Patterns in Nuclear and Mitochondrial DNA Reveal Historical and Recent Isolation in the Black-Tailed Godwit (Limosa limosa)
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{"title"=>"Patterns in nuclear and mitochondrial DNA reveal historical and recent isolation in the black-tailed godwit (Limosa limosa)", "type"=>"journal", "authors"=>[{"first_name"=>"Krijn B.", "last_name"=>"Trimbos", "scopus_author_id"=>"7801508396"}, {"first_name"=>"Camiel", "last_name"=>"Doorenweerd", "scopus_author_id"=>"55062310800"}, {"first_name"=>"Ken", "last_name"=>"Kraaijeveld", "scopus_author_id"=>"6701738590"}, {"first_name"=>"C. J.M.", "last_name"=>"Musters", "scopus_author_id"=>"6602415002"}, {"first_name"=>"Niko M.", "last_name"=>"Groen", "scopus_author_id"=>"6602199184"}, {"first_name"=>"Peterde", "last_name"=>"Knijff", "scopus_author_id"=>"56147027300"}, {"first_name"=>"Theunis", "last_name"=>"Piersma", "scopus_author_id"=>"7005941801"}, {"first_name"=>"Geert R.", "last_name"=>"De Snoo", "scopus_author_id"=>"6701724408"}], "year"=>2014, "source"=>"PLoS ONE", "identifiers"=>{"sgr"=>"84897553005", "pmid"=>"24416186", "isbn"=>"1932-6203, 1932-6203", "pui"=>"372763042", "issn"=>"19326203", "scopus"=>"2-s2.0-84897553005", "doi"=>"10.1371/journal.pone.0083949"}, "id"=>"5d93def2-fae3-39ee-b1fd-290e652d0d6d", "abstract"=>"On the basis of morphological differences, three subspecies of Black-tailed Godwit (Limosa limosa) have been recognized (L. l. limosa, L. l. islandica and L. l. melanuroides). In previous studies mitochondrial DNA (mtDNA) sequence data showed minimal genetic divergence between the three subspecies and an absence of sub-structuring within L. l. limosa. Here, population genetic structure and phylogeographic patterns have been analyzed using COI, HVR1 and HVR2 mtDNA sequence data as well as 12 microsatellite loci (nuDNA). The nuDNA data suggest genetic differentiation between L. l. limosa from Sweden and The Netherlands, between L. l. limosa and L. l. islandica, but not between L. l. limosa and L. l. melanuroides. However, the mtDNA data were not consistent with the nuDNA pattern. mtDNA did support a split between L. l. melanuroides and L. l. limosa/L. l. islandica and also demonstrated two L. l. limosa haplotype clusters that were not geographically isolated. This genetic structure can be explained by a scenario of isolation of L. l. melanuroides from L. l. limosa in Beringia during the Last Glacial Maximum. During the Pleistocene separation of L. l. islandica from L. l. limosa occurred, followed by colonization of Iceland by the L. l. islandica during the Holocene. Within L. l. limosa founder events, followed by population expansion, took place during the Holocene also. According to the patterns observed in both markers together and their geographic separation, we propose that the three traditional subspecies indeed represent three separate genetic units.", "link"=>"http://www.mendeley.com/research/patterns-nuclear-mitochondrial-dna-reveal-historical-recent-isolation-blacktailed-godwit-limosa-limo", "reader_count"=>23, "reader_count_by_academic_status"=>{"Professor > Associate Professor"=>1, "Librarian"=>2, "Researcher"=>6, "Student > Doctoral Student"=>1, "Student > Ph. D. Student"=>6, "Other"=>1, "Student > Master"=>1, "Student > Bachelor"=>3, "Lecturer"=>1, "Professor"=>1}, "reader_count_by_user_role"=>{"Professor > Associate Professor"=>1, "Librarian"=>2, "Researcher"=>6, "Student > Doctoral Student"=>1, "Student > Ph. D. Student"=>6, "Other"=>1, "Student > Master"=>1, "Student > Bachelor"=>3, "Lecturer"=>1, "Professor"=>1}, "reader_count_by_subject_area"=>{"Biochemistry, Genetics and Molecular Biology"=>3, "Agricultural and Biological Sciences"=>18, "Chemistry"=>1, "Social Sciences"=>1}, "reader_count_by_subdiscipline"=>{"Chemistry"=>{"Chemistry"=>1}, "Social Sciences"=>{"Social Sciences"=>1}, "Agricultural and Biological Sciences"=>{"Agricultural and Biological Sciences"=>18}, "Biochemistry, Genetics and Molecular Biology"=>{"Biochemistry, Genetics and Molecular Biology"=>3}}, "reader_count_by_country"=>{"Netherlands"=>1, "Portugal"=>1}, "group_count"=>1}

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Figshare

  • {"files"=>["https://ndownloader.figshare.com/files/1344579"], "description"=>"<p>Below the diagonal: D values for the microsatellite loci; above the diagonal: pairwise Φst for mtDNA HVR sequences. Confidence Intervals not overlapping with zero for D values and significant P values after sequential bonferroni correction for Φst are indicated by *.</p>", "links"=>[], "tags"=>["ecology", "Evolutionary biology", "Evolutionary systematics", "phylogenetics", "Organismal evolution", "Animal evolution", "Evolutionary genetics", "population genetics", "genetics", "Population biology", "Zoology", "Animal phylogenetics", "Ornithology", "microsatellite", "loci", "pairwise", "mtdna", "hvr"], "article_id"=>898921, "categories"=>["Biological Sciences"], "users"=>["Krijn B. Trimbos", "Camiel Doorenweerd", "Ken Kraaijeveld", "C. J. M. Musters", "Niko M. Groen", "Peter de Knijff", "Theunis Piersma", "Geert R. De Snoo"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0083949.t003", "stats"=>{"downloads"=>1, "page_views"=>18, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_D_values_for_the_microsatellite_loci_and_pairwise_934_st_for_mtDNA_HVR_sequences_/898921", "title"=>"D values for the microsatellite loci and pairwise Φst for mtDNA HVR sequences.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2014-01-09 03:55:27"}
  • {"files"=>["https://ndownloader.figshare.com/files/1344578"], "description"=>"<p>Analysis of the mitochondrial HVR sequences for the three <i>Limosa limosa</i> subspecies. The colors indicate the sample locations. The support values of the maximum likelihood analysis are plotted on the respective branches. Additionally, a median-joining network of 89 HVR mtDNA sequences is depicted. Different clusters are indicated with a/b/c/d. The red arrow indicates one individual (H072) which was found on Iceland but sorted close to <i>L. l. limosa</i> haplotypes.</p>", "links"=>[], "tags"=>["ecology", "Evolutionary biology", "Evolutionary systematics", "phylogenetics", "Organismal evolution", "Animal evolution", "Evolutionary genetics", "population genetics", "genetics", "Population biology", "Zoology", "Animal phylogenetics", "Ornithology", "median", "joining", "mitochondrial", "hvr1", "hvr2"], "article_id"=>898920, "categories"=>["Biological Sciences"], "users"=>["Krijn B. Trimbos", "Camiel Doorenweerd", "Ken Kraaijeveld", "C. J. M. Musters", "Niko M. Groen", "Peter de Knijff", "Theunis Piersma", "Geert R. De Snoo"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0083949.g004", "stats"=>{"downloads"=>6, "page_views"=>44, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Maximum_Likelihood_tree_and_median_joining_network_of_the_mitochondrial_HVR1_and_HVR2_regions_/898920", "title"=>"Maximum Likelihood tree and median joining network of the mitochondrial HVR1 and HVR2 regions.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2014-01-09 03:55:27"}
  • {"files"=>["https://ndownloader.figshare.com/files/1344573"], "description"=>"<p>Above: mean log likelihood Ln P(X|K) and DeltaK as a function of the number of genetic clusters (K) averaged over 5 consecutive STRUCTURE runs for each K (error bars indicate one standard deviation). Below: representation of the assignment values, estimated relative contribution of each member of the population to that individual's microsatellite-based genome, per individual at the different sample locations for K = 4. The red arrow indicates sample H072.</p>", "links"=>[], "tags"=>["ecology", "Evolutionary biology", "Evolutionary systematics", "phylogenetics", "Organismal evolution", "Animal evolution", "Evolutionary genetics", "population genetics", "genetics", "Population biology", "Zoology", "Animal phylogenetics", "Ornithology", "deltak", "microsatellite"], "article_id"=>898915, "categories"=>["Biological Sciences"], "users"=>["Krijn B. Trimbos", "Camiel Doorenweerd", "Ken Kraaijeveld", "C. J. M. Musters", "Niko M. Groen", "Peter de Knijff", "Theunis Piersma", "Geert R. De Snoo"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0083949.g002", "stats"=>{"downloads"=>2, "page_views"=>137, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Mean_log_likelihood_DeltaK_and_assignment_value_plot_of_microsatellite_STRUCTURE_analysis_/898915", "title"=>"Mean log likelihood, DeltaK and assignment value plot of microsatellite STRUCTURE analysis.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2014-01-09 03:55:27"}
  • {"files"=>["https://ndownloader.figshare.com/files/1344581"], "description"=>"<p>Region, Sample location, number of samples per sample location used for microsatellite analysis (nuDNA), number of samples per sample location used for HVR mtDNA analysis (HVR), number of samples per sample location used for COI mtDNA analysis (COI) and the <i>Limosa</i> species or <i>Limosa limosa</i> subspecies per sample location.</p>", "links"=>[], "tags"=>["ecology", "Evolutionary biology", "Evolutionary systematics", "phylogenetics", "Organismal evolution", "Animal evolution", "Evolutionary genetics", "population genetics", "genetics", "Population biology", "Zoology", "Animal phylogenetics", "Ornithology"], "article_id"=>898923, "categories"=>["Biological Sciences"], "users"=>["Krijn B. Trimbos", "Camiel Doorenweerd", "Ken Kraaijeveld", "C. J. M. Musters", "Niko M. Groen", "Peter de Knijff", "Theunis Piersma", "Geert R. De Snoo"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0083949.t001", "stats"=>{"downloads"=>1, "page_views"=>12, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Geographical_and_genetic_information_of_the_used_samples_/898923", "title"=>"Geographical and genetic information of the used samples.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2014-01-09 03:55:27"}
  • {"files"=>["https://ndownloader.figshare.com/files/1344580"], "description"=>"<p>Sample location and <i>Limosa limosa</i> subspecies; number of sequence alignments (n), haplotype diversity (h), number of haplotypes (nh) for COI and HVR mtDNA; and number of individuals (n), absolute number of alleles (A), allelic richness (A<sub>R</sub>), number of private alleles (P<sub>a</sub>) and inbreeding coefficient (F<sub>IS</sub>) for microsatellite fragment analysis (Msats).</p>", "links"=>[], "tags"=>["ecology", "Evolutionary biology", "Evolutionary systematics", "phylogenetics", "Organismal evolution", "Animal evolution", "Evolutionary genetics", "population genetics", "genetics", "Population biology", "Zoology", "Animal phylogenetics", "Ornithology", "mitochondrial", "sequences", "microsatellite"], "article_id"=>898922, "categories"=>["Biological Sciences"], "users"=>["Krijn B. Trimbos", "Camiel Doorenweerd", "Ken Kraaijeveld", "C. J. M. Musters", "Niko M. Groen", "Peter de Knijff", "Theunis Piersma", "Geert R. De Snoo"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0083949.t002", "stats"=>{"downloads"=>0, "page_views"=>9, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Genetic_diversity_values_of_mitochondrial_sequences_and_microsatellite_fragment_lengths_/898922", "title"=>"Genetic diversity values of mitochondrial sequences and microsatellite fragment lengths.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2014-01-09 03:55:27"}
  • {"files"=>["https://ndownloader.figshare.com/files/1344575"], "description"=>"<p>Maximum Likelihood based on COI barcode mitochondrial sequences of <i>Limosa</i> with <i>Limnodromus</i> as outgroup <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0083949#pone.0083949-Thomas1\" target=\"_blank\">[55]</a>. Aside from the barcode sequences generated for this study, public sequences for <i>Limosa haemastica</i>, <i>Limosa fedoa</i>, <i>Limosa lapponica</i>, <i>Limnodromus scolopaceus</i> and <i>Limnodromus griseus</i> available through BOLD were included as well, indicated by their BOLD ID.</p>", "links"=>[], "tags"=>["ecology", "Evolutionary biology", "Evolutionary systematics", "phylogenetics", "Organismal evolution", "Animal evolution", "Evolutionary genetics", "population genetics", "genetics", "Population biology", "Zoology", "Animal phylogenetics", "Ornithology", "mitochondrial", "coi"], "article_id"=>898917, "categories"=>["Biological Sciences"], "users"=>["Krijn B. Trimbos", "Camiel Doorenweerd", "Ken Kraaijeveld", "C. J. M. Musters", "Niko M. Groen", "Peter de Knijff", "Theunis Piersma", "Geert R. De Snoo"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0083949.g003", "stats"=>{"downloads"=>0, "page_views"=>17, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Maximum_Likelihood_tree_mitochondrial_COI_region_/898917", "title"=>"Maximum Likelihood tree mitochondrial COI region.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2014-01-09 03:55:27"}
  • {"files"=>["https://ndownloader.figshare.com/files/1344568"], "description"=>"<p>Sample locations of the Black-tailed Godwit <i>Limosa limosa</i>. <i>L. l. limosa</i>: the Netherlands, Mid-Germany, Northern Germany, Denmark, Sweden, Belarus/Moscow, Kazachstan/SW Russia; <i>L. l. islandica</i>: Iceland; and <i>L. l. melanuroides</i>: Eastern Russia/Selanga delta.</p>", "links"=>[], "tags"=>["ecology", "Evolutionary biology", "Evolutionary systematics", "phylogenetics", "Organismal evolution", "Animal evolution", "Evolutionary genetics", "population genetics", "genetics", "Population biology", "Zoology", "Animal phylogenetics", "Ornithology", "locations", "black-tailed", "godwit"], "article_id"=>898913, "categories"=>["Biological Sciences"], "users"=>["Krijn B. Trimbos", "Camiel Doorenweerd", "Ken Kraaijeveld", "C. J. M. Musters", "Niko M. Groen", "Peter de Knijff", "Theunis Piersma", "Geert R. De Snoo"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0083949.g001", "stats"=>{"downloads"=>0, "page_views"=>23, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Sample_locations_of_the_Black_tailed_Godwit_Limosa_limosa_/898913", "title"=>"Sample locations of the Black-tailed Godwit <i>Limosa limosa</i>.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2014-01-09 03:55:27"}

PMC Usage Stats | Further Information

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Relative Metric

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