Alfaro Lab - Publications

Publications

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2012 Santana, S.E., Lynch Alfaro, J. W. and Alfaro, M. 2012. Adaptive evolution of facial colour patterns in Neotropical primates. Proceedings of the Royal Society B: Biological Sciences.
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2011 Jaffe, A. L., G. J. Slater, and M. E. Alfaro. The evolution of island gigantism and body size variation in tortoises and turtles. Biology Letters 7:558-561.

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2011 Alfaro, J. W., L. Matthews, A. H. Boyette, S. J. Macfarlan, K. A. Phillips, T. Falotico, E. Ottoni, M. Verderane, P. Izar, M. Schulte, A. Melin, L. Fedigan, C. Janson, and M. E. Alfaro. 2011. Anointing variation across wild capuchin populations: a review of material preferences, bout frequency and anointing sociality in Cebus and Sapajus. Am J Primatol, in press.

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2011 Eastman, J. M., M. E. Alfaro, P. Joyce, A. L. Hipp, and L. J. Harmon. 2011. A novel comparative method for identifying shifts in the rate of character evolution on trees. Evolution 65 (online in advance of publication)

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2011 Dornburg, A., B. Sidlauskas, F. Santini, L. Sorenson, Near, T. J., and M. E. Alfaro. The influence of an innovative locomotor strategy on the phenotypic diversification of triggerfishes (Family: Balistidae). Evolution 65:1912-1926.

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2011 Brock, C. D., L. J. Harmon, and M. E. Alfaro. Testing for temporal variation in diversification rates when sampling is incomplete and nonrandom. Syst Biol 60:410-419.
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2011 Huelsenbeck, J. P., M. E. Alfaro, and M. A. Suchard. 2011. Biologically inspired phylogenetic models strongly outperform the No Common Mechanism model. Systematic Biology 60:225-232.
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2010 Slater, G. J., S. A. Price, F. Santini, and M. E. Alfaro. Diversity versus disparity and the radiation of modern cetaceans. Proc Biol Sci 277:3097-3104.
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2010 Rabosky, D. L., and M. E. Alfaro. Evolutionary bangs and whimpers: methodological advances and conceptual frameworks for studying exceptional diversification. Syst Biol 59:615-618.
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2010 Mehta, R. S., A. B. Ward, M. E. Alfaro, and P. C. Wainwright. 2010. Elongation of the body in eels. Integr Comp Biol 50:1091-1105.

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2009 M. E. Alfaro, F. Santini, C. D. Brock, H. Alamillo, A. Dornburg, D. L. Rabosky, G. Carnevale, and L.J. Harmon. 2009. Nine exceptional radiations plus high turnover explain species diversity in jawed vertebrates. PNAS 32: 13410-13414.

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2009 F. Santini, L.J. Harmon, G. Carnevale, and M. E. Alfaro. 2009. Did genome duplication drive the origin of teleosts? A comparative study of diversification in ray-finned fishes. BMC Evolutionary Biology 9:194.

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2009 M. E. Alfaro, C.D. Brock, B.L. Banbury, and P. C. Wainwright. 2009. Does evolutionary innovation in pharyngeal jaws lead to rapid lineage diversification in labrid fishes? BMC Evolutionary Biology 9:255.

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2009 S. E. Vincent, M. C. Brandley, A. Herrel, M. E. Alfaro. 2009. Convergence in trophic morphology and feeding performance among piscivorous natricine snakes. J Evolution Biol. 22:1203-1211.

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2009 T. B. Waltzek, G. O. Kelley, M. E. Alfaro, T. Kurobe, A. J. Davison, and R. P. Hedrick 2009. Phylogenetic relationships in the family Alloherpesviride. Diseases of Aquatic Organisms 84:179-194.

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2008 A. Dornburg, F. Santini, and M. E. Alfaro. 2008. Influence of model averaging on clade posteriors: An example using the triggerfishes (Balistidae). Systematic Biology, 57:905-919.

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2008 Clark, J. R., R. H. Ree, M. E. Alfaro, M. G. King, W. L. Wagner, and E. H. Roalson. 2008. A Comparative Study in Ancestral Range Reconstruction Methods: Retracing the Uncertain Histories of Insular Lineages. Syst Biol 57:693-707.

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2008 Collar, D. C., P. C. Wainwright, and M. E. Alfaro. 2008. Integrated diversification of locomotion and feeding in labrid fishes. Biol Lett 4:84-86.

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2008 Herrel, A., S. E. Vincent, M. E. Alfaro, W. Van, S, B. Vanhooydonck, and D. J. Irschick. 2008. Morphological convergence as a consequence of extreme functional demands: examples from the feeding system of natricine snakes. J Evolution Biol 21:1438-1448.

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2008 L. L. Smith, J. L. Fessler, M. E. Alfaro, J.T. Streelman, and M.W. Westneat. 2008. Phylogenetic relationships and the evolution of regulatory gene sequences in the parrotfishes. Molecular Phylogenetics and Evolution. 49:136-52.
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2008 M. E. Alfaro, D. R. Karns, H. K. Voris, and B. L. Stuart. 2008. Phylogeny, Evolutionary History, and Biogeography of Oriental-Australian Rear-fanged Water Snakes (Colubridae: Homalopsidae) Inferred from Mitochondrial and Nuclear DNA Sequences. Molecular Phylogenetics and Evolution 46:576-93.
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2007 A. Storfer, M. E. Alfaro, B.J. Ridenhour, J. K. Jancovich, S. G. Mech, M. J. Parris, J. P. Collins. 2007. Phylogenetic concordance analysis shows an emerging pathogen is novel and endemic. Ecology Letters 10: 1075-1083.
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2007 M. E. Alfaro, C. D. Brock, and F. Santini. 2007. Do reefs drive diversification in marine teleosts? Evidence from the pufferfishes and their allies (Order Tetraodontiformes) Evolution 61:2104-2126.
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2006 M. E. Alfaro & J. P. Huelsenbeck. 2006. Comparative performance of Bayesian and AIC-based measures of phylogenetic model uncertainty. Systematic Biology 55: 89-96.
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2006 M. E. Alfaro and M.T. Holder. 2006. The posterior and the prior in Bayesian phylogenetics. Annual Review of Ecology, Evolution, and Systematics 37:19-42.
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2005 M. E. Alfaro, D. I. Bolnick, and P. C. Wainwright. 2005. Evolutionary consequences of a redundant map of morphology to mechanics: an example using the jaws of labrid fishes. American Naturalist 165:E140-E154.
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2005 M. W. Westneat and M. E. Alfaro. 2005. Phylogenetic relationships and evolutionary history of the reef fish family Labridae. Mol. Phyl. Evol. 36:370-390.
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2005 M. W. Westneat, M. E. Alfaro, P. C. Wainwright, D. Bellwood, and J. Fessler. 2005. Local phylogenetic divergence and global evolutionary convergence of skull function in reef fishes of the family Labridae. Proc. Roy. Soc. 272:1471-2954.
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2005 P. C. Wainwright, M. E. Alfaro, D. I. Bolnick, and C. D. Hulsey. 2005. Many-to-one mapping of form to function: a general principle of organismal design? Integrative and Comparative Biology 45:256-262.
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2004 Huelsenbeck, J. H., Larget, B., and M. E. Alfaro. 2004. Bayesian phylogenetic model selection using reversible jump Markov chain Monte Carlo. Molecular Biology and Evolution 21:1123-1133.
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2004 K. D. Clements, M. E. Alfaro, J. Fessler and M. W. Westneat. 2004. Relationships of the Temperate Australasian Labrid Fish Tribe Odacini (Perciformes: Teleostei). Molecular Phylogenetics and Evolution 32:575-587.
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2004 M. E. Alfaro, D. I. Bolnick, P. C. Wainwright. 2004. Evolutionary dynamics of complex biomechanical systems: an example using the four-bar. Evolution 58:495-503.
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2004 M. E. Alfaro, D. R. Karns, H. K. Voris, E. Abernathy, and S. L. Sellins. 2004. Phylogeography of Cerberus (Serpentes: Homalopsinae): Diversification of a coastal marine snake in Southeast Asia. Journal of Biogeography 31:1277-1292.
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2003 M. E. Alfaro. 2003. Sweeping and striking: a kinematic study of the trunk during prey capture in three thamnophiine snakes. Journal of Experimental Biology. 206:2381-2392.
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2003 M. E. Alfaro, S. Zoller, and F. Lutzoni. 2003. Bayes or bootstrap? A simulation study comparing the performance of Bayesian Markov chain Monte Carlo sampling and bootstrapping in assessing phylogenetic confidence. Molecular Biology and Evolution. 20:255-266. Recognized in the 2005 Editor’s report as the most cited paper in Molecular Biology and Evolution for 2003. (This paper has now been cited 287 times).
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2002 H. K. Voris, M. E. Alfaro, D. R. Karns, E. Loomis, J. Murphy, L. Starnes, and E. Thompson. 2002. Phylogenetic relationships of Southeast Asian Water snakes (Homalopsinae) inferred from mitochondrial DNA sequences. Copeia 2002:906-915.
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2002 J. T. Streelman, M. E. Alfaro, M. W. Westneat, D. R. Bellwood, and S. A. Karl. 2002. Evolutionary history of the parrotfishes: biogeography, ecomorphology, and comparative diversity. Evolution 56:961-971.
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2002 M. E. Alfaro. 2002. Forward attack modes of aquatic feeding garter snakes: a comparison of specialists and generalists. Functional Ecology 16:204-215.
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2001 M. E. Alfaro, A. Herrel. 2001. Major issues of feeding motor control in vertebrates. American Zoologist 41:1243-1247.
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2001 M. E. Alfaro, and S. J. Arnold. 2001. Molecular systematics and evolution of Regina and the thamnophiine snakes. Molecular Phylogenetics and Evolution 16:408-423.
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2001 M. E. Alfaro, J. Janovetz, and M. W. Westneat. 2001. Motor control across trophic strategies: variability and constraint in the feeding system of biting and suction feeding fishes. American Zoologist 41:1266-1279.
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1999 M. E. Alfaro and M. W. Westneat. 1999. Motor patterns of herbivorous feeding: Electromyographic analysis of biting in the parrotfishes Scarus iseri and Cetoscarus bicolor. Brain, Behavior and Evolution. 54:205-222.