Michael Alfaro

Michael Edward Alfaro

Professor, Ecology And Evolutionary Biology, University of California Los Angeles

Professor, Institute for Society And Genetics, University of California Los Angeles


  1. Dornburg A, Zapfe KL, Williams R, Alfaro ME, Morris R, Adachi H, Flores J, Santini F, Near TJ, Frédérich B. Considering decoupled phenotypic diversification between ontogenetic phases in macroevolution: An example using Triggerfishes (Balistidae).. Systematic biology, 2024.
  2. Tsai WLE, Escalona M, Garrett KL, Terrill RS, Sahasrabudhe R, Nguyen O, Beraut E, Seligmann W, Fairbairn CW, Harrigan RJ, McCormack JE, Alfaro ME, Smith TB, Bay RA. A highly contiguous genome assembly for the Yellow Warbler (Setophaga petechia).. The Journal of heredity, 2024.
  3. Smith JE, Natterson-Horowitz B, Mueller MM, Alfaro ME. Mechanisms of equality and inequality in mammalian societies.. Philosophical transactions of the Royal Society of London. Series B, Biological sciences, 2023.
  4. Ghezelayagh A, Harrington RC, Burress ED, Campbell MA, Buckner JC, Chakrabarty P, Glass JR, McCraney WT, Unmack PJ, Thacker CE, Alfaro ME, Friedman ST, Ludt WB, Cowman PF, Friedman M, Price SA, Dornburg A, Faircloth BC, Wainwright PC, Near TJ. Prolonged morphological expansion of spiny-rayed fishes following the end-Cretaceous.. Nature ecology & evolution, 2022.
  5. Van Gorp MJW, Goyens J, Alfaro ME, Van Wassenbergh S. Keels of boxfish carapaces strongly improve stabilization against roll.. Journal of the Royal Society, Interface, 2022.
  6. Melo BF, Sidlauskas BL, Near TJ, Roxo FF, Ghezelayagh A, Ochoa LE, Stiassny MLJ, Arroyave J, Chang J, Faircloth BC, MacGuigan DJ, Harrington RC, Benine RC, Burns MD, Hoekzema K, Sanches NC, Maldonado-Ocampo JA, Castro RMC, Foresti F, Alfaro ME, Oliveira C. Accelerated Diversification Explains the Exceptional Species Richness of Tropical Characoid Fishes.. Systematic biology, 2021.
  7. Snedden CE, Makanani SK, Schwartz ST, Gamble A, Blakey RV, Borremans B, Helman SK, Espericueta L, Valencia A, Endo A, Alfaro ME, Lloyd-Smith JO. SARS-CoV-2: Cross-scale Insights from Ecology and Evolution.. Trends in microbiology, 2021.
  8. Stiller J, da Fonseca RR, Alfaro ME, Faircloth BC, Wilson NG, Rouse GW. Using ultraconserved elements to track the influence of sea-level change on leafy seadragon populations.. Molecular ecology, 2020.
  9. Campbell MA, Buser TJ, Alfaro ME, López JA. Addressing incomplete lineage sorting and paralogy in the inference of uncertain salmonid phylogenetic relationships.. PeerJ, 2020.
  10. McCraney WT, Thacker CE, Alfaro ME. Supermatrix phylogeny resolves goby lineages and reveals unstable root of Gobiaria.. Molecular phylogenetics and evolution, 2020.
  11. Chang J, Rabosky DL, Alfaro ME. Estimating Diversification Rates on Incompletely Sampled Phylogenies: Theoretical Concerns and Practical Solutions.. Systematic biology, 2020.
  12. Ochoa LE, Datovo A, DoNascimiento C, Roxo FF, Sabaj MH, Chang J, Melo BF, Silva GSC, Foresti F, Alfaro M, Oliveira C. Phylogenomic analysis of trichomycterid catfishes (Teleostei: Siluriformes) inferred from ultraconserved elements.. Scientific reports, 2020.
  13. Gjesfjeld E, Silvestro D, Chang J, Koch B, Foster JG, Alfaro ME. A quantitative workflow for modeling diversification in material culture.. PloS one, 2020.
  14. Haridas S, Albert R, Binder M, Bloem J, LaButti K, Salamov A, Andreopoulos B, Baker SE, Barry K, Bills G, Bluhm BH, Cannon C, Castanera R, Culley DE, Daum C, Ezra D, González JB, Henrissat B, Kuo A, Liang C, Lipzen A, Lutzoni F, Magnuson J, Mondo SJ, Nolan M, Ohm RA, Pangilinan J, Park HJ, Ramírez L, Alfaro M, Sun H, Tritt A, Yoshinaga Y, Zwiers LH, Turgeon BG, Goodwin SB, Spatafora JW, Crous PW, Grigoriev IV. 101 Dothideomycetes genomes: A test case for predicting lifestyles and emergence of pathogens.. Studies in mycology, 2020.
  15. Friedman M, Feilich KL, Beckett HT, Alfaro ME, Faircloth BC, Cerný D, Miya M, Near TJ, Harrington RC. A phylogenomic framework for pelagiarian fishes (Acanthomorpha: Percomorpha) highlights mosaic radiation in the open ocean.. Proceedings. Biological sciences, 2019.
  16. Phuong MA, Alfaro ME, Mahardika GN, Marwoto RM, Prabowo RE, von Rintelen T, Vogt PWH, Hendricks JR, Puillandre N. Lack of Signal for the Impact of Conotoxin Gene Diversity on Speciation Rates in Cone Snails.. Systematic biology, 2019.
  17. Alfaro ME, Karan EA, Schwartz ST, Shultz AJ. The Evolution of Color Pattern in Butterflyfishes (Chaetodontidae).. Integrative and comparative biology, 2019.
  18. Alda F, Tagliacollo VA, Bernt MJ, Waltz BT, Ludt WB, Faircloth BC, Alfaro ME, Albert JS, Chakrabarty P. Resolving Deep Nodes in an Ancient Radiation of Neotropical Fishes in the Presence of Conflicting Signals from Incomplete Lineage Sorting.. Systematic biology, 2019.
  19. Hulsey CD, Alfaro ME, Zheng J, Meyer A, Holzman R. Pleiotropic jaw morphology links the evolution of mechanical modularity and functional feeding convergence in Lake Malawi cichlids.. Proceedings. Biological sciences, 2019.
  20. Roxo FF, Ochoa LE, Sabaj MH, Lujan NK, Covain R, Silva GSC, Melo BF, Albert JS, Chang J, Foresti F, Alfaro ME, Oliveira C. Phylogenomic reappraisal of the Neotropical catfish family Loricariidae (Teleostei: Siluriformes) using ultraconserved elements.. Molecular phylogenetics and evolution, 2019.
  21. Burin G, Alencar LRV, Chang J, Alfaro ME, Quental TB. How Well Can We Estimate Diversity Dynamics for Clades in Diversity Decline?. Systematic biology, 2019.
  22. Lutzoni F, Nowak MD, Alfaro ME, Reeb V, Miadlikowska J, Krug M, Arnold AE, Lewis LA, Swofford DL, Hibbett D, Hilu K, James TY, Quandt D, Magallón S. Contemporaneous radiations of fungi and plants linked to symbiosis.. Nature communications, 2018.
  23. Darrin Hulsey C, Zheng J, Holzman R, Alfaro ME, Olave M, Meyer A. Phylogenomics of a putatively convergent novelty: did hypertrophied lips evolve once or repeatedly in Lake Malawi cichlid fishes?. BMC evolutionary biology, 2018.
  24. DiBattista JD, Alfaro ME, Sorenson L, Choat JH, Hobbs JA, Sinclair-Taylor TH, Rocha LA, Chang J, Luiz OJ, Cowman PF, Friedman M, Berumen ML. Ice ages and butterflyfishes: Phylogenomics elucidates the ecological and evolutionary history of reef fishes in an endemism hotspot.. Ecology and evolution, 2018.
  25. Rabosky DL, Chang J, Title PO, Cowman PF, Sallan L, Friedman M, Kaschner K, Garilao C, Near TJ, Coll M, Alfaro ME. An inverse latitudinal gradient in speciation rate for marine fishes.. Nature, 2018.
  26. Alfaro ME. Resolving the ray-finned fish tree of life.. Proceedings of the National Academy of Sciences of the United States of America, 2018.
  27. Tolkoff MR, Alfaro ME, Baele G, Lemey P, Suchard MA. Phylogenetic Factor Analysis.. Systematic biology, 2018.
  28. Gilbert PS, Wu J, Simon MW, Sinsheimer JS, Alfaro ME. Filtering nucleotide sites by phylogenetic signal to noise ratio increases confidence in the Neoaves phylogeny generated from ultraconserved elements.. Molecular phylogenetics and evolution, 2018.
  29. Lima MGM, Silva-Júnior JSE, Cerný 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.. Molecular phylogenetics and evolution, 2018.
  30. Alfaro ME, Faircloth BC, Harrington RC, Sorenson L, Friedman M, Thacker CE, Oliveros CH, Cerný D, Near TJ. Explosive diversification of marine fishes at the Cretaceous-Palaeogene boundary.. Nature ecology & evolution, 2018.
  31. Wainwright PC, Santini F, Bellwood DR, Robertson DR, Rocha LA, Alfaro ME. Phylogenetics and geography of speciation in New World Halichoeres wrasses.. Molecular phylogenetics and evolution, 2017.
  32. Chakrabarty P, Faircloth BC, Alda F, Ludt WB, Mcmahan CD, Near TJ, Dornburg A, Albert JS, Arroyave J, Stiassny MLJ, Sorenson L, Alfaro ME. Phylogenomic Systematics of Ostariophysan Fishes: Ultraconserved Elements Support the Surprising Non-Monophyly of Characiformes.. Systematic biology, 2017.
  33. Campbell MA, Alfaro ME, Belasco M, López JA. Early-branching euteleost relationships: areas of congruence between concatenation and coalescent model inferences.. PeerJ, 2017.
  34. Ochoa LE, Roxo FF, DoNascimiento C, Sabaj MH, Datovo A, Alfaro M, Oliveira C. Multilocus analysis of the catfish family Trichomycteridae (Teleostei: Ostariophysi: Siluriformes) supporting a monophyletic Trichomycterinae.. Molecular phylogenetics and evolution, 2017.
  35. Frédérich B, Santini F, Konow N, Schnitzler J, Lecchini D, Alfaro ME. Body shape convergence driven by small size optimum in marine angelfishes.. Biology letters, 2017.
  36. Hulsey CD, Zheng J, Faircloth BC, Meyer A, Alfaro ME. Phylogenomic analysis of Lake Malawi cichlid fishes: Further evidence that the three-stage model of diversification does not fit.. Molecular phylogenetics and evolution, 2017.
  37. Longo SJ, Faircloth BC, Meyer A, Westneat MW, Alfaro ME, Wainwright PC. Phylogenomic analysis of a rapid radiation of misfit fishes (Syngnathiformes) using ultraconserved elements.. Molecular phylogenetics and evolution, 2017.
  38. Harrington RC, Faircloth BC, Eytan RI, Smith WL, Near TJ, Alfaro ME, Friedman M. Phylogenomic analysis of carangimorph fishes reveals flatfish asymmetry arose in a blink of the evolutionary eye.. BMC evolutionary biology, 2016.
  39. Alfaro ME. Evolution: Bioluminescent Courtship as an Engine of Diversity.. Current biology : CB, 2016.
  40. Phuong MA, Mahardika GN, Alfaro ME. Dietary breadth is positively correlated with venom complexity in cone snails.. BMC genomics, 2016.
  41. Santini F, Sorenson L, Alfaro ME. Phylogeny and biogeography of hogfishes and allies (Bodianus, Labridae).. Molecular phylogenetics and evolution, 2016.
  42. McGee MD, Faircloth BC, Borstein SR, Zheng J, Darrin Hulsey C, Wainwright PC, Alfaro ME. Replicated divergence in cichlid radiations mirrors a major vertebrate innovation.. Proceedings. Biological sciences, 2016.
  43. Blumstein DT, Buckner J, Shah S, Patel S, Alfaro ME, Natterson-Horowitz B. A clinical research pathway towards developing new insights into cardiomyopathy.. Evolution, medicine, and public health, 2015.
  44. Blumstein DT, Buckner J, Shah S, Patel S, Alfaro ME, Natterson-Horowitz B. The evolution of capture myopathy in hooved mammals: a model for human stress cardiomyopathy?. Evolution, medicine, and public health, 2015.
  45. Gilbert PS, Chang J, Pan C, Sobel EM, Sinsheimer JS, Faircloth BC, Alfaro ME. Genome-wide ultraconserved elements exhibit higher phylogenetic informativeness than traditional gene markers in percomorph fishes.. Molecular phylogenetics and evolution, 2015.
  46. Iglesias TL, Dornburg A, Brandley MC, Alfaro ME, Warren DL. Life in the unthinking depths: energetic constraints on encephalization in marine fishes.. Journal of evolutionary biology, 2015.
  47. Van Wassenbergh S, van Manen K, Marcroft TA, Alfaro ME, Stamhuis EJ. Boxfish swimming paradox resolved: forces by the flow of water around the body promote manoeuvrability.. Journal of the Royal Society, Interface, 2015.
  48. Collar DC, Wainwright PC, Alfaro ME, Revell LJ, Mehta RS. Biting disrupts integration to spur skull evolution in eels.. Nature communications, 2014.
  49. Lynch Alfaro JW, Boubli JP, Paim FP, Ribas CC, Silva MN, Messias MR, Röhe F, Mercês MP, Silva Júnior JS, Silva CR, Pinho GM, Koshkarian G, Nguyen MT, Harada ML, Rabelo RM, Queiroz HL, Alfaro ME, Farias IP. Biogeography of squirrel monkeys (genus Saimiri): South-central Amazon origin and rapid pan-Amazonian diversification of a lowland primate.. Molecular phylogenetics and evolution, 2014.
  50. Boubli JP, Ribas C, Lynch Alfaro JW, Alfaro ME, da Silva MN, Pinho GM, Farias IP. Spatial and temporal patterns of diversification on the Amazon: A test of the riverine hypothesis for all diurnal primates of Rio Negro and Rio Branco in Brazil.. Molecular phylogenetics and evolution, 2014.
  51. Wright KA, Wright BW, Ford SM, Fragaszy D, Izar P, Norconk M, Masterson T, Hobbs DG, Alfaro ME, Lynch Alfaro JW. The effects of ecology and evolutionary history on robust capuchin morphological diversity.. Molecular phylogenetics and evolution, 2014.
  52. Frédérich B, Olivier D, Litsios G, Alfaro ME, Parmentier E. Trait decoupling promotes evolutionary diversification of the trophic and acoustic system of damselfishes.. Proceedings. Biological sciences, 2014.
  53. Sorenson L, Santini F, Alfaro ME. The effect of habitat on modern shark diversification.. Journal of evolutionary biology, 2014.
  54. Buckner JC, Lynch Alfaro JW, Rylands AB, Alfaro ME. Biogeography of the marmosets and tamarins (Callitrichidae).. Molecular phylogenetics and evolution, 2014.
  55. Collar DC, Reece JS, Alfaro ME, Wainwright PC, Mehta RS. Imperfect morphological convergence: variable changes in cranial structures underlie transitions to durophagy in moray eels.. The American naturalist, 2014.
  56. Pennell MW, Eastman JM, Slater GJ, Brown JW, Uyeda JC, FitzJohn RG, Alfaro ME, Harmon LJ. geiger v2.0: an expanded suite of methods for fitting macroevolutionary models to phylogenetic trees.. Bioinformatics (Oxford, England), 2014.
  57. Walker JA, Alfaro ME, Noble MM, Fulton CJ. Body fineness ratio as a predictor of maximum prolonged-swimming speed in coral reef fishes.. PloS one, 2013.
  58. Santini F, Kong X, Sorenson L, Carnevale G, Mehta RS, Alfaro ME. A multi-locus molecular timescale for the origin and diversification of eels (Order: Anguilliformes).. Molecular phylogenetics and evolution, 2013.
  59. Faircloth BC, Sorenson L, Santini F, Alfaro ME. A Phylogenomic Perspective on the Radiation of Ray-Finned Fishes Based upon Targeted Sequencing of Ultraconserved Elements (UCEs).. PloS one, 2013.
  60. Santini F, Sorenson L, Alfaro ME. A new phylogeny of tetraodontiform fishes (Tetraodontiformes, Acanthomorpha) based on 22 loci.. Molecular phylogenetics and evolution, 2013.
  61. Santini F, Sorenson L, Alfaro ME. A new multi-locus timescale reveals the evolutionary basis of diversity patterns in triggerfishes and filefishes (Balistidae, Monacanthidae; Tetraodontiformes).. Molecular phylogenetics and evolution, 2013.
  62. Stoltzfus A, Lapp H, Matasci N, Deus H, Sidlauskas B, Zmasek CM, Vaidya G, Pontelli E, Cranston K, Vos R, Webb CO, Harmon LJ, Pirrung M, O'Meara B, Pennell MW, Mirarab S, Rosenberg MS, Balhoff JP, Bik HM, Heath TA, Midford PE, Brown JW, McTavish EJ, Sukumaran J, Westneat M, Alfaro ME, Steele A, Jordan G. Phylotastic! Making tree-of-life knowledge accessible, reusable and convenient.. BMC bioinformatics, 2013.
  63. Sorenson L, Santini F, Carnevale G, Alfaro ME. A multi-locus timetree of surgeonfishes (Acanthuridae, Percomorpha), with revised family taxonomy.. Molecular phylogenetics and evolution, 2013.
  64. Santini F, Nguyen MT, Sorenson L, Waltzek TB, Lynch Alfaro JW, Eastman JM, Alfaro ME. Do habitat shifts drive diversification in teleost fishes? An example from the pufferfishes (Tetraodontidae).. Journal of evolutionary biology, 2013.
  65. Santana SE, Alfaro JL, Noonan A, Alfaro ME. Adaptive response to sociality and ecology drives the diversification of facial colour patterns in catarrhines.. Nature communications, 2013.
  66. Rabosky DL, Santini F, Eastman J, Smith SA, Sidlauskas B, Chang J, Alfaro ME. Rates of speciation and morphological evolution are correlated across the largest vertebrate radiation.. Nature communications, 2013.
  67. Victor BC, Alfaro ME, Sorenson L. Rediscovery of Sagittalarva inornata n. gen., n. comb. (Gilbert, 1890) (Perciformes: Labridae), a long-lost deepwater fish from the eastern Pacific Ocean: a case study of a forensic approach to taxonomy using DNA barcoding.. Zootaxa, 2013.
  68. Frédérich B, Sorenson L, Santini F, Slater GJ, Alfaro ME. Iterative ecological radiation and convergence during the evolutionary history of damselfishes (Pomacentridae).. The American naturalist, 2012.
  69. Santini F, Sorenson L, Marcroft T, Dornburg A, Alfaro ME. A multilocus molecular phylogeny of boxfishes (Aracanidae, Ostraciidae; Tetraodontiformes).. Molecular phylogenetics and evolution, 2012.
  70. Rabosky DL, Slater GJ, Alfaro ME. Clade age and species richness are decoupled across the eukaryotic tree of life.. PLoS biology, 2012.
  71. Slater GJ, Harmon LJ, Alfaro ME. Integrating fossils with molecular phylogenies improves inference of trait evolution.. Evolution; international journal of organic evolution, 2012.
  72. Waltzek TB, Marty GD, Alfaro ME, Bennett WR, Garver KA, Haulena M, Weber ES, Hedrick RP. Systemic iridovirus from threespine stickleback Gasterosteus aculeatus represents a new megalocytivirus species (family Iridoviridae).. Diseases of aquatic organisms, 2012.
  73. Boubli JP, Rylands AB, Farias IP, Alfaro ME, Alfaro JL. Cebus phylogenetic relationships: a preliminary reassessment of the diversity of the untufted capuchin monkeys.. American journal of primatology, 2012.
  74. Santana SE, Lynch Alfaro J, Alfaro ME. Adaptive evolution of facial colour patterns in Neotropical primates.. Proceedings. Biological sciences, 2012.
  75. Slater GJ, Harmon LJ, Wegmann D, Joyce P, Revell LJ, Alfaro ME. Fitting models of continuous trait evolution to incompletely sampled comparative data using approximate Bayesian computation.. Evolution; international journal of organic evolution, 2011.
  76. Santana SE, Dial TO, Eiting TP, Alfaro ME. Roosting ecology and the evolution of pelage markings in bats.. PloS one, 2011.
  77. Eastman JM, Alfaro ME, Joyce P, Hipp AL, Harmon LJ. A novel comparative method for identifying shifts in the rate of character evolution on trees.. Evolution; international journal of organic evolution, 2011.
  78. Alfaro JW, Matthews L, Boyette AH, Macfarlan SJ, Phillips KA, Falótico T, Ottoni E, Verderane M, Izar P, Schulte M, Melin A, Fedigan L, Janson C, Alfaro ME. Anointing variation across wild capuchin populations: a review of material preferences, bout frequency and anointing sociality in Cebus and Sapajus.. American journal of primatology, 2011.
  79. Dornburg A, Sidlauskas B, Santini F, Sorenson L, Near TJ, Alfaro ME. The influence of an innovative locomotor strategy on the phenotypic diversification of triggerfish (family: Balistidae).. Evolution; international journal of organic evolution, 2011.
  80. Brock CD, Harmon LJ, Alfaro ME. Testing for temporal variation in diversification rates when sampling is incomplete and nonrandom.. Systematic biology, 2011.
  81. Jaffe AL, Slater GJ, Alfaro ME. The evolution of island gigantism and body size variation in tortoises and turtles.. Biology letters, 2011.
  82. Huelsenbeck JP, Alfaro ME, Suchard MA. Biologically inspired phylogenetic models strongly outperform the no common mechanism model.. Systematic biology, 2011.
  83. Rabosky DL, Alfaro ME. Evolutionary bangs and whimpers: methodological advances and conceptual frameworks for studying exceptional diversification.. Systematic biology, 2010.
  84. Mehta RS, Ward AB, Alfaro ME, Wainwright PC. Elongation of the body in eels.. Integrative and comparative biology, 2010.
  85. Slater GJ, Price SA, Santini F, Alfaro ME. Diversity versus disparity and the radiation of modern cetaceans.. Proceedings. Biological sciences, 2010.
  86. Alfaro M, Santini F. Evolutionary biology: A flourishing of fish forms.. Nature, 2010.
  87. Alfaro ME, Brock CD, Banbury BL, Wainwright PC. Does evolutionary innovation in pharyngeal jaws lead to rapid lineage diversification in labrid fishes?. BMC evolutionary biology, 2009.
  88. Santini F, Harmon LJ, Carnevale G, Alfaro ME. Did genome duplication drive the origin of teleosts? A comparative study of diversification in ray-finned fishes.. BMC evolutionary biology, 2009.
  89. Alfaro ME, Santini F, Brock C, Alamillo H, Dornburg A, Rabosky DL, Carnevale G, Harmon LJ. Nine exceptional radiations plus high turnover explain species diversity in jawed vertebrates.. Proceedings of the National Academy of Sciences of the United States of America, 2009.
  90. Waltzek TB, Kelley GO, Alfaro ME, Kurobe T, Davison AJ, Hedrick RP. Phylogenetic relationships in the family Alloherpesviridae.. Diseases of aquatic organisms, 2009.
  91. Vincent SE, Brandley MC, Herrel A, Alfaro ME. Convergence in trophic morphology and feeding performance among piscivorous natricine snakes.. Journal of evolutionary biology, 2009.
  92. Dornburg A, Santini F, Alfaro ME. The influence of model averaging on clade posteriors: an example using the triggerfishes (Family Balistidae).. Systematic biology, 2008.
  93. Clark JR, Ree RH, Alfaro ME, King MG, Wagner WL, Roalson EH. A comparative study in ancestral range reconstruction methods: retracing the uncertain histories of insular lineages.. Systematic biology, 2008.
  94. Smith LL, Fessler JL, Alfaro ME, Streelman JT, Westneat MW. Phylogenetic relationships and the evolution of regulatory gene sequences in the parrotfishes.. Molecular phylogenetics and evolution, 2008.
  95. Herrel A, Vincent SE, Alfaro ME, VAN Wassenbergh S, Vanhooydonck B, Irschick DJ. Morphological convergence as a consequence of extreme functional demands: examples from the feeding system of natricine snakes.. Journal of evolutionary biology, 2008.
  96. Collar DC, Wainwright PC, Alfaro ME. Integrated diversification of locomotion and feeding in labrid fishes.. Biology letters, 2008.
  97. Alfaro ME, Karns DR, Voris HK, Brock CD, Stuart BL. Phylogeny, evolutionary history, and biogeography of Oriental-Australian rear-fanged water snakes (Colubroidea: Homalopsidae) inferred from mitochondrial and nuclear DNA sequences.. Molecular phylogenetics and evolution, 2007.
  98. Storfer A, Alfaro ME, Ridenhour BJ, Jancovich JK, Mech SG, Parris MJ, Collins JP. Phylogenetic concordance analysis shows an emerging pathogen is novel and endemic.. Ecology letters, 2007.
  99. Alfaro ME, Santini F, Brock CD. Do reefs drive diversification in marine teleosts? Evidence from the pufferfishes and their allies (Order Tetraodontiformes).. Evolution; international journal of organic evolution, 2007.
  100. Dantas BM, Lucena EA, Dantas AL, Araújo F, Rebelo AM, Terán M, Paolino A, Hermida JC, Rojo AM, Puerta JA, Morales J, Bejerano GM, Alfaro M, Ruiz MA, Videla R, Piñones O, González S, Navarro T, Melo D, Cruz-Suárez R. A protocol for the calibration of gamma cameras to estimate internal contamination in emergency situations.. Radiation protection dosimetry, 2007.
  101. Alfaro ME, Huelsenbeck JP. Comparative performance of Bayesian and AIC-based measures of phylogenetic model uncertainty.. Systematic biology, 2006.
  102. Westneat MW, Alfaro ME. Phylogenetic relationships and evolutionary history of the reef fish family Labridae.. Molecular phylogenetics and evolution, 2005.
  103. Westneat MW, Alfaro ME, Wainwright PC, Bellwood DR, Grubich JR, Fessler JL, Clements KD, Smith LL. Local phylogenetic divergence and global evolutionary convergence of skull function in reef fishes of the family Labridae.. Proceedings. Biological sciences, 2005.
  104. Alfaro ME, Bolnick DI, Wainwright PC. Evolutionary consequences of many-to-one mapping of jaw morphology to mechanics in labrid fishes.. The American naturalist, 2005.
  105. Wainwright PC, Alfaro ME, Bolnick DI, Hulsey CD. Many-to-One Mapping of Form to Function: A General Principle in Organismal Design?. Integrative and comparative biology, 2005.
  106. Clements KD, Alfaro ME, Fessler JL, Westneat MW. Relationships of the temperate Australasian labrid fish tribe Odacini (Perciformes; Teleostei).. Molecular phylogenetics and evolution, 2004.
  107. Huelsenbeck JP, Larget B, Alfaro ME. Bayesian phylogenetic model selection using reversible jump Markov chain Monte Carlo.. Molecular biology and evolution, 2004.
  108. Alfaro ME, Bolnick DI, Wainwright PC. Evolutionary dynamics of complex biomechanical systems: an example using the four-bar mechanism.. Evolution; international journal of organic evolution, 2004.
  109. Alfaro ME. Sweeping and striking: a kinematic study of the trunk during prey capture in three thamnophiine snakes.. The Journal of experimental biology, 2003.
  110. Alfaro ME, Zoller S, Lutzoni F. 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, 2003.
  111. Streelman JT, Alfaro M, Westneat MW, Bellwood DR, Karl SA. Evolutionary history of the parrotfishes: biogeography, ecomorphology, and comparative diversity.. Evolution; international journal of organic evolution, 2002.
  112. Alfaro ME, Arnold SJ. Molecular systematics and evolution of Regina and the thamnophiine snakes.. Molecular phylogenetics and evolution, 2001.
  113. Alfaro M, Westneat MW. Motor patterns of herbivorous feeding: electromyographic analysis of biting in the parrotfishes Cetoscarus bicolor and Scarus iseri.. Brain, behavior and evolution, 1999.
  114. Esquivel R, Zúñiga JA, Alfaro M, Kotcher E. Trypanosomes of Costa Rican feral mmamals.. The Journal of parasitology, 1967.