Revealing Less Derived Nature of Cartilaginous Fish Genomes with Their Evolutionary Time Scale Inferred with Nuclear Genes
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{"title"=>"Revealing Less Derived Nature of Cartilaginous Fish Genomes with Their Evolutionary Time Scale Inferred with Nuclear Genes", "type"=>"journal", "authors"=>[{"first_name"=>"Adina J.", "last_name"=>"Renz", "scopus_author_id"=>"35208802500"}, {"first_name"=>"Axel", "last_name"=>"Meyer", "scopus_author_id"=>"7401840299"}, {"first_name"=>"Shigehiro", "last_name"=>"Kuraku", "scopus_author_id"=>"6602515031"}], "year"=>2013, "source"=>"PLoS ONE", "identifiers"=>{"sgr"=>"84879330929", "doi"=>"10.1371/journal.pone.0066400", "isbn"=>"1932-6203", "pmid"=>"23825540", "issn"=>"19326203", "scopus"=>"2-s2.0-84879330929", "pui"=>"369184503"}, "id"=>"792488de-04ac-3fe1-9a4d-e8a7ff199293", "abstract"=>"Cartilaginous fishes, divided into Holocephali (chimaeras) and Elasmoblanchii (sharks, rays and skates), occupy a key phylogenetic position among extant vertebrates in reconstructing their evolutionary processes. Their accurate evolutionary time scale is indispensable for better understanding of the relationship between phenotypic and molecular evolution of cartilaginous fishes. However, our current knowledge on the time scale of cartilaginous fish evolution largely relies on estimates using mitochondrial DNA sequences. In this study, making the best use of the still partial, but large-scale sequencing data of cartilaginous fish species, we estimate the divergence times between the major cartilaginous fish lineages employing nuclear genes. By rigorous orthology assessment based on available genomic and transcriptomic sequence resources for cartilaginous fishes, we selected 20 protein-coding genes in the nuclear genome, spanning 2973 amino acid residues. Our analysis based on the Bayesian inference resulted in the mean divergence time of 421 Ma, the late Silurian, for the Holocephali-Elasmobranchii split, and 306 Ma, the late Carboniferous, for the split between sharks and rays/skates. By applying these results and other documented divergence times, we measured the relative evolutionary rate of the Hox A cluster sequences in the cartilaginous fish lineages, which resulted in a lower substitution rate with a factor of at least 2.4 in comparison to tetrapod lineages. The obtained time scale enables mapping phenotypic and molecular changes in a quantitative framework. It is of great interest to corroborate the less derived nature of cartilaginous fish at the molecular level as a genome-wide phenomenon.", "link"=>"http://www.mendeley.com/research/revealing-less-derived-nature-cartilaginous-fish-genomes-evolutionary-time-scale-inferred-nuclear-ge", "reader_count"=>39, "reader_count_by_academic_status"=>{"Unspecified"=>1, "Professor > Associate Professor"=>2, "Researcher"=>6, "Student > Doctoral Student"=>1, "Student > Ph. D. Student"=>9, "Student > Postgraduate"=>3, "Student > Master"=>9, "Other"=>1, "Student > Bachelor"=>6, "Professor"=>1}, "reader_count_by_user_role"=>{"Unspecified"=>1, "Professor > Associate Professor"=>2, "Researcher"=>6, "Student > Doctoral Student"=>1, "Student > Ph. D. Student"=>9, "Student > Postgraduate"=>3, "Student > Master"=>9, "Other"=>1, "Student > Bachelor"=>6, "Professor"=>1}, "reader_count_by_subject_area"=>{"Unspecified"=>1, "Biochemistry, Genetics and Molecular Biology"=>7, "Agricultural and Biological Sciences"=>27, "Medicine and Dentistry"=>1, "Psychology"=>1, "Immunology and Microbiology"=>1, "Earth and Planetary Sciences"=>1}, "reader_count_by_subdiscipline"=>{"Medicine and Dentistry"=>{"Medicine and Dentistry"=>1}, "Psychology"=>{"Psychology"=>1}, "Immunology and Microbiology"=>{"Immunology and Microbiology"=>1}, "Earth and Planetary Sciences"=>{"Earth and Planetary Sciences"=>1}, "Agricultural and Biological Sciences"=>{"Agricultural and Biological Sciences"=>27}, "Biochemistry, Genetics and Molecular Biology"=>{"Biochemistry, Genetics and Molecular Biology"=>7}, "Unspecified"=>{"Unspecified"=>1}}, "reader_count_by_country"=>{"Sweden"=>2, "United States"=>1, "United Kingdom"=>1, "Australia"=>1, "France"=>1}, "group_count"=>0}

Scopus | Further Information

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Figshare

  • {"files"=>["https://ndownloader.figshare.com/files/1100190"], "description"=>"<p>Distances (number of substitutions per site) were calculated by codeml for different pairs of species using <i>Callorhinchus milii</i> (<i>Cm</i>) as outgroup. Applying divergence times estimated in this study (306 Ma) as well as previous studies (203 Ma, 312 Ma and 330 Ma), evolutionary rates were calculated for three chondrichthyans and four tetrapod species. Abbreviations: aa, amino acid; Ma, million years ago; <i>Hf</i>, <i>Heterodontus francisci</i>; <i>Sc</i>, <i>Scyliorhinus canicula</i>; <i>Le</i>, <i>Leucoraja erinacea</i>; <i>Gg</i>, <i>Gallus gallus</i>; <i>Hs</i>, <i>Homo sapiens</i>; <i>Ac</i>, <i>Anolis carolinensis</i>; <i>Xt</i>, <i>Xenopus tropicalis</i>; O, Last common ancestor of the two selected species.</p>", "links"=>[], "tags"=>["Evolutionary biology", "Forms of evolution", "Divergent evolution", "Organismal evolution", "Animal evolution", "Comparative genomics", "Evolutionary genetics", "Genomic evolution", "population genetics", "Marine biology", "Zoology", "Animal phylogenetics", "Ichthyology", "evolutionary", "rates", "chondrichthyan", "tetrapod"], "article_id"=>730784, "categories"=>["Biological Sciences"], "users"=>["Adina J. Renz", "Axel Meyer", "Shigehiro Kuraku"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0066400.t003", "stats"=>{"downloads"=>4, "page_views"=>13, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Distances_and_evolutionary_rates_for_chondrichthyan_and_tetrapod_representatives_/730784", "title"=>"Distances and evolutionary rates for chondrichthyan and tetrapod representatives.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2013-06-25 01:48:57"}
  • {"files"=>["https://ndownloader.figshare.com/files/1100188"], "description"=>"<p>The log-likelihood difference (Δlog<i>L</i>) between the ML tree and the topology based on the generally accepted species phylogeny is shown with standard error. The topology of the ML tree is shown in newick format. The number of amino acid sites used for tree inference is shown for each gene, as well as their corresponding shape parameter α for gamma distribution. Abbreviations: aa, amino acid; ML, maximum likelihood tree; Dm, <i>Drosophila melanogaster</i>; Ds, <i>Drosophila simulans</i>; Ci, <i>Ciona intestinalis</i>; Cm, chimaeras; Sh, sharks; Ry, rays/skates; Fr, <i>Takifugu rubripes</i>; Ol, <i>Oryzias latipes</i>; Dr, <i>Danio rerio</i>; Hs, <i>Homo sapiens</i>; Md, <i>Monodelphis domestica</i>; Gg, <i>Gallus gallus</i>; Xt, <i>Xenopus tropicalis</i>.</p>", "links"=>[], "tags"=>["Evolutionary biology", "Forms of evolution", "Divergent evolution", "Organismal evolution", "Animal evolution", "Comparative genomics", "Evolutionary genetics", "Genomic evolution", "population genetics", "Marine biology", "Zoology", "Animal phylogenetics", "Ichthyology", "genes", "divergence"], "article_id"=>730782, "categories"=>["Biological Sciences"], "users"=>["Adina J. Renz", "Axel Meyer", "Shigehiro Kuraku"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0066400.t001", "stats"=>{"downloads"=>2, "page_views"=>2, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Overview_of_nuclear_genes_used_for_the_divergence_time_analysis_/730782", "title"=>"Overview of nuclear genes used for the divergence time analysis.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2013-06-25 01:48:57"}
  • {"files"=>["https://ndownloader.figshare.com/files/1100186"], "description"=>"<p>Timetree produced by MCMCTREE in PAML 4.4 <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0066400#pone.0066400-Yang1\" target=\"_blank\">[62]</a> implementing the relaxed molecular clock method. A total of 19 time constraints (see Table S2) used for the calculation are shown as arrowheads at the eleven nodes. 2973 amino acid sites were analyzed derived from a total of 20 nuclear genes. Horizontal bars indicate 95% confidence intervals (CI) of the divergence time estimates. All estimates and 95% CIs are listed in <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0066400#pone-0066400-t001\" target=\"_blank\">Table 1</a>. The marginal densities obtained in TRACER 1.5 are shown in light grey above the bars. Rates given by MCMCTREE are shown above the individual branches.</p>", "links"=>[], "tags"=>["Evolutionary biology", "Forms of evolution", "Divergent evolution", "Organismal evolution", "Animal evolution", "Comparative genomics", "Evolutionary genetics", "Genomic evolution", "population genetics", "Marine biology", "Zoology", "Animal phylogenetics", "Ichthyology", "timetree"], "article_id"=>730780, "categories"=>["Biological Sciences"], "users"=>["Adina J. Renz", "Axel Meyer", "Shigehiro Kuraku"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0066400.g004", "stats"=>{"downloads"=>0, "page_views"=>4, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Estimated_timetree_of_vertebrates_/730780", "title"=>"Estimated timetree of vertebrates.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-06-25 01:48:57"}
  • {"files"=>["https://ndownloader.figshare.com/files/1100183"], "description"=>"<p>This gene is listed as candidate #9 in <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0066400#pone-0066400-t001\" target=\"_blank\">Table 1</a>. The tree was reconstructed with the maximum-likelihood (ML) method (see <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0066400#s4\" target=\"_blank\">Methods</a>). Bootstrap values were calculated with 100 resamplings. Support values at nodes indicate, in order, probabilities in the ML and the neighbor-joining (NJ) analysis. 119 amino acid sites were included for tree inference (shape parameter for gamma distribution α = 0.38). Note that the topology of this ML tree is not consistent with the generally accepted species phylogeny, but the log-likelihood of the tree topology consistent with the species phylogeny was not significantly lower than that of the ML tree (<a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0066400#pone-0066400-t001\" target=\"_blank\">Table 1</a>). For this reason, this gene was included in the final dataset.</p>", "links"=>[], "tags"=>["Evolutionary biology", "Forms of evolution", "Divergent evolution", "Organismal evolution", "Animal evolution", "Comparative genomics", "Evolutionary genetics", "Genomic evolution", "population genetics", "Marine biology", "Zoology", "Animal phylogenetics", "Ichthyology", "binding"], "article_id"=>730777, "categories"=>["Biological Sciences"], "users"=>["Adina J. Renz", "Axel Meyer", "Shigehiro Kuraku"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0066400.g003", "stats"=>{"downloads"=>0, "page_views"=>5, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Phylogenetic_tree_of_RAN_binding_protein_1_genes_/730777", "title"=>"Phylogenetic tree of<i>RAN binding protein 1</i> genes.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-06-25 01:48:57"}
  • {"files"=>["https://ndownloader.figshare.com/files/1100182"], "description"=>"<p>See <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0066400#s4\" target=\"_blank\">Methods</a> for details of elasmobranch EST assembly and gene prediction on <i>C. milii</i> genomic genomic contigs. Abbreviations: EST, expressed sequence tags; GSS, genome survey sequence.</p>", "links"=>[], "tags"=>["Evolutionary biology", "Forms of evolution", "Divergent evolution", "Organismal evolution", "Animal evolution", "Comparative genomics", "Evolutionary genetics", "Genomic evolution", "population genetics", "Marine biology", "Zoology", "Animal phylogenetics", "Ichthyology", "divergence", "estimation"], "article_id"=>730776, "categories"=>["Biological Sciences"], "users"=>["Adina J. Renz", "Axel Meyer", "Shigehiro Kuraku"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0066400.g002", "stats"=>{"downloads"=>0, "page_views"=>9, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Work_flow_of_gene_family_selection_for_divergence_time_estimation_within_chondrichthyans_/730776", "title"=>"Work flow of gene family selection for divergence time estimation within chondrichthyans.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-06-25 01:48:57"}
  • {"files"=>["https://ndownloader.figshare.com/files/1100180"], "description"=>"<p>Species tree illustrating the relationship of all chondrichthyan species employed in our analyses, either in the divergence time study or evolutionary rate analysis (see text for alternative views of the phylogenetic relationship). Circles indicate the nodes referred to in the divergence time analysis. Widths of triangles are proportional to the numbers of species for individual groups according to Compagno et al. <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0066400#pone.0066400-Compagno1\" target=\"_blank\">[69]</a>.</p>", "links"=>[], "tags"=>["Evolutionary biology", "Forms of evolution", "Divergent evolution", "Organismal evolution", "Animal evolution", "Comparative genomics", "Evolutionary genetics", "Genomic evolution", "population genetics", "Marine biology", "Zoology", "Animal phylogenetics", "Ichthyology", "chondrichthyan"], "article_id"=>730774, "categories"=>["Biological Sciences"], "users"=>["Adina J. Renz", "Axel Meyer", "Shigehiro Kuraku"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0066400.g001", "stats"=>{"downloads"=>0, "page_views"=>5, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Relationship_of_chondrichthyan_species_/730774", "title"=>"Relationship of chondrichthyan species.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-06-25 01:48:57"}
  • {"files"=>["https://ndownloader.figshare.com/files/1100191", "https://ndownloader.figshare.com/files/1100193", "https://ndownloader.figshare.com/files/1100196"], "description"=>"<div><p>Cartilaginous fishes, divided into Holocephali (chimaeras) and Elasmoblanchii (sharks, rays and skates), occupy a key phylogenetic position among extant vertebrates in reconstructing their evolutionary processes. Their accurate evolutionary time scale is indispensable for better understanding of the relationship between phenotypic and molecular evolution of cartilaginous fishes. However, our current knowledge on the time scale of cartilaginous fish evolution largely relies on estimates using mitochondrial DNA sequences. In this study, making the best use of the still partial, but large-scale sequencing data of cartilaginous fish species, we estimate the divergence times between the major cartilaginous fish lineages employing nuclear genes. By rigorous orthology assessment based on available genomic and transcriptomic sequence resources for cartilaginous fishes, we selected 20 protein-coding genes in the nuclear genome, spanning 2973 amino acid residues. Our analysis based on the Bayesian inference resulted in the mean divergence time of 421 Ma, the late Silurian, for the Holocephali-Elasmobranchii split, and 306 Ma, the late Carboniferous, for the split between sharks and rays/skates. By applying these results and other documented divergence times, we measured the relative evolutionary rate of the Hox A cluster sequences in the cartilaginous fish lineages, which resulted in a lower substitution rate with a factor of at least 2.4 in comparison to tetrapod lineages. The obtained time scale enables mapping phenotypic and molecular changes in a quantitative framework. It is of great interest to corroborate the less derived nature of cartilaginous fish at the molecular level as a genome-wide phenomenon.</p></div>", "links"=>[], "tags"=>["Evolutionary biology", "Forms of evolution", "Divergent evolution", "Organismal evolution", "Animal evolution", "Comparative genomics", "Evolutionary genetics", "Genomic evolution", "population genetics", "Marine biology", "Zoology", "Animal phylogenetics", "Ichthyology", "derived", "cartilaginous", "genomes", "evolutionary", "inferred"], "article_id"=>730785, "categories"=>["Biological Sciences"], "users"=>["Adina J. Renz", "Axel Meyer", "Shigehiro Kuraku"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0066400.s001", "https://dx.doi.org/10.1371/journal.pone.0066400.s002", "https://dx.doi.org/10.1371/journal.pone.0066400.s003"], "stats"=>{"downloads"=>11, "page_views"=>6, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Revealing_Less_Derived_Nature_of_Cartilaginous_Fish_Genomes_with_Their_Evolutionary_Time_Scale_Inferred_with_Nuclear_Genes_/730785", "title"=>"Revealing Less Derived Nature of Cartilaginous Fish Genomes with Their Evolutionary Time Scale Inferred with Nuclear Genes", "pos_in_sequence"=>0, "defined_type"=>4, "published_date"=>"2013-06-25 01:48:57"}
  • {"files"=>["https://ndownloader.figshare.com/files/1100189"], "description"=>"<p>Divergence time estimates (posterior mean) and their 95% confidence intervals (CIs) in Ma (million years from present) for eleven nodes indicated in <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0066400#pone-0066400-g004\" target=\"_blank\">Figure 4</a>. See Table S2 for details of the time constraints. Different minimum constraints of node #11 resulted in different divergence time estimates.</p>", "links"=>[], "tags"=>["Evolutionary biology", "Forms of evolution", "Divergent evolution", "Organismal evolution", "Animal evolution", "Comparative genomics", "Evolutionary genetics", "Genomic evolution", "population genetics", "Marine biology", "Zoology", "Animal phylogenetics", "Ichthyology", "divergence"], "article_id"=>730783, "categories"=>["Biological Sciences"], "users"=>["Adina J. Renz", "Axel Meyer", "Shigehiro Kuraku"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0066400.t002", "stats"=>{"downloads"=>1, "page_views"=>4, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Estimated_divergence_times_/730783", "title"=>"Estimated divergence times.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2013-06-25 01:48:57"}

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Relative Metric

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