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{"title"=>"A novel widespread cryptic species and phylogeographic patterns within several giant clam species (cardiidae: Tridacna) from the Indo-Pacific ocean", "type"=>"journal", "authors"=>[{"first_name"=>"Thomas", "last_name"=>"Huelsken", "scopus_author_id"=>"24335434400"}, {"first_name"=>"Jude", "last_name"=>"Keyse", "scopus_author_id"=>"55388098100"}, {"first_name"=>"Libby", "last_name"=>"Liggins", "scopus_author_id"=>"24474607700"}, {"first_name"=>"Shane", "last_name"=>"Penny", "scopus_author_id"=>"24279081700"}, {"first_name"=>"Eric A.", "last_name"=>"Treml", "scopus_author_id"=>"23101663700"}, {"first_name"=>"Cynthia", "last_name"=>"Riginos", "scopus_author_id"=>"6603230581"}], "year"=>2013, "source"=>"PLoS ONE", "identifiers"=>{"pui"=>"372425432", "issn"=>"19326203", "isbn"=>"1932-6203", "doi"=>"10.1371/journal.pone.0080858", "scopus"=>"2-s2.0-84896692318", "pmid"=>"24278333", "sgr"=>"84896692318"}, "id"=>"9a2e0e16-95f0-3d27-83c1-9e3032d708a6", "abstract"=>"Giant clams (genus Tridacna) are iconic coral reef animals of the Indian and Pacific Oceans, easily recognizable by their massive shells and vibrantly colored mantle tissue. Most Tridacna species are listed by CITES and the IUCN Redlist, as their populations have been extensively harvested and depleted in many regions. Here, we survey Tridacna crocea and Tridacna maxima from the eastern Indian and western Pacific Oceans for mitochondrial (COI and 16S) and nuclear (ITS) sequence variation and consolidate these data with previous published results using phylogenetic analyses. We find deep intraspecific differentiation within both T. crocea and T. maxima. In T. crocea we describe a previously undocumented phylogeographic division to the east of Cenderawasih Bay (northwest New Guinea), whereas for T. maxima the previously described, distinctive lineage of Cenderawasih Bay can be seen to also typify western Pacific populations. Furthermore, we find an undescribed, monophyletic group that is evolutionarily distinct from named Tridacna species at both mitochondrial and nuclear loci. This cryptic taxon is geographically widespread with a range extent that minimally includes much of the central Indo-Pacific region. Our results reinforce the emerging paradigm that cryptic species are common among marine invertebrates, even for conspicuous and culturally significant taxa. Additionally, our results add to identified locations of genetic differentiation across the central Indo-Pacific and highlight how phylogeographic patterns may differ even between closely related and co-distributed species.", "link"=>"http://www.mendeley.com/research/novel-widespread-cryptic-species-phylogeographic-patterns-within-several-giant-clam-species-cardiida-1", "reader_count"=>68, "reader_count_by_academic_status"=>{"Unspecified"=>1, "Professor > Associate Professor"=>2, "Researcher"=>14, "Student > Doctoral Student"=>3, "Student > Ph. D. Student"=>19, "Student > Postgraduate"=>2, "Student > Master"=>12, "Other"=>1, "Student > Bachelor"=>9, "Lecturer"=>2, "Professor"=>3}, "reader_count_by_user_role"=>{"Unspecified"=>1, "Professor > Associate Professor"=>2, "Researcher"=>14, "Student > Doctoral Student"=>3, "Student > Ph. D. Student"=>19, "Student > Postgraduate"=>2, "Student > Master"=>12, "Other"=>1, "Student > Bachelor"=>9, "Lecturer"=>2, "Professor"=>3}, "reader_count_by_subject_area"=>{"Unspecified"=>2, "Environmental Science"=>9, "Biochemistry, Genetics and Molecular Biology"=>3, "Agricultural and Biological Sciences"=>44, "Arts and Humanities"=>1, "Chemical Engineering"=>1, "Chemistry"=>1, "Computer Science"=>1, "Earth and Planetary Sciences"=>6}, "reader_count_by_subdiscipline"=>{"Chemistry"=>{"Chemistry"=>1}, "Earth and Planetary Sciences"=>{"Earth and Planetary Sciences"=>6}, "Agricultural and Biological Sciences"=>{"Agricultural and Biological Sciences"=>44}, "Computer Science"=>{"Computer Science"=>1}, "Biochemistry, Genetics and Molecular Biology"=>{"Biochemistry, Genetics and Molecular Biology"=>3}, "Unspecified"=>{"Unspecified"=>2}, "Environmental Science"=>{"Environmental Science"=>9}, "Chemical Engineering"=>{"Chemical Engineering"=>1}, "Arts and Humanities"=>{"Arts and Humanities"=>1}}, "reader_count_by_country"=>{"United States"=>2, "Japan"=>1, "Brazil"=>1, "South Africa"=>1, "United Kingdom"=>1, "Portugal"=>1, "Germany"=>1}, "group_count"=>2}

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• http://doi.org/10.1080/13235818.2014.940662
• http://doi.org/10.1111/jbi.13163
• http://doi.org/10.1093/icesjms/fsw184
• http://doi.org/10.1007/s12526-014-0265-9
• http://doi.org/10.1111/bij.12665
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• http://doi.org/10.1111/jbi.13797
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• http://doi.org/10.1016/j.actao.2015.10.009
• http://doi.org/10.1007/s12526-017-0678-3
• http://doi.org/10.1093/mollus/eyw001
• http://doi.org/10.2983/035.038.0303
• http://doi.org/10.1007/s11692-015-9356-1
• http://doi.org/10.1016/j.ympev.2016.08.013
• http://doi.org/10.2983/035.036.0306
• http://doi.org/10.1016/j.biocon.2014.11.004
• http://doi.org/10.1007/s12526-017-0715-2
• http://doi.org/10.1071/IS15032
• http://doi.org/10.1080/13235818.2016.1181141
• http://doi.org/10.1371/journal.pone.0157659
• http://doi.org/10.1007/s12526-017-0794-0
• http://doi.org/10.1093/mollus/eyz033
• http://doi.org/10.1007/s00227-014-2545-0
• http://doi.org/10.1016/j.ympev.2017.06.018

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{"EMBL"=>170, "UNIPROT"=>34}

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• {"id"=>"403285044040445952", "text"=>"A Novel Widespread Cryptic Species and Phylogeographic Patterns in Several Giant Clam Species http://t.co/sICcIQX86a http://t.co/htQAUhYUMH", "created_at"=>"2013-11-20T22:13:42Z", "user"=>"PLOSONE", "user_name"=>"PLOS ONE", "user_profile_image"=>"http://pbs.twimg.com/profile_images/2429958559/mzjl6as5u2m09r2erof6_normal.jpeg"}
• {"id"=>"403287737534386176", "text"=>"RT @PLOSONE: A Novel Widespread Cryptic Species and Phylogeographic Patterns in Several Giant Clam Species http://t.co/sICcIQX86a http://t.…", "created_at"=>"2013-11-20T22:24:24Z", "user"=>"alscientist", "user_name"=>"حيدر علي Haedar PhD", "user_profile_image"=>"http://pbs.twimg.com/profile_images/378800000757731195/3d6b49e8f6eaaf5e219f6d7a5d57f6fa_normal.jpeg"}
• {"id"=>"403508978631462913", "text"=>"RT @PLOSONE: A Novel Widespread Cryptic Species and Phylogeographic Patterns in Several Giant Clam Species http://t.co/sICcIQX86a http://t.…", "created_at"=>"2013-11-21T13:03:32Z", "user"=>"bio_utmn", "user_name"=>"bio", "user_profile_image"=>"http://pbs.twimg.com/profile_images/378800000504733108/a4aef3842334f55af59f58a9fa5e8d92_normal.jpeg"}
• {"id"=>"403993614298017792", "text"=>"New Giant Clam species http://t.co/7QVeBH89kX\nhttp://t.co/BcIik3JwoH", "created_at"=>"2013-11-22T21:09:18Z", "user"=>"FemoraleShells", "user_name"=>"Femorale Shells", "user_profile_image"=>"http://pbs.twimg.com/profile_images/1595996123/FemoConchasmall_normal.jpg"}
• {"id"=>"405448113600487425", "text"=>"For more on this cool clam & others in the Indo-Pacific , check out this cryptic clams study in @PLOSONE: http://t.co/VO28oag46i", "created_at"=>"2013-11-26T21:28:57Z", "user"=>"SaraMynott", "user_name"=>"Sara Mynott", "user_profile_image"=>"http://pbs.twimg.com/profile_images/3199241905/c7b11fd1ad49367a962ffd8ab009bd4f_normal.jpeg"}
• {"id"=>"413678788694642688", "text"=>"Cryptic species in Giant Clams? Read all about it here: http://t.co/QGbMjNmvbt", "created_at"=>"2013-12-19T14:34:43Z", "user"=>"Drew_Lab", "user_name"=>"Joshua Drew", "user_profile_image"=>"http://pbs.twimg.com/profile_images/3444291770/b68009ef610612af64fa6daba8b31340_normal.jpeg"}
• {"id"=>"413680516911869952", "text"=>"RT @Drew_Lab: Cryptic species in Giant Clams? Read all about it here: http://t.co/QGbMjNmvbt", "created_at"=>"2013-12-19T14:41:35Z", "user"=>"mt_ur_mind", "user_name"=>"Milton Tan", "user_profile_image"=>"http://pbs.twimg.com/profile_images/3615148923/a813cb7e9ec26883830ed9bab784b2b2_normal.png"}
• {"id"=>"413686675337125888", "text"=>"RT @Drew_Lab: Cryptic species in Giant Clams? Read all about it here: http://t.co/QGbMjNmvbt", "created_at"=>"2013-12-19T15:06:04Z", "user"=>"SeSimmonds", "user_name"=>"Sara Simmonds", "user_profile_image"=>"http://pbs.twimg.com/profile_images/3379755936/3ff393d9464e34b2fab4dd812104909e_normal.jpeg"}

Wikipedia | Further Information

• {"title"=>"Boring clam", "url"=>"http://en.wikipedia.org/wiki/Boring_clam", "timestamp"=>"2018-12-26T00:38:04Z"}
• {"title"=>"Tridacna", "url"=>"http://en.wikipedia.org/wiki/Tridacna", "timestamp"=>"2018-08-24T12:40:58Z"}
• {"title"=>"Maxima clam", "url"=>"http://en.wikipedia.org/wiki/Maxima_clam", "timestamp"=>"2019-01-07T03:34:10Z"}
• {"title"=>"Tridacna", "url"=>"http://es.wikipedia.org/wiki/Tridacna", "timestamp"=>"2017-05-12T17:02:04Z"}
• {"title"=>"Tridacna crocea", "url"=>"http://es.wikipedia.org/wiki/Tridacna_crocea", "timestamp"=>"2018-10-02T08:40:14Z"}
• {"title"=>"Trai tai tượng lớn", "url"=>"http://vi.wikipedia.org/wiki/Trai_tai_tượng_lớn", "timestamp"=>"2018-08-14T04:27:21Z"}
• {"title"=>"Tridacna crocea", "url"=>"http://vi.wikipedia.org/wiki/Tridacna_crocea", "timestamp"=>"2018-05-07T09:49:57Z"}
• {"title"=>"Tridacna", "url"=>"http://fi.wikipedia.org/wiki/Tridacna", "timestamp"=>"2017-01-23T19:40:10Z"}
• {"title"=>"Tridacna", "url"=>"http://hu.wikipedia.org/wiki/Tridacna", "timestamp"=>"2019-02-23T09:23:08Z"}

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• {"month"=>"5", "year"=>"2019", "pdf_views"=>"22", "xml_views"=>"0", "html_views"=>"18"}
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• {"month"=>"8", "year"=>"2019", "pdf_views"=>"6", "xml_views"=>"4", "html_views"=>"18"}
• {"month"=>"9", "year"=>"2019", "pdf_views"=>"9", "xml_views"=>"0", "html_views"=>"31"}
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• {"month"=>"12", "year"=>"2019", "pdf_views"=>"8", "xml_views"=>"0", "html_views"=>"24"}
• {"month"=>"1", "year"=>"2020", "pdf_views"=>"10", "xml_views"=>"0", "html_views"=>"20"}
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Figshare

• {"files"=>["https://ndownloader.figshare.com/files/1289825"], "description"=>"<p>Major lineages on networks are colored and the geographic extent of each lineage is indicated on the map. Relative frequencies of each haplotype are not depicted; each haplotype is shown in equal size (see text). Dots on maps indicate sampling locations and locations with two distinct sympatric lineages are shown as bisected circles (not indicative of relative frequencies). Support for monophyly of major clades among <i>COI</i> trees is based on 100 percent consistency of each branch among all equally parsimonious trees (a randomly chosen tree is depicted). Among <i>16S</i> trees, the single most parsimonious tree for <i>T. sp</i>. and <i>T. maxima</i> are shown, and for <i>T. crocea</i> both green and blue lineages were present in all six equally parsimonious trees. Colors indicate geographic locations of haplotypes and internal branches are in gray.</p>", "links"=>[], "tags"=>["parsimony", "trees", "sampling", "locations"], "article_id"=>858142, "categories"=>["Biological Sciences", "Ecology", "Earth and Environmental Sciences"], "users"=>["Thomas Huelsken", "Jude Keyse", "Libby Liggins", "Shane Penny", "Eric A. Treml", "Cynthia Riginos"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0080858.g005", "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Unrooted_parsimony_trees_and_sampling_locations_for_Tridacna_crocea_Tridacna_sp_and_Tridacna_maxima_/858142", "title"=>"Unrooted parsimony trees and sampling locations for <i>Tridacna crocea</i>, <i>Tridacna sp</i>., and <i>Tridacna maxima</i>.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-11-20 03:21:23"}
• {"files"=>["https://ndownloader.figshare.com/files/1289822"], "description"=>"<p>The topology shown is a time calibrated maximum clade credibility tree inferred with StarBEAST under a birth-death model. Bayesian posterior probabilities from StarBEAST and MrBayes are above branches and RAxML bootstrap support percentages are below branches. Individuals with two accession numbers include both <i>COI</i> and <i>16S</i> sequences. Individuals that are underlined also appear in <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0080858#pone-0080858-g004\" target=\"_blank\">Fig. 4</a>.</p>", "links"=>[], "tags"=>["relationships", "concatenated", "mitochondrial", "dna"], "article_id"=>858139, "categories"=>["Biological Sciences", "Ecology", "Earth and Environmental Sciences"], "users"=>["Thomas Huelsken", "Jude Keyse", "Libby Liggins", "Shane Penny", "Eric A. Treml", "Cynthia Riginos"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0080858.g002", "stats"=>{"downloads"=>1, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Species_relationships_within_Tridacna_based_on_concatenated_mitochondrial_DNA_COI_and_16S_sequences_/858139", "title"=>"Species relationships within <i>Tridacna</i> based on concatenated mitochondrial DNA (<i>COI</i> and <i>16S</i>) sequences.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-11-20 03:21:23"}
• {"files"=>["https://ndownloader.figshare.com/files/1289821"], "description"=>"<p>The light grey outline represents the lowest Pleistocene sea level (120 m depth contour).</p>", "links"=>[], "tags"=>[], "article_id"=>858138, "categories"=>["Biological Sciences", "Ecology", "Earth and Environmental Sciences"], "users"=>["Thomas Huelsken", "Jude Keyse", "Libby Liggins", "Shane Penny", "Eric A. Treml", "Cynthia Riginos"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0080858.g001", "stats"=>{"downloads"=>8, "page_views"=>4, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Study_region_/858138", "title"=>"Study region.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-11-20 03:21:23"}
• {"files"=>["https://ndownloader.figshare.com/files/1289833"], "description"=>"<div><p>Giant clams (genus <i>Tridacna</i>) are iconic coral reef animals of the Indian and Pacific Oceans, easily recognizable by their massive shells and vibrantly colored mantle tissue. Most <i>Tridacna</i> species are listed by CITES and the IUCN Redlist, as their populations have been extensively harvested and depleted in many regions. Here, we survey <i>Tridacna crocea</i> and <i>Tridacna maxima</i> from the eastern Indian and western Pacific Oceans for mitochondrial (<i>COI</i> and <i>16S</i>) and nuclear (<i>ITS</i>) sequence variation and consolidate these data with previous published results using phylogenetic analyses. We find deep intraspecific differentiation within both <i>T. crocea</i> and <i>T. maxima</i>. In <i>T. crocea</i> we describe a previously undocumented phylogeographic division to the east of Cenderawasih Bay (northwest New Guinea), whereas for <i>T. maxima</i> the previously described, distinctive lineage of Cenderawasih Bay can be seen to also typify western Pacific populations. Furthermore, we find an undescribed, monophyletic group that is evolutionarily distinct from named <i>Tridacna</i> species at both mitochondrial and nuclear loci. This cryptic taxon is geographically widespread with a range extent that minimally includes much of the central Indo-Pacific region. Our results reinforce the emerging paradigm that cryptic species are common among marine invertebrates, even for conspicuous and culturally significant taxa. Additionally, our results add to identified locations of genetic differentiation across the central Indo-Pacific and highlight how phylogeographic patterns may differ even between closely related and co-distributed species.</p></div>", "links"=>[], "tags"=>["cryptic", "phylogeographic", "patterns", "clam", "indo-pacific"], "article_id"=>858147, "categories"=>["Biological Sciences", "Ecology", "Earth and Environmental Sciences"], "users"=>["Thomas Huelsken", "Jude Keyse", "Libby Liggins", "Shane Penny", "Eric A. Treml", "Cynthia Riginos"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0080858", "stats"=>{"downloads"=>3, "page_views"=>29, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/A_Novel_Widespread_Cryptic_Species_and_Phylogeographic_Patterns_within_Several_Giant_Clam_Species_Cardiidae_Tridacna_from_the_Indo_Pacific_Ocean/858147", "title"=>"A Novel Widespread Cryptic Species and Phylogeographic Patterns within Several Giant Clam Species (Cardiidae: <i>Tridacna</i>) from the Indo-Pacific Ocean", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2013-11-20 03:21:23"}
• {"files"=>["https://ndownloader.figshare.com/files/1289824"], "description"=>"<p>Unalignable regions have been excluded. Bayesian posterior probabilities are above branches and RAxML bootstrap support percentages are below branches.</p>", "links"=>[], "tags"=>["relationships", "mrbayes"], "article_id"=>858141, "categories"=>["Biological Sciences", "Ecology", "Earth and Environmental Sciences"], "users"=>["Thomas Huelsken", "Jude Keyse", "Libby Liggins", "Shane Penny", "Eric A. Treml", "Cynthia Riginos"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0080858.g004", "stats"=>{"downloads"=>1, "page_views"=>9, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Species_relationships_within_Tridacna_based_an_ITS_MrBayes_consensus_tree_/858141", "title"=>"Species relationships within <i>Tridacna</i> based an <i>ITS</i> MrBayes consensus tree.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-11-20 03:21:23"}
• {"files"=>["https://ndownloader.figshare.com/files/1289823"], "description"=>"<p>MrBayesian consensus trees constructed for each gene region using all available data. Although different species and regions have differential representation, the two gene trees are concordant, as is expected for linked loci. Thus, overall patterns are consistent among research groups. Branch colors correspond to distinct lineages whose geographic distributions are described in <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0080858#pone-0080858-g005\" target=\"_blank\">Fig. 5</a>.</p>", "links"=>[], "tags"=>["phylogenetic", "trees", "mitochondrial"], "article_id"=>858140, "categories"=>["Biological Sciences", "Ecology", "Earth and Environmental Sciences"], "users"=>["Thomas Huelsken", "Jude Keyse", "Libby Liggins", "Shane Penny", "Eric A. Treml", "Cynthia Riginos"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0080858.g003", "stats"=>{"downloads"=>1, "page_views"=>15, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Bayesian_phylogenetic_trees_for_mitochondrial_CO1_and_16S_/858140", "title"=>"Bayesian phylogenetic trees for mitochondrial <i>CO1</i> and <i>16S</i>.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-11-20 03:21:23"}
• {"files"=>["https://ndownloader.figshare.com/files/1289831"], "description"=>"<p>A) <i>Tridacna maxima</i> from Hibernia Reef, WA, Australia. Accession No# P.52722 (Museum Art Gallery Northern Territory (MAGNT)), original identification based on morphology, B) <i>Tridacna sp.</i> from Five Finger Reef, South of Coral Bay, Ningaloo Marine Park, WA, Australia. Accession No#. P.51911 (Museum Art Gallery Northern Territory (MAGNT)), C) <i>Tridacna maxima</i>, from north western WA, Australia, unregistered (Museum Art Gallery Northern Territory (MAGNT)). Photo credit: Shane Penny.</p>", "links"=>[], "tags"=>["mtdna", "demonstrating", "valve", "morphology"], "article_id"=>858145, "categories"=>["Biological Sciences", "Ecology", "Earth and Environmental Sciences"], "users"=>["Thomas Huelsken", "Jude Keyse", "Libby Liggins", "Shane Penny", "Eric A. Treml", "Cynthia Riginos"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0080858.g006", "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_An_individual_with_Tridacna_sp_mtDNA_demonstrating_valve_morphology_consistent_with_Tridacna_maxima_/858145", "title"=>"An individual with <i>Tridacna sp.</i> mtDNA demonstrating valve morphology consistent with <i>Tridacna maxima</i>.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-11-20 03:21:23"}

PMC Usage Stats | Further Information

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Relative Metric

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F1000Prime