Investigating Concordance among Genetic Data, Subspecies Circumscriptions and Hostplant Use in the Nymphalid Butterfly Polygonia faunus
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{"title"=>"Investigating concordance among genetic data, subspecies circumscriptions and hostplant use in the Nymphalid butterfly Polygonia faunus", "type"=>"journal", "authors"=>[{"first_name"=>"Ullasa", "last_name"=>"Kodandaramaiah", "scopus_author_id"=>"22938074800"}, {"first_name"=>"Elisabet", "last_name"=>"Weingartner", "scopus_author_id"=>"12785384500"}, {"first_name"=>"Niklas", "last_name"=>"Janz", "scopus_author_id"=>"7005955238"}, {"first_name"=>"Michael", "last_name"=>"Leski", "scopus_author_id"=>"57197179407"}, {"first_name"=>"Jessica", "last_name"=>"Slove", "scopus_author_id"=>"36626218100"}, {"first_name"=>"Andrew", "last_name"=>"Warren", "scopus_author_id"=>"7201588708"}, {"first_name"=>"Sören", "last_name"=>"Nylin", "scopus_author_id"=>"7004462501"}], "year"=>2012, "source"=>"PLoS ONE", "identifiers"=>{"pui"=>"365316178", "sgr"=>"84864245306", "issn"=>"19326203", "pmid"=>"22844425", "scopus"=>"2-s2.0-84864245306", "doi"=>"10.1371/journal.pone.0041058", "isbn"=>"1932-6203 (Electronic)\\n1932-6203 (Linking)"}, "id"=>"8fc1ee26-339a-356b-b7e9-bfc77a482940", "abstract"=>"Subspecies are commonly used taxonomic units to formally describe intraspecific geographic variation in morphological traits. However, the concept of subspecies is not clearly defined, and there is little agreement about what they represent in terms of evolutionary units, and whether they can be used as reliably useful units in conservation, evolutionary theory and taxonomy. We here investigate whether the morphologically well-characterized subspecies in the North American butterfly Polygonia faunus are supported by genetic data from mitochondrial sequences and eight microsatellite loci. We also investigate the phylogeographic structure of P. faunus and test whether similarities in host-plant use among populations are related to genetic similarity. Neither the nuclear nor the mitochondrial data corroborated subspecies groupings. We found three well defined genetic clusters corresponding to California, Arizona and (New Mexico+Colorado). There was little structuring among the remaining populations, probably due to gene flow across populations. We found no support for the hypothesis that similarities in host use are related to genetic proximity. The results indicate that the species underwent a recent rapid expansion, probably from two glacial refugia in western North America. The mitochondrial haplotype network indicates at least two independent expansion phases into eastern North America. Our results clearly demonstrate that subspecies in P. faunus do not conform to the structuring of genetic variation. More studies on insects and other invertebrates are needed to better understand the scope of this phenomenon. The results of this study will be crucial in designing further experiments to understand the evolution of hostplant utilization in this species.", "link"=>"http://www.mendeley.com/research/investigating-concordance-among-genetic-data-subspecies-circumscriptions-hostplant-nymphalid-butterf", "reader_count"=>36, "reader_count_by_academic_status"=>{"Professor > Associate Professor"=>3, "Researcher"=>10, "Student > Ph. D. Student"=>11, "Student > Postgraduate"=>3, "Student > Master"=>4, "Other"=>1, "Student > Bachelor"=>2, "Lecturer > Senior Lecturer"=>1, "Professor"=>1}, "reader_count_by_user_role"=>{"Professor > Associate Professor"=>3, "Researcher"=>10, "Student > Ph. D. Student"=>11, "Student > Postgraduate"=>3, "Student > Master"=>4, "Other"=>1, "Student > Bachelor"=>2, "Lecturer > Senior Lecturer"=>1, "Professor"=>1}, "reader_count_by_subject_area"=>{"Unspecified"=>1, "Biochemistry, Genetics and Molecular Biology"=>5, "Agricultural and Biological Sciences"=>28, "Social Sciences"=>1, "Earth and Planetary Sciences"=>1}, "reader_count_by_subdiscipline"=>{"Social Sciences"=>{"Social Sciences"=>1}, "Earth and Planetary Sciences"=>{"Earth and Planetary Sciences"=>1}, "Agricultural and Biological Sciences"=>{"Agricultural and Biological Sciences"=>28}, "Biochemistry, Genetics and Molecular Biology"=>{"Biochemistry, Genetics and Molecular Biology"=>5}, "Unspecified"=>{"Unspecified"=>1}}, "reader_count_by_country"=>{"China"=>1, "Brazil"=>1, "France"=>1, "Portugal"=>1, "India"=>1}, "group_count"=>0}

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Figshare

  • {"files"=>["https://ndownloader.figshare.com/files/315297", "https://ndownloader.figshare.com/files/315311"], "description"=>"<div><p>Subspecies are commonly used taxonomic units to formally describe intraspecific geographic variation in morphological traits. However, the concept of subspecies is not clearly defined, and there is little agreement about what they represent in terms of evolutionary units, and whether they can be used as reliably useful units in conservation, evolutionary theory and taxonomy. We here investigate whether the morphologically well-characterized subspecies in the North American butterfly <em>Polygonia faunus</em> are supported by genetic data from mitochondrial sequences and eight microsatellite loci. We also investigate the phylogeographic structure of <em>P. faunus</em> and test whether similarities in host-plant use among populations are related to genetic similarity. Neither the nuclear nor the mitochondrial data corroborated subspecies groupings. We found three well defined genetic clusters corresponding to California, Arizona and (New Mexico+Colorado). There was little structuring among the remaining populations, probably due to gene flow across populations. We found no support for the hypothesis that similarities in host use are related to genetic proximity. The results indicate that the species underwent a recent rapid expansion, probably from two glacial refugia in western North America. The mitochondrial haplotype network indicates at least two independent expansion phases into eastern North America. Our results clearly demonstrate that subspecies in <em>P. faunus</em> do not conform to the structuring of genetic variation. More studies on insects and other invertebrates are needed to better understand the scope of this phenomenon. The results of this study will be crucial in designing further experiments to understand the evolution of hostplant utilization in this species.</p> </div>", "links"=>[], "tags"=>["investigating", "concordance", "subspecies", "circumscriptions", "hostplant", "nymphalid"], "article_id"=>122219, "categories"=>["Evolutionary Biology"], "users"=>["Ullasa Kodandaramaiah", "Elisabet Weingartner", "Niklas Janz", "Michael Leski", "Jessica Slove", "Andrew Warren", "Sören Nylin"], "doi"=>[nil, nil], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/Investigating_Concordance_among_Genetic_Data_Subspecies_Circumscriptions_and_Hostplant_Use_in_the_Nymphalid_Butterfly_em_Polygonia_faunus_em_/122219", "title"=>"Investigating Concordance among Genetic Data, Subspecies Circumscriptions and Hostplant Use in the Nymphalid Butterfly <em>Polygonia faunus</em>", "pos_in_sequence"=>0, "defined_type"=>4, "published_date"=>"2012-07-23 00:36:59"}
  • {"files"=>["https://ndownloader.figshare.com/files/604684"], "description"=>"<p>Shown are representative photographs of the Polygonia faunus subspecies: a) ‘faunus’, 8 miles northwest of Fraserdale, Ontario; b) ‘smythi’, Cooper Creek Wildlife Management Area, 11 miles southeast of Blairsville, Georgia; c) ‘arcticus’, Bug Creek, 15 miles southwest of Aklavik, NWT, Canada; d) ‘hylas’, 0.25 miles west of Turquoise Lake Reservoir, Leadville, Colorado; and e), ‘rusticus’, Lewis Creek, Sugar Pines, California. Fresh vouchers of subspecies ‘fulvescens’ were unavailable for this study. The distribution map of each subspecies is illustrated in f). Diamonds indicate the location of the specimens shown in a-e). A blend zone exists at the ‘rusticus’/’arcticus’ interface, and probably at the ‘faunus’/’arcticus’ and ‘arcticus’/’hylas’ interfaces (not illustrated).</p>", "links"=>[], "tags"=>["Evolutionary biology"], "article_id"=>275177, "categories"=>["Evolutionary Biology"], "users"=>["Ullasa Kodandaramaiah", "Elisabet Weingartner", "Niklas Janz", "Michael Leski", "Jessica Slove", "Andrew Warren", "Sören Nylin"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0041058.g001"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Subspecies_of_Polygonia_faunus_and_distribution_map_/275177", "title"=>"Subspecies of <i>Polygonia faunus</i> and distribution map.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2012-07-23 01:26:17"}
  • {"files"=>["https://ndownloader.figshare.com/files/604896"], "description"=>"<p>Each circle represents a haplotype and is approximately proportional in area to the number of individuals possessing the haplotype. The smallest circles represent missing haplotypes. Each haplotype is named using the following convention: The alphabets preceding the hyphen indicate the subspecies as listed in b), and the alphabets following the hyphen indicate the populations in which the haplotype was recovered, with each population abbreviated according to the list in d). Widespread haplotypes, i.e., those occurring in more than two populations, have a ‘WS’ after the hyphen. For the three haplotypes found in more than one subspecies, c) lists the numbers of individuals for each; d) is the legend to the patterns representing each population on the network.</p>", "links"=>[], "tags"=>["parsimony", "35", "mitochondrial", "haplotypes", "reconstructed", "tcs"], "article_id"=>275382, "categories"=>["Evolutionary Biology"], "users"=>["Ullasa Kodandaramaiah", "Elisabet Weingartner", "Niklas Janz", "Michael Leski", "Jessica Slove", "Andrew Warren", "Sören Nylin"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0041058.g002"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_The_statistical_parsimony_network_of_35_Polygonia_faunus_mitochondrial_haplotypes_identified_in_the_study_reconstructed_using_the_software_TCS_v1_21_/275382", "title"=>"The statistical parsimony network of 35 <i>Polygonia faunus</i> mitochondrial haplotypes identified in the study, reconstructed using the software TCS v1.21.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2012-07-23 01:29:42"}
  • {"files"=>["https://ndownloader.figshare.com/files/605007"], "description"=>"<p>Numbers above branches are bootstrap support values greater than 50%. The length of branch leading to the outgroup is not to scale.</p>", "links"=>[], "tags"=>["phylogeny", "mtdna", "haplotypes", "inferred"], "article_id"=>275498, "categories"=>["Evolutionary Biology"], "users"=>["Ullasa Kodandaramaiah", "Elisabet Weingartner", "Niklas Janz", "Michael Leski", "Jessica Slove", "Andrew Warren", "Sören Nylin"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0041058.g003"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Maximum_Likelihood_phylogeny_of_mtDNA_haplotypes_inferred_in_RaXML_/275498", "title"=>"Maximum Likelihood phylogeny of mtDNA haplotypes inferred in RaXML.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2012-07-23 01:31:38"}
  • {"files"=>["https://ndownloader.figshare.com/files/605069"], "description"=>"<p>Each genetic cluster is represented by a colour. Every individual is represented by a single vertical line with coloured segments depicting the estimated proportion of ancestry from a given cluster. a) Results from the analysis where individuals were grouped into populations <i>a priori</i>; K = 5. b) Results from the analysis where individuals were grouped into subspecies <i>a priori</i>; K = 6.</p>", "links"=>[], "tags"=>["inferred", "microsatellite"], "article_id"=>275563, "categories"=>["Evolutionary Biology"], "users"=>["Ullasa Kodandaramaiah", "Elisabet Weingartner", "Niklas Janz", "Michael Leski", "Jessica Slove", "Andrew Warren", "Sören Nylin"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0041058.g004"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Population_structure_inferred_in_STRUCTURE_based_on_microsatellite_data_/275563", "title"=>"Population structure inferred in STRUCTURE based on microsatellite data.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2012-07-23 01:32:43"}
  • {"files"=>["https://ndownloader.figshare.com/files/605151"], "description"=>"<p>Idaho, Quebec and Georgia were excluded from the analysis since they were represented by less than five individuals.</p>", "links"=>[], "tags"=>["mitochondrial", "haplotypes", "haplotype"], "article_id"=>275641, "categories"=>["Evolutionary Biology"], "users"=>["Ullasa Kodandaramaiah", "Elisabet Weingartner", "Niklas Janz", "Michael Leski", "Jessica Slove", "Andrew Warren", "Sören Nylin"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0041058.t001"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Number_of_mitochondrial_haplotypes_and_haplotype_diversity_values_of_each_population_/275641", "title"=>"Number of mitochondrial haplotypes and haplotype diversity values of each population.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2012-07-23 01:34:01"}
  • {"files"=>["https://ndownloader.figshare.com/files/605178"], "description"=>"<p>Values significantly different in the exact tests of differentiation are in bold. Population abbreviations are as in <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0041058#pone-0041058-t001\" target=\"_blank\">Table 1</a> and <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0041058#pone-0041058-g002\" target=\"_blank\">Figure 2</a>.</p>", "links"=>[], "tags"=>["populations", "calculated", "mitochondrial", "haplotype", "frequencies"], "article_id"=>275669, "categories"=>["Evolutionary Biology"], "users"=>["Ullasa Kodandaramaiah", "Elisabet Weingartner", "Niklas Janz", "Michael Leski", "Jessica Slove", "Andrew Warren", "Sören Nylin"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0041058.t002"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Pairwise_ST_values_between_populations_calculated_from_mitochondrial_haplotype_frequencies_in_Arlequin_/275669", "title"=>"Pairwise Ф<sub>ST</sub> values between populations calculated from mitochondrial haplotype frequencies in Arlequin.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2012-07-23 01:34:29"}
  • {"files"=>["https://ndownloader.figshare.com/files/605216"], "description"=>"<p>Values significantly different in the exact tests of differentiation are in bold.</p>", "links"=>[], "tags"=>["subspecies", "calculated", "mitochondrial", "haplotype", "frequencies"], "article_id"=>275704, "categories"=>["Evolutionary Biology"], "users"=>["Ullasa Kodandaramaiah", "Elisabet Weingartner", "Niklas Janz", "Michael Leski", "Jessica Slove", "Andrew Warren", "Sören Nylin"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0041058.t003"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Pairwise_ST_values_between_subspecies_calculated_from_mitochondrial_haplotype_frequencies_in_Arlequin_/275704", "title"=>"Pairwise Ф<sub>ST</sub> values between subspecies calculated from mitochondrial haplotype frequencies in Arlequin.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2012-07-23 01:35:04"}
  • {"files"=>["https://ndownloader.figshare.com/files/605257"], "description"=>"<p>Observed heterozygosity values significantly lower than expected are in bold. The second column lists the lengths of repeat units for each locus.</p>", "links"=>[], "tags"=>["observed", "heterozygosity", "genotyping", "137", "individuals", "microsatellite"], "article_id"=>275741, "categories"=>["Evolutionary Biology"], "users"=>["Ullasa Kodandaramaiah", "Elisabet Weingartner", "Niklas Janz", "Michael Leski", "Jessica Slove", "Andrew Warren", "Sören Nylin"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0041058.t004"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Allelic_variability_expected_and_observed_heterozygosity_values_estimated_from_genotyping_137_Polygonia_faunus_individuals_for_8_microsatellite_loci_/275741", "title"=>"Allelic variability, expected and observed heterozygosity values estimated from genotyping 137 <i>Polygonia faunus</i> individuals for 8 microsatellite loci.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2012-07-23 01:35:41"}
  • {"files"=>["https://ndownloader.figshare.com/files/605293"], "description"=>"<p>Numbers to the left of the diagonal are calculated in Arlequin without correcting for the presence of null alleles. Values in bold are significantly greater than zero. Numbers to the right of the diagonal are F<sub>ST</sub> values calculated in FreeNA after ENA correction for null alleles. Population abbreviations are as in <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0041058#pone-0041058-t001\" target=\"_blank\">Table 1</a> and <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0041058#pone-0041058-g002\" target=\"_blank\">Figure 2</a>.</p>", "links"=>[], "tags"=>["populations", "calculated", "microsatellite"], "article_id"=>275781, "categories"=>["Evolutionary Biology"], "users"=>["Ullasa Kodandaramaiah", "Elisabet Weingartner", "Niklas Janz", "Michael Leski", "Jessica Slove", "Andrew Warren", "Sören Nylin"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0041058.t005"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Pairwise_F_ST_values_between_populations_calculated_from_the_microsatellite_data_/275781", "title"=>"Pairwise F<sub>ST</sub> values between populations calculated from the microsatellite data.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2012-07-23 01:36:21"}
  • {"files"=>["https://ndownloader.figshare.com/files/605319"], "description"=>"<p>Numbers to the left of the diagonal are calculated in Arlequin without correcting for the presence of null alleles. Values in bold are significantly greater than zero. Numbers to the right of the diagonal are F<sub>ST</sub> values calculated in FreeNA after ENA correction for null alleles.</p>", "links"=>[], "tags"=>["subspecies", "calculated", "microsatellite"], "article_id"=>275812, "categories"=>["Evolutionary Biology"], "users"=>["Ullasa Kodandaramaiah", "Elisabet Weingartner", "Niklas Janz", "Michael Leski", "Jessica Slove", "Andrew Warren", "Sören Nylin"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0041058.t006"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Pairwise_F_ST_values_between_subspecies_calculated_from_the_microsatellite_data_/275812", "title"=>"Pairwise F<sub>ST</sub> values between subspecies calculated from the microsatellite data.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2012-07-23 01:36:52"}

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Relative Metric

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