Comparative Phylogeography of Direct-Developing Frogs (Anura: Craugastoridae: Pristimantis) in the Southern Andes of Colombia
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{"title"=>"Comparative Phylogeography of Direct-Developing Frogs (Anura: Craugastoridae: Pristimantis) in the Southern Andes of Colombia", "type"=>"journal", "authors"=>[{"first_name"=>"Juan C.", "last_name"=>"García-R", "scopus_author_id"=>"55366173300"}, {"first_name"=>"Andrew J.", "last_name"=>"Crawford", "scopus_author_id"=>"55536426000"}, {"first_name"=>"Ángela María", "last_name"=>"Mendoza", "scopus_author_id"=>"57193119745"}, {"first_name"=>"Oscar", "last_name"=>"Ospina", "scopus_author_id"=>"55204515600"}, {"first_name"=>"Heiber", "last_name"=>"Cardenas", "scopus_author_id"=>"7006647396"}, {"first_name"=>"Fernando", "last_name"=>"Castro", "scopus_author_id"=>"43160919700"}], "year"=>2012, "source"=>"PLoS ONE", "identifiers"=>{"pui"=>"365720817", "issn"=>"19326203", "isbn"=>"1932-6203", "doi"=>"10.1371/journal.pone.0046077", "scopus"=>"2-s2.0-84866675709", "pmid"=>"23049941", "sgr"=>"84866675709"}, "id"=>"e9a52bb7-c92a-3f9d-a101-e9a6448263f7", "abstract"=>"The Andes of South America hosts perhaps the highest amphibian species diversity in the world, and a sizable component of that diversity is comprised of direct-developing frogs of the genus Pristimantis (Anura: Craugastoridae). In order to better understand the initial stages of species formation in these frogs, this study quantified local-scale spatial genetic structuring in three species of Pristimantis. DNA sequences of two mitochondrial gene fragments (16S and COI) were obtained from P. brevifrons, P. palmeri and P. jubatus at different locations in the Cordillera Occidental. We found high levels of genetic diversity in the three species, with highly structured populations (as measured by F(ST)) in P. brevifrons and P. palmeri while P. jubatus showed panmixia. Large effective population sizes, inferred from the high levels of genetic diversity, were found in the three species and two highly divergent lineages were detected within P. jubatus and P. palmeri. Estimated divergence times among populations within P. brevifrons and P. palmeri coincide with the Pleistocene, perhaps due to similar responses to climatic cycling or recent geological history. Such insights have important implications for linking alpha and beta diversity, suggesting regional scale patterns may be associated with local scale processes in promoting differentiation among populations in the Andes.", "link"=>"http://www.mendeley.com/research/comparative-phylogeography-directdeveloping-frogs-anura-craugastoridae-pristimantis-southern-andes-c", "reader_count"=>99, "reader_count_by_academic_status"=>{"Unspecified"=>5, "Professor > Associate Professor"=>2, "Student > Doctoral Student"=>9, "Researcher"=>13, "Student > Ph. D. Student"=>16, "Student > Postgraduate"=>6, "Student > Master"=>17, "Other"=>4, "Student > Bachelor"=>17, "Lecturer > Senior Lecturer"=>1, "Professor"=>9}, "reader_count_by_user_role"=>{"Unspecified"=>5, "Professor > Associate Professor"=>2, "Student > Doctoral Student"=>9, "Researcher"=>13, "Student > Ph. D. Student"=>16, "Student > Postgraduate"=>6, "Student > Master"=>17, "Other"=>4, "Student > Bachelor"=>17, "Lecturer > Senior Lecturer"=>1, "Professor"=>9}, "reader_count_by_subject_area"=>{"Unspecified"=>5, "Environmental Science"=>6, "Biochemistry, Genetics and Molecular Biology"=>2, "Agricultural and Biological Sciences"=>85, "Business, Management and Accounting"=>1}, "reader_count_by_subdiscipline"=>{"Agricultural and Biological Sciences"=>{"Agricultural and Biological Sciences"=>85}, "Business, Management and Accounting"=>{"Business, Management and Accounting"=>1}, "Biochemistry, Genetics and Molecular Biology"=>{"Biochemistry, Genetics and Molecular Biology"=>2}, "Unspecified"=>{"Unspecified"=>5}, "Environmental Science"=>{"Environmental Science"=>6}}, "reader_count_by_country"=>{"Colombia"=>3, "Puerto Rico"=>1, "United States"=>2, "Brazil"=>4, "South Africa"=>1, "United Kingdom"=>1, "Mexico"=>1, "France"=>1, "Germany"=>1, "Spain"=>1}, "group_count"=>2}

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  • {"files"=>["https://ndownloader.figshare.com/files/570906"], "description"=>"*<p>Transect refers to the straight distance along which samples were collected at each site. The three sites for <i>P. jubatus</i> are contained within the Munchique National Park (<a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0046077#pone-0046077-g002\" target=\"_blank\">Fig. 2</a>).</p>", "links"=>[], "tags"=>["Evolutionary biology"], "article_id"=>241402, "categories"=>["Evolutionary Biology"], "users"=>["Juan C. García-R", "Andrew J. Crawford", "Ángela María Mendoza", "Oscar Ospina", "Heiber Cardenas", "Fernando Castro"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0046077.t002", "stats"=>{"downloads"=>1, "page_views"=>8, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Sampling_locations_/241402", "title"=>"Sampling locations.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2012-09-25 00:23:22"}
  • {"files"=>["https://ndownloader.figshare.com/files/570557"], "description"=>"<p>Branches represent inferred mutational steps, where more than three mutations are denoted by the number of substitutions. The size of the circle is proportional to the number of individuals found for each haplotype. The two highly divergent specimens from Peñas Blancas in <i>P. palmeri</i> and one from Munchique National Park in <i>P. jubatus</i> were included in the networks.</p>", "links"=>[], "tags"=>["mitochondrial", "dna", "haplotypes", "16s", "coi"], "article_id"=>241044, "categories"=>["Evolutionary Biology"], "users"=>["Juan C. García-R", "Andrew J. Crawford", "Ángela María Mendoza", "Oscar Ospina", "Heiber Cardenas", "Fernando Castro"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0046077.g001", "stats"=>{"downloads"=>1, "page_views"=>5, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Networks_of_mitochondrial_DNA_haplotypes_for_16S_left_and_COI_right_from_P_brevifrons_P_palmeri_and_P_jubatus_/241044", "title"=>"Networks of mitochondrial DNA haplotypes for 16S (left) and COI (right) from <i>P. brevifrons, P. palmeri</i> and <i>P. jubatus</i>.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2012-09-25 00:17:24"}
  • {"files"=>["https://ndownloader.figshare.com/files/570875"], "description"=>"<p><i>F</i><sub>ST</sub> estimated and confidence limits (in parentheses) between pairs of populations of <i>P. brevifrons</i> and <i>P. palmeri</i> using mtDNA sequences from the 16S and COI genes combined.</p>", "links"=>[], "tags"=>["limits", "pairs", "populations", "mtdna", "sequences", "16s", "coi", "genes"], "article_id"=>241364, "categories"=>["Evolutionary Biology"], "users"=>["Juan C. García-R", "Andrew J. Crawford", "Ángela María Mendoza", "Oscar Ospina", "Heiber Cardenas", "Fernando Castro"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0046077.t001", "stats"=>{"downloads"=>1, "page_views"=>4, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_F_ST_estimated_and_confidence_limits_in_parentheses_between_pairs_of_populations_of_P_brevifrons_and_P_palmeri_using_mtDNA_sequences_from_the_16S_and_COI_genes_combined_/241364", "title"=>"<i>F</i><sub>ST</sub> estimated and confidence limits (in parentheses) between pairs of populations of <i>P. brevifrons</i> and <i>P. palmeri</i> using mtDNA sequences from the 16S and COI genes combined.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2012-09-25 00:22:44"}
  • {"files"=>["https://ndownloader.figshare.com/files/570948"], "description"=>"<p>N  =  number of sequences, h  =  number of haplotypes, S  =  segregating sites, <i>θ<sub>W</sub></i>  =  population mutation rate per site, π  =  nucleotide diversity per site, D<sub>T</sub>  =  Tajima’s D statistic <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0046077#pone.0046077-Tajima1\" target=\"_blank\">[73]</a>. An asterisk (*) in the D<sub>T</sub> column indicates a significant deviation from the expected value under neutrality (D<sub>T</sub> = 0) as calculated from coalescence simulations. D<sub>T</sub> values in <b>bold</b> obtained for <i>P. jubatus</i> when the divergent sample UVC15842 was excluded. N.A.  =  Not Applicable. Indels and sites with missing data were not taken into account in pairwise comparisons.</p>", "links"=>[], "tags"=>["polymorphism", "mitochondrial", "dna", "sequences", "populations"], "article_id"=>241437, "categories"=>["Evolutionary Biology"], "users"=>["Juan C. García-R", "Andrew J. Crawford", "Ángela María Mendoza", "Oscar Ospina", "Heiber Cardenas", "Fernando Castro"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0046077.t003", "stats"=>{"downloads"=>1, "page_views"=>9, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Genetic_polymorphism_data_for_mitochondrial_DNA_sequences_from_the_Pristimantis_populations_in_this_study_/241437", "title"=>"Genetic polymorphism data for mitochondrial DNA sequences from the <i>Pristimantis</i> populations in this study.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2012-09-25 00:23:57"}
  • {"files"=>["https://ndownloader.figshare.com/files/301450", "https://ndownloader.figshare.com/files/301543", "https://ndownloader.figshare.com/files/301629", "https://ndownloader.figshare.com/files/301695"], "description"=>"<div><p>The Andes of South America hosts perhaps the highest amphibian species diversity in the world, and a sizable component of that diversity is comprised of direct-developing frogs of the genus <em>Pristimantis</em> (Anura: Craugastoridae). In order to better understand the initial stages of species formation in these frogs, this study quantified local-scale spatial genetic structuring in three species of <em>Pristimantis</em>. DNA sequences of two mitochondrial gene fragments (16S and COI) were obtained from <em>P. brevifrons</em>, <em>P. palmeri</em> and <em>P. jubatus</em> at different locations in the Cordillera Occidental. We found high levels of genetic diversity in the three species, with highly structured populations (as measured by <em>F</em><sub>ST</sub>) in <em>P. brevifrons</em> and <em>P. palmeri</em> while <em>P. jubatus</em> showed panmixia. Large effective population sizes, inferred from the high levels of genetic diversity, were found in the three species and two highly divergent lineages were detected within <em>P. jubatus</em> and <em>P. palmeri</em>. Estimated divergence times among populations within <em>P. brevifrons</em> and <em>P. palmeri</em> coincide with the Pleistocene, perhaps due to similar responses to climatic cycling or recent geological history. Such insights have important implications for linking alpha and beta diversity, suggesting regional scale patterns may be associated with local scale processes in promoting differentiation among populations in the Andes.</p> </div>", "links"=>[], "tags"=>["comparative", "phylogeography", "direct-developing", "frogs", "andes", "colombia"], "article_id"=>119447, "categories"=>["Evolutionary Biology"], "users"=>["Juan C. García-R", "Andrew J. Crawford", "Ángela María Mendoza", "Oscar Ospina", "Heiber Cardenas", "Fernando Castro"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0046077.s001", "https://dx.doi.org/10.1371/journal.pone.0046077.s002", "https://dx.doi.org/10.1371/journal.pone.0046077.s003", "https://dx.doi.org/10.1371/journal.pone.0046077.s004"], "stats"=>{"downloads"=>3, "page_views"=>9, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/Comparative_Phylogeography_of_Direct_Developing_Frogs_Anura_Craugastoridae_Pristimantis_in_the_Southern_Andes_of_Colombia/119447", "title"=>"Comparative Phylogeography of Direct-Developing Frogs (Anura: Craugastoridae: <em>Pristimantis</em>) in the Southern Andes of Colombia", "pos_in_sequence"=>0, "defined_type"=>4, "published_date"=>"2012-09-25 02:37:27"}
  • {"files"=>["https://ndownloader.figshare.com/files/570833"], "description"=>"*<p>indicates that HPD estimates are unreliable because the tail of the distribution did not reach zero.</p>", "links"=>[], "tags"=>["ima", "parameter", "theta", "divergence", "times", "highest", "posterior", "intervals", "populations", "pairwise", "comparisons", "coi", "16s"], "article_id"=>241311, "categories"=>["Evolutionary Biology"], "users"=>["Juan C. García-R", "Andrew J. Crawford", "Ángela María Mendoza", "Oscar Ospina", "Heiber Cardenas", "Fernando Castro"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0046077.t004", "stats"=>{"downloads"=>1, "page_views"=>11, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Estimates_obtained_from_IMa_for_the_population_size_parameter_theta_N_e_gene_flow_Nm_and_divergence_times_t_and_90_highest_posterior_density_HPD_intervals_for_populations_of_P_brevifrons_one_pairwise_comparison_among_two_localities_and_P_palmeri_three_pa/241311", "title"=>"Estimates obtained from IMa for the population size parameter theta (<i>N<sub>e</sub></i>), gene flow (<i>Nm</i>) and divergence times (<i>t</i>) and 90% highest posterior density (HPD) intervals for populations of <i>P. brevifrons</i> (one pairwise comparison among two localities) and <i>P. palmeri</i> (three pairwise comparisons among three localities), based on the combined COI and 16S data.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2012-09-25 00:21:51"}

PMC Usage Stats | Further Information

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Relative Metric

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