The Effect of Inappropriate Calibration: Three Case Studies in Molecular Ecology
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{"title"=>"The effect of inappropriate calibration: Three case studies in molecular ecology", "type"=>"journal", "authors"=>[{"first_name"=>"Simon Y.W.", "last_name"=>"Ho", "scopus_author_id"=>"7403716888"}, {"first_name"=>"Urmas", "last_name"=>"Saarma", "scopus_author_id"=>"6508125252"}, {"first_name"=>"Ross", "last_name"=>"Barnett", "scopus_author_id"=>"36776853100"}, {"first_name"=>"James", "last_name"=>"Haile", "scopus_author_id"=>"35503255600"}, {"first_name"=>"Beth", "last_name"=>"Shapiro", "scopus_author_id"=>"7402300615"}], "year"=>2008, "source"=>"PLoS ONE", "identifiers"=>{"issn"=>"19326203", "scopus"=>"2-s2.0-45449120082", "sgr"=>"45449120082", "pui"=>"351850767", "isbn"=>"1932-6203 (Electronic)\\r1932-6203 (Linking)", "pmid"=>"18286172", "doi"=>"10.1371/journal.pone.0001615"}, "id"=>"7741d307-9849-3135-91ca-395e3d066063", "abstract"=>"Time-scales estimated from sequence data play an important role in molecular ecology. They can be used to draw correlations between evolutionary and palaeoclimatic events, to measure the tempo of speciation, and to study the demographic history of an endangered species. In all of these studies, it is paramount to have accurate estimates of time-scales and substitution rates. Molecular ecological studies typically focus on intraspecific data that have evolved on genealogical scales, but often these studies inappropriately employ deep fossil calibrations or canonical substitution rates (e.g., 1% per million years for birds and mammals) for calibrating estimates of divergence times. These approaches can yield misleading estimates of molecular time-scales, with significant impacts on subsequent evolutionary and ecological inferences. We illustrate this calibration problem using three case studies: avian speciation in the late Pleistocene, the demographic history of bowhead whales, and the Pleistocene biogeography of brown bears. For each data set, we compare the date estimates that are obtained using internal and external calibration points. In all three cases, the conclusions are significantly altered by the application of revised, internally-calibrated substitution rates. Collectively, the results emphasise the importance of judicious selection of calibrations for analyses of recent evolutionary events.", "link"=>"http://www.mendeley.com/research/effect-inappropriate-calibration-three-case-studies-molecular-ecology", "reader_count"=>280, "reader_count_by_academic_status"=>{"Unspecified"=>4, "Professor > Associate Professor"=>16, "Researcher"=>72, "Student > Doctoral Student"=>12, "Student > Ph. D. Student"=>75, "Student > Postgraduate"=>14, "Other"=>10, "Student > Master"=>22, "Student > Bachelor"=>38, "Lecturer"=>5, "Lecturer > Senior Lecturer"=>3, "Professor"=>9}, "reader_count_by_user_role"=>{"Unspecified"=>4, "Professor > Associate Professor"=>16, "Researcher"=>72, "Student > Doctoral Student"=>12, "Student > Ph. D. Student"=>75, "Student > Postgraduate"=>14, "Other"=>10, "Student > Master"=>22, "Student > Bachelor"=>38, "Lecturer"=>5, "Lecturer > Senior Lecturer"=>3, "Professor"=>9}, "reader_count_by_subject_area"=>{"Unspecified"=>7, "Agricultural and Biological Sciences"=>198, "Arts and Humanities"=>29, "Veterinary Science and Veterinary Medicine"=>1, "Chemistry"=>1, "Computer Science"=>1, "Earth and Planetary Sciences"=>8, "Engineering"=>2, "Environmental Science"=>14, "Biochemistry, Genetics and Molecular Biology"=>16, "Medicine and Dentistry"=>1, "Immunology and Microbiology"=>1, "Linguistics"=>1}, "reader_count_by_subdiscipline"=>{"Medicine and Dentistry"=>{"Medicine and Dentistry"=>1}, "Unspecified"=>{"Unspecified"=>7}, "Environmental Science"=>{"Environmental Science"=>14}, "Arts and Humanities"=>{"Arts and Humanities"=>29}, "Engineering"=>{"Engineering"=>2}, "Chemistry"=>{"Chemistry"=>1}, "Earth and Planetary Sciences"=>{"Earth and Planetary Sciences"=>8}, "Immunology and Microbiology"=>{"Immunology and Microbiology"=>1}, "Agricultural and Biological Sciences"=>{"Agricultural and Biological Sciences"=>198}, "Computer Science"=>{"Computer Science"=>1}, "Linguistics"=>{"Linguistics"=>1}, "Biochemistry, Genetics and Molecular Biology"=>{"Biochemistry, Genetics and Molecular Biology"=>16}, "Veterinary Science and Veterinary Medicine"=>{"Veterinary Science and Veterinary Medicine"=>1}}, "reader_count_by_country"=>{"United States"=>15, "Japan"=>1, "Malaysia"=>1, "Portugal"=>3, "Switzerland"=>1, "Spain"=>3, "New Zealand"=>1, "Netherlands"=>3, "Sweden"=>1, "China"=>1, "Brazil"=>5, "Denmark"=>1, "Italy"=>1, "South Africa"=>2, "Mexico"=>1, "Nigeria"=>3, "France"=>3, "Chile"=>2, "Germany"=>2}, "group_count"=>4}

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Figshare

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  • {"files"=>["https://ndownloader.figshare.com/files/937519"], "description"=>"a<p>Range of 22 divergence time estimates</p>", "links"=>[], "tags"=>["estimates", "calibrations", "sets", "presented"], "article_id"=>607964, "categories"=>["Ecology"], "users"=>["Simon Y. W. Ho", "Urmas Saarma", "Ross Barnett", "James Haile", "Beth Shapiro"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0001615.t003", "stats"=>{"downloads"=>1, "page_views"=>7, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Summary_of_estimates_made_using_internal_and_external_calibrations_for_the_three_data_sets_presented_in_this_study_/607964", "title"=>"Summary of estimates made using internal and external calibrations for the three data sets presented in this study", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2013-02-21 11:03:57"}
  • {"files"=>["https://ndownloader.figshare.com/files/937487"], "description"=>"a<p>All taxa are members of Order Passeriformes, with the exception of Picidae (Order Piciformes).</p>b<p>Gamma-corrected distance estimated by Weir and Schluter <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0001615#pone.0001615-Weir2\" target=\"_blank\">[42]</a>.</p>c<p>Divergence times older than 250 kyr are italicised.</p>", "links"=>[], "tags"=>["estimates", "conspecific", "phylogroups", "22"], "article_id"=>607929, "categories"=>["Ecology"], "users"=>["Simon Y. W. Ho", "Urmas Saarma", "Ross Barnett", "James Haile", "Beth Shapiro"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0001615.t001", "stats"=>{"downloads"=>1, "page_views"=>15, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Divergence_time_estimates_for_conspecific_phylogroups_from_22_bird_species_/607929", "title"=>"Divergence time estimates for conspecific phylogroups from 22 bird species", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2013-02-21 11:03:46"}
  • {"files"=>["https://ndownloader.figshare.com/files/937549"], "description"=>"<p>Bayesian age estimates for nodes labelled in <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0001615#pone-0001615-g003\" target=\"_blank\">Figure 3</a></p>", "links"=>[], "tags"=>["estimates", "nodes", "labelled"], "article_id"=>607992, "categories"=>["Ecology"], "users"=>["Simon Y. W. Ho", "Urmas Saarma", "Ross Barnett", "James Haile", "Beth Shapiro"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0001615.t002", "stats"=>{"downloads"=>0, "page_views"=>3, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Bayesian_age_estimates_for_nodes_labelled_in_Figure_3_/607992", "title"=>"Bayesian age estimates for nodes labelled in Figure 3", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2013-02-21 11:04:09"}

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  • {"unique-ip"=>"4", "full-text"=>"3", "pdf"=>"1", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2020", "month"=>"12"}
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Relative Metric

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