Northern Bobwhite (Colinus virginianus) Mitochondrial Population Genomics Reveals Structure, Divergence, and Evidence for Heteroplasmy
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{"title"=>"Northern bobwhite (Colinus virginianus) mitochondrial population genomics reveals structure, divergence, and evidence for heteroplasmy", "type"=>"journal", "authors"=>[{"first_name"=>"Yvette A.", "last_name"=>"Halley", "scopus_author_id"=>"55681504800"}, {"first_name"=>"David L.", "last_name"=>"Oldeschulte", "scopus_author_id"=>"57113731600"}, {"first_name"=>"Eric K.", "last_name"=>"Bhattarai", "scopus_author_id"=>"6504601884"}, {"first_name"=>"Joshua", "last_name"=>"Hill", "scopus_author_id"=>"57112909100"}, {"first_name"=>"Richard P.", "last_name"=>"Metz", "scopus_author_id"=>"56471408800"}, {"first_name"=>"Charles D.", "last_name"=>"Johnson", "scopus_author_id"=>"55636319041"}, {"first_name"=>"Steven M.", "last_name"=>"Presley", "scopus_author_id"=>"6701360608"}, {"first_name"=>"Rebekah E.", "last_name"=>"Ruzicka", "scopus_author_id"=>"54684794500"}, {"first_name"=>"Dale", "last_name"=>"Rollins", "scopus_author_id"=>"7102639256"}, {"first_name"=>"Markus J.", "last_name"=>"Peterson", "scopus_author_id"=>"7402271293"}, {"first_name"=>"William J.", "last_name"=>"Murphy", "scopus_author_id"=>"7401510455"}, {"first_name"=>"Christopher M.", "last_name"=>"Seabury", "scopus_author_id"=>"13806485400"}], "year"=>2015, "source"=>"PLoS ONE", "identifiers"=>{"pmid"=>"26713762", "issn"=>"19326203", "sgr"=>"84957998888", "pui"=>"608080588", "scopus"=>"2-s2.0-84957998888", "isbn"=>"1932-6203 (Electronic)\\r1932-6203 (Linking)", "doi"=>"10.1371/journal.pone.0144913"}, "id"=>"804f56f3-681b-3680-992a-b595a684ef9d", "abstract"=>"Herein, we evaluated the concordance of population inferences and conclusions resulting from the analysis of short mitochondrial fragments (i.e., partial or complete D-Loop nucleotide sequences) versus complete mitogenome sequences for 53 bobwhites representing six ecoregions across TX and OK (USA). Median joining (MJ) haplotype networks demonstrated that analyses performed using small mitochondrial fragments were insufficient for estimating the true (i.e., complete) mitogenome haplotype structure, corresponding levels of divergence, and maternal population history of our samples. Notably, discordant demographic inferences were observed when mismatch distributions of partial (i.e., partial D-Loop) versus complete mitogenome sequences were compared, with the reduction in mitochondrial genomic information content observed to encourage spurious inferences in our samples. A probabilistic approach to variant prediction for the complete bobwhite mitogenomes revealed 344 segregating sites corresponding to 347 total mutations, including 49 putative nonsynonymous single nucleotide variants (SNVs) distributed across 12 protein coding genes. Evidence of gross heteroplasmy was observed for 13 bobwhites, with 10 of the 13 heteroplasmies involving one moderate to high frequency SNV. Haplotype network and phylogenetic analyses for the complete bobwhite mitogenome sequences revealed two divergent maternal lineages (dXY = 0.00731; FST = 0.849; P < 0.05), thereby supporting the potential for two putative subspecies. However, the diverged lineage (n = 103 variants) almost exclusively involved bobwhites geographically classified as Colinus virginianus texanus, which is discordant with the expectations of previous geographic subspecies designations. Tests of adaptive evolution for functional divergence (MKT), frequency distribution tests (D, FS) and phylogenetic analyses (RAxML) provide no evidence for positive selection or hybridization with the sympatric scaled quail (Callipepla squamata) as being explanatory factors for the two bobwhite maternal lineages observed. Instead, our analyses support the supposition that two diverged maternal lineages have survived from pre-expansion to post-expansion population(s), with the segregation of some slightly deleterious nonsynonymous mutations.", "link"=>"http://www.mendeley.com/research/northern-bobwhite-colinus-virginianus-mitochondrial-population-genomics-reveals-structure-divergence", "reader_count"=>14, "reader_count_by_academic_status"=>{"Unspecified"=>1, "Student > Doctoral Student"=>3, "Researcher"=>4, "Student > Ph. D. Student"=>2, "Student > Master"=>3, "Professor"=>1}, "reader_count_by_user_role"=>{"Unspecified"=>1, "Student > Doctoral Student"=>3, "Researcher"=>4, "Student > Ph. D. Student"=>2, "Student > Master"=>3, "Professor"=>1}, "reader_count_by_subject_area"=>{"Unspecified"=>1, "Environmental Science"=>1, "Biochemistry, Genetics and Molecular Biology"=>3, "Agricultural and Biological Sciences"=>7, "Medicine and Dentistry"=>1, "Social Sciences"=>1}, "reader_count_by_subdiscipline"=>{"Medicine and Dentistry"=>{"Medicine and Dentistry"=>1}, "Social Sciences"=>{"Social Sciences"=>1}, "Agricultural and Biological Sciences"=>{"Agricultural and Biological Sciences"=>7}, "Biochemistry, Genetics and Molecular Biology"=>{"Biochemistry, Genetics and Molecular Biology"=>3}, "Unspecified"=>{"Unspecified"=>1}, "Environmental Science"=>{"Environmental Science"=>1}}, "reader_count_by_country"=>{"United Kingdom"=>1}, "group_count"=>2}

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Figshare

  • {"files"=>["https://ndownloader.figshare.com/files/2617497"], "description"=>"<p>(A) MJ haplotype network for 353 bp of the mitochondrial D-Loop [<a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0144913#pone.0144913.ref003\" target=\"_blank\">3</a>] (n = 54, including 1 heteroplasmic minor allele haplotype). (B) MJ haplotype network for the complete D-Loop (1,152 bp; n = 55, including 2 heteroplasmic minor allele haplotypes). (C) MJ haplotype network for the complete mitogenome (16,709 bp including gaps; n = 66, including 13 heteroplasmic minor allele haplotypes). Default weights for SNPs and indels were used (10 and 20, respectively), with node sizes proportional to haplotype frequency, and branch lengths drawn to scale. Red dots indicate median vectors. The complete mitogenome haplotypes were observed to form two divergent clusters (i.e., Group 1, Group 2; n = 103 variants). Pairwise <i>F</i><sub>ST</sub> values (below diagonal) with standard errors (above diagonal) were computed to assess genetic differentiation between the two clusters, with the asterisk (*) indicating a significant <i>F</i><sub>ST</sub> value (<i>P</i> < 0.05). Fig 1C includes three complete mitogenome haplotypes for bobwhites lawfully harvested from active surrogating pastures (i.e., pen release sites = S), and one haplotype from a lawfully harvested pen-released bobwhite (P). (R) designates the reference mitogenome [<a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0144913#pone.0144913.ref036\" target=\"_blank\">36</a>].</p>", "links"=>[], "tags"=>["mitochondrial genomic information content", "Phylogenetic analyses", "Colinus virginianus texanus", "OK", "lineage", "snv", "Mitochondrial Population Genomics", "fst", "variant", "i.e", "12 protein coding genes", "mj", "fs", "inference", "usa", "mitogenome haplotype structure", "mkt", "tx", "mitochondrial fragments", "bobwhite mitogenome sequences", "mitogenome sequences"], "article_id"=>1630738, "categories"=>["Biological Sciences", "Ecology"], "users"=>["Yvette A. Halley", "David L. Oldeschulte", "Eric K. Bhattarai", "Joshua Hill", "Richard P. Metz", "Charles D. Johnson", "Steven M. Presley", "Rebekah E. Ruzicka", "Dale Rollins", "Markus J. Peterson", "William J. Murphy", "Christopher M. Seabury"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0144913.g001", "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Median_joining_MJ_haplotype_networks_64_constructed_for_partial_and_complete_bobwhite_mitogenome_sequences_with_heteroplasmic_minor_allele_haplotypes_and_color_coded_geographic_subspecies_designations_1_3_/1630738", "title"=>"Median joining (MJ) haplotype networks [64] constructed for partial and complete bobwhite mitogenome sequences, with heteroplasmic minor allele haplotypes, and color-coded geographic subspecies designations [1–3].", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2016-01-05 14:54:25"}
  • {"files"=>["https://ndownloader.figshare.com/files/2617498"], "description"=>"<p>(A) MJ haplotype network for 353 bp of the mitochondrial D-Loop [<a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0144913#pone.0144913.ref003\" target=\"_blank\">3</a>] (n = 54, including 1 heteroplasmic minor allele haplotype). (B) MJ haplotype network for the complete D-Loop (1,152 bp; n = 55, including 2 heteroplasmic minor allele haplotypes). (C) MJ haplotype network for the complete mitogenome (16,709 bp including gaps; n = 66, including 13 heteroplasmic minor allele haplotypes). Default weights for SNPs and indels were used (10 and 20, respectively), with node sizes proportional to haplotype frequency, and branch lengths drawn to scale. Red dots indicate median vectors. The complete mitogenome haplotypes were observed to form two divergent clusters (i.e., Group 1, Group 2; n = 103 variants). Pairwise <i>F</i><sub>ST</sub> values (below diagonal) with standard errors (above diagonal) were computed to assess genetic differentiation between the two clusters, with the asterisk (*) indicating a significant <i>F</i><sub>ST</sub> value (<i>P</i> < 0.05). Fig 2C includes three complete mitogenome haplotypes for bobwhites harvested from active surrogating pastures (i.e., pen release sites = S), and one haplotype from a lawfully harvested pen-released bobwhite (P). (R) designates the reference mitogenome [<a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0144913#pone.0144913.ref036\" target=\"_blank\">36</a>].</p>", "links"=>[], "tags"=>["mitochondrial genomic information content", "Phylogenetic analyses", "Colinus virginianus texanus", "OK", "lineage", "snv", "Mitochondrial Population Genomics", "fst", "variant", "i.e", "12 protein coding genes", "mj", "fs", "inference", "usa", "mitogenome haplotype structure", "mkt", "tx", "mitochondrial fragments", "bobwhite mitogenome sequences", "mitogenome sequences"], "article_id"=>1630739, "categories"=>["Biological Sciences", "Ecology"], "users"=>["Yvette A. Halley", "David L. Oldeschulte", "Eric K. Bhattarai", "Joshua Hill", "Richard P. Metz", "Charles D. Johnson", "Steven M. Presley", "Rebekah E. Ruzicka", "Dale Rollins", "Markus J. Peterson", "William J. Murphy", "Christopher M. Seabury"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0144913.g002", "stats"=>{"downloads"=>1, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Median_joining_MJ_haplotype_networks_64_constructed_for_partial_and_complete_bobwhite_mitogenome_sequences_with_heteroplasmic_minor_allele_haplotypes_and_color_coded_assignments_to_U_S_Environmental_Protection_Agency_level_III_ecoregions_http_archive_epa/1630739", "title"=>"Median joining (MJ) haplotype networks [64] constructed for partial and complete bobwhite mitogenome sequences, with heteroplasmic minor allele haplotypes, and color-coded assignments to U.S. Environmental Protection Agency level III ecoregions (http://archive.epa.gov/wed/ecoregions/web/html/level_iii_iv-2.html).", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2016-01-05 14:54:27"}
  • {"files"=>["https://ndownloader.figshare.com/files/2617499"], "description"=>"<p>(A) 353 bp of the mitochondrial D-Loop [<a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0144913#pone.0144913.ref003\" target=\"_blank\">3</a>] (n = 54, including 1 heteroplasmic minor allele haplotype). (B) Complete D-Loop (1,151 bp excluding gaps; n = 55, including 2 heteroplasmic minor allele haplotypes). (C) Complete mitogenome (16,698 bp excluding gaps; n = 66, including 13 heteroplasmic minor allele haplotypes). The x-axis represents the number of pairwise differences (mismatches) and the y-axis represents the frequency of these differences. The observed mismatch distribution (dashed line) is compared to the expected distribution (red line) for a stable population (i.e., constant population size).</p>", "links"=>[], "tags"=>["mitochondrial genomic information content", "Phylogenetic analyses", "Colinus virginianus texanus", "OK", "lineage", "snv", "Mitochondrial Population Genomics", "fst", "variant", "i.e", "12 protein coding genes", "mj", "fs", "inference", "usa", "mitogenome haplotype structure", "mkt", "tx", "mitochondrial fragments", "bobwhite mitogenome sequences", "mitogenome sequences"], "article_id"=>1630740, "categories"=>["Biological Sciences", "Ecology"], "users"=>["Yvette A. Halley", "David L. Oldeschulte", "Eric K. Bhattarai", "Joshua Hill", "Richard P. Metz", "Charles D. Johnson", "Steven M. Presley", "Rebekah E. Ruzicka", "Dale Rollins", "Markus J. Peterson", "William J. Murphy", "Christopher M. Seabury"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0144913.g003", "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Bobwhite_Mismatch_Distributions_/1630740", "title"=>"Bobwhite Mismatch Distributions.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2016-01-05 14:54:25"}
  • {"files"=>["https://ndownloader.figshare.com/files/2617500"], "description"=>"<p>Phylogeny of all bobwhite mitogenomes (n = 66, including 13 heteroplasmic minor allele haplotypes) in conjunction with mitogenomes for the scaled quail (<i>Callipepla squamata</i>), tawny-faced quail (<i>Rhynchortyx cinctus</i>) [<a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0144913#pone.0144913.ref037\" target=\"_blank\">37</a>], and stone partridge (<i>Ptilopachus petrosus</i>) [<a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0144913#pone.0144913.ref037\" target=\"_blank\">37</a>]. The asterisk (*) denotes a pen-released (n = 1) origin, and ‘^’ denotes bobwhites sampled from active surrogating pastures (i.e., pen release sites; n = 3). Terminal taxa noted with “H” and “L” refers to the high frequency (i.e., major) and low frequency (i.e., minor) heteroplasmic haplotypes, respectively. Individual bobwhites are labeled with laboratory identifiers (Q, SQ, T), with REF indicating the bobwhite reference sequence (GenBank Accession AWGT00000000.1), and KJ914548.1 indicating a bobwhite GenBank Accession [<a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0144913#pone.0144913.ref037\" target=\"_blank\">37</a>] included in our analyses. The maximum likelihood phylogeny was constructed with RAxML 7.2.8 [<a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0144913#pone.0144913.ref096\" target=\"_blank\">96</a>] using a GTR+Γ model of sequence evolution, with bootstrap support values based on 1,000 pseudoreplicates.</p>", "links"=>[], "tags"=>["mitochondrial genomic information content", "Phylogenetic analyses", "Colinus virginianus texanus", "OK", "lineage", "snv", "Mitochondrial Population Genomics", "fst", "variant", "i.e", "12 protein coding genes", "mj", "fs", "inference", "usa", "mitogenome haplotype structure", "mkt", "tx", "mitochondrial fragments", "bobwhite mitogenome sequences", "mitogenome sequences"], "article_id"=>1630741, "categories"=>["Biological Sciences", "Ecology"], "users"=>["Yvette A. Halley", "David L. Oldeschulte", "Eric K. Bhattarai", "Joshua Hill", "Richard P. Metz", "Charles D. Johnson", "Steven M. Presley", "Rebekah E. Ruzicka", "Dale Rollins", "Markus J. Peterson", "William J. Murphy", "Christopher M. Seabury"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0144913.g004", "stats"=>{"downloads"=>1, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Maximum_Likelihood_based_Phylogeny_Constructed_with_Expanded_Taxon_Sampling_/1630741", "title"=>"Maximum Likelihood-based Phylogeny Constructed with Expanded Taxon Sampling.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2016-01-05 14:54:27"}
  • {"files"=>["https://ndownloader.figshare.com/files/2617501"], "description"=>"<p>(A) The observed mismatch distribution (dashed line) for bobwhite Group 1 (n = 49) as compared to the expected distribution (red line) for a stable population (i.e., constant population size). (B) The observed mismatch distribution (dashed line) for bobwhite Group 2 (n = 17) as compared to the expected distribution (red line) for a stable population (i.e., constant population size). (C) The observed mismatch distribution (dashed line) for bobwhite Group 1 (n = 49) as compared to the expected distribution (red line) for a growth-decline model. (D) The observed mismatch distribution (dashed line) for bobwhite Group 2 (n = 17) as compared to the expected distribution (red line) for a growth-decline model.</p>", "links"=>[], "tags"=>["mitochondrial genomic information content", "Phylogenetic analyses", "Colinus virginianus texanus", "OK", "lineage", "snv", "Mitochondrial Population Genomics", "fst", "variant", "i.e", "12 protein coding genes", "mj", "fs", "inference", "usa", "mitogenome haplotype structure", "mkt", "tx", "mitochondrial fragments", "bobwhite mitogenome sequences", "mitogenome sequences"], "article_id"=>1630742, "categories"=>["Biological Sciences", "Ecology"], "users"=>["Yvette A. Halley", "David L. Oldeschulte", "Eric K. Bhattarai", "Joshua Hill", "Richard P. Metz", "Charles D. Johnson", "Steven M. Presley", "Rebekah E. Ruzicka", "Dale Rollins", "Markus J. Peterson", "William J. Murphy", "Christopher M. Seabury"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0144913.g005", "stats"=>{"downloads"=>1, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Bobwhite_Historical_Demography_Inferred_From_Complete_Mitogenome_Sequences_/1630742", "title"=>"Bobwhite Historical Demography Inferred From Complete Mitogenome Sequences.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2016-01-05 14:54:28"}
  • {"files"=>["https://ndownloader.figshare.com/files/2617503", "https://ndownloader.figshare.com/files/2617504"], "description"=>"<div><p>Herein, we evaluated the concordance of population inferences and conclusions resulting from the analysis of short mitochondrial fragments (i.e., partial or complete D-Loop nucleotide sequences) versus complete mitogenome sequences for 53 bobwhites representing six ecoregions across TX and OK (USA). Median joining (MJ) haplotype networks demonstrated that analyses performed using small mitochondrial fragments were insufficient for estimating the true (i.e., complete) mitogenome haplotype structure, corresponding levels of divergence, and maternal population history of our samples. Notably, discordant demographic inferences were observed when mismatch distributions of partial (i.e., partial D-Loop) versus complete mitogenome sequences were compared, with the reduction in mitochondrial genomic information content observed to encourage spurious inferences in our samples. A probabilistic approach to variant prediction for the complete bobwhite mitogenomes revealed 344 segregating sites corresponding to 347 total mutations, including 49 putative nonsynonymous single nucleotide variants (SNVs) distributed across 12 protein coding genes. Evidence of gross heteroplasmy was observed for 13 bobwhites, with 10 of the 13 heteroplasmies involving one moderate to high frequency SNV. Haplotype network and phylogenetic analyses for the complete bobwhite mitogenome sequences revealed two divergent maternal lineages (<i>d</i><sub>XY</sub> = 0.00731; <i>F</i><sub>ST</sub> = 0.849; <i>P</i> < 0.05), thereby supporting the potential for two putative subspecies. However, the diverged lineage (n = 103 variants) almost exclusively involved bobwhites geographically classified as <i>Colinus virginianus texanus</i>, which is discordant with the expectations of previous geographic subspecies designations. Tests of adaptive evolution for functional divergence (MKT), frequency distribution tests (<i>D</i>, <i>F</i><sub>S</sub>) and phylogenetic analyses (RAxML) provide no evidence for positive selection or hybridization with the sympatric scaled quail (<i>Callipepla squamata</i>) as being explanatory factors for the two bobwhite maternal lineages observed. Instead, our analyses support the supposition that two diverged maternal lineages have survived from pre-expansion to post-expansion population(s), with the segregation of some slightly deleterious nonsynonymous mutations.</p></div>", "links"=>[], "tags"=>["mitochondrial genomic information content", "Phylogenetic analyses", "Colinus virginianus texanus", "OK", "lineage", "snv", "Mitochondrial Population Genomics", "fst", "variant", "i.e", "12 protein coding genes", "mj", "fs", "inference", "usa", "mitogenome haplotype structure", "mkt", "tx", "mitochondrial fragments", "bobwhite mitogenome sequences", "mitogenome sequences"], "article_id"=>1630744, "categories"=>["Biological Sciences", "Ecology"], "users"=>["Yvette A. Halley", "David L. Oldeschulte", "Eric K. Bhattarai", "Joshua Hill", "Richard P. Metz", "Charles D. Johnson", "Steven M. Presley", "Rebekah E. Ruzicka", "Dale Rollins", "Markus J. Peterson", "William J. Murphy", "Christopher M. Seabury"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0144913.s001", "https://dx.doi.org/10.1371/journal.pone.0144913.s002"], "stats"=>{"downloads"=>1, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/Northern_Bobwhite_Colinus_virginianus_Mitochondrial_Population_Genomics_Reveals_Structure_Divergence_and_Evidence_for_Heteroplasmy/1630744", "title"=>"Northern Bobwhite (<i>Colinus virginianus</i>) Mitochondrial Population Genomics Reveals Structure, Divergence, and Evidence for Heteroplasmy", "pos_in_sequence"=>0, "defined_type"=>4, "published_date"=>"2016-01-05 14:54:27"}

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{"start_date"=>"2015-01-01T00:00:00Z", "end_date"=>"2015-12-31T00:00:00Z", "subject_areas"=>[]}
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