A Phylogenomic Perspective on the Radiation of Ray-Finned Fishes Based upon Targeted Sequencing of Ultraconserved Elements (UCEs)
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{"title"=>"A Phylogenomic Perspective on the Radiation of Ray-Finned Fishes Based upon Targeted Sequencing of Ultraconserved Elements (UCEs)", "type"=>"journal", "authors"=>[{"first_name"=>"Brant C.", "last_name"=>"Faircloth", "scopus_author_id"=>"8437891300"}, {"first_name"=>"Laurie", "last_name"=>"Sorenson", "scopus_author_id"=>"37065176100"}, {"first_name"=>"Francesco", "last_name"=>"Santini", "scopus_author_id"=>"35725922400"}, {"first_name"=>"Michael E.", "last_name"=>"Alfaro", "scopus_author_id"=>"7004720066"}], "year"=>2013, "source"=>"PLoS ONE", "identifiers"=>{"sgr"=>"84879162598", "doi"=>"10.1371/journal.pone.0065923", "pui"=>"369142325", "pmid"=>"23824177", "scopus"=>"2-s2.0-84879162598", "issn"=>"19326203", "isbn"=>"10.1371/journal.pone.0065923", "arxiv"=>"1210.0120"}, "id"=>"6dcf6709-0faa-30b7-b931-ee3b29d22729", "abstract"=>"Ray-finned fishes constitute the dominant radiation of vertebrates with over 30,000 species. Although molecular phylogenetics has begun to disentangle major evolutionary relationships within this vast section of the Tree of Life, there is no widely available approach for efficiently collecting phylogenomic data within fishes, leaving much of the enormous potential of massively parallel sequencing technologies for resolving major radiations in ray-finned fishes unrealized. Here, we provide a genomic perspective on longstanding questions regarding the diversification of major groups of ray-finned fishes through targeted enrichment of ultraconserved nuclear DNA elements (UCEs) and their flanking sequence. Our workflow efficiently and economically generates data sets that are orders of magnitude larger than those produced by traditional approaches and is well-suited to working with museum specimens. Analysis of the UCE data set recovers a well-supported phylogeny at both shallow and deep time-scales that supports a monophyletic relationship between Amia and Lepisosteus (Holostei) and reveals elopomorphs and then osteoglossomorphs to be the earliest diverging teleost lineages. Divergence time estimation based upon 14 fossil calibrations reveals that crown teleosts appeared ~270 Ma at the end of the Permian and that elopomorphs, osteoglossomorphs, ostarioclupeomorphs, and euteleosts diverged from one another by 205 Ma during the Triassic. Our approach additionally reveals that sequence capture of UCE regions and their flanking sequence offers enormous potential for resolving phylogenetic relationships within ray-finned fishes.", "link"=>"http://www.mendeley.com/research/phylogenomic-perspective-radiation-rayfinned-fishes-based-upon-targeted-sequencing-ultraconserved-el", "reader_count"=>242, "reader_count_by_academic_status"=>{"Unspecified"=>1, "Professor > Associate Professor"=>12, "Researcher"=>51, "Student > Doctoral Student"=>15, "Student > Ph. D. Student"=>79, "Student > Postgraduate"=>9, "Other"=>6, "Student > Master"=>39, "Student > Bachelor"=>18, "Lecturer"=>2, "Professor"=>10}, "reader_count_by_user_role"=>{"Unspecified"=>1, "Professor > Associate Professor"=>12, "Researcher"=>51, "Student > Doctoral Student"=>15, "Student > Ph. D. Student"=>79, "Student > Postgraduate"=>9, "Other"=>6, "Student > Master"=>39, "Student > Bachelor"=>18, "Lecturer"=>2, "Professor"=>10}, "reader_count_by_subject_area"=>{"Unspecified"=>7, "Engineering"=>2, "Environmental Science"=>15, "Biochemistry, Genetics and Molecular Biology"=>23, "Agricultural and Biological Sciences"=>181, "Arts and Humanities"=>1, "Physics and Astronomy"=>1, "Chemistry"=>1, "Social Sciences"=>1, "Computer Science"=>3, "Immunology and Microbiology"=>1, "Earth and Planetary Sciences"=>6}, "reader_count_by_subdiscipline"=>{"Engineering"=>{"Engineering"=>2}, "Chemistry"=>{"Chemistry"=>1}, "Social Sciences"=>{"Social Sciences"=>1}, "Physics and Astronomy"=>{"Physics and Astronomy"=>1}, "Immunology and Microbiology"=>{"Immunology and Microbiology"=>1}, "Earth and Planetary Sciences"=>{"Earth and Planetary Sciences"=>6}, "Agricultural and Biological Sciences"=>{"Agricultural and Biological Sciences"=>181}, "Computer Science"=>{"Computer Science"=>3}, "Biochemistry, Genetics and Molecular Biology"=>{"Biochemistry, Genetics and Molecular Biology"=>23}, "Unspecified"=>{"Unspecified"=>7}, "Environmental Science"=>{"Environmental Science"=>15}, "Arts and Humanities"=>{"Arts and Humanities"=>1}}, "reader_count_by_country"=>{"Colombia"=>1, "United States"=>9, "United Kingdom"=>4, "Spain"=>2, "Canada"=>1, "Sweden"=>3, "Brazil"=>6, "South Africa"=>1, "Mexico"=>2, "Australia"=>2, "France"=>1, "Chile"=>1, "Germany"=>1}, "group_count"=>3}

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Figshare

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Relative Metric

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