Papers using diversitree

2014/in press

Arbuckle K., Bennett C.M., and Speed M.P. 2014. A simple measure of the strength of convergent evolution. Methods in Ecology and Evolution in press. [ doi ]
Bouchenak-Khelladi Y., Muasya A.M., and Linder H.P. 2014. A revised evolutionary history of poales: origins and diversification. Botanical Journal of the Linnean Society 175:4-16. [ doi ]
Cantalapiedra J.L., FitzJohn R.G., Kuhn T.S., Demiguel M.H.F.D., Azanza B., Morales J., and Mooers A.O. 2014. Dietary innovations spurred the diversification of ruminants during the caenozoic. Proceedings of the Royal Society of London, Series B Biological Sciences in press. [ doi ]
Cieslak A., Fresneda J., and Ribera I. 2014. Life-history specialization was not an evolutionary dead-end in Pyrenean cave beetles. Proceedings of the Royal Society of London, Series B Biological Sciences 281:20132978. [ doi ]
Denton J.S.S. 2014. Seven-locus molecular phylogeny of Myctophiformes (Teleostei; Scopelomorpha) highlights the utility of the order for studies of deep-sea evolution. Molecular Phylogenetics and Evolution in press. [ doi ]
Givnish T.J., Barfuss M.H.J., Ee B.V., Riina R., Schulte K., Horres R., Gonsiska P.A., Jabaily R.S., Crayn D.M., Smith J.A.C., Winter K., Brown G.K., Evans T.M., Holst B.K., Luther H., Till W., Zizka G., Berry P.E., and Sytsma K.J. 2014. Adaptive radiation, correlated and contingent evolution, and net species diversification in bromeliaceae. Molecular Phylogenetics and Evolution 71:55-78. [ doi ]
Hendry C.R., Guiher T.J., and Pyron R.A. 2014. Ecological divergence and sexual selection drive sexual size dimorphism in new world pitvipers (Serpentes: Viperidae). Journal of Evolutionary Biology in press. [ doi ]
Hernández-Hernández T., Brown J.W., Schlumpberger B.O., Eguiarte L.E., and Magallón S. 2014. Beyond aridification: multiple explanations for the elevated diversification of cacti in the new world succulent biome. New Phytologist 202:1382-1397. [ doi ]
Humphreys A.M. and Barraclough T.G. 2014. The evolutionary reality of higher taxa in mammals. Proceedings of the Royal Society of London, Series B Biological Sciences 281:20132750. [ doi ]
Iles W.J., Lee C., Sokoloff D.D., Remizowa M.V., Yadav S.R., Barrett M.D., Barrett R.L., Macfarlane T.D., Rudall P.J., and Graham S.W. 2014. Reconstructing the age and historical biogeography of the ancient flowering-plant family Hydatellaceae (Nymphaeales). BMC Evolutionary Biology 14:102. [ doi ]
Käfer J., de Boer H.J., Mousset S., Kool A., Dufay M., and Marais G.A.B. 2014. Dioecy is associated with higher diversification rates in flowering plants. Journal of Evolutionary Biology in press. [ doi ]
Käfer J. and Mousset S. 2014. Standard sister-clade comparison fails when testing derived character states. Systematic Biology in press. [ doi ]
Macqueen D.J. and Johnston I.A. 2014. A well-constrained estimate for the timing of the salmonid whole genome duplication reveals major decoupling from species diversification. Proceedings of the Royal Society of London, Series B Biological Sciences 281:20132881. [ doi ]
Ohutcen E., Hamper B., and Vamosi J.C. 2014. Diversification in monkeyflowers: An investigation of the effects of elevation and floral color in the genus Mimulus. International Journal of Evolutionary Biology 2014:382453. [ doi ]
Price S.L., Powell S., Kronauer D.J.C., Tran L.A.P., Pierce N.E., and Wayne R.K. 2014. Renewed diversification is associated with new ecological opportunity in the Neotropical turtle ants. Journal of Evolutionary Biology in press. [ doi ]
Rolland J., Condamine F.L., Jiguet F., and Morlon H. 2014a. Faster speciation and reduced extinction in the tropics contribute to the mammalian latitudinal diversity gradient. PLOS Biology 12:e1001775. [ doi ]
Rolland J., Jiguet F., Jonsson K.A., Condamine F.L., and Morlon H. 2014b. Settling down of seasonal migrants promotes bird diversification. Proceedings of the Royal Society of London, Series B Biological Sciences 281:20140473. [ doi ]
Sachs J.L., Skophammer R.G., Bansal N., and Stajich J.E. 2014. Evolutionary origins and diversification of proteobacterial mutualists. Proceedings of the Royal Society of London, Series B Biological Sciences in press. [ doi ]
Tran L.A.P. 2014. The role of ecological opportunity in shaping disparate diversification trajectories in a bicontinental primate radiation. Proceedings of the Royal Society of London, Series B Biological Sciences 281:20131979. [ doi ]
Vos J.D., Hughes C.E., G M Schneeweiss B.R.M., and Conti E. 2014a. Heterostyly accelerates diversification via reduced extinction in primroses. Proceedings of the Royal Society of London, Series B Biological Sciences 281:20140075. [ doi ]
Vos J.M.D., Wüest R.O., and Conti E. 2014b. small and ugly? phylogenetic analyses of the "selfing syndrome" reveal complex evolutionary fates of monomorphic primrose flowers. Evolution in press. [ doi ]
Williams J.H., Taylor M.L., and O'Meara B.C. 2014. Repeated evolution of tricellular (and bicellular) pollen. American Journal of Botany in press. [ doi ]
Willis C.G., Baskin C.C., Baskin J.M., Auld J.R., Venable D.L., Cavender-Bares J., Donohue K., Rubio de Casas R., and The NESCent Germination Working Group. 2014. The evolution of seed dormancy: environmental cues, evolutionary hubs, and diversification of the seed plants. New Phytologist in press. [ doi ]
Xianga X.G., Wanga W., Lia R.Q., Lina L., Liub Y., Zhouc Z.K., Lia Z.Y., and Chen Z.D. 2014. Large-scale phylogenetic analyses reveal fagalean diversification promoted by the interplay of diaspores and environments in the Paleogene. Perspectives in Plant Ecology, Evolution and Systematics 16:101-110. [ doi ]
Zhan S.H., Glick L., Tsigenopoulos C.S., Otto S.P., and Mayrose I. 2014. Comparative analysis reveals that polyploidy does not decelerate diversification in fish. Journal of Evolutionary Biology in press. [ doi ]

2013

Beaulieu J.M. and Donoghue M.J. 2013. Fruit evolution and diversification in campanulid angiosperms. Evolution in press. [ doi ]
Blanco-Pastor J.L. and Vargas P. 2013. Autecological traits determined two evolutionary strategies in Mediterranean plants during the Quaternary: low differentiation and range expansion versus geographical speciation in Linaria. Molecular Ecology in press. [ doi ]
Bloom D.D., Wier J.T., Piller K.R., and Lovejoy N.R. 2013. Do freshwater fishes diversify faster than marine fishes? a test using state-dependent diversification analyses and molecular phylogenetics of new world silversides (Atherinopsidae). Evolution in press. [ doi ]
Buerki S., Manning J.C., and Forest F. 2013. Spatio-temporal history of the disjunct family Tecophilaeaceae: a tale involving the colonization of three Mediterranean-type ecosystems. Annals of Botany in press. [ doi ]
Cardillo M. and Pratt R. 2013. Evolution of a hotspot genus: geographic variation in speciation and extinction rates in Banksia (proteaceae). BMC Evolutionary Biology 13:155. [ doi ]
Fernández-Mazuecos M., Blanco-Pastor J.L., Gómez J.M., and Vargas P. 2013. Corolla morphology influences diversification rates in bifid toadflaxes (Linaria sect. Versicolores). Annals of Botany in press. [ doi ]
Forest F., Goldblatt P., Maning J.C., Baker D., Colville J.F., Devey D.S., Jose S., KAye M., and Buerki S. 2013. Pollinator shifts as triggers of speciation in painted petal irises (Lapeirousia: Iridaceae). Annals of Botany in press. [ doi ]
Garcia-Porta J. and Ord T.J. 2013. Key innovations and island colonization as engines of evolutionary diversiﬁcation: a comparative test with the australasian diplodactyloid geckos. Journal of Evolutionary Biology in press. [ doi ]
Igić B. and Busch J.W. 2013. Is self-fertilization an evolutionary dead end? New Phytologist in press. [ doi ]
Klimov P.B. and O'Connor B. 2013. Is permanent parasitism reversible? - critical evidence from early evolution of house dust mites. Systematic Biology in press. [ doi ]
Lambert S.M. and Wiens J.J. 2013. Evolution of viviparity: a phylogenetic test of the cold-climate hypothesis in phrynosomatid lizards. Evolution in press. [ doi ]
Lancaster L.T. and Kay K.M. 2013. Origin and diversification of the California flora: re-examining classic hypotheses with molecular phylogenies. Evolution in press. [ doi ]
Leslie A.B., Beaulieu J.M., Crane P.R., and Donoghue M.J. 2013. Explaining the distribution of breeding and dispersal syndromes in conifers. Proceedings of the Royal Society of London, Series B Biological Sciences 280:20131812. [ doi ]
Litsios G., Wüest E.O., Kostikova A., Fores F., Lexer C., Linder H.P., Pearman P.B., Zimmerman N.E., and Salamin N. 2013. Effects of a fire response trait on diversification in replicated radiations. Evolution in press. [ doi ]
Lorion J., Kiel S., Faure B., Kawato M., Ho S.Y.W., Marshall B., Tsuchida S., Miyazaki J.I., and Fujiwara Y. 2013. Adaptive radiation of chemosymbiotic deep-sea mussels. Proceedings of the Royal Society of London, Series B Biological Sciences in press. [ doi ]
Machac A., Storch D., and Wiens J.J. 2013. Ecological causes of decelerating diversification in carnivoran mammals. Evolution in press. [ doi ]
Maia R., Rubenstein D.R., and Shawkey M.D. 2013. Key ornamental innovations facilitate diversification in an avian radiation. Proceedings of the National Acadamy of Sciences, USA in press. [ doi ]
Maliska M.E., Pennell M.W., and Swalla B.J. 2013. Developmental mode influences diversification in ascidians. Proceedings of the Royal Society B 9. [ doi ]
Poon A.F.Y., Walker L.W., Murray H., McCloskey R.M., Harrigan P.R., and Liang R.H. 2013. Mapping the shapes of phylogenetic trees from human and zoonotic rna viruses. PLOS One 8:e78122. [ doi ]
Pyron R.A. and Burbrink F.T. 2013. Early origin of viviparity and multiple reversions to oviparity in squamate reptiles. Ecology Letters in press. [ doi ]
Sachs J.L., Skophammer R.G., Bansal N., and Stajich J.E. 2013. Evolutionary origins and diversification of proteobacterial mutualists. Proceedings of the Royal Society of London, Series B Biological Sciences in press. [ doi ]
Santini F., Nguyen M.T.T., Sorenson L., Waltzek T.B., Lynch Alfaro J.W., Eastman J.M., and Alfaro M.E. 2013a. Do habitat shifts drive diversification in teleost fishes? an example from the pufferfishes (Tetraodontidae). Journal of Evolutionary Biology in press. [ doi ]
Santini F., Sorenson L., and Alfaro M.E. 2013b. A new multi-locus timescale reveals the evolutionary basis of diversity patterns in triggerfishes and filefishes (Balistidae, Monacanthidae; Tetraodontiformes). Molecular Phylogenetics and Evolution 69:165-176. [ doi ]
Scarpino S.V., Hunt P.J., Garcia-De-Leon F.J., Juenger T.E., Schartl M., and Kirkpatrick M. 2013. Evolution of a genetic incompatibility in the genus Xiphophorus. Molecular Biology and Evolution 30:2302-2310. [ doi ]
Soltis D.E., Mort M.E., Latvis M., Mavrodiev E.V., O'Meara B.C., Soltis P.S., Burleigh J.C., and Rubio de Casas R. 2013. Phylogenetic relationships and character evolution analysis of Saxifragales using a supermatrix approach. American Journal of Botany in press. [ doi ]
Svensson E.I. and Waller J.T. 2013. Ecology and sexual selection: Evolution of wing pigmentation in calopterygid damselflies in relation to latitude, sexual dimorphism, and speciation. The American Naturalist in press. [ doi ]
Verdú M. and Pasusas J.G. 2013. Syndrome-driven diversification in a Mediterranean ecosystem. Evolution in press. [ doi ]
Wiens J., Kozak K.H., and Silva N. 2013. Diversity and niche evolution along aridity gradients in North American lizards (Phtynosomatidae). Evolution in press. [ doi ]

2012

Avaria-Llautureo J., Hernández C.E., Boric-Bargetto D., Canales-Aguirre C.B., Morales-Pallero B., and Rodríguez-Serrano E. 2012. Body size evolution in extant Oryzomyini rodents: Cope's rule or miniaturization? PloS One 7:e34654. [ doi ]
Bardon L., Chamagne J., Dexter K.G., Sothers C.A., Prance G.T., and Chave J. 2012. Origin and evolution of Chrysobalanaceae: insights into the evolution of plants in the Neotropics. Botanical Journal of the Linnean Society in press. [ doi ]
Bergmann P.J. and Irschick D.J. 2012. Vertebral evolution and the diversification of squamate reptiles. Evolution 66:1044-1058. [ doi ]
Betancur-R R., Ortí G., Stein A.M., Marceniuk A.P., and Pyron R.A. 2012. Apparent signal of competition limiting diversiﬁcation after ecological transitions from marine to freshwater habitats. Ecology Letters in press. [ doi ]
Boucher F.C., Thuiller W., Roquet C., Douzet R., Aubert S., Alvarez N., and Lavergne S. 2012. Reconstructing the origins of high-alpine niches and cushion life form in the genus Androsace s.l. (Primulaceae). Evolution 66:1255-1268. [ doi ]
Buerki S., Jose S., Yadav S.R., Goldblatt P., Manning J.C., and Forest F. 2012. Contrasting biogeographic and diversification patterns in two mediterranean-type ecosystems. PLos ONE 7:e39377. [ doi ]
Burbrink F.T., Ruane S., and Pyron R.A. 2012. When are adaptive radiations replicated in areas? ecological opportunity and unexceptional diversification in west indian dipsadine snakes (Colubridae: Alsophiini). Journal of Biogeography 39:465-475. [ doi ]
Claramunt S., Derryberry E.P., Brumfield R.T., and Remsen Jr J.V. 2012a. Ecological opportunity and diversification in a continental radiation of birds: Climbing adaptations and cladogenesis in the furnariidae. The American Naturalist 179:649-666. [ doi ]
Claramunt S., Derryberry E.P., Remsen Jr J.V., and Brumfield R.T. 2012b. High dispersal ability inhibits speciation in a continental radiation of passerine birds. Proceedings of the Royal Society of London, Series B Biological Sciences 279:1567-1574. [ doi ]
Drummond C.S., Eastwood R.J., Miotto S.T., , and Hughes C.E. 2012. Multiple continental radiations and correlates of diversification in Lupinus (Leguminosae): Testing for key innovation with incomplete taxon sampling. Systematic Biology in press. [ doi ]
Dumont E.R., Dávalos L.M., Goldberg A., Santana S.E., Rex K., and Voigt C.C. 2012. Morphological innovation, diversification and invasion of a new adaptive zone. Proceedings of the Royal Society of London, Series B Biological Sciences 279:1797-1805. [ doi ]
Floudas D., Binder M., Riley R., Barry K., Blanchette R.A., Henrissat B., Martínez A.T., Otillar R., Spatafora J.W., Yadav J.S., Aerts A., Benoit I., Boyd A., Carlson A., Copeland A., Coutinho P.M., de Vries R.P., Ferreira P., Findley K., Foster B., Gaskell J., Glotzer D., Górecki P., Heitman J., Hesse C., Hori C., Igarashi K., Jurgens J.A., Kallen N., Kersten P., Kohler A., Kües U., Kumar T.K.A., Kuo A., LaButti K., Larrondo L.F., Lindquist E., Ling A., Lombard V., Lucas S., Lundell T., Martin R., McLaughlin D.J., Morgenstern I., Morin E., Murat C., Nagy L.G., Nolan M., Ohm R.A., Patyshakuliyeva A., Rokas A., nas F.J.R.D., Sabat G., Salamov A., Samejima M., Schmutz J., Slot J.C., John F.S., Stenlid J., Sun H., Sun S., Syed K., Tsang A., Wiebenga A., Young D., Pisabarro A., Eastwood D.C., Martin F., Cullen D., Grigoriev I.V., and Hibbett D.S. 2012. The paleozoic origin of enzymatic lignin decomposition reconstructed from 31 fungal genomes. Science 336:1715-1719. [ doi ]
Gamble T., Greenbaum E., Jackman T.R., Russell A.P., and Bauer A.M. 2012. Repeated origin and loss of adhesive toepads in geckos. PLoS One 7:e39429. [ doi ]
Goldberg E.E. and Igić B. 2012. Tempo and mode in plant breeding system evolution. Evolution in press. [ doi ]
Gómez J.M. and Verdú M. 2012. Mutualism with plants drives primate diversification. Systematic Biology in press. [ doi ]
Grass Phylogeny Working Group II. 2012. New grass phylogeny resolves deep evolutionary relationships and discovers C₄ origins. New Phytologist 193:304-312. [ doi ]
Hugall A.F. and Stuart-Fox D. 2012. Accelerated speciation in colour-polymorphic birds. Nature in press. [ doi ]
Hutter C.R., Guayasamin J.M., and Wiens J.J. 2013. Explaining andean megadiversity: the evolutionary and ecological causes of glassfrog elevational richness patterns. Ecology Letters in press. [ doi ]
Ikeda H., Nishikawa M., and Sota T. 2012. Loss of flight promotes beetle diversification. Nature Communications 3:648. [ doi ]
Litsios G., Sims C.A., Wëst R.O., Pearman B., Zimmermann N.E., and Salamin N. 2012. Mutualism with sea anemones triggered the adaptive radiation of clownfishes. BMC Evolutionary Biology 12:212. [ doi ]
Machac A., Zrzavy J., Smrckova J., and Storch D. 2012. Temperature dependence of evolutionary diversification: differences between two contrasting model taxa support the metabolic theory of ecology. Journal of Evolutionary Biology in press. [ doi ]
Magnuson-Ford K. and Otto S.P. 2012. Linking the investigations of character evolution and species diversification. The American Naturalist in press. [ doi ]
McDaniel S.F., Atwood J., and Burleigh J.G. 2012. Recurrent evolution of dioecy in bryophytes. Evolution in press. [ doi ]
Miglietta M.P. and Cunningham C.W. 2012. Evolution of life cycle, colony morphology and host-specificity in the family Hydractiniidae (Hydrozoa, Cnidaria). Evolution in press. [ doi ]
Price S.A., Hopkins S.S.B., Smith K.K., and Roth V.L. 2012. Tempo of trophic evolution and its impact on mammalian diversification. Proceedings of the National Acadamy of Sciences, USA in press. [ doi ]
Pyron R.A. and Burbrink F.T. 2012. Trait-dependent diversification and the impact of palaeontological data on evolutionary hypothesis testing in New World ratsnakes (tribe Lampropeltini). Journal of Evolutionary Biology 25:497-508. [ doi ]
Rojas D., Vale Á., Ferrero V., and Navarro L. 2012. The role of frugivory in the diversification of bats in the Neotropics. Journal of Biogeography in press. [ doi ]
Ross L., Hardy N.B., Okusu A., and Normark B.B. 2012. Large population size predicts the distribution of asexuality in scale insects. Evolution in press. [ doi ]
Scott J.E., Lack J.B., and Rabosa M.J. 2012. On the reversibility of mandibular symphyseal fusion. Evolution in press. [ doi ]
Syme A.E. and Oakley T.H. 2012. Dispersal between shallow and abyssal seas and evolutionary loss and regain of compound eyes in cylindroleberidid ostracods: Conflicting conclusions from different comparative methods. Systematic Biology 61:314-336. [ doi ]
Valente L.M., Manning J.C., Goldblatt P., and Vargas P. 2012. Did pollination shifts drive diversification in southern African Gladiolus? Evaluating the model of pollinator-driven speciation. The American Naturalist 180:83-98. [ doi ]
Weber M.G. and Keeler K.H. 2012. The phylogenetic distribution of extrafloral nectaries in plants. Annals of Botany in press. [ doi ]
Weir J.T. and Mursleen S. 2012. Diversity-dependent cladogenesis and trait evolution in the adaptive radiation of the auks (aves: Alcidae). Evolution in press. [ doi ]
Winger B.M., Lovette I.J., and Winkler D.W. 2012. Ancestry and evolution of seasonal migration in the Parulidae. Proceedings of the Royal Society of London, Series B Biological Sciences 279:610-618. [ doi ]
Zimkus B.M., Lawson L., Loader S.P., and Hanken J. 2012. Terrestrialization, miniaturization and rates of diversification in african puddle frogs (Anura: Phrynobatrachidae). PloS ONE 7:e35118. [ doi ]

2011

Cánovas F.G., Mota C.F., Serrão E.A., and Pearson G.A. 2011. Driving south: a multi-gene phylogeny of the brown algal family Fucaceae reveals relationships and recent drivers of a marine radiation. BMC Evolutionary Biology 11:371. [ doi ]
Cantalapiedra J.L., Fernández M.H., and Morales J. 2011. Biomic specialization and speciation rates in ruminants (cetartiodactyla, mammalia): A test of the resource-use hypothesis at the global scale. PloS One 6:e28749. [ doi ]
Eastman J.M. and Storfer A. 2011. Correlations of life-history and distributional-range variation with salamander diversification rates: Evidence for species selection. Systematic Biology 60:503-518. [ doi ]
Johnson M.T.J., FitzJohn R.G., Smith S.D., Rausher M.D., and Otto S.P. 2011. Loss of sexual recombination and segregation is associated with increased diversification in evening primroses. Evolution 65:3230-3240. [ doi ]
Matthews L.J., Arnold C., Machanda Z., and Nunn C.L. 2011. Primate extinction risk and historical patterns of speciation and extinction in relation to body mass. Proceedings of the Royal Society of London, Series B Biological Sciences 278:1246-1263. [ doi ]
Mayrose I., Zhan S.H., Rothfels C.J., Magnuson-Ford K., Barker M.S., Rieseberg L.H., and Otto S.P. 2011. Recently formed polyploid plants diversify at lower rates. Science 333:1257. [ doi ]
Olalla-Tárraga M.Á., McInnes L., Bini L.M., Diniz-Filho J.A.F., Fritz S.A., Hawkins B.A., Hortal J., Orme C.D.L., Rahbek C., Rodríguez M.Á., and Purvis A. 2011. Climatic niche conservatism and the evolutionary dynamics in species range boundaries: global congruence across mammals and amphibians. Journal of Biogeography 38:2237-2247. [ doi ]
Raia P., Carotenuto F., Eronen J.R., and Fortelius M. 2011. Longer in the tooth, shorter in the record? the evolutionary correlates of hypsodonty in Neogene ruminants. Proceedings of the Royal Society of London, Series B Biological Sciences 278:3474-3481. [ doi ]
Valente L.M., Savolainen V., Manning J.C., Goldblatt P., and Vargas P. 2011. Explaining disparities in species richness between Mediterranean floristic regions: a case study in Gladiolus (Iridaceae). Global Ecology and Biogeography 20:881-892. [ doi ]
Wilson A.W., Binder M., and Hibbett D.S. 2011. Effects of gasteroid fruiting body morphology on diversification rates in three independent clades of fungi estimated using binary state speciation and extinction analysis. Evolution 65:1305-1322. [ doi ]

2010

Anacker B.L., Whittall J.B., Goldberg E.E., and Harrison S.P. 2010. Origins and consequences of serpentine endemism in the california flora. Evolution 65:365-376. [ doi ]
FitzJohn R.G. 2010. Quantitative traits and diversification. Systematic Biology 59:619-633. [ doi ]
Goldberg E.E., Kohn J.R., Lande R., Robertson K.A., Smith S.A., and Igić B. 2010. Species selection maintains self-incompatibility. Science 330:493-495. [ doi ]
Lancaster L.T. 2010. Molecular evolutionary rates predict both extinction and speciation in temperate angiosperm lineages. BMC Evolutionary Biology 10:162. [ doi ]

2009

FitzJohn R.G., Maddison W.P., and Otto S.P. 2009. Estimating trait-dependent speciation and extinction rates from incompletely resolved phylogenies. systematic biology 58:595-611. Systematic Biology 58:595-611. [ doi ]