldwide Sheep Populations

            The diversity of populations in domestic species offers great opportunities to study genome response to selection. The recently published Sheep HapMap dataset is a great example of characterization of the world wide genetic diversity in sheep. In this study, we re-analyzed the Sheep HapMap dataset to identify selection signatures in worldwide sheep populations. Compared to previous analyses, we made use of statistical methods that (i) take account of the hierarchical structure of sheep populations, (ii) make use of linkage disequilibrium information and (iii) focus specifically on either recent or older selection signatures. We show that this allows pinpointing several new selection signatures in the sheep genome and distinguishing those related to modern breeding objectives and to earlier post-domestication constraints. The newly identified regions, together with the ones previously identified, reveal the extensive genome response to selection on morphology, color and adaptation to new environments.
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              Domesticating Animals in Africa: Implications of Genetic and Archaeological Findings

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                Author and article information

                Contributors
                Role: ConceptualizationRole: Data curationRole: Formal analysisRole: InvestigationRole: MethodologyRole: SupervisionRole: ValidationRole: VisualizationRole: Writing – original draftRole: Writing – review & editing
                Role: Data curationRole: Formal analysisRole: InvestigationRole: MethodologyRole: ValidationRole: VisualizationRole: Writing – original draftRole: Writing – review & editing
                Role: InvestigationRole: Resources
                Role: InvestigationRole: Resources
                Role: Formal analysis
                Role: Funding acquisitionRole: Methodology
                Role: Investigation
                Role: Investigation
                Role: Investigation
                Role: Funding acquisitionRole: MethodologyRole: Project administrationRole: ResourcesRole: SupervisionRole: ValidationRole: Writing – review & editing
                Role: Editor
                Journal
                PLoS One
                PLoS ONE
                plos
                plosone
                PLoS ONE
                Public Library of Science (San Francisco, CA USA )
                1932-6203
                29 June 2017
                2017
                : 12
                : 6
                : e0179021
                Affiliations
                [1 ]Animal Genomics and Improvement Laboratory, Agricultural Research Service, United States Department of Agriculture, Beltsville, Maryland, United States of America
                [2 ]School of Life Sciences, University of Nottingham, Nottingham, United Kingdom
                [3 ]Acceligen of Recombinetics Incorporated, Saint Paul, Minnesota, United States of America
                [4 ]Dale Bumpers Small Farms Research Station, Agricultural Research Service, United States Department of Agriculture, Booneville, Arkansas, United States of America
                [5 ]Katahdin Hair Sheep International, Fayetteville, Arkansas, United States of America
                [6 ]Department of Animal and Poultry Sciences, Virginia Tech, Blacksburg, Virginia, United States of America
                China Agricultural University, CHINA
                Author notes

                Competing Interests: The authors have declared that no competing interests exist.

                Author information
                http://orcid.org/0000-0001-9395-8346
                Article
                PONE-D-16-39180
                10.1371/journal.pone.0179021
                5490989
                28662044
                c718dc07-2b50-4b4d-a6ca-8dbd61f5a7d3

                This is an open access article, free of all copyright, and may be freely reproduced, distributed, transmitted, modified, built upon, or otherwise used by anyone for any lawful purpose. The work is made available under the Creative Commons CC0 public domain dedication.

                History
                : 24 October 2016
                : 23 May 2017
                Page count
                Figures: 4, Tables: 2, Pages: 16
                Funding
                Funded by: funder-id http://dx.doi.org/10.13039/100000200, United States Agency for International Development;
                Award ID: 8042-31000-104-21R
                Award Recipient :
                The authors received no specific funding for this work.
                Categories
                Research Article
                Biology and Life Sciences
                Organisms
                Animals
                Vertebrates
                Amniotes
                Mammals
                Ruminants
                Sheep
                People and places
                Geographical locations
                North America
                Caribbean
                Biology and Life Sciences
                Evolutionary Biology
                Evolutionary Systematics
                Phylogenetics
                Phylogenetic Analysis
                Biology and Life Sciences
                Taxonomy
                Evolutionary Systematics
                Phylogenetics
                Phylogenetic Analysis
                Computer and Information Sciences
                Data Management
                Taxonomy
                Evolutionary Systematics
                Phylogenetics
                Phylogenetic Analysis
                Biology and Life Sciences
                Agriculture
                Animal Products
                Wool
                Biology and Life Sciences
                Evolutionary Biology
                Evolutionary Processes
                Introgression
                Engineering and Technology
                Structural Engineering
                Structural Analysis
                People and places
                Geographical locations
                North America
                Caribbean
                Barbados
                Biology and Life Sciences
                Organisms
                Animals
                Animal Types
                Domestic Animals
                Biology and Life Sciences
                Zoology
                Animal Types
                Domestic Animals
                Custom metadata
                All the data required to replicate this study are publically available. Genotype files unique to this article (West African, St Croix, Bergamesca) can be found on the NAL repository. The dataset (doi: 10.15482/USDA.ADC/1351110) is now published and can be accessed via http://dx.doi.org/10.15482/USDA.ADC/1351110. The remainder of the genotype files used for purpose of comparison are available in the ISGC website ( http://www.sheephapmap.org/). Interested researchers can access the data by agreeing to the Terms of Access ( http://www.sheephapmap.org/termsofaccess.php).

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