Publications

My publications are also listed on Google Scholar and ORCID .

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Recent Publications

  1. [1]W.T. McCraney, C.E. Thacker, B.C. Faircloth, R.C. Harrington, T.J. Near, M.E. Alfaro, Explosion of goby fish diversity at the Eocene-Oligocene transition, Molecular Phylogenetics and Evolution 207 (2025) 108342. DOI
  2. [2]E.A. Karan, J.R. Hodge, M.E. Alfaro, Eyespot function in butterflyfishes (Chaetodontidae): comparing evidence for aposematism, automimicry, and predator mimicry, Biological Journal of the Linnean Society 144 (2025) blae122. DOI
  3. [3]W.L.E. Tsai, M. Escalona, K.L. Garrett, R.S. Terrill, R. Sahasrabudhe, O. Nguyen, E. Beraut, W. Seligmann, C.W. Fairbairn, R.J. Harrigan, J.E. McCormack, M.E. Alfaro, T.B. Smith, R.A. Bay, A highly contiguous genome assembly for the Yellow Warbler (Setophaga petechia), Journal of Heredity 115 (2024) 317–325. DOI
  4. [4]A. Dornburg, K.L. Zapfe, R. Williams, M.E. Alfaro, R. Morris, H. Adachi, J. Flores, Considering decoupled phenotypic diversification between ontogenetic phases in macroevolution: An example using Triggerfishes (Balistidae), Systematic Biology 73 (2024) 434–454. DOI
  5. [5]J.E. Smith, B. Natterson-Horowitz, M.M. Mueller, M.E. Alfaro, Mechanisms of equality and inequality in mammalian societies, Philosophical Transactions of the Royal Society B 378 (2023) 20220307. DOI
  6. [6]A. Ghezelayagh, R.C. Harrington, E.D. Burress, M.A. Campbell, J.C. Buckner, M.E. Alfaro, Prolonged morphological expansion of spiny-rayed fishes following the end-Cretaceous, Nature Ecology and Evolution 6 (2022) 1211–1220. DOI
  7. [7]M.J.W. Van Gorp, J. Goyens, M.E. Alfaro, S. Van Wassenbergh, Keels of boxfish carapaces strongly improve stabilization against roll, Journal of the Royal Society Interface 19 (2022) 20210942. DOI
  8. [8]J.E. Smith, B. Natterson-Horowitz, M.E. Alfaro, The nature of privilege: intergenerational wealth in animal societies, Behavioral Ecology 33 (2022) 1–6. DOI
  9. [9]B.F. Melo, B.L. Sidlauskas, T.J. Near, F.F. Roxo, A. Ghezelayagh, L.E. Ochoa, M.E. Alfaro, Accelerated diversification explains the exceptional species richness of tropical characoid fishes, Systematic Biology 71 (2022) 78–92. DOI
  10. [10]S.T. Schwartz, M.E. Alfaro, Sashimi: A toolkit for facilitating high-throughput organismal image segmentation using deep learning, Methods in Ecology and Evolution 12 (2021) 2341–2354. DOI

All Publications

  1. [1]W.T. McCraney, C.E. Thacker, B.C. Faircloth, R.C. Harrington, T.J. Near, M.E. Alfaro, Explosion of goby fish diversity at the Eocene-Oligocene transition, Molecular Phylogenetics and Evolution 207 (2025) 108342. DOI
  2. [2]E.A. Karan, J.R. Hodge, M.E. Alfaro, Eyespot function in butterflyfishes (Chaetodontidae): comparing evidence for aposematism, automimicry, and predator mimicry, Biological Journal of the Linnean Society 144 (2025) blae122. DOI
  3. [3]W.L.E. Tsai, M. Escalona, K.L. Garrett, R.S. Terrill, R. Sahasrabudhe, O. Nguyen, E. Beraut, W. Seligmann, C.W. Fairbairn, R.J. Harrigan, J.E. McCormack, M.E. Alfaro, T.B. Smith, R.A. Bay, A highly contiguous genome assembly for the Yellow Warbler (Setophaga petechia), Journal of Heredity 115 (2024) 317–325. DOI
  4. [4]A. Dornburg, K.L. Zapfe, R. Williams, M.E. Alfaro, R. Morris, H. Adachi, J. Flores, Considering decoupled phenotypic diversification between ontogenetic phases in macroevolution: An example using Triggerfishes (Balistidae), Systematic Biology 73 (2024) 434–454. DOI
  5. [5]J.E. Smith, B. Natterson-Horowitz, M.M. Mueller, M.E. Alfaro, Mechanisms of equality and inequality in mammalian societies, Philosophical Transactions of the Royal Society B 378 (2023) 20220307. DOI
  6. [6]A. Ghezelayagh, R.C. Harrington, E.D. Burress, M.A. Campbell, J.C. Buckner, M.E. Alfaro, Prolonged morphological expansion of spiny-rayed fishes following the end-Cretaceous, Nature Ecology and Evolution 6 (2022) 1211–1220. DOI
  7. [7]M.J.W. Van Gorp, J. Goyens, M.E. Alfaro, S. Van Wassenbergh, Keels of boxfish carapaces strongly improve stabilization against roll, Journal of the Royal Society Interface 19 (2022) 20210942. DOI
  8. [8]J.E. Smith, B. Natterson-Horowitz, M.E. Alfaro, The nature of privilege: intergenerational wealth in animal societies, Behavioral Ecology 33 (2022) 1–6. DOI
  9. [9]B.F. Melo, B.L. Sidlauskas, T.J. Near, F.F. Roxo, A. Ghezelayagh, L.E. Ochoa, M.E. Alfaro, Accelerated diversification explains the exceptional species richness of tropical characoid fishes, Systematic Biology 71 (2022) 78–92. DOI
  10. [10]S.T. Schwartz, M.E. Alfaro, Sashimi: A toolkit for facilitating high-throughput organismal image segmentation using deep learning, Methods in Ecology and Evolution 12 (2021) 2341–2354. DOI
  11. [11]C.E. Snedden, S.K. Makanani, S.T. Schwartz, A. Gamble, R.V. Blakey, M.E. Alfaro, SARS-CoV-2: cross-scale insights from ecology and evolution, Trends in Microbiology 29 (2021) 593–605. DOI
  12. [12]J. Stiller, R.R. da Fonseca, M.E. Alfaro, B.C. Faircloth, N.G. Wilson, G.W. Rouse, Using ultraconserved elements to track the influence of sea-level change on leafy seadragon populations, Molecular Ecology 30 (2021) 1364–1380. DOI
  13. [13]P. Duchen, M.L. Alfaro, J. Rolland, N. Salamin, D. Silvestro, On the effect of asymmetrical trait inheritance on models of trait evolution, Systematic Biology 70 (2021) 376–388. DOI
  14. [14]W.T. McCraney, C.E. Thacker, M.E. Alfaro, Supermatrix phylogeny resolves goby lineages and reveals unstable root of Gobiaria, Molecular Phylogenetics and Evolution 151 (2020) 106862. DOI
  15. [15]M.A. Campbell, T.J. Buser, M.E. Alfaro, J.A. López, Addressing incomplete lineage sorting and paralogy in the inference of uncertain salmonid phylogenetic relationships, PeerJ 8 (2020) e9389. DOI
  16. [16]J. Chang, D.L. Rabosky, M.E. Alfaro, Estimating diversification rates on incompletely sampled phylogenies: theoretical concerns and practical solutions, Systematic Biology 69 (2020) 602–611. DOI
  17. [17]B.C. Faircloth, F. Alda, K. Hoekzema, M.D. Burns, C. Oliveira, J.S. Albert, M.E. Alfaro, A target enrichment bait set for studying relationships among ostariophysan fishes, Copeia 108 (2020) 47–60. DOI
  18. [18]L.E. Ochoa, A. Datovo, C. DoNascimiento, F.F. Roxo, M.H. Sabaj, J. Chang, M.E. Alfaro, Phylogenomic analysis of trichomycterid catfishes (Teleostei: Siluriformes) inferred from ultraconserved elements, Scientific Reports 10 (2020) 2697. DOI
  19. [19]E. Gjesfjeld, D. Silvestro, J. Chang, B. Koch, J.G. Foster, M.E. Alfaro, A quantitative workflow for modeling diversification in material culture, PLoS ONE 15 (2020) e0227579. DOI
  20. [20]M. Friedman, K.L. Feilich, H.T. Beckett, M.E. Alfaro, B.C. Faircloth, D. Černý, A phylogenomic framework for pelagiarian fishes (Acanthomorpha: Percomorpha) highlights mosaic radiation in the open ocean, Proceedings of the Royal Society B 286 (2019) 20191502. DOI
  21. [21]M.E. Alfaro, E.A. Karan, S.T. Schwartz, A.J. Shultz, The evolution of color pattern in butterflyfishes (Chaetodontidae), Integrative and Comparative Biology 59 (2019) 604–615. DOI
  22. [22]M.A. Phuong, M.E. Alfaro, G.N. Mahardika, R.M. Marwoto, R.E. Prabowo, Lack of signal for the impact of conotoxin gene diversity on speciation rates in cone snails, Systematic Biology 68 (2019) 781–796. DOI
  23. [23]J. Chang, D.L. Rabosky, S.A. Smith, M.E. Alfaro, An R package and online resource for macroevolutionary studies using the ray-finned fish tree of life, Methods in Ecology and Evolution 10 (2019) 1118–1124. DOI
  24. [24]F. Alda, V.A. Tagliacollo, M.J. Bernt, B.T. Waltz, W.B. Ludt, B.C. Faircloth, M.E. Alfaro, Resolving deep nodes in an ancient radiation of neotropical fishes in the presence of conflicting signals from incomplete lineage sorting, Systematic Biology 68 (2019) 573–593. DOI
  25. [25]F.F. Roxo, L.E. Ochoa, M.H. Sabaj, N.K. Lujan, R. Covain, G.S.C. Silva, B.F. Melo, M.E. Alfaro, Phylogenomic reappraisal of the Neotropical catfish family Loricariidae (Teleostei: Siluriformes) using ultraconserved elements, Molecular Phylogenetics and Evolution 135 (2019) 148–165. DOI
  26. [26]C.D. Hulsey, M.E. Alfaro, J. Zheng, A. Meyer, R. Holzman, Pleiotropic jaw morphology links the evolution of mechanical modularity and functional feeding convergence in Lake Malawi cichlids, Proceedings of the Royal Society B 286 (2019) 20182358. DOI
  27. [27]G. Burin, L.R.V. Alencar, J. Chang, M.E. Alfaro, T.B. Quental, How well can we estimate diversity dynamics for clades in diversity decline?, Systematic Biology 68 (2019) 47–62. DOI
  28. [28]F. Lutzoni, M.D. Nowak, M.E. Alfaro, V. Reeb, J. Miadlikowska, M. Krug, Contemporaneous radiations of fungi and plants linked to symbiosis, Nature Communications 9 (2018) 5451. DOI
  29. [29]C.D. Hulsey, J. Zheng, R. Holzman, M.E. Alfaro, M. Olave, A. Meyer, Phylogenomics of a putatively convergent novelty: did hypertrophied lips evolve once or repeatedly in Lake Malawi cichlid fishes?, BMC Evolutionary Biology 18 (2018) 179. DOI
  30. [30]J.D. DiBattista, M.E. Alfaro, L. Sorenson, J.H. Choat, J.P.A. Hobbs, Ice ages and butterflyfishes: Phylogenomics elucidates the ecological and evolutionary history of reef fishes in an endemism hotspot, Ecology and Evolution 8 (2018) 10989–11008. DOI
  31. [31]P.S. Gilbert, J. Wu, M.W. Simon, J.S. Sinsheimer, M.E. Alfaro, Filtering nucleotide sites by phylogenetic signal to noise ratio increases confidence in the Neoaves phylogeny generated from ultraconserved elements, Molecular Phylogenetics and Evolution 126 (2018) 116–128. DOI
  32. [32]D.L. Rabosky, J. Chang, P.F. Cowman, L. Sallan, M. Friedman, K. Kaschner, M.E. Alfaro, An inverse latitudinal gradient in speciation rate for marine fishes, Nature 559 (2018) 392–395. DOI
  33. [33]M.G.M. Lima, J.S. Silva-Júnior, D. Černý, J.C. Buckner, A. Aleixo, J. Chang, M.E. Alfaro, A phylogenomic perspective on the robust capuchin monkey (Sapajus) radiation: First evidence for extensive population admixture across South America, Molecular Phylogenetics and Evolution 124 (2018) 137–150. DOI
  34. [34]M.E. Alfaro, Resolving the ray-finned fish tree of life, Proceedings of the National Academy of Sciences 115 (2018) 6107–6109. DOI
  35. [35]M.R. Tolkoff, M.E. Alfaro, G. Baele, P. Lemey, M.A. Suchard, Phylogenetic factor analysis, Systematic Biology 67 (2018) 384–399. DOI
  36. [36]M.E. Alfaro, B.C. Faircloth, R.C. Harrington, L. Sorenson, M. Friedman, Explosive diversification of marine fishes at the Cretaceous-Palaeogene boundary, Nature Ecology and Evolution 2 (2018) 688–696. DOI
  37. [37]P.C. Wainwright, F. Santini, D.R. Bellwood, D.R. Robertson, L.A. Rocha, M.E. Alfaro, Phylogenetics and geography of speciation in New World Halichoeres wrasses, Molecular Phylogenetics and Evolution 121 (2018) 35–45. DOI
  38. [38]M.E. Alfaro, The Fish Tree of Life, Annual Review of Ecology, Evolution, and Systematics 48 (2017).
  39. [39]B. Frédérich, F. Santini, N. Konow, J. Schnitzler, D. Lecchini, M.E. Alfaro, Body shape convergence driven by small size optimum in marine angelfishes, Biology Letters 13 (2017) 20170154. DOI
  40. [40]M.G.M. Lima, J.C. Buckner, J.S. Silva-Júnior, A. Aleixo, A.B. Martins, J.P. Boubli, M.E. Alfaro, Capuchin monkey biogeography: understanding Sapajus Pleistocene range expansion and the current sympatry between Cebus and Sapajus, Journal of Biogeography 44 (2017) 810–820. DOI
  41. [41]L.E. Ochoa, F.F. Roxo, C. DoNascimiento, M.H. Sabaj, A. Datovo, M.E. Alfaro, Multilocus analysis of the catfish family Trichomycteridae (Teleostei: Ostariophysi: Siluriformes) supporting a monophyletic Trichomycterinae, Molecular Phylogenetics and Evolution 115 (2017) 71–81. DOI
  42. [42]M.A. Campbell, M.E. Alfaro, M. Belasco, J. Andrés López, Early-branching euteleost relationships: Areas of congruence between concatenation and coalescent model inferences, PeerJ 2017 (2017). DOI
  43. [43]P. Chakrabarty, B.C. Faircloth, F. Alda, W.B. Ludt, C.D. McMahan, T.J. Near, A. Dornburg, J.S. Albert, J. Arroyave, M.L.J. Stiassny, L. Sorenson, M.E. Alfaro, Phylogenomic Systematics of Ostariophysan Fishes: Ultraconserved Elements Support the Surprising Non-Monophyly of Characiformes, Systematic Biology 66 (2017) 881–895. DOI
  44. [44]C.D. Hulsey, J. Zheng, B.C. Faircloth, A. Meyer, M.E. 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 (2017) 40–48. DOI
  45. [45]S.J. Longo, B.C. Faircloth, A. Meyer, M.W. Westneat, M.E. Alfaro, P.C. Wainwright, Phylogenomic analysis of a rapid radiation of misfit fishes (Syngnathiformes) using ultraconserved elements, Molecular Phylogenetics and Evolution 113 (2017) 33–48. DOI
  46. [46]J. Chang, M.E. Alfaro, Crowdsourced geometric morphometrics enable rapid large-scale collection and analysis of phenotypic data, Methods in Ecology and Evolution 7 (2016) 472–482. DOI
  47. [47]M.A. Phuong, G.N. Mahardika, M.E. Alfaro, Dietary breadth is positively correlated with venom complexity in cone snails, BMC Genomics 17 (2016). DOI
  48. [48]L.R.V. Alencar, T.B. Quental, F.G. Grazziotin, M.L. Alfaro, M. Martins, M. Venzon, H. Zaher, Diversification in vipers: Phylogenetic relationships, time of divergence and shifts in speciation rates, Molecular Phylogenetics and Evolution 105 (2016) 50–62. DOI
  49. [49]M.E. Alfaro, Evolution: Bioluminescent Courtship as an Engine of Diversity, Current Biology 26 (2016) R667–R669. DOI
  50. [50]R.C. Harrington, B.C. Faircloth, R.I. Eytan, W.L. Smith, T.J. Near, M.E. Alfaro, M. Friedman, Phylogenomic analysis of carangimorph fishes reveals flatfish asymmetry arose in a blink of the evolutionary eye, BMC Evolutionary Biology 16 (2016). DOI
  51. [51]F. Santini, L. Sorenson, M.E. Alfaro, Phylogeny and biogeography of hogfishes and allies (Bodianus, Labridae), Molecular Phylogenetics and Evolution 99 (2016) 1–6. DOI
  52. [52]M.D. McGee, B.C. Faircloth, S.R. Borstein, J. Zheng, C.D. Hulsey, P.C. Wainwright, M.E. Alfaro, Replicated divergence in cichlid radiations mirrors a major vertebrate innovation, Proceedings of the Royal Society B: Biological Sciences 283 (2016). DOI
  53. [53]J.W. Lynch Alfaro, J.P. Boubli, F.P. Paim, C.C. Ribas, M.N.F.D. Silva, M.R. Messias, F. Röhe, M.P. Mercês, J.S. Silva Júnior, C.R. Silva, G.M. Pinho, G. Koshkarian, M.T.T. Nguyen, M.L. Harada, R.M. Rabelo, H.L. Queiroz, M.E. Alfaro, I.P. Farias, Biogeography of squirrel monkeys (genus Saimiri): South-central Amazon origin and rapid pan-Amazonian diversification of a lowland primate, Molecular Phylogenetics and Evolution 82 (2015) 436–454. DOI
  54. [54]J.C. Buckner, J.W. Lynch Alfaro, A.B. Rylands, M.E. Alfaro, Biogeography of the marmosets and tamarins (Callitrichidae), Molecular Phylogenetics and Evolution 82 (2015) 413–425. DOI
  55. [55]P.S. Gilbert, J. Chang, C. Pan, E.M. Sobel, J.S. Sinsheimer, B.C. Faircloth, M.E. Alfaro, Genome-wide ultraconserved elements exhibit higher phylogenetic informativeness than traditional gene markers in percomorph fishes, Molecular Phylogenetics and Evolution 92 (2015) 140–146. DOI
  56. [56]T.L. Iglesias, A. Dornburg, M.C. Brandley, M.E. Alfaro, D.L. Warren, Life in the unthinking depths: Energetic constraints on encephalization in marine fishes, Journal of Evolutionary Biology 28 (2015) 1080–1090. DOI
  57. [57]J.P. Boubli, C. Ribas, J.W. Lynch Alfaro, M.E. Alfaro, M.N.F. da Silva, G.M. Pinho, I.P. Farias, 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 82 (2015) 400–412. DOI
  58. [58]K.A. Wright, B.W. Wright, S.M. Ford, D. Fragaszy, P. Izar, M. Norconk, T. Masterson, D.G. Hobbs, M.E. Alfaro, J.W. Lynch Alfaro, The effects of ecology and evolutionary history on robust capuchin morphological diversity, Molecular Phylogenetics and Evolution 82 (2015) 455–466. DOI
  59. [59]D.C. Collar, P.C. Wainwright, M.E. Alfaro, L.J. Revell, R.S. Mehta, Biting disrupts integration to spur skull evolution in eels, Nature Communications 5 (2014). DOI
  60. [60]M.W. Pennell, J.M. Eastman, G.J. Slater, J.W. Brown, J.C. Uyeda, R.G. Fitzjohn, M.E. Alfaro, L.J. Harmon, Geiger v2.0: An expanded suite of methods for fitting macroevolutionary models to phylogenetic trees, Bioinformatics 30 (2014) 2216–2218. DOI
  61. [61]D.C. Collar, J.S. Reece, M.E. Alfaro, P.C. Wainwright, R.S. Mehta, Imperfect morphological convergence: Variable changes in cranial structures underlie transitions to durophagy in moray eels, American Naturalist 183 (2014). DOI
  62. [62]L. Sorenson, F. Santini, M.E. Alfaro, The effect of habitat on modern shark diversification, Journal of Evolutionary Biology 27 (2014) 1536–1548. DOI
  63. [63]B. Frédérich, D. Olivier, G. Litsios, M.E. Alfaro, E. Parmentier, Trait decoupling promotes evolutionary diversification of the trophic and acoustic system of damselfishes, Proceedings of the Royal Society B: Biological Sciences 281 (2014). DOI
  64. [64]B.C. Faircloth, L. Sorenson, F. Santini, M.E. Alfaro, A Phylogenomic Perspective on the Radiation of Ray-Finned Fishes Based upon Targeted Sequencing of Ultraconserved Elements (UCEs), PLoS ONE 8 (2013). DOI
  65. [65]F. Santini, X. Kong, L. Sorenson, G. Carnevale, R.S. Mehta, M.E. Alfaro, A multi-locus molecular timescale for the origin and diversification of eels (Order: Anguilliformes), Molecular Phylogenetics and Evolution 69 (2013) 884–894. DOI
  66. [66]L. Sorenson, F. Santini, G. Carnevale, M.E. Alfaro, A multi-locus timetree of surgeonfishes (Acanthuridae, Percomorpha), with revised family taxonomy, Molecular Phylogenetics and Evolution 68 (2013) 150–160. DOI
  67. [67]F. Santini, L. Sorenson, T. Marcroft, A. Dornburg, M.E. Alfaro, A multilocus molecular phylogeny of boxfishes (Aracanidae, Ostraciidae; Tetraodontiformes), Molecular Phylogenetics and Evolution 66 (2013) 153–160. DOI
  68. [68]F. Santini, L. Sorenson, M.E. Alfaro, A new multi-locus timescale reveals the evolutionary basis of diversity patterns in triggerfishes and filefishes (Balistidae, Monacanthidae; Tetraodontiformes), Molecular Phylogenetics and Evolution 69 (2013) 165–176. DOI
  69. [69]F. Santini, L. Sorenson, M.E. Alfaro, A new phylogeny of tetraodontiform fishes (Tetraodontiformes, Acanthomorpha) based on 22 loci, Molecular Phylogenetics and Evolution 69 (2013) 177–187. DOI
  70. [70]S.E. Santana, J.L. Alfaro, A. Noonan, M.E. Alfaro, Adaptive response to sociality and ecology drives the diversification of facial colour patterns in catarrhines, Nature Communications 4 (2013). DOI
  71. [71]J.A. Walker, M.E. Alfaro, M.M. Noble, C.J. Fulton, Body Fineness Ratio as a Predictor of Maximum Prolonged-Swimming Speed in Coral Reef Fishes, PLoS ONE 8 (2013). DOI
  72. [72]F. Santini, M.T.T. Nguyen, L. Sorenson, T.B. Waltzek, J.W. Lynch Alfaro, J.M. Eastman, M.E. Alfaro, Do habitat shifts drive diversification in teleost fishes? An example from the pufferfishes (Tetraodontidae), Journal of Evolutionary Biology 26 (2013) 1003–1018. DOI
  73. [73]B. Frédérich, L. Sorenson, F. Santini, G.J. Slater, M.E. Alfaro, Iterative ecological radiation and convergence during the evolutionary history of damselfishes (Pomacentridae), American Naturalist 181 (2013) 94–113. DOI
  74. [74]A. Stoltzfus, H. Lapp, N. Matasci, H. Deus, B. Sidlauskas, C.M. Zmasek, G. Vaidya, E. Pontelli, K. Cranston, R. Vos, C.O. Webb, L.J. Harmon, M. Pirrung, B. O’Meara, M.W. Pennell, S. Mirarab, M.S. Rosenberg, J.P. Balhoff, H.M. Bik, T.A. Heath, P.E. Midford, J.W. Brown, E.J. McTavish, J. Sukumaran, M. Westneat, M.E. Alfaro, A. Steele, G. Jordan, Phylotastic! Making tree-of-life knowledge accessible, reusable and convenient, BMC Bioinformatics 14 (2013). DOI
  75. [75]D.L. Rabosky, F. Santini, J. Eastman, S.A. Smith, B. Sidlauskas, J. Chang, M.E. Alfaro, Rates of speciation and morphological evolution are correlated across the largest vertebrate radiation, Nature Communications 4 (2013). DOI
  76. [76]B.C. Victor, M.E. Alfaro, L. Sorenson, 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 3669 (2013) 551–570. DOI
  77. [77]S.E. Santana, J.L. Alfaro, M.E. Alfaro, Adaptive evolution of facial colour patterns in Neotropical primates, Proceedings of the Royal Society B: Biological Sciences 279 (2012) 2204–2211. DOI
  78. [78]J.W.L. Alfaro, L. Matthews, A.H. Boyette, S.J. MacFarlan, K.A. Phillips, T. Falótico, E. Ottoni, M. Verderane, P. Izar, M. Schulte, A. Melin, L. Fedigan, C. Janson, M.E. Alfaro, Anointing variation across wild capuchin populations: A review of material preferences, bout frequency and anointing sociality in Cebus and Sapajus, American Journal of Primatology 74 (2012) 299–314. DOI
  79. [79]J.P. Boubli, A.B. Rylands, I.P. Farias, M.E. Alfaro, J.L. Alfaro, Cebus Phylogenetic Relationships: A Preliminary Reassessment of the Diversity of the Untufted Capuchin Monkeys, American Journal of Primatology 74 (2012) 381–393. DOI
  80. [80]D.L. Rabosky, G.J. Slater, M.E. Alfaro, Clade Age and Species Richness Are Decoupled Across the Eukaryotic Tree of Life, PLoS Biology 10 (2012). DOI
  81. [81]J.W. Lynch Alfaro, J.P. Boubli, L.E. Olson, A. Di Fiore, B. Wilson, G.A. Gutiérrez-Espeleta, K.L. Chiou, M. Schulte, S. Neitzel, V. Ross, D. Schwochow, M.T.T. Nguyen, I. Farias, C.H. Janson, M.E. Alfaro, Explosive Pleistocene range expansion leads to widespread Amazonian sympatry between robust and gracile capuchin monkeys, Journal of Biogeography 39 (2012) 272–288. DOI
  82. [82]G.J. Slater, L.J. Harmon, D. Wegmann, P. Joyce, L.J. Revell, M.E. Alfaro, Fitting models of continuous trait evolution to incompletely sampled comparative data using approximate bayesian computation, Evolution 66 (2012) 752–762. DOI
  83. [83]G.J. Slater, L.J. Harmon, M.E. Alfaro, Integrating fossils with molecular phylogenies improves inference of trait evolution, Evolution 66 (2012) 3931–3944. DOI
  84. [84]T.B. Waltzek, G.D. Marty, M.E. Alfaro, W.R. Bennett, K.A. Garver, M. Haulena, E.S. Weber III, R.P. Hedrick, Systemic iridovirus from threespine stickleback Gasterosteus aculeatus represents a new megalocytivirus species (family Iridoviridae), Diseases of Aquatic Organisms 98 (2012) 41–56. DOI
  85. [85]J.M. Eastman, M.E. Alfaro, P. Joyce, A.L. Hipp, L.J. Harmon, A Novel comparative method for identifying shifts in the rate of character evolution on trees, Evolution 65 (2011) 3578–3589. DOI
  86. [86]J.P. Huelsenbeck, M.E. Alfaro, M.A. Suchard, Biologically inspired phylogenetic models strongly outperform the no common mechanism model, Systematic Biology 60 (2011) 225–232. DOI
  87. [87]S.E. Santana, T.O. Dial, T.P. Eiting, M.E. Alfaro, Roosting ecology and the evolution of pelage markings in bats, PLoS ONE 6 (2011). DOI
  88. [88]C.D. Brock, L.J. Harmon, M.E. Alfaro, Testing for temporal variation in diversification rates when sampling is incomplete and nonrandom, Systematic Biology 60 (2011) 410–419. DOI
  89. [89]A.L. Jaffe, G.J. Slater, M.E. Alfaro, The evolution of island gigantism and body size variation in tortoises and turtles, Biology Letters 7 (2011) 558–561. DOI
  90. [90]A. Dornburg, B. Sidlauskas, F. Santini, L. Sorenson, T.J. Near, M.E. Alfaro, The influence of an innovative locomotor strategy on the phenotypic diversification of triggerfish (family: Balistidae), Evolution 65 (2011) 1912–1926. DOI
  91. [91]G.J. Slater, S.A. Price, F. Santini, M.E. Alfaro, Diversity versus disparity and the radiation of modern cetaceans, Proceedings of the Royal Society B: Biological Sciences 277 (2010) 3097–3104. DOI
  92. [92]R.S. Mehta, A.B. Ward, M.E. Alfaro, P.C. Wainwright, Elongation of the body in Eels, Integrative and Comparative Biology 50 (2010) 1091–1105. DOI
  93. [93]D.L. Rabosky, M.E. Alfaro, Evolutionary bangs and whimpers: Methodological advances and conceptual frameworks for studying exceptional diversification, Systematic Biology 59 (2010) 615–618. DOI
  94. [94]M. Alfaro, F. Santini, Evolutionary biology: A flourishing of fish forms, Nature 464 (2010) 840–842. DOI
  95. [95]S.E. Vincent, M.C. Brandley, A. Herrel, M.E. Alfaro, Convergence in trophic morphology and feeding performance among piscivorous natricine snakes, Journal of Evolutionary Biology 22 (2009) 1203–1211. DOI
  96. [96]F. Santini, L.J. Harmon, G. Carnevale, M.E. Alfaro, Did genome duplication drive the origin of teleosts? A comparative study of diversification in ray-finned fishes, BMC Evolutionary Biology 9 (2009). DOI
  97. [97]M.E. Alfaro, C.D. Brock, B.L. Banbury, P.C. Wainwright, Does evolutionary innovation in pharyngeal jaws lead to rapid lineage diversification in labrid fishes?, BMC Evolutionary Biology 9 (2009). DOI
  98. [98]M.E. Alfaro, F. Santini, C. Brock, H. Alamillo, A. Dornburg, D.L. Rabosky, G. Carnevale, L.J. Harmon, 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 106 (2009) 13410–13414. DOI
  99. [99]T.B. Waltzek, G.O. Kelley, M.E. Alfaro, T. Kurobe, A.J. Davison, R.P. Hedrick, Phylogenetic relationships in the family Alloherpesviridae, Diseases of Aquatic Organisms 84 (2009) 179–194. DOI
  100. [100]J.R. Clark, R.H. Ree, M.E. Alfaro, M.G. King, W.L. Wagner, E.H. Roalson, A comparative study in ancestral range reconstruction methods: Retracing the uncertain histories of insular lineages, Systematic Biology 57 (2008) 693–707. DOI
  101. [101]D.C. Collar, P.C. Wainwright, M.E. Alfaro, Integrated diversification of locomotion and feeding in labrid fishes, Biology Letters 4 (2008) 84–86. DOI
  102. [102]A. Herrel, S.E. Vincent, M.E. Alfaro, S. Van Wassenbergh, B. Vanhooydonck, D.J. Irschick, Morphological convergence as a consequence of extreme functional demands: Examples from the feeding system of natricine snakes, Journal of Evolutionary Biology 21 (2008) 1438–1448. DOI
  103. [103]L.L. Smith, J.L. Fessler, M.E. Alfaro, J.T. Streelman, M.W. Westneat, Phylogenetic relationships and the evolution of regulatory gene sequences in the parrotfishes, Molecular Phylogenetics and Evolution 49 (2008) 136–152. DOI
  104. [104]M.E. Alfaro, D.R. Karns, H.K. Voris, C.D. Brock, B.L. Stuart, 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 46 (2008) 576–593. DOI
  105. [105]A. Dornburg, F. Santini, M.E. Alfaro, The influence of model averaging on clade posteriors: An example using the triggerfishes (Family Balistidae), Systematic Biology 57 (2008) 905–919. DOI
  106. [106]M.E. Alfaro, F. Santini, C.D. Brock, Do reefs drive diversification in marine teleosts? Evidence from the pufferfish and their allies (order tetraodontiformes), Evolution 61 (2007) 2104–2126. DOI
  107. [107]A. Storfer, M.E. Alfaro, B.J. Ridenhour, J.K. Jancovich, S.G. Mech, M.J. Parris, J.P. Collins, Phylogenetic concordance analysis shows an emerging pathogen is novel and endemic, Ecology Letters 10 (2007) 1075–1083. DOI
  108. [108]M. Alfaro, J. Huelsenbeck, Comparative performance of Bayesian and AIC-based measures of phylogenetic model uncertainty, Systematic Biology 55 (2006) 89–96. DOI
  109. [109]M.E. Alfaro, M.T. Holder, The posterior and the prior in Bayesian phylogenetics, Annual Review of Ecology, Evolution, and Systematics 37 (2006) 19–42. DOI
  110. [110]M.E. Alfaro, D.I. Bolnick, P.C. Wainwright, Evolutionary consequences of many-to-one mapping of jaw morphology to mechanics in labrid fishes., The American Naturalist 165 (2005). DOI
  111. [111]M.W. Westneat, M.E. Alfaro, P.C. Wainwright, D.R. Bellwood, J.R. Grubich, J.L. Fessler, K.D. Clements, L.L. Smith, Local phylogenetic divergence and global evolutionary convergence of skull function in reef fishes of the family Labridae, Proceedings of the Royal Society B: Biological Sciences 272 (2005) 993–1000. DOI
  112. [112]P.C. Wainwright, M.E. Alfaro, D.I. Bolnick, C.D. Hulsey, Many-to-one mapping of form to function: A general principle in organismal design?, Integrative and Comparative Biology 45 (2005) 256–262. DOI
  113. [113]M.W. Westneat, M.E. Alfaro, Phylogenetic relationships and evolutionary history of the reef fish family Labridae, Molecular Phylogenetics and Evolution 36 (2005) 370–390. DOI
  114. [114]J.P. Huelsenbeck, B. Larget, M.E. Alfaro, Bayesian phylogenetic model selection using reversible jump Markov chain Monte Carlo, Molecular Biology and Evolution 21 (2004) 1123–1133. DOI
  115. [115]M.E. Alfaro, D.I. Bolnick, P.C. Wainwright, Evolutionary dynamics of complex biomechanical systems: An example using the four-bar mechanism, Evolution 58 (2004) 495–503. DOI
  116. [116]M.E. Alfaro, D.R. Karns, H.K. Voris, E. Abernathy, S.L. Sellins, Phylogeny of Cerberus (Serpentes: Homalopsinae) and phylogeography of Cerberus rynchops: Diversification of a coastal marine snake in Southeast Asia, Journal of Biogeography 31 (2004) 1277–1292. DOI
  117. [117]K.D. Clements, M.E. Alfaro, J.L. Fessler, M.W. Westneat, Relationships of the temperate Australasian labrid fish tribe Odacini (Perciformes; Teleostei), Molecular Phylogenetics and Evolution 32 (2004) 575–587. DOI
  118. [118]M.E. Alfaro, S. Zoller, F. Lutzoni, 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 20 (2003) 255–266. DOI
  119. [119]M.E. Alfaro, Sweeping and striking: A kinematic study of the trunk during prey capture in three thamnophiine snakes, Journal of Experimental Biology 206 (2003) 2381–2392. DOI
  120. [120]J.T. Streelman, M. Alfaro, M.W. Westneat, D.R. Bellwood, S.A. Karl, Evolutionary history of the parrotfishes: Biogeography, ecomorphology, and comparative diversity, Evolution 56 (2002) 961–971. DOI
  121. [121]M.E. Alfaro, Forward attack modes of aquatic feeding garter snakes, Functional Ecology 16 (2002) 204–215. DOI
  122. [122]H.K. Voris, M.E. Alfaro, D.R. Karns, G.L. Starnes, E. Thompson, J.C. Murphy, Phylogenetic relationships of the Oriental-Australian rear-fanged water snakes (Colubridae: Homalopsinae) based on mitochondrial DNA sequences, Copeia (2002) 906–915. DOI
  123. [123]M.E. Alfaro, S.J. Arnold, Molecular systematics and evolution of Regina and the Thamnophiine snakes, Molecular Phylogenetics and Evolution 21 (2001) 408–423. DOI
  124. [124]M.E. Alfaro, Motor control across trophic strategies: Muscle activity of biting and suction feeding fishes, American Zoologist 41 (2001) 1266–1279. DOI
  125. [125]M. Alfaro, M.W. Westneat, Motor patterns of herbivorous feeding: Electromyographic analysis of biting in the parrotfishes Cetoscarus bicolor and Scarus iseri, Brain, Behavior and Evolution 54 (1999) 205–222. DOI