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Items: 1 to 50 of 88

1.

An inverse latitudinal gradient in speciation rate for marine fishes.

Rabosky DL, Chang J, Title PO, Cowman PF, Sallan L, Friedman M, Kaschner K, Garilao C, Near TJ, Coll M, Alfaro ME.

Nature. 2018 Jul 4. doi: 10.1038/s41586-018-0273-1. [Epub ahead of print]

PMID:
29973726
2.

Resolving the ray-finned fish tree of life.

Alfaro ME.

Proc Natl Acad Sci U S A. 2018 Jun 12;115(24):6107-6109. doi: 10.1073/pnas.1807018115. Epub 2018 May 30. No abstract available.

PMID:
29848635
3.

Filtering nucleotide sites by phylogenetic signal to noise ratio increases confidence in the Neoaves phylogeny generated from ultraconserved elements.

Gilbert PS, Wu J, Simon MW, Sinsheimer JS, Alfaro ME.

Mol Phylogenet Evol. 2018 Sep;126:116-128. doi: 10.1016/j.ympev.2018.03.033. Epub 2018 Apr 4.

PMID:
29626666
4.

A phylogenomic perspective on the robust capuchin monkey (Sapajus) radiation: First evidence for extensive population admixture across South America.

Lima MGM, Silva-Júnior JSE, Černý D, Buckner JC, Aleixo A, Chang J, Zheng J, Alfaro ME, Martins A, Di Fiore A, Boubli JP, Lynch Alfaro JW.

Mol Phylogenet Evol. 2018 Jul;124:137-150. doi: 10.1016/j.ympev.2018.02.023. Epub 2018 Mar 12.

PMID:
29545109
5.

Explosive diversification of marine fishes at the Cretaceous-Palaeogene boundary.

Alfaro ME, Faircloth BC, Harrington RC, Sorenson L, Friedman M, Thacker CE, Oliveros CH, Černý D, Near TJ.

Nat Ecol Evol. 2018 Apr;2(4):688-696. doi: 10.1038/s41559-018-0494-6. Epub 2018 Mar 12.

PMID:
29531346
6.

Phylogenetics and geography of speciation in New World Halichoeres wrasses.

Wainwright PC, Santini F, Bellwood DR, Robertson DR, Rocha LA, Alfaro ME.

Mol Phylogenet Evol. 2018 Apr;121:35-45. doi: 10.1016/j.ympev.2017.12.028. Epub 2017 Dec 28.

PMID:
29289544
7.

Phylogenetic Factor Analysis.

Tolkoff MR, Alfaro ME, Baele G, Lemey P, Suchard MA.

Syst Biol. 2018 May 1;67(3):384-399. doi: 10.1093/sysbio/syx066.

PMID:
28950376
8.

Early-branching euteleost relationships: areas of congruence between concatenation and coalescent model inferences.

Campbell MA, Alfaro ME, Belasco M, López JA.

PeerJ. 2017 Sep 8;5:e3548. doi: 10.7717/peerj.3548. eCollection 2017.

9.

Body shape convergence driven by small size optimum in marine angelfishes.

Frédérich B, Santini F, Konow N, Schnitzler J, Lecchini D, Alfaro ME.

Biol Lett. 2017 Jun;13(6). pii: 20170154. doi: 10.1098/rsbl.2017.0154.

10.

Phylogenomic analysis of Lake Malawi cichlid fishes: Further evidence that the three-stage model of diversification does not fit.

Hulsey CD, Zheng J, Faircloth BC, Meyer A, Alfaro ME.

Mol Phylogenet Evol. 2017 Sep;114:40-48. doi: 10.1016/j.ympev.2017.05.027. Epub 2017 Jun 1.

PMID:
28579077
11.

Phylogenomic analysis of a rapid radiation of misfit fishes (Syngnathiformes) using ultraconserved elements.

Longo SJ, Faircloth BC, Meyer A, Westneat MW, Alfaro ME, Wainwright PC.

Mol Phylogenet Evol. 2017 Aug;113:33-48. doi: 10.1016/j.ympev.2017.05.002. Epub 2017 May 6.

PMID:
28487262
12.

Phylogenomic Systematics of Ostariophysan Fishes: Ultraconserved Elements Support the Surprising Non-Monophyly of Characiformes.

Chakrabarty P, Faircloth BC, Alda F, Ludt WB, Mcmahan CD, Near TJ, Dornburg A, Albert JS, Arroyave J, Stiassny MLJ, Sorenson L, Alfaro ME.

Syst Biol. 2017 Nov 1;66(6):881-895. doi: 10.1093/sysbio/syx038.

PMID:
28334176
13.

Phylogenomic analysis of carangimorph fishes reveals flatfish asymmetry arose in a blink of the evolutionary eye.

Harrington RC, Faircloth BC, Eytan RI, Smith WL, Near TJ, Alfaro ME, Friedman M.

BMC Evol Biol. 2016 Oct 21;16(1):224.

14.

Evolution: Bioluminescent Courtship as an Engine of Diversity.

Alfaro ME.

Curr Biol. 2016 Jul 25;26(14):R667-9. doi: 10.1016/j.cub.2016.05.061.

15.

Dietary breadth is positively correlated with venom complexity in cone snails.

Phuong MA, Mahardika GN, Alfaro ME.

BMC Genomics. 2016 May 26;17:401. doi: 10.1186/s12864-016-2755-6.

16.

Phylogeny and biogeography of hogfishes and allies (Bodianus, Labridae).

Santini F, Sorenson L, Alfaro ME.

Mol Phylogenet Evol. 2016 Jun;99:1-6. doi: 10.1016/j.ympev.2016.02.011. Epub 2016 Mar 2.

PMID:
26944013
17.

Replicated divergence in cichlid radiations mirrors a major vertebrate innovation.

McGee MD, Faircloth BC, Borstein SR, Zheng J, Darrin Hulsey C, Wainwright PC, Alfaro ME.

Proc Biol Sci. 2016 Jan 13;283(1822). pii: 20151413. doi: 10.1098/rspb.2015.1413.

18.

A clinical research pathway towards developing new insights into cardiomyopathy.

Blumstein DT, Buckner J, Shah S, Patel S, Alfaro ME, Natterson-Horowitz B.

Evol Med Public Health. 2015 Sep 28;2015(1):280. doi: 10.1093/emph/eov024. No abstract available.

19.

The evolution of capture myopathy in hooved mammals: a model for human stress cardiomyopathy?

Blumstein DT, Buckner J, Shah S, Patel S, Alfaro ME, Natterson-Horowitz B.

Evol Med Public Health. 2015 Jul 21;2015(1):195-203. doi: 10.1093/emph/eov015.

20.

Genome-wide ultraconserved elements exhibit higher phylogenetic informativeness than traditional gene markers in percomorph fishes.

Gilbert PS, Chang J, Pan C, Sobel EM, Sinsheimer JS, Faircloth BC, Alfaro ME.

Mol Phylogenet Evol. 2015 Nov;92:140-6. doi: 10.1016/j.ympev.2015.05.027. Epub 2015 Jun 12.

21.

Life in the unthinking depths: energetic constraints on encephalization in marine fishes.

Iglesias TL, Dornburg A, Brandley MC, Alfaro ME, Warren DL.

J Evol Biol. 2015 May;28(5):1080-90. doi: 10.1111/jeb.12631. Epub 2015 Apr 22.

22.

Boxfish swimming paradox resolved: forces by the flow of water around the body promote manoeuvrability.

Van Wassenbergh S, van Manen K, Marcroft TA, Alfaro ME, Stamhuis EJ.

J R Soc Interface. 2015 Feb 6;12(103). pii: 20141146. doi: 10.1098/rsif.2014.1146.

23.

Biting disrupts integration to spur skull evolution in eels.

Collar DC, Wainwright PC, Alfaro ME, Revell LJ, Mehta RS.

Nat Commun. 2014 Nov 17;5:5505. doi: 10.1038/ncomms6505.

PMID:
25399532
24.

Biogeography of squirrel monkeys (genus Saimiri): South-central Amazon origin and rapid pan-Amazonian diversification of a lowland primate.

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.

Mol Phylogenet Evol. 2015 Jan;82 Pt B:436-54. doi: 10.1016/j.ympev.2014.09.004. Epub 2014 Oct 8.

25.

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.

Boubli JP, Ribas C, Lynch Alfaro JW, Alfaro ME, da Silva MN, Pinho GM, Farias IP.

Mol Phylogenet Evol. 2015 Jan;82 Pt B:400-12. doi: 10.1016/j.ympev.2014.09.005. Epub 2014 Oct 5.

PMID:
25285613
26.

The effects of ecology and evolutionary history on robust capuchin morphological diversity.

Wright KA, Wright BW, Ford SM, Fragaszy D, Izar P, Norconk M, Masterson T, Hobbs DG, Alfaro ME, Lynch Alfaro JW.

Mol Phylogenet Evol. 2015 Jan;82 Pt B:455-66. doi: 10.1016/j.ympev.2014.08.009. Epub 2014 Sep 4.

PMID:
25194323
27.

Trait decoupling promotes evolutionary diversification of the trophic and acoustic system of damselfishes.

Frédérich B, Olivier D, Litsios G, Alfaro ME, Parmentier E.

Proc Biol Sci. 2014 Aug 22;281(1789):20141047. doi: 10.1098/rspb.2014.1047.

28.

The effect of habitat on modern shark diversification.

Sorenson L, Santini F, Alfaro ME.

J Evol Biol. 2014 Aug;27(8):1536-48. doi: 10.1111/jeb.12405. Epub 2014 May 30.

29.

Biogeography of the marmosets and tamarins (Callitrichidae).

Buckner JC, Lynch Alfaro JW, Rylands AB, Alfaro ME.

Mol Phylogenet Evol. 2015 Jan;82 Pt B:413-25. doi: 10.1016/j.ympev.2014.04.031. Epub 2014 May 20.

PMID:
24857784
30.

Imperfect morphological convergence: variable changes in cranial structures underlie transitions to durophagy in moray eels.

Collar DC, Reece JS, Alfaro ME, Wainwright PC, Mehta RS.

Am Nat. 2014 Jun;183(6):E168-84. doi: 10.1086/675810. Epub 2014 Apr 24.

PMID:
24823828
31.

geiger v2.0: an expanded suite of methods for fitting macroevolutionary models to phylogenetic trees.

Pennell MW, Eastman JM, Slater GJ, Brown JW, Uyeda JC, FitzJohn RG, Alfaro ME, Harmon LJ.

Bioinformatics. 2014 Aug 1;30(15):2216-8. doi: 10.1093/bioinformatics/btu181. Epub 2014 Apr 10.

PMID:
24728855
32.

Adaptive response to sociality and ecology drives the diversification of facial colour patterns in catarrhines.

Santana SE, Alfaro JL, Noonan A, Alfaro ME.

Nat Commun. 2013;4:2765. doi: 10.1038/ncomms3765.

PMID:
24212362
33.

Body fineness ratio as a predictor of maximum prolonged-swimming speed in coral reef fishes.

Walker JA, Alfaro ME, Noble MM, Fulton CJ.

PLoS One. 2013 Oct 18;8(10):e75422. doi: 10.1371/journal.pone.0075422. eCollection 2013.

34.

A multi-locus molecular timescale for the origin and diversification of eels (Order: Anguilliformes).

Santini F, Kong X, Sorenson L, Carnevale G, Mehta RS, Alfaro ME.

Mol Phylogenet Evol. 2013 Dec;69(3):884-94. doi: 10.1016/j.ympev.2013.06.016. Epub 2013 Jul 2.

PMID:
23831455
35.

A Phylogenomic Perspective on the Radiation of Ray-Finned Fishes Based upon Targeted Sequencing of Ultraconserved Elements (UCEs).

Faircloth BC, Sorenson L, Santini F, Alfaro ME.

PLoS One. 2013 Jun 18;8(6):e65923. doi: 10.1371/journal.pone.0065923. Print 2013.

36.

Rates of speciation and morphological evolution are correlated across the largest vertebrate radiation.

Rabosky DL, Santini F, Eastman J, Smith SA, Sidlauskas B, Chang J, Alfaro ME.

Nat Commun. 2013;4:1958. doi: 10.1038/ncomms2958.

PMID:
23739623
37.

A new phylogeny of tetraodontiform fishes (Tetraodontiformes, Acanthomorpha) based on 22 loci.

Santini F, Sorenson L, Alfaro ME.

Mol Phylogenet Evol. 2013 Oct;69(1):177-87. doi: 10.1016/j.ympev.2013.05.014. Epub 2013 May 31.

PMID:
23727595
38.

A new multi-locus timescale reveals the evolutionary basis of diversity patterns in triggerfishes and filefishes (Balistidae, Monacanthidae; Tetraodontiformes).

Santini F, Sorenson L, Alfaro ME.

Mol Phylogenet Evol. 2013 Oct;69(1):165-76. doi: 10.1016/j.ympev.2013.05.015. Epub 2013 May 30.

PMID:
23727054
39.

Phylotastic! Making tree-of-life knowledge accessible, reusable and convenient.

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.

BMC Bioinformatics. 2013 May 13;14:158. doi: 10.1186/1471-2105-14-158.

40.

A multi-locus timetree of surgeonfishes (Acanthuridae, Percomorpha), with revised family taxonomy.

Sorenson L, Santini F, Carnevale G, Alfaro ME.

Mol Phylogenet Evol. 2013 Jul;68(1):150-60. doi: 10.1016/j.ympev.2013.03.014. Epub 2013 Mar 28.

PMID:
23542000
41.

Do habitat shifts drive diversification in teleost fishes? An example from the pufferfishes (Tetraodontidae).

Santini F, Nguyen MT, Sorenson L, Waltzek TB, Lynch Alfaro JW, Eastman JM, Alfaro ME.

J Evol Biol. 2013 May;26(5):1003-18. doi: 10.1111/jeb.12112. Epub 2013 Mar 15.

43.

Iterative ecological radiation and convergence during the evolutionary history of damselfishes (Pomacentridae).

Frédérich B, Sorenson L, Santini F, Slater GJ, Alfaro ME.

Am Nat. 2013 Jan;181(1):94-113. doi: 10.1086/668599. Epub 2012 Dec 3.

PMID:
23234848
44.

Integrating fossils with molecular phylogenies improves inference of trait evolution.

Slater GJ, Harmon LJ, Alfaro ME.

Evolution. 2012 Dec;66(12):3931-44. doi: 10.1111/j.1558-5646.2012.01723.x. Epub 2012 Jul 10.

PMID:
23206147
45.

A multilocus molecular phylogeny of boxfishes (Aracanidae, Ostraciidae; Tetraodontiformes).

Santini F, Sorenson L, Marcroft T, Dornburg A, Alfaro ME.

Mol Phylogenet Evol. 2013 Jan;66(1):153-60. doi: 10.1016/j.ympev.2012.09.022. Epub 2012 Oct 2.

PMID:
23036494
46.

Clade age and species richness are decoupled across the eukaryotic tree of life.

Rabosky DL, Slater GJ, Alfaro ME.

PLoS Biol. 2012 Aug;10(8):e1001381. doi: 10.1371/journal.pbio.1001381. Epub 2012 Aug 28.

47.

Systemic iridovirus from threespine stickleback Gasterosteus aculeatus represents a new megalocytivirus species (family Iridoviridae).

Waltzek TB, Marty GD, Alfaro ME, Bennett WR, Garver KA, Haulena M, Weber ES 3rd, Hedrick RP.

Dis Aquat Organ. 2012 Feb 17;98(1):41-56. doi: 10.3354/dao02415.

PMID:
22422128
48.

Fitting models of continuous trait evolution to incompletely sampled comparative data using approximate Bayesian computation.

Slater GJ, Harmon LJ, Wegmann D, Joyce P, Revell LJ, Alfaro ME.

Evolution. 2012 Mar;66(3):752-762. doi: 10.1111/j.1558-5646.2011.01474.x. Epub 2011 Oct 21.

PMID:
22380438
49.

Cebus phylogenetic relationships: a preliminary reassessment of the diversity of the untufted capuchin monkeys.

Boubli JP, Rylands AB, Farias IP, Alfaro ME, Alfaro JL.

Am J Primatol. 2012 Apr;74(4):381-93. doi: 10.1002/ajp.21998. Epub 2012 Feb 6.

PMID:
22311697
50.

Adaptive evolution of facial colour patterns in Neotropical primates.

Santana SE, Lynch Alfaro J, Alfaro ME.

Proc Biol Sci. 2012 Jun 7;279(1736):2204-11. doi: 10.1098/rspb.2011.2326. Epub 2012 Jan 11.

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