Michael E Alfaro
Affiliation: University of California
- Bayes or bootstrap? A simulation study comparing the performance of Bayesian Markov chain Monte Carlo sampling and bootstrapping in assessing phylogenetic confidenceMichael 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...
- Evolutionary dynamics of complex biomechanical systems: an example using the four-bar mechanismMichael 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...
- Evolutionary consequences of many-to-one mapping of jaw morphology to mechanics in labrid fishesMichael 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...
- Comparative performance of Bayesian and AIC-based measures of phylogenetic model uncertaintyMichael 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.]...
- 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....
- Rates of speciation and morphological evolution are correlated across the largest vertebrate radiationDaniel 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...
- Integrating fossils with molecular phylogenies improves inference of trait evolutionGraham 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...
- Clade age and species richness are decoupled across the eukaryotic tree of lifeDaniel 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...
- Biting disrupts integration to spur skull evolution in eelsDavid C Collar
Department of Evolution and Ecology, University of California, Davis, California 95616, USA
Nat Commun 5:5505. 2014..Our results suggest that behavioural transitions can change the evolutionary potential of the vertebrate skeleton by altering functional relationships among structures. ..
- Fitting models of continuous trait evolution to incompletely sampled comparative data using approximate Bayesian computationGraham 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...
- 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....
- Bayesian phylogenetic model selection using reversible jump Markov chain Monte CarloJohn 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....
- Imperfect morphological convergence: variable changes in cranial structures underlie transitions to durophagy in moray eelsDavid 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...
- 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....
- Integrated diversification of locomotion and feeding in labrid fishesDavid 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...
- geiger v2.0: an expanded suite of methods for fitting macroevolutionary models to phylogenetic treesMatthew 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..0, a complete overhaul of the popular R package geiger. We have reimplemented existing methods with more efficient algorithms and have developed several new approaches for accomodating heterogeneous models and data types...
- Adaptive evolution of facial colour patterns in Neotropical primatesSharlene 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...
- Elongation of the body in eelsRita 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...
- Nine exceptional radiations plus high turnover explain species diversity in jawed vertebratesMichael 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....
- Phylogenetic relationships in the family AlloherpesviridaeThomas 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...
- Replicated divergence in cichlid radiations mirrors a major vertebrate innovationMatthew D McGee
Department of Evolution and Ecology, University of California, Davis, CA 95616, USA
Proc Biol Sci 283:. 2016....
- Biologically inspired phylogenetic models strongly outperform the no common mechanism modelJohn 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)...
- Local phylogenetic divergence and global evolutionary convergence of skull function in reef fishes of the family LabridaeMark 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...
- Phylogenetic relationships and evolutionary history of the reef fish family LabridaeMark 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...
- Phylogenetic concordance analysis shows an emerging pathogen is novel and endemicAndrew 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...
- Phylogeny, evolutionary history, and biogeography of Oriental-Australian rear-fanged water snakes (Colubroidea: Homalopsidae) inferred from mitochondrial and nuclear DNA sequencesMichael 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...
- 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...
- Sweeping and striking: a kinematic study of the trunk during prey capture in three thamnophiine snakesMichael 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...