Archaeogenetic Evidence of Ancient Nubian Barley Evolution from Six to Two-Row Indicates Local Adaptation
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{"title"=>"Archaeogenetic evidence of ancient nubian barley evolution from six to two-row indicates local adaptation", "type"=>"journal", "authors"=>[{"first_name"=>"Sarah A.", "last_name"=>"Palmer", "scopus_author_id"=>"7402329301"}, {"first_name"=>"Jonathan D.", "last_name"=>"Moore", "scopus_author_id"=>"55641662900"}, {"first_name"=>"Alan J.", "last_name"=>"Clapham", "scopus_author_id"=>"6603104256"}, {"first_name"=>"Pamela", "last_name"=>"Rose", "scopus_author_id"=>"7201668918"}, {"first_name"=>"Robin G.", "last_name"=>"Allaby", "scopus_author_id"=>"6602620692"}], "year"=>2009, "source"=>"PLoS ONE", "identifiers"=>{"issn"=>"19326203", "scopus"=>"2-s2.0-67749144187", "sgr"=>"67749144187", "pui"=>"354999830", "isbn"=>"1932-6203 (Electronic)\\n1932-6203 (Linking)", "pmid"=>"19623249", "doi"=>"10.1371/journal.pone.0006301"}, "id"=>"9fb1ec5b-84c2-30ca-a415-0ef86721ae51", "abstract"=>"BACKGROUND Archaeobotanical samples of barley (Hordeum vulgare L.) found at Qasr Ibrim display a two-row phenotype that is unique to the region of archaeological sites upriver of the first cataract of the Nile, characterised by the development of distinctive lateral bracts. The phenotype occurs throughout all strata at Qasr Ibrim, which range in age from 3000 to a few hundred years. METHODOLOGY AND FINDINGS We extracted ancient DNA from barley samples from the entire range of occupancy of the site, and studied the Vrs1 gene responsible for row number in extant barley. Surprisingly, we found a discord between the genotype and phenotype in all samples; all the barley had a genotype consistent with the six-row condition. These results indicate a six-row ancestry for the Qasr Ibrim barley, followed by a reassertion of the two-row condition. Modelling demonstrates that this sequence of evolutionary events requires a strong selection pressure. CONCLUSIONS The two-row phenotype at Qasr Ibrim is caused by a different mechanism to that in extant barley. The strength of selection required for this mechanism to prevail indicates that the barley became locally adapted in the region in response to a local selection pressure. The consistency of the genotype/phenotype discord over time supports a scenario of adoption of this barley type by successive cultures, rather than the importation of new barley varieties associated with individual cultures.", "link"=>"http://www.mendeley.com/research/archaeogenetic-evidence-ancient-nubian-barley-evolution-six-tworow-indicates-local-adaptation", "reader_count"=>59, "reader_count_by_academic_status"=>{"Professor > Associate Professor"=>4, "Librarian"=>2, "Student > Doctoral Student"=>2, "Researcher"=>15, "Student > Ph. D. Student"=>15, "Student > Postgraduate"=>1, "Student > Master"=>5, "Other"=>2, "Student > Bachelor"=>6, "Lecturer"=>1, "Lecturer > Senior Lecturer"=>1, "Professor"=>5}, "reader_count_by_user_role"=>{"Professor > Associate Professor"=>4, "Librarian"=>2, "Student > Doctoral Student"=>2, "Researcher"=>15, "Student > Ph. D. Student"=>15, "Student > Postgraduate"=>1, "Student > Master"=>5, "Other"=>2, "Student > Bachelor"=>6, "Lecturer"=>1, "Lecturer > Senior Lecturer"=>1, "Professor"=>5}, "reader_count_by_subject_area"=>{"Unspecified"=>1, "Biochemistry, Genetics and Molecular Biology"=>5, "Agricultural and Biological Sciences"=>38, "Arts and Humanities"=>7, "Social Sciences"=>6, "Computer Science"=>1, "Economics, Econometrics and Finance"=>1}, "reader_count_by_subdiscipline"=>{"Social Sciences"=>{"Social Sciences"=>6}, "Economics, Econometrics and Finance"=>{"Economics, Econometrics and Finance"=>1}, "Agricultural and Biological Sciences"=>{"Agricultural and Biological Sciences"=>38}, "Computer Science"=>{"Computer Science"=>1}, "Biochemistry, Genetics and Molecular Biology"=>{"Biochemistry, Genetics and Molecular Biology"=>5}, "Unspecified"=>{"Unspecified"=>1}, "Arts and Humanities"=>{"Arts and Humanities"=>7}}, "reader_count_by_country"=>{"New Zealand"=>2, "Czech Republic"=>1, "Norway"=>1, "United States"=>2, "Denmark"=>1, "United Kingdom"=>2, "France"=>1}, "group_count"=>2}

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  • {"files"=>["https://ndownloader.figshare.com/files/890149"], "description"=>"<p><i>(A)</i> Analysis of Qasr Ibrim barley for haplotype specific polymorphisms <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0006301#pone.0006301-Komatsuda1\" target=\"_blank\">[9]</a>. SNPs coloured in red indicate <i>vrs1</i> loss of function mutations.–indicates where sequencing data were not available. <i>(B)</i> Phylogenetic tree of <i>Vrs1</i> alleles indicating the position of the Qasr Ibrim barley within the vrs1.a1 clade.</p>", "links"=>[], "tags"=>["locus", "qasr", "ibrim"], "article_id"=>560603, "categories"=>["Evolutionary Biology"], "users"=>["Sarah A. Palmer", "Jonathan D. Moore", "Alan J. Clapham", "Pamela Rose", "Robin G. Allaby"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0006301.g003", "stats"=>{"downloads"=>1, "page_views"=>3, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Characterisation_of_Vrs1_locus_in_Qasr_Ibrim_barley_/560603", "title"=>"Characterisation of <i>Vrs1</i> locus in Qasr Ibrim barley.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2009-07-22 00:10:03"}
  • {"files"=>["https://ndownloader.figshare.com/files/889993"], "description"=>"<p>DNA extracted per Barley seed plotted on a logarithmic scale against the years BP of the assemblage from which each sample was recovered. Error bars indicate the range of years BP of each strata from which samples were taken.</p>", "links"=>[], "tags"=>["archaeological", "dna"], "article_id"=>560452, "categories"=>["Evolutionary Biology"], "users"=>["Sarah A. Palmer", "Jonathan D. Moore", "Alan J. Clapham", "Pamela Rose", "Robin G. Allaby"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0006301.g002", "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Recoverable_archaeological_DNA_quantity_over_time_/560452", "title"=>"Recoverable archaeological DNA quantity over time.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2009-07-22 00:07:32"}
  • {"files"=>["https://ndownloader.figshare.com/files/441577", "https://ndownloader.figshare.com/files/441606", "https://ndownloader.figshare.com/files/441637", "https://ndownloader.figshare.com/files/441667", "https://ndownloader.figshare.com/files/441707", "https://ndownloader.figshare.com/files/441735"], "description"=>"<div><h3>Background</h3><p>Archaeobotanical samples of barley (<em>Hordeum vulgare</em> L.) found at Qasr Ibrim display a two-row phenotype that is unique to the region of archaeological sites upriver of the first cataract of the Nile, characterised by the development of distinctive lateral bracts. The phenotype occurs throughout all strata at Qasr Ibrim, which range in age from 3000 to a few hundred years.</p><h3>Methodology and Findings</h3><p>We extracted ancient DNA from barley samples from the entire range of occupancy of the site, and studied the <em>Vrs1</em> gene responsible for row number in extant barley. Surprisingly, we found a discord between the genotype and phenotype in all samples; all the barley had a genotype consistent with the six-row condition. These results indicate a six-row ancestry for the Qasr Ibrim barley, followed by a reassertion of the two-row condition. Modelling demonstrates that this sequence of evolutionary events requires a strong selection pressure.</p><h3>Conclusions</h3><p>The two-row phenotype at Qasr Ibrim is caused by a different mechanism to that in extant barley. The strength of selection required for this mechanism to prevail indicates that the barley became locally adapted in the region in response to a local selection pressure. The consistency of the genotype/phenotype discord over time supports a scenario of adoption of this barley type by successive cultures, rather than the importation of new barley varieties associated with individual cultures.</p></div>", "links"=>[], "tags"=>["archaeogenetic", "nubian", "barley", "two-row", "indicates", "adaptation"], "article_id"=>147041, "categories"=>["Evolutionary Biology"], "users"=>["Sarah A. Palmer", "Jonathan D. Moore", "Alan J. Clapham", "Pamela Rose", "Robin G. Allaby"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0006301.s001", "https://dx.doi.org/10.1371/journal.pone.0006301.s002", "https://dx.doi.org/10.1371/journal.pone.0006301.s003", "https://dx.doi.org/10.1371/journal.pone.0006301.s004", "https://dx.doi.org/10.1371/journal.pone.0006301.s005", "https://dx.doi.org/10.1371/journal.pone.0006301.s006"], "stats"=>{"downloads"=>11, "page_views"=>12, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/Archaeogenetic_Evidence_of_Ancient_Nubian_Barley_Evolution_from_Six_to_Two_Row_Indicates_Local_Adaptation/147041", "title"=>"Archaeogenetic Evidence of Ancient Nubian Barley Evolution from Six to Two-Row Indicates Local Adaptation", "pos_in_sequence"=>0, "defined_type"=>4, "published_date"=>"2009-07-22 01:57:21"}
  • {"files"=>["https://ndownloader.figshare.com/files/889856"], "description"=>"<p>Locations of archaeological excavations at Tell el-Amarna, Qasr Ibrim, and Nauri and the cataracts along the River Nile are indicated.</p>", "links"=>[], "tags"=>["evolutionary biology/evolutionary and comparative genetics", "evolutionary biology/paleontology", "evolutionary biology/plant genomes and evolution"], "article_id"=>560314, "categories"=>["Evolutionary Biology"], "users"=>["Sarah A. Palmer", "Jonathan D. Moore", "Alan J. Clapham", "Pamela Rose", "Robin G. Allaby"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0006301.g001", "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Map_of_Nubia_/560314", "title"=>"Map of Nubia.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2009-07-22 00:05:14"}
  • {"files"=>["https://ndownloader.figshare.com/files/890246"], "description"=>"<p>Modelling of generations to fixation of recessive six-rowed alleles in homozygous two-rowed barley crops by automatic selection using realistic constraints (Population size: 10<sup>6</sup>; Out-crossing rate: 2%; Six- to two-rowed fecundity ratio: 2.0) the a six-row individual is introduced into a population of 10<sup>6</sup> two-row plants.</p>", "links"=>[], "tags"=>["two-row"], "article_id"=>560705, "categories"=>["Evolutionary Biology"], "users"=>["Sarah A. Palmer", "Jonathan D. Moore", "Alan J. Clapham", "Pamela Rose", "Robin G. Allaby"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0006301.g004", "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Six_row_introduction_to_two_row_populations_/560705", "title"=>"Six-row introduction to two-row populations.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2009-07-22 00:11:45"}

PMC Usage Stats | Further Information

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  • {"unique-ip"=>"5", "full-text"=>"9", "pdf"=>"2", "abstract"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2016", "month"=>"3"}
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  • {"unique-ip"=>"4", "full-text"=>"5", "pdf"=>"0", "abstract"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"4", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2016", "month"=>"6"}
  • {"unique-ip"=>"6", "full-text"=>"8", "pdf"=>"2", "abstract"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"1", "supp-data"=>"3", "cited-by"=>"0", "year"=>"2016", "month"=>"7"}
  • {"unique-ip"=>"4", "full-text"=>"4", "pdf"=>"3", "abstract"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2016", "month"=>"8"}
  • {"unique-ip"=>"9", "full-text"=>"11", "pdf"=>"2", "abstract"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"2", "supp-data"=>"4", "cited-by"=>"0", "year"=>"2016", "month"=>"9"}
  • {"unique-ip"=>"6", "full-text"=>"5", "pdf"=>"2", "abstract"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"2", "supp-data"=>"2", "cited-by"=>"0", "year"=>"2016", "month"=>"10"}
  • {"unique-ip"=>"5", "full-text"=>"6", "pdf"=>"1", "abstract"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2016", "month"=>"11"}
  • {"unique-ip"=>"6", "full-text"=>"8", "pdf"=>"1", "abstract"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2016", "month"=>"12"}
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  • {"unique-ip"=>"6", "full-text"=>"6", "pdf"=>"0", "abstract"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2017", "month"=>"2"}
  • {"unique-ip"=>"8", "full-text"=>"7", "pdf"=>"3", "abstract"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2017", "month"=>"3"}
  • {"unique-ip"=>"4", "full-text"=>"5", "pdf"=>"1", "abstract"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2017", "month"=>"4"}
  • {"unique-ip"=>"6", "full-text"=>"14", "pdf"=>"4", "abstract"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2017", "month"=>"5"}
  • {"unique-ip"=>"5", "full-text"=>"5", "pdf"=>"0", "abstract"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2017", "month"=>"6"}
  • {"unique-ip"=>"5", "full-text"=>"5", "pdf"=>"2", "abstract"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2017", "month"=>"7"}
  • {"unique-ip"=>"5", "full-text"=>"5", "pdf"=>"0", "abstract"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2017", "month"=>"8"}
  • {"unique-ip"=>"8", "full-text"=>"8", "pdf"=>"1", "abstract"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2017", "month"=>"9"}
  • {"unique-ip"=>"6", "full-text"=>"5", "pdf"=>"1", "abstract"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2017", "month"=>"10"}
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  • {"unique-ip"=>"11", "full-text"=>"14", "pdf"=>"2", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2019", "month"=>"1"}
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  • {"unique-ip"=>"17", "full-text"=>"20", "pdf"=>"2", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"1", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2018", "month"=>"5"}
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  • {"unique-ip"=>"12", "full-text"=>"8", "pdf"=>"3", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"3", "cited-by"=>"0", "year"=>"2018", "month"=>"7"}
  • {"unique-ip"=>"10", "full-text"=>"12", "pdf"=>"3", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2018", "month"=>"8"}
  • {"unique-ip"=>"9", "full-text"=>"9", "pdf"=>"1", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2018", "month"=>"10"}
  • {"unique-ip"=>"18", "full-text"=>"17", "pdf"=>"2", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"7", "cited-by"=>"0", "year"=>"2018", "month"=>"11"}
  • {"unique-ip"=>"10", "full-text"=>"11", "pdf"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2018", "month"=>"9"}
  • {"unique-ip"=>"16", "full-text"=>"18", "pdf"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2018", "month"=>"12"}
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  • {"unique-ip"=>"22", "full-text"=>"19", "pdf"=>"6", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"2", "supp-data"=>"2", "cited-by"=>"0", "year"=>"2019", "month"=>"4"}
  • {"unique-ip"=>"11", "full-text"=>"12", "pdf"=>"1", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2019", "month"=>"5"}
  • {"unique-ip"=>"12", "full-text"=>"10", "pdf"=>"7", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2019", "month"=>"8"}
  • {"unique-ip"=>"7", "full-text"=>"6", "pdf"=>"2", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"1", "cited-by"=>"0", "year"=>"2019", "month"=>"9"}
  • {"unique-ip"=>"12", "full-text"=>"12", "pdf"=>"2", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2019", "month"=>"10"}
  • {"unique-ip"=>"9", "full-text"=>"1", "pdf"=>"13", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2019", "month"=>"12"}
  • {"unique-ip"=>"13", "full-text"=>"19", "pdf"=>"2", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"1", "cited-by"=>"1", "year"=>"2020", "month"=>"2"}
  • {"unique-ip"=>"18", "full-text"=>"15", "pdf"=>"6", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"1", "cited-by"=>"0", "year"=>"2020", "month"=>"3"}
  • {"unique-ip"=>"9", "full-text"=>"9", "pdf"=>"2", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2020", "month"=>"4"}
  • {"unique-ip"=>"10", "full-text"=>"10", "pdf"=>"5", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2020", "month"=>"5"}
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Relative Metric

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