Phylogenetic Diversity Theory Sheds Light on the Structure of Microbial Communities
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{"title"=>"Phylogenetic Diversity Theory Sheds Light on the Structure of Microbial Communities", "type"=>"journal", "authors"=>[{"first_name"=>"James P.", "last_name"=>"O'Dwyer", "scopus_author_id"=>"26536493300"}, {"first_name"=>"Steven W.", "last_name"=>"Kembel", "scopus_author_id"=>"8682558800"}, {"first_name"=>"Jessica L.", "last_name"=>"Green", "scopus_author_id"=>"55463724300"}], "year"=>2012, "source"=>"PLoS Computational Biology", "identifiers"=>{"pui"=>"368067305", "issn"=>"1553734X", "isbn"=>"1553-7358 (Electronic)\\n1553-734X (Linking)", "doi"=>"10.1371/journal.pcbi.1002832", "scopus"=>"2-s2.0-84872038980", "pmid"=>"23284280", "sgr"=>"84872038980"}, "id"=>"c8246ebb-0f63-3459-b6a9-8a4f327612d1", "abstract"=>"Microbial communities are typically large, diverse, and complex, and identifying and understanding the processes driving their structure has implications ranging from ecosystem stability to human health and well-being. Phylogenetic data gives us a new insight into these processes, providing a more informative perspective on functional and trait diversity than taxonomic richness alone. But the sheer scale of high resolution phylogenetic data also presents a new challenge to ecological theory. We bring a sampling theory perspective to microbial communities, considering a local community of co-occuring organisms as a sample from a larger regional pool, and apply our framework to make analytical predictions for local phylogenetic diversity arising from a given metacommunity and community assembly process. We characterize community assembly in terms of quantitative descriptions of clustered, random and overdispersed sampling, which have been associated with hypotheses of environmental filtering and competition. Using our approach, we analyze large microbial communities from the human microbiome, uncovering significant variation in diversity across habitats relative to the null hypothesis of random sampling.", "link"=>"http://www.mendeley.com/research/phylogenetic-diversity-theory-sheds-light-structure-microbial-communities", "reader_count"=>196, "reader_count_by_academic_status"=>{"Unspecified"=>3, "Professor > Associate Professor"=>11, "Researcher"=>45, "Student > Doctoral Student"=>10, "Student > Ph. D. Student"=>74, "Student > Postgraduate"=>4, "Other"=>5, "Student > Master"=>19, "Student > Bachelor"=>11, "Professor"=>13}, "reader_count_by_user_role"=>{"Unspecified"=>3, "Professor > Associate Professor"=>11, "Researcher"=>45, "Student > Doctoral Student"=>10, "Student > Ph. D. Student"=>74, "Student > Postgraduate"=>4, "Other"=>5, "Student > Master"=>19, "Student > Bachelor"=>11, "Professor"=>13}, "reader_count_by_subject_area"=>{"Unspecified"=>10, "Agricultural and Biological Sciences"=>134, "Business, Management and Accounting"=>1, "Computer Science"=>4, "Earth and Planetary Sciences"=>1, "Engineering"=>2, "Environmental Science"=>20, "Biochemistry, Genetics and Molecular Biology"=>8, "Mathematics"=>3, "Medicine and Dentistry"=>4, "Design"=>1, "Physics and Astronomy"=>3, "Social Sciences"=>1, "Immunology and Microbiology"=>3}, "reader_count_by_subdiscipline"=>{"Medicine and Dentistry"=>{"Medicine and Dentistry"=>4}, "Social Sciences"=>{"Social Sciences"=>1}, "Physics and Astronomy"=>{"Physics and Astronomy"=>3}, "Mathematics"=>{"Mathematics"=>3}, "Unspecified"=>{"Unspecified"=>10}, "Environmental Science"=>{"Environmental Science"=>20}, "Design"=>{"Design"=>1}, "Engineering"=>{"Engineering"=>2}, "Earth and Planetary Sciences"=>{"Earth and Planetary Sciences"=>1}, "Immunology and Microbiology"=>{"Immunology and Microbiology"=>3}, "Agricultural and Biological Sciences"=>{"Agricultural and Biological Sciences"=>134}, "Computer Science"=>{"Computer Science"=>4}, "Business, Management and Accounting"=>{"Business, Management and Accounting"=>1}, "Biochemistry, Genetics and Molecular Biology"=>{"Biochemistry, Genetics and Molecular Biology"=>8}}, "reader_count_by_country"=>{"Colombia"=>2, "United States"=>22, "Japan"=>1, "Philippines"=>1, "United Kingdom"=>3, "Spain"=>3, "India"=>1, "Canada"=>3, "Sweden"=>2, "China"=>1, "Brazil"=>2, "Mexico"=>1, "Italy"=>1, "South Africa"=>1, "France"=>5, "Chile"=>1, "Germany"=>2}, "group_count"=>9}

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Figshare

  • {"files"=>["https://ndownloader.figshare.com/files/519635"], "description"=>"<p>We show a comparison of actual PD with expected PD under random sampling for three habitats: nose, hair and forehead. Solid lines represent expected PD from random sampling as a function of expected number of tips, dashed lines represent an upper bound on the 95% confidence interval computed using the variance in sampled PD (see Supplementary Information). Points represent actual PD from each of seven human subjects on one sampling day, with subjects labeled by a letter (M or F indicating male or female) and an identifying number. On the top row the reference metacommunity is all reads from <i>that</i> specified habitat, pooled across all seven subjects, and on the bottom row the metacommunity is all sampled reads across all subjects <i>and</i> all habitats. Our central conclusion is that while most samples are consistent with phylogenetic clustering, irrespective of the metacommunity, a minority of communities are consistent with overdispersed sampling from the smaller metacommunity, but clustered sampling from the larger.</p>", "links"=>[], "tags"=>["ecology", "Community Ecology", "Community assembly", "microbial ecology", "theoretical ecology", "metacommunity", "samples", "clustered"], "article_id"=>190128, "categories"=>["Biological Sciences"], "users"=>["James P. O'Dwyer", "Steven W. Kembel", "Jessica L. Green"], "doi"=>"https://dx.doi.org/10.1371/journal.pcbi.1002832.g006", "stats"=>{"downloads"=>0, "page_views"=>12, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Changing_metacommunity_scale_can_change_whether_samples_appear_clustered_or_overdispersed_/190128", "title"=>"Changing metacommunity scale can change whether samples appear clustered or overdispersed.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2012-12-20 00:02:08"}
  • {"files"=>["https://ndownloader.figshare.com/files/281947", "https://ndownloader.figshare.com/files/281995"], "description"=>"<div><p>Microbial communities are typically large, diverse, and complex, and identifying and understanding the processes driving their structure has implications ranging from ecosystem stability to human health and well-being. Phylogenetic data gives us a new insight into these processes, providing a more informative perspective on functional and trait diversity than taxonomic richness alone. But the sheer scale of high resolution phylogenetic data also presents a new challenge to ecological theory. We bring a sampling theory perspective to microbial communities, considering a local community of co-occuring organisms as a sample from a larger regional pool, and apply our framework to make analytical predictions for local phylogenetic diversity arising from a given metacommunity and community assembly process. We characterize community assembly in terms of quantitative descriptions of clustered, random and overdispersed sampling, which have been associated with hypotheses of environmental filtering and competition. Using our approach, we analyze large microbial communities from the human microbiome, uncovering significant variation in diversity across habitats relative to the null hypothesis of random sampling.</p> </div>", "links"=>[], "tags"=>["ecology", "Community Ecology", "Community assembly", "microbial ecology", "theoretical ecology", "phylogenetic", "sheds", "microbial", "communities"], "article_id"=>115591, "categories"=>["Biological Sciences"], "users"=>["James P. O'Dwyer", "Steven W. Kembel", "Jessica L. Green"], "doi"=>["https://dx.doi.org/10.1371/journal.pcbi.1002832.s001", "https://dx.doi.org/10.1371/journal.pcbi.1002832.s002"], "stats"=>{"downloads"=>4, "page_views"=>30, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/Phylogenetic_Diversity_Theory_Sheds_Light_on_the_Structure_of_Microbial_Communities__/115591", "title"=>"Phylogenetic Diversity Theory Sheds Light on the Structure of Microbial Communities", "pos_in_sequence"=>0, "defined_type"=>4, "published_date"=>"2012-12-20 01:33:11"}
  • {"files"=>["https://ndownloader.figshare.com/files/519288"], "description"=>"<p>All edges are labeled by their length, and the table shows the total edge-length summed across all edges with a given number of upstream tips. Number of tips appears in the left column, and the total edge-length associated with that number of tips, , is shown in the right column. For example, the circled edge has length two, and has two tips downstream, and therefore contributes length to .</p>", "links"=>[], "tags"=>["ecology", "Community Ecology", "Community assembly", "microbial ecology", "theoretical ecology", "edge-length", "abundance"], "article_id"=>189781, "categories"=>["Biological Sciences"], "users"=>["James P. O'Dwyer", "Steven W. Kembel", "Jessica L. Green"], "doi"=>"https://dx.doi.org/10.1371/journal.pcbi.1002832.g002", "stats"=>{"downloads"=>2, "page_views"=>3, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_The_Edge_length_Abundance_Distribution_for_a_community_with_four_individuals_/189781", "title"=>"The Edge-length Abundance Distribution, , for a community with four individuals.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2012-12-20 02:43:01"}
  • {"files"=>["https://ndownloader.figshare.com/files/519470"], "description"=>"<p>As an approximation to the real communities in <a href=\"http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1002832#pcbi-1002832-g003\" target=\"_blank\">Figure 3</a>, we take . The resulting expected PD for Binomial sampling is close to a power law as a function of number of tips sampled, with . We show the corresponding result for Poisson sampling, representing sampling with replacement which is identical to the binomial result until sample size becomes large. Finally, we show two negative binomial schemes with different clustering parameters, , (see Supplementary Information). These parameters are consistent with different degrees of phylogenetic clustering, which leads in general to smaller sampled PD for a given number of tips.</p>", "links"=>[], "tags"=>["ecology", "Community Ecology", "Community assembly", "microbial ecology", "theoretical ecology", "pd", "taken", "metacommunity", "power-law", "edge-length", "abundance", "sampling"], "article_id"=>189954, "categories"=>["Biological Sciences"], "users"=>["James P. O'Dwyer", "Steven W. Kembel", "Jessica L. Green"], "doi"=>"https://dx.doi.org/10.1371/journal.pcbi.1002832.g004", "stats"=>{"downloads"=>1, "page_views"=>7, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Expected_PD_for_a_sample_taken_from_a_theoretical_metacommunity_with_a_power_law_Edge_length_Abundance_Distribution_for_various_sampling_schemes_/189954", "title"=>"Expected PD for a sample taken from a theoretical metacommunity with a power-law Edge-length Abundance Distribution, for various sampling schemes.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2012-12-20 02:45:54"}
  • {"files"=>["https://ndownloader.figshare.com/files/519198"], "description"=>"<p>In (A), (B) and (C) we adapt this framework for a microbial community, the human microbiome, for different definitions of the local community and the reference metacommunity. (A) shows microbiota from a single body habitat, thought of as a sample from the pool of microbiota found in the same habitat on different human subjects. (B) shows the same local community, but thought of as a sample from all microbiota across multiple humans. Finally, the local community in (C) is all microbiota from a single human subject, while the metacommunity is again microbiota from multiple habitats across multiple humans.</p>", "links"=>[], "tags"=>["ecology", "Community Ecology", "Community assembly", "microbial ecology", "theoretical ecology", "metacommunity", "casts", "biodiversity", "coexisting", "sampling", "larger"], "article_id"=>189680, "categories"=>["Biological Sciences"], "users"=>["James P. O'Dwyer", "Steven W. Kembel", "Jessica L. Green"], "doi"=>"https://dx.doi.org/10.1371/journal.pcbi.1002832.g001", "stats"=>{"downloads"=>0, "page_views"=>6, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_The_local_community_and_metacommunity_framework_casts_local_biodiversity_of_coexisting_species_in_terms_of_a_sampling_process_from_a_larger_reference_pool_or_metacommunity_/189680", "title"=>"The local community and metacommunity framework casts local biodiversity of coexisting species in terms of a sampling process from a larger reference pool, or metacommunity.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2012-12-20 02:41:20"}
  • {"files"=>["https://ndownloader.figshare.com/files/519744"], "description"=>"<p>We show a comparison of actual PD with expected PD for multiple habitats and subjects. The lefthand panel shows the PD of all habitats sampled from subject F1, with the solid line indicating the expected phylogenetic diversity of a random sample from a metacommunity comprising all reads taken from all subjects, and the dotted line representing an upper bound on the corresponding 95% confidence interval. The right hand panel shows the total branch length for all reads sampled from each subject (again including F1 in black), with solid and dotted lines as on the left hand-side. When local samples are grouped into a single community for each microbiome, all microbiome communities are consistent with clustered sampling. On the other hand, we observe a wide range of variation in habitat PD relative to random sampling.</p>", "links"=>[], "tags"=>["ecology", "Community Ecology", "Community assembly", "microbial ecology", "theoretical ecology", "reveals", "clustered", "overdispersed"], "article_id"=>190231, "categories"=>["Biological Sciences"], "users"=>["James P. O'Dwyer", "Steven W. Kembel", "Jessica L. Green"], "doi"=>"https://dx.doi.org/10.1371/journal.pcbi.1002832.g007", "stats"=>{"downloads"=>1, "page_views"=>5, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Increasing_local_community_resolution_reveals_a_diversity_of_clustered_and_overdispersed_local_samples_/190231", "title"=>"Increasing local community resolution reveals a diversity of clustered and overdispersed local samples.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2012-12-20 00:03:51"}
  • {"files"=>["https://ndownloader.figshare.com/files/519525"], "description"=>"<p>The score is calculated in terms of expected shared branch length and expected total branch length for the two samples. The black line is for samples of the same size, and colored lines are for various differences in sample size, . As becomes a larger fraction of mean sample size, there is an increasing deviation from the expectation value for equal samples sizes, indicating that an appropriate normalization accounting for differing sample sizes is potentially crucial in computing phylogenetic beta diversity for differently-sized samples.</p>", "links"=>[], "tags"=>["ecology", "Community Ecology", "Community assembly", "microbial ecology", "theoretical ecology", "normalized", "samples", "taken"], "article_id"=>190017, "categories"=>["Biological Sciences"], "users"=>["James P. O'Dwyer", "Steven W. Kembel", "Jessica L. Green"], "doi"=>"https://dx.doi.org/10.1371/journal.pcbi.1002832.g005", "stats"=>{"downloads"=>3, "page_views"=>13, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Unifrac_score_normalized_for_different_sample_sizes_for_two_random_samples_taken_from_the_same_theoretical_metacommunity_/190017", "title"=>"Unifrac score normalized for different sample sizes, for two random samples taken from the same theoretical metacommunity.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2012-12-20 00:00:17"}
  • {"files"=>["https://ndownloader.figshare.com/files/519369"], "description"=>"<p>Here we compute the EAD for trees inferred from 16S bacterial microbiome sequences using FastTree <a href=\"http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1002832#pcbi.1002832-Price1\" target=\"_blank\">[47]</a>, for sequences obtained from 7 human subjects across 26 different habitats on a single sample date <a href=\"http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1002832#pcbi.1002832-Costello1\" target=\"_blank\">[11]</a>. On the y-axis is total edge-length summed across all edges with a given number of downstream tips (see <a href=\"http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1002832#pcbi-1002832-g002\" target=\"_blank\">Figure 2</a>) and on the x axis is number of tips grouped into bins, a method commonly used in plotting Species Abundance Distributions <a href=\"http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1002832#pcbi.1002832-Preston1\" target=\"_blank\">[15]</a>. (A) Sequences from all individuals across all body habitats (B–D) Sequences taken from different habitats pooled from all seven subjects. (E–F) Sequences taken from a single subject.</p>", "links"=>[], "tags"=>["ecology", "Community Ecology", "Community assembly", "microbial ecology", "theoretical ecology", "edge-length", "abundance", "follows", "power-law"], "article_id"=>189855, "categories"=>["Biological Sciences"], "users"=>["James P. O'Dwyer", "Steven W. Kembel", "Jessica L. Green"], "doi"=>"https://dx.doi.org/10.1371/journal.pcbi.1002832.g003", "stats"=>{"downloads"=>1, "page_views"=>38, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_The_Edge_length_Abundance_Distribution_EAD_follows_an_approximately_power_law_distribution_/189855", "title"=>"The Edge-length Abundance Distribution (EAD) follows an approximately power-law distribution.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2012-12-20 02:44:15"}

PMC Usage Stats | Further Information

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  • {"unique-ip"=>"2", "full-text"=>"2", "pdf"=>"0", "abstract"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2018", "month"=>"1"}
  • {"unique-ip"=>"10", "full-text"=>"9", "pdf"=>"3", "abstract"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"1", "supp-data"=>"0", "cited-by"=>"1", "year"=>"2018", "month"=>"3"}
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  • {"unique-ip"=>"31", "full-text"=>"27", "pdf"=>"1", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"7", "supp-data"=>"0", "cited-by"=>"1", "year"=>"2018", "month"=>"4"}
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Relative Metric

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