Recent Courses

E&S SCI M216 | EE BIOL M200A - Evolutionary Biology
EE BIOL 194B - Research Group or Internship Seminars: Ecology and Evolutionary Biology
EE BIOL C177 | EE BIOL C234 - Practical Computing for Evolutionary Biologists and Ecologists

Research Areas

Conservation Biology, Evolutionary Biology, Marine Biology, Theory

Research Interests

The central goal of my research program is to understand the factors that govern the evolutionary dynamics of organismal diversification. How can we explain the uneven patterns of species richness and morphological diversity across the Tree of Life? Where is macroevolutionary theory adequate to explain diversity patterns and where must new models and methods be developed? Does morphological diversity always signal mechanical, functional, or ecological diversity? To address these questions, I work on two main systems: coral reef fishes and neotropical primates. My research approach is interdisciplinary and quantitative and crosses traditional boundaries among molecular phylogenetics, evolutionary morphology, and theoretical evolution. I construct evolutionary trees using phylogenomic approaches, test evolutionary hypotheses using phylogenetic statis- tical methods; use models of trait evolution to explore form-function dynamics identify and quantify organismal diversity using morphological and functional morphological techniques

Selected Publications

C. Darrin Hulsey, Jimmy Zheng, Roi Holzman, Michael E. Alfaro, Melisa Olave and Axel Meyer, "Phylogenomics of a putatively convergent novelty: did hypertrophied lips evolve once or repeatedly in Lake Malawi cichlid fishes?", BMC Evolutionary Biology, 18 : - (2018) [link].

Peter C Wainwright, Francesco Santini, David R Bellwood, D Ross Robertson, Luiz A Rocha, Michael E Alfaro, "Phylogenetics and geography of speciation in New World Halichoeres wrasses", Molecular Phylogenetics and Evolution, 121 : 35-45 (2018) [link].

Max R Tolkoff Michael E Alfaro Guy Baele Philippe Lemey Marc A Suchard, "Phylogenetic factor analysis", Systematic Biology, 67 (3): 384-399 (2018) [link].

Alfaro, ME, "[PDF] from pnas.org
UC-eLinks
Resolving the ray-finned fish tree of life", PNAS, 115 (24): 6107-6109 (2018) .

Lima MGM, Silva-Junior JSE, Cerny D, Buckner JC, Aleixo A, Chang J, Zheng J, Alfaro ME, Martins A, Di Fiore A, Boubli JP, Lynch Alfaro JW, "A phylogenomic perspective on the robust capuchin monkey (Sapajus) radiation: First evidence for extensive population admixture across South America", Mol Phylogenet Evol, 115 (24): 137-150 (2018) [link].

Rabosky, D.L.
Chang, J.
Title, P.O.
Cowman, P.F.
Sallan, L.
Friedman, M.
Kaschner, K.
Garilao, C.
Near, T.J.
Coll, M.
Alfaro, M.E., "An inverse latitudinal gradient in speciation rate for marine fishes", Nature, 559 : 392-395 (2018) [link].

Gilbert, Princess S; Wu, Jing; Simon, Margaret W; Sinsheimer, Janet S; Alfaro, Michael E, "Filtering nucleotide sites by phylogenetic signal to noise ratio increases confidence in the Neoaves phylogeny generated from ultraconserved elements", Mol. Phylogenet. Evol, 126 : 116-128 (2018) [link].

Prosanta Chakrabarty, Brant C Faircloth, Fernando Alda, William B Ludt, Caleb D Mcmahan, Thomas J Near, Alex Dornburg, James S Albert, Jairo Arroyave, Melanie LJ Stiassny, Laurie Sorenson, Michael E Alfaro, "Phylogenomic Systematics of Ostariophysan Fishes: Ultraconserved Elements Support the Surprising Non-Monophyly of Characiformes", Systematic Biology, 66 : 881-895 (2017) [link].

Luz E Ochoa, Fabio F Roxo, Carlos DoNascimiento, Mark H Sabaj, Alessio Datovo, Michael Alfaro, Claudio Oliveira, "Multilocus analysis of the catfish family Trichomycteridae (Teleostei: Ostariophysi: Siluriformes) supporting a monophyletic Trichomycterinae", Molecular Phylogenetics and Evolution, 115 : 71-81 (2017) [link].

CD Hulsey, J Zheng, BC Faircloth, A Meyer, ME Alfaro, "Phylogenomic analysis of Lake Malawi cichlid fishes: further evidence that the three-stage model of diversification does not fit", Molecular Phylogenetics and Evolution, 114 : 40-48 (2017) [link].