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}, "data": { "key": "X2RH3WIG", "version": 192, "parentItem": "E3VBTNJJ", "itemType": "attachment", "linkMode": "linked_url", "title": "PubMed entry", "accessDate": "2017-03-02T23:18:32Z", "url": "http://www.ncbi.nlm.nih.gov/pubmed/28166715", "note": "", "contentType": "text/html", "charset": "", "tags": [], "relations": {}, "dateAdded": "2017-03-02T23:21:38Z", "dateModified": "2017-03-02T23:21:38Z" } }, { "key": "P8B76ADF", "version": 192, "library": { "type": "group", "id": 115830, "name": "Computational Evolution Group", "links": { "alternate": { "href": "https://www.zotero.org/groups/computational_evolution_group", "type": "text/html" } } }, "links": { "self": { "href": "https://api.zotero.org/groups/115830/items/P8B76ADF", "type": "application/json" }, "alternate": { "href": "https://www.zotero.org/groups/computational_evolution_group/items/P8B76ADF", "type": "text/html" }, "up": { "href": "https://api.zotero.org/groups/115830/items/2KN6GH8V", "type": "application/json" } }, "meta": { "createdByUser": { "id": 1202954, "username": "alexeidrummond", "name": "Alexei Drummond", "links": { "alternate": { "href": "https://www.zotero.org/alexeidrummond", "type": "text/html" } } } }, "data": { "key": "P8B76ADF", "version": 192, "parentItem": "2KN6GH8V", "itemType": "attachment", "linkMode": "linked_url", "title": "PubMed entry", "accessDate": "2017-03-02T23:19:22Z", "url": "http://www.ncbi.nlm.nih.gov/pubmed/27189573", "note": "", "contentType": "text/html", "charset": "", "tags": [], "relations": {}, "dateAdded": "2017-03-02T23:21:38Z", "dateModified": "2017-03-02T23:21:38Z" } }, { "key": "BTUA6WC5", "version": 192, "library": { "type": "group", "id": 115830, "name": "Computational Evolution Group", "links": { "alternate": { "href": "https://www.zotero.org/groups/computational_evolution_group", "type": "text/html" } } }, "links": { "self": { "href": "https://api.zotero.org/groups/115830/items/BTUA6WC5", "type": "application/json" }, "alternate": { "href": "https://www.zotero.org/groups/computational_evolution_group/items/BTUA6WC5", "type": "text/html" } }, "meta": { "createdByUser": { "id": 1202954, "username": "alexeidrummond", "name": "Alexei Drummond", "links": { "alternate": { "href": "https://www.zotero.org/alexeidrummond", "type": "text/html" } } }, "creatorSummary": "Vaughan et al.", "parsedDate": "2017-02", "numChildren": 1 }, "data": { "key": "BTUA6WC5", "version": 192, "itemType": "journalArticle", "title": "Inferring Ancestral Recombination Graphs from Bacterial Genomic Data", "creators": [ { "creatorType": "author", "firstName": "Timothy G.", "lastName": "Vaughan" }, { "creatorType": "author", "firstName": "David", "lastName": "Welch" }, { "creatorType": "author", "firstName": "Alexei J.", "lastName": "Drummond" }, { "creatorType": "author", "firstName": "Patrick J.", "lastName": "Biggs" }, { "creatorType": "author", "firstName": "Tessy", "lastName": "George" }, { "creatorType": "author", "firstName": "Nigel P.", "lastName": "French" } ], "abstractNote": "Homologous recombination is a central feature of bacterial evolution, yet it confounds traditional phylogenetic methods. While a number of methods specific to bacterial evolution have been developed, none of these permit joint inference of a bacterial recombination graph and associated parameters. In this article, we present a new method which addresses this shortcoming. Our method uses a novel Markov chain Monte Carlo algorithm to perform phylogenetic inference under the ClonalOrigin model. We demonstrate the utility of our method by applying it to ribosomal multilocus sequence typing data sequenced from pathogenic and nonpathogenic Escherichia coli serotype O157 and O26 isolates collected in rural New Zealand. The method is implemented as an open source BEAST 2 package, Bacter, which is available via the project web page at http://tgvaughan.github.io/bacter.", "publicationTitle": "Genetics", "publisher": "", "place": "", "date": "Feb 2017", "volume": "205", "issue": "2", "section": "", "partNumber": "", "partTitle": "", "pages": "857-870", "series": "", "seriesTitle": "", "seriesText": "", "journalAbbreviation": "Genetics", "DOI": "10.1534/genetics.116.193425", "citationKey": "", "url": "", "accessDate": "", "PMID": "", "PMCID": "", "ISSN": "1943-2631", "archive": "", "archiveLocation": "", "shortTitle": "", "language": "eng", "libraryCatalog": "PubMed", "callNumber": "", "rights": "", "extra": "PMID: 28007885\nPMCID: PMC5289856", "tags": [ { "tag": "bacterial evolution", "type": 1 }, { "tag": "phylogenetic inference", "type": 1 }, { "tag": "recombination", "type": 1 } ], "collections": [ "NK3JMAQM" ], "relations": {}, "dateAdded": "2017-03-02T23:21:38Z", "dateModified": "2017-03-02T23:21:38Z" } }, { "key": "J3IK96GP", "version": 192, "library": { "type": "group", "id": 115830, "name": "Computational Evolution Group", "links": { "alternate": { "href": "https://www.zotero.org/groups/computational_evolution_group", "type": "text/html" } } }, "links": { "self": { "href": "https://api.zotero.org/groups/115830/items/J3IK96GP", "type": "application/json" }, "alternate": { "href": "https://www.zotero.org/groups/computational_evolution_group/items/J3IK96GP", "type": "text/html" } }, "meta": { "createdByUser": { "id": 1202954, "username": "alexeidrummond", "name": "Alexei Drummond", "links": { "alternate": { "href": "https://www.zotero.org/alexeidrummond", "type": "text/html" } } }, "creatorSummary": "Gavryushkina et al.", "parsedDate": "2017-01-01", "numChildren": 1 }, "data": { "key": "J3IK96GP", "version": 192, "itemType": "journalArticle", "title": "Bayesian Total-Evidence Dating Reveals the Recent Crown Radiation of Penguins", "creators": [ { "creatorType": "author", "firstName": "Alexandra", "lastName": "Gavryushkina" }, { "creatorType": "author", "firstName": "Tracy A.", "lastName": "Heath" }, { "creatorType": "author", "firstName": "Daniel T.", "lastName": "Ksepka" }, { "creatorType": "author", "firstName": "Tanja", "lastName": "Stadler" }, { "creatorType": "author", "firstName": "David", "lastName": "Welch" }, { "creatorType": "author", "firstName": "Alexei J.", "lastName": "Drummond" } ], "abstractNote": "", "publicationTitle": "Systematic Biology", "publisher": "", "place": "", "date": "Jan 01, 2017", "volume": "66", "issue": "1", "section": "", "partNumber": "", "partTitle": "", "pages": "57-73", "series": "", "seriesTitle": "", "seriesText": "", "journalAbbreviation": "Syst. Biol.", "DOI": "10.1093/sysbio/syw060", "citationKey": "", "url": "", "accessDate": "", "PMID": "", "PMCID": "", "ISSN": "1076-836X", "archive": "", "archiveLocation": "", "shortTitle": "", "language": "eng", "libraryCatalog": "PubMed", "callNumber": "", "rights": "", "extra": "PMID: 28173531", "tags": [], "collections": [ "NK3JMAQM" ], "relations": {}, "dateAdded": "2017-03-02T23:21:38Z", "dateModified": "2017-03-02T23:21:38Z" } }, { "key": "XHGQGAJX", "version": 192, "library": { "type": "group", "id": 115830, "name": "Computational Evolution Group", "links": { "alternate": { "href": "https://www.zotero.org/groups/computational_evolution_group", "type": "text/html" } } }, "links": { "self": { "href": "https://api.zotero.org/groups/115830/items/XHGQGAJX", "type": "application/json" }, "alternate": { "href": "https://www.zotero.org/groups/computational_evolution_group/items/XHGQGAJX", "type": "text/html" } }, "meta": { "createdByUser": { "id": 1202954, "username": "alexeidrummond", "name": "Alexei Drummond", "links": { "alternate": { "href": "https://www.zotero.org/alexeidrummond", "type": "text/html" } } }, "creatorSummary": "Gavryushkin and Drummond", "parsedDate": "2016-08-21", "numChildren": 1 }, "data": { "key": "XHGQGAJX", "version": 192, "itemType": "journalArticle", "title": "The space of ultrametric phylogenetic trees", "creators": [ { "creatorType": "author", "firstName": "Alex", "lastName": "Gavryushkin" }, { "creatorType": "author", "firstName": "Alexei J.", "lastName": "Drummond" } ], "abstractNote": "The reliability of a phylogenetic inference method from genomic sequence data is ensured by its statistical consistency. Bayesian inference methods produce a sample of phylogenetic trees from the posterior distribution given sequence data. Hence the question of statistical consistency of such methods is equivalent to the consistency of the summary of the sample. More generally, statistical consistency is ensured by the tree space used to analyse the sample. In this paper, we consider two standard parameterisations of phylogenetic time-trees used in evolutionary models: inter-coalescent interval lengths and absolute times of divergence events. For each of these parameterisations we introduce a natural metric space on ultrametric phylogenetic trees. We compare the introduced spaces with existing models of tree space and formulate several formal requirements that a metric space on phylogenetic trees must possess in order to be a satisfactory space for statistical analysis, and justify them. We show that only a few known constructions of the space of phylogenetic trees satisfy these requirements. However, our results suggest that these basic requirements are not enough to distinguish between the two metric spaces we introduce and that the choice between metric spaces requires additional properties to be considered. Particularly, that the summary tree minimising the square distance to the trees from the sample might be different for different parameterisations. This suggests that further fundamental insight is needed into the problem of statistical consistency of phylogenetic inference methods.", "publicationTitle": "Journal of Theoretical Biology", "publisher": "", "place": "", "date": "Aug 21, 2016", "volume": "403", "issue": "", "section": "", "partNumber": "", "partTitle": "", "pages": "197-208", "series": "", "seriesTitle": "", "seriesText": "", "journalAbbreviation": "J. Theor. Biol.", "DOI": "10.1016/j.jtbi.2016.05.001", "citationKey": "", "url": "", "accessDate": "", "PMID": "", "PMCID": "", "ISSN": "1095-8541", "archive": "", "archiveLocation": "", "shortTitle": "", "language": "eng", "libraryCatalog": "PubMed", "callNumber": "", "rights": "", "extra": "PMID: 27188249", "tags": [ { "tag": "CAT(0)", "type": 1 }, { "tag": "Curvature", "type": 1 }, { "tag": "Geodesic", "type": 1 }, { "tag": "Phylogenetic tree", "type": 1 }, { "tag": "Posterior distribution summary", "type": 1 }, { "tag": "Simplicial complex", "type": 1 }, { "tag": "Time-tree", "type": 1 }, { "tag": "Ultrametric tree", "type": 1 }, { "tag": "phylogenetic inference", "type": 1 } ], "collections": [ "NK3JMAQM" ], "relations": {}, "dateAdded": "2017-03-02T23:21:38Z", "dateModified": "2017-03-02T23:21:38Z" } }, { "key": "JM4FE95G", "version": 192, "library": { "type": "group", "id": 115830, "name": "Computational Evolution Group", "links": { "alternate": { "href": "https://www.zotero.org/groups/computational_evolution_group", "type": "text/html" } } }, "links": { "self": { "href": "https://api.zotero.org/groups/115830/items/JM4FE95G", "type": "application/json" }, "alternate": { "href": "https://www.zotero.org/groups/computational_evolution_group/items/JM4FE95G", "type": "text/html" } }, "meta": { "createdByUser": { "id": 1202954, "username": "alexeidrummond", "name": "Alexei Drummond", "links": { "alternate": { "href": "https://www.zotero.org/alexeidrummond", "type": "text/html" } } }, "creatorSummary": "Drummond and Stadler", "parsedDate": "2016-07-19", "numChildren": 1 }, "data": { "key": "JM4FE95G", "version": 192, "itemType": "journalArticle", "title": "Bayesian phylogenetic estimation of fossil ages", "creators": [ { "creatorType": "author", "firstName": "Alexei J.", "lastName": "Drummond" }, { "creatorType": "author", "firstName": "Tanja", "lastName": "Stadler" } ], "abstractNote": "Recent advances have allowed for both morphological fossil evidence and molecular sequences to be integrated into a single combined inference of divergence dates under the rule of Bayesian probability. In particular, the fossilized birth-death tree prior and the Lewis-Mk model of discrete morphological evolution allow for the estimation of both divergence times and phylogenetic relationships between fossil and extant taxa. We exploit this statistical framework to investigate the internal consistency of these models by producing phylogenetic estimates of the age of each fossil in turn, within two rich and well-characterized datasets of fossil and extant species (penguins and canids). We find that the estimation accuracy of fossil ages is generally high with credible intervals seldom excluding the true age and median relative error in the two datasets of 5.7% and 13.2%, respectively. The median relative standard error (RSD) was 9.2% and 7.2%, respectively, suggesting good precision, although with some outliers. In fact, in the two datasets we analyse, the phylogenetic estimate of fossil age is on average less than 2 Myr from the mid-point age of the geological strata from which it was excavated. The high level of internal consistency found in our analyses suggests that the Bayesian statistical model employed is an adequate fit for both the geological and morphological data, and provides evidence from real data that the framework used can accurately model the evolution of discrete morphological traits coded from fossil and extant taxa. We anticipate that this approach will have diverse applications beyond divergence time dating, including dating fossils that are temporally unconstrained, testing of the 'morphological clock', and for uncovering potential model misspecification and/or data errors when controversial phylogenetic hypotheses are obtained based on combined divergence dating analyses.This article is part of the themed issue 'Dating species divergences using rocks and clocks'.", "publicationTitle": "Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences", "publisher": "", "place": "", "date": "Jul 19, 2016", "volume": "371", "issue": "1699", "section": "", "partNumber": "", "partTitle": "", "pages": "", "series": "", "seriesTitle": "", "seriesText": "", "journalAbbreviation": "Philos. Trans. R. Soc. Lond., B, Biol. Sci.", "DOI": "10.1098/rstb.2015.0129", "citationKey": "", "url": "", "accessDate": "", "PMID": "", "PMCID": "", "ISSN": "1471-2970", "archive": "", "archiveLocation": "", "shortTitle": "", "language": "eng", "libraryCatalog": "PubMed", "callNumber": "", "rights": "", "extra": "PMID: 27325827\nPMCID: PMC4920331", "tags": [ { "tag": "Bayesian phylogenetics", "type": 1 }, { "tag": "divergence time dating", "type": 1 }, { "tag": "fossil dating", "type": 1 }, { "tag": "morphological clock", "type": 1 }, { "tag": "morphological evolution", "type": 1 }, { "tag": "phylogenetic inference", "type": 1 } ], "collections": [ "NK3JMAQM" ], "relations": {}, "dateAdded": "2017-03-02T23:21:38Z", "dateModified": "2017-03-02T23:21:38Z" } }, { "key": "PBEIHJ32", "version": 192, "library": { "type": "group", "id": 115830, "name": "Computational Evolution Group", "links": { "alternate": { "href": "https://www.zotero.org/groups/computational_evolution_group", "type": "text/html" } } }, "links": { "self": { "href": "https://api.zotero.org/groups/115830/items/PBEIHJ32", "type": "application/json" }, "alternate": { "href": "https://www.zotero.org/groups/computational_evolution_group/items/PBEIHJ32", "type": "text/html" }, "up": { "href": "https://api.zotero.org/groups/115830/items/J3IK96GP", "type": "application/json" } }, "meta": { "createdByUser": { "id": 1202954, "username": "alexeidrummond", "name": "Alexei Drummond", "links": { "alternate": { "href": "https://www.zotero.org/alexeidrummond", "type": "text/html" } } } }, "data": { "key": "PBEIHJ32", "version": 192, "parentItem": "J3IK96GP", "itemType": "attachment", "linkMode": "linked_url", "title": "PubMed entry", "accessDate": "2017-03-02T23:18:51Z", "url": "http://www.ncbi.nlm.nih.gov/pubmed/28173531", "note": "", "contentType": "text/html", "charset": "", "tags": [], "relations": {}, "dateAdded": "2017-03-02T23:21:38Z", "dateModified": "2017-03-02T23:21:38Z" } }, { "key": "N92BEM89", "version": 192, "library": { "type": "group", 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"itemType": "attachment", "linkMode": "linked_url", "title": "PubMed entry", "accessDate": "2017-03-02T23:19:10Z", "url": "http://www.ncbi.nlm.nih.gov/pubmed/27188249", "note": "", "contentType": "text/html", "charset": "", "tags": [], "relations": {}, "dateAdded": "2017-03-02T23:21:38Z", "dateModified": "2017-03-02T23:21:38Z" } }, { "key": "3NREJUGK", "version": 192, "library": { "type": "group", "id": 115830, "name": "Computational Evolution Group", "links": { "alternate": { "href": "https://www.zotero.org/groups/computational_evolution_group", "type": "text/html" } } }, "links": { "self": { "href": "https://api.zotero.org/groups/115830/items/3NREJUGK", "type": "application/json" }, "alternate": { "href": "https://www.zotero.org/groups/computational_evolution_group/items/3NREJUGK", "type": "text/html" }, "up": { "href": "https://api.zotero.org/groups/115830/items/JM4FE95G", "type": "application/json" } }, "meta": { "createdByUser": { "id": 1202954, "username": "alexeidrummond", "name": "Alexei Drummond", "links": { "alternate": { "href": "https://www.zotero.org/alexeidrummond", "type": "text/html" } } } }, "data": { "key": "3NREJUGK", "version": 192, "parentItem": "JM4FE95G", "itemType": "attachment", "linkMode": "linked_url", "title": "PubMed entry", "accessDate": "2017-03-02T23:19:37Z", "url": "http://www.ncbi.nlm.nih.gov/pubmed/27325827", "note": "", "contentType": "text/html", "charset": "", "tags": [], "relations": {}, "dateAdded": "2017-03-02T23:21:38Z", "dateModified": "2017-03-02T23:21:38Z" } }, { "key": "E3VBTNJJ", "version": 192, "library": { "type": "group", "id": 115830, "name": "Computational Evolution Group", "links": { "alternate": { "href": "https://www.zotero.org/groups/computational_evolution_group", "type": "text/html" } } }, "links": { "self": { "href": "https://api.zotero.org/groups/115830/items/E3VBTNJJ", "type": "application/json" }, "alternate": { "href": "https://www.zotero.org/groups/computational_evolution_group/items/E3VBTNJJ", "type": "text/html" } }, "meta": { "createdByUser": { "id": 1202954, "username": "alexeidrummond", "name": "Alexei Drummond", "links": { "alternate": { "href": "https://www.zotero.org/alexeidrummond", "type": "text/html" } } }, "creatorSummary": "Bouckaert and Drummond", "parsedDate": "2017-02-06", "numChildren": 1 }, "data": { "key": "E3VBTNJJ", "version": 192, "itemType": "journalArticle", "title": "bModelTest: Bayesian phylogenetic site model averaging and model comparison", "creators": [ { "creatorType": "author", "firstName": "Remco R.", "lastName": "Bouckaert" }, { "creatorType": "author", "firstName": "Alexei J.", "lastName": "Drummond" } ], "abstractNote": "BACKGROUND: Reconstructing phylogenies through Bayesian methods has many benefits, which include providing a mathematically sound framework, providing realistic estimates of uncertainty and being able to incorporate different sources of information based on formal principles. Bayesian phylogenetic analyses are popular for interpreting nucleotide sequence data, however for such studies one needs to specify a site model and associated substitution model. Often, the parameters of the site model is of no interest and an ad-hoc or additional likelihood based analysis is used to select a single site model.\nRESULTS: bModelTest allows for a Bayesian approach to inferring and marginalizing site models in a phylogenetic analysis. It is based on trans-dimensional Markov chain Monte Carlo (MCMC) proposals that allow switching between substitution models as well as estimating the posterior probability for gamma-distributed rate heterogeneity, a proportion of invariable sites and unequal base frequencies. The model can be used with the full set of time-reversible models on nucleotides, but we also introduce and demonstrate the use of two subsets of time-reversible substitution models.\nCONCLUSION: With the new method the site model can be inferred (and marginalized) during the MCMC analysis and does not need to be pre-determined, as is now often the case in practice, by likelihood-based methods. The method is implemented in the bModelTest package of the popular BEAST 2 software, which is open source, licensed under the GNU Lesser General Public License and allows joint site model and tree inference under a wide range of models.", "publicationTitle": "BMC evolutionary biology", "publisher": "", "place": "", "date": "Feb 06, 2017", "volume": "17", "issue": "1", "section": "", "partNumber": "", "partTitle": "", "pages": "42", "series": "", "seriesTitle": "", "seriesText": "", "journalAbbreviation": "BMC Evol. Biol.", "DOI": "10.1186/s12862-017-0890-6", "citationKey": "", "url": "", "accessDate": "", "PMID": "", "PMCID": "", "ISSN": "1471-2148", "archive": "", "archiveLocation": "", "shortTitle": "bModelTest", "language": "eng", "libraryCatalog": "PubMed", "callNumber": "", "rights": "", "extra": "PMID: 28166715\nPMCID: PMC5294809", "tags": [ { "tag": "Model selection", "type": 1 }, { "tag": "ModelTest", "type": 1 }, { "tag": "Phylogenetic model averaging", "type": 1 }, { "tag": "Phylogenetic model comparison", "type": 1 }, { "tag": "Site model", "type": 1 }, { "tag": "Statistical phylogenetics", "type": 1 }, { "tag": "Substitution model", "type": 1 }, { "tag": "model averaging", "type": 1 }, { "tag": "model comparison", "type": 1 } ], "collections": [ "NK3JMAQM" ], "relations": {}, "dateAdded": "2017-03-02T23:21:38Z", "dateModified": "2017-03-02T23:21:38Z" } }, { "key": "F9VCWKGK", "version": 192, "library": { "type": "group", "id": 115830, "name": "Computational Evolution Group", "links": { "alternate": { "href": "https://www.zotero.org/groups/computational_evolution_group", "type": "text/html" } } }, "links": { "self": { "href": "https://api.zotero.org/groups/115830/items/F9VCWKGK", "type": "application/json" }, "alternate": { "href": "https://www.zotero.org/groups/computational_evolution_group/items/F9VCWKGK", "type": "text/html" } }, "meta": { "createdByUser": { "id": 1202954, "username": "alexeidrummond", "name": "Alexei Drummond", "links": { "alternate": { "href": "https://www.zotero.org/alexeidrummond", "type": "text/html" } } }, "creatorSummary": "Ogilvie et al.", "parsedDate": "2016-05", "numChildren": 1 }, "data": { "key": "F9VCWKGK", "version": 192, "itemType": "journalArticle", "title": "Computational Performance and Statistical Accuracy of *BEAST and Comparisons with Other Methods", "creators": [ { "creatorType": "author", "firstName": "Huw A.", "lastName": "Ogilvie" }, { "creatorType": "author", "firstName": "Joseph", "lastName": "Heled" }, { "creatorType": "author", "firstName": "Dong", "lastName": "Xie" }, { "creatorType": "author", "firstName": "Alexei J.", "lastName": "Drummond" } ], "abstractNote": "Under the multispecies coalescent model of molecular evolution, gene trees have independent evolutionary histories within a shared species tree. In comparison, supermatrix concatenation methods assume that gene trees share a single common genealogical history, thereby equating gene coalescence with species divergence. The multispecies coalescent is supported by previous studies which found that its predicted distributions fit empirical data, and that concatenation is not a consistent estimator of the species tree. *BEAST, a fully Bayesian implementation of the multispecies coalescent, is popular but computationally intensive, so the increasing size of phylogenetic data sets is both a computational challenge and an opportunity for better systematics. Using simulation studies, we characterize the scaling behavior of *BEAST, and enable quantitative prediction of the impact increasing the number of loci has on both computational performance and statistical accuracy. Follow-up simulations over a wide range of parameters show that the statistical performance of *BEAST relative to concatenation improves both as branch length is reduced and as the number of loci is increased. Finally, using simulations based on estimated parameters from two phylogenomic data sets, we compare the performance of a range of species tree and concatenation methods to show that using *BEAST with tens of loci can be preferable to using concatenation with thousands of loci. Our results provide insight into the practicalities of Bayesian species tree estimation, the number of loci required to obtain a given level of accuracy and the situations in which supermatrix or summary methods will be outperformed by the fully Bayesian multispecies coalescent.", "publicationTitle": "Systematic Biology", "publisher": "", "place": "", "date": "May 2016", "volume": "65", "issue": "3", "section": "", "partNumber": "", "partTitle": "", "pages": "381-396", "series": "", "seriesTitle": "", "seriesText": "", "journalAbbreviation": "Syst. Biol.", "DOI": "10.1093/sysbio/syv118", "citationKey": "", "url": "", "accessDate": "", "PMID": "", "PMCID": "", "ISSN": "1076-836X", "archive": "", "archiveLocation": "", "shortTitle": "", "language": "eng", "libraryCatalog": "PubMed", "callNumber": "", "rights": "", "extra": "PMID: 26821913\nPMCID: PMC4851174", "tags": [ { "tag": "Bayesian phylogenetics", "type": 1 }, { "tag": "Concatenation", "type": 1 }, { "tag": "Gene tree", "type": 1 }, { "tag": "Multispecies coalescent", "type": 1 }, { "tag": "Phylogenomics", "type": 1 }, { "tag": "Species tree", "type": 1 }, { "tag": "Supermatrix", "type": 1 } ], "collections": [ "NK3JMAQM" ], "relations": {}, "dateAdded": "2017-03-02T23:21:38Z", "dateModified": "2017-03-02T23:21:38Z" } }, { "key": "2KN6GH8V", "version": 192, "library": { "type": "group", "id": 115830, "name": "Computational Evolution Group", "links": { "alternate": { "href": "https://www.zotero.org/groups/computational_evolution_group", "type": "text/html" } } }, "links": { "self": { "href": "https://api.zotero.org/groups/115830/items/2KN6GH8V", "type": "application/json" }, "alternate": { "href": "https://www.zotero.org/groups/computational_evolution_group/items/2KN6GH8V", "type": "text/html" } }, "meta": { "createdByUser": { "id": 1202954, "username": "alexeidrummond", "name": "Alexei Drummond", "links": { "alternate": { "href": "https://www.zotero.org/alexeidrummond", "type": "text/html" } } }, "creatorSummary": "Kühnert et al.", "parsedDate": "2016-08", "numChildren": 1 }, "data": { "key": "2KN6GH8V", "version": 192, "itemType": "journalArticle", "title": "Phylodynamics with Migration: A Computational Framework to Quantify Population Structure from Genomic Data", "creators": [ { "creatorType": "author", "firstName": "Denise", "lastName": "Kühnert" }, { "creatorType": "author", "firstName": "Tanja", "lastName": "Stadler" }, { "creatorType": "author", "firstName": "Timothy G.", "lastName": "Vaughan" }, { "creatorType": "author", "firstName": "Alexei J.", "lastName": "Drummond" } ], "abstractNote": "When viruses spread, outbreaks can be spawned in previously unaffected regions. Depending on the time and mode of introduction, each regional outbreak can have its own epidemic dynamics. The migration and phylodynamic processes are often intertwined and need to be taken into account when analyzing temporally and spatially structured virus data. In this article, we present a fully probabilistic approach for the joint reconstruction of phylodynamic history in structured populations (such as geographic structure) based on a multitype birth-death process. This approach can be used to quantify the spread of a pathogen in a structured population. Changes in epidemic dynamics through time within subpopulations are incorporated through piecewise constant changes in transmission parameters.We analyze a global human influenza H3N2 virus data set from a geographically structured host population to demonstrate how seasonal dynamics can be inferred simultaneously with the phylogeny and migration process. Our results suggest that the main migration path among the northern, tropical, and southern region represented in the sample analyzed here is the one leading from the tropics to the northern region. Furthermore, the time-dependent transmission dynamics between and within two HIV risk groups, heterosexuals and injecting drug users, in the Latvian HIV epidemic are investigated. Our analyses confirm that the Latvian HIV epidemic peaking around 2001 was mainly driven by the injecting drug user risk group.", "publicationTitle": "Molecular Biology and Evolution", "publisher": "", "place": "", "date": "Aug 2016", "volume": "33", "issue": "8", "section": "", "partNumber": "", "partTitle": "", "pages": "2102-2116", "series": "", "seriesTitle": "", "seriesText": "", "journalAbbreviation": "Mol. Biol. Evol.", "DOI": "10.1093/molbev/msw064", "citationKey": "", "url": "", "accessDate": "", "PMID": "", "PMCID": "", "ISSN": "1537-1719", "archive": "", "archiveLocation": "", "shortTitle": "Phylodynamics with Migration", "language": "eng", "libraryCatalog": "PubMed", "callNumber": "", "rights": "", "extra": "PMID: 27189573\nPMCID: PMC4948704", "tags": [ { "tag": "Bayesian inference", "type": 1 }, { "tag": "Phylogeography", "type": 1 }, { "tag": "biogeography", "type": 1 }, { "tag": "birth-death model", "type": 1 }, { "tag": "epidemiology", "type": 1 }, { "tag": "infectious diseases", "type": 1 } ], "collections": [ "NK3JMAQM" ], "relations": {}, "dateAdded": "2017-03-02T23:21:38Z", "dateModified": "2017-03-02T23:21:38Z" } }, { "key": "B3A22FDJ", "version": 190, "library": { "type": "group", "id": 115830, "name": "Computational Evolution Group", "links": { "alternate": { "href": "https://www.zotero.org/groups/computational_evolution_group", "type": "text/html" } } }, "links": { "self": { "href": "https://api.zotero.org/groups/115830/items/B3A22FDJ", "type": "application/json" }, "alternate": { "href": "https://www.zotero.org/groups/computational_evolution_group/items/B3A22FDJ", "type": "text/html" } }, "meta": { "createdByUser": { "id": 1202954, "username": "alexeidrummond", "name": "Alexei Drummond", "links": { "alternate": { "href": "https://www.zotero.org/alexeidrummond", "type": "text/html" } } }, "creatorSummary": "Drummond and Bouckaert", "parsedDate": "2015", "numChildren": 0 }, "data": { "key": "B3A22FDJ", "version": 190, "itemType": "book", "title": "Bayesian evolutionary analysis ; with BEAST", "creators": [ { "creatorType": "author", "firstName": "Alexei J.", "lastName": "Drummond" }, { "creatorType": "author", "firstName": "Remco R.", "lastName": "Bouckaert" } ], "abstractNote": "", "series": "", "seriesNumber": "", "volume": "", "numberOfVolumes": "", "edition": "", "date": "2015", "publisher": "Cambridge University Press", "place": "Cambridge, United Kingdom", "originalDate": "", "originalPublisher": "", "originalPlace": "", "format": "", "numPages": "", "ISBN": "9781107019652", "DOI": "", "citationKey": "", "url": "", "accessDate": "", "ISSN": "", "archive": "", "archiveLocation": "", "shortTitle": "", "language": "", "libraryCatalog": "Library of Congress ISBN", "callNumber": "QH83 .D78 2015", "rights": "", "extra": "", "tags": [ { "tag": "Bayesian statistical decision theory", "type": 1 }, { "tag": "Cladistic analysis", "type": 1 }, { "tag": "Data processing", "type": 1 } ], "collections": [ "NK3JMAQM" ], "relations": {}, "dateAdded": "2015-10-12T21:32:30Z", "dateModified": "2015-10-12T23:19:21Z" } }, { "key": "IE2ZA9HU", "version": 193, "library": { "type": "group", "id": 115830, "name": "Computational Evolution Group", "links": { "alternate": { "href": "https://www.zotero.org/groups/computational_evolution_group", "type": "text/html" } } }, "links": { "self": { "href": "https://api.zotero.org/groups/115830/items/IE2ZA9HU", "type": "application/json" }, "alternate": { "href": "https://www.zotero.org/groups/computational_evolution_group/items/IE2ZA9HU", "type": "text/html" } }, "meta": { "createdByUser": { "id": 1202954, "username": "alexeidrummond", "name": "Alexei Drummond", "links": { "alternate": { "href": "https://www.zotero.org/alexeidrummond", "type": "text/html" } } }, "creatorSummary": "Ogilvie et al.", "parsedDate": "2015-06-21", "numChildren": 2 }, "data": { "key": "IE2ZA9HU", "version": 193, "itemType": "journalArticle", "title": "Computational Performance and Statistical Accuracy of *BEAST and Comparisons with Other Methods", "creators": [ { "creatorType": "author", "firstName": "Huw A.", "lastName": "Ogilvie" }, { "creatorType": "author", "firstName": "Joseph", "lastName": "Heled" }, { "creatorType": "author", "firstName": "Dong", "lastName": "Xie" }, { "creatorType": "author", "firstName": "Alexei J.", "lastName": "Drummond" } ], "abstractNote": "Under the multispecies coalescent model of molecular evolution, gene trees have independent evolutionary histories within a shared species tree. In comparison, supermatrix concatenation methods assume that gene trees share a single common genealogical history, thereby equating gene coalescence with species divergence. The multispecies coalescent is supported by previous studies which found that its predicted distributions fit empirical data, and that concatenation is not a consistent estimator of the species tree. *BEAST, a fully Bayesian implementation of the multispecies coalescent, is popular but computationally intensive, so the increasing size of phylogenetic data sets is both a computational challenge and an opportunity for better systematics. Using simulation studies, we characterize the scaling behaviour of *BEAST, and enable quantitative prediction of the impact increasing the number of loci has on both computational performance and statistical accuracy. Follow up simulations over a wide range of parameters show that the statistical performance of *BEAST relative to concatenation improves both as branch length is reduced and as the number of loci is increased. Finally, using simulations based on estimated parameters from two phylogenomic data sets, we compare the performance of a range of species tree and concatenation methods to show that using *BEAST with tens of loci can be preferable to using concatenation with thousands of loci. Our results provide insight into the practicalities of Bayesian species tree estimation, the number of loci required to obtain a given level of accuracy and the situations in which supermatrix or summary methods will be outperformed by the fully Bayesian multispecies coalescent.", "publicationTitle": "arXiv:1506.06446 [q-bio]", "publisher": "", "place": "", "date": "2015-06-21", "volume": "", "issue": "", "section": "", "partNumber": "", "partTitle": "", "pages": "", "series": "", "seriesTitle": "", "seriesText": "", "journalAbbreviation": "", "DOI": "", "citationKey": "", "url": "http://arxiv.org/abs/1506.06446", "accessDate": "2015-10-12T21:40:34Z", "PMID": "", "PMCID": "", "ISSN": "", "archive": "", "archiveLocation": "", "shortTitle": "", "language": "", "libraryCatalog": "arXiv.org", "callNumber": "", "rights": "", "extra": "arXiv: 1506.06446", "tags": [ { "tag": "Quantitative Biology - Populations and Evolution", "type": 1 } ], "collections": [], "relations": {}, "dateAdded": "2015-10-12T21:40:57Z", "dateModified": "2015-10-12T21:40:57Z" } }, { "key": "VGMCSI8H", "version": 193, "library": { "type": "group", "id": 115830, "name": "Computational Evolution Group", "links": { "alternate": { "href": "https://www.zotero.org/groups/computational_evolution_group", "type": "text/html" } } }, "links": { "self": { "href": "https://api.zotero.org/groups/115830/items/VGMCSI8H", "type": "application/json" }, "alternate": { "href": "https://www.zotero.org/groups/computational_evolution_group/items/VGMCSI8H", "type": "text/html" } }, "meta": { "createdByUser": { "id": 1202954, "username": "alexeidrummond", "name": "Alexei Drummond", "links": { "alternate": { "href": "https://www.zotero.org/alexeidrummond", "type": "text/html" } } }, "creatorSummary": "Gavryushkina et al.", "parsedDate": "2015-06-15", "numChildren": 2 }, "data": { "key": "VGMCSI8H", "version": 193, "itemType": "journalArticle", "title": "Bayesian total evidence dating reveals the recent crown radiation of penguins", "creators": [ { "creatorType": "author", "firstName": "Alexandra", "lastName": "Gavryushkina" }, { "creatorType": "author", "firstName": "Tracy A.", "lastName": "Heath" }, { "creatorType": "author", "firstName": "Daniel T.", "lastName": "Ksepka" }, { "creatorType": "author", "firstName": "Tanja", "lastName": "Stadler" }, { "creatorType": "author", "firstName": "David", "lastName": "Welch" }, { "creatorType": "author", "firstName": "Alexei J.", "lastName": "Drummond" } ], "abstractNote": "The total evidence approach to divergence-time dating uses molecular and morphological data of extant and fossil species to infer phylogenetic relationships, species divergence times, and macroevolutionary parameters in a single coherent framework. Current model-based implementations of this approach lack an appropriate model for the tree describing the diversification and fossilisation process which can result in erroneous conclusions. We address this shortcoming by providing a total evidence method implemented in a Bayesian framework. This approach uses a mechanistic tree prior to describe the underlying diversification process that generated the tree of extant and fossil taxa. Previous attempts to apply the total-evidence approach have used tree priors that do not account for the possibility that fossil samples may be direct ancestors of other samples. The fossilised birth-death process explicitly models the diversification, fossilisation, and sampling processes and naturally allows for sampled ancestors. This model was recently applied to estimate divergence times based on molecular data and fossil occurrence dates. We incorporate the fossilised birth-death model and a model of morphological trait evolution into a Bayesian total-evidence approach to dating species phylogenies. We apply this method to extant and fossil penguins and show that the modern penguins radiated much more recently than has been previously estimated, with the basal divergence in the crown clade occurring at~12.5 Ma and most splits leading to extant species occurring in the last 2 million years. Our results demonstrate that including stem-fossil diversity can greatly improve the estimates of the divergence times of crown taxa. The method is available in BEAST2 (v2.3) software www.beast2.org with packages SA (v1.1.3) and morph-models (v1.0.1) installed.", "publicationTitle": "arXiv:1506.04797 [q-bio]", "publisher": "", "place": "", "date": "2015-06-15", "volume": "", "issue": "", "section": "", "partNumber": "", "partTitle": "", "pages": "", "series": "", "seriesTitle": "", "seriesText": "", "journalAbbreviation": "", "DOI": "", "citationKey": "", "url": "http://arxiv.org/abs/1506.04797", "accessDate": "2015-10-12T21:40:24Z", "PMID": "", "PMCID": "", "ISSN": "", "archive": "", "archiveLocation": "", "shortTitle": "", "language": "", "libraryCatalog": "arXiv.org", "callNumber": "", "rights": "", "extra": "arXiv: 1506.04797", "tags": [ { "tag": "Quantitative Biology - Populations and Evolution", "type": 1 } ], "collections": [], "relations": {}, "dateAdded": "2015-10-12T21:40:57Z", "dateModified": "2015-10-12T21:40:57Z" } }, { "key": "59XT4XR7", "version": 189, "library": { "type": "group", "id": 115830, 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"charset": "", "filename": "", "md5": null, "mtime": null, "tags": [], "relations": {}, "dateAdded": "2015-10-12T21:40:57Z", "dateModified": "2015-10-12T21:40:57Z" } }, { "key": "5V7C9EZ8", "version": 186, "library": { "type": "group", "id": 115830, "name": "Computational Evolution Group", "links": { "alternate": { "href": "https://www.zotero.org/groups/computational_evolution_group", "type": "text/html" } } }, "links": { "self": { "href": "https://api.zotero.org/groups/115830/items/5V7C9EZ8", "type": "application/json" }, "alternate": { "href": "https://www.zotero.org/groups/computational_evolution_group/items/5V7C9EZ8", "type": "text/html" } }, "meta": { "createdByUser": { "id": 1202954, "username": "alexeidrummond", "name": "Alexei Drummond", "links": { "alternate": { "href": "https://www.zotero.org/alexeidrummond", "type": "text/html" } } }, "creatorSummary": "Drummond and Bouckaert", "parsedDate": "2015", "numChildren": 0 }, "data": { "key": "5V7C9EZ8", "version": 186, "itemType": "book", "title": "Bayesian evolutionary analysis ; with BEAST 2", "creators": [ { "creatorType": "author", "firstName": "Alexei J.", "lastName": "Drummond" }, { "creatorType": "author", "firstName": "Remco R.", "lastName": "Bouckaert" } ], "abstractNote": "", "series": "", "seriesNumber": "", "volume": "", "numberOfVolumes": "", "edition": "", "date": "2015", "publisher": "Cambridge University Press", "place": "Cambridge, United Kingdom", "originalDate": "", "originalPublisher": "", "originalPlace": "", "format": "", "numPages": "", "ISBN": "9781107019652", "DOI": "", "citationKey": "", "url": "", "accessDate": "", "ISSN": "", "archive": "", "archiveLocation": "", "shortTitle": "", "language": "", "libraryCatalog": "Library of Congress ISBN", "callNumber": "QH83 .D78 2015", "rights": "", "extra": "", "tags": [ { "tag": "Bayesian statistical decision theory", "type": 1 }, { "tag": "Cladistic analysis", "type": 1 }, { "tag": "Data processing", "type": 1 } ], "collections": [], "relations": {}, "dateAdded": "2015-10-12T21:32:56Z", "dateModified": "2015-10-12T21:32:56Z" } }, { "key": "9WTQ8JP2", "version": 184, "library": { "type": "group", "id": 115830, "name": "Computational Evolution Group", "links": { "alternate": { "href": "https://www.zotero.org/groups/computational_evolution_group", "type": "text/html" } } }, "links": { "self": { "href": "https://api.zotero.org/groups/115830/items/9WTQ8JP2", "type": "application/json" }, "alternate": { "href": "https://www.zotero.org/groups/computational_evolution_group/items/9WTQ8JP2", "type": "text/html" }, "up": { "href": "https://api.zotero.org/groups/115830/items/WZ3P3WTD", "type": "application/json" } }, "meta": { "createdByUser": { "id": 1202954, "username": "alexeidrummond", "name": "Alexei Drummond", "links": { "alternate": { "href": "https://www.zotero.org/alexeidrummond", "type": "text/html" } } } }, "data": { "key": "9WTQ8JP2", "version": 184, "parentItem": "WZ3P3WTD", "itemType": "attachment", "linkMode": "linked_url", "title": "PubMed entry", "accessDate": "2015-10-12T21:25:23Z", "url": "http://www.ncbi.nlm.nih.gov/pubmed/26445670", "note": "", "contentType": "text/html", "charset": "", "tags": [], "relations": {}, "dateAdded": "2015-10-12T21:25:23Z", "dateModified": "2015-10-12T21:25:23Z" } }, { "key": "WZ3P3WTD", "version": 184, "library": { "type": "group", "id": 115830, "name": "Computational Evolution Group", "links": { "alternate": { "href": "https://www.zotero.org/groups/computational_evolution_group", "type": "text/html" } } }, "links": { "self": { "href": "https://api.zotero.org/groups/115830/items/WZ3P3WTD", "type": "application/json" }, "alternate": { "href": "https://www.zotero.org/groups/computational_evolution_group/items/WZ3P3WTD", "type": "text/html" } }, "meta": { "createdByUser": { "id": 1202954, "username": "alexeidrummond", "name": "Alexei Drummond", "links": { "alternate": { "href": "https://www.zotero.org/alexeidrummond", "type": "text/html" } } }, "creatorSummary": "Drummond et al.", "parsedDate": "2015", "numChildren": 1 }, "data": { "key": "WZ3P3WTD", "version": 184, "itemType": "journalArticle", "title": "Evaluating a multigene environmental DNA approach for biodiversity assessment", "creators": [ { "creatorType": "author", "firstName": "Alexei J.", "lastName": "Drummond" }, { "creatorType": "author", "firstName": "Richard D.", "lastName": "Newcomb" }, { "creatorType": "author", "firstName": "Thomas R.", "lastName": "Buckley" }, { "creatorType": "author", "firstName": "Dong", "lastName": "Xie" }, { "creatorType": "author", "firstName": "Andrew", "lastName": "Dopheide" }, { "creatorType": "author", "firstName": "Benjamin Cm", "lastName": "Potter" }, { "creatorType": "author", "firstName": "Joseph", "lastName": "Heled" }, { "creatorType": "author", "firstName": "Howard A.", "lastName": "Ross" }, { "creatorType": "author", "firstName": "Leah", "lastName": "Tooman" }, { "creatorType": "author", "firstName": "Stefanie", "lastName": "Grosser" }, { "creatorType": "author", "firstName": "Duckchul", "lastName": "Park" }, { "creatorType": "author", "firstName": "Nicholas J.", "lastName": "Demetras" }, { "creatorType": "author", "firstName": "Mark I.", "lastName": "Stevens" }, { "creatorType": "author", "firstName": "James C.", "lastName": "Russell" }, { "creatorType": "author", "firstName": "Sandra H.", "lastName": "Anderson" }, { "creatorType": "author", "firstName": "Anna", "lastName": "Carter" }, { "creatorType": "author", "firstName": "Nicola", "lastName": "Nelson" } ], "abstractNote": "BACKGROUND: There is an increasing demand for rapid biodiversity assessment tools that have a broad taxonomic coverage. Here we evaluate a suite of environmental DNA (eDNA) markers coupled with next generation sequencing (NGS) that span the tree of life, comparing them with traditional biodiversity monitoring tools within ten 20×20 meter plots along a 700 meter elevational gradient.\nRESULTS: From six eDNA datasets (one from each of 16S, 18S, ITS, trnL and two from COI) we identified sequences from 109 NCBI taxonomy-defined phyla or equivalent, ranging from 31 to 60 for a given eDNA marker. Estimates of alpha and gamma diversity were sensitive to the number of sequence reads, whereas beta diversity estimates were less sensitive. The average within-plot beta diversity was lower than between plots for all markers. The soil beta diversity of COI and 18S markers showed the strongest response to the elevational variation of the eDNA markers (COI: r=0.49, p<0.001; 18S: r=0.48, p<0.001). Furthermore pairwise beta diversities for these two markers were strongly correlated with those calculated from traditional vegetation and invertebrate biodiversity measures.\nCONCLUSIONS: Using a soil-based eDNA approach, we demonstrate that standard phylogenetic markers are capable of recovering sequences from a broad diversity of eukaryotes, in addition to prokaryotes by 16S. The COI and 18S eDNA markers are the best proxies for aboveground biodiversity based on the high correlation between the pairwise beta diversities of these markers and those obtained using traditional methods.", "publicationTitle": "GigaScience", "publisher": "", "place": "", "date": "2015", "volume": "4", "issue": "", "section": "", "partNumber": "", "partTitle": "", "pages": "46", "series": "", "seriesTitle": "", "seriesText": "", "journalAbbreviation": "Gigascience", "DOI": "10.1186/s13742-015-0086-1", "citationKey": "", "url": "", "accessDate": "", "PMID": "", "PMCID": "", "ISSN": "2047-217X", "archive": "", "archiveLocation": "", "shortTitle": "", "language": "eng", "libraryCatalog": "PubMed", "callNumber": "", "rights": "", "extra": "PMID: 26445670\nPMCID: PMC4595072", "tags": [], "collections": [ "NK3JMAQM" ], "relations": {}, "dateAdded": "2015-10-12T21:25:23Z", "dateModified": "2015-10-12T21:25:23Z" } }, { "key": "UK93A5QT", "version": 183, "library": { "type": "group", "id": 115830, "name": "Computational Evolution Group", "links": { "alternate": { "href": "https://www.zotero.org/groups/computational_evolution_group", "type": "text/html" } } }, "links": { "self": { "href": "https://api.zotero.org/groups/115830/items/UK93A5QT", "type": "application/json" }, "alternate": { "href": "https://www.zotero.org/groups/computational_evolution_group/items/UK93A5QT", "type": "text/html" } }, "meta": { "createdByUser": { "id": 1210522, "username": "guindon", "name": "", "links": { "alternate": { "href": "https://www.zotero.org/guindon", "type": "text/html" } } }, "creatorSummary": "Stadler et al.", "parsedDate": "2015", "numChildren": 0 }, "data": { "key": "UK93A5QT", "version": 183, "itemType": "journalArticle", "title": "How well can the exponential-growth coalescent approximate constant-rate birth–death population dynamics?", "creators": [ { "creatorType": "author", "firstName": "Tanja", "lastName": "Stadler" }, { "creatorType": "author", "firstName": "Timothy G.", "lastName": "Vaughan" }, { "creatorType": "author", "firstName": "Alex", "lastName": "Gavryushkin" }, { "creatorType": "author", "firstName": "Stephane", "lastName": "Guindon" }, { "creatorType": "author", "firstName": "Denise", "lastName": "Kühnert" }, { "creatorType": "author", "firstName": "Gabriel E.", "lastName": "Leventhal" }, { "creatorType": "author", "firstName": "Alexei J.", "lastName": "Drummond" } ], "abstractNote": "", "publicationTitle": "Proceedings of the Royal Society of London B: Biological Sciences", "publisher": "", "place": "", "date": "2015", "volume": "282", "issue": "1806", "section": "", "partNumber": "", "partTitle": "", "pages": "20150420", "series": "", "seriesTitle": "", "seriesText": "", "journalAbbreviation": "", "DOI": "", "citationKey": "", "url": "http://rspb.royalsocietypublishing.org/content/282/1806/20150420.abstract", "accessDate": "2015-05-10T21:45:30Z", "PMID": "", "PMCID": "", "ISSN": "", "archive": "", "archiveLocation": "", "shortTitle": "", "language": "", "libraryCatalog": "Google Scholar", "callNumber": "", "rights": "", "extra": "", "tags": [], "collections": [ "NK3JMAQM" ], "relations": {}, "dateAdded": "2015-05-10T21:47:52Z", "dateModified": "2015-05-10T21:47:52Z" } } ]