Inferring the Dynamics of Diversification: A Coalescent Approach
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{"title"=>"Inferring the dynamics of diversification: A coalescent approach", "type"=>"journal", "authors"=>[{"first_name"=>"Hélène", "last_name"=>"Morlon", "scopus_author_id"=>"24537368500"}, {"first_name"=>"Matthew D.", "last_name"=>"Potts", "scopus_author_id"=>"7102163967"}, {"first_name"=>"Joshua B.", "last_name"=>"Plotkin", "scopus_author_id"=>"7006104476"}], "year"=>2010, "source"=>"PLoS Biology", "identifiers"=>{"isbn"=>"1545-7885", "pui"=>"359761809", "issn"=>"15449173", "pmid"=>"20927410", "doi"=>"10.1371/journal.pbio.1000493", "sgr"=>"77957907040", "scopus"=>"2-s2.0-77957907040"}, "id"=>"e25efd1c-3a16-3be1-b20b-574c8fbe2aeb", "abstract"=>"A novel approach to infer diversification dynamics shows that biodiversity is still expanding but at a slower rate than in the past.", "link"=>"http://www.mendeley.com/research/inferring-dynamics-diversification-coalescent-approach", "reader_count"=>330, "reader_count_by_academic_status"=>{"Unspecified"=>2, "Professor > Associate Professor"=>28, "Researcher"=>88, "Student > Doctoral Student"=>14, "Student > Ph. D. Student"=>97, "Student > Postgraduate"=>16, "Student > Master"=>26, "Other"=>9, "Student > Bachelor"=>10, "Lecturer"=>7, "Lecturer > Senior Lecturer"=>2, "Professor"=>31}, "reader_count_by_user_role"=>{"Unspecified"=>2, "Professor > Associate Professor"=>28, "Researcher"=>88, "Student > Doctoral Student"=>14, "Student > Ph. D. Student"=>97, "Student > Postgraduate"=>16, "Student > Master"=>26, "Other"=>9, "Student > Bachelor"=>10, "Lecturer"=>7, "Lecturer > Senior Lecturer"=>2, "Professor"=>31}, "reader_count_by_subject_area"=>{"Unspecified"=>7, "Engineering"=>1, "Environmental Science"=>28, "Biochemistry, Genetics and Molecular Biology"=>11, "Mathematics"=>5, "Agricultural and Biological Sciences"=>252, "Medicine and Dentistry"=>1, "Psychology"=>12, "Social Sciences"=>1, "Earth and Planetary Sciences"=>9, "Economics, Econometrics and Finance"=>2, "Linguistics"=>1}, "reader_count_by_subdiscipline"=>{"Engineering"=>{"Engineering"=>1}, "Medicine and Dentistry"=>{"Medicine and Dentistry"=>1}, "Social Sciences"=>{"Social Sciences"=>1}, "Psychology"=>{"Psychology"=>12}, "Earth and Planetary Sciences"=>{"Earth and Planetary Sciences"=>9}, "Economics, Econometrics and Finance"=>{"Economics, Econometrics and Finance"=>2}, "Agricultural and Biological Sciences"=>{"Agricultural and Biological Sciences"=>252}, "Linguistics"=>{"Linguistics"=>1}, "Biochemistry, Genetics and Molecular Biology"=>{"Biochemistry, Genetics and Molecular Biology"=>11}, "Mathematics"=>{"Mathematics"=>5}, "Unspecified"=>{"Unspecified"=>7}, "Environmental Science"=>{"Environmental Science"=>28}}, "reader_count_by_country"=>{"Reunion"=>1, "United States"=>26, "Japan"=>1, "United Kingdom"=>5, "Switzerland"=>3, "Portugal"=>3, "Spain"=>4, "India"=>3, "New Zealand"=>1, "Sweden"=>5, "Austria"=>1, "Norway"=>1, "China"=>1, "Finland"=>1, "Brazil"=>8, "Poland"=>1, "South Africa"=>1, "France"=>8, "Australia"=>4, "Chile"=>1, "Germany"=>5}, "group_count"=>10}

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Figshare

  • {"files"=>["https://ndownloader.figshare.com/files/412125"], "description"=>"<div><p>Recent analyses of the fossil record and molecular phylogenies suggest that there are fundamental limits to biodiversity, possibly arising from constraints in the availability of space, resources, or ecological niches. Under this hypothesis, speciation rates decay over time and biodiversity eventually saturates, with new species emerging only when others are driven to extinction. This view of macro-evolution contradicts an alternative hypothesis that biodiversity is unbounded, with species ever accumulating as they find new niches to occupy. These contrasting theories of biodiversity dynamics yield fundamentally different explanations for the disparity in species richness across taxa and regions. Here, we test whether speciation rates have decayed or remained constant over time, and whether biodiversity is saturated or still expanding. We first derive a general likelihood expression for internode distances in a phylogeny, based on the well-known coalescent process from population genetics. This expression accounts for either time-constant or time-variable rates, time-constant or time-variable diversity, and completely or incompletely sampled phylogenies. We then compare the performance of different diversification scenarios in explaining a set of 289 phylogenies representing amphibians, arthropods, birds, mammals, mollusks, and flowering plants. Our results indicate that speciation rates typically decay over time, but that diversity is still expanding at present. The evidence for expanding-diversity models suggests that an upper limit to biodiversity has not yet been reached, or that no such limit exists.</p></div>", "links"=>[], "tags"=>["inferring", "coalescent"], "article_id"=>141412, "categories"=>["Ecology", "Evolutionary Biology"], "users"=>["Hélène Morlon", "Matthew D. Potts", "Joshua B. Plotkin"], "doi"=>["https://dx.doi.org/10.1371/journal.pbio.1000493"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/Inferring_the_Dynamics_of_Diversification_A_Coalescent_Approach/141412", "title"=>"Inferring the Dynamics of Diversification: A Coalescent Approach", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2010-09-28 00:23:32"}
  • {"files"=>["https://ndownloader.figshare.com/files/827939"], "description"=>"<p>Schematic illustration of the nine diversification models considered in our analyses. The models can be classified according to three broad criteria: diversity is either expanding over time (in red, Models 3–6) or saturated (Models 1 and 2); rates either vary over time (in blue, Models 2, 4a–4d, and 6) or they are constant over time (Models 1, 3, and 5); and extinctions are either present (in green, Models 1–4) or absent (Models 5 and 6). There are four flavors of models that exhibit expanding diversity with time-varying rates and positive extinction: the speciation rate (λ) varies over time while the extinction rate (μ) is constant (Model 4a); the extinction rate varies over time while the speciation rate is constant (Model 4b); both rates vary over time with a constant extinction fraction (; Model 4c); and both rates vary independently over time (Model 4d). When they vary, rates either decay or grow exponentially. The parameters of each model are shown in <a href=\"http://www.plosbiology.org/article/info:doi/10.1371/journal.pbio.1000493#pbio-1000493-t001\" target=\"_blank\">Table 1</a>.</p>", "links"=>[], "tags"=>["ecology", "ecology/community ecology and biodiversity", "ecology/evolutionary ecology", "ecology/theoretical ecology", "Evolutionary biology", "evolutionary biology/evolutionary ecology"], "article_id"=>498296, "categories"=>["Ecology", "Evolutionary Biology"], "users"=>["Hélène Morlon", "Matthew D. Potts", "Joshua B. Plotkin"], "doi"=>["https://dx.doi.org/10.1371/journal.pbio.1000493.g001"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Models_of_diversification_/498296", "title"=>"Models of diversification.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2010-09-28 02:18:16"}
  • {"files"=>["https://ndownloader.figshare.com/files/828099"], "description"=>"<p>Phylogenies simulated under a model with saturated diversity and a constant turnover rate (Model 1) have short terminal branches compared to phylogenies simulated under the pure-birth process (Yule model; Model 5). With saturated diversity but decaying turnover rates, terminal branches become longer (Model 2). Compared to the pure-birth process (Model 5), the presence of extinction pushes phylogenetic nodes towards the tips (Model 3), whereas a decay in speciation rate pushes them towards the root (Model 6). In the presence of both extinction and a decay in speciation rate (Model 4), however, these two effects counteract, producing a phylogeny that appears similar to the pure-birth model. All phylogenies were simulated with the same initial speciation rate (six speciation events per time unit). The extinction rate in Models 3 and 4a was identical (three speciation events per time unit). The exponential variation in speciation rate in Models 2, 4a, and 6 was identical (0.25 per time unit). Note the different time scales.</p>", "links"=>[], "tags"=>["phylogenies", "resulting", "diversification"], "article_id"=>498470, "categories"=>["Ecology", "Evolutionary Biology"], "users"=>["Hélène Morlon", "Matthew D. Potts", "Joshua B. Plotkin"], "doi"=>["https://dx.doi.org/10.1371/journal.pbio.1000493.g002"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Example_phylogenies_resulting_from_different_diversification_models_/498470", "title"=>"Example phylogenies resulting from different diversification models.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2010-09-28 02:21:10"}
  • {"files"=>["https://ndownloader.figshare.com/files/828202"], "description"=>"<p>The figure shows maximum likelihood parameter estimates for phylogenies simulated under Model 4a (extinction rate is constant over time and speciation rate decays exponentially). The true, simulated parameters of diversification are indicated by dashed lines (expressed in number of events per time unit). Points and error bars indicate the median and 95% quantile range of the maximum likelihood parameter estimates, across 1,000 simulated phylogenies for each parameter set. The right column shows the estimated extinction rate at present, compared to its true, simulated value. Before estimating parameters, species were randomly sampled from the simulated phylogenies. In the left and middle columns the sampling fraction <i>f</i> ranged from 10% of species (poorly sampled) to 100% of species (fully sampled). In the right column, <i>f</i> = 75% of species were sampled. MRCA, time at the most recent common ancestor.</p>", "links"=>[], "tags"=>["coalescent", "provides", "robust", "estimates", "diversification", "rates", "incompletely", "sampled"], "article_id"=>498559, "categories"=>["Ecology", "Evolutionary Biology"], "users"=>["Hélène Morlon", "Matthew D. Potts", "Joshua B. Plotkin"], "doi"=>["https://dx.doi.org/10.1371/journal.pbio.1000493.g003"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_The_coalescent_method_provides_robust_estimates_of_diversification_rates_from_incompletely_sampled_phylogenies_/498559", "title"=>"The coalescent method provides robust estimates of diversification rates from incompletely sampled phylogenies.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2010-09-28 02:22:39"}
  • {"files"=>["https://ndownloader.figshare.com/files/828297"], "description"=>"<p>Each bar represents the probability—measured as the Akaike weight—that the phylogeny arises from the corresponding model, among the set of nine models considered. The phylogeny of the genus <i>Bursera</i>, comprising 73% of known species in that genus, overwhelmingly supports Model 2. Thus, the <i>Bursera</i> phylogeny is consistent with the hypotheses that diversity is saturated and that the turnover rate varies over time. The phylogeny of the genus <i>Bicyclus</i>, comprising 68% of known species, is consistent with the hypotheses that diversity is expanding and that speciation rates vary. The phylogeny of the genus <i>Cicindela</i>, comprising 84% of recognized species, is also largely consistent with the hypotheses that diversity expands and rates vary. However, the dynamics of diversification are less clear-cut in the <i>Cicindela</i> phylogeny, because models with saturated diversity and constant rates also have positive probabilities. Although there is high confidence for the presence of extinction in the phylogeny of <i>Bursera</i>, models with or without extinction are about equally likely in the phylogenies of <i>Bicyclus</i> and <i>Cicindela</i>. Models with time-varying diversification rates are written in blue text.</p>", "links"=>[], "tags"=>["diversification", "empirical"], "article_id"=>498669, "categories"=>["Ecology", "Evolutionary Biology"], "users"=>["Hélène Morlon", "Matthew D. Potts", "Joshua B. Plotkin"], "doi"=>["https://dx.doi.org/10.1371/journal.pbio.1000493.g004"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Dynamics_of_diversification_in_three_empirical_phylogenies_/498669", "title"=>"Dynamics of diversification in three empirical phylogenies.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2010-09-28 02:24:29"}
  • {"files"=>["https://ndownloader.figshare.com/files/828408"], "description"=>"<p>The red histogram shows, for each of the 289 phylogenies, the relative probability of the best model with expanding diversity versus the best model with saturated diversity. The blue histogram shows the relative probability of the best model with time-varying rates versus the best model with constant rates. The green histogram shows the relative probability of the best model with positive extinction versus the best model without extinction. The relative probabilities of two models are calculated using their Akaike weights. Most empirical phylogenies are consistent with the hypotheses that diversity is expanding (in red) and that speciation rates vary through time (in blue). Extinction is not detected in most phylogenies (in green).</p>", "links"=>[], "tags"=>["diversification", "289", "empirical"], "article_id"=>498778, "categories"=>["Ecology", "Evolutionary Biology"], "users"=>["Hélène Morlon", "Matthew D. Potts", "Joshua B. Plotkin"], "doi"=>["https://dx.doi.org/10.1371/journal.pbio.1000493.g005"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Dynamics_of_diversification_among_289_empirical_phylogenies_/498778", "title"=>"Dynamics of diversification among 289 empirical phylogenies.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2010-09-28 02:26:18"}
  • {"files"=>["https://ndownloader.figshare.com/files/828469"], "description"=>"<p>The final column indicates, for each model, the number and percentage of the 289 empirical phylogenies for which the model exhibits the lowest AICc.</p>", "links"=>[], "tags"=>["diversification", "empirical"], "article_id"=>498835, "categories"=>["Ecology", "Evolutionary Biology"], "users"=>["Hélène Morlon", "Matthew D. Potts", "Joshua B. Plotkin"], "doi"=>["https://dx.doi.org/10.1371/journal.pbio.1000493.t001"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Nine_diversification_models_their_parameters_and_empirical_support_/498835", "title"=>"Nine diversification models, their parameters, and empirical support.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2010-09-28 02:27:15"}

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Relative Metric

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