Artigo Acesso aberto Revisado por pares

A coalescent perspective on delimiting and naming species: a reply to Bauer et al.

2010; Royal Society; Volume: 278; Issue: 1705 Linguagem: Inglês

10.1098/rspb.2010.1864

ISSN

1471-2954

Autores

Matthew K. Fujita, Adam D. Leaché,

Tópico(s)

Forest Ecology and Biodiversity Studies

Resumo

Restricted accessMoreSectionsView Full TextView PDF ToolsAdd to favoritesDownload CitationsTrack Citations ShareShare onFacebookTwitterLinked InRedditEmail Cite this article Fujita Matthew K. and Leaché Adam D. 2011A coalescent perspective on delimiting and naming species: a reply to Bauer et al.Proc. R. Soc. B.278493–495http://doi.org/10.1098/rspb.2010.1864SectionRestricted accessComments and invited repliesA coalescent perspective on delimiting and naming species: a reply to Bauer et al. Matthew K. Fujita Matthew K. Fujita Museum of Comparative Zoology, Department of Organismic and Evolutionary Biology, Harvard University, 26 Oxford Street, Cambridge, MA 02138, USA [email protected] Google Scholar Find this author on PubMed Search for more papers by this author and Adam D. Leaché Adam D. Leaché Burke Museum and Department of Biology, University of Washington, Seattle, WA 98195, USA Google Scholar Find this author on PubMed Search for more papers by this author Matthew K. Fujita Matthew K. Fujita Museum of Comparative Zoology, Department of Organismic and Evolutionary Biology, Harvard University, 26 Oxford Street, Cambridge, MA 02138, USA [email protected] Google Scholar Find this author on PubMed and Adam D. Leaché Adam D. Leaché Burke Museum and Department of Biology, University of Washington, Seattle, WA 98195, USA Google Scholar Find this author on PubMed Published:20 October 2010https://doi.org/10.1098/rspb.2010.1864References1Darwin C.. 1859 The origin of species, 1st edn. Cambridge, MA: Harvard University Press. Google Scholar2Leaché A. D.& Fujita M. K.. 2010 Bayesian species delimitation in West African forest geckos (Hemidactylus fasciatus). Proc. R. Soc. B 277, 3071–3077.doi:10.1098/rspb.2010.0662 (doi:10.1098/rspb.2010.0662). Link, ISI, Google Scholar3Bauer A. M., et al. 2011 Availability of new Bayesian-delimited gecko names and the importance of character-based species descriptions. Proc. R. Soc. B 278, 490–492. Link, ISI, Google Scholar4ICZN (International Commission on Zoological Nomenclature). 1999 International Code of Zoological Nomenclature, 4th edn. London, UK: International Trust for Zoological Nomenclature. Google Scholar5Isaac N. J., Mallet J.& Mace G. M.. 2004 Taxonomic inflation: its influence on macroecology and conservation. Trends Ecol. Evol. 19, 464–469.doi:10.1016/j.tree.2004.06.004 (doi:10.1016/j.tree.2004.06.004). Crossref, PubMed, ISI, Google Scholar6Coyne J. A.& Orr H. A.. 2003 Speciation. Sunderland, MA: Sinauer Associates. Google Scholar7White M. J. D.. 1978 Modes of speciation. San Francisco, CA: W. H. Freeman and Company. Google Scholar8Yang Z.& Rannala B.. 2010 Bayesian species delimitation using multilocus sequence data. Proc. Natl Acad. Sci. USA 107, 9264–9269.doi:10.1073/pnas.0913022107 (doi:10.1073/pnas.0913022107). Crossref, PubMed, ISI, Google Scholar9Rannala B.& Yang Z.. 2003 Bayes estimation of species divergence times and ancestral population sizes using DNA sequences from multiple loci. Genetics 164, 1645–1656. Crossref, PubMed, ISI, Google Scholar10de Queiroz K.. 1998 The general lineage concept of species, species criteria, and the process of speciation: a conceptual unification and terminological recommendations. Endless forms: species and speciation (eds , Howard D. J.& Berlocher S. H.), pp. 57–75. Oxford, UK: Oxford University Press. Google Scholar11Carstens B. C.& Knowles L. L.. 2007 Estimating species phylogeny from gene-tree probabilities despite incomplete lineage sorting: an example from Melanoplus grasshoppers. Syst. Biol. 56, 400–411.doi:10.1080/10635150701405560 (doi:10.1080/10635150701405560). Crossref, PubMed, ISI, Google Scholar12Knowles L. L.& Carstens B. C.. 2007 Delimiting species without monophyletic gene trees. Syst. Biol. 56, 887–895.doi:10.1080/10635150701701091 (doi:10.1080/10635150701701091). Crossref, PubMed, ISI, Google Scholar13Edwards S. V.. 2009 Is a new and general theory of molecular systematics emerging? Evolution 63, 1–19.doi:10.1111/j.1558-5646.2008.00549.x (doi:10.1111/j.1558-5646.2008.00549.x). Crossref, PubMed, ISI, Google Scholar14Carstens B. C.& Dewey T. A.. 2010 Species delimitation using a combined coalescent and information-theoretic approach: an example from North American myotis bats. Syst. Biol. 59, 400–414.doi:10.1093/sysbio/syq024 (doi:10.1093/sysbio/syq024). Crossref, PubMed, ISI, Google Scholar15Padial J. M., Miralles A., De la Riva I.& Vences M.. 2010 The integrative future of taxonomy. Front. Zool. 7, 16.doi:10.1186/1742-9994-7-16 (doi:10.1186/1742-9994-7-16). Crossref, PubMed, ISI, Google Scholar16Ezard T. H. G., Pearson P. N.& Purvis A.. 2010 Algorithmic approaches to aid species' delimitation in multidimensional morphospace. BMC Evol. Biol. 10, 175.doi:10.1186/1471-2148-10-175 (doi:10.1186/1471-2148-10-175). Crossref, PubMed, ISI, Google Scholar Previous ArticleNext Article VIEW FULL TEXT DOWNLOAD PDF FiguresRelatedReferencesDetailsCited by Ebach M (2022) AI and the Modern Hubris Goethe in the Age of Artificial Intelligence, 10.1007/978-981-19-6741-2_2, (13-25), . Burbrink F and Ruane S Contemporary Philosophy and Methods for Studying Speciation and Delimiting Species, Ichthyology & Herpetology, 10.1643/h2020073, 109:3 Leaché A, Davis H, Singhal S, Fujita M, Lahti M and Zamudio K (2021) Phylogenomic Assessment of Biodiversity Using a Reference-Based Taxonomy: An Example With Horned Lizards (Phrynosoma), Frontiers in Ecology and Evolution, 10.3389/fevo.2021.678110, 9 Mason N, Fletcher N, Gill B, Funk W and Zamudio K (2020) Coalescent-based species delimitation is sensitive to geographic sampling and isolation by distance, Systematics and Biodiversity, 10.1080/14772000.2020.1730475, 18:3, (269-280), Online publication date: 2-Apr-2020. Rull V (2020) Neotropical Diversification: Historical Overview and Conceptual Insights Neotropical Diversification: Patterns and Processes, 10.1007/978-3-030-31167-4_2, (13-49), . Villamil J, Avila L, Morando M, Sites J, Leaché A, Maneyro R and Camargo A (2019) Coalescent-based species delimitation in the sand lizards of the Liolaemus wiegmannii complex (Squamata: Liolaemidae), Molecular Phylogenetics and Evolution, 10.1016/j.ympev.2019.05.024, 138, (89-101), Online publication date: 1-Sep-2019. Yang L, Kong H, Huang J and Kang M (2019) Different species or genetically divergent populations? Integrative species delimitation of the Primulina hochiensis complex from isolated karst habitats, Molecular Phylogenetics and Evolution, 10.1016/j.ympev.2018.12.011, 132, (219-231), Online publication date: 1-Mar-2019. Johnson N, Smith C, Pfeiffer J, Randklev C, Williams J and Austin J (2018) Integrative taxonomy resolves taxonomic uncertainty for freshwater mussels being considered for protection under the U.S. Endangered Species Act, Scientific Reports, 10.1038/s41598-018-33806-z, 8:1 Lagourgue L, Puillandre N and Payri C (2018) Exploring the Udoteaceae diversity (Bryopsidales, Chlorophyta) in the Caribbean region based on molecular and morphological data, Molecular Phylogenetics and Evolution, 10.1016/j.ympev.2018.06.023, 127, (758-769), Online publication date: 1-Oct-2018. Reyes-Velasco J, Manthey J, Bourgeois Y, Freilich X, Boissinot S and Chiang T (2018) Revisiting the phylogeography, demography and taxonomy of the frog genus Ptychadena in the Ethiopian highlands with the use of genome-wide SNP data, PLOS ONE, 10.1371/journal.pone.0190440, 13:2, (e0190440) Ramírez-Reyes T, Piñero D, Flores-Villela O and Vázquez-Domínguez E (2017) Molecular systematics, species delimitation and diversification patterns of the Phyllodactylus lanei complex (Gekkota: Phyllodactylidae) in Mexico, Molecular Phylogenetics and Evolution, 10.1016/j.ympev.2017.07.008, 115, (82-94), Online publication date: 1-Oct-2017. Díaz-Cárdenas B, Ruiz-Sanchez E, Castro-Felix P, Castañeda-Gaytán G, Ruiz-Santana S and Gadsden H (2017) Species delimitation of the blue-spotted spiny lizard within a multilocus, multispecies coalescent framework, results in the recognition of a new Sceloporus species, Molecular Phylogenetics and Evolution, 10.1016/j.ympev.2017.04.004, 111, (185-195), Online publication date: 1-Jun-2017. Willis S and Chiang T (2017) One species or four? Yes!...and, no. Or, arbitrary assignment of lineages to species obscures the diversification processes of Neotropical fishes, PLOS ONE, 10.1371/journal.pone.0172349, 12:2, (e0172349) Liu F, Wang M, Damm U, Crous P and Cai L (2016) Species boundaries in plant pathogenic fungi: a Colletotrichum case study, BMC Evolutionary Biology, 10.1186/s12862-016-0649-5, 16:1, Online publication date: 1-Dec-2016. Rocha S, Perera A, Bunbury N, Kaiser-Bunbury C and Harris D (2016) Speciation history and species-delimitation within the Seychelles Bronze geckos, Ailuronyx spp.: molecular and morphological evidence , Biological Journal of the Linnean Society, 10.1111/bij.12895, Online publication date: 1-Oct-2016. Pyron R, Hsieh F, Lemmon A, Lemmon E and Hendry C (2016) Integrating phylogenomic and morphological data to assess candidate species-delimitation models in brown and red-bellied snakes ( Storeria ) , Zoological Journal of the Linnean Society, 10.1111/zoj.12392, 177:4, (937-949), Online publication date: 1-Aug-2016. Phiri E and Daniels S (2016) Multilocus coalescent species delimitation reveals widespread cryptic differentiation among Drakensberg mountain-living freshwater crabs (Decapoda : Potamonautes), Invertebrate Systematics, 10.1071/IS15035, 30:1, (60), . Toussaint E, Morinière J, Müller C, Kunte K, Turlin B, Hausmann A and Balke M (2015) Comparative molecular species delimitation in the charismatic Nawab butterflies (Nymphalidae, Charaxinae, Polyura), Molecular Phylogenetics and Evolution, 10.1016/j.ympev.2015.05.015, 91, (194-209), Online publication date: 1-Oct-2015. Blair C, Méndez de la Cruz F, Law C and Murphy R (2015) Molecular phylogenetics and species delimitation of leaf-toed geckos (Phyllodactylidae: Phyllodactylus) throughout the Mexican tropical dry forest, Molecular Phylogenetics and Evolution, 10.1016/j.ympev.2015.01.003, 84, (254-265), Online publication date: 1-Mar-2015. Hedin M (2015) High-stakes species delimitation in eyeless cave spiders ( Cicurina, Dictynidae, Araneae) from central Texas , Molecular Ecology, 10.1111/mec.13036, 24:2, (346-361), Online publication date: 1-Jan-2015. Zhang C, Rannala B and Yang Z (2014) Bayesian Species Delimitation Can Be Robust to Guide-Tree Inference Errors, Systematic Biology, 10.1093/sysbio/syu052, 63:6, (993-1004), Online publication date: 1-Nov-2014. Meyer-Wachsmuth I, Curini Galletti M, Jondelius U and Fontaneto D (2014) Hyper-Cryptic Marine Meiofauna: Species Complexes in Nemertodermatida, PLoS ONE, 10.1371/journal.pone.0107688, 9:9, (e107688) Su Y, Wang J, Villanueva R, Nuñeza O, Lin C and Heaney L (2014) Hopping out of Mindanao: Miocene-Pliocene geological processes and cross-island dispersal as major drivers of diversity for Philippine treehoppers, Journal of Biogeography, 10.1111/jbi.12296, 41:7, (1277-1290), Online publication date: 1-Jul-2014. Leaché A, Fujita M, Minin V and Bouckaert R (2014) Species Delimitation using Genome-Wide SNP Data, Systematic Biology, 10.1093/sysbio/syu018, 63:4, (534-542), Online publication date: 1-Jul-2014. Edwards D and Knowles L (2014) Species detection and individual assignment in species delimitation: can integrative data increase efficacy?, Proceedings of the Royal Society B: Biological Sciences, 281:1777, Online publication date: 22-Feb-2014. Barley A, White J, Diesmos A and Brown R (2013) THE CHALLENGE OF SPECIES DELIMITATION AT THE EXTREMES: DIVERSIFICATION WITHOUT MORPHOLOGICAL CHANGE IN PHILIPPINE SUN SKINKS, Evolution, 10.1111/evo.12219, 67:12, (3556-3572), Online publication date: 1-Dec-2013. Satler J, Carstens B and Hedin M (2013) Multilocus Species Delimitation in a Complex of Morphologically Conserved Trapdoor Spiders (Mygalomorphae, Antrodiaetidae, Aliatypus), Systematic Biology, 10.1093/sysbio/syt041, 62:6, (805-823), Online publication date: 1-Nov-2013. McKay B, Mays H, Wu Y, Li H, Yao C, Nishiumi I and Zou F (2013) An empirical comparison of character-based and coalescent-based approaches to species delimitation in a young avian complex, Molecular Ecology, 10.1111/mec.12446, 22:19, (4943-4957), Online publication date: 1-Oct-2013. Miralles A, Vences M and Fontaneto D (2013) New Metrics for Comparison of Taxonomies Reveal Striking Discrepancies among Species Delimitation Methods in Madascincus Lizards, PLoS ONE, 10.1371/journal.pone.0068242, 8:7, (e68242) Sistrom M, Donnellan S and Hutchinson M (2013) Delimiting species in recent radiations with low levels of morphological divergence: A case study in Australian Gehyra geckos, Molecular Phylogenetics and Evolution, 10.1016/j.ympev.2013.03.007, 68:1, (135-143), Online publication date: 1-Jul-2013. Rasoloarison R, Weisrock D, Yoder A, Rakotondravony D and Kappeler P (2013) Two New Species of Mouse Lemurs (Cheirogaleidae: Microcebus) from Eastern Madagascar, International Journal of Primatology, 10.1007/s10764-013-9672-1, 34:3, (455-469), Online publication date: 1-Jun-2013. Leavitt S, Fernández-Mendoza F, Pérez-Ortega S, Sohrabi M, Divakar P, Lumbsch T and St. Clair L (2013) DNA barcode identification of lichen-forming fungal species in the Rhizoplaca melanophthalma species-complex (Lecanorales, Lecanoraceae), including five new species, MycoKeys, 10.3897/mycokeys.7.4508, 7, (1-22) Jörger K and Schrödl M (2013) How to describe a cryptic species? Practical challenges of molecular taxonomy, Frontiers in Zoology, 10.1186/1742-9994-10-59, 10:1, (59), . Nuñez J, Vejar-Pardo A, Guzmán B, Barriga E and Gallardo C (2012) Phylogenetic and mixed Yule-coalescent analyses reveal cryptic lineages within two South American marine snails of the genus Crepipatella (Gastropoda: Calyptraeidae) , Invertebrate Biology, 10.1111/ivb.12003, 131:4, (301-311), Online publication date: 1-Dec-2012. Camargo A, Morando M, Avila L and Sites J (2012) SPECIES DELIMITATION WITH ABC AND OTHER COALESCENT-BASED METHODS: A TEST OF ACCURACY WITH SIMULATIONS AND AN EMPIRICAL EXAMPLE WITH LIZARDS OF THE LIOLAEMUS DARWINII COMPLEX (SQUAMATA: LIOLAEMIDAE), Evolution, 10.1111/j.1558-5646.2012.01640.x, 66:9, (2834-2849), Online publication date: 1-Sep-2012. Fujita M, Leaché A, Burbrink F, McGuire J and Moritz C (2012) Coalescent-based species delimitation in an integrative taxonomy, Trends in Ecology & Evolution, 10.1016/j.tree.2012.04.012, 27:9, (480-488), Online publication date: 1-Sep-2012. Zhang C, Zhang D, Zhu T and Yang Z (2011) Evaluation of a Bayesian Coalescent Method of Species Delimitation, Systematic Biology, 10.1093/sysbio/syr071, 60:6, (747-761), Online publication date: 1-Dec-2011. Leavitt S, Johnson L, Goward T and St. Clair L (2011) Species delimitation in taxonomically difficult lichen-forming fungi: An example from morphologically and chemically diverse Xanthoparmelia (Parmeliaceae) in North America, Molecular Phylogenetics and Evolution, 10.1016/j.ympev.2011.05.012, 60:3, (317-332), Online publication date: 1-Sep-2011. Falk B, Luke Mahler D and Perkins S (2011) Tree-based delimitation of morphologically ambiguous taxa: A study of the lizard malaria parasites on the Caribbean island of Hispaniola, International Journal for Parasitology, 10.1016/j.ijpara.2011.05.004, 41:9, (967-980), Online publication date: 1-Aug-2011. This Issue22 February 2011Volume 278Issue 1705 Article InformationDOI:https://doi.org/10.1098/rspb.2010.1864Published by:Royal SocietyOnline ISSN:1471-2954History: Manuscript received31/08/2010Manuscript accepted01/10/2010Published online20/10/2010Published in print22/02/2011 License:This Journal is © 2010 The Royal Society Citations and impact Subjectsevolutiontaxonomy and systematics Large datasets are available through Proceedings B's partnership with Dryad

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