An Estimation of Erinaceidae Phylogeny: A Combined Analysis Approach
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{"title"=>"An estimation of erinaceidae phylogeny: A combined analysis approach", "type"=>"journal", "authors"=>[{"first_name"=>"Kai", "last_name"=>"He", "scopus_author_id"=>"57200171386"}, {"first_name"=>"Jian Hai", "last_name"=>"Chen", "scopus_author_id"=>"55258647900"}, {"first_name"=>"Gina C.", "last_name"=>"Gould", "scopus_author_id"=>"55258815600"}, {"first_name"=>"Nobuyuki", "last_name"=>"Yamaguchi", "scopus_author_id"=>"7402846932"}, {"first_name"=>"Huai Sen", "last_name"=>"Ai", "scopus_author_id"=>"55258058600"}, {"first_name"=>"Ying Xiang", "last_name"=>"Wang", "scopus_author_id"=>"7601494131"}, {"first_name"=>"Ya Ping", "last_name"=>"Zhang", "scopus_author_id"=>"55881841300"}, {"first_name"=>"Xue Long", "last_name"=>"Jiang", "scopus_author_id"=>"8283762400"}], "year"=>2012, "source"=>"PLoS ONE", "identifiers"=>{"scopus"=>"2-s2.0-84862657923", "pui"=>"365066140", "sgr"=>"84862657923", "isbn"=>"1932-6203 (Electronic)\\r1932-6203 (Linking)", "issn"=>"19326203", "pmid"=>"22745729", "doi"=>"10.1371/journal.pone.0039304"}, "id"=>"babb2b35-a352-3c19-abc6-cfb1311dcb4f", "abstract"=>"BACKGROUND: Erinaceidae is a family of small mammals that include the spiny hedgehogs (Erinaceinae) and the silky-furred moonrats and gymnures (Galericinae). These animals are widely distributed across Eurasia and Africa, from the tundra to the tropics and the deserts to damp forests. The importance of these animals lies in the fact that they are the oldest known living placental mammals, which are well represented in the fossil record, a rarity fact given their size and vulnerability to destruction during fossilization. Although the Family has been well studied, their phylogenetic relationships remain controversial. To test previous phylogenetic hypotheses, we combined molecular and morphological data sets, including representatives of all the genera.\\n\\nMETHODOLOGY AND PRINCIPAL FINDINGS: We included in the analyses 3,218 bp mitochondrial genes, one hundred and thirty-five morphological characters, twenty-two extant erinaceid taxa, and five outgroup taxa. Phylogenetic relationships were reconstructed using both partitioned and combined data sets. As in previous analyses, our results strongly support the monophyly of both subfamilies (Galericinae and Erinaceinae), the Hylomys group (to include Neotetracus and Neohylomys), and a sister-relationship of Atelerix and Erinaceus. As well, we verified that the extremely long branch lengths within the Galericinae are consistent with their fossil records. Not surprisingly, we found significant incongruence between the phylogenetic signals of the genes and the morphological characters, specifically in the case of Hylomys parvus, Mesechinus, and relationships between Hemiechinus and Paraechinus.\\n\\nCONCLUSIONS: Although we discovered new clues to understanding the evolutionary relationships within the Erinaceidae, our results nonetheless, strongly suggest that more robust analyses employing more complete taxon sampling (to include fossils) and multiple unlinked genes would greatly enhance our understanding of the Erinaceidae. Until then, we have left the nomenclature of the taxa unchanged; hence it does not yet precisely reflect their phylogenetic relationships or the depth of their genetic diversity.", "link"=>"http://www.mendeley.com/research/estimation-erinaceidae-phylogeny-combined-analysis-approach", "reader_count"=>45, "reader_count_by_academic_status"=>{"Unspecified"=>1, "Professor > Associate Professor"=>4, "Student > Doctoral Student"=>3, "Researcher"=>7, "Student > Ph. D. Student"=>10, "Student > Postgraduate"=>2, "Other"=>4, "Student > Master"=>4, "Student > Bachelor"=>6, "Lecturer"=>2, "Professor"=>2}, "reader_count_by_user_role"=>{"Unspecified"=>1, "Professor > Associate Professor"=>4, "Student > Doctoral Student"=>3, "Researcher"=>7, "Student > Ph. D. Student"=>10, "Student > Postgraduate"=>2, "Other"=>4, "Student > Master"=>4, "Student > Bachelor"=>6, "Lecturer"=>2, "Professor"=>2}, "reader_count_by_subject_area"=>{"Engineering"=>1, "Unspecified"=>1, "Environmental Science"=>4, "Biochemistry, Genetics and Molecular Biology"=>2, "Agricultural and Biological Sciences"=>31, "Medicine and Dentistry"=>1, "Business, Management and Accounting"=>1, "Computer Science"=>2, "Earth and Planetary Sciences"=>2}, "reader_count_by_subdiscipline"=>{"Engineering"=>{"Engineering"=>1}, "Medicine and Dentistry"=>{"Medicine and Dentistry"=>1}, "Earth and Planetary Sciences"=>{"Earth and Planetary Sciences"=>2}, "Agricultural and Biological Sciences"=>{"Agricultural and Biological Sciences"=>31}, "Computer Science"=>{"Computer Science"=>2}, "Business, Management and Accounting"=>{"Business, Management and Accounting"=>1}, "Biochemistry, Genetics and Molecular Biology"=>{"Biochemistry, Genetics and Molecular Biology"=>2}, "Unspecified"=>{"Unspecified"=>1}, "Environmental Science"=>{"Environmental Science"=>4}}, "reader_count_by_country"=>{"United States"=>2, "United Kingdom"=>1, "Bulgaria"=>1, "Portugal"=>1, "Spain"=>1}, "group_count"=>0}

Scopus | Further Information

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Figshare

  • {"files"=>["https://ndownloader.figshare.com/files/620576"], "description"=>"<p>Photograph of the Shrew Gymnure (<i>Neotetracus sinensis</i>) from Yunnan, China.</p>", "links"=>[], "tags"=>["genetics and genomics", "Evolutionary biology"], "article_id"=>291065, "categories"=>["Genetics", "Evolutionary Biology"], "users"=>["Kai He", "Jian-Hai Chen", "Gina C. Gould", "Nobuyuki Yamaguchi", "Huai-Sen Ai", "Ying-Xiang Wang", "Ya-Ping Zhang", "Xue-Long Jiang"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0039304.g003", "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_A_living_gymnure_/291065", "title"=>"A living gymnure.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2012-06-20 00:17:45"}
  • {"files"=>["https://ndownloader.figshare.com/files/620679"], "description"=>"<p>Phylogenetic relationships of Erinaceidae proposed by: (a) Corbet <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0039304#pone.0039304-Corbet1\" target=\"_blank\">[1]</a>; (b) Frost et al. <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0039304#pone.0039304-Frost1\" target=\"_blank\">[17]</a>; (c) Ruedi and Fumagalli <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0039304#pone.0039304-Ruedi1\" target=\"_blank\">[16]</a>; (d) Jenkins and Robinson <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0039304#pone.0039304-Jenkins1\" target=\"_blank\">[13]</a>; (e) and (f) Bannikova et al. <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0039304#pone.0039304-Bannikova1\" target=\"_blank\">[14]</a>; (g) Grenyer and Purvis <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0039304#pone.0039304-Grenyer1\" target=\"_blank\">[12]</a>.</p>", "links"=>[], "tags"=>["phylogenetic"], "article_id"=>291173, "categories"=>["Genetics", "Evolutionary Biology"], "users"=>["Kai He", "Jian-Hai Chen", "Gina C. Gould", "Nobuyuki Yamaguchi", "Huai-Sen Ai", "Ying-Xiang Wang", "Ya-Ping Zhang", "Xue-Long Jiang"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0039304.g004", "stats"=>{"downloads"=>1, "page_views"=>6, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Previous_phylogenetic_hypotheses_/291173", "title"=>"Previous phylogenetic hypotheses.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2012-06-20 00:19:33"}
  • {"files"=>["https://ndownloader.figshare.com/files/620943"], "description"=>"<p>Result of Bayesian phylogenetic analyses of three mitochondrial genes. Node numbers indicate Bayesian posterior probabilities.</p>", "links"=>[], "tags"=>["genetics and genomics", "Evolutionary biology"], "article_id"=>291432, "categories"=>["Genetics", "Evolutionary Biology"], "users"=>["Kai He", "Jian-Hai Chen", "Gina C. Gould", "Nobuyuki Yamaguchi", "Huai-Sen Ai", "Ying-Xiang Wang", "Ya-Ping Zhang", "Xue-Long Jiang"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0039304.g006", "stats"=>{"downloads"=>0, "page_views"=>7, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Mitochondrial_phylogeny_/291432", "title"=>"Mitochondrial phylogeny.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2012-06-20 00:23:52"}
  • {"files"=>["https://ndownloader.figshare.com/files/620815"], "description"=>"<p>Morphological strict consensus trees for 23 species using equal weighted (a) and unequal weighted (b), non-dental (c) and dental-only characters (d). Numbers above branches indicate bootstrap values, those below the branches indicate Bremer supports.</p>", "links"=>[], "tags"=>["phylogeny", "22"], "article_id"=>291305, "categories"=>["Genetics", "Evolutionary Biology"], "users"=>["Kai He", "Jian-Hai Chen", "Gina C. Gould", "Nobuyuki Yamaguchi", "Huai-Sen Ai", "Ying-Xiang Wang", "Ya-Ping Zhang", "Xue-Long Jiang"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0039304.g005", "stats"=>{"downloads"=>11, "page_views"=>8, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Morphological_phylogeny_of_22_erinaceids_/291305", "title"=>"Morphological phylogeny of 22 erinaceids.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2012-06-20 00:21:45"}
  • {"files"=>["https://ndownloader.figshare.com/files/621069"], "description"=>"<p>Result of Bayesian phylogenetic analyses using combined genes or genes-morphology combined data set including 14 erinaceids species (a) and 22 species (b). Node numbers indicate Bayesian posterior probabilities. Only one value is presented if the posterior probabilities are identical. Taxa shaded in grey have no available gene sequences in this study.</p>", "links"=>[], "tags"=>["genetics and genomics", "Evolutionary biology"], "article_id"=>291562, "categories"=>["Genetics", "Evolutionary Biology"], "users"=>["Kai He", "Jian-Hai Chen", "Gina C. Gould", "Nobuyuki Yamaguchi", "Huai-Sen Ai", "Ying-Xiang Wang", "Ya-Ping Zhang", "Xue-Long Jiang"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0039304.g007", "stats"=>{"downloads"=>1, "page_views"=>15, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Combined_data_phylogeny_/291562", "title"=>"Combined-data phylogeny.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2012-06-20 00:26:02"}
  • {"files"=>["https://ndownloader.figshare.com/files/323042", "https://ndownloader.figshare.com/files/323079", "https://ndownloader.figshare.com/files/323098", "https://ndownloader.figshare.com/files/323147", "https://ndownloader.figshare.com/files/323319", "https://ndownloader.figshare.com/files/323507"], "description"=>"<div><h3>Background</h3><p>Erinaceidae is a family of small mammals that include the spiny hedgehogs (Erinaceinae) and the silky-furred moonrats and gymnures (Galericinae). These animals are widely distributed across Eurasia and Africa, from the tundra to the tropics and the deserts to damp forests. The importance of these animals lies in the fact that they are the oldest known living placental mammals, which are well represented in the fossil record, a rarity fact given their size and vulnerability to destruction during fossilization. Although the Family has been well studied, their phylogenetic relationships remain controversial. To test previous phylogenetic hypotheses, we combined molecular and morphological data sets, including representatives of all the genera.</p> <h3>Methodology and Principal Findings</h3><p>We included in the analyses 3,218 bp mitochondrial genes, one hundred and thirty-five morphological characters, twenty-two extant erinaceid taxa, and five outgroup taxa. Phylogenetic relationships were reconstructed using both partitioned and combined data sets. As in previous analyses, our results strongly support the monophyly of both subfamilies (Galericinae and Erinaceinae), the <em>Hylomys</em> group (to include <em>Neotetracus</em> and <em>Neohylomys</em>), and a sister-relationship of <em>Atelerix</em> and <em>Erinaceus</em>. As well, we verified that the extremely long branch lengths within the Galericinae are consistent with their fossil records. Not surprisingly, we found significant incongruence between the phylogenetic signals of the genes and the morphological characters, specifically in the case of <em>Hylomys parvus, Mesechinus</em>, and relationships between <em>Hemiechinus</em> and <em>Paraechinus</em>.</p> <h3>Conclusions</h3><p>Although we discovered new clues to understanding the evolutionary relationships within the Erinaceidae, our results nonetheless, strongly suggest that more robust analyses employing more complete taxon sampling (to include fossils) and multiple unlinked genes would greatly enhance our understanding of the Erinaceidae. Until then, we have left the nomenclature of the taxa unchanged; hence it does not yet precisely reflect their phylogenetic relationships or the depth of their genetic diversity.</p> </div>", "links"=>[], "tags"=>["estimation", "erinaceidae"], "article_id"=>123755, "categories"=>["Genetics", "Evolutionary Biology"], "users"=>["Kai He", "Jian-Hai Chen", "Gina C. Gould", "Nobuyuki Yamaguchi", "Huai-Sen Ai", "Ying-Xiang Wang", "Ya-Ping Zhang", "Xue-Long Jiang"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0039304.s001", "https://dx.doi.org/10.1371/journal.pone.0039304.s002", "https://dx.doi.org/10.1371/journal.pone.0039304.s003", "https://dx.doi.org/10.1371/journal.pone.0039304.s004", "https://dx.doi.org/10.1371/journal.pone.0039304.s005", "https://dx.doi.org/10.1371/journal.pone.0039304.s006"], "stats"=>{"downloads"=>18, "page_views"=>22, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/An_Estimation_of_Erinaceidae_Phylogeny_A_Combined_Analysis_Approach/123755", "title"=>"An Estimation of Erinaceidae Phylogeny: A Combined Analysis Approach", "pos_in_sequence"=>0, "defined_type"=>4, "published_date"=>"2012-06-20 01:02:35"}
  • {"files"=>["https://ndownloader.figshare.com/files/621324"], "description"=>"*<p>Sequences downloaded from GenBank.</p>#<p>Only used for additional <i>CYT B</i> analysis of <i>Hylomys</i>.</p>", "links"=>[], "tags"=>["sequences"], "article_id"=>291820, "categories"=>["Genetics", "Evolutionary Biology"], "users"=>["Kai He", "Jian-Hai Chen", "Gina C. Gould", "Nobuyuki Yamaguchi", "Huai-Sen Ai", "Ying-Xiang Wang", "Ya-Ping Zhang", "Xue-Long Jiang"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0039304.t001", "stats"=>{"downloads"=>3, "page_views"=>36, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Samples_and_sequences_used_in_this_study_/291820", "title"=>"Samples and sequences used in this study.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2012-06-20 00:30:20"}
  • {"files"=>["https://ndownloader.figshare.com/files/620431"], "description"=>"<p>Modified based on Corbet et al. <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0039304#pone.0039304-Corbet1\" target=\"_blank\">[1]</a> and IUCN red list (iucnredlist.org). Galericinae: Ehg, <i>Echinosorex gymnura</i>; Hm, <i>Hylomys megalotis</i>; Hp, <i>Hylomys parvus</i>; Hs, <i>Hylomys suillus</i>; Nhh, <i>Neohylomys hainanensis</i>; NS, <i>Neotetracus sinensis</i>; Poa, <i>Podogymnura aureospinula</i>; Pot, <i>Podogymnura truei</i>. Erinaceinae: Aa, <i>Atelerix albiventris</i>; Af, <i>Atelerix frontalis</i>; Al, <i>Atelerix algirus</i>; As, <i>Atelerix sclateri</i>; Ea, <i>Erinaceus amurensis</i>; Ec, <i>Erinaceus concolor</i>; Ee, <i>Erinaceus europaeus</i>; Er, <i>Erinaceus roumanicus</i>; Ha, <i>Hemiechinus auritus</i>; Hc, <i>Hemiechinus collaris</i>; Md, <i>Mesechinus dauuricus</i>; Mh, <i>Mesechinus hughi</i>; Pe, <i>Paraechinus aethiopicus</i>; Ph, <i>Paraechinus hypomelas</i>; Pn, <i>Paraechinus nudiventris</i>; Pm, <i>Paraechinus micropus</i>.</p>", "links"=>[], "tags"=>["erinaceidae"], "article_id"=>290921, "categories"=>["Genetics", "Evolutionary Biology"], "users"=>["Kai He", "Jian-Hai Chen", "Gina C. Gould", "Nobuyuki Yamaguchi", "Huai-Sen Ai", "Ying-Xiang Wang", "Ya-Ping Zhang", "Xue-Long Jiang"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0039304.g002", "stats"=>{"downloads"=>3, "page_views"=>96, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Distribution_of_the_Family_Erinaceidae_and_its_component_species_/290921", "title"=>"Distribution of the Family Erinaceidae and its component species.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2012-06-20 00:15:21"}
  • {"files"=>["https://ndownloader.figshare.com/files/621406"], "description"=>"*<p>EDL6 and EDH6 were used for <i>Hylomys</i> and <i>Neotetracus</i>. L14724_hk3 and H15443_hk1 were used for <i>Neohylomys</i>. L14724_hk4 and H15427 were used for <i>Mesechinus dauuricus</i>. L14724_hk4 and H15915_hk4 were used for the other species.</p>", "links"=>[], "tags"=>["pcr"], "article_id"=>291897, "categories"=>["Genetics", "Evolutionary Biology"], "users"=>["Kai He", "Jian-Hai Chen", "Gina C. Gould", "Nobuyuki Yamaguchi", "Huai-Sen Ai", "Ying-Xiang Wang", "Ya-Ping Zhang", "Xue-Long Jiang"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0039304.t002", "stats"=>{"downloads"=>1, "page_views"=>39, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Primers_used_in_PCR_reaction_and_sequencing_/291897", "title"=>"Primers used in PCR reaction and sequencing.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2012-06-20 00:31:37"}
  • {"files"=>["https://ndownloader.figshare.com/files/621217"], "description"=>"<p>Result of Bayesian phylogenetic analyses of <i>Hylomys</i> based on partial <i>CYT B</i> genes. Node numbers indicate Bayesian posterior probabilities. Distribution of the two major clades was divided by the Kra Isthmus.</p>", "links"=>[], "tags"=>["phylogeny"], "article_id"=>291707, "categories"=>["Genetics", "Evolutionary Biology"], "users"=>["Kai He", "Jian-Hai Chen", "Gina C. Gould", "Nobuyuki Yamaguchi", "Huai-Sen Ai", "Ying-Xiang Wang", "Ya-Ping Zhang", "Xue-Long Jiang"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0039304.g008", "stats"=>{"downloads"=>0, "page_views"=>7, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Hylomys_phylogeny_based_on_partial_CYT_B_/291707", "title"=>"<i>Hylomys</i> phylogeny based on partial <i>CYT B</i>.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2012-06-20 00:28:27"}
  • {"files"=>["https://ndownloader.figshare.com/files/620290"], "description"=>"<p>Photograph of the Daurian Hedgehog (<i>Mesechinus dauuricus</i>) from Liaoning, China.</p>", "links"=>[], "tags"=>["genetics and genomics", "Evolutionary biology"], "article_id"=>290780, "categories"=>["Genetics", "Evolutionary Biology"], "users"=>["Kai He", "Jian-Hai Chen", "Gina C. Gould", "Nobuyuki Yamaguchi", "Huai-Sen Ai", "Ying-Xiang Wang", "Ya-Ping Zhang", "Xue-Long Jiang"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0039304.g001", "stats"=>{"downloads"=>1, "page_views"=>20, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_A_Living_hedgehog_/290780", "title"=>"A Living hedgehog.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2012-06-20 00:13:00"}
  • {"files"=>["https://ndownloader.figshare.com/files/621363"], "description"=>"<p>Phylogenetic analyses performed in this study.</p>", "links"=>[], "tags"=>["analyses", "performed"], "article_id"=>291850, "categories"=>["Genetics", "Evolutionary Biology"], "users"=>["Kai He", "Jian-Hai Chen", "Gina C. Gould", "Nobuyuki Yamaguchi", "Huai-Sen Ai", "Ying-Xiang Wang", "Ya-Ping Zhang", "Xue-Long Jiang"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0039304.t003", "stats"=>{"downloads"=>1, "page_views"=>33, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Phylogenetic_analyses_performed_in_this_study_/291850", "title"=>"Phylogenetic analyses performed in this study.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2012-06-20 00:30:50"}

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Relative Metric

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