Michael E. Alfaro - Publications

Ecology and Evolutionary Biology University of California, Los Angeles, Los Angeles, CA 
biomechanics, evolution of ideas

119 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2022 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, et al. Prolonged morphological expansion of spiny-rayed fishes following the end-Cretaceous. Nature Ecology & Evolution. PMID 35835827 DOI: 10.1038/s41559-022-01801-3  0.825
2021 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, ... ... Alfaro ME, et al. Accelerated Diversification Explains the Exceptional Species Richness of Tropical Characoid Fishes. Systematic Biology. PMID 34097063 DOI: 10.1093/sysbio/syab040  0.836
2020 Campbell MA, Buser TJ, Alfaro ME, López JA. Addressing incomplete lineage sorting and paralogy in the inference of uncertain salmonid phylogenetic relationships. Peerj. 8: e9389. PMID 32685284 DOI: 10.7717/Peerj.9389  0.458
2020 Tyler McCraney W, Thacker CE, Alfaro ME. Supermatrix phylogeny resolves goby lineages and reveals unstable root of Gobiaria. Molecular Phylogenetics and Evolution. 106862. PMID 32473335 DOI: 10.1016/J.Ympev.2020.106862  0.505
2020 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. 10: 2697. PMID 32060350 DOI: 10.1038/S41598-020-59519-W  0.657
2020 Gjesfjeld E, Silvestro D, Chang J, Koch B, Foster JG, Alfaro ME. A quantitative workflow for modeling diversification in material culture. Plos One. 15: e0227579. PMID 32027685 DOI: 10.1371/Journal.Pone.0227579  0.5
2020 Faircloth BC, Alda F, Hoekzema K, Burns MD, Oliveira C, Albert JS, Melo BF, Ochoa LE, Roxo FF, Chakrabarty P, Sidlauskas BL, Alfaro ME. A Target Enrichment Bait Set for Studying Relationships among Ostariophysan Fishes Copeia. 108: 47. DOI: 10.1643/Cg-18-139  0.734
2019 Chang J, Rabosky DL, Alfaro ME. Estimating diversification rates on incompletely-sampled phylogenies: theoretical concerns and practical solutions. Systematic Biology. PMID 31804691 DOI: 10.1093/Sysbio/Syz081  0.695
2019 Friedman M, Feilich KL, Beckett HT, Alfaro ME, Faircloth BC, Černý 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. 286: 20191502. PMID 31506051 DOI: 10.1098/Rspb.2019.1502  0.727
2019 Alfaro ME, Karan E, Schwartz ST, Shultz AJ. The Evolution of Color Pattern in Butterflyfishes (Chaetodontidae). Integrative and Comparative Biology. PMID 31292612 DOI: 10.1093/Icb/Icz119  0.778
2019 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. 286: 20182358. PMID 30963830 DOI: 10.1098/Rspb.2018.2358  0.795
2019 Phuong MA, Alfaro ME, Mahardika GN, Marwoto RM, Prabowo RE, von Rintelen T, Wh Vogt P, Hendricks JR, Puillandre N. Lack of signal for the impact of conotoxin gene diversity on speciation rates in cone snails. Systematic Biology. PMID 30816949 DOI: 10.1093/Sysbio/Syz016  0.472
2019 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. PMID 30802595 DOI: 10.1016/J.Ympev.2019.02.017  0.667
2019 Burin G, Alencar LRV, Chang J, Alfaro ME, Quental TB. How Well Can We Estimate Diversity Dynamics for Clades in Diversity Decline? Systematic Biology. 68: 47-62. PMID 30544232 DOI: 10.1093/Sysbio/Syy037  0.601
2019 Chang J, Rabosky DL, Smith SA, Alfaro ME. An r package and online resource for macroevolutionary studies using the ray‐finned fish tree of life Methods in Ecology and Evolution. 10: 1118-1124. DOI: 10.1111/2041-210X.13182  0.71
2018 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. 9: 5451. PMID 30575731 DOI: 10.1038/S41467-018-07849-9  0.316
2018 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. PMID 30521024 DOI: 10.1093/Sysbio/Syy085  0.436
2018 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. 8: 10989-11008. PMID 30519422 DOI: 10.1002/Ece3.4566  0.777
2018 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. 18: 179. PMID 30486792 DOI: 10.1186/S12862-018-1296-9  0.642
2018 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. PMID 29973726 DOI: 10.1038/S41586-018-0273-1  0.815
2018 Alfaro ME. Resolving the ray-finned fish tree of life. Proceedings of the National Academy of Sciences of the United States of America. PMID 29848635 DOI: 10.1073/Pnas.1807018115  0.5
2018 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. PMID 29626666 DOI: 10.1016/J.Ympev.2018.03.033  0.753
2018 Lima MGM, de Sousa E Silva-Júnior J, Černý 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. PMID 29545109 DOI: 10.1016/J.Ympev.2018.02.023  0.707
2018 Alfaro ME, Faircloth BC, Harrington RC, Sorenson L, Friedman M, Thacker CE, Oliveros CH, Černý D, Near TJ. Explosive diversification of marine fishes at the Cretaceous-Palaeogene boundary. Nature Ecology & Evolution. PMID 29531346 DOI: 10.1038/S41559-018-0494-6  0.693
2017 Wainwright PC, Santini F, Bellwood DR, Ross Robertson D, Rocha LA, Alfaro ME. Phylogenetics and geography of speciation in New World Halichoeres wrasses. Molecular Phylogenetics and Evolution. PMID 29289544 DOI: 10.1016/J.Ympev.2017.12.028  0.644
2017 Tolkoff MR, Alfaro ME, Baele G, Lemey P, Suchard MA. Phylogenetic Factor Analysis. Systematic Biology. PMID 28950376 DOI: 10.1093/Sysbio/Syx066  0.353
2017 Campbell MA, Alfaro ME, Belasco M, López JA. Early-branching euteleost relationships: areas of congruence between concatenation and coalescent model inferences. Peerj. 5: e3548. PMID 28929008 DOI: 10.7717/Peerj.3548  0.474
2017 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. 115: 71-81. PMID 28716740 DOI: 10.1016/J.Ympev.2017.07.007  0.436
2017 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. 13. PMID 28615351 DOI: 10.1098/Rsbl.2017.0154  0.381
2017 Darrin Hulsey C, 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. PMID 28579077 DOI: 10.1016/J.Ympev.2017.05.027  0.472
2017 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. PMID 28487262 DOI: 10.1016/J.Ympev.2017.05.002  0.829
2017 Chakrabarty P, Faircloth BC, Alda F, Ludt WB, McMahan CD, Near TJ, Dornburg A, Albert JS, Arroyave J, Stiassny ML, Sorenson L, Alfaro ME. Phylogenomic Systematics of Ostariophysan fishes: Ultraconserved Elements Support the Surprising Non-monophyly of Characiformes. Systematic Biology. PMID 28334176 DOI: 10.1093/Sysbio/Syx038  0.799
2017 Lima MGM, Buckner JC, Silva-Júnior JdSe, Aleixo A, Martins AB, Boubli JP, Link A, Farias IP, da Silva MN, Röhe F, Queiroz H, Chiou KL, Di Fiore A, Alfaro ME, Lynch Alfaro JW. Capuchin monkey biogeography: understanding Sapajus Pleistocene range expansion and the current sympatry between Cebus and Sapajus Journal of Biogeography. 44: 810-820. DOI: 10.1111/Jbi.12945  0.682
2016 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. 16: 224. PMID 27769164 DOI: 10.1186/S12862-016-0786-X  0.65
2016 Alfaro ME. Evolution: Bioluminescent Courtship as an Engine of Diversity. Current Biology : Cb. 26: R667-9. PMID 27458910 DOI: 10.1016/J.Cub.2016.05.061  0.421
2016 Phuong MA, Mahardika GN, Alfaro ME. Dietary breadth is positively correlated with venom complexity in cone snails. Bmc Genomics. 17: 401. PMID 27229931 DOI: 10.1186/S12864-016-2755-6  0.479
2016 Santini F, Sorenson L, Alfaro ME. Phylogeny and biogeography of hogfishes and allies (Bodianus, Labridae). Molecular Phylogenetics and Evolution. PMID 26944013 DOI: 10.1016/J.Ympev.2016.02.011  0.72
2016 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 / the Royal Society. 283. PMID 26763694 DOI: 10.1098/Rspb.2015.1413  0.795
2016 Gjesfjeld E, Chang J, Silvestro D, Kelty C, Alfaro ME. Competition and Extinction Explain the Evolution of Diversity in American Automobiles Palgrave Communications. 2: 16038. DOI: 10.1057/Palcomms.2016.19  0.551
2015 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. PMID 26415642 DOI: 10.1093/Emph/Eov024  0.603
2015 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. PMID 26198189 DOI: 10.1093/Emph/Eov015  0.608
2015 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. 92: 140-146. PMID 26079130 DOI: 10.1016/J.Ympev.2015.05.027  0.761
2015 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. 28: 1080-90. PMID 25818759 DOI: 10.1111/Jeb.12631  0.616
2015 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, ... ... Alfaro ME, et al. Biogeography of squirrel monkeys (genus Saimiri): South-central Amazon origin and rapid pan-Amazonian diversification of a lowland primate. Molecular Phylogenetics and Evolution. 82: 436-54. PMID 25305518 DOI: 10.1016/J.Ympev.2014.09.004  0.464
2015 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. 82: 400-12. PMID 25285613 DOI: 10.1016/J.Ympev.2014.09.005  0.469
2015 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. 82: 455-66. PMID 25194323 DOI: 10.1016/J.Ympev.2014.08.009  0.632
2015 Buckner JC, Lynch Alfaro JW, Rylands AB, Alfaro ME. Biogeography of the marmosets and tamarins (Callitrichidae). Molecular Phylogenetics and Evolution. 82: 413-25. PMID 24857784 DOI: 10.1016/J.Ympev.2014.04.031  0.674
2015 Chang J, Alfaro ME. Crowdsourced geometric morphometrics enable rapid large-scale collection and analysis of phenotypic data Methods in Ecology and Evolution. DOI: 10.1111/2041-210X.12508  0.567
2014 Collar DC, Wainwright PC, Alfaro ME, Revell LJ, Mehta RS. Biting disrupts integration to spur skull evolution in eels. Nature Communications. 5: 5505. PMID 25399532 DOI: 10.1038/Ncomms6505  0.691
2014 Peši? V, Chatterjee T, Alfaro M, Schizas NV. A new species of Litarachna (Acari, Hydrachnidia, Pontarachnidae) from a Caribbean mesophotic coral ecosystem. Zookeys. 89-97. PMID 25147451 DOI: 10.3897/zookeys.425.8110  0.325
2014 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 / the Royal Society. 281: 20141047. PMID 24990683 DOI: 10.1098/Rspb.2014.1047  0.436
2014 Sorenson L, Santini F, Alfaro ME. The effect of habitat on modern shark diversification. Journal of Evolutionary Biology. 27: 1536-48. PMID 24890604 DOI: 10.1111/Jeb.12405  0.733
2014 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. 183: E168-84. PMID 24823828 DOI: 10.1086/675810  0.704
2014 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). 30: 2216-8. PMID 24728855 DOI: 10.1093/Bioinformatics/Btu181  0.304
2013 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. 3669: 551-70. PMID 26312357 DOI: 10.11646/Zootaxa.3669.4.8  0.693
2013 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. 4: 2765. PMID 24212362 DOI: 10.1038/Ncomms3765  0.381
2013 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. 8: e75422. PMID 24204575 DOI: 10.1371/Journal.Pone.0075422  0.722
2013 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. 69: 884-94. PMID 23831455 DOI: 10.1016/J.Ympev.2013.06.016  0.775
2013 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. 8: e65923. PMID 23824177 DOI: 10.1371/Journal.Pone.0065923  0.714
2013 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. 4: 1958. PMID 23739623 DOI: 10.1038/Ncomms2958  0.827
2013 Santini F, Sorenson L, Alfaro ME. A new phylogeny of tetraodontiform fishes (Tetraodontiformes, Acanthomorpha) based on 22 loci. Molecular Phylogenetics and Evolution. 69: 177-87. PMID 23727595 DOI: 10.1016/J.Ympev.2013.05.014  0.75
2013 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. 69: 165-76. PMID 23727054 DOI: 10.1016/J.Ympev.2013.05.015  0.769
2013 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, ... Alfaro ME, et al. Phylotastic! Making tree-of-life knowledge accessible, reusable and convenient. Bmc Bioinformatics. 14: 158. PMID 23668630 DOI: 10.1186/1471-2105-14-158  0.777
2013 Sorenson L, Santini F, Carnevale G, Alfaro ME. A multi-locus timetree of surgeonfishes (Acanthuridae, Percomorpha), with revised family taxonomy. Molecular Phylogenetics and Evolution. 68: 150-60. PMID 23542000 DOI: 10.1016/J.Ympev.2013.03.014  0.726
2013 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. 26: 1003-18. PMID 23496826 DOI: 10.1111/Jeb.12112  0.75
2013 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. 181: 94-113. PMID 23234848 DOI: 10.1086/668599  0.721
2013 Santini F, Sorenson L, Marcroft T, Dornburg A, Alfaro ME. A multilocus molecular phylogeny of boxfishes (Aracanidae, Ostraciidae; Tetraodontiformes). Molecular Phylogenetics and Evolution. 66: 153-60. PMID 23036494 DOI: 10.1016/J.Ympev.2012.09.022  0.735
2013 Rocha LA, Bernal MA, Gaither MR, Alfaro ME. Massively parallel DNA sequencing: the new frontier in biogeography Frontiers of Biogeography. 5. DOI: 10.21425/F5Fbg16189  0.314
2013 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. 3669: 551-570. DOI: 10.11646/zootaxa.3669.4.8  0.576
2012 Slater GJ, Harmon LJ, Alfaro ME. Integrating fossils with molecular phylogenies improves inference of trait evolution. Evolution; International Journal of Organic Evolution. 66: 3931-44. PMID 23206147 DOI: 10.1111/J.1558-5646.2012.01723.X  0.398
2012 Rabosky DL, Slater GJ, Alfaro ME. Clade age and species richness are decoupled across the eukaryotic tree of life. Plos Biology. 10: e1001381. PMID 22969411 DOI: 10.1371/Journal.Pbio.1001381  0.714
2012 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. 98: 41-56. PMID 22422128 DOI: 10.3354/Dao02415  0.456
2012 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. 66: 752-62. PMID 22380438 DOI: 10.1111/J.1558-5646.2011.01474.X  0.392
2012 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. 74: 381-93. PMID 22311697 DOI: 10.1002/Ajp.21998  0.357
2012 Santana SE, Lynch Alfaro J, Alfaro ME. Adaptive evolution of facial colour patterns in Neotropical primates. Proceedings. Biological Sciences / the Royal Society. 279: 2204-11. PMID 22237906 DOI: 10.1098/Rspb.2011.2326  0.45
2012 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. 74: 299-314. PMID 21769906 DOI: 10.1002/Ajp.20971  0.345
2012 Lynch Alfaro JW, Boubli JP, Olson LE, Di Fiore A, Wilson B, Gutiérrez-Espeleta GA, Chiou KL, Schulte M, Neitzel S, Ross V, Schwochow D, Nguyen MTT, Farias I, Janson CH, Alfaro ME. Explosive Pleistocene range expansion leads to widespread Amazonian sympatry between robust and gracile capuchin monkeys Journal of Biogeography. 39: 272-288. DOI: 10.1111/J.1365-2699.2011.02609.X  0.457
2011 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. 65: 3578-89. PMID 22133227 DOI: 10.1111/J.1558-5646.2011.01401.X  0.409
2011 Santana SE, Dial TO, Eiting TP, Alfaro ME. Roosting ecology and the evolution of pelage markings in bats. Plos One. 6: e25845. PMID 21991371 DOI: 10.1371/Journal.Pone.0025845  0.453
2011 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. 65: 1912-26. PMID 21729047 DOI: 10.1111/J.1558-5646.2011.01275.X  0.82
2011 Brock CD, Harmon LJ, Alfaro ME. Testing for temporal variation in diversification rates when sampling is incomplete and nonrandom. Systematic Biology. 60: 410-9. PMID 21378083 DOI: 10.1093/Sysbio/Syr007  0.355
2011 Jaffe AL, Slater GJ, Alfaro ME. The evolution of island gigantism and body size variation in tortoises and turtles. Biology Letters. 7: 558-61. PMID 21270022 DOI: 10.1098/Rsbl.2010.1084  0.337
2011 Huelsenbeck JP, Alfaro ME, Suchard MA. Biologically inspired phylogenetic models strongly outperform the no common mechanism model. Systematic Biology. 60: 225-32. PMID 21252385 DOI: 10.1093/Sysbio/Syq089  0.335
2010 Mehta RS, Ward AB, Alfaro ME, Wainwright PC. Elongation of the body in eels. Integrative and Comparative Biology. 50: 1091-105. PMID 21558261 DOI: 10.1093/Icb/Icq075  0.709
2010 Rabosky DL, Alfaro ME. Evolutionary bangs and whimpers: methodological advances and conceptual frameworks for studying exceptional diversification. Systematic Biology. 59: 615-8. PMID 20947700 DOI: 10.1093/Sysbio/Syq061  0.575
2010 Slater GJ, Price SA, Santini F, Alfaro ME. Diversity versus disparity and the radiation of modern cetaceans. Proceedings. Biological Sciences / the Royal Society. 277: 3097-104. PMID 20484243 DOI: 10.1098/Rspb.2010.0408  0.671
2010 Alfaro M, Santini F. Evolutionary biology: A flourishing of fish forms. Nature. 464: 840-2. PMID 20376139 DOI: 10.1038/464840A  0.383
2009 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. 9: 255. PMID 19849854 DOI: 10.1186/1471-2148-9-255  0.812
2009 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. 9: 194. PMID 19664233 DOI: 10.1186/1471-2148-9-194  0.468
2009 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. 106: 13410-4. PMID 19633192 DOI: 10.1073/Pnas.0811087106  0.83
2009 Waltzek TB, Kelley GO, Alfaro ME, Kurobe T, Davison AJ, Hedrick RP. Phylogenetic relationships in the family Alloherpesviridae. Diseases of Aquatic Organisms. 84: 179-94. PMID 19565695 DOI: 10.3354/Dao02023  0.372
2009 Vincent SE, Brandley MC, Herrel A, Alfaro ME. Convergence in trophic morphology and feeding performance among piscivorous natricine snakes. Journal of Evolutionary Biology. 22: 1203-11. PMID 19389153 DOI: 10.1111/J.1420-9101.2009.01739.X  0.423
2008 Dornburg A, Santini F, Alfaro ME. The influence of model averaging on clade posteriors: an example using the triggerfishes (Family Balistidae). Systematic Biology. 57: 905-19. PMID 19085332 DOI: 10.1080/10635150802562392  0.451
2008 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. 57: 693-707. PMID 18853357 DOI: 10.1080/10635150802426473  0.435
2008 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. 49: 136-52. PMID 18621133 DOI: 10.1016/J.Ympev.2008.06.008  0.668
2008 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. 21: 1438-48. PMID 18547353 DOI: 10.1111/J.1420-9101.2008.01552.X  0.38
2008 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. 46: 576-93. PMID 18182308 DOI: 10.1016/J.Ympev.2007.10.024  0.509
2008 Collar DC, Wainwright PC, Alfaro ME. Integrated diversification of locomotion and feeding in labrid fishes. Biology Letters. 4: 84-6. PMID 18077241 DOI: 10.1098/Rsbl.2007.0509  0.597
2008 O'Meara B, Alfaro M, Bell C, Bolker B, Butler M, Cowan P, Vienne Dd, Desper R, Felsenstein J, Harmon L, Heibl C, Hipp A, Hunt G, Jombart T, Kembel S, et al. Comparative methods in R hackathon Nature Precedings. DOI: 10.1038/Npre.2008.2126.1  0.737
2007 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. 61: 2104-26. PMID 17915358 DOI: 10.1111/J.1558-5646.2007.00182.X  0.53
2007 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. 10: 1075-83. PMID 17850337 DOI: 10.1111/J.1461-0248.2007.01102.X  0.3
2006 Alfaro ME, Holder MT. The posterior and the prior in Bayesian phylogenetics Annual Review of Ecology, Evolution, and Systematics. 37: 19-42. DOI: 10.1146/Annurev.Ecolsys.37.091305.110021  0.317
2005 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. 45: 256-62. PMID 21676769 DOI: 10.1093/Icb/45.2.256  0.789
2005 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 / the Royal Society. 272: 993-1000. PMID 16024356 DOI: 10.1098/Rspb.2004.3013  0.821
2005 Westneat MW, Alfaro ME. Phylogenetic relationships and evolutionary history of the reef fish family Labridae. Molecular Phylogenetics and Evolution. 36: 370-90. PMID 15955516 DOI: 10.1016/J.Ympev.2005.02.001  0.717
2005 Alfaro ME, Bolnick DI, Wainwright PC. Evolutionary consequences of many-to-one mapping of jaw morphology to mechanics in labrid fishes. The American Naturalist. 165: E140-54. PMID 15937739 DOI: 10.1086/429564  0.716
2004 Clements KD, Alfaro ME, Fessler JL, Westneat MW. Relationships of the temperate Australasian labrid fish tribe Odacini (Perciformes; Teleostei). Molecular Phylogenetics and Evolution. 32: 575-87. PMID 15223039 DOI: 10.1016/J.Ympev.2004.02.003  0.726
2004 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. 58: 495-503. PMID 15119434 DOI: 10.1111/J.0014-3820.2004.Tb01673.X  0.737
2004 Alfaro ME, Karns DR, Voris HK, Abernathy E, Sellins SL. Phylogeny of Cerberus (Serpentes: Homalopsinae) and phylogeography of Cerberus rynchops: Diversification of a coastal marine snake in Southeast Asia Journal of Biogeography. 31: 1277-1292. DOI: 10.1111/J.1365-2699.2004.01114.X  0.461
2003 Alfaro ME. Sweeping and striking: a kinematic study of the trunk during prey capture in three thamnophiine snakes. The Journal of Experimental Biology. 206: 2381-92. PMID 12796455 DOI: 10.1242/Jeb.00424  0.343
2003 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. 20: 255-66. PMID 12598693 DOI: 10.1093/Molbev/Msg028  0.314
2002 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. 56: 961-71. PMID 12093031 DOI: 10.1111/J.0014-3820.2002.Tb01408.X  0.72
2002 Voris HK, Alfaro ME, Karns DR, Starnes GL, Thompson E, Murphy JC. Phylogenetic relationships of the Oriental-Australian rear-fanged water snakes (Colubridae: Homalopsinae) based on mitochondrial DNA sequences Copeia. 906-915. DOI: 10.1643/0045-8511(2002)002[0906:Protoa]2.0.Co;2  0.508
2002 Streelman JT, Alfaro M, Westneat MW, Bellwood DR, Karl SA. EVOLUTIONARY HISTORY OF THE PARROTFISHES: BIOGEOGRAPHY, ECOMORPHOLOGY, AND COMPARATIVE DIVERSITY Evolution. 56: 961. DOI: 10.1554/0014-3820(2002)056[0961:EHOTPB]2.0.CO;2  0.328
2001 Alfaro ME, Arnold SJ. Molecular systematics and evolution of Regina and the thamnophiine snakes. Molecular Phylogenetics and Evolution. 21: 408-23. PMID 11741383 DOI: 10.1006/Mpev.2001.1024  0.46
2001 Alfaro ME. Motor control across trophic strategies: Muscle activity of biting and suction feeding fishes American Zoologist. 41: 1266-1279. DOI: 10.1668/0003-1569(2001)041[1266:Mcatsm]2.0.Co;2  0.363
2001 Alfaro ME, Janovetz J, Westneat MW. Motor Control Across Trophic Strategies: Muscle Activity of Biting and Suction Feeding Fishes1 American Zoologist. 41: 1266-1279. DOI: 10.1668/0003-1569(2001)041[1266:MCATSM]2.0.CO;2  0.493
2001 Alfaro ME, Herrel A. Introduction: Major Issues of Feeding Motor Control in Vertebrates1 Integrative and Comparative Biology. 41: 1243-1247. DOI: 10.1668/0003-1569(2001)041[1243:Imiofm]2.0.Co;2  0.342
1999 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. 54: 205-22. PMID 10592383 DOI: 10.1159/000006624  0.607
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