Phylogeography of the Endangered Otago Skink, Oligosoma otagense: Population Structure, Hybridisation and Genetic Diversity in Captive Populations
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{"title"=>"Phylogeography of the endangered Otago skink, Oligosoma otagense: population structure, hybridisation and genetic diversity in captive populations.", "type"=>"journal", "authors"=>[{"first_name"=>"David G.", "last_name"=>"Chapple", "scopus_author_id"=>"8363653900"}, {"first_name"=>"Alisha", "last_name"=>"Birkett", "scopus_author_id"=>"55545715800"}, {"first_name"=>"Kimberly A.", "last_name"=>"Miller", "scopus_author_id"=>"35190787300"}, {"first_name"=>"Charles H.", "last_name"=>"Daugherty", "scopus_author_id"=>"7006324578"}, {"first_name"=>"Dianne M.", "last_name"=>"Gleeson", "scopus_author_id"=>"7005315532"}], "year"=>2012, "source"=>"PloS one", "identifiers"=>{"scopus"=>"2-s2.0-84871886310", "doi"=>"10.1371/journal.pone.0034599", "sgr"=>"84871886310", "isbn"=>"1932-6203", "pmid"=>"22511953", "issn"=>"19326203", "pui"=>"366360165"}, "id"=>"e81087ca-eee6-3934-a01e-d9e9a6c6aac1", "abstract"=>"Climatic cooling and substantial tectonic activity since the late Miocene have had a pronounced influence on the evolutionary history of the fauna of New Zealand's South Island. However, many species have recently experienced dramatic range reductions due to habitat fragmentation and the introduction of mammalian predators and competitors. These anthropogenic impacts have been particularly severe in the tussock grasslands of the Otago region. The Otago skink (Oligosoma otagense), endemic to the region, is one of the most critically endangered vertebrates in New Zealand. We use mitochondrial DNA sequence data to investigate the evolutionary history of the Otago skink, examine its population genetic structure, and assess the level of genetic diversity in the individuals in the captive breeding program. Our data indicate that the Otago skink diverged from its closest relatives in the Miocene, consistent with the commencement of tectonic uplift of the Southern Alps. However, there is evidence for past introgression with the scree skink (O. waimatense) in the northern Otago-southern Canterbury region. The remnant populations in eastern Otago and western Otago are estimated to have diverged in the mid-Pliocene, with no haplotypes shared between these two regions. This divergence accounts for 95% of the genetic diversity in the species. Within both regions there is strong genetic structure among populations, although shared haplotypes are generally evident between adjacent localities. Although substantial genetic diversity is present in the captive population, all individuals originate from the eastern region and the majority had haplotypes that were not evident in the intensively managed populations at Macraes Flat. Our data indicate that eastern and western populations should continue to be regarded as separate management units. Knowledge of the genetic diversity of the breeding stock will act to inform the captive management of the Otago skink and contribute to a key recovery action for the species.", "link"=>"http://www.mendeley.com/research/phylogeography-endangered-otago-skink-oligosoma-otagense-population-structure-hybridisation-genetic", "reader_count"=>29, "reader_count_by_academic_status"=>{"Unspecified"=>1, "Professor > Associate Professor"=>2, "Researcher"=>4, "Student > Ph. D. Student"=>5, "Student > Master"=>9, "Other"=>1, "Student > Bachelor"=>6, "Lecturer > Senior Lecturer"=>1}, "reader_count_by_user_role"=>{"Unspecified"=>1, "Professor > Associate Professor"=>2, "Researcher"=>4, "Student > Ph. D. Student"=>5, "Student > Master"=>9, "Other"=>1, "Student > Bachelor"=>6, "Lecturer > Senior Lecturer"=>1}, "reader_count_by_subject_area"=>{"Unspecified"=>1, "Environmental Science"=>3, "Biochemistry, Genetics and Molecular Biology"=>3, "Agricultural and Biological Sciences"=>20, "Psychology"=>1, "Earth and Planetary Sciences"=>1}, "reader_count_by_subdiscipline"=>{"Psychology"=>{"Psychology"=>1}, "Earth and Planetary Sciences"=>{"Earth and Planetary Sciences"=>1}, "Agricultural and Biological Sciences"=>{"Agricultural and Biological Sciences"=>20}, "Biochemistry, Genetics and Molecular Biology"=>{"Biochemistry, Genetics and Molecular Biology"=>3}, "Unspecified"=>{"Unspecified"=>1}, "Environmental Science"=>{"Environmental Science"=>3}}, "reader_count_by_country"=>{"New Zealand"=>1, "Portugal"=>1}, "group_count"=>0}

Scopus | Further Information

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Figshare

  • {"files"=>["https://ndownloader.figshare.com/files/654672"], "description"=>"<p>Asterisks indicate statistical significance following Bonferroni correction (adjusted significance level 0.005).</p>", "links"=>[], "tags"=>["otago", "skink"], "article_id"=>325160, "categories"=>["Evolutionary Biology", "Genetics", "Ecology"], "users"=>["David G. Chapple", "Alisha Birkett", "Kimberly A. Miller", "Charles H. Daugherty", "Dianne M. Gleeson"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0034599.t006", "stats"=>{"downloads"=>3, "page_views"=>10, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/Pairwise_sub_ST_sub_among_the_five_Otago_skink_populations_/325160", "title"=>"Pairwise Φ<sub>ST</sub> among the five Otago skink populations.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2013-02-20 06:35:56"}
  • {"files"=>["https://ndownloader.figshare.com/files/654631"], "description"=>"<p>Mean TrN genetic distances between <i>control region</i> haplotypes.</p>", "links"=>[], "tags"=>["trn", "distances"], "article_id"=>325124, "categories"=>["Evolutionary Biology", "Genetics", "Ecology"], "users"=>["David G. Chapple", "Alisha Birkett", "Kimberly A. Miller", "Charles H. Daugherty", "Dianne M. Gleeson"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0034599.t005", "stats"=>{"downloads"=>2, "page_views"=>23, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/Mean_TrN_genetic_distances_between_i_control_region_i_haplotypes_/325124", "title"=>"Mean TrN genetic distances between <i>control region</i> haplotypes.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2013-02-20 06:35:46"}
  • {"files"=>["https://ndownloader.figshare.com/files/654398"], "description"=>"<p>Each circle represents one haplotype and the size indicates the number of individuals with each haplotype. The lines indicate one base pair change between sequences. The different colours indicate the population(s) in which each haplotype is found. A) Wild Otago skink populations, B) Wild and captive Otago skinks, C) Wild Otago skinks and introgressed scree skinks.</p>", "links"=>[], "tags"=>["haplotype", "otago"], "article_id"=>324887, "categories"=>["Evolutionary Biology", "Genetics", "Ecology"], "users"=>["David G. Chapple", "Alisha Birkett", "Kimberly A. Miller", "Charles H. Daugherty", "Dianne M. Gleeson"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0034599.g003", "stats"=>{"downloads"=>2, "page_views"=>25, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_i_Control_region_i_haplotype_network_for_the_Otago_skink_/324887", "title"=>"<i>Control region</i> haplotype network for the Otago skink.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-02-20 06:34:34"}
  • {"files"=>["https://ndownloader.figshare.com/files/654179"], "description"=>"<p>The distribution of <i>O. otagense</i> (black circles), <i>O. waimatense</i> (blue squares), <i>O. acrinasum</i> (green circles), <i>O. infrapunctatum</i> (red triangles), <i>O. taumakae</i> (orange square), and <i>O. pikitanga</i> (purple circle) is indicated. Several localities mentioned in the text are highlighted, including the locations of the <i>O. otagense</i> and <i>O. waimatense</i> samples used in this study. The dashed line indicates the estimated former distribution of <i>O. otagense </i><a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0034599#pone.0034599-Whitaker1\" target=\"_blank\">[26]</a>. The distribution data is adapted from the Department of Conservation's BioWeb Herpetofauna database. Inset: Major geographic regions of New Zealand.</p>", "links"=>[], "tags"=>["otago", "skink", "zealand"], "article_id"=>324662, "categories"=>["Evolutionary Biology", "Genetics", "Ecology"], "users"=>["David G. Chapple", "Alisha Birkett", "Kimberly A. Miller", "Charles H. Daugherty", "Dianne M. Gleeson"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0034599.g001", "stats"=>{"downloads"=>2, "page_views"=>12, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/Distribution_of_the_Otago_skink_and_several_closely_related_species_of_New_Zealand_skinks_/324662", "title"=>"Distribution of the Otago skink and several closely related species of New Zealand skinks.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-02-20 06:33:20"}
  • {"files"=>["https://ndownloader.figshare.com/files/654277"], "description"=>"<p>The lineage contains five other species: <i>O. waimatense</i>, <i>O. acrinasum</i>, <i>O. infrapunctatum</i>, <i>O. pikitanga</i>, and <i>O. taumakae</i>. The phylogeny is based upon 1834 bp of mitochondrial DNA sequence data (<i>ND2</i>, <i>ND4</i> &amp; Cytochrome b). Two measures of branch support are indicated with ML bootstraps (500 replicates) on the left and Bayesian posterior probabilities on the right (only values over 50 and 0.7, respectively, are shown).</p>", "links"=>[], "tags"=>["phylogram", "zealand", "skink", "lineage", "containing", "otago"], "article_id"=>324767, "categories"=>["Evolutionary Biology", "Genetics", "Ecology"], "users"=>["David G. Chapple", "Alisha Birkett", "Kimberly A. Miller", "Charles H. Daugherty", "Dianne M. Gleeson"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0034599.g002", "stats"=>{"downloads"=>10, "page_views"=>56, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/Maximum_Likelihood_ML_phylogram_for_the_New_Zealand_skink_lineage_containing_the_Otago_skink_i_Oligosoma_otagense_i_/324767", "title"=>"Maximum Likelihood (ML) phylogram for the New Zealand skink lineage containing the Otago skink (<i>Oligosoma otagense</i>).", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-02-20 06:33:56"}
  • {"files"=>["https://ndownloader.figshare.com/files/654598"], "description"=>"<p><i>n</i> = sample size, <i>h</i> = number of haplotypes (the specific haplotypes present are indicated), <i>Hd</i> = haplotypic diversity, <i>M</i> = total number of mutations, <i>S</i> = number of segregating (polymorphic) sites, π = nucleotide diversity, RI = raggedness index, SSD = sum of squared deviations. Asterisks indicate significant Tajima's <i>D</i>, Fu's <i>F</i>s statistic, RI and SSD values.</p>", "links"=>[], "tags"=>["otago", "skink", "populations"], "article_id"=>325092, "categories"=>["Evolutionary Biology", "Genetics", "Ecology"], "users"=>["David G. Chapple", "Alisha Birkett", "Kimberly A. Miller", "Charles H. Daugherty", "Dianne M. Gleeson"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0034599.t004", "stats"=>{"downloads"=>1, "page_views"=>14, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/Estimates_of_genetic_diversity_mitochondrial_i_control_region_i_within_Otago_skink_populations_and_regions_/325092", "title"=>"Estimates of genetic diversity (mitochondrial <i>control region</i>) within Otago skink populations and regions.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2013-02-20 06:35:36"}
  • {"files"=>["https://ndownloader.figshare.com/files/654574"], "description"=>"<p>Mean model-corrected genetic distances (<i>ND2</i>, <i>ND4</i>, Cytochrome b) between the Otago skink and several closely-related species.</p>", "links"=>[], "tags"=>["model-corrected", "distances", "cytochrome", "otago", "skink", "closely-related"], "article_id"=>325057, "categories"=>["Evolutionary Biology", "Genetics", "Ecology"], "users"=>["David G. Chapple", "Alisha Birkett", "Kimberly A. Miller", "Charles H. Daugherty", "Dianne M. Gleeson"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0034599.t003", "stats"=>{"downloads"=>6, "page_views"=>21, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/Mean_model_corrected_genetic_distances_i_ND2_i_i_ND4_i_Cytochrome_b_between_the_Otago_skink_and_several_closely_related_species_/325057", "title"=>"Mean model-corrected genetic distances (<i>ND2</i>, <i>ND4</i>, Cytochrome b) between the Otago skink and several closely-related species.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2013-02-20 06:35:23"}
  • {"files"=>["https://ndownloader.figshare.com/files/654493"], "description"=>"<p>Samples with CD or FT codes were obtained from the National Frozen Tissue Collection (NFTC) housed at Victoria University of Wellington, New Zealand. Samples with RE codes were obtained from ethanol preserved specimens housed at Te Papa, National Museum of New Zealand, Wellington (S codes refer to specimens from the former Ecology Division collection, now housed at Te Papa).</p>", "links"=>[], "tags"=>["genbank", "accession", "numbers", "samples", "phylogenetic"], "article_id"=>324978, "categories"=>["Evolutionary Biology", "Genetics", "Ecology"], "users"=>["David G. Chapple", "Alisha Birkett", "Kimberly A. Miller", "Charles H. Daugherty", "Dianne M. Gleeson"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0034599.t001", "stats"=>{"downloads"=>1, "page_views"=>7, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/Locality_information_and_GenBank_accession_numbers_for_samples_used_in_the_phylogenetic_analyses_/324978", "title"=>"Locality information and GenBank accession numbers for samples used in the phylogenetic analyses.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2013-02-20 06:35:02"}
  • {"files"=>["https://ndownloader.figshare.com/files/654531"], "description"=>"<p>The letters L and H refer to the light and heavy strands. Values in ‘5’ position' refer to the position of the 5′ position in the complete <i>Eumeces egregius</i> mtDNA sequence <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0034599#pone.0034599-Kumazawa1\" target=\"_blank\">[96]</a>.</p>", "links"=>[], "tags"=>["primers"], "article_id"=>325023, "categories"=>["Evolutionary Biology", "Genetics", "Ecology"], "users"=>["David G. Chapple", "Alisha Birkett", "Kimberly A. Miller", "Charles H. Daugherty", "Dianne M. Gleeson"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0034599.t002", "stats"=>{"downloads"=>3, "page_views"=>8, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/Oligonucleotide_primers_used_in_this_study_/325023", "title"=>"Oligonucleotide primers used in this study.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2013-02-20 06:35:13"}

PMC Usage Stats | Further Information

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Relative Metric

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