Comprehensive Phylogenetic Reconstruction of Amoebozoa Based on Concatenated Analyses of SSU-rDNA and Actin Genes
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{"title"=>"Comprehensive phylogenetic reconstruction of amoebozoa based on concatenated analyses of SSU-rDNA and actin genes", "type"=>"journal", "authors"=>[{"first_name"=>"Daniel J.G.", "last_name"=>"Lahr", "scopus_author_id"=>"23978171500"}, {"first_name"=>"Jessica", "last_name"=>"Grant", "scopus_author_id"=>"23008107900"}, {"first_name"=>"Truc", "last_name"=>"Nguyen", "scopus_author_id"=>"37077832900"}, {"first_name"=>"Jian Hua", "last_name"=>"Lin", "scopus_author_id"=>"55709978800"}, {"first_name"=>"Laura A.", "last_name"=>"Katz", "scopus_author_id"=>"7202789639"}], "year"=>2011, "source"=>"PLoS ONE", "identifiers"=>{"issn"=>"19326203", "pui"=>"362231782", "sgr"=>"79960855196", "doi"=>"10.1371/journal.pone.0022780", "scopus"=>"2-s2.0-79960855196", "isbn"=>"10.1371/journal.pone.0022780", "pmid"=>"21829512"}, "id"=>"caeaedfa-9e23-3cbf-a04c-6eec300fa645", "abstract"=>"Evolutionary relationships within Amoebozoa have been the subject of controversy for two reasons: 1) paucity of morphological characters in traditional surveys and 2) haphazard taxonomic sampling in modern molecular reconstructions. These along with other factors have prevented the erection of a definitive system that resolves confidently both higher and lower-level relationships. Additionally, the recent recognition that many protosteloid amoebae are in fact scattered throughout the Amoebozoa suggests that phylogenetic reconstructions have been excluding an extensive and integral group of organisms. Here we provide a comprehensive phylogenetic reconstruction based on 139 taxa using molecular information from both SSU-rDNA and actin genes. We provide molecular data for 13 of those taxa, 12 of which had not been previously characterized. We explored the dataset extensively by generating 18 alternative reconstructions that assess the effect of missing data, long-branched taxa, unstable taxa, fast evolving sites and inclusion of environmental sequences. We compared reconstructions with each other as well as against previously published phylogenies. Our analyses show that many of the morphologically established lower-level relationships (defined here as relationships roughly equivalent to Order level or below) are congruent with molecular data. However, the data are insufficient to corroborate or reject the large majority of proposed higher-level relationships (above the Order-level), with the exception of Tubulinea, Archamoebae and Myxogastrea, which are consistently recovered. Moreover, contrary to previous expectations, the inclusion of available environmental sequences does not significantly improve the Amoebozoa reconstruction. This is probably because key amoebozoan taxa are not easily amplified by environmental sequencing methodology due to high rates of molecular evolution and regular occurrence of large indels and introns. Finally, in an effort to facilitate future sampling of key amoebozoan taxa, we provide a novel methodology for genome amplification and cDNA extraction from single or a few cells, a method that is culture-independent and allows both photodocumentation and extraction of multiple genes from natural samples.", "link"=>"http://www.mendeley.com/research/comprehensive-phylogenetic-reconstruction-amoebozoa-based-concatenated-analyses-ssurdna-actin-genes", "reader_count"=>61, "reader_count_by_academic_status"=>{"Unspecified"=>1, "Professor > Associate Professor"=>2, "Student > Doctoral Student"=>6, "Researcher"=>15, "Student > Ph. D. Student"=>15, "Student > Postgraduate"=>3, "Student > Master"=>7, "Other"=>1, "Student > Bachelor"=>7, "Professor"=>4}, "reader_count_by_user_role"=>{"Unspecified"=>1, "Professor > Associate Professor"=>2, "Student > Doctoral Student"=>6, "Researcher"=>15, "Student > Ph. D. Student"=>15, "Student > Postgraduate"=>3, "Student > Master"=>7, "Other"=>1, "Student > Bachelor"=>7, "Professor"=>4}, "reader_count_by_subject_area"=>{"Unspecified"=>6, "Environmental Science"=>1, "Biochemistry, Genetics and Molecular Biology"=>2, "Agricultural and Biological Sciences"=>43, "Chemistry"=>1, "Immunology and Microbiology"=>4, "Earth and Planetary Sciences"=>4}, "reader_count_by_subdiscipline"=>{"Chemistry"=>{"Chemistry"=>1}, "Immunology and Microbiology"=>{"Immunology and Microbiology"=>4}, "Earth and Planetary Sciences"=>{"Earth and Planetary Sciences"=>4}, "Agricultural and Biological Sciences"=>{"Agricultural and Biological Sciences"=>43}, "Biochemistry, Genetics and Molecular Biology"=>{"Biochemistry, Genetics and Molecular Biology"=>2}, "Unspecified"=>{"Unspecified"=>6}, "Environmental Science"=>{"Environmental Science"=>1}}, "reader_count_by_country"=>{"Canada"=>1, "United States"=>3, "Brazil"=>2, "France"=>2, "Portugal"=>1, "Germany"=>2, "Spain"=>1, "India"=>2}, "group_count"=>2}

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Figshare

  • {"files"=>["https://ndownloader.figshare.com/files/751117"], "description"=>"<p><b>1a–c. </b><i>Cryptodifflugia operculata</i>: a) Scanning electron micrograph (SEM) of <i>C. operculata</i> in ventral view, showing the distinctive mucous operculum covering the aperture; b) Dorsal view of two <i>C. operculata</i> with a cytoplasmic connection, this state is often seen in culture; c) Differential interference contrast images (DIC) of 3 connected <i>C. operculata</i> individuals. Scale bars are 5 µm. <b>1d–f</b>. Light microscopy images of the <i>Arcella mitrata</i> individual that was genome amplified to generate the sequences used in this study: d) lateral view showing the typical polygonal profile; e) top view of the same individual, focal plane at the middle of test height; f) top view of the same individual, focal plane at bottom of test height, showing the characteristic rippled apertural margin. Scale bars are 100 µm. <b>1g–i</b>. Hoffman modulation contrast (HMC) images of cultured individuals of <i>Arcella gibbosa</i>: g) lateral view showing hemispherical profile and pseudopods; h) another individual showing the shell's ridges and depressions; i) lateral view of a third individual. Scale bars are 60 µm. <b>1j–l</b>. <i>Arcella discoides</i>: j) HMC image of a cultured individual; k) SEM image showing the thin lateral profile; l) close-up on the apertural margin of individual in k, showing pores surrounding the aperture. Scale bars for j, k are 30 µm, for l 3 µm. <b>1m–n</b>. DIC images of cultured <i>Pyxidicula operculata</i>: m) focal plane at middle of test height showing the nucleus and one contractile vacuole; n) focal plane at the bottom of a different individual, surrounded by bacteria on which it was feeding. Scale bars are 10 µm. <b>1o–r</b>. DIC images of ‘<i>Govecia fonbrunei</i>’ ATCC® 50196: o) Encysted individual; p) resting individual, note the hyaline covering visible at the top margin; q) individual shape immediately after excystation; r) initial stages of locomotion. Scale bars are 10 µm. <b>1s–t</b>. HMC images of <i>Hyalosphenia papilio</i>: s) close up on one of the individuals that was genome amplified to obtain sequences in this study, scale bar 30 µm; t) a more general view of the same individual, scale bar 50 µm. <b>1u–y</b>. Images of ‘<i>Stereomyxa ramosa</i>’ ATCC® 50982: u,v) Phase contrast images of a cultured individual; x) protargol staining, showing the single nucleus; y) DIC image of a ‘<i>S. ramosa</i>’ showing the variety of pseudopods it can produce. Scale bars are 20 µm. <b>1z–a′</b>. HIC images of <i>Nebela carinata</i>: z) a lateral profile of one of the individuals used to obtain sequences in this study, this image shows the characteristic rim around the margin of the shell; a′) same individual observed in the typical raised shell locomotive position. Scale bars are 20 µm. <b>1b′–e′</b>. ‘<i>Stygamoeba regulata</i>’ ATCC® 50892: b′) sedentary shape; c′) beginning of movement morphology; d′) start of monopodial movement; e′) polypodial movement. Scale bars are 5 µm. <b>1f′–h′</b>. Three images of isolate CHINC-5 ATCC® 50979 (misidentified as <i>Sexangularia</i>) showing locomotive form. The absence of a shell, among other significant characters, indicates the identification as <i>Sexangularia</i> is incorrect. Note the finger-like pseudopods, similar to dactylopodids. Scale bars are 10 µm. Images of ATCC® isolates were generated by Jeffrey Cole and kindly provided by Robert Molestina, director of ATCC® collections, except for images on isolate CHINC-5 ATCC® 50979 provided by O. Roger Anderson.</p>", "links"=>[], "tags"=>["amoeboid", "lineages"], "article_id"=>421481, "categories"=>["Microbiology", "Physics", "Biochemistry", "Biophysics", "Molecular Biology", "Genetics", "Evolutionary Biology"], "users"=>["Daniel J. G. Lahr", "Jessica Grant", "Truc Nguyen", "Jian Hua Lin", "Laura A. Katz"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0022780.g001", "stats"=>{"downloads"=>2, "page_views"=>26, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Morphology_of_the_amoeboid_lineages_isolated_for_this_study_/421481", "title"=>"Morphology of the amoeboid lineages isolated for this study.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2011-07-28 00:24:41"}
  • {"files"=>["https://ndownloader.figshare.com/files/751796"], "description"=>"<p>Tree length is the total length of the tree. Treeness index is the ratio of tree length that is in internal branches over the total tree length. Leaf Stability values are averaged over all taxa in 1000 boostrap reconstructions. The 95% Confidence Interval refers to Leaf Stability values.</p>", "links"=>[], "tags"=>["indices", "16", "raxml", "reconstructions"], "article_id"=>422165, "categories"=>["Microbiology", "Physics", "Biochemistry", "Biophysics", "Molecular Biology", "Genetics", "Evolutionary Biology"], "users"=>["Daniel J. G. Lahr", "Jessica Grant", "Truc Nguyen", "Jian Hua Lin", "Laura A. Katz"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0022780.t005", "stats"=>{"downloads"=>1, "page_views"=>13, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Summary_of_tree_indices_obtained_for_16_RAxML_reconstructions_reconstructions_/422165", "title"=>"Summary of tree indices obtained for 16 RAxML reconstructions reconstructions.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2011-07-28 00:36:05"}
  • {"files"=>["https://ndownloader.figshare.com/files/751619"], "description"=>"<p>Triangles indicate multiple paralogs (number indicated in parenthesis), the length of triangle is equal to the length of longest branching paralog within the group.</p>", "links"=>[], "tags"=>["actin", "140"], "article_id"=>421990, "categories"=>["Microbiology", "Physics", "Biochemistry", "Biophysics", "Molecular Biology", "Genetics", "Evolutionary Biology"], "users"=>["Daniel J. G. Lahr", "Jessica Grant", "Truc Nguyen", "Jian Hua Lin", "Laura A. Katz"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0022780.g004", "stats"=>{"downloads"=>1, "page_views"=>19, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Reconstruction_of_actin_gene_family_evolution_in_Amoebozoa_using_140_paralogs_/421990", "title"=>"Reconstruction of actin gene family evolution in Amoebozoa, using 140 paralogs.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2011-07-28 00:33:10"}
  • {"files"=>["https://ndownloader.figshare.com/files/751728"], "description"=>"<p>*denotes that the group is invaded by one incertae sedis taxon;</p><p>**excluding <i>Saccamoeba limax</i> ATCC® 30942.</p><p>All reconstructions performed on RaxML, except the two indicated by (B) on Mr. Bayes. Bootstrap and posterior probability values above 95 and 0.95 respectively are in bold. Notes: nm – non-monophyletic; - not enough taxa to test the group in reconstruction; DS Myxogastrea – dark spored myxogastrids; LS Myxogastrea – light spored myxogastrids; Am+Hart – Amoebidae+Hartmannellidae; <i>Sty</i>+<i>Ver</i> – <i>Stygamoeba+Vermistella</i>; Dic+pro – Dictyosteliida+protosporangiids; FD – taxon as defined in Fiore-Donno et al. <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0022780#pone.0022780-FioreDonno2\" target=\"_blank\">[22]</a>; S – taxon as defined in Smirnov et al. <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0022780#pone.0022780-Smirnov3\" target=\"_blank\">[15]</a>; CS – taxon as defined in Cavalier-Smith et al. <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0022780#pone.0022780-CavalierSmith2\" target=\"_blank\">[14]</a>.</p>", "links"=>[], "tags"=>["bootstrap", "18", "reconstructions", "relationships", "suggested"], "article_id"=>422095, "categories"=>["Microbiology", "Physics", "Biochemistry", "Biophysics", "Molecular Biology", "Genetics", "Evolutionary Biology"], "users"=>["Daniel J. G. Lahr", "Jessica Grant", "Truc Nguyen", "Jian Hua Lin", "Laura A. Katz"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0022780.t003", "stats"=>{"downloads"=>1, "page_views"=>3, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Summary_of_bootstrap_values_obtained_in_all_18_reconstructions_for_previously_proposed_relationships_and_hypothesis_suggested_in_the_current_report_/422095", "title"=>"Summary of bootstrap values obtained in all 18 reconstructions for previously proposed relationships and hypothesis suggested in the current report.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2011-07-28 00:34:55"}
  • {"files"=>["https://ndownloader.figshare.com/files/751756"], "description"=>"<p>A list detailing which taxa were included in each reconstruction is available as Supplementary <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0022780#pone.0022780.s003\" target=\"_blank\">Table S1</a>. Taxa # - number of taxa included in reconstruction; Sites – number of sites included in alignment for each of SSU-rDNA and actin genes; Removal of amb sites – method used for dealing with ambiguously aligned sites: Manual indicates that sites were hand curated, and Automated indicates usage of the GUIDANCE algorithm <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0022780#pone.0022780-Penn1\" target=\"_blank\">[79]</a>.</p>", "links"=>[], "tags"=>["datasets", "generated", "phylogenetic"], "article_id"=>422126, "categories"=>["Microbiology", "Physics", "Biochemistry", "Biophysics", "Molecular Biology", "Genetics", "Evolutionary Biology"], "users"=>["Daniel J. G. Lahr", "Jessica Grant", "Truc Nguyen", "Jian Hua Lin", "Laura A. Katz"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0022780.t002", "stats"=>{"downloads"=>0, "page_views"=>2, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Concatenated_datasets_generated_to_perform_phylogenetic_analyses_/422126", "title"=>"Concatenated datasets generated to perform phylogenetic analyses.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2011-07-28 00:35:26"}
  • {"files"=>["https://ndownloader.figshare.com/files/751690"], "description"=>"a<p>The SSU-rDNA for <i>Paraflabellula hoguae</i> ATCC® 30733 has been published previously <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0022780#pone.0022780-AmaralZettler1\" target=\"_blank\">[8]</a>. We have obtained an identical sequence from our independently retrieved DNA.</p>b<p>Morphological analysis confirms this isolate is not <i>Sexangularia</i>, mislabeled in the ATCC® collection.</p><p>Source indicates origin of the organism, GenBank numbers are listed for both SSU-rDNA and actin genes. Name in single quotes indicate that identification provided by ATCC® may be incorrect.</p>", "links"=>[], "tags"=>["characterized", "amoebozoa"], "article_id"=>422059, "categories"=>["Microbiology", "Physics", "Biochemistry", "Biophysics", "Molecular Biology", "Genetics", "Evolutionary Biology"], "users"=>["Daniel J. G. Lahr", "Jessica Grant", "Truc Nguyen", "Jian Hua Lin", "Laura A. Katz"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0022780.t001", "stats"=>{"downloads"=>0, "page_views"=>2, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Newly_characterized_Amoebozoa_lineages_/422059", "title"=>"Newly characterized Amoebozoa lineages.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2011-07-28 00:34:19"}
  • {"files"=>["https://ndownloader.figshare.com/files/378312", "https://ndownloader.figshare.com/files/378326", "https://ndownloader.figshare.com/files/378350", "https://ndownloader.figshare.com/files/378369", "https://ndownloader.figshare.com/files/378382", "https://ndownloader.figshare.com/files/378408"], "description"=>"<div><p>Evolutionary relationships within Amoebozoa have been the subject of controversy for two reasons: 1) paucity of morphological characters in traditional surveys and 2) haphazard taxonomic sampling in modern molecular reconstructions. These along with other factors have prevented the erection of a definitive system that resolves confidently both higher and lower-level relationships. Additionally, the recent recognition that many protosteloid amoebae are in fact scattered throughout the Amoebozoa suggests that phylogenetic reconstructions have been excluding an extensive and integral group of organisms. Here we provide a comprehensive phylogenetic reconstruction based on 139 taxa using molecular information from both SSU-rDNA and actin genes. We provide molecular data for 13 of those taxa, 12 of which had not been previously characterized. We explored the dataset extensively by generating 18 alternative reconstructions that assess the effect of missing data, long-branched taxa, unstable taxa, fast evolving sites and inclusion of environmental sequences. We compared reconstructions with each other as well as against previously published phylogenies. Our analyses show that many of the morphologically established lower-level relationships (defined here as relationships roughly equivalent to Order level or below) are congruent with molecular data. However, the data are insufficient to corroborate or reject the large majority of proposed higher-level relationships (above the Order-level), with the exception of Tubulinea, Archamoebae and Myxogastrea, which are consistently recovered. Moreover, contrary to previous expectations, the inclusion of available environmental sequences does not significantly improve the Amoebozoa reconstruction. This is probably because key amoebozoan taxa are not easily amplified by environmental sequencing methodology due to high rates of molecular evolution and regular occurrence of large indels and introns. Finally, in an effort to facilitate future sampling of key amoebozoan taxa, we provide a novel methodology for genome amplification and cDNA extraction from single or a few cells, a method that is culture-independent and allows both photodocumentation and extraction of multiple genes from natural samples.</p> </div>", "links"=>[], "tags"=>["phylogenetic", "reconstruction", "amoebozoa", "based", "concatenated", "analyses", "ssu-rdna", "actin", "genes"], "article_id"=>134780, "categories"=>["Microbiology", "Physics", "Biochemistry", "Biophysics", "Molecular Biology", "Genetics", "Evolutionary Biology"], "users"=>["Daniel J. G. Lahr", "Jessica Grant", "Truc Nguyen", "Jian Hua Lin", "Laura A. Katz"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0022780.s001", "https://dx.doi.org/10.1371/journal.pone.0022780.s002", "https://dx.doi.org/10.1371/journal.pone.0022780.s003", "https://dx.doi.org/10.1371/journal.pone.0022780.s004", "https://dx.doi.org/10.1371/journal.pone.0022780.s005", "https://dx.doi.org/10.1371/journal.pone.0022780.s006"], "stats"=>{"downloads"=>16, "page_views"=>5, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/Comprehensive_Phylogenetic_Reconstruction_of_Amoebozoa_Based_on_Concatenated_Analyses_of_SSU_rDNA_and_Actin_Genes/134780", "title"=>"Comprehensive Phylogenetic Reconstruction of Amoebozoa Based on Concatenated Analyses of SSU-rDNA and Actin Genes", "pos_in_sequence"=>0, "defined_type"=>4, "published_date"=>"2011-07-28 01:19:40"}
  • {"files"=>["https://ndownloader.figshare.com/files/751823"], "description"=>"<p>Values are comparing our best phylogeny against phylogenies where proposed relationships were constrained. None of the hypotheses can be rejected, since all p values are above the 0.05 threshold. wkh – weighted Kishino-Hasegawa test; au – approximately unbiased test; wsh – weighted Shimodaira-Hasegawa test; FD – taxon as defined in Fiore-Donno et al. <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0022780#pone.0022780-FioreDonno2\" target=\"_blank\">[22]</a>; S – taxon as defined in Smirnov et al. <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0022780#pone.0022780-Smirnov3\" target=\"_blank\">[15]</a>; CS – taxon as defined in Cavalier-Smith et al. <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0022780#pone.0022780-CavalierSmith2\" target=\"_blank\">[14]</a>.</p>", "links"=>[], "tags"=>["unbiased"], "article_id"=>422197, "categories"=>["Microbiology", "Physics", "Biochemistry", "Biophysics", "Molecular Biology", "Genetics", "Evolutionary Biology"], "users"=>["Daniel J. G. Lahr", "Jessica Grant", "Truc Nguyen", "Jian Hua Lin", "Laura A. Katz"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0022780.t004", "stats"=>{"downloads"=>1, "page_views"=>7, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Summary_of_values_obtained_from_approximately_unbiased_test_/422197", "title"=>"Summary of values obtained from approximately unbiased test.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2011-07-28 00:36:37"}
  • {"files"=>["https://ndownloader.figshare.com/files/751488"], "description"=>"<p>This reconstruction is the best maximum likelihood tree obtained from the dataset Manual139, which we consider exhibits the optimal combination of tree indices and taxonomic coverage. Both Bayesian posterior probabilities and bootstrap supports are plotted on branches of interest. Branches without any support indication had bootstrap support of less than 70. The three well-supported higher-level groupings are shaded gray. The lower-level, morphologically consistent relationships are indicated. The novel relationships uncovered in the current study are in bold, and the suggested name for the group is shown in single quotes. Terminals in bold indicate lineages for which we are providing novel molecular information. Dashed brackets represent lower-level groups that are morphologically consistent but not recovered in this reconstruction. All branches are drawn to scale, except the branches leading to Myxomycetes, <i>Lindbladia</i>, <i>Vannella</i> CAZ6/I and <i>Clydonnella</i> which were trimmed to half-length for display purposes.</p>", "links"=>[], "tags"=>["reconstruction", "concatenated", "ssu-rdna", "actin", "genes", "139"], "article_id"=>421852, "categories"=>["Microbiology", "Physics", "Biochemistry", "Biophysics", "Molecular Biology", "Genetics", "Evolutionary Biology"], "users"=>["Daniel J. G. Lahr", "Jessica Grant", "Truc Nguyen", "Jian Hua Lin", "Laura A. Katz"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0022780.g003", "stats"=>{"downloads"=>1, "page_views"=>8, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Phylogenetic_reconstruction_of_the_Amoebozoa_based_on_concatenated_analysis_of_SSU_rDNA_and_actin_genes_of_139_lineages_/421852", "title"=>"Phylogenetic reconstruction of the Amoebozoa, based on concatenated analysis of SSU-rDNA and actin genes of 139 lineages.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2011-07-28 00:30:52"}
  • {"files"=>["https://ndownloader.figshare.com/files/751364"], "description"=>"<p>Grey boxes indicate a dataset, grey arrows indicate phylogenetic analyses performed on that dataset. Black arrows and boxes indicate other types of analyses performed on particular datasets, and the black dotted lines indicate the final analyses performed to obtain scores for each phylogenetic reconstruction.</p>", "links"=>[], "tags"=>["pipeline", "implemented", "phylogenetic"], "article_id"=>421734, "categories"=>["Microbiology", "Physics", "Biochemistry", "Biophysics", "Molecular Biology", "Genetics", "Evolutionary Biology"], "users"=>["Daniel J. G. Lahr", "Jessica Grant", "Truc Nguyen", "Jian Hua Lin", "Laura A. Katz"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0022780.g002", "stats"=>{"downloads"=>0, "page_views"=>3, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Computational_pipeline_implemented_for_phylogenetic_analysis_/421734", "title"=>"Computational pipeline implemented for phylogenetic analysis.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2011-07-28 00:28:54"}

PMC Usage Stats | Further Information

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  • {"unique-ip"=>"11", "full-text"=>"12", "pdf"=>"2", "abstract"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"1", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2017", "month"=>"3"}
  • {"unique-ip"=>"14", "full-text"=>"17", "pdf"=>"1", "abstract"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"4", "supp-data"=>"6", "cited-by"=>"1", "year"=>"2017", "month"=>"4"}
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  • {"unique-ip"=>"11", "full-text"=>"6", "pdf"=>"2", "abstract"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"8", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2018", "month"=>"1"}
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  • {"unique-ip"=>"13", "full-text"=>"12", "pdf"=>"2", "abstract"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"4", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2018", "month"=>"3"}
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  • {"unique-ip"=>"13", "full-text"=>"12", "pdf"=>"3", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2018", "month"=>"6"}
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  • {"unique-ip"=>"13", "full-text"=>"16", "pdf"=>"1", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2018", "month"=>"12"}
  • {"unique-ip"=>"20", "full-text"=>"21", "pdf"=>"2", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"2", "cited-by"=>"0", "year"=>"2018", "month"=>"11"}
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  • {"unique-ip"=>"11", "full-text"=>"14", "pdf"=>"5", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"1", "supp-data"=>"6", "cited-by"=>"0", "year"=>"2019", "month"=>"3"}
  • {"unique-ip"=>"10", "full-text"=>"12", "pdf"=>"2", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2019", "month"=>"4"}
  • {"unique-ip"=>"14", "full-text"=>"16", "pdf"=>"1", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2019", "month"=>"5"}
  • {"unique-ip"=>"8", "full-text"=>"8", "pdf"=>"2", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2019", "month"=>"8"}
  • {"unique-ip"=>"15", "full-text"=>"16", "pdf"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"1", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2019", "month"=>"9"}
  • {"unique-ip"=>"12", "full-text"=>"53", "pdf"=>"2", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"4", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2019", "month"=>"10"}
  • {"unique-ip"=>"13", "full-text"=>"12", "pdf"=>"3", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2019", "month"=>"12"}

Relative Metric

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