Michael E Alfaro

Summary

Affiliation: University of California
Country: USA

Publications

  1. pmc Phylotastic! Making tree-of-life knowledge accessible, reusable and convenient
    Arlin Stoltzfus
    Institute for Bioscience and Biotechnology Research, Biosystems and Biomaterials Division, National Institute of Standards and Technology, Gaithersburg, MD 20899, USA
    BMC Bioinformatics 14:158. 2013
  2. 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
  3. pmc Did genome duplication drive the origin of teleosts? A comparative study of diversification in ray-finned fishes
    Francesco Santini
    Department of Ecology and Evolutionary Biology, University of California at Los Angeles, 651 Charles Young Dr, South, Los Angeles, CA 90095, USA
    BMC Evol Biol 9:194. 2009
  4. 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
  5. doi request reprint A multi-locus molecular timescale for the origin and diversification of eels (Order: Anguilliformes)
    Francesco Santini
    University of California Los Angeles, Department of Ecology and Evolutionary Biology, 610 Charles E Young Drive South, Los Angeles, CA 90095, USA Università degli Studi di Torino, Dipartimento di Scienze della Terra, Via Valperga Caluso 35, 10125 Torino, Italy Electronic address
    Mol Phylogenet Evol 69:884-94. 2013
  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 A new phylogeny of tetraodontiform fishes (Tetraodontiformes, Acanthomorpha) based on 22 loci
    Francesco Santini
    University of California Los Angeles, Department of Ecology and Evolutionary Biology, 610 Charles E Young Drive South, Los Angeles, CA 90095, USA
    Mol Phylogenet Evol 69:177-87. 2013
  8. doi request reprint A new multi-locus timescale reveals the evolutionary basis of diversity patterns in triggerfishes and filefishes (Balistidae, Monacanthidae; Tetraodontiformes)
    Francesco Santini
    University of California Los Angeles, Department of Ecology and Evolutionary Biology, 610 Charles E Young Drive South, Los Angeles, CA 90095, USA
    Mol Phylogenet Evol 69:165-76. 2013
  9. doi request reprint A multilocus molecular phylogeny of boxfishes (Aracanidae, Ostraciidae; Tetraodontiformes)
    Francesco Santini
    Department of Ecology and Evolutionary Biology, University of California Los Angeles, 610 Young Drive South, Los Angeles, CA 90095, USA
    Mol Phylogenet Evol 66:153-60. 2013
  10. doi request reprint A multi-locus timetree of surgeonfishes (Acanthuridae, Percomorpha), with revised family taxonomy
    Laurie Sorenson
    University of California Los Angeles, Department of Ecology and Evolutionary Biology, 610 Charles E Young Drive South, Los Angeles, CA 90095, USA
    Mol Phylogenet Evol 68:150-60. 2013

Detail Information

Publications28

  1. pmc Phylotastic! Making tree-of-life knowledge accessible, reusable and convenient
    Arlin Stoltzfus
    Institute for Bioscience and Biotechnology Research, Biosystems and Biomaterials Division, National Institute of Standards and Technology, Gaithersburg, MD 20899, USA
    BMC Bioinformatics 14:158. 2013
    ..Such a system could become a sustainable community resource if implemented as a distributed system of loosely coupled parts that interact through clearly defined interfaces...
  2. 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
    ....
  3. pmc Did genome duplication drive the origin of teleosts? A comparative study of diversification in ray-finned fishes
    Francesco Santini
    Department of Ecology and Evolutionary Biology, University of California at Los Angeles, 651 Charles Young Dr, South, Los Angeles, CA 90095, USA
    BMC Evol Biol 9:194. 2009
    ..However, one critical assumption of this hypothesis, that diversification rates in teleosts increased soon after the acquisition of a duplicated genome, has never been tested...
  4. 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
    ....
  5. doi request reprint A multi-locus molecular timescale for the origin and diversification of eels (Order: Anguilliformes)
    Francesco Santini
    University of California Los Angeles, Department of Ecology and Evolutionary Biology, 610 Charles E Young Drive South, Los Angeles, CA 90095, USA Università degli Studi di Torino, Dipartimento di Scienze della Terra, Via Valperga Caluso 35, 10125 Torino, Italy Electronic address
    Mol Phylogenet Evol 69:884-94. 2013
    ..Most major (family level) lineages originated between the end of the Cretaceous and Early Eocene, suggesting that anguilliform radiation may have been facilitated by the recovery of marine ecosystems following the KP extinction...
  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 A new phylogeny of tetraodontiform fishes (Tetraodontiformes, Acanthomorpha) based on 22 loci
    Francesco Santini
    University of California Los Angeles, Department of Ecology and Evolutionary Biology, 610 Charles E Young Drive South, Los Angeles, CA 90095, USA
    Mol Phylogenet Evol 69:177-87. 2013
    ....
  8. doi request reprint A new multi-locus timescale reveals the evolutionary basis of diversity patterns in triggerfishes and filefishes (Balistidae, Monacanthidae; Tetraodontiformes)
    Francesco Santini
    University of California Los Angeles, Department of Ecology and Evolutionary Biology, 610 Charles E Young Drive South, Los Angeles, CA 90095, USA
    Mol Phylogenet Evol 69:165-76. 2013
    ....
  9. doi request reprint A multilocus molecular phylogeny of boxfishes (Aracanidae, Ostraciidae; Tetraodontiformes)
    Francesco Santini
    Department of Ecology and Evolutionary Biology, University of California Los Angeles, 610 Young Drive South, Los Angeles, CA 90095, USA
    Mol Phylogenet Evol 66:153-60. 2013
    ....
  10. doi request reprint A multi-locus timetree of surgeonfishes (Acanthuridae, Percomorpha), with revised family taxonomy
    Laurie Sorenson
    University of California Los Angeles, Department of Ecology and Evolutionary Biology, 610 Charles E Young Drive South, Los Angeles, CA 90095, USA
    Mol Phylogenet Evol 68:150-60. 2013
    ..Based on our molecular analyses, in conjunction with the large body of morphological evidence, we recommend dissolving the genus Ctenochaetus into the genus Acanthurus...
  11. 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...
  12. 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...
  13. 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...
  14. 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...
  15. doi request reprint The influence of an innovative locomotor strategy on the phenotypic diversification of triggerfish (family: Balistidae)
    Alex Dornburg
    Department of Ecology and Evolutionary Biology, Yale University, New Haven, Connecticut 06520, USA
    Evolution 65:1912-26. 2011
    ..Together these findings suggest that the acquisition of a distinctive mode of locomotion drove an early radiation of shape and function in triggerfish, but not an early radiation of species...
  16. 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
    ....
  17. 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...
  18. 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...
  19. pmc Diversity versus disparity and the radiation of modern cetaceans
    Graham J Slater
    Department of Ecology and Evolutionary Biology, University of California at Los Angeles, Los Angeles, CA 90025, USA
    Proc Biol Sci 277:3097-104. 2010
    ....
  20. ncbi request reprint geiger v2.0: an expanded suite of methods for fitting macroevolutionary models to phylogenetic trees
    Matthew W Pennell
    Department of Biological Sciences and Institute for Bioinformatics and Evolutionary Studies, University of Idaho, Moscow, ID 83844, Department of Paleobiology, National Museum of Natural History, Smithsonian Institution, Washington, DC 20013, Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI 48109, USA, Department of Biological Sciences, Macquarie University, Sydney, NSW 2109, Australia and Department of Ecology and Evolutionary Biology, University of California, Los Angeles, Los Angeles, CA 90095, USA
    Bioinformatics 30:2216-8. 2014
    ..r-project.org/web/packages/geiger/. All source code is also available on github http://github.com/mwpennell/geiger-v2. geiger v2.0 depends on the ape package...
  21. 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...
  22. ncbi 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...
  23. 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...
  24. doi request reprint Anointing variation across wild capuchin populations: a review of material preferences, bout frequency and anointing sociality in Cebus and Sapajus
    Jessica W Lynch Alfaro
    Center for Society and Genetics, University of California Los Angeles, Los Angeles, California 90095, USA
    Am J Primatol 74:299-314. 2012
    ..We review anointing in the context of other Neotropical primate rubbing behaviors and consider the evidence for anointing as self-medication; as a mechanism for enhanced sociality; and as a behavioral response to chemical stimuli...
  25. 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)...
  26. 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
    ....
  27. 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...