Diversity of Aplochiton Fishes (Galaxiidea) and the Taxonomic Resurrection of A. marinus
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{"title"=>"Diversity of Aplochiton Fishes (Galaxiidea) and the Taxonomic Resurrection of A. marinus", "type"=>"journal", "authors"=>[{"first_name"=>"Dominique", "last_name"=>"Alò"}, {"first_name"=>"Cristián", "last_name"=>"Correa"}, {"first_name"=>"Carlos", "last_name"=>"Arias"}, {"first_name"=>"Leyla", "last_name"=>"Cárdenas"}], "year"=>2013, "source"=>"PLoS ONE", "identifiers"=>{"scopus"=>"2-s2.0-84897918271", "doi"=>"10.1371/journal.pone.0071577", "pui"=>"563050601", "sgr"=>"84897918271", "issn"=>"1932-6203", "pmid"=>"23977079"}, "id"=>"8b16ca8f-771f-3657-89af-1de00fb82c5e", "abstract"=>"Aplochiton is a small genus of galaxiid fishes endemic to Patagonia and the Falkland Islands whose taxonomy is insufficiently resolved. Recent genetic analyses confirmed the existence of only two closely related species, Aplochiton taeniatus and Aplochiton zebra, while a third controversial species, Aplochiton marinus, remained lost to synonymy with A. taeniatus. Using an integrative taxonomy framework, we studied original samples and published sequences from a broad range in western Patagonia and the Falkland Islands, and generated robust species hypotheses based on single-locus (Cytochrome Oxidase subunit I; COI) species-delineation methods and known diagnostic morphological characters analyzed in a multivariate context. Results revealed three distinct evolutionary lineages that morphologically resemble, in important respects, existing nominal species descriptions. Interestingly, the lineage associated with A. marinus was unambiguously identifiable (100% accuracy) both from the genetic and morphological viewpoints. In contrast, the morphology of A. taeniatus and A. zebra overlapped substantially, mainly due to the high variability of A. taeniatus. Discriminant function analysis aided the identification of these species with 83.9% accuracy. Hence, for their unambiguous identification, genetic screening is needed. A. marinus has seldom been documented, and when recorded, it has always been found in sites with clear marine influence. It is possible that only A. marinus preserves a life cycle related to the sea akin to the hypothesized ancestral galaxiid. We did not find evidence of claimed diadromy in A. taeniatus or A. zebra, and, therefore, these should be regarded as freshwater species. Finally, a lack of phylogeographic patterns and overrepresentation of uncommon haplotypes suggested demographic expansions in recent evolutionary time, especially of A. zebra, in line with the hypothesis of large-scale range expansion and lineage spread in western Patagonia.", "link"=>"http://www.mendeley.com/research/diversity-aplochiton-fishes-galaxiidea-taxonomic-resurrection-marinus", "reader_count"=>35, "reader_count_by_academic_status"=>{"Unspecified"=>1, "Professor > Associate Professor"=>2, "Researcher"=>4, "Student > Ph. D. Student"=>7, "Student > Postgraduate"=>2, "Student > Master"=>8, "Other"=>3, "Student > Bachelor"=>6, "Lecturer"=>1, "Professor"=>1}, "reader_count_by_user_role"=>{"Unspecified"=>1, "Professor > Associate Professor"=>2, "Researcher"=>4, "Student > Ph. D. Student"=>7, "Student > Postgraduate"=>2, "Student > Master"=>8, "Other"=>3, "Student > Bachelor"=>6, "Lecturer"=>1, "Professor"=>1}, "reader_count_by_subject_area"=>{"Engineering"=>2, "Unspecified"=>1, "Environmental Science"=>4, "Agricultural and Biological Sciences"=>26, "Computer Science"=>1, "Earth and Planetary Sciences"=>1}, "reader_count_by_subdiscipline"=>{"Engineering"=>{"Engineering"=>2}, "Earth and Planetary Sciences"=>{"Earth and Planetary Sciences"=>1}, "Agricultural and Biological Sciences"=>{"Agricultural and Biological Sciences"=>26}, "Computer Science"=>{"Computer Science"=>1}, "Unspecified"=>{"Unspecified"=>1}, "Environmental Science"=>{"Environmental Science"=>4}}, "reader_count_by_country"=>{"Colombia"=>1, "Chile"=>2}, "group_count"=>1}

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Figshare

  • {"files"=>["https://ndownloader.figshare.com/files/1175335"], "description"=>"<p>Each leaf of the tree is labeled with individual ID-code (this study; n = 60 sequences), haplotype accession number, or outgroup species name (refer to <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0071577#pone-0071577-t004\" target=\"_blank\">Table 4</a>). Branch support is indicated nearby nodes for inferences based on maximum likelihood (ML, bootstrap), Bayesian Inference (BI, posterior probability), and parsimony (P, bootstrap) (i.e. ML/BI/P); values <0.50 not shown. <i>Cytochrome Oxidase I</i> haplotype (<i>COI</i>-HT) correspond to those in Vanhaecke <i>et al. </i><a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0071577#pone.0071577-Vanhaecke1\" target=\"_blank\">[7]</a> when matching, or to the new haplotypes described here. The first letters of <i>COI</i>-HT stand for haplogroups that were associated with species: A (associated with AZ), B (AT), and C (AM). Additional data are shown with an alternating shaded background to aid the visual separation of each sampling site listed as ''Site'' on the second column (unavailable for sequences downloaded from Genbank). Std. Length is standard length in cm. Stomach displays either the bulbous (□) or elongated (▪) shape. HD ratio is head length to head depth ratio (%), with head depth measured posterior to eye orbit (dashed line corresponds to that in <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0071577#pone-0071577-g003\" target=\"_blank\">Figure 3</a>-A, for reference). Pattern refers to skin color patterns; dark chevron blotches (▴), dark spots (•) and unclear/no pattern (○). Morph corresponds to morphological identification; letters are initials of the second word (species) in binomial names. Morphological identification was accomplished by reference to Stomach and Pattern (M), or by jackknife identification using linear discriminant analysis based on all five characters analyzed (T and Z; method indicated by *). Note several discrepancies between morphological and barcoding identifications. Some fish photos further illustrate <i>Aplochiton</i> phenotypic diversity (IDs correspond tree leaf labels).</p>", "links"=>[], "tags"=>["diagnostic", "morphological", "characters"], "article_id"=>776736, "categories"=>["Biological Sciences", "Information And Computing Sciences", "Ecology", "Earth and Environmental Sciences"], "users"=>["Dominique Alò", "Cristián Correa", "Carlos Arias", "Leyla Cárdenas"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0071577.g002", "stats"=>{"downloads"=>0, "page_views"=>8, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Maximum_likelihood_tree_and_three_traditional_diagnostic_morphological_characters_for_Aplochiton_/776736", "title"=>"Maximum likelihood tree and three traditional diagnostic morphological characters for <i>Aplochiton</i>.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-08-19 04:56:51"}
  • {"files"=>["https://ndownloader.figshare.com/files/1175348", "https://ndownloader.figshare.com/files/1175351", "https://ndownloader.figshare.com/files/1175353"], "description"=>"<div><p><i>Aplochiton</i> is a small genus of galaxiid fishes endemic to Patagonia and the Falkland Islands whose taxonomy is insufficiently resolved. Recent genetic analyses confirmed the existence of only two closely related species, <i>Aplochiton taeniatus</i> and <i>Aplochiton zebra</i>, while a third controversial species, <i>Aplochiton marinus,</i> remained lost to synonymy with <i>A. taeniatus</i>. Using an integrative taxonomy framework, we studied original samples and published sequences from a broad range in western Patagonia and the Falkland Islands, and generated robust species hypotheses based on single-locus (<i>Cytochrome Oxidase</i> subunit <i>I</i>; <i>COI</i>) species-delineation methods and known diagnostic morphological characters analyzed in a multivariate context. Results revealed three distinct evolutionary lineages that morphologically resemble, in important respects, existing nominal species descriptions. Interestingly, the lineage associated with <i>A. marinus</i> was unambiguously identifiable (100% accuracy) both from the genetic and morphological viewpoints. In contrast, the morphology of <i>A. taeniatus</i> and <i>A. zebra</i> overlapped substantially, mainly due to the high variability of <i>A. taeniatus</i>. Discriminant function analysis aided the identification of these species with 83.9% accuracy. Hence, for their unambiguous identification, genetic screening is needed. <i>A. marinus</i> has seldom been documented, and when recorded, it has always been found in sites with clear marine influence. It is possible that only <i>A. marinus</i> preserves a life cycle related to the sea akin to the hypothesized ancestral galaxiid. We did not find evidence of claimed diadromy in <i>A. taeniatus</i> or <i>A. zebra</i>, and, therefore, these should be regarded as freshwater species. Finally, a lack of phylogeographic patterns and overrepresentation of uncommon haplotypes suggested demographic expansions in recent evolutionary time, especially of <i>A. zebra</i>, in line with the hypothesis of large-scale range expansion and lineage spread in western Patagonia.</p></div>", "links"=>[], "tags"=>["fishes", "taxonomic", "resurrection"], "article_id"=>776749, "categories"=>["Biological Sciences", "Information And Computing Sciences", "Ecology", "Earth and Environmental Sciences"], "users"=>["Dominique Alò", "Cristián Correa", "Carlos Arias", "Leyla Cárdenas"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0071577.s001", "https://dx.doi.org/10.1371/journal.pone.0071577.s002", "https://dx.doi.org/10.1371/journal.pone.0071577.s003"], "stats"=>{"downloads"=>1, "page_views"=>11, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/Diversity_of_Aplochiton_Fishes_Galaxiidea_and_the_Taxonomic_Resurrection_of_A_marinus_/776749", "title"=>"Diversity of <i>Aplochiton</i> Fishes (Galaxiidea) and the Taxonomic Resurrection of <i>A. marinus</i>", "pos_in_sequence"=>0, "defined_type"=>4, "published_date"=>"2013-08-19 04:56:51"}
  • {"files"=>["https://ndownloader.figshare.com/files/1175344"], "description"=>"<p>Levels of significance: >5% (n.s.), 5% (*), 1% (**), and 0.1% (***), but 5% significance level of F<sub>S</sub> was indicated when P<0.02 <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0071577#pone.0071577-Fu1\" target=\"_blank\">[56]</a>. In one occasion, Mantel test could not be conducted due to insufficient number of populations (!). Species acronyms as in <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0071577#pone-0071577-g001\" target=\"_blank\">Figure 1</a>.</p>", "links"=>[], "tags"=>["variance", "partitioning", "isolation-by-distance", "neutrality"], "article_id"=>776745, "categories"=>["Biological Sciences", "Information And Computing Sciences", "Ecology", "Earth and Environmental Sciences"], "users"=>["Dominique Alò", "Cristián Correa", "Carlos Arias", "Leyla Cárdenas"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0071577.t003", "stats"=>{"downloads"=>2, "page_views"=>34, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Genetic_variance_partitioning_AMOVA_isolation_by_distance_Mantel_tests_and_neutrality_tests_D_and_F_S_/776745", "title"=>"Genetic variance partitioning (AMOVA), isolation-by-distance (Mantel tests) and neutrality tests (D and F<sub>S</sub>).", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2013-08-19 04:56:51"}
  • {"files"=>["https://ndownloader.figshare.com/files/1175343"], "description"=>"<p>Genetic distances (mean (SD)) are K2P distances (boldface) and distances obtained from the best GTR+I+G model (non-bold). Species acronyms as in <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0071577#pone-0071577-g001\" target=\"_blank\">Figure 1</a>; in addition, <i>Galaxias platei</i> (GP) and <i>Galaxias maculatus</i> (GM) were included as outgroups.</p>", "links"=>[], "tags"=>["intra-specific", "pairwise"], "article_id"=>776744, "categories"=>["Biological Sciences", "Information And Computing Sciences", "Ecology", "Earth and Environmental Sciences"], "users"=>["Dominique Alò", "Cristián Correa", "Carlos Arias", "Leyla Cárdenas"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0071577.t001", "stats"=>{"downloads"=>1, "page_views"=>10, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Inter_off_diagonal_and_intra_specific_diagonal_pairwise_genetic_distances_/776744", "title"=>"Inter- (off-diagonal) and intra-specific (diagonal) pairwise genetic distances.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2013-08-19 04:56:51"}
  • {"files"=>["https://ndownloader.figshare.com/files/1175341"], "description"=>"<p>Includes 31 AT (•) and 31 AZ (▴) used as training dataset for heteroscedastic linear discriminant function analysis based on four morphological characters. Misidentified cases (16.13%; ○) correspond to incorrect jackknifed predictions.</p>", "links"=>[], "tags"=>["scatter-plot", "overlapping"], "article_id"=>776742, "categories"=>["Biological Sciences", "Information And Computing Sciences", "Ecology", "Earth and Environmental Sciences"], "users"=>["Dominique Alò", "Cristián Correa", "Carlos Arias", "Leyla Cárdenas"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0071577.g004", "stats"=>{"downloads"=>0, "page_views"=>3, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Discriminant_space_scatter_plot_for_overlapping_morphospecies_/776742", "title"=>"Discriminant space scatter-plot for overlapping morphospecies.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-08-19 04:56:51"}
  • {"files"=>["https://ndownloader.figshare.com/files/1175338"], "description"=>"<p>(A) Post-orbital head depth to head length ratio. (B) Caudal peduncle depth to standard length ratio. (C) Pre-dorsal length to standard length ratio.</p>", "links"=>[], "tags"=>["distributions", "morphometric", "characters"], "article_id"=>776739, "categories"=>["Biological Sciences", "Information And Computing Sciences", "Ecology", "Earth and Environmental Sciences"], "users"=>["Dominique Alò", "Cristián Correa", "Carlos Arias", "Leyla Cárdenas"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0071577.g003", "stats"=>{"downloads"=>0, "page_views"=>7, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Kernell_density_distributions_by_species_haplogroup_of_the_three_morphometric_characters_analyzed_/776739", "title"=>"Kernell density distributions by species/haplogroup of the three morphometric characters analyzed (%).", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-08-19 04:56:51"}
  • {"files"=>["https://ndownloader.figshare.com/files/1175331"], "description"=>"<p>Distribution ranges of <i>A. taeniatus</i> (AT) and <i>A. zebra</i> (AZ) have been confused due to equivocal morphological identification, and herein are displayed together (insert, dark area). <i>A. marinus</i> (AM) is easier to identify, however, it has been recorded only in a few regions (insert, filled circles). The sampling sites of this study (main map) are indicated with <i>Cytochrome Oxidase I</i> (<i>COI</i>) haplogroup symbols (legend); in brackets, the sample size followed by haplotype richness. Approximate maximum Patagonian ice sheet extent and shorelines during the Pleistocene were modified from references <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0071577#pone.0071577-Glasser1\" target=\"_blank\">[82]</a> and <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0071577#pone.0071577-Ponce1\" target=\"_blank\">[83]</a>, respectively.</p>", "links"=>[], "tags"=>["sampling"], "article_id"=>776733, "categories"=>["Biological Sciences", "Information And Computing Sciences", "Ecology", "Earth and Environmental Sciences"], "users"=>["Dominique Alò", "Cristián Correa", "Carlos Arias", "Leyla Cárdenas"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0071577.g001", "stats"=>{"downloads"=>0, "page_views"=>5, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Aplochiton_distribution_range_and_sampling_sites_/776733", "title"=>"<i>Aplochiton</i> distribution range and sampling sites.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-08-19 04:56:51"}
  • {"files"=>["https://ndownloader.figshare.com/files/1175346"], "description"=>"<p>Species acronyms as in <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0071577#pone-0071577-g001\" target=\"_blank\">Figure 1</a>.</p>", "links"=>[], "tags"=>["accession", "numbers", "barcode-region", "haplotype", "sequences"], "article_id"=>776747, "categories"=>["Biological Sciences", "Information And Computing Sciences", "Ecology", "Earth and Environmental Sciences"], "users"=>["Dominique Alò", "Cristián Correa", "Carlos Arias", "Leyla Cárdenas"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0071577.t004", "stats"=>{"downloads"=>1, "page_views"=>8, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_GenBank_accession_numbers_for_the_barcode_region_haplotype_sequences_analyzed_/776747", "title"=>"GenBank accession numbers for the barcode-region haplotype sequences analyzed.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2013-08-19 04:56:51"}
  • {"files"=>["https://ndownloader.figshare.com/files/1175345"], "description"=>"<p>For each discriminative components obtained from heteroscedastic linear discriminant function analysis, both the loadings of morphological variables and Pearson correlation coefficients are shown (the latter in brackets; significant correlations in boldface). *Dark chevron blotches on fish sides were indexed as 0; unclear/no dark patterns were indexed as 1.</p>", "links"=>[], "tags"=>["morphological", "variables", "discriminant"], "article_id"=>776746, "categories"=>["Biological Sciences", "Information And Computing Sciences", "Ecology", "Earth and Environmental Sciences"], "users"=>["Dominique Alò", "Cristián Correa", "Carlos Arias", "Leyla Cárdenas"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0071577.t002", "stats"=>{"downloads"=>0, "page_views"=>6, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Influence_of_morphological_variables_on_discriminant_functions_/776746", "title"=>"Influence of morphological variables on discriminant functions.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2013-08-19 04:56:51"}

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Relative Metric

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