A Phylogenomic Approach to Vertebrate Phylogeny Supports a Turtle-Archosaur Affinity and a Possible Paraphyletic Lissamphibia
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{"title"=>"A Phylogenomic Approach to Vertebrate Phylogeny Supports a Turtle-Archosaur Affinity and a Possible Paraphyletic Lissamphibia", "type"=>"journal", "authors"=>[{"first_name"=>"Jonathan J.", "last_name"=>"Fong", "scopus_author_id"=>"8512758000"}, {"first_name"=>"Jeremy M.", "last_name"=>"Brown", "scopus_author_id"=>"55724444100"}, {"first_name"=>"Matthew K.", "last_name"=>"Fujita", "scopus_author_id"=>"7403991388"}, {"first_name"=>"Bastien", "last_name"=>"Boussau", "scopus_author_id"=>"25221331300"}], "year"=>2012, "source"=>"PLoS ONE", "identifiers"=>{"sgr"=>"84868678250", "doi"=>"10.1371/journal.pone.0048990", "pui"=>"366025071", "pmid"=>"23145043", "scopus"=>"2-s2.0-84868678250", "issn"=>"19326203", "isbn"=>"1932-6203"}, "id"=>"5539e690-cec7-3be1-81fe-5ad0b82c8269", "abstract"=>"In resolving the vertebrate tree of life, two fundamental questions remain: 1) what is the phylogenetic position of turtles within amniotes, and 2) what are the relationships between the three major lissamphibian (extant amphibian) groups? These relationships have historically been difficult to resolve, with five different hypotheses proposed for turtle placement, and four proposed branching patterns within Lissamphibia. We compiled a large cDNA/EST dataset for vertebrates (75 genes for 129 taxa) to address these outstanding questions. Gene-specific phylogenetic analyses revealed a great deal of variation in preferred topology, resulting in topologically ambiguous conclusions from the combined dataset. Due to consistent preferences for the same divergent topologies across genes, we suspected systematic phylogenetic error as a cause of some variation. Accordingly, we developed and tested a novel statistical method that identifies sites that have a high probability of containing biased signal for a specific phylogenetic relationship. After removing putatively biased sites, support emerged for a sister relationship between turtles and either crocodilians or archosaurs, as well as for a caecilian-salamander sister relationship within Lissamphibia, with Lissamphibia potentially paraphyletic.", "link"=>"http://www.mendeley.com/research/phylogenomic-approach-vertebrate-phylogeny-supports-turtlearchosaur-affinity-possible-paraphyletic-l", "reader_count"=>116, "reader_count_by_academic_status"=>{"Unspecified"=>2, "Professor > Associate Professor"=>3, "Researcher"=>27, "Student > Doctoral Student"=>7, "Student > Ph. D. Student"=>20, "Student > Postgraduate"=>7, "Student > Master"=>24, "Other"=>4, "Student > Bachelor"=>14, "Lecturer"=>1, "Professor"=>7}, "reader_count_by_user_role"=>{"Unspecified"=>2, "Professor > Associate Professor"=>3, "Researcher"=>27, "Student > Doctoral Student"=>7, "Student > Ph. D. Student"=>20, "Student > Postgraduate"=>7, "Student > Master"=>24, "Other"=>4, "Student > Bachelor"=>14, "Lecturer"=>1, "Professor"=>7}, "reader_count_by_subject_area"=>{"Unspecified"=>4, "Environmental Science"=>4, "Biochemistry, Genetics and Molecular Biology"=>5, "Agricultural and Biological Sciences"=>84, "Veterinary Science and Veterinary Medicine"=>1, "Chemistry"=>1, "Computer Science"=>2, "Earth and Planetary Sciences"=>15}, "reader_count_by_subdiscipline"=>{"Chemistry"=>{"Chemistry"=>1}, "Earth and Planetary Sciences"=>{"Earth and Planetary Sciences"=>15}, "Agricultural and Biological Sciences"=>{"Agricultural and Biological Sciences"=>84}, "Computer Science"=>{"Computer Science"=>2}, "Biochemistry, Genetics and Molecular Biology"=>{"Biochemistry, Genetics and Molecular Biology"=>5}, "Unspecified"=>{"Unspecified"=>4}, "Environmental Science"=>{"Environmental Science"=>4}, "Veterinary Science and Veterinary Medicine"=>{"Veterinary Science and Veterinary Medicine"=>1}}, "reader_count_by_country"=>{"Reunion"=>1, "United States"=>3, "Japan"=>1, "Philippines"=>1, "Serbia and Montenegro"=>1, "Brazil"=>3, "United Kingdom"=>2, "France"=>1, "Chile"=>1, "Germany"=>1}, "group_count"=>4}

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Figshare

  • {"files"=>["https://ndownloader.figshare.com/files/547134"], "description"=>"<p>Uncertainties in the vertebrate phylogeny examined in this study. (A) The five alternative hypotheses for the placement of turtles within amniotes 1) turtles as basal amniotes, 2) turtles as basal sauropsids, 3) turtle-lepidosaur sister group, 4) turtle-archosaur sister group, and 5) turtle-crocodilian sister group. (B) monophyletic and (C) paraphyletic alternative hypotheses for lissamphibian (extant amphibians) relationships.</p>", "links"=>[], "tags"=>["hypotheses", "vertebrate"], "article_id"=>217626, "categories"=>["Mathematics", "Biological Sciences", "Genetics", "Evolutionary Biology"], "users"=>["Jonathan J. Fong", "Jeremy M. Brown", "Matthew K. Fujita", "Bastien Boussau"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0048990.g001", "stats"=>{"downloads"=>1, "page_views"=>7, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Alternative_hypotheses_in_the_vertebrate_phylogeny_/217626", "title"=>"Alternative hypotheses in the vertebrate phylogeny.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2012-11-07 02:07:06"}
  • {"files"=>["https://ndownloader.figshare.com/files/292378", "https://ndownloader.figshare.com/files/292538", "https://ndownloader.figshare.com/files/292578", "https://ndownloader.figshare.com/files/292699", "https://ndownloader.figshare.com/files/292759", "https://ndownloader.figshare.com/files/292830", "https://ndownloader.figshare.com/files/292902", "https://ndownloader.figshare.com/files/292955"], "description"=>"<div><p>In resolving the vertebrate tree of life, two fundamental questions remain: 1) what is the phylogenetic position of turtles within amniotes, and 2) what are the relationships between the three major lissamphibian (extant amphibian) groups? These relationships have historically been difficult to resolve, with five different hypotheses proposed for turtle placement, and four proposed branching patterns within Lissamphibia. We compiled a large cDNA/EST dataset for vertebrates (75 genes for 129 taxa) to address these outstanding questions. Gene-specific phylogenetic analyses revealed a great deal of variation in preferred topology, resulting in topologically ambiguous conclusions from the combined dataset. Due to consistent preferences for the same divergent topologies across genes, we suspected systematic phylogenetic error as a cause of some variation. Accordingly, we developed and tested a novel statistical method that identifies sites that have a high probability of containing biased signal for a specific phylogenetic relationship. After removing putatively biased sites, support emerged for a sister relationship between turtles and either crocodilians or archosaurs, as well as for a caecilian-salamander sister relationship within Lissamphibia, with Lissamphibia potentially paraphyletic.</p> </div>", "links"=>[], "tags"=>["phylogenomic", "vertebrate", "phylogeny", "supports", "turtle-archosaur", "affinity", "paraphyletic", "lissamphibia"], "article_id"=>117550, "categories"=>["Mathematics", "Biological Sciences", "Genetics", "Evolutionary Biology"], "users"=>["Jonathan J. Fong", "Jeremy M. Brown", "Matthew K. Fujita", "Bastien Boussau"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0048990.s001", "https://dx.doi.org/10.1371/journal.pone.0048990.s002", "https://dx.doi.org/10.1371/journal.pone.0048990.s003", "https://dx.doi.org/10.1371/journal.pone.0048990.s004", "https://dx.doi.org/10.1371/journal.pone.0048990.s005", "https://dx.doi.org/10.1371/journal.pone.0048990.s006", "https://dx.doi.org/10.1371/journal.pone.0048990.s007", "https://dx.doi.org/10.1371/journal.pone.0048990.s008"], "stats"=>{"downloads"=>33, "page_views"=>42, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/A_Phylogenomic_Approach_to_Vertebrate_Phylogeny_Supports_a_Turtle_Archosaur_Affinity_and_a_Possible_Paraphyletic_Lissamphibia__/117550", "title"=>"A Phylogenomic Approach to Vertebrate Phylogeny Supports a Turtle-Archosaur Affinity and a Possible Paraphyletic Lissamphibia", "pos_in_sequence"=>0, "defined_type"=>4, "published_date"=>"2012-11-07 02:05:50"}
  • {"files"=>["https://ndownloader.figshare.com/files/547255"], "description"=>"<p>(A) The phylogenetic position of turtles within amniotes when all major groups were present and (B) when no crocodilians were present. (C) The relationships between major lissamphibian groups. The “other” category includes topologies that do not match any of the previously proposed hypotheses, usually with a major amniote group being paraphyletic.</p>", "links"=>[], "tags"=>["genetics and genomics", "Computational biology", "Evolutionary biology", "mathematics"], "article_id"=>217745, "categories"=>["Mathematics", "Biological Sciences", "Genetics", "Evolutionary Biology"], "users"=>["Jonathan J. Fong", "Jeremy M. Brown", "Matthew K. Fujita", "Bastien Boussau"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0048990.g002", "stats"=>{"downloads"=>1, "page_views"=>2, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Phylogenetic_results_from_individual_gene_analyses_/217745", "title"=>"Phylogenetic results from individual gene analyses.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2012-11-07 02:09:05"}
  • {"files"=>["https://ndownloader.figshare.com/files/547529"], "description"=>"<p>Varying amounts of suspect sites were removed and tested. A) Position of turtles in the amniote phylogeny using three descriptive statistics (site-rates, %GC, and %missing), B) position of turtles in the amniote phylogeny using two descriptive statistics (excluding %GC), C) interrelationships of Lissamphibian groups using three descriptive statistics (site-rates, %GC, and %missing), D) interrelationships of Lissamphibian groups using two descriptive statistics (excluding %GC). The percentage in each column represents the percentage of sites removed from the dataset. Values in cells represent p-values, “X” denotes the best tree, and trees statistically indistinguishable from the best tree are in bold font (Approximately Unbiased topology test p-value >5%).</p>", "links"=>[], "tags"=>["filtered"], "article_id"=>218030, "categories"=>["Mathematics", "Biological Sciences", "Genetics", "Evolutionary Biology"], "users"=>["Jonathan J. Fong", "Jeremy M. Brown", "Matthew K. Fujita", "Bastien Boussau"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0048990.t002", "stats"=>{"downloads"=>4, "page_views"=>2, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Phylogenetic_results_from_filtered_datasets_/218030", "title"=>"Phylogenetic results from filtered datasets.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2012-11-07 02:13:50"}
  • {"files"=>["https://ndownloader.figshare.com/files/547464"], "description"=>"<p>Consensus phylogeny from datasets with the 10% most putatively biased sites removed. (A) Turtles are either the sister group to Crocodilians or Archosauria. (B) Lissamphibia: salamanders (Caudata) and caecilians (Gymnophiona) are sister groups, and this group is either the sister group to frogs (Procera hypothesis) or Amniota (rendering Lissamphibia paraphyletic). RAxML bootstrap values are at nodes, with “*” representing support ≥95.</p>", "links"=>[], "tags"=>["vertebrate"], "article_id"=>217962, "categories"=>["Mathematics", "Biological Sciences", "Genetics", "Evolutionary Biology"], "users"=>["Jonathan J. Fong", "Jeremy M. Brown", "Matthew K. Fujita", "Bastien Boussau"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0048990.g004", "stats"=>{"downloads"=>0, "page_views"=>1, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Consensus_vertebrate_phylogeny_/217962", "title"=>"Consensus vertebrate phylogeny.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2012-11-07 02:12:42"}
  • {"files"=>["https://ndownloader.figshare.com/files/547563"], "description"=>"<p>Summary of results from phylogenetic analyses for turtle placement within the amniote phylogeny, and relationships of Lissamphibia (extant amphibians). Individual gene and concatenated analyses were performed. For individual gene analyses, percentages denote the proportion of genes supporting the hypothesis. For the concatenated analyses, the cell with “X” for each column denote the most likely topology based on RAxML likelihood scores, while the numbers in cells represent p-values based on approximately unbiased topology tests (Shimodaira 2002). Cells in bold font denote statistically indistinguishable topologies (p-value>0.05) from the most likely topology. Sixteen total concatenated analyses were performed (4 data transformations × 4 datasets). Data were transformed in an attempt to reduce the rate of evolution: NUCL = complete nucleotide dataset, N12 = 1<sup>st</sup> and 2<sup>nd</sup> codon positions only (Edwards et al. 1991, Blouin et al. 1998), DEGEN1 = codon degeneracy (Regier et al. 2010), AA = amino acids (Meyer 1994). Three different datasets were compiled in attempts to minimize the amount of missing data: 16 taxa (reduced taxon set to include the taxa with the most complete data for each major vertebrate group), 31 genes (for turtle question, genes with representatives from all the major groups in question), 26 genes (for lissamphibian question, genes with representatives from all the major groups in question). The last column summarizes the results from phylogenetic analyses when removing the 19 most quickly evolving genes (25% of total genes).</p>", "links"=>[], "tags"=>["phylogenetic"], "article_id"=>218062, "categories"=>["Mathematics", "Biological Sciences", "Genetics", "Evolutionary Biology"], "users"=>["Jonathan J. Fong", "Jeremy M. Brown", "Matthew K. Fujita", "Bastien Boussau"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0048990.t001", "stats"=>{"downloads"=>0, "page_views"=>6, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Summary_of_phylogenetic_results_from_different_datasets_/218062", "title"=>"Summary of phylogenetic results from different datasets.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2012-11-07 02:14:22"}
  • {"files"=>["https://ndownloader.figshare.com/files/547358"], "description"=>"<p>Steps of the new statistical methodology to identify and filter out sites that contain putative non-phylogenetic signal (i.e. biased sites). Analyses pertaining to the phylogenetic position of turtles are used in this example.</p>", "links"=>[], "tags"=>["diagram", "filtering"], "article_id"=>217855, "categories"=>["Mathematics", "Biological Sciences", "Genetics", "Evolutionary Biology"], "users"=>["Jonathan J. Fong", "Jeremy M. Brown", "Matthew K. Fujita", "Bastien Boussau"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0048990.g003", "stats"=>{"downloads"=>0, "page_views"=>2, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Flow_diagram_of_data_filtering_method_/217855", "title"=>"Flow diagram of data filtering method.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2012-11-07 02:10:55"}

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Relative Metric

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