Variation at Innate Immunity Toll-Like Receptor Genes in a Bottlenecked Population of a New Zealand Robin
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{"title"=>"Variation at Innate Immunity Toll-Like Receptor Genes in a Bottlenecked Population of a New Zealand Robin", "type"=>"journal", "authors"=>[{"first_name"=>"Catherine E.", "last_name"=>"Grueber", "scopus_author_id"=>"24080444100"}, {"first_name"=>"Graham P.", "last_name"=>"Wallis", "scopus_author_id"=>"7102196704"}, {"first_name"=>"Tania M.", "last_name"=>"King", "scopus_author_id"=>"7403270253"}, {"first_name"=>"Ian G.", "last_name"=>"Jamieson", "scopus_author_id"=>"7004916616"}], "year"=>2012, "source"=>"PLoS ONE", "identifiers"=>{"pmid"=>"23024782", "doi"=>"10.1371/journal.pone.0045011", "sgr"=>"84866398771", "isbn"=>"1932-6203", "scopus"=>"2-s2.0-84866398771", "issn"=>"19326203", "pui"=>"365667815"}, "id"=>"5d61b323-496e-3c46-bf4f-b6e111d94af2", "abstract"=>"Toll-like receptors (TLRs) are an ancient family of genes encoding transmembrane proteins that bind pathogen-specific molecules and initiate both innate and adaptive aspects of the immune response. Our goal was to determine whether these genes show sufficient genetic diversity in a bottlenecked population to be a useful addition or alternative to the more commonly employed major histocompatibility complex (MHC) genotyping in a conservation genetics context. We amplified all known avian TLR genes in a severely bottlenecked population of New Zealand's Stewart Island robin (Petroica australis rakiura), for which reduced microsatellite diversity was previously observed. We genotyped 17-24 birds from a reintroduced island population (including the 12 founders) for nine genes, seven of which were polymorphic. We observed a total of 24 single-nucleotide polymorphisms overall, 15 of which were non-synonymous, representing up to five amino-acid variants at a locus. One locus (TLR1LB) showed evidence of past directional selection. Results also confirmed a passerine duplication of TLR7. The levels of TLR diversity that we observe are sufficient to justify their further use in addressing conservation genetic questions, even in bottlenecked populations.", "link"=>"http://www.mendeley.com/research/variation-innate-immunity-tolllike-receptor-genes-bottlenecked-population-new-zealand-robin", "reader_count"=>75, "reader_count_by_academic_status"=>{"Professor > Associate Professor"=>3, "Student > Doctoral Student"=>7, "Researcher"=>15, "Student > Ph. D. Student"=>20, "Student > Postgraduate"=>3, "Other"=>1, "Student > Master"=>14, "Student > Bachelor"=>9, "Lecturer"=>1, "Lecturer > Senior Lecturer"=>1, "Professor"=>1}, "reader_count_by_user_role"=>{"Professor > Associate Professor"=>3, "Student > Doctoral Student"=>7, "Researcher"=>15, "Student > Ph. D. Student"=>20, "Student > Postgraduate"=>3, "Other"=>1, "Student > Master"=>14, "Student > Bachelor"=>9, "Lecturer"=>1, "Lecturer > Senior Lecturer"=>1, "Professor"=>1}, "reader_count_by_subject_area"=>{"Engineering"=>1, "Unspecified"=>1, "Environmental Science"=>4, "Biochemistry, Genetics and Molecular Biology"=>3, "Agricultural and Biological Sciences"=>63, "Medicine and Dentistry"=>2, "Economics, Econometrics and Finance"=>1}, "reader_count_by_subdiscipline"=>{"Engineering"=>{"Engineering"=>1}, "Medicine and Dentistry"=>{"Medicine and Dentistry"=>2}, "Economics, Econometrics and Finance"=>{"Economics, Econometrics and Finance"=>1}, "Agricultural and Biological Sciences"=>{"Agricultural and Biological Sciences"=>63}, "Biochemistry, Genetics and Molecular Biology"=>{"Biochemistry, Genetics and Molecular Biology"=>3}, "Unspecified"=>{"Unspecified"=>1}, "Environmental Science"=>{"Environmental Science"=>4}}, "reader_count_by_country"=>{"New Zealand"=>2, "United States"=>2, "Brazil"=>1, "United Kingdom"=>3, "South Africa"=>2, "Mexico"=>1, "Germany"=>1, "India"=>1}, "group_count"=>2}

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Figshare

  • {"files"=>["https://ndownloader.figshare.com/files/576725"], "description"=>"1<p>Numbers in brackets are the number of offspring used to infer the genotypes of the missing 11<sup>th</sup> (female) and 12<sup>th</sup> (male) founders. See <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0045011#s2\" target=\"_blank\">Methods</a>.</p>2<p>Nucleotide diversity (×10<sup>4</sup>).</p>3<p>These five birds are also the offspring of the 10<sup>th</sup> founder that could not be genotyped for this locus.</p>4<p><i>TLR7</i> primers co-amplified two loci, excludes SNPs that clearly do not follow Mendelian inheritance (likely to be fixed differences). Genotypes could not be inferred.</p>5<p>Length of cloned product (see <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0045011#s3\" target=\"_blank\">Results</a>); initial, population-level sequence analyses were based on directly sequenced PCR products (sequence length = 947 bp).</p>", "links"=>[], "tags"=>["exons", "encoding", "pathogen-recognition", "extracellular", "domains", "toll-like", "receptor", "genes", "stewart", "robin", "australis", "founders", "ulva"], "article_id"=>247199, "categories"=>["Evolutionary Biology"], "users"=>["Catherine E. Grueber", "Graham P. Wallis", "Tania M. King", "Ian G. Jamieson"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0045011.t001", "stats"=>{"downloads"=>4, "page_views"=>7, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Polymorphism_of_the_exons_encoding_the_pathogen_recognition_extracellular_domains_of_Toll_like_receptor_genes_among_Stewart_Island_robin_Petroica_australis_rakiura_founders_of_Ulva_Island_/247199", "title"=>"Polymorphism of the exons encoding the pathogen-recognition extracellular domains of Toll-like receptor genes among Stewart Island robin <i>Petroica australis rakiura</i> founders of Ulva Island.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2012-09-14 01:59:59"}
  • {"files"=>["https://ndownloader.figshare.com/files/576675"], "description"=>"1<p><i>TLR7</i> is excluded from this table because locus-specific heterozygosities could not be inferred (see <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0045011#s3\" target=\"_blank\">Results</a>).</p>2<p>Hardy-Weinberg exact test.</p>", "links"=>[], "tags"=>["heterozygosity", "estimates", "toll-like", "receptor", "loci", "genotyped", "12", "ulva", "amino-acid"], "article_id"=>247157, "categories"=>["Evolutionary Biology"], "users"=>["Catherine E. Grueber", "Graham P. Wallis", "Tania M. King", "Ian G. Jamieson"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0045011.t002", "stats"=>{"downloads"=>0, "page_views"=>3, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Observed_H_O_and_expected_heterozygosity_H_E_estimates_for_seven_Toll_like_receptor_loci_genotyped_among_the_12_Ulva_Island_founders_based_on_amino_acid_variants_/247157", "title"=>"Observed (<i>H</i><sub>O</sub>) and expected heterozygosity (<i>H</i><sub>E</sub>) estimates for seven Toll-like receptor loci genotyped among the 12 Ulva Island founders, based on amino-acid variants.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2012-09-14 01:59:17"}
  • {"files"=>["https://ndownloader.figshare.com/files/304453", "https://ndownloader.figshare.com/files/304517", "https://ndownloader.figshare.com/files/304582"], "description"=>"<div><p>Toll-like receptors (TLRs) are an ancient family of genes encoding transmembrane proteins that bind pathogen-specific molecules and initiate both innate and adaptive aspects of the immune response. Our goal was to determine whether these genes show sufficient genetic diversity in a bottlenecked population to be a useful addition or alternative to the more commonly employed major histocompatibility complex (MHC) genotyping in a conservation genetics context. We amplified all known avian TLR genes in a severely bottlenecked population of New Zealand's Stewart Island robin (<em>Petroica australis rakiura</em>), for which reduced microsatellite diversity was previously observed. We genotyped 17–24 birds from a reintroduced island population (including the 12 founders) for nine genes, seven of which were polymorphic. We observed a total of 24 single-nucleotide polymorphisms overall, 15 of which were non-synonymous, representing up to five amino-acid variants at a locus. One locus (<em>TLR1LB</em>) showed evidence of past directional selection. <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0045011#s3\">Results</a> also confirmed a passerine duplication of <em>TLR7</em>. The levels of TLR diversity that we observe are sufficient to justify their further use in addressing conservation genetic questions, even in bottlenecked populations.</p> </div>", "links"=>[], "tags"=>["innate", "immunity", "toll-like", "receptor", "genes", "bottlenecked", "zealand", "robin"], "article_id"=>120047, "categories"=>["Evolutionary Biology"], "users"=>["Catherine E. Grueber", "Graham P. Wallis", "Tania M. King", "Ian G. Jamieson"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0045011.s001", "https://dx.doi.org/10.1371/journal.pone.0045011.s002", "https://dx.doi.org/10.1371/journal.pone.0045011.s003"], "stats"=>{"downloads"=>1, "page_views"=>4, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/Variation_at_Innate_Immunity_Toll_Like_Receptor_Genes_in_a_Bottlenecked_Population_of_a_New_Zealand_Robin/120047", "title"=>"Variation at Innate Immunity Toll-Like Receptor Genes in a Bottlenecked Population of a New Zealand Robin", "pos_in_sequence"=>0, "defined_type"=>4, "published_date"=>"2012-09-14 00:00:47"}

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Relative Metric

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