[ { "key": "I3E6HEHF", "version": 22, "library": { "type": "group", "id": 203572, "name": "Museum of Vertebrate Zoology", "links": { "alternate": { "href": "https://www.zotero.org/groups/museum_of_vertebrate_zoology", "type": "text/html" } } }, "links": { "self": { "href": "https://api.zotero.org/groups/203572/items/I3E6HEHF", "type": "application/json" }, "alternate": { "href": "https://www.zotero.org/groups/museum_of_vertebrate_zoology/items/I3E6HEHF", "type": "text/html" } }, "meta": { "createdByUser": { "id": 115811, "username": "mkoo", "name": "Michelle Koo", "links": { "alternate": { "href": "https://www.zotero.org/mkoo", "type": "text/html" } } }, "creatorSummary": "Wake", "parsedDate": "2006", "numChildren": 0 }, "data": { "key": "I3E6HEHF", "version": 22, "itemType": "journalArticle", "title": "PROBLEMS WITH SPECIES: PATTERNS AND PROCESSES OF SPECIES FORMATION IN SALAMANDERS", "creators": [ { "creatorType": "author", "firstName": "David B.", "lastName": "Wake" } ], "abstractNote": "", "publicationTitle": "Annals of the Missouri Botanical Garden", "publisher": "", "place": "", "date": "2006", "volume": "93", "issue": "1", "section": "", "partNumber": "", "partTitle": "", "pages": "8-23", "series": "", "seriesTitle": "", "seriesText": "", "journalAbbreviation": "Annals of the Missouri Botanical Garden", "DOI": "10.3417/0026-6493(2006)93[8:PWSPAP]2.0.CO;2", "citationKey": "", "url": "http://www.bioone.org/doi/full/10.3417/0026-6493%282006%2993%5B8%3APWSPAP%5D2.0.CO%3B2", "accessDate": "2011-08-17T06:18:42Z", "PMID": "", "PMCID": "", "ISSN": "0026-6493", "archive": "", "archiveLocation": "", "shortTitle": "PROBLEMS WITH SPECIES", "language": "", "libraryCatalog": "CrossRef", "callNumber": "", "rights": "", "extra": "", "tags": [], "collections": [], "relations": {}, "dateAdded": "2013-09-10T17:36:56Z", "dateModified": "2013-09-10T17:36:56Z" } }, { "key": "4CHK2A6N", "version": 21, "library": { "type": "group", "id": 203572, "name": "Museum of Vertebrate Zoology", "links": { "alternate": { "href": "https://www.zotero.org/groups/museum_of_vertebrate_zoology", "type": "text/html" } } }, "links": { "self": { "href": "https://api.zotero.org/groups/203572/items/4CHK2A6N", "type": "application/json" }, "alternate": { "href": "https://www.zotero.org/groups/museum_of_vertebrate_zoology/items/4CHK2A6N", "type": "text/html" } }, "meta": { "createdByUser": { "id": 115811, "username": "mkoo", "name": "Michelle Koo", "links": { "alternate": { "href": "https://www.zotero.org/mkoo", "type": "text/html" } } }, "creatorSummary": "Pearson", "parsedDate": "1953-02", "numChildren": 0 }, "data": { "key": "4CHK2A6N", "version": 21, "itemType": "journalArticle", "title": "Use of Caves by Hummingbirds and Other Species at High Altitudes in Peru", "creators": [ { "creatorType": "author", "firstName": "Oliver P.", "lastName": "Pearson" } ], "abstractNote": "", "publicationTitle": "The Condor", "publisher": "", "place": "", "date": "Jan. - Feb., 1953", "volume": "55", "issue": "1", "section": "", "partNumber": "", "partTitle": "", "pages": "17-20", "series": "", "seriesTitle": "", "seriesText": "", "journalAbbreviation": "", "DOI": "", "citationKey": "", "url": "http://www.jstor.org/stable/1364918", "accessDate": "2010-10-01T17:37:44Z", "PMID": "", "PMCID": "", "ISSN": "00105422", "archive": "", "archiveLocation": "", "shortTitle": "", "language": "", "libraryCatalog": "JSTOR", "callNumber": "", "rights": "", "extra": "ArticleType: research-article / Full publication date: Jan. - Feb., 1953 / Copyright © 1953 Cooper Ornithological Society", "tags": [], "collections": [], "relations": {}, "dateAdded": "2013-09-10T17:34:56Z", "dateModified": "2013-09-10T17:34:56Z" } }, { "key": "2BXH5BUF", "version": 20, "library": { "type": "group", "id": 203572, "name": "Museum of Vertebrate Zoology", "links": { "alternate": { "href": "https://www.zotero.org/groups/museum_of_vertebrate_zoology", "type": "text/html" } } }, "links": { "self": { "href": "https://api.zotero.org/groups/203572/items/2BXH5BUF", "type": "application/json" }, "alternate": { "href": "https://www.zotero.org/groups/museum_of_vertebrate_zoology/items/2BXH5BUF", "type": "text/html" } }, "meta": { "createdByUser": { "id": 115811, "username": "mkoo", "name": "Michelle Koo", "links": { "alternate": { "href": "https://www.zotero.org/mkoo", "type": "text/html" } } }, "lastModifiedByUser": { "id": 1563364, "username": "MVZpubs", "name": "", "links": { "alternate": { "href": "https://www.zotero.org/mvzpubs", "type": "text/html" } } }, "creatorSummary": "Fujita et al.", "parsedDate": "2012", "numChildren": 0 }, "data": { "key": "2BXH5BUF", "version": 20, "itemType": "journalArticle", "title": "Coalescent-based species delimitation in an integrative taxonomy", "creators": [ { "creatorType": "author", "firstName": "Matthew K.", "lastName": "Fujita" }, { "creatorType": "author", "firstName": "Adam D.", "lastName": "Leaché" }, { "creatorType": "author", "firstName": "Frank T.", "lastName": "Burbrink" }, { "creatorType": "author", "firstName": "Jimmy A.", "lastName": "McGuire" }, { "creatorType": "author", "firstName": "Craig", "lastName": "Moritz" } ], "abstractNote": "The statistical rigor of species delimitation has increased dramatically over the past decade. Coalescent theory provides powerful models for population genetic inference, and is now increasingly important in phylogenetics and speciation research. By applying probabilistic models, coalescent-based species delimitation provides clear and objective testing of alternative hypotheses of evolutionary independence. As acquisition of multilocus data becomes increasingly automated, coalescent-based species delimitation will improve the discovery, resolution, consistency, and stability of the taxonomy of species. Along with other tools and data types, coalescent-based species delimitation will play an important role in an integrative taxonomy that emphasizes the identification of species limits and the processes that have promoted lineage diversification.", "publicationTitle": "Trends in Ecology & Evolution", "publisher": "", "place": "", "date": "2012", "volume": "", "issue": "", "section": "", "partNumber": "", "partTitle": "", "pages": "", "series": "", "seriesTitle": "", "seriesText": "", "journalAbbreviation": "", "DOI": "10.1016/j.tree.2012.04.012", "citationKey": "", "url": "http://www.sciencedirect.com/science/article/pii/S0169534712001000", "accessDate": "2012-05-31T04:17:06Z", "PMID": "", "PMCID": "", "ISSN": "0169-5347", "archive": "", "archiveLocation": "", "shortTitle": "", "language": "", "libraryCatalog": "ScienceDirect", "callNumber": "", "rights": "", "extra": "", "tags": [], "collections": [], "relations": {}, "dateAdded": "2013-08-30T22:06:08Z", "dateModified": "2013-09-10T16:03:15Z" } }, { "key": "K4U286SH", "version": 19, "library": { "type": "group", "id": 203572, "name": "Museum of Vertebrate Zoology", "links": { "alternate": { "href": "https://www.zotero.org/groups/museum_of_vertebrate_zoology", "type": "text/html" } } }, "links": { "self": { "href": "https://api.zotero.org/groups/203572/items/K4U286SH", "type": "application/json" }, "alternate": { "href": "https://www.zotero.org/groups/museum_of_vertebrate_zoology/items/K4U286SH", "type": "text/html" } }, "meta": { "createdByUser": { "id": 115811, "username": "mkoo", "name": "Michelle Koo", "links": { "alternate": { "href": "https://www.zotero.org/mkoo", "type": "text/html" } } }, "creatorSummary": "Rowe et al.", "parsedDate": "2011-03", "numChildren": 1 }, "data": { "key": "K4U286SH", "version": 19, "itemType": "journalArticle", "title": "Recent and rapid speciation with limited morphological disparity in the genus Rattus", "creators": [ { "creatorType": "author", "firstName": "Kevin C", "lastName": "Rowe" }, { "creatorType": "author", "firstName": "Ken P", "lastName": "Aplin" }, { "creatorType": "author", "firstName": "Peter R", "lastName": "Baverstock" }, { "creatorType": "author", "firstName": "Craig", "lastName": "Moritz" } ], "abstractNote": "Recent and rapid radiations provide rich material to examine the factors that drive speciation. Most recent and rapid radiations that have been well-characterized involve species that exhibit overt ecomorphological differences associated with clear partitioning of ecological niches in sympatry. The most diverse genus of rodents, Rattus (66 species), evolved fairly recently, but without overt ecomorphological divergence among species. We used multilocus molecular phylogenetic data and five fossil calibrations to estimate the tempo of diversification in Rattus, and their radiation on Australia and New Guinea (Sahul, 24 species). Based on our analyses, the genus Rattus originated at a date centered on the Pliocene-Pleistocene boundary (1.84-3.17 Ma) with a subsequent colonization of Sahul in the middle Pleistocene (0.85-1.28 Ma). Given these dates, the per lineage diversification rates in Rattus and Sahulian Rattus are among the highest reported for vertebrates (1.1-1.9 and 1.6-3.0 species per lineage per million years, respectively). Despite their rapid diversification, Rattus display little ecomorphological divergence among species and do not fit clearly into current models of adaptive radiations. Lineage through time plots and ancestral state reconstruction of ecological characters suggest that diversification of Sahulian Rattus was most rapid early on as they expanded into novel ecological conditions. However, rapid lineage accumulation occurred even when morphological disparity within lineages was low suggesting that future studies consider other phenotypes in the diversification of Rattus.", "publicationTitle": "Systematic biology", "publisher": "", "place": "", "date": "Mar 2011", "volume": "60", "issue": "2", "section": "", "partNumber": "", "partTitle": "", "pages": "188-203", "series": "", "seriesTitle": "", "seriesText": "", "journalAbbreviation": "Syst. Biol.", "DOI": "10.1093/sysbio/syq092", "citationKey": "", "url": "", "accessDate": "", "PMID": "", "PMCID": "", "ISSN": "1076-836X", "archive": "", "archiveLocation": "", "shortTitle": "", "language": "eng", "libraryCatalog": "NCBI PubMed", "callNumber": "", "rights": "", "extra": "PMID: 21239388", "tags": [ { "tag": "Animals", "type": 1 }, { "tag": "Fossils", "type": 1 }, { "tag": "Genetic Speciation", "type": 1 }, { "tag": "Murinae", "type": 1 }, { "tag": "Phylogeny", "type": 1 }, { "tag": "Rats", "type": 1 } ], "collections": [], "relations": {}, "dateAdded": "2013-08-30T23:08:17Z", "dateModified": "2013-08-30T23:08:17Z" } }, { "key": "QMGF9J5U", "version": 19, "library": { "type": "group", "id": 203572, "name": "Museum of Vertebrate Zoology", "links": { "alternate": { "href": "https://www.zotero.org/groups/museum_of_vertebrate_zoology", "type": "text/html" } } }, "links": { "self": { "href": "https://api.zotero.org/groups/203572/items/QMGF9J5U", "type": "application/json" }, "alternate": { "href": "https://www.zotero.org/groups/museum_of_vertebrate_zoology/items/QMGF9J5U", "type": "text/html" }, "up": { "href": "https://api.zotero.org/groups/203572/items/K4U286SH", "type": "application/json" } }, "meta": { "createdByUser": { "id": 115811, "username": "mkoo", "name": "Michelle Koo", "links": { "alternate": { "href": "https://www.zotero.org/mkoo", "type": "text/html" } } } }, "data": { "key": "QMGF9J5U", "version": 19, "parentItem": "K4U286SH", "itemType": "attachment", "linkMode": "linked_url", "title": "PubMed entry", "accessDate": "2013-08-30T23:08:17Z", "url": "http://www.ncbi.nlm.nih.gov/pubmed/21239388", "note": "", "contentType": "text/html", "charset": "", "tags": [], "relations": {}, "dateAdded": "2013-08-30T23:08:17Z", "dateModified": "2013-08-30T23:08:17Z" } }, { "key": "DVENE2HQ", "version": 18, "library": { "type": "group", "id": 203572, "name": "Museum of Vertebrate Zoology", "links": { "alternate": { "href": "https://www.zotero.org/groups/museum_of_vertebrate_zoology", "type": "text/html" } } }, "links": { "self": { "href": "https://api.zotero.org/groups/203572/items/DVENE2HQ", "type": "application/json" }, "alternate": { "href": "https://www.zotero.org/groups/museum_of_vertebrate_zoology/items/DVENE2HQ", "type": "text/html" }, "up": { "href": "https://api.zotero.org/groups/203572/items/SNQ7V5EP", "type": "application/json" } }, "meta": { "createdByUser": { "id": 115811, "username": "mkoo", "name": "Michelle Koo", "links": { "alternate": { "href": "https://www.zotero.org/mkoo", "type": "text/html" } } } }, "data": { "key": "DVENE2HQ", "version": 18, "parentItem": "SNQ7V5EP", "itemType": "attachment", "linkMode": "linked_url", "title": "PubMed entry", "accessDate": "2013-08-30T23:07:49Z", "url": "http://www.ncbi.nlm.nih.gov/pubmed/22030727", "note": "", "contentType": "text/html", "charset": "", "tags": [], "relations": {}, "dateAdded": "2013-08-30T23:07:49Z", "dateModified": "2013-08-30T23:07:49Z" } }, { "key": "SNQ7V5EP", "version": 18, "library": { "type": "group", "id": 203572, "name": "Museum of Vertebrate Zoology", "links": { "alternate": { "href": "https://www.zotero.org/groups/museum_of_vertebrate_zoology", "type": "text/html" } } }, "links": { "self": { "href": "https://api.zotero.org/groups/203572/items/SNQ7V5EP", "type": "application/json" }, "alternate": { "href": "https://www.zotero.org/groups/museum_of_vertebrate_zoology/items/SNQ7V5EP", "type": "text/html" } }, "meta": { "createdByUser": { "id": 115811, "username": "mkoo", "name": "Michelle Koo", "links": { "alternate": { "href": "https://www.zotero.org/mkoo", "type": "text/html" } } }, "creatorSummary": "Hoskin et al.", "parsedDate": "2011-11", "numChildren": 1 }, "data": { "key": "SNQ7V5EP", "version": 18, "itemType": "journalArticle", "title": "Persistence in peripheral refugia promotes phenotypic divergence and speciation in a rainforest frog", "creators": [ { "creatorType": "author", "firstName": "Conrad J", "lastName": "Hoskin" }, { "creatorType": "author", "firstName": "Maria", "lastName": "Tonione" }, { "creatorType": "author", "firstName": "Megan", "lastName": "Higgie" }, { "creatorType": "author", "firstName": "Jason B", "lastName": "Mackenzie" }, { "creatorType": "author", "firstName": "Stephen E", "lastName": "Williams" }, { "creatorType": "author", "firstName": "Jeremy", "lastName": "Vanderwal" }, { "creatorType": "author", "firstName": "Craig", "lastName": "Moritz" } ], "abstractNote": "It is well established from the fossil record and phylogeographic analyses that late Quaternary climate fluctuations led to substantial changes in species' distribution, but whether and how these fluctuations resulted in phenotypic divergence and speciation is less clear. This question can be addressed through detailed analysis of traits relevant to ecology and mating within and among intraspecific lineages that persisted in separate refugia. In a biogeographic system (the Australian Wet Tropics [AWT]) with a well-established history of refugial isolation during Pleistocene glacial periods, we tested whether climate-mediated changes in distribution drove genetic and phenotypic divergence in the rainforest frog Cophixalus ornatus. We combined paleomodeling and multilocus genetics to demonstrate long-term persistence within, and isolation among, one central and two peripheral refugia. In contrast to other AWT vertebrates, the three major lineages differ in ecologically relevant morphology and in mating call, reflecting divergent selection and/or genetic drift in the peripheral isolates. Divergence in mating call and contact zone analyses suggest that the lineages now represent distinct species. The results show that climate shifts can promote genetic and phenotypic divergence and, potentially, speciation and direct attention toward incorporating adaptive traits into phylogeographic studies to better resolve the mechanisms of speciation.", "publicationTitle": "The American naturalist", "publisher": "", "place": "", "date": "Nov 2011", "volume": "178", "issue": "5", "section": "", "partNumber": "", "partTitle": "", "pages": "561-578", "series": "", "seriesTitle": "", "seriesText": "", "journalAbbreviation": "Am. Nat.", "DOI": "10.1086/662164", "citationKey": "", "url": "", "accessDate": "", "PMID": "", "PMCID": "", "ISSN": "1537-5323", "archive": "", "archiveLocation": "", "shortTitle": "", "language": "eng", "libraryCatalog": "NCBI PubMed", "callNumber": "", "rights": "", "extra": "PMID: 22030727", "tags": [ { "tag": "Animals", "type": 1 }, { "tag": "Anura", "type": 1 }, { "tag": "Cell Nucleus", "type": 1 }, { "tag": "Climate Change", "type": 1 }, { "tag": "DNA, Mitochondrial", "type": 1 }, { "tag": "Ecosystem", "type": 1 }, { "tag": "Female", "type": 1 }, { "tag": "Genetic Speciation", "type": 1 }, { "tag": "Male", "type": 1 }, { "tag": "Models, Biological", "type": 1 }, { "tag": "Molecular Sequence Data", "type": 1 }, { "tag": "Phylogeny", "type": 1 }, { "tag": "Phylogeography", "type": 1 }, { "tag": "Polymerase Chain Reaction", "type": 1 }, { "tag": "Queensland", "type": 1 }, { "tag": "RNA, Ribosomal, 16S", "type": 1 }, { "tag": "Reproductive Isolation", "type": 1 }, { "tag": "Vocalization, Animal", "type": 1 } ], "collections": [], "relations": {}, "dateAdded": "2013-08-30T23:07:49Z", "dateModified": "2013-08-30T23:07:49Z" } }, { "key": "ZBPCAHBF", "version": 17, "library": { "type": "group", "id": 203572, "name": "Museum of Vertebrate Zoology", "links": { "alternate": { "href": "https://www.zotero.org/groups/museum_of_vertebrate_zoology", "type": "text/html" } } }, "links": { "self": { "href": "https://api.zotero.org/groups/203572/items/ZBPCAHBF", "type": "application/json" }, "alternate": { "href": "https://www.zotero.org/groups/museum_of_vertebrate_zoology/items/ZBPCAHBF", "type": "text/html" } }, "meta": { "createdByUser": { "id": 115811, "username": "mkoo", "name": "Michelle Koo", "links": { "alternate": { "href": "https://www.zotero.org/mkoo", "type": "text/html" } } }, "creatorSummary": "Moritz et al.", "parsedDate": "2009-04-07", "numChildren": 1 }, "data": { "key": "ZBPCAHBF", "version": 17, "itemType": "journalArticle", "title": "Identification and dynamics of a cryptic suture zone in tropical rainforest", "creators": [ { "creatorType": "author", "firstName": "C", "lastName": "Moritz" }, { "creatorType": "author", "firstName": "C J", "lastName": "Hoskin" }, { "creatorType": "author", "firstName": "J B", "lastName": "MacKenzie" }, { "creatorType": "author", "firstName": "B L", "lastName": "Phillips" }, { "creatorType": "author", "firstName": "M", "lastName": "Tonione" }, { "creatorType": "author", "firstName": "N", "lastName": "Silva" }, { "creatorType": "author", "firstName": "J", "lastName": "VanDerWal" }, { "creatorType": "author", "firstName": "S E", "lastName": "Williams" }, { "creatorType": "author", "firstName": "C H", "lastName": "Graham" } ], "abstractNote": "Suture zones, shared regions of secondary contact between long-isolated lineages, are natural laboratories for studying divergence and speciation. For tropical rainforest, the existence of suture zones and their significance for speciation has been controversial. Using comparative phylogeographic evidence, we locate a morphologically cryptic suture zone in the Australian Wet Tropics rainforest. Fourteen out of 18 contacts involve morphologically cryptic phylogeographic lineages, with mtDNA sequence divergences ranging from 2 to 15 per cent. Contact zones are significantly clustered in a suture zone located between two major Quaternary refugia. Within this area, there is a trend for secondary contacts to occur in regions with low environmental suitability relative to both adjacent refugia and, by inference, the parental lineages. The extent and form of reproductive isolation among interacting lineages varies across species, ranging from random admixture to speciation, in one case via reinforcement. Comparative phylogeographic studies, combined with environmental analysis at a fine-scale and across varying climates, can generate new insights into suture zone formation and to diversification processes in species-rich tropical rainforests. As arenas for evolutionary experimentation, suture zones merit special attention for conservation.", "publicationTitle": "Proceedings. Biological sciences / The Royal Society", "publisher": "", "place": "", "date": "Apr 7, 2009", "volume": "276", "issue": "1660", "section": "", "partNumber": "", "partTitle": "", "pages": "1235-1244", "series": "", "seriesTitle": "", "seriesText": "", "journalAbbreviation": "Proc. Biol. Sci.", "DOI": "10.1098/rspb.2008.1622", "citationKey": "", "url": "", "accessDate": "", "PMID": "", "PMCID": "", "ISSN": "0962-8452", "archive": "", "archiveLocation": "", "shortTitle": "", "language": "eng", "libraryCatalog": "NCBI PubMed", "callNumber": "", "rights": "", "extra": "PMID: 19203915", "tags": [ { "tag": "Amphibians", "type": 1 }, { "tag": "Animals", "type": 1 }, { "tag": "Australia", "type": 1 }, { "tag": "Biological Evolution", "type": 1 }, { "tag": "DNA, Mitochondrial", "type": 1 }, { "tag": "Demography", "type": 1 }, { "tag": "Reptiles", "type": 1 }, { "tag": "Trees", "type": 1 }, { "tag": "Tropical Climate", "type": 1 } ], "collections": [], "relations": {}, "dateAdded": "2013-08-30T23:07:29Z", "dateModified": "2013-08-30T23:07:29Z" } }, { "key": "ASSKUPQC", "version": 17, "library": { "type": "group", "id": 203572, "name": "Museum of Vertebrate Zoology", "links": { "alternate": { "href": "https://www.zotero.org/groups/museum_of_vertebrate_zoology", "type": "text/html" } } }, "links": { "self": { "href": "https://api.zotero.org/groups/203572/items/ASSKUPQC", "type": "application/json" }, "alternate": { "href": "https://www.zotero.org/groups/museum_of_vertebrate_zoology/items/ASSKUPQC", "type": "text/html" }, "up": { "href": "https://api.zotero.org/groups/203572/items/ZBPCAHBF", "type": "application/json" } }, "meta": { "createdByUser": { "id": 115811, "username": "mkoo", "name": "Michelle Koo", "links": { "alternate": { "href": "https://www.zotero.org/mkoo", "type": "text/html" } } } }, "data": { "key": "ASSKUPQC", "version": 17, "parentItem": "ZBPCAHBF", "itemType": "attachment", "linkMode": "linked_url", "title": "PubMed entry", "accessDate": "2013-08-30T23:07:29Z", "url": "http://www.ncbi.nlm.nih.gov/pubmed/19203915", "note": "", "contentType": "text/html", "charset": "", "tags": [], "relations": {}, "dateAdded": "2013-08-30T23:07:29Z", "dateModified": "2013-08-30T23:07:29Z" } }, { "key": "NRGP2G4J", "version": 16, "library": { "type": "group", "id": 203572, "name": "Museum of Vertebrate Zoology", "links": { "alternate": { "href": "https://www.zotero.org/groups/museum_of_vertebrate_zoology", "type": "text/html" } } }, "links": { "self": { "href": "https://api.zotero.org/groups/203572/items/NRGP2G4J", "type": "application/json" }, "alternate": { "href": "https://www.zotero.org/groups/museum_of_vertebrate_zoology/items/NRGP2G4J", "type": "text/html" } }, "meta": { "createdByUser": { "id": 115811, "username": "mkoo", "name": "Michelle Koo", "links": { "alternate": { "href": "https://www.zotero.org/mkoo", "type": "text/html" } } }, "creatorSummary": "Oza et al.", "parsedDate": "2012-01", "numChildren": 1 }, "data": { "key": "NRGP2G4J", "version": 16, "itemType": "journalArticle", "title": "Recent speciation and limited phylogeographic structure in Mixophyes frogs from the Australian Wet Tropics", "creators": [ { "creatorType": "author", "firstName": "Anuja U", "lastName": "Oza" }, { "creatorType": "author", "firstName": "Katharine E", "lastName": "Lovett" }, { "creatorType": "author", "firstName": "Stephen E", "lastName": "Williams" }, { "creatorType": "author", "firstName": "Craig", "lastName": "Moritz" } ], "abstractNote": "Through a combination of macroecological, paleoecological, and phylogeographical analyses, the rainforests of the Australian Wet Tropics (AWT) have emerged as a useful model for understanding sensitivity of species to past climatic change and, hence, for predicting vulnerability to future change. To extend the ecological breadth of comparative phylogeographic analyses, we investigate a clade of myobatrachid frogs, Mixophyes, a genus of large, stream-breeding but terrestrial frogs, three species of which are endemic to rainforests of the AWT. Here we (i) combine mtDNA, allozyme, and morphological data to refine knowledge of the geographic and environmental distribution of each taxon, (ii) resolve relationships among species, and (iii) use mtDNA phylogeography to infer responses of the three taxa to late-Pleistocene and Holocene climatic change. Each of the three species (Mixophyes carbinensis, Mixophyes coggeri, and Mixophyes schevilli) is effectively diagnosed by mtDNA, with the two small-bodied, allopatric species (M. carbinensis and M. schevilli) being sister-taxa. Mixophyes have a very different history from other AWT amphibians, with more recent speciation (net divergences <5%) and much lower and geographically unstructured mtDNA diversity within each species. The combination of low diversity (θ(Π)<0.36%) and strong signals of recent population expansion (Fu's Fs<0) suggests very high sensitivity to climate-driven rainforest dynamics, perhaps due to their large body size, low population density, and their requirement for both wet forest-floor litter and streams suitable for breeding. The results further emphasize the heterogeneity of species' responses to climate change and suggest that species dependent on multiple habitat types could be especially vulnerable.", "publicationTitle": "Molecular phylogenetics and evolution", "publisher": "", "place": "", "date": "Jan 2012", "volume": "62", "issue": "1", "section": "", "partNumber": "", "partTitle": "", "pages": "407-413", "series": "", "seriesTitle": "", "seriesText": "", "journalAbbreviation": "Mol. Phylogenet. Evol.", "DOI": "10.1016/j.ympev.2011.10.010", "citationKey": "", "url": "", "accessDate": "", "PMID": "", "PMCID": "", "ISSN": "1095-9513", "archive": "", "archiveLocation": "", "shortTitle": "", "language": "eng", "libraryCatalog": "NCBI PubMed", "callNumber": "", "rights": "", "extra": "PMID: 22063263", "tags": [ { "tag": "Animals", "type": 1 }, { "tag": "Anura", "type": 1 }, { "tag": "Female", "type": 1 }, { "tag": "Genes, Mitochondrial", "type": 1 }, { "tag": "Genetic Speciation", "type": 1 }, { "tag": "Genetic Variation", "type": 1 }, { "tag": "Haplotypes", "type": 1 }, { "tag": "Isoenzymes", "type": 1 }, { "tag": "Male", "type": 1 }, { "tag": "Models, Genetic", "type": 1 }, { "tag": "Multilocus Sequence Typing", "type": 1 }, { "tag": "Phylogeny", "type": 1 }, { "tag": "Phylogeography", "type": 1 }, { "tag": "Queensland", "type": 1 }, { "tag": "RNA, Ribosomal, 16S", "type": 1 }, { "tag": "Tropical Climate", "type": 1 } ], "collections": [], "relations": {}, "dateAdded": "2013-08-30T23:07:12Z", "dateModified": "2013-08-30T23:07:12Z" } }, { "key": "5WHJCS94", "version": 16, "library": { "type": "group", "id": 203572, "name": "Museum of Vertebrate Zoology", "links": { "alternate": { "href": "https://www.zotero.org/groups/museum_of_vertebrate_zoology", "type": "text/html" } } }, "links": { "self": { "href": "https://api.zotero.org/groups/203572/items/5WHJCS94", "type": "application/json" }, "alternate": { "href": "https://www.zotero.org/groups/museum_of_vertebrate_zoology/items/5WHJCS94", "type": "text/html" }, "up": { "href": "https://api.zotero.org/groups/203572/items/NRGP2G4J", "type": "application/json" } }, "meta": { "createdByUser": { "id": 115811, "username": "mkoo", "name": "Michelle Koo", "links": { "alternate": { "href": "https://www.zotero.org/mkoo", "type": "text/html" } } } }, "data": { "key": "5WHJCS94", "version": 16, "parentItem": "NRGP2G4J", "itemType": "attachment", "linkMode": "linked_url", "title": "PubMed entry", "accessDate": "2013-08-30T23:07:12Z", "url": "http://www.ncbi.nlm.nih.gov/pubmed/22063263", "note": "", "contentType": "text/html", "charset": "", "tags": [], "relations": {}, "dateAdded": "2013-08-30T23:07:12Z", "dateModified": "2013-08-30T23:07:12Z" } }, { "key": "VNFA42QT", "version": 15, "library": { "type": "group", "id": 203572, "name": "Museum of Vertebrate Zoology", "links": { "alternate": { "href": "https://www.zotero.org/groups/museum_of_vertebrate_zoology", "type": "text/html" } } }, "links": { "self": { "href": "https://api.zotero.org/groups/203572/items/VNFA42QT", "type": "application/json" }, "alternate": { "href": "https://www.zotero.org/groups/museum_of_vertebrate_zoology/items/VNFA42QT", "type": "text/html" } }, "meta": { "createdByUser": { "id": 115811, "username": "mkoo", "name": "Michelle Koo", "links": { "alternate": { "href": "https://www.zotero.org/mkoo", "type": "text/html" } } }, "creatorSummary": "Carnaval et al.", "parsedDate": "2009-02-06", "numChildren": 1 }, "data": { "key": "VNFA42QT", "version": 15, "itemType": "journalArticle", "title": "Stability predicts genetic diversity in the Brazilian Atlantic forest hotspot", "creators": [ { "creatorType": "author", "firstName": "Ana Carolina", "lastName": "Carnaval" }, { "creatorType": "author", "firstName": "Michael J", "lastName": "Hickerson" }, { "creatorType": "author", "firstName": "Célio F B", "lastName": "Haddad" }, { "creatorType": "author", "firstName": "Miguel T", "lastName": "Rodrigues" }, { "creatorType": "author", "firstName": "Craig", "lastName": "Moritz" } ], "abstractNote": "Biodiversity hotspots, representing regions with high species endemism and conservation threat, have been mapped globally. Yet, biodiversity distribution data from within hotspots are too sparse for effective conservation in the face of rapid environmental change. Using frogs as indicators, ecological niche models under paleoclimates, and simultaneous Bayesian analyses of multispecies molecular data, we compare alternative hypotheses of assemblage-scale response to late Quaternary climate change. This reveals a hotspot within the Brazilian Atlantic forest hotspot. We show that the southern Atlantic forest was climatically unstable relative to the central region, which served as a large climatic refugium for neotropical species in the late Pleistocene. This sets new priorities for conservation in Brazil and establishes a validated approach to biodiversity prediction in other understudied, species-rich regions.", "publicationTitle": "Science (New York, N.Y.)", "publisher": "", "place": "", "date": "Feb 6, 2009", "volume": "323", "issue": "5915", "section": "", "partNumber": "", "partTitle": "", "pages": "785-789", "series": "", "seriesTitle": "", "seriesText": "", "journalAbbreviation": "Science", "DOI": "10.1126/science.1166955", "citationKey": "", "url": "", "accessDate": "", "PMID": "", "PMCID": "", "ISSN": "1095-9203", "archive": "", "archiveLocation": "", "shortTitle": "", "language": "eng", "libraryCatalog": "NCBI PubMed", "callNumber": "", "rights": "", "extra": "PMID: 19197066", "tags": [ { "tag": "Animals", "type": 1 }, { "tag": "Anura", "type": 1 }, { "tag": "Bayes Theorem", "type": 1 }, { "tag": "Biodiversity", "type": 1 }, { "tag": "Brazil", "type": 1 }, { "tag": "Conservation of Natural Resources", "type": 1 }, { "tag": "DNA, Mitochondrial", "type": 1 }, { "tag": "Demography", "type": 1 }, { "tag": "Ecosystem", "type": 1 }, { "tag": "Geography", "type": 1 }, { "tag": "Molecular Sequence Data", "type": 1 }, { "tag": "Mutation", "type": 1 }, { "tag": "Phylogeny", "type": 1 }, { "tag": "Population Dynamics", "type": 1 }, { "tag": "Time", "type": 1 }, { "tag": "Trees", "type": 1 }, { "tag": "Tropical Climate", "type": 1 } ], "collections": [], "relations": {}, "dateAdded": "2013-08-30T23:06:47Z", "dateModified": "2013-08-30T23:06:47Z" } }, { "key": "7QFPPWDQ", "version": 15, "library": { "type": "group", "id": 203572, "name": "Museum of Vertebrate Zoology", "links": { "alternate": { "href": "https://www.zotero.org/groups/museum_of_vertebrate_zoology", "type": "text/html" } } }, "links": { "self": { "href": "https://api.zotero.org/groups/203572/items/7QFPPWDQ", "type": "application/json" }, "alternate": { "href": "https://www.zotero.org/groups/museum_of_vertebrate_zoology/items/7QFPPWDQ", "type": "text/html" }, "up": { "href": "https://api.zotero.org/groups/203572/items/VNFA42QT", "type": "application/json" } }, "meta": { "createdByUser": { "id": 115811, "username": "mkoo", "name": "Michelle Koo", "links": { "alternate": { "href": "https://www.zotero.org/mkoo", "type": "text/html" } } } }, "data": { "key": "7QFPPWDQ", "version": 15, "parentItem": "VNFA42QT", "itemType": "attachment", "linkMode": "linked_url", "title": "PubMed entry", "accessDate": "2013-08-30T23:06:47Z", "url": "http://www.ncbi.nlm.nih.gov/pubmed/19197066", "note": "", "contentType": "text/html", "charset": "", "tags": [], "relations": {}, "dateAdded": "2013-08-30T23:06:47Z", "dateModified": "2013-08-30T23:06:47Z" } }, { "key": "BDBBRBIG", "version": 14, "library": { "type": "group", "id": 203572, "name": "Museum of Vertebrate Zoology", "links": { "alternate": { "href": "https://www.zotero.org/groups/museum_of_vertebrate_zoology", "type": "text/html" } } }, "links": { "self": { "href": "https://api.zotero.org/groups/203572/items/BDBBRBIG", "type": "application/json" }, "alternate": { "href": "https://www.zotero.org/groups/museum_of_vertebrate_zoology/items/BDBBRBIG", "type": "text/html" }, "up": { "href": "https://api.zotero.org/groups/203572/items/9BX9VRVK", "type": "application/json" } }, "meta": { "createdByUser": { "id": 115811, "username": "mkoo", "name": "Michelle Koo", "links": { "alternate": { "href": "https://www.zotero.org/mkoo", "type": "text/html" } } } }, "data": { "key": "BDBBRBIG", "version": 14, "parentItem": "9BX9VRVK", "itemType": "attachment", "linkMode": "linked_url", "title": "PubMed entry", "accessDate": "2013-08-30T23:06:34Z", "url": "http://www.ncbi.nlm.nih.gov/pubmed/22166838", "note": "", "contentType": "text/html", "charset": "", "tags": [], "relations": {}, "dateAdded": "2013-08-30T23:06:34Z", "dateModified": "2013-08-30T23:06:34Z" } }, { "key": "9BX9VRVK", "version": 14, "library": { "type": "group", "id": 203572, "name": "Museum of Vertebrate Zoology", "links": { "alternate": { "href": "https://www.zotero.org/groups/museum_of_vertebrate_zoology", "type": "text/html" } } }, "links": { "self": { "href": "https://api.zotero.org/groups/203572/items/9BX9VRVK", "type": "application/json" }, "alternate": { "href": "https://www.zotero.org/groups/museum_of_vertebrate_zoology/items/9BX9VRVK", "type": "text/html" } }, "meta": { "createdByUser": { "id": 115811, "username": "mkoo", "name": "Michelle Koo", "links": { "alternate": { "href": "https://www.zotero.org/mkoo", "type": "text/html" } } }, "creatorSummary": "Fouquet et al.", "parsedDate": "2012-03", "numChildren": 1 }, "data": { "key": "9BX9VRVK", "version": 14, "itemType": "journalArticle", "title": "Molecular phylogeny and morphometric analyses reveal deep divergence between Amazonia and Atlantic Forest species of Dendrophryniscus", "creators": [ { "creatorType": "author", "firstName": "Antoine", "lastName": "Fouquet" }, { "creatorType": "author", "firstName": "Renato", "lastName": "Recoder" }, { "creatorType": "author", "firstName": "Mauro, Jr", "lastName": "Teixeira" }, { "creatorType": "author", "firstName": "José", "lastName": "Cassimiro" }, { "creatorType": "author", "firstName": "Renata Cecília", "lastName": "Amaro" }, { "creatorType": "author", "firstName": "Agustín", "lastName": "Camacho" }, { "creatorType": "author", "firstName": "Roberta", "lastName": "Damasceno" }, { "creatorType": "author", "firstName": "Ana Carolina", "lastName": "Carnaval" }, { "creatorType": "author", "firstName": "Craig", "lastName": "Moritz" }, { "creatorType": "author", "firstName": "Miguel Trefaut", "lastName": "Rodrigues" } ], "abstractNote": "Dendrophryniscus is an early diverging clade of bufonids represented by few small-bodied species distributed in Amazonia and the Atlantic Forest. We used mitochondrial (414 bp of 12S, 575 bp of 16S genes) and nuclear DNA (785 bp of RAG-1) to investigate phylogenetic relationships and the timing of diversification within the genus. These molecular data were gathered from 23 specimens from 19 populations, including eight out of the 10 nominal species of the genus as well as Rhinella boulengeri. Analyses also included sequences of representatives of 18 other bufonid genera that were publically available. We also examined morphological characters to analyze differences within Dendrophryniscus. We found deep genetic divergence between an Amazonian and an Atlantic Forest clade, dating back to Eocene. Morphological data corroborate this distinction. We thus propose to assign the Amazonian species to a new genus, Amazonella. The species currently named R. boulengeri, which has been previously assigned to the genus Rhamphophryne, is shown to be closely related to Dendrophryniscus species. Our findings illustrate cryptic trends in bufonid morphological evolution, and point to a deep history of persistence and diversification within the Amazonian and Atlantic rainforests. We discuss our results in light of available paleoecological data and the biogeographic patterns observed in other similarly distributed groups.", "publicationTitle": "Molecular phylogenetics and evolution", "publisher": "", "place": "", "date": "Mar 2012", "volume": "62", "issue": "3", "section": "", "partNumber": "", "partTitle": "", "pages": "826-838", "series": "", "seriesTitle": "", "seriesText": "", "journalAbbreviation": "Mol. Phylogenet. Evol.", "DOI": "10.1016/j.ympev.2011.11.023", "citationKey": "", "url": "", "accessDate": "", "PMID": "", "PMCID": "", "ISSN": "1095-9513", "archive": "", "archiveLocation": "", "shortTitle": "", "language": "eng", "libraryCatalog": "NCBI PubMed", "callNumber": "", "rights": "", "extra": "PMID: 22166838", "tags": [ { "tag": "Animals", "type": 1 }, { "tag": "Biological Evolution", "type": 1 }, { "tag": "Bufonidae", "type": 1 }, { "tag": "DNA, Mitochondrial", "type": 1 }, { "tag": "Genes, RAG-1", "type": 1 }, { "tag": "Genes, rRNA", "type": 1 }, { "tag": "Molecular Sequence Data", "type": 1 }, { "tag": "Phylogeny", "type": 1 }, { "tag": "Phylogeography", "type": 1 } ], "collections": [], "relations": {}, "dateAdded": "2013-08-30T23:06:34Z", "dateModified": "2013-08-30T23:06:34Z" } }, { "key": "ZM7NK5FV", "version": 13, "library": { "type": "group", "id": 203572, "name": "Museum of Vertebrate Zoology", "links": { "alternate": { "href": "https://www.zotero.org/groups/museum_of_vertebrate_zoology", "type": "text/html" } } }, "links": { "self": { "href": "https://api.zotero.org/groups/203572/items/ZM7NK5FV", "type": "application/json" }, "alternate": { "href": "https://www.zotero.org/groups/museum_of_vertebrate_zoology/items/ZM7NK5FV", "type": "text/html" }, "up": { "href": "https://api.zotero.org/groups/203572/items/W48X3WBS", "type": "application/json" } }, "meta": { "createdByUser": { "id": 115811, "username": "mkoo", "name": "Michelle Koo", "links": { "alternate": { "href": "https://www.zotero.org/mkoo", "type": "text/html" } } } }, "data": { "key": "ZM7NK5FV", "version": 13, "parentItem": "W48X3WBS", "itemType": "attachment", "linkMode": "linked_url", "title": "PubMed entry", "accessDate": "2013-08-30T23:06:16Z", "url": "http://www.ncbi.nlm.nih.gov/pubmed/18588990", "note": "", "contentType": "text/html", "charset": "", "tags": [], "relations": {}, "dateAdded": "2013-08-30T23:06:16Z", "dateModified": "2013-08-30T23:06:16Z" } }, { "key": "W48X3WBS", "version": 13, "library": { "type": "group", "id": 203572, "name": "Museum of Vertebrate Zoology", "links": { "alternate": { "href": "https://www.zotero.org/groups/museum_of_vertebrate_zoology", "type": "text/html" } } }, "links": { "self": { "href": "https://api.zotero.org/groups/203572/items/W48X3WBS", "type": "application/json" }, "alternate": { "href": "https://www.zotero.org/groups/museum_of_vertebrate_zoology/items/W48X3WBS", "type": "text/html" } }, "meta": { "createdByUser": { "id": 115811, "username": "mkoo", "name": "Michelle Koo", "links": { "alternate": { "href": "https://www.zotero.org/mkoo", "type": "text/html" } } }, "creatorSummary": "Geurgas et al.", "parsedDate": "2008-10", "numChildren": 1 }, "data": { "key": "W48X3WBS", "version": 13, "itemType": "journalArticle", "title": "The genus Coleodactylus (Sphaerodactylinae, Gekkota) revisited: a molecular phylogenetic perspective", "creators": [ { "creatorType": "author", "firstName": "Silvia Rodrigues", "lastName": "Geurgas" }, { "creatorType": "author", "firstName": "Miguel Trefaut", "lastName": "Rodrigues" }, { "creatorType": "author", "firstName": "Craig", "lastName": "Moritz" } ], "abstractNote": "Nucleotide sequence data from a mitochondrial gene (16S) and two nuclear genes (c-mos, RAG-1) were used to evaluate the monophyly of the genus Coleodactylus, to provide the first phylogenetic hypothesis of relationships among its species in a cladistic framework, and to estimate the relative timing of species divergences. Maximum Parsimony, Maximum Likelihood and Bayesian analyses of the combined data sets retrieved Coleodactylus as a monophyletic genus, although weakly supported. Species were recovered as two genetically and morphological distinct clades, with C. amazonicus populations forming the sister taxon to the meridionalis group (C. brachystoma, C. meridionalis, C. natalensis, and C. septentrionalis). Within this group, C. septentrionalis was placed as the sister taxon to a clade comprising the rest of the species, C. meridionalis was recovered as the sister species to C. brachystoma, and C. natalensis was found nested within C. meridionalis. Divergence time estimates based on penalized likelihood and Bayesian dating methods do not support the previous hypothesis based on the Quaternary rain forest fragmentation model proposed to explain the diversification of the genus. The basal cladogenic event between major lineages of Coleodactylus was estimated to have occurred in the late Cretaceous (72.6+/-1.77 Mya), approximately at the same point in time than the other genera of Sphaerodactylinae diverged from each other. Within the meridionalis group, the split between C. septentrionalis and C. brachystoma+C. meridionalis was placed in the Eocene (46.4+/-4.22 Mya), and the divergence between C. brachystoma and C. meridionalis was estimated to have occurred in the Oligocene (29.3+/-4.33 Mya). Most intraspecific cladogenesis occurred through Miocene to Pliocene, and only for two conspecific samples and for C. natalensis could a Quaternary differentiation be assumed (1.9+/-1.3 Mya).", "publicationTitle": "Molecular phylogenetics and evolution", "publisher": "", "place": "", "date": "Oct 2008", "volume": "49", "issue": "1", "section": "", "partNumber": "", "partTitle": "", "pages": "92-101", "series": "", "seriesTitle": "", "seriesText": "", "journalAbbreviation": "Mol. Phylogenet. Evol.", "DOI": "10.1016/j.ympev.2008.05.043", "citationKey": "", "url": "", "accessDate": "", "PMID": "", "PMCID": "", "ISSN": "1095-9513", "archive": "", "archiveLocation": "", "shortTitle": "The genus Coleodactylus (Sphaerodactylinae, Gekkota) revisited", "language": "eng", "libraryCatalog": "NCBI PubMed", "callNumber": "", "rights": "", "extra": "PMID: 18588990", "tags": [ { "tag": "Animals", "type": 1 }, { "tag": "Bayes Theorem", "type": 1 }, { "tag": "DNA, Mitochondrial", "type": 1 }, { "tag": "Evolution, Molecular", "type": 1 }, { "tag": "Genes, Mitochondrial", "type": 1 }, { "tag": "Genes, RAG-1", "type": 1 }, { "tag": "Genes, mos", "type": 1 }, { "tag": "Genes, rRNA", "type": 1 }, { "tag": "Genetic Speciation", "type": 1 }, { "tag": "Likelihood Functions", "type": 1 }, { "tag": "Lizards", "type": 1 }, { "tag": "Mitochondria", "type": 1 }, { "tag": "Models, Genetic", "type": 1 }, { "tag": "Phylogeny", "type": 1 }, { "tag": "RNA, Ribosomal, 16S", "type": 1 }, { "tag": "Sequence Analysis, DNA", "type": 1 }, { "tag": "Sequence Homology, Nucleic Acid", "type": 1 }, { "tag": "Species Specificity", "type": 1 } ], "collections": [], "relations": {}, "dateAdded": "2013-08-30T23:06:16Z", "dateModified": "2013-08-30T23:06:16Z" } }, { "key": "E2UGCPK4", "version": 12, "library": { "type": "group", "id": 203572, "name": "Museum of Vertebrate Zoology", "links": { "alternate": { "href": "https://www.zotero.org/groups/museum_of_vertebrate_zoology", "type": "text/html" } } }, "links": { "self": { "href": "https://api.zotero.org/groups/203572/items/E2UGCPK4", "type": "application/json" }, "alternate": { "href": "https://www.zotero.org/groups/museum_of_vertebrate_zoology/items/E2UGCPK4", "type": "text/html" }, "up": { "href": "https://api.zotero.org/groups/203572/items/MJR7R9U7", "type": "application/json" } }, "meta": { "createdByUser": { "id": 115811, "username": "mkoo", "name": "Michelle Koo", "links": { "alternate": { "href": "https://www.zotero.org/mkoo", "type": "text/html" } } } }, "data": { "key": "E2UGCPK4", "version": 12, "parentItem": "MJR7R9U7", "itemType": "attachment", "linkMode": "linked_url", "title": "PubMed entry", "accessDate": "2013-08-30T23:05:26Z", "url": "http://www.ncbi.nlm.nih.gov/pubmed/20519219", "note": "", "contentType": "text/html", "charset": "", "tags": [], "relations": {}, "dateAdded": "2013-08-30T23:05:26Z", "dateModified": "2013-08-30T23:05:26Z" } }, { "key": "MJR7R9U7", "version": 12, "library": { "type": "group", "id": 203572, "name": "Museum of Vertebrate Zoology", "links": { "alternate": { "href": "https://www.zotero.org/groups/museum_of_vertebrate_zoology", "type": "text/html" } } }, "links": { "self": { "href": "https://api.zotero.org/groups/203572/items/MJR7R9U7", "type": "application/json" }, "alternate": { "href": "https://www.zotero.org/groups/museum_of_vertebrate_zoology/items/MJR7R9U7", "type": "text/html" } }, "meta": { "createdByUser": { "id": 115811, "username": "mkoo", "name": "Michelle Koo", "links": { "alternate": { "href": "https://www.zotero.org/mkoo", "type": "text/html" } } }, "creatorSummary": "Leaché and Fujita", "parsedDate": "2010-10-22", "numChildren": 1 }, "data": { "key": "MJR7R9U7", "version": 12, "itemType": "journalArticle", "title": "Bayesian species delimitation in West African forest geckos (Hemidactylus fasciatus)", "creators": [ { "creatorType": "author", "firstName": "Adam D", "lastName": "Leaché" }, { "creatorType": "author", "firstName": "Matthew K", "lastName": "Fujita" } ], "abstractNote": "Genealogical data are an important source of evidence for delimiting species, yet few statistical methods are available for calculating the probabilities associated with different species delimitations. Bayesian species delimitation uses reversible-jump Markov chain Monte Carlo (rjMCMC) in conjunction with a user-specified guide tree to estimate the posterior distribution for species delimitation models containing different numbers of species. We apply Bayesian species delimitation to investigate the speciation history of forest geckos (Hemidactylus fasciatus) from tropical West Africa using five nuclear loci (and mtDNA) for 51 specimens representing 10 populations. We find that species diversity in H. fasciatus is currently underestimated, and describe three new species to reflect the most conservative estimate for the number of species in this complex. We examine the impact of the guide tree, and the prior distributions on ancestral population sizes () and root age (τ(0)), on the posterior probabilities for species delimitation. Mis-specification of the guide tree or the prior distribution for can result in strong support for models containing more species. We describe a new statistic for summarizing the posterior distribution of species delimitation models, called speciation probabilities, which summarize the posterior support for each speciation event on the starting guide tree.", "publicationTitle": "Proceedings. Biological sciences / The Royal Society", "publisher": "", "place": "", "date": "Oct 22, 2010", "volume": "277", "issue": "1697", "section": "", "partNumber": "", "partTitle": "", "pages": "3071-3077", "series": "", "seriesTitle": "", "seriesText": "", "journalAbbreviation": "Proc. Biol. Sci.", "DOI": "10.1098/rspb.2010.0662", "citationKey": "", "url": "", "accessDate": "", "PMID": "", "PMCID": "", "ISSN": "1471-2954", "archive": "", "archiveLocation": "", "shortTitle": "", "language": "eng", "libraryCatalog": "NCBI PubMed", "callNumber": "", "rights": "", "extra": "PMID: 20519219", "tags": [ { "tag": "Animals", "type": 1 }, { "tag": "Bayes Theorem", "type": 1 }, { "tag": "Biodiversity", "type": 1 }, { "tag": "Genetic Speciation", "type": 1 }, { "tag": "Lizards", "type": 1 }, { "tag": "Markov Chains", "type": 1 }, { "tag": "Monte Carlo Method", "type": 1 }, { "tag": "Population Density", "type": 1 }, { "tag": "Population Dynamics", "type": 1 } ], "collections": [], "relations": {}, "dateAdded": "2013-08-30T23:05:26Z", "dateModified": "2013-08-30T23:05:26Z" } }, { "key": "3GNKDGU7", "version": 11, "library": { "type": "group", "id": 203572, "name": "Museum of Vertebrate Zoology", "links": { "alternate": { "href": "https://www.zotero.org/groups/museum_of_vertebrate_zoology", "type": "text/html" } } }, "links": { "self": { "href": "https://api.zotero.org/groups/203572/items/3GNKDGU7", "type": "application/json" }, "alternate": { "href": "https://www.zotero.org/groups/museum_of_vertebrate_zoology/items/3GNKDGU7", "type": "text/html" }, "up": { "href": "https://api.zotero.org/groups/203572/items/FVR36T87", "type": "application/json" } }, "meta": { "createdByUser": { "id": 115811, "username": "mkoo", "name": "Michelle Koo", "links": { "alternate": { "href": "https://www.zotero.org/mkoo", "type": "text/html" } } } }, "data": { "key": "3GNKDGU7", "version": 11, "parentItem": "FVR36T87", "itemType": "attachment", "linkMode": "linked_url", "title": "PubMed entry", "accessDate": "2013-08-30T23:02:50Z", "url": "http://www.ncbi.nlm.nih.gov/pubmed/20961901", "note": "", "contentType": "text/html", "charset": "", "tags": [], "relations": {}, "dateAdded": "2013-08-30T23:02:50Z", "dateModified": "2013-08-30T23:02:50Z" } }, { "key": "FVR36T87", "version": 11, "library": { "type": "group", "id": 203572, "name": "Museum of Vertebrate Zoology", "links": { "alternate": { "href": "https://www.zotero.org/groups/museum_of_vertebrate_zoology", "type": "text/html" } } }, "links": { "self": { "href": "https://api.zotero.org/groups/203572/items/FVR36T87", "type": "application/json" }, "alternate": { "href": "https://www.zotero.org/groups/museum_of_vertebrate_zoology/items/FVR36T87", "type": "text/html" } }, "meta": { "createdByUser": { "id": 115811, "username": "mkoo", "name": "Michelle Koo", "links": { "alternate": { "href": "https://www.zotero.org/mkoo", "type": "text/html" } } }, "creatorSummary": "Bauer et al.", "parsedDate": "2011-02-22", "numChildren": 1 }, "data": { "key": "FVR36T87", "version": 11, "itemType": "journalArticle", "title": "Availability of new Bayesian-delimited gecko names and the importance of character-based species descriptions", "creators": [ { "creatorType": "author", "firstName": "Aaron M", "lastName": "Bauer" }, { "creatorType": "author", "firstName": "James F", "lastName": "Parham" }, { "creatorType": "author", "firstName": "Rafe M", "lastName": "Brown" }, { "creatorType": "author", "firstName": "Bryan L", "lastName": "Stuart" }, { "creatorType": "author", "firstName": "Lee", "lastName": "Grismer" }, { "creatorType": "author", "firstName": "Theodore J", "lastName": "Papenfuss" }, { "creatorType": "author", "firstName": "Wolfgang", "lastName": "Böhme" }, { "creatorType": "author", "firstName": "Jay M", "lastName": "Savage" }, { "creatorType": "author", "firstName": "Salvador", "lastName": "Carranza" }, { "creatorType": "author", "firstName": "Jesse L", "lastName": "Grismer" }, { "creatorType": "author", "firstName": "Philipp", "lastName": "Wagner" }, { "creatorType": "author", "firstName": "Andreas", "lastName": "Schmitz" }, { "creatorType": "author", "firstName": "Natalia B", "lastName": "Ananjeva" }, { "creatorType": "author", "firstName": "Robert F", "lastName": "Inger" } ], "abstractNote": "", "publicationTitle": "Proceedings. Biological sciences / The Royal Society", "publisher": "", "place": "", "date": "Feb 22, 2011", "volume": "278", "issue": "1705", "section": "", "partNumber": "", "partTitle": "", "pages": "490-492; discussion 493-495", "series": "", "seriesTitle": "", "seriesText": "", "journalAbbreviation": "Proc. Biol. Sci.", "DOI": "10.1098/rspb.2010.1330", "citationKey": "", "url": "", "accessDate": "", "PMID": "", "PMCID": "", "ISSN": "1471-2954", "archive": "", "archiveLocation": "", "shortTitle": "", "language": "eng", "libraryCatalog": "NCBI PubMed", "callNumber": "", "rights": "", "extra": "PMID: 20961901", "tags": [ { "tag": "Animals", "type": 1 }, { "tag": "Bayes Theorem", "type": 1 }, { "tag": "Genetic Speciation", "type": 1 }, { "tag": "Lizards", "type": 1 }, { "tag": "Species Specificity", "type": 1 }, { "tag": "Terminology as Topic", "type": 1 } ], "collections": [], "relations": {}, "dateAdded": "2013-08-30T23:02:50Z", "dateModified": "2013-08-30T23:02:50Z" } }, { "key": "BBHUCUX6", "version": 10, "library": { "type": "group", "id": 203572, "name": "Museum of Vertebrate Zoology", "links": { "alternate": { "href": "https://www.zotero.org/groups/museum_of_vertebrate_zoology", "type": "text/html" } } }, "links": { "self": { "href": "https://api.zotero.org/groups/203572/items/BBHUCUX6", "type": "application/json" }, "alternate": { "href": "https://www.zotero.org/groups/museum_of_vertebrate_zoology/items/BBHUCUX6", "type": "text/html" } }, "meta": { "createdByUser": { "id": 115811, "username": "mkoo", "name": "Michelle Koo", "links": { "alternate": { "href": "https://www.zotero.org/mkoo", "type": "text/html" } } }, "creatorSummary": "Moritz et al.", "parsedDate": "2008-10-10", "numChildren": 0 }, "data": { "key": "BBHUCUX6", "version": 10, "itemType": "journalArticle", "title": "Impact of a Century of Climate Change on Small-Mammal Communities in Yosemite National Park, USA", "creators": [ { "creatorType": "author", "firstName": "Craig", "lastName": "Moritz" }, { "creatorType": "author", "firstName": "James L.", "lastName": "Patton" }, { "creatorType": "author", "firstName": "Chris J.", "lastName": "Conroy" }, { "creatorType": "author", "firstName": "Juan L.", "lastName": "Parra" }, { "creatorType": "author", "firstName": "Gary C.", "lastName": "White" }, { "creatorType": "author", "firstName": "Steven R.", "lastName": "Beissinger" } ], "abstractNote": "We provide a century-scale view of small-mammal responses to global warming, without confounding effects of land-use change, by repeating Grinnell's early-20th century survey across a 3000-meter-elevation gradient that spans Yosemite National Park, California, USA. Using occupancy modeling to control for variation in detectability, we show substantial ([~]500 meters on average) upward changes in elevational limits for half of 28 species monitored, consistent with the observed [~]3{degrees}C increase in minimum temperatures. Formerly low-elevation species expanded their ranges and high-elevation species contracted theirs, leading to changed community composition at mid- and high elevations. Elevational replacement among congeners changed because species' responses were idiosyncratic. Though some high-elevation species are threatened, protection of elevation gradients allows other species to respond via migration.", "publicationTitle": "Science", "publisher": "", "place": "", "date": "October 10, 2008", "volume": "322", "issue": "5899", "section": "", "partNumber": "", "partTitle": "", "pages": "261-264", "series": "", "seriesTitle": "", "seriesText": "", "journalAbbreviation": "", "DOI": "10.1126/science.1163428", "citationKey": "", "url": "http://www.sciencemag.org/cgi/content/abstract/322/5899/261", "accessDate": "2009-02-19T04:21:00Z", "PMID": "", "PMCID": "", "ISSN": "", "archive": "", "archiveLocation": "", "shortTitle": "", "language": "", "libraryCatalog": "HighWire", "callNumber": "", "rights": "", "extra": "", "tags": [ { "tag": "Climate Change" }, { "tag": "Grinnell Resurvey project" }, { "tag": "Sierra Nevada" }, { "tag": "Yosemite" } ], "collections": [], "relations": {}, "dateAdded": "2013-08-30T22:19:05Z", "dateModified": "2013-08-30T22:19:05Z" } }, { "key": "9AV8NUUR", "version": 9, "library": { "type": "group", "id": 203572, "name": "Museum of Vertebrate Zoology", "links": { "alternate": { "href": "https://www.zotero.org/groups/museum_of_vertebrate_zoology", "type": "text/html" } } }, "links": { "self": { "href": "https://api.zotero.org/groups/203572/items/9AV8NUUR", "type": "application/json" }, "alternate": { "href": "https://www.zotero.org/groups/museum_of_vertebrate_zoology/items/9AV8NUUR", "type": "text/html" } }, "meta": { "createdByUser": { "id": 115811, "username": "mkoo", "name": "Michelle Koo", "links": { "alternate": { "href": "https://www.zotero.org/mkoo", "type": "text/html" } } }, "creatorSummary": "Wieczorek et al.", "parsedDate": "2012-01-06", "numChildren": 0 }, "data": { "key": "9AV8NUUR", "version": 9, "itemType": "journalArticle", "title": "Darwin Core: An Evolving Community-Developed Biodiversity Data Standard", "creators": [ { "creatorType": "author", "firstName": "John", "lastName": "Wieczorek" }, { "creatorType": "author", "firstName": "David", "lastName": "Bloom" }, { "creatorType": "author", "firstName": "Robert", "lastName": "Guralnick" }, { "creatorType": "author", "firstName": "Stan", "lastName": "Blum" }, { "creatorType": "author", "firstName": "Markus", "lastName": "Döring" }, { "creatorType": "author", "firstName": "Renato", "lastName": "Giovanni" }, { "creatorType": "author", "firstName": "Tim", "lastName": "Robertson" }, { "creatorType": "author", "firstName": "David", "lastName": "Vieglais" } ], "abstractNote": "Biodiversity data derive from myriad sources stored in various formats on many distinct hardware and software platforms. An essential step towards understanding global patterns of biodiversity is to provide a standardized view of these heterogeneous data sources to improve interoperability. Fundamental to this advance are definitions of common terms. This paper describes the evolution and development of Darwin Core, a data standard for publishing and integrating biodiversity information. We focus on the categories of terms that define the standard, differences between simple and relational Darwin Core, how the standard has been implemented, and the community processes that are essential for maintenance and growth of the standard. We present case-study extensions of the Darwin Core into new research communities, including metagenomics and genetic resources. We close by showing how Darwin Core records are integrated to create new knowledge products documenting species distributions and changes due to environmental perturbations.", "publicationTitle": "PLoS ONE", "publisher": "", "place": "", "date": "January 6, 2012", "volume": "7", "issue": "1", "section": "", "partNumber": "", "partTitle": "", "pages": "e29715", "series": "", "seriesTitle": "", "seriesText": "", "journalAbbreviation": "PLoS ONE", "DOI": "10.1371/journal.pone.0029715", "citationKey": "", "url": "http://dx.doi.org/10.1371/journal.pone.0029715", "accessDate": "2013-02-07T00:42:48Z", "PMID": "", "PMCID": "", "ISSN": "", "archive": "", "archiveLocation": "", "shortTitle": "Darwin Core", "language": "", "libraryCatalog": "PLoS ONE", "callNumber": "", "rights": "", "extra": "", "tags": [], "collections": [], "relations": {}, "dateAdded": "2013-08-30T22:17:51Z", "dateModified": "2013-08-30T22:17:51Z" } }, { "key": "H5IUNK8P", "version": 8, "library": { "type": "group", "id": 203572, "name": "Museum of Vertebrate Zoology", "links": { "alternate": { "href": "https://www.zotero.org/groups/museum_of_vertebrate_zoology", "type": "text/html" } } }, "links": { "self": { "href": "https://api.zotero.org/groups/203572/items/H5IUNK8P", "type": "application/json" }, "alternate": { "href": "https://www.zotero.org/groups/museum_of_vertebrate_zoology/items/H5IUNK8P", "type": "text/html" } }, "meta": { "createdByUser": { "id": 115811, "username": "mkoo", "name": "Michelle Koo", "links": { "alternate": { "href": "https://www.zotero.org/mkoo", "type": "text/html" } } }, "creatorSummary": "Smith et al.", "parsedDate": "2013", "numChildren": 0 }, "data": { "key": "H5IUNK8P", "version": 8, "itemType": "journalArticle", "title": "Evaluation of species distribution models by resampling of sites surveyed a century ago by Joseph Grinnell", "creators": [ { "creatorType": "author", "firstName": "Adam B.", "lastName": "Smith" }, { "creatorType": "author", "firstName": "Maria J.", "lastName": "Santos" }, { "creatorType": "author", "firstName": "Michelle S.", "lastName": "Koo" }, { "creatorType": "author", "firstName": "Karen M. C.", "lastName": "Rowe" }, { "creatorType": "author", "firstName": "Kevin C.", "lastName": "Rowe" }, { "creatorType": "author", "firstName": "James L.", "lastName": "Patton" }, { "creatorType": "author", "firstName": "John D.", "lastName": "Perrine" }, { "creatorType": "author", "firstName": "Steven R.", "lastName": "Beissinger" }, { "creatorType": "author", "firstName": "Craig", "lastName": "Moritz" } ], "abstractNote": "Species distribution models (SDMs) are commonly applied to predict species’ responses to anticipated global change, but lack of data from future time periods precludes assessment of their reliability. Instead, performance against test data in the same era is assumed to correlate with accuracy in the future. Moreover, high-confidence absence data is required for testing model accuracy but is often unavailable since a species may be present when undetected. Here we evaluate the performance of eight SDMs trained with historic (1900–1939) or modern (1970–2009) climate data and occurrence records for 18 mammalian species. Models were projected to the same or the opposing time period and evaluated with data obtained from surveys conducted by Joseph Grinnell and his colleagues in the Sierra Nevada of California from 1900 to 1939 and modern resurveys from 2003 to 2011. Occupancy modeling was used to confidently assign absences at test sites where species were undetected. SDMs were evaluated using species’ presences combined with this high-confidence absence (HCA) set, a low-confidence set in which non-detections were assumed to indicate absence (LCA), and randomly located ‘pseudoabsences’ (PSA). Model performance increased significantly with the quality of absences (mean AUC ± SE: 0.76 ± 0.01 for PSA, 0.79 ± 0.01 for LCA, and 0.81 ± 0.01 for HCA), and apparent differences between SDMs declined as the quality of test absences increased. Models projecting across time performed as well as when projecting within the same time period when assessed with threshold-independent metrics. However, accuracy of presence and absence predictions sometimes declined in cross-era projections. Although most variation in performance occurred among species, autecological traits were only weakly correlated with model accuracy. Our study indicates that a) the quality of evaluation data affects assessments of model performance; b) within-era performance correlates positively but unreliably with cross-era performance; and c) SDMs can be reliably but cautiously projected across time.", "publicationTitle": "Ecography", "publisher": "", "place": "", "date": "2013", "volume": "", "issue": "", "section": "", "partNumber": "", "partTitle": "", "pages": "no–no", "series": "", "seriesTitle": "", "seriesText": "", "journalAbbreviation": "", "DOI": "10.1111/j.1600-0587.2013.00107.x", "citationKey": "", "url": "http://onlinelibrary.wiley.com/doi/10.1111/j.1600-0587.2013.00107.x/abstract", "accessDate": "2013-04-25T17:36:19Z", "PMID": "", "PMCID": "", "ISSN": "1600-0587", "archive": "", "archiveLocation": "", "shortTitle": "", "language": "en", "libraryCatalog": "Wiley Online Library", "callNumber": "", "rights": "© 2013 The Authors", "extra": "", "tags": [ { "tag": "Grinnell Resurvey project" }, { "tag": "Species Distribution Modeling" } ], "collections": [], "relations": {}, "dateAdded": "2013-08-30T22:16:43Z", "dateModified": "2013-08-30T22:16:43Z" } }, { "key": "NH5ATHMJ", "version": 8, "library": { "type": "group", "id": 203572, "name": "Museum of Vertebrate Zoology", "links": { "alternate": { "href": "https://www.zotero.org/groups/museum_of_vertebrate_zoology", "type": "text/html" } } }, "links": { "self": { "href": "https://api.zotero.org/groups/203572/items/NH5ATHMJ", "type": "application/json" }, "alternate": { "href": "https://www.zotero.org/groups/museum_of_vertebrate_zoology/items/NH5ATHMJ", "type": "text/html" } }, "meta": { "createdByUser": { "id": 115811, "username": "mkoo", "name": "Michelle Koo", "links": { "alternate": { "href": "https://www.zotero.org/mkoo", "type": "text/html" } } }, "creatorSummary": "Leaché et al.", "parsedDate": "2009-07-28", "numChildren": 0 }, "data": { "key": "NH5ATHMJ", "version": 8, "itemType": "journalArticle", "title": "Quantifying ecological, morphological, and genetic variation to delimit species in the coast horned lizard species complex (Phrynosoma)", "creators": [ { "creatorType": "author", "firstName": "Adam D.", "lastName": "Leaché" }, { "creatorType": "author", "firstName": "Michelle S.", "lastName": "Koo" }, { "creatorType": "author", "firstName": "Carol L.", "lastName": "Spencer" }, { "creatorType": "author", "firstName": "Theodore J.", "lastName": "Papenfuss" }, { "creatorType": "author", "firstName": "Robert N.", "lastName": "Fisher" }, { "creatorType": "author", "firstName": "Jimmy A.", "lastName": "McGuire" } ], "abstractNote": "Lineage separation and divergence form a temporally extended process whereby populations may diverge genetically, morphologically, or ecologically, and these contingent properties of species provide the operational criteria necessary for species delimitation. We inferred the historical process of lineage formation in the coast horned lizard () species complex by evaluating a diversity of operational species criteria, including divergence in mtDNA (98 specimens; 2,781 bp) and nuclear loci (−, 1,054 bp; 529 bp), ecological niches (11 bioclimatic variables; 285 unique localities), and cranial horn shapes (493 specimens; 16 landmarks). A phylogenetic analysis of mtDNA recovers 5 phylogeographic groups arranged latitudinally along the Baja California Peninsula and in California. The 2 southern phylogeographic groups exhibit concordance between genetic, morphological, and ecological divergence; however, differentiation is weak or absent at more recent levels defined by phylogeographic breaks in California. Interpreting these operational species criteria together suggests that there are 3 ecologically divergent and morphologically diagnosable species within the complex. Our 3-species taxonomic hypothesis invokes a deep coalescence event when fitting the mtDNA genealogy into the species tree, which is not unexpected for populations that have diverged recently. Although the hypothesis that the 3 phylogeographic groups distributed across California each represent distinctive species is not supported by all of the operational species criteria evaluated in this study, the conservation status of the imperiled populations represented by these genealogical units remains critical.", "publicationTitle": "Proceedings of the National Academy of Sciences", "publisher": "", "place": "", "date": "July 28, 2009", "volume": "106", "issue": "30", "section": "", "partNumber": "", "partTitle": "", "pages": "12418-12423", "series": "", "seriesTitle": "", "seriesText": "", "journalAbbreviation": "", "DOI": "10.1073/pnas.0906380106", "citationKey": "", "url": "http://www.pnas.org/content/106/30/12418.abstract", "accessDate": "2009-08-04T17:29:03Z", "PMID": "", "PMCID": "", "ISSN": "", "archive": "", "archiveLocation": "", "shortTitle": "", "language": "", "libraryCatalog": "PNAS", "callNumber": "", "rights": "", "extra": "", "tags": [ { "tag": "Phrynosoma" }, { "tag": "Phylogeography" }, { "tag": "Species delimitation" } ], "collections": [], "relations": {}, "dateAdded": "2013-08-30T22:16:33Z", "dateModified": "2013-08-30T22:16:33Z" } } ]