Michael E Alfaro

Summary

Affiliation: University of California
Country: USA

Publications

  1. ncbi request reprint Bayes or bootstrap? A simulation study comparing the performance of Bayesian Markov chain Monte Carlo sampling and bootstrapping in assessing phylogenetic confidence
    Michael E Alfaro
    Evolution and Ecology, University of California, Davis, USA
    Mol Biol Evol 20:255-66. 2003
  2. ncbi request reprint Evolutionary dynamics of complex biomechanical systems: an example using the four-bar mechanism
    Michael E Alfaro
    Section of Evolution and Ecology, One Shields Avenue, University of California, Davis, California 95616, USA
    Evolution 58:495-503. 2004
  3. ncbi request reprint Evolutionary consequences of many-to-one mapping of jaw morphology to mechanics in labrid fishes
    Michael E Alfaro
    Section of Evolution and Ecology, University of California, Davis, California, 95616, USA
    Am Nat 165:E140-54. 2005
  4. ncbi request reprint Comparative performance of Bayesian and AIC-based measures of phylogenetic model uncertainty
    Michael E Alfaro
    School of Biological Sciences, P O Box 644236, Pullman, Washington 99164 4236, USA
    Syst Biol 55:89-96. 2006
  5. ncbi request reprint Do reefs drive diversification in marine teleosts? Evidence from the pufferfishes and their allies (Order Tetraodontiformes)
    Michael E Alfaro
    School of Biological Sciences, Washington State University, Pullman, Washington 99164, USA
    Evolution 61:2104-26. 2007
  6. doi request reprint Rates of speciation and morphological evolution are correlated across the largest vertebrate radiation
    Daniel L Rabosky
    Department of Integrative Biology, Museum of Vertebrate Zoology, University of California, Berkeley, California 94609, USA
    Nat Commun 4:1958. 2013
  7. doi request reprint Integrating fossils with molecular phylogenies improves inference of trait evolution
    Graham J Slater
    Department of Ecology and Evolutionary Biology, University of California, 610 Charles E Young Drive South, Los Angeles, California 90095 1606, USA
    Evolution 66:3931-44. 2012
  8. pmc Clade age and species richness are decoupled across the eukaryotic tree of life
    Daniel L Rabosky
    Department of Integrative Biology and Museum of Vertebrate Zoology, University of California, Berkeley, California, USA
    PLoS Biol 10:e1001381. 2012
  9. doi request reprint Fitting models of continuous trait evolution to incompletely sampled comparative data using approximate Bayesian computation
    Graham J Slater
    Department of Ecology and Evolutionary Biology, University of California, Los Angeles, California 90095 1606, USA
    Evolution 66:752-62. 2012
  10. pmc Does evolutionary innovation in pharyngeal jaws lead to rapid lineage diversification in labrid fishes?
    Michael E Alfaro
    University of California, Los Angeles, CA 90095 1606, USA
    BMC Evol Biol 9:255. 2009

Detail Information

Publications25

  1. ncbi request reprint Bayes or bootstrap? A simulation study comparing the performance of Bayesian Markov chain Monte Carlo sampling and bootstrapping in assessing phylogenetic confidence
    Michael E Alfaro
    Evolution and Ecology, University of California, Davis, USA
    Mol Biol Evol 20:255-66. 2003
    ..BMCMC-PP provided high support values for correct topological bipartitions with fewer characters than was needed for nonparametric bootstrap...
  2. ncbi request reprint Evolutionary dynamics of complex biomechanical systems: an example using the four-bar mechanism
    Michael E Alfaro
    Section of Evolution and Ecology, One Shields Avenue, University of California, Davis, California 95616, USA
    Evolution 58:495-503. 2004
    ..We suggest that partial decoupling of morphology and mechanics due to redundancy is a major factor in morphological diversification...
  3. ncbi request reprint Evolutionary consequences of many-to-one mapping of jaw morphology to mechanics in labrid fishes
    Michael E Alfaro
    Section of Evolution and Ecology, University of California, Davis, California, 95616, USA
    Am Nat 165:E140-54. 2005
    ..Many-to-one mapping may be an important factor in generating the uneven patterns of diversity in physiological traits...
  4. ncbi request reprint Comparative performance of Bayesian and AIC-based measures of phylogenetic model uncertainty
    Michael E Alfaro
    School of Biological Sciences, P O Box 644236, Pullman, Washington 99164 4236, USA
    Syst Biol 55:89-96. 2006
    ..AIC; Akaike weights; Bayesian phylogenetics; model averaging; model selection; model uncertainty; posterior probability; reversible jump.]...
  5. ncbi request reprint Do reefs drive diversification in marine teleosts? Evidence from the pufferfishes and their allies (Order Tetraodontiformes)
    Michael E Alfaro
    School of Biological Sciences, Washington State University, Pullman, Washington 99164, USA
    Evolution 61:2104-26. 2007
    ....
  6. doi request reprint Rates of speciation and morphological evolution are correlated across the largest vertebrate radiation
    Daniel L Rabosky
    Department of Integrative Biology, Museum of Vertebrate Zoology, University of California, Berkeley, California 94609, USA
    Nat Commun 4:1958. 2013
    ..Alternatively, these findings are consistent with the hypothesis that phenotypic 'evolvability'-the capacity of organisms to evolve-shapes the dynamics of speciation through time at the largest phylogenetic scales...
  7. doi request reprint Integrating fossils with molecular phylogenies improves inference of trait evolution
    Graham J Slater
    Department of Ecology and Evolutionary Biology, University of California, 610 Charles E Young Drive South, Los Angeles, California 90095 1606, USA
    Evolution 66:3931-44. 2012
    ..Our approach highlights the importance of considering fossil information when making macroevolutionary inference, and provides a way to integrate the kind of sparse fossil information that is available to most evolutionary biologists...
  8. pmc Clade age and species richness are decoupled across the eukaryotic tree of life
    Daniel L Rabosky
    Department of Integrative Biology and Museum of Vertebrate Zoology, University of California, Berkeley, California, USA
    PLoS Biol 10:e1001381. 2012
    ..These results imply that a fundamentally different interpretative paradigm may be needed in the study of phylogenetic diversity patterns in many groups of organisms...
  9. doi request reprint Fitting models of continuous trait evolution to incompletely sampled comparative data using approximate Bayesian computation
    Graham J Slater
    Department of Ecology and Evolutionary Biology, University of California, Los Angeles, California 90095 1606, USA
    Evolution 66:752-62. 2012
    ..ABC approaches can provide a useful alternative set of tools for future macroevolutionary studies where likelihood-dependent approaches are lacking...
  10. pmc Does evolutionary innovation in pharyngeal jaws lead to rapid lineage diversification in labrid fishes?
    Michael E Alfaro
    University of California, Los Angeles, CA 90095 1606, USA
    BMC Evol Biol 9:255. 2009
    ....
  11. ncbi request reprint Bayesian phylogenetic model selection using reversible jump Markov chain Monte Carlo
    John P Huelsenbeck
    Section of Ecology, Behavior and Evolution, Division of Biological Sciences, University of California, San Diego, USA
    Mol Biol Evol 21:1123-33. 2004
    ....
  12. ncbi request reprint Imperfect morphological convergence: variable changes in cranial structures underlie transitions to durophagy in moray eels
    David C Collar
    Department of Evolution and Ecology, University of California, Davis, California 95616
    Am Nat 183:E168-84. 2014
    ..Our results reveal a pattern of imperfect convergence, which suggests shared selection may actually promote diversification because lineages often differ in their phenotypic responses to similar selective demands...
  13. doi request reprint Systemic iridovirus from threespine stickleback Gasterosteus aculeatus represents a new megalocytivirus species (family Iridoviridae)
    Thomas B Waltzek
    Department of Medicine and Epidemiology, University of California, Davis, CA 95616, USA
    Dis Aquat Organ 98:41-56. 2012
    ....
  14. pmc Integrated diversification of locomotion and feeding in labrid fishes
    David C Collar
    Section of Evolution and Ecology, University of California, Davis, CA 95616, USA
    Biol Lett 4:84-6. 2008
    ..These results indicate that the labrid radiation involved a strong connection between locomotion and feeding abilities...
  15. pmc Adaptive evolution of facial colour patterns in Neotropical primates
    Sharlene E Santana
    UCLA Center for Society and Genetics, University of California, Los Angeles, CA 90095, USA
    Proc Biol Sci 279:2204-11. 2012
    ..Our results demonstrate the interaction of behavioural and ecological factors in shaping one of the most outstanding facial diversities of any mammalian lineage...
  16. doi request reprint Elongation of the body in eels
    Rita S Mehta
    Department of Ecology and Evolutionary Biology, 100 Schaffer Road, University of California, Santa Cruz, CA 95060, USA
    Integr Comp Biol 50:1091-105. 2010
    ..Lastly, we point out that a diverse range of derived behaviors such as head- and tail-first burrowing, rotational feeding, and knotting around prey are only found in long cylindrical vertebrates...
  17. doi request reprint Phylogenetic relationships in the family Alloherpesviridae
    Thomas B Waltzek
    Department of Medicine and Epidemiology, School of Veterinary Medicine, University of California, Davis, California 95616, USA
    Dis Aquat Organ 84:179-94. 2009
    ..A comparison of virus and host phylogenies suggested that closely related HVs in this family may have coevolved with their hosts, whereas significant codiversification was not apparent for the more distantly related viruses...
  18. pmc Nine exceptional radiations plus high turnover explain species diversity in jawed vertebrates
    Michael E Alfaro
    Department of Ecology and Evolutionary Biology, University of California, Los Angeles, CA 90095, USA
    Proc Natl Acad Sci U S A 106:13410-4. 2009
    ....
  19. pmc Biologically inspired phylogenetic models strongly outperform the no common mechanism model
    John P Huelsenbeck
    Department of Integrative Biology, University of California, Berkeley, CA 94720 3140, USA
    Syst Biol 60:225-32. 2011
    ..With the realistic NCM in the background, then, most parsimonious trees have greatest power to explain available observations. -Farris (2008)...
  20. ncbi request reprint Phylogenetic relationships and evolutionary history of the reef fish family Labridae
    Mark W Westneat
    Department of Zoology, Field Museum of Natural History, Chicago, IL 60605 2496, USA
    Mol Phylogenet Evol 36:370-90. 2005
    ..Functional novelties in the feeding apparatus have allowed labrid fishes to occupy nearly every feeding guild in reef environments, and trophic variation is a central axis of diversification in this family...
  21. pmc Local phylogenetic divergence and global evolutionary convergence of skull function in reef fishes of the family Labridae
    Mark W Westneat
    Department of Zoology, Field Museum of Natural History, Chicago, IL 60605, USA
    Proc Biol Sci 272:993-1000. 2005
    ..Divergence of close relatives, convergence among higher clades and several unusual 'breakthroughs' in skull function characterize the evolution of functional complexity in one of the most diverse groups of reef fishes...
  22. ncbi request reprint Phylogenetic concordance analysis shows an emerging pathogen is novel and endemic
    Andrew Storfer
    School of Biological Sciences, Washington State University, Pullman, WA 99164 4236, USA
    Ecol Lett 10:1075-83. 2007
    ..Thus, our analysis of intraspecific phylogenetic concordance revealed that human introduction of viruses is the mechanism underlying tree non-concordance and possibly disease emergence via artificial selection...
  23. ncbi request reprint Relationships of the temperate Australasian labrid fish tribe Odacini (Perciformes; Teleostei)
    Kendall D Clements
    School of Biological Sciences, University of Auckland, Auckland, New Zealand
    Mol Phylogenet Evol 32:575-87. 2004
    ..Either herbivory evolved twice in the odacines, or herbivory evolved once with two reversions to carnivory. The latter hypothesis appears more likely in the light of odacine feeding biology...
  24. ncbi request reprint Sweeping and striking: a kinematic study of the trunk during prey capture in three thamnophiine snakes
    Michael E Alfaro
    Committee on Evolutionary Biology, 1025 E 57th Street, University of Chicago, Chicago, IL 60637, USA
    J Exp Biol 206:2381-92. 2003
    ..elegans, although N. rhombifer typically had a short strike distance. N. rhombifer struck significantly faster than T. elegans. Aquatic prey capture diversity appears to reflect ecological diversity in thamnophiine snakes...
  25. doi request reprint Phylogeny, evolutionary history, and biogeography of Oriental-Australian rear-fanged water snakes (Colubroidea: Homalopsidae) inferred from mitochondrial and nuclear DNA sequences
    Michael E Alfaro
    School of Biological Sciences, Washington State University, Pullman, WA 99164, USA
    Mol Phylogenet Evol 46:576-93. 2008
    ..We discuss several Miocene and Pliocene paleogeographic factors that might underlie observed patterns of temporal diversification and biogeography...