Michael Edward Alfaro

Title(s)Professor, Ecology And Evolutionary Biology
SchoolCollege of Letters and Science
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    Title(s)Professor, Institute for Society And Genetics


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    Publications listed below are automatically derived from MEDLINE/PubMed and other sources, which might result in incorrect or missing publications. Researchers can login to make corrections and additions, or contact us for help. to make corrections and additions.
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    Altmetrics Details PMC Citations indicate the number of times the publication was cited by articles in PubMed Central, and the Altmetric score represents citations in news articles and social media. (Note that publications are often cited in additional ways that are not shown here.) Fields are based on how the National Library of Medicine (NLM) classifies the publication's journal and might not represent the specific topic of the publication. Translation tags are based on the publication type and the MeSH terms NLM assigns to the publication. Some publications (especially newer ones and publications not in PubMed) might not yet be assigned Field or Translation tags.) Click a Field or Translation tag to filter the publications.
    1. A highly contiguous genome assembly for the Yellow Warbler (Setophaga petechia). J Hered. 2024 May 09; 115(3):317-325. 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. PMID: 38401156; PMCID: PMC11081134.
      View in: PubMed   Mentions:    Fields:    Translation:Animals
    2. Considering decoupled phenotypic diversification between ontogenetic phases in macroevolution: An example using Triggerfishes (Balistidae). Syst Biol. 2024 Mar 15. Dornburg A, Zapfe KL, Williams R, Alfaro ME, Morris R, Adachi H, Flores J, Santini F, Near TJ, Frédérich B. PMID: 38490727.
      View in: PubMed   Mentions:    Fields:    
    3. Mechanisms of equality and inequality in mammalian societies. Philos Trans R Soc Lond B Biol Sci. 2023 08 14; 378(1883):20220307. Smith JE, Natterson-Horowitz B, Mueller MM, Alfaro ME. PMID: 37381860; PMCID: PMC10291435.
      View in: PubMed   Mentions: 6     Fields:    Translation:Animals
    4. Prolonged morphological expansion of spiny-rayed fishes following the end-Cretaceous. Nat Ecol Evol. 2022 08; 6(8):1211-1220. 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. PMID: 35835827.
      View in: PubMed   Mentions: 17     Fields:    Translation:Animals
    5. Keels of boxfish carapaces strongly improve stabilization against roll. J R Soc Interface. 2022 04; 19(189):20210942. Van Gorp MJW, Goyens J, Alfaro ME, Van Wassenbergh S. PMID: 35472270; PMCID: PMC9042571.
      View in: PubMed   Mentions: 1     Fields:    Translation:Animals
    6. Accelerated Diversification Explains the Exceptional Species Richness of Tropical Characoid Fishes. Syst Biol. 2021 12 16; 71(1):78-92. 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. PMID: 34097063; PMCID: PMC9034337.
      View in: PubMed   Mentions: 13     Fields:    Translation:Animals
    7. SARS-CoV-2: Cross-scale Insights from Ecology and Evolution. Trends Microbiol. 2021 07; 29(7):593-605. 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. PMID: 33893024; PMCID: PMC7997387.
      View in: PubMed   Mentions: 9     Fields:    Translation:HumansAnimalsCells
    8. Using ultraconserved elements to track the influence of sea-level change on leafy seadragon populations. Mol Ecol. 2021 Mar; 30(6):1364-1380. Stiller J, da Fonseca RR, Alfaro ME, Faircloth BC, Wilson NG, Rouse GW. PMID: 33217068.
      View in: PubMed   Mentions: 7     Fields:    Translation:Animals
    9. Addressing incomplete lineage sorting and paralogy in the inference of uncertain salmonid phylogenetic relationships. PeerJ. 2020; 8:e9389. Campbell MA, Buser TJ, Alfaro ME, López JA. PMID: 32685284; PMCID: PMC7337038.
      View in: PubMed   Mentions: 2     Fields:    
    10. Supermatrix phylogeny resolves goby lineages and reveals unstable root of Gobiaria. Mol Phylogenet Evol. 2020 10; 151:106862. McCraney WT, Thacker CE, Alfaro ME. PMID: 32473335.
      View in: PubMed   Mentions: 14     Fields:    Translation:Animals
    11. Estimating Diversification Rates on Incompletely Sampled Phylogenies: Theoretical Concerns and Practical Solutions. Syst Biol. 2020 05 01; 69(3):602-611. Chang J, Rabosky DL, Alfaro ME. PMID: 31804691.
      View in: PubMed   Mentions: 21     Fields:    
    12. Phylogenomic analysis of trichomycterid catfishes (Teleostei: Siluriformes) inferred from ultraconserved elements. Sci Rep. 2020 02 14; 10(1):2697. Ochoa LE, Datovo A, DoNascimiento C, Roxo FF, Sabaj MH, Chang J, Melo BF, Silva GSC, Foresti F, Alfaro M, Oliveira C. PMID: 32060350; PMCID: PMC7021825.
      View in: PubMed   Mentions: 3     Fields:    Translation:Animals
    13. A quantitative workflow for modeling diversification in material culture. PLoS One. 2020; 15(2):e0227579. Gjesfjeld E, Silvestro D, Chang J, Koch B, Foster JG, Alfaro ME. PMID: 32027685; PMCID: PMC7004301.
      View in: PubMed   Mentions: 3     Fields:    
    14. 101 Dothideomycetes genomes: A test case for predicting lifestyles and emergence of pathogens. Stud Mycol. 2020 Jun; 96:141-153. 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. PMID: 32206138; PMCID: PMC7082219.
      View in: PubMed   Mentions: 69  
    15. A phylogenomic framework for pelagiarian fishes (Acanthomorpha: Percomorpha) highlights mosaic radiation in the open ocean. Proc Biol Sci. 2019 09 11; 286(1910):20191502. Friedman M, Feilich KL, Beckett HT, Alfaro ME, Faircloth BC, Cerný D, Miya M, Near TJ, Harrington RC. PMID: 31506051; PMCID: PMC6742994.
      View in: PubMed   Mentions: 14     Fields:    Translation:Animals
    16. Lack of Signal for the Impact of Conotoxin Gene Diversity on Speciation Rates in Cone Snails. Syst Biol. 2019 09 01; 68(5):781-796. Phuong MA, Alfaro ME, Mahardika GN, Marwoto RM, Prabowo RE, von Rintelen T, Vogt PWH, Hendricks JR, Puillandre N. PMID: 30816949; PMCID: PMC6934442.
      View in: PubMed   Mentions: 7     Fields:    Translation:Animals
    17. The Evolution of Color Pattern in Butterflyfishes (Chaetodontidae). Integr Comp Biol. 2019 09 01; 59(3):604-615. Alfaro ME, Karan EA, Schwartz ST, Shultz AJ. PMID: 31292612.
      View in: PubMed   Mentions: 5     Fields:    Translation:Animals
    18. Resolving Deep Nodes in an Ancient Radiation of Neotropical Fishes in the Presence of Conflicting Signals from Incomplete Lineage Sorting. Syst Biol. 2019 07 01; 68(4):573-593. Alda F, Tagliacollo VA, Bernt MJ, Waltz BT, Ludt WB, Faircloth BC, Alfaro ME, Albert JS, Chakrabarty P. PMID: 30521024.
      View in: PubMed   Mentions: 15     Fields:    Translation:AnimalsCells
    19. Pleiotropic jaw morphology links the evolution of mechanical modularity and functional feeding convergence in Lake Malawi cichlids. Proc Biol Sci. 2019 02 27; 286(1897):20182358. Hulsey CD, Alfaro ME, Zheng J, Meyer A, Holzman R. PMID: 30963830; PMCID: PMC6408893.
      View in: PubMed   Mentions: 7     Fields:    Translation:Animals
    20. Phylogenomic reappraisal of the Neotropical catfish family Loricariidae (Teleostei: Siluriformes) using ultraconserved elements. Mol Phylogenet Evol. 2019 06; 135:148-165. Roxo FF, Ochoa LE, Sabaj MH, Lujan NK, Covain R, Silva GSC, Melo BF, Albert JS, Chang J, Foresti F, Alfaro ME, Oliveira C. PMID: 30802595.
      View in: PubMed   Mentions: 20     Fields:    Translation:AnimalsCells
    21. How Well Can We Estimate Diversity Dynamics for Clades in Diversity Decline? Syst Biol. 2019 01 01; 68(1):47-62. Burin G, Alencar LRV, Chang J, Alfaro ME, Quental TB. PMID: 30544232.
      View in: PubMed   Mentions: 10     Fields:    
    22. Contemporaneous radiations of fungi and plants linked to symbiosis. Nat Commun. 2018 12 21; 9(1):5451. 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. PMID: 30575731; PMCID: PMC6303338.
      View in: PubMed   Mentions: 62     Fields:    Translation:Animals
    23. Phylogenomics of a putatively convergent novelty: did hypertrophied lips evolve once or repeatedly in Lake Malawi cichlid fishes? BMC Evol Biol. 2018 11 29; 18(1):179. Darrin Hulsey C, Zheng J, Holzman R, Alfaro ME, Olave M, Meyer A. PMID: 30486792; PMCID: PMC6263179.
      View in: PubMed   Mentions: 6     Fields:    Translation:Animals
    24. Ice ages and butterflyfishes: Phylogenomics elucidates the ecological and evolutionary history of reef fishes in an endemism hotspot. Ecol Evol. 2018 Nov; 8(22):10989-11008. 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. PMID: 30519422; PMCID: PMC6262737.
      View in: PubMed   Mentions: 2  
    25. An inverse latitudinal gradient in speciation rate for marine fishes. Nature. 2018 07; 559(7714):392-395. Rabosky DL, Chang J, Title PO, Cowman PF, Sallan L, Friedman M, Kaschner K, Garilao C, Near TJ, Coll M, Alfaro ME. PMID: 29973726.
      View in: PubMed   Mentions: 187     Fields:    Translation:Animals
    26. Resolving the ray-finned fish tree of life. Proc Natl Acad Sci U S A. 2018 06 12; 115(24):6107-6109. Alfaro ME. PMID: 29848635; PMCID: PMC6004464.
      View in: PubMed   Mentions: 2     Fields:    Translation:Animals
    27. Phylogenetic Factor Analysis. Syst Biol. 2018 May 01; 67(3):384-399. Tolkoff MR, Alfaro ME, Baele G, Lemey P, Suchard MA. PMID: 28950376; PMCID: PMC5920329.
      View in: PubMed   Mentions: 8     Fields:    Translation:Animals
    28. Filtering nucleotide sites by phylogenetic signal to noise ratio increases confidence in the Neoaves phylogeny generated from ultraconserved elements. Mol Phylogenet Evol. 2018 09; 126:116-128. Gilbert PS, Wu J, Simon MW, Sinsheimer JS, Alfaro ME. PMID: 29626666; PMCID: PMC6217972.
      View in: PubMed   Mentions: 4     Fields:    Translation:AnimalsCells
    29. A phylogenomic perspective on the robust capuchin monkey (Sapajus) radiation: First evidence for extensive population admixture across South America. Mol Phylogenet Evol. 2018 07; 124:137-150. 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. PMID: 29545109.
      View in: PubMed   Mentions: 13     Fields:    Translation:Animals
    30. Explosive diversification of marine fishes at the Cretaceous-Palaeogene boundary. Nat Ecol Evol. 2018 04; 2(4):688-696. Alfaro ME, Faircloth BC, Harrington RC, Sorenson L, Friedman M, Thacker CE, Oliveros CH, Cerný D, Near TJ. PMID: 29531346.
      View in: PubMed   Mentions: 55     Fields:    Translation:Animals
    31. Phylogenetics and geography of speciation in New World Halichoeres wrasses. Mol Phylogenet Evol. 2018 04; 121:35-45. Wainwright PC, Santini F, Bellwood DR, Robertson DR, Rocha LA, Alfaro ME. PMID: 29289544.
      View in: PubMed   Mentions: 5     Fields:    Translation:Animals
    32. Phylogenomic Systematics of Ostariophysan Fishes: Ultraconserved Elements Support the Surprising Non-Monophyly of Characiformes. Syst Biol. 2017 Nov 01; 66(6):881-895. Chakrabarty P, Faircloth BC, Alda F, Ludt WB, Mcmahan CD, Near TJ, Dornburg A, Albert JS, Arroyave J, Stiassny MLJ, Sorenson L, Alfaro ME. PMID: 28334176.
      View in: PubMed   Mentions: 20     Fields:    Translation:AnimalsCells
    33. Early-branching euteleost relationships: areas of congruence between concatenation and coalescent model inferences. PeerJ. 2017; 5:e3548. Campbell MA, Alfaro ME, Belasco M, López JA. PMID: 28929008; PMCID: PMC5592902.
      View in: PubMed   Mentions: 2     Fields:    
    34. Multilocus analysis of the catfish family Trichomycteridae (Teleostei: Ostariophysi: Siluriformes) supporting a monophyletic Trichomycterinae. Mol Phylogenet Evol. 2017 10; 115:71-81. Ochoa LE, Roxo FF, DoNascimiento C, Sabaj MH, Datovo A, Alfaro M, Oliveira C. PMID: 28716740.
      View in: PubMed   Mentions: 4     Fields:    Translation:AnimalsCells
    35. Body shape convergence driven by small size optimum in marine angelfishes. Biol Lett. 2017 Jun; 13(6). Frédérich B, Santini F, Konow N, Schnitzler J, Lecchini D, Alfaro ME. PMID: 28615351; PMCID: PMC5493737.
      View in: PubMed   Mentions: 4     Fields:    Translation:Animals
    36. Phylogenomic analysis of Lake Malawi cichlid fishes: Further evidence that the three-stage model of diversification does not fit. Mol Phylogenet Evol. 2017 09; 114:40-48. Hulsey CD, Zheng J, Faircloth BC, Meyer A, Alfaro ME. PMID: 28579077.
      View in: PubMed   Mentions: 11     Fields:    Translation:Animals
    37. Phylogenomic analysis of a rapid radiation of misfit fishes (Syngnathiformes) using ultraconserved elements. Mol Phylogenet Evol. 2017 08; 113:33-48. Longo SJ, Faircloth BC, Meyer A, Westneat MW, Alfaro ME, Wainwright PC. PMID: 28487262.
      View in: PubMed   Mentions: 18     Fields:    Translation:AnimalsCells
    38. Phylogenomic analysis of carangimorph fishes reveals flatfish asymmetry arose in a blink of the evolutionary eye. BMC Evol Biol. 2016 Oct 21; 16(1):224. Harrington RC, Faircloth BC, Eytan RI, Smith WL, Near TJ, Alfaro ME, Friedman M. PMID: 27769164; PMCID: PMC5073739.
      View in: PubMed   Mentions: 36     Fields:    Translation:Animals
    39. Evolution: Bioluminescent Courtship as an Engine of Diversity. Curr Biol. 2016 07 25; 26(14):R667-9. Alfaro ME. PMID: 27458910.
      View in: PubMed   Mentions:    Fields:    Translation:Animals
    40. Dietary breadth is positively correlated with venom complexity in cone snails. BMC Genomics. 2016 May 26; 17:401. Phuong MA, Mahardika GN, Alfaro ME. PMID: 27229931; PMCID: PMC4880860.
      View in: PubMed   Mentions: 56     Fields:    Translation:AnimalsCells
    41. Phylogeny and biogeography of hogfishes and allies (Bodianus, Labridae). Mol Phylogenet Evol. 2016 06; 99:1-6. Santini F, Sorenson L, Alfaro ME. PMID: 26944013.
      View in: PubMed   Mentions:    Fields:    Translation:Animals
    42. Replicated divergence in cichlid radiations mirrors a major vertebrate innovation. Proc Biol Sci. 2016 Jan 13; 283(1822). McGee MD, Faircloth BC, Borstein SR, Zheng J, Darrin Hulsey C, Wainwright PC, Alfaro ME. PMID: 26763694; PMCID: PMC4721080.
      View in: PubMed   Mentions: 17     Fields:    Translation:Animals
    43. A clinical research pathway towards developing new insights into cardiomyopathy. Evol Med Public Health. 2015 Sep 28; 2015(1):280. Blumstein DT, Buckner J, Shah S, Patel S, Alfaro ME, Natterson-Horowitz B. PMID: 26415642; PMCID: PMC4606057.
      View in: PubMed   Mentions:
    44. The evolution of capture myopathy in hooved mammals: a model for human stress cardiomyopathy? Evol Med Public Health. 2015 Jul 21; 2015(1):195-203. Blumstein DT, Buckner J, Shah S, Patel S, Alfaro ME, Natterson-Horowitz B. PMID: 26198189; PMCID: PMC4538952.
      View in: PubMed   Mentions: 13  
    45. Genome-wide ultraconserved elements exhibit higher phylogenetic informativeness than traditional gene markers in percomorph fishes. Mol Phylogenet Evol. 2015 Nov; 92:140-6. Gilbert PS, Chang J, Pan C, Sobel EM, Sinsheimer JS, Faircloth BC, Alfaro ME. PMID: 26079130; PMCID: PMC4583375.
      View in: PubMed   Mentions: 24     Fields:    Translation:AnimalsCells
    46. Life in the unthinking depths: energetic constraints on encephalization in marine fishes. J Evol Biol. 2015 May; 28(5):1080-90. Iglesias TL, Dornburg A, Brandley MC, Alfaro ME, Warren DL. PMID: 25818759.
      View in: PubMed   Mentions: 2     Fields:    Translation:Animals
    47. Boxfish swimming paradox resolved: forces by the flow of water around the body promote manoeuvrability. J R Soc Interface. 2015 Feb 06; 12(103). Van Wassenbergh S, van Manen K, Marcroft TA, Alfaro ME, Stamhuis EJ. PMID: 25505133; PMCID: PMC4305415.
      View in: PubMed   Mentions: 12     Fields:    Translation:Animals
    48. Biting disrupts integration to spur skull evolution in eels. Nat Commun. 2014 Nov 17; 5:5505. Collar DC, Wainwright PC, Alfaro ME, Revell LJ, Mehta RS. PMID: 25399532.
      View in: PubMed   Mentions: 19     Fields:    Translation:Animals
    49. Biogeography of squirrel monkeys (genus Saimiri): South-central Amazon origin and rapid pan-Amazonian diversification of a lowland primate. Mol Phylogenet Evol. 2015 Jan; 82 Pt B:436-54. 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. PMID: 25305518.
      View in: PubMed   Mentions: 26     Fields:    Translation:Animals
    50. 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. Mol Phylogenet Evol. 2015 Jan; 82 Pt B:400-12. Boubli JP, Ribas C, Lynch Alfaro JW, Alfaro ME, da Silva MN, Pinho GM, Farias IP. PMID: 25285613.
      View in: PubMed   Mentions: 24     Fields:    Translation:Animals
    51. The effects of ecology and evolutionary history on robust capuchin morphological diversity. Mol Phylogenet Evol. 2015 Jan; 82 Pt B:455-66. Wright KA, Wright BW, Ford SM, Fragaszy D, Izar P, Norconk M, Masterson T, Hobbs DG, Alfaro ME, Lynch Alfaro JW. PMID: 25194323.
      View in: PubMed   Mentions: 4     Fields:    Translation:Animals
    52. Trait decoupling promotes evolutionary diversification of the trophic and acoustic system of damselfishes. Proc Biol Sci. 2014 Aug 22; 281(1789):20141047. Frédérich B, Olivier D, Litsios G, Alfaro ME, Parmentier E. PMID: 24990683; PMCID: PMC4100519.
      View in: PubMed   Mentions: 9     Fields:    Translation:Animals
    53. The effect of habitat on modern shark diversification. J Evol Biol. 2014 Aug; 27(8):1536-48. Sorenson L, Santini F, Alfaro ME. PMID: 24890604.
      View in: PubMed   Mentions: 24     Fields:    Translation:Animals
    54. Biogeography of the marmosets and tamarins (Callitrichidae). Mol Phylogenet Evol. 2015 Jan; 82 Pt B:413-25. Buckner JC, Lynch Alfaro JW, Rylands AB, Alfaro ME. PMID: 24857784.
      View in: PubMed   Mentions: 26     Fields:    Translation:Animals
    55. Imperfect morphological convergence: variable changes in cranial structures underlie transitions to durophagy in moray eels. Am Nat. 2014 Jun; 183(6):E168-84. Collar DC, Reece JS, Alfaro ME, Wainwright PC, Mehta RS. PMID: 24823828.
      View in: PubMed   Mentions: 16     Fields:    Translation:Animals
    56. geiger v2.0: an expanded suite of methods for fitting macroevolutionary models to phylogenetic trees. Bioinformatics. 2014 Aug 01; 30(15):2216-8. Pennell MW, Eastman JM, Slater GJ, Brown JW, Uyeda JC, FitzJohn RG, Alfaro ME, Harmon LJ. PMID: 24728855.
      View in: PubMed   Mentions: 228     Fields:    
    57. Body fineness ratio as a predictor of maximum prolonged-swimming speed in coral reef fishes. PLoS One. 2013; 8(10):e75422. Walker JA, Alfaro ME, Noble MM, Fulton CJ. PMID: 24204575; PMCID: PMC3799785.
      View in: PubMed   Mentions: 7     Fields:    Translation:Animals
    58. A multi-locus molecular timescale for the origin and diversification of eels (Order: Anguilliformes). Mol Phylogenet Evol. 2013 Dec; 69(3):884-94. Santini F, Kong X, Sorenson L, Carnevale G, Mehta RS, Alfaro ME. PMID: 23831455.
      View in: PubMed   Mentions: 11     Fields:    Translation:AnimalsCells
    59. A Phylogenomic Perspective on the Radiation of Ray-Finned Fishes Based upon Targeted Sequencing of Ultraconserved Elements (UCEs). PLoS One. 2013; 8(6):e65923. Faircloth BC, Sorenson L, Santini F, Alfaro ME. PMID: 23824177; PMCID: PMC3688804.
      View in: PubMed   Mentions: 88     Fields:    Translation:AnimalsCells
    60. A new phylogeny of tetraodontiform fishes (Tetraodontiformes, Acanthomorpha) based on 22 loci. Mol Phylogenet Evol. 2013 Oct; 69(1):177-87. Santini F, Sorenson L, Alfaro ME. PMID: 23727595.
      View in: PubMed   Mentions: 9     Fields:    Translation:AnimalsCells
    61. A new multi-locus timescale reveals the evolutionary basis of diversity patterns in triggerfishes and filefishes (Balistidae, Monacanthidae; Tetraodontiformes). Mol Phylogenet Evol. 2013 Oct; 69(1):165-76. Santini F, Sorenson L, Alfaro ME. PMID: 23727054.
      View in: PubMed   Mentions: 9     Fields:    Translation:AnimalsCells
    62. Phylotastic! Making tree-of-life knowledge accessible, reusable and convenient. BMC Bioinformatics. 2013 May 13; 14:158. 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. PMID: 23668630; PMCID: PMC3669619.
      View in: PubMed   Mentions: 12     Fields:    
    63. A multi-locus timetree of surgeonfishes (Acanthuridae, Percomorpha), with revised family taxonomy. Mol Phylogenet Evol. 2013 Jul; 68(1):150-60. Sorenson L, Santini F, Carnevale G, Alfaro ME. PMID: 23542000.
      View in: PubMed   Mentions: 18     Fields:    Translation:Animals
    64. Do habitat shifts drive diversification in teleost fishes? An example from the pufferfishes (Tetraodontidae). J Evol Biol. 2013 May; 26(5):1003-18. Santini F, Nguyen MT, Sorenson L, Waltzek TB, Lynch Alfaro JW, Eastman JM, Alfaro ME. PMID: 23496826.
      View in: PubMed   Mentions: 19     Fields:    Translation:Animals
    65. 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; 3669:551-70. Victor BC, Alfaro ME, Sorenson L. PMID: 26312357.
      View in: PubMed   Mentions: 1     Fields:    Translation:Animals
    66. Adaptive response to sociality and ecology drives the diversification of facial colour patterns in catarrhines. Nat Commun. 2013; 4:2765. Santana SE, Alfaro JL, Noonan A, Alfaro ME. PMID: 24212362.
      View in: PubMed   Mentions: 17     Fields:    Translation:Animals
    67. Rates of speciation and morphological evolution are correlated across the largest vertebrate radiation. Nat Commun. 2013; 4:1958. Rabosky DL, Santini F, Eastman J, Smith SA, Sidlauskas B, Chang J, Alfaro ME. PMID: 23739623.
      View in: PubMed   Mentions: 162     Fields:    Translation:Animals
    68. Iterative ecological radiation and convergence during the evolutionary history of damselfishes (Pomacentridae). Am Nat. 2013 Jan; 181(1):94-113. Frédérich B, Sorenson L, Santini F, Slater GJ, Alfaro ME. PMID: 23234848.
      View in: PubMed   Mentions: 32     Fields:    Translation:AnimalsCells
    69. A multilocus molecular phylogeny of boxfishes (Aracanidae, Ostraciidae; Tetraodontiformes). Mol Phylogenet Evol. 2013 Jan; 66(1):153-60. Santini F, Sorenson L, Marcroft T, Dornburg A, Alfaro ME. PMID: 23036494.
      View in: PubMed   Mentions: 9     Fields:    Translation:AnimalsCells
    70. Clade age and species richness are decoupled across the eukaryotic tree of life. PLoS Biol. 2012 Aug; 10(8):e1001381. Rabosky DL, Slater GJ, Alfaro ME. PMID: 22969411; PMCID: PMC3433737.
      View in: PubMed   Mentions: 55     Fields:    Translation:Animals
    71. Integrating fossils with molecular phylogenies improves inference of trait evolution. Evolution. 2012 Dec; 66(12):3931-44. Slater GJ, Harmon LJ, Alfaro ME. PMID: 23206147.
      View in: PubMed   Mentions: 83     Fields:    Translation:Animals
    72. Systemic iridovirus from threespine stickleback Gasterosteus aculeatus represents a new megalocytivirus species (family Iridoviridae). Dis Aquat Organ. 2012 Feb 17; 98(1):41-56. Waltzek TB, Marty GD, Alfaro ME, Bennett WR, Garver KA, Haulena M, Weber ES, Hedrick RP. PMID: 22422128.
      View in: PubMed   Mentions: 5     Fields:    Translation:AnimalsCells
    73. Cebus phylogenetic relationships: a preliminary reassessment of the diversity of the untufted capuchin monkeys. Am J Primatol. 2012 Apr; 74(4):381-93. Boubli JP, Rylands AB, Farias IP, Alfaro ME, Alfaro JL. PMID: 22311697.
      View in: PubMed   Mentions: 13     Fields:    Translation:Animals
    74. Adaptive evolution of facial colour patterns in Neotropical primates. Proc Biol Sci. 2012 Jun 07; 279(1736):2204-11. Santana SE, Lynch Alfaro J, Alfaro ME. PMID: 22237906; PMCID: PMC3321701.
      View in: PubMed   Mentions: 26     Fields:    Translation:Animals
    75. Fitting models of continuous trait evolution to incompletely sampled comparative data using approximate Bayesian computation. Evolution. 2012 Mar; 66(3):752-762. Slater GJ, Harmon LJ, Wegmann D, Joyce P, Revell LJ, Alfaro ME. PMID: 22380438.
      View in: PubMed   Mentions: 16     Fields:    Translation:Animals
    76. Roosting ecology and the evolution of pelage markings in bats. PLoS One. 2011; 6(10):e25845. Santana SE, Dial TO, Eiting TP, Alfaro ME. PMID: 21991371; PMCID: PMC3185059.
      View in: PubMed   Mentions: 8     Fields:    Translation:Animals
    77. A novel comparative method for identifying shifts in the rate of character evolution on trees. Evolution. 2011 Dec; 65(12):3578-89. Eastman JM, Alfaro ME, Joyce P, Hipp AL, Harmon LJ. PMID: 22133227.
      View in: PubMed   Mentions: 68     Fields:    Translation:Animals
    78. Anointing variation across wild capuchin populations: a review of material preferences, bout frequency and anointing sociality in Cebus and Sapajus. Am J Primatol. 2012 Apr; 74(4):299-314. 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. PMID: 21769906.
      View in: PubMed   Mentions: 11     Fields:    Translation:Animals
    79. The influence of an innovative locomotor strategy on the phenotypic diversification of triggerfish (family: Balistidae). Evolution. 2011 Jul; 65(7):1912-26. Dornburg A, Sidlauskas B, Santini F, Sorenson L, Near TJ, Alfaro ME. PMID: 21729047.
      View in: PubMed   Mentions: 19     Fields:    Translation:Animals
    80. Testing for temporal variation in diversification rates when sampling is incomplete and nonrandom. Syst Biol. 2011 Jul; 60(4):410-9. Brock CD, Harmon LJ, Alfaro ME. PMID: 21378083.
      View in: PubMed   Mentions: 22     Fields:    
    81. The evolution of island gigantism and body size variation in tortoises and turtles. Biol Lett. 2011 Aug 23; 7(4):558-61. Jaffe AL, Slater GJ, Alfaro ME. PMID: 21270022; PMCID: PMC3130210.
      View in: PubMed   Mentions: 20     Fields:    Translation:Animals
    82. Biologically inspired phylogenetic models strongly outperform the no common mechanism model. Syst Biol. 2011 Mar; 60(2):225-32. Huelsenbeck JP, Alfaro ME, Suchard MA. PMID: 21252385; PMCID: PMC3038349.
      View in: PubMed   Mentions: 6     Fields:    
    83. Evolutionary bangs and whimpers: methodological advances and conceptual frameworks for studying exceptional diversification. Syst Biol. 2010 Dec; 59(6):615-8. Rabosky DL, Alfaro ME. PMID: 20947700.
      View in: PubMed   Mentions: 3     Fields:    
    84. Elongation of the body in eels. Integr Comp Biol. 2010 Dec; 50(6):1091-105. Mehta RS, Ward AB, Alfaro ME, Wainwright PC. PMID: 21558261.
      View in: PubMed   Mentions: 12     Fields:    Translation:Animals
    85. Diversity versus disparity and the radiation of modern cetaceans. Proc Biol Sci. 2010 Oct 22; 277(1697):3097-104. Slater GJ, Price SA, Santini F, Alfaro ME. PMID: 20484243; PMCID: PMC2982053.
      View in: PubMed   Mentions: 74     Fields:    Translation:Animals
    86. Evolutionary biology: A flourishing of fish forms. Nature. 2010 Apr 08; 464(7290):840-2. Alfaro M, Santini F. PMID: 20376139.
      View in: PubMed   Mentions: 2     Fields:    Translation:Animals
    87. Does evolutionary innovation in pharyngeal jaws lead to rapid lineage diversification in labrid fishes? BMC Evol Biol. 2009 Oct 22; 9:255. Alfaro ME, Brock CD, Banbury BL, Wainwright PC. PMID: 19849854; PMCID: PMC2779191.
      View in: PubMed   Mentions: 23     Fields:    Translation:Animals
    88. Did genome duplication drive the origin of teleosts? A comparative study of diversification in ray-finned fishes. BMC Evol Biol. 2009 Aug 08; 9:194. Santini F, Harmon LJ, Carnevale G, Alfaro ME. PMID: 19664233; PMCID: PMC2743667.
      View in: PubMed   Mentions: 101     Fields:    Translation:Animals
    89. Nine exceptional radiations plus high turnover explain species diversity in jawed vertebrates. Proc Natl Acad Sci U S A. 2009 Aug 11; 106(32):13410-4. Alfaro ME, Santini F, Brock C, Alamillo H, Dornburg A, Rabosky DL, Carnevale G, Harmon LJ. PMID: 19633192; PMCID: PMC2715324.
      View in: PubMed   Mentions: 235     Fields:    Translation:Animals
    90. Phylogenetic relationships in the family Alloherpesviridae. Dis Aquat Organ. 2009 Apr 27; 84(3):179-94. Waltzek TB, Kelley GO, Alfaro ME, Kurobe T, Davison AJ, Hedrick RP. PMID: 19565695.
      View in: PubMed   Mentions: 45     Fields:    Translation:AnimalsCells
    91. Convergence in trophic morphology and feeding performance among piscivorous natricine snakes. J Evol Biol. 2009 Jun; 22(6):1203-11. Vincent SE, Brandley MC, Herrel A, Alfaro ME. PMID: 19389153.
      View in: PubMed   Mentions: 9     Fields:    Translation:Animals
    92. The influence of model averaging on clade posteriors: an example using the triggerfishes (Family Balistidae). Syst Biol. 2008 Dec; 57(6):905-19. Dornburg A, Santini F, Alfaro ME. PMID: 19085332.
      View in: PubMed   Mentions: 10     Fields:    Translation:Animals
    93. A comparative study in ancestral range reconstruction methods: retracing the uncertain histories of insular lineages. Syst Biol. 2008 Oct; 57(5):693-707. Clark JR, Ree RH, Alfaro ME, King MG, Wagner WL, Roalson EH. PMID: 18853357.
      View in: PubMed   Mentions: 17     Fields:    Translation:Animals
    94. Phylogenetic relationships and the evolution of regulatory gene sequences in the parrotfishes. Mol Phylogenet Evol. 2008 Oct; 49(1):136-52. Smith LL, Fessler JL, Alfaro ME, Streelman JT, Westneat MW. PMID: 18621133; PMCID: PMC3418665.
      View in: PubMed   Mentions: 16     Fields:    Translation:AnimalsCells
    95. Morphological convergence as a consequence of extreme functional demands: examples from the feeding system of natricine snakes. J Evol Biol. 2008 Sep; 21(5):1438-48. Herrel A, Vincent SE, Alfaro ME, VAN Wassenbergh S, Vanhooydonck B, Irschick DJ. PMID: 18547353.
      View in: PubMed   Mentions: 9     Fields:    Translation:Animals
    96. Integrated diversification of locomotion and feeding in labrid fishes. Biol Lett. 2008 Feb 23; 4(1):84-6. Collar DC, Wainwright PC, Alfaro ME. PMID: 18077241; PMCID: PMC2412936.
      View in: PubMed   Mentions: 5     Fields:    Translation:Animals
    97. Phylogeny, evolutionary history, and biogeography of Oriental-Australian rear-fanged water snakes (Colubroidea: Homalopsidae) inferred from mitochondrial and nuclear DNA sequences. Mol Phylogenet Evol. 2008 Feb; 46(2):576-93. Alfaro ME, Karns DR, Voris HK, Brock CD, Stuart BL. PMID: 18182308.
      View in: PubMed   Mentions: 6     Fields:    Translation:AnimalsCells
    98. Phylogenetic concordance analysis shows an emerging pathogen is novel and endemic. Ecol Lett. 2007 Nov; 10(11):1075-83. Storfer A, Alfaro ME, Ridenhour BJ, Jancovich JK, Mech SG, Parris MJ, Collins JP. PMID: 17850337.
      View in: PubMed   Mentions: 17     Fields:    Translation:HumansAnimalsCellsPHPublic Health
    99. Do reefs drive diversification in marine teleosts? Evidence from the pufferfishes and their allies (Order Tetraodontiformes). Evolution. 2007 Sep; 61(9):2104-26. Alfaro ME, Santini F, Brock CD. PMID: 17915358.
      View in: PubMed   Mentions: 39     Fields:    Translation:Animals
    100. A protocol for the calibration of gamma cameras to estimate internal contamination in emergency situations. Radiat Prot Dosimetry. 2007; 127(1-4):253-7. 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. PMID: 17562649.
      View in: PubMed   Mentions: 1     Fields:    Translation:PHPublic Health
    101. Comparative performance of Bayesian and AIC-based measures of phylogenetic model uncertainty. Syst Biol. 2006 Feb; 55(1):89-96. Alfaro ME, Huelsenbeck JP. PMID: 16507526.
      View in: PubMed   Mentions: 14     Fields:    
    102. Phylogenetic relationships and evolutionary history of the reef fish family Labridae. Mol Phylogenet Evol. 2005 Aug; 36(2):370-90. Westneat MW, Alfaro ME. PMID: 15955516.
      View in: PubMed   Mentions: 50     Fields:    Translation:AnimalsCells
    103. Local phylogenetic divergence and global evolutionary convergence of skull function in reef fishes of the family Labridae. Proc Biol Sci. 2005 May 22; 272(1567):993-1000. Westneat MW, Alfaro ME, Wainwright PC, Bellwood DR, Grubich JR, Fessler JL, Clements KD, Smith LL. PMID: 16024356; PMCID: PMC1599880.
      View in: PubMed   Mentions: 39     Fields:    Translation:AnimalsCells
    104. Evolutionary consequences of many-to-one mapping of jaw morphology to mechanics in labrid fishes. Am Nat. 2005 Jun; 165(6):E140-54. Alfaro ME, Bolnick DI, Wainwright PC. PMID: 15937739.
      View in: PubMed   Mentions: 54     Fields:    Translation:Animals
    105. Many-to-One Mapping of Form to Function: A General Principle in Organismal Design? Integr Comp Biol. 2005 Apr; 45(2):256-62. Wainwright PC, Alfaro ME, Bolnick DI, Hulsey CD. PMID: 21676769.
      View in: PubMed   Mentions: 100     Fields:    
    106. Relationships of the temperate Australasian labrid fish tribe Odacini (Perciformes; Teleostei). Mol Phylogenet Evol. 2004 Aug; 32(2):575-87. Clements KD, Alfaro ME, Fessler JL, Westneat MW. PMID: 15223039.
      View in: PubMed   Mentions: 10     Fields:    Translation:Animals
    107. Bayesian phylogenetic model selection using reversible jump Markov chain Monte Carlo. Mol Biol Evol. 2004 Jun; 21(6):1123-33. Huelsenbeck JP, Larget B, Alfaro ME. PMID: 15034130.
      View in: PubMed   Mentions: 133     Fields:    
    108. Evolutionary dynamics of complex biomechanical systems: an example using the four-bar mechanism. Evolution. 2004 Mar; 58(3):495-503. Alfaro ME, Bolnick DI, Wainwright PC. PMID: 15119434.
      View in: PubMed   Mentions: 37     Fields:    Translation:Animals
    109. Sweeping and striking: a kinematic study of the trunk during prey capture in three thamnophiine snakes. J Exp Biol. 2003 Jul; 206(Pt 14):2381-92. Alfaro ME. PMID: 12796455.
      View in: PubMed   Mentions: 2     Fields:    Translation:Animals
    110. Bayes or bootstrap? A simulation study comparing the performance of Bayesian Markov chain Monte Carlo sampling and bootstrapping in assessing phylogenetic confidence. Mol Biol Evol. 2003 Feb; 20(2):255-66. Alfaro ME, Zoller S, Lutzoni F. PMID: 12598693.
      View in: PubMed   Mentions: 168     Fields:    
    111. Evolutionary history of the parrotfishes: biogeography, ecomorphology, and comparative diversity. Evolution. 2002 May; 56(5):961-71. Streelman JT, Alfaro M, Westneat MW, Bellwood DR, Karl SA. PMID: 12093031.
      View in: PubMed   Mentions: 37     Fields:    Translation:AnimalsCells
    112. Molecular systematics and evolution of Regina and the thamnophiine snakes. Mol Phylogenet Evol. 2001 Dec; 21(3):408-23. Alfaro ME, Arnold SJ. PMID: 11741383.
      View in: PubMed   Mentions: 11     Fields:    Translation:AnimalsCells
    113. Motor patterns of herbivorous feeding: electromyographic analysis of biting in the parrotfishes Cetoscarus bicolor and Scarus iseri. Brain Behav Evol. 1999 Oct; 54(4):205-22. Alfaro M, Westneat MW. PMID: 10592383.
      View in: PubMed   Mentions:    Fields:    Translation:AnimalsCells
    114. Trypanosomes of Costa Rican feral mmamals. J Parasitol. 1967 Oct; 53(5):951-5. Esquivel R, Zúñiga JA, Alfaro M, Kotcher E. PMID: 6062080.
      View in: PubMed   Mentions: 2     Fields:    Translation:Animals
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