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Ayala, Francisco J.

TitleUniversity Professor and Bren Professor
InstitutionUniversity of California, Irvine
DepartmentEcology & Evolutionary Biology
Address353 Steinhaus Hall
Zot 2525
CA 92697
Phone(949) 824-8293, 8294
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    Collapse Research 
    Collapse Research Activities and Funding
    MARC U*STAR at the University of California, Irvine
    NIH/NIGMS T34GM069337Sep 1, 2003 - May 31, 2020
    Role: Principal Investigator
    MINORITY PREDOCTORAL FELLOWSHIP PROGRAM
    NIH/NIGMS F31GM014846Mar 19, 1992
    Role: Principal Investigator
    EVOLUTIONARY GENETICS OF A MODEL SYSTEM
    NIH/NIGMS P01GM042397Jul 1, 1991 - Jun 30, 1997
    Role: Principal Investigator

    Collapse Bibliographic 
    Collapse Publications
    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.
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    1. An R, Tang Y, Chen L, Cai H, Lai DH, Liu K, Wan L, Gong L, Yu L, Luo Q, Shen J, Lun ZR, Ayala F, Du J. Encephalitis is mediated by ROP18 of Toxoplasma gondii, a severe pathogen in AIDS patients. Proc Natl Acad Sci U S A. 2018 Jun 05; 115(23):E5344-E5352. PMID: 29784816.
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    2. Cela-Conde CJ, Ayala F. Art and brain coevolution. Prog Brain Res. 2018; 237:41-60. PMID: 29779746.
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    3. Puig Giribets M, García Guerreiro MP, Santos M, Ayala F, Tarrío R, Rodríguez-Trelles F. Chromosomal inversions promote genomic islands of concerted evolution of Hsp70 genes in the Drosophila subobscura species subgroup. Mol Ecol. 2018 Feb 07. PMID: 29412486.
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    4. Shen J, Lai DH, Wilson RA, Chen YF, Wang LF, Yu ZL, Li MY, He P, Hide G, Sun X, Yang TB, Wu ZD, Ayala F, Lun ZR. Nitric oxide blocks the development of the human parasite Schistosoma japonicum. Proc Natl Acad Sci U S A. 2017 Sep 19; 114(38):10214-10219. PMID: 28874579.
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    5. Balakirev ES, Saveliev PA, Ayala F. Complete Mitochondrial Genomes of the Cherskii's Sculpin Cottus czerskii and Siberian Taimen Hucho taimen Reveal GenBank Entry Errors: Incorrect Species Identification and Recombinant Mitochondrial Genome. Evol Bioinform Online. 2017; 13:1176934317726783. PMID: 28890653.
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    6. Ayala F, Cela-Conde CJ. Which brain networks related to art perception are we talking about?: Comment on "Move me, astonish me… delight my eyes and brain: The Vienna Integrated Model of top-down and bottom-up processes in Art Perception (VIMAP) and corresponding affective, evaluative, and neurophysiological correlates" by Matthew Pelowski et al. Phys Life Rev. 2017 07; 21:133-134. PMID: 28528962.
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    7. Tibayrenc M, Ayala F. Relevant units of analysis for applied and basic research dealing with neglected transmissible diseases: The predominant clonal evolution model of pathogenic microorganisms. PLoS Negl Trop Dis. 2017 Apr; 11(4):e0005293. PMID: 28448491.
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    8. Qin A, Lai DH, Liu Q, Huang W, Wu YP, Chen X, Yan S, Xia H, Hide G, Lun ZR, Ayala F, Xiang AP. Guanylate-binding protein 1 (GBP1) contributes to the immunity of human mesenchymal stromal cells against Toxoplasma gondii. Proc Natl Acad Sci U S A. 2017 02 07; 114(6):1365-1370. PMID: 28123064.
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    9. Karadjian G, Hassanin A, Saintpierre B, Gembu Tungaluna GC, Ariey F, Ayala F, Landau I, Duval L. Highly rearranged mitochondrial genome in Nycteria parasites (Haemosporidia) from bats. Proc Natl Acad Sci U S A. 2016 08 30; 113(35):9834-9. PMID: 27528689; PMCID: PMC5024609 [Available on 02/28/17].
    10. Avise JC, Bowen BW, Ayala F. In the light of evolution X: Comparative phylogeography. Proc Natl Acad Sci U S A. 2016 07 19; 113(29):7957-61. PMID: 27432955; PMCID: PMC4961136.
    11. Dai J, Wang X, Ayala F. Medical Informatics and the "Three Long, One Short" Problem of Large Urban Hospitals in China. JAMA. 2016 Jul 19; 316(3):269-70. PMID: 27434438.
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    12. Balakirev ES, Anisimova M, Pavlyuchkov VA, Ayala F. DNA polymorphism and selection at the bindin locus in three Strongylocentrotus sp. (Echinoidea). BMC Genet. 2016 05 12; 17(1):66. PMID: 27176219; PMCID: PMC4866015.
    13. Makanga B, Yangari P, Rahola N, Rougeron V, Elguero E, Boundenga L, Moukodoum ND, Okouga AP, Arnathau C, Durand P, Willaume E, Ayala D, Fontenille D, Ayala F, Renaud F, Ollomo B, Prugnolle F, Paupy C. Ape malaria transmission and potential for ape-to-human transfers in Africa. Proc Natl Acad Sci U S A. 2016 May 10; 113(19):5329-34. PMID: 27071123; PMCID: PMC4868493 [Available on 11/10/16].
    14. Zhou Q, Gu J, Lun ZR, Ayala F, Li Z. Two distinct cytokinesis pathways drive trypanosome cell division initiation from opposite cell ends. Proc Natl Acad Sci U S A. 2016 Mar 22; 113(12):3287-92. PMID: 26929336; PMCID: PMC4812729 [Available on 09/22/16].
    15. Balakirev ES, Romanov NS, Ayala F. Complete mitochondrial genome of the Kamchatka grayling Thymallus mertensii (Salmoniformes, Salmonidae). Mitochondrial DNA A DNA Mapp Seq Anal. 2017 01; 28(1):135-136. PMID: 26709442.
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    16. Tibayrenc M, Ayala F. Reproductive clonality in protozoan pathogens--truth or artifact? A comment on Ramírez and Llewellyn. Mol Ecol. 2015 Dec; 24(23):5778-81. PMID: 26607214.
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    17. Balakirev ES, Parensky VA, Kovalev MY, Ayala F. Complete mitochondrial genome of the white char Salvelinus albus (Salmoniformes, Salmonidae). Mitochondrial DNA A DNA Mapp Seq Anal. 2016 09; 27(5):3753-4. PMID: 26358825.
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    18. Tibayrenc M, Ayala F. How clonal are Neisseria species? The epidemic clonality model revisited. Proc Natl Acad Sci U S A. 2015 Jul 21; 112(29):8909-13. PMID: 26195766; PMCID: PMC4517260.
    19. Tibayrenc M, Avise JC, Ayala F. In the light of evolution IX: Clonal reproduction: Alternatives to sex. Proc Natl Acad Sci U S A. 2015 Jul 21; 112(29):8824-6. PMID: 26195755; PMCID: PMC4517246.
    20. Ayala F. Cloning humans? Biological, ethical, and social considerations. Proc Natl Acad Sci U S A. 2015 Jul 21; 112(29):8879-86. PMID: 26195738; PMCID: PMC4517218.
    21. Lun ZR, Lai DH, Wen YZ, Zheng LL, Shen JL, Yang TB, Zhou WL, Qu LH, Hide G, Ayala F. Cancer in the parasitic protozoans Trypanosoma brucei and Toxoplasma gondii. Proc Natl Acad Sci U S A. 2015 Jul 21; 112(29):8835-42. PMID: 26195778; PMCID: PMC4517281.
    22. Tibayrenc M, Ayala F. The population genetics of Trypanosoma cruzi revisited in the light of the predominant clonal evolution model. Acta Trop. 2015 Nov; 151:156-65. PMID: 26188332.
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    23. Tibayrenc M, Ayala F. Response to Rougeron et al.: Leishmania population genetics: clonality, selfing and aneuploidy. Trends Parasitol. 2015 Jul; 31(7):279-80. PMID: 26142921.
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    24. Elguero E, Délicat-Loembet LM, Rougeron V, Arnathau C, Roche B, Becquart P, Gonzalez JP, Nkoghe D, Sica L, Leroy EM, Durand P, Ayala F, Ollomo B, Renaud F, Prugnolle F. Malaria continues to select for sickle cell trait in Central Africa. Proc Natl Acad Sci U S A. 2015 Jun 02; 112(22):7051-4. PMID: 25941403; PMCID: PMC4460506.
    25. Guo HM, Gao JM, Luo YL, Wen YZ, Zhang YL, Hide G, Zhou WL, Ayala F, Lun ZR. Infection by Toxoplasma gondii, a severe parasite in neonates and AIDS patients, causes impaired anion secretion in airway epithelia. Proc Natl Acad Sci U S A. 2015 Apr 07; 112(14):4435-40. PMID: 25831498; PMCID: PMC4394305.
    26. Ayala F. Science, evolution and natural selection: in praise of Darwin at the Stazione Zoologica Anton Dohrn of Naples. Hist Philos Life Sci. 2015; 36(3):444-55. PMID: 26013200.
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    27. Balakirev ES, Parensky VA, Ayala F. Complete mitochondrial genomes of the anadromous and resident forms of the lamprey Lethenteron camtschaticum. Mitochondrial DNA A DNA Mapp Seq Anal. 2016 05; 27(3):1730-1. PMID: 25242184.
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    28. Liao JY, Guo YH, Zheng LL, Li Y, Xu WL, Zhang YC, Zhou H, Lun ZR, Ayala F, Qu LH. Both endo-siRNAs and tRNA-derived small RNAs are involved in the differentiation of primitive eukaryote Giardia lamblia. Proc Natl Acad Sci U S A. 2014 Sep 30; 111(39):14159-64. PMID: 25225396; PMCID: PMC4191773.
    29. Arnaud-Haond S, Moalic Y, Barnabé C, Ayala F, Tibayrenc M. Discriminating micropathogen lineages and their reticulate evolution through graph theory-based network analysis: the case of Trypanosoma cruzi, the agent of Chagas disease. PLoS One. 2014; 9(8):e103213. PMID: 25148574; PMCID: PMC4141739.
    30. Tomasini N, Lauthier JJ, Ayala F, Tibayrenc M, Diosque P. How often do they have sex? A comparative analysis of the population structure of seven eukaryotic microbial pathogens. PLoS One. 2014; 9(7):e103131. PMID: 25054834; PMCID: PMC4108389.
    31. Skyrms B, Avise JC, Ayala F. In the light of evolution VIII: Darwinian thinking in the social sciences. Introduction. Proc Natl Acad Sci U S A. 2014 Jul 22; 111 Suppl 3:10781-4. PMID: 25202765; PMCID: PMC4113919.
    32. Balakirev ES, Romanov NS, Ayala F. Complete mitochondrial genome of Sakhalin taimen Parahucho perryi (Salmoniformes, Salmonidae) without two frame-disrupting indels in the ND4 gene. Mitochondrial DNA A DNA Mapp Seq Anal. 2016; 27(2):1020-1. PMID: 24938084.
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    33. Balakirev ES, Romanov NS, Ayala F. Complete mitochondrial genomes of the Northern (Salvelinus malma) and Southern (Salvelinus curilus) Dolly Varden chars (Salmoniformes, Salmonidae). Mitochondrial DNA A DNA Mapp Seq Anal. 2016; 27(2):1016-7. PMID: 24919504.
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    34. Balakirev ES, Romanov NS, Ayala F. Complete mitochondrial genome of blunt-snouted lenok Brachymystax tumensis (Salmoniformes, Salmonidae). Mitochondrial DNA A DNA Mapp Seq Anal. 2016; 27(2):882-3. PMID: 24865917.
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    35. Balakirev ES, Romanov NS, Mikheev PB, Ayala F. Complete mitochondrial genome of Siberian taimen, Hucho taimen not introgressed by the lenok subspecies, Brachymystax lenok and B. lenok tsinlingensis. Mitochondrial DNA A DNA Mapp Seq Anal. 2016; 27(2):815-6. PMID: 24845441.
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    36. Machin A, Telleria J, Brizard JP, Demettre E, Séveno M, Ayala F, Tibayrenc M. Trypanosoma cruzi: gene expression surveyed by proteomic analysis reveals interaction between different genotypes in mixed in vitro cultures. PLoS One. 2014; 9(4):e95442. PMID: 24748035; PMCID: PMC3991653.
    37. Tibayrenc M, Ayala F. Cryptosporidium,Giardia, Cryptococcus, Pneumocystis genetic variability: cryptic biological species or clonal near-clades? PLoS Pathog. 2014 Apr; 10(4):e1003908. PMID: 24722548; PMCID: PMC3983055.
    38. Yalcindag E, Rougeron V, Elguero E, Arnathau C, Durand P, Brisse S, Diancourt L, Aubouy A, Becquart P, D'Alessandro U, Fontenille D, Gamboa D, Maestre A, Ménard D, Musset L, Noya O, Veron V, Wide A, Carme B, Legrand E, Chevillon C, Ayala F, Renaud F, Prugnolle F. Patterns of selection on Plasmodium falciparum erythrocyte-binding antigens after the colonization of the New World. Mol Ecol. 2014 Apr; 23(8):1979-93. PMID: 24834503.
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    39. Balakirev ES, Chechetkin VR, Lobzin VV, Ayala F. Computational methods of identification of pseudogenes based on functionality: entropy and GC content. Methods Mol Biol. 2014; 1167:41-62. PMID: 24823770.
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    40. Tibayrenc M, Ayala F. New insights into clonality and panmixia in Plasmodium and toxoplasma. Adv Parasitol. 2014; 84:253-68. PMID: 24480316.
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    41. Balakirev ES, Romanov NS, Mikheev PB, Ayala F. Mitochondrial DNA variation and introgression in Siberian taimen Hucho taimen. PLoS One. 2013; 8(8):e71147. PMID: 23951096.
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    42. Cela-Conde CJ, Gutiérrez Lombardo R, Avise JC, Ayala F. In the light of evolution VII: The human mental machinery. Proc Natl Acad Sci U S A. 2013 Jun 18; 110 Suppl 2:10339-42. PMID: 23754413; PMCID: PMC3690619.
    43. Zheng LL, Wen YZ, Yang JH, Liao JY, Shao P, Xu H, Zhou H, Wen JZ, Lun ZR, Ayala F, Qu LH. Comparative transcriptome analysis of small noncoding RNAs in different stages of Trypanosoma brucei. RNA. 2013 Jul; 19(7):863-75. PMID: 23704326; PMCID: PMC3683921.
    44. Prugnolle F, Rougeron V, Becquart P, Berry A, Makanga B, Rahola N, Arnathau C, Ngoubangoye B, Menard S, Willaume E, Ayala F, Fontenille D, Ollomo B, Durand P, Paupy C, Renaud F. Diversity, host switching and evolution of Plasmodium vivax infecting African great apes. Proc Natl Acad Sci U S A. 2013 May 14; 110(20):8123-8. PMID: 23637341; PMCID: PMC3657773.
    45. Tibayrenc M, Ayala F. How clonal are Trypanosoma and Leishmania? Trends Parasitol. 2013 Jun; 29(6):264-9. PMID: 23602631.
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    46. Ayala F. Walter Monroe Fitch (May 21, 1929 - March 10, 2011): a memorial tribute. Infect Genet Evol. 2012 Oct; 12(7):1587-9. PMID: 23087917.
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    47. Tibayrenc M, Ayala F. Reproductive clonality of pathogens: a perspective on pathogenic viruses, bacteria, fungi, and parasitic protozoa. Proc Natl Acad Sci U S A. 2012 Nov 27; 109(48):E3305-13. PMID: 22949662; PMCID: PMC3511763.
    48. Balakirev ES, Krupnova TN, Ayala F. DNA variation in the phenotypically-diverse brown alga Saccharina japonica. BMC Plant Biol. 2012 Jul 11; 12:108. PMID: 22784095; PMCID: PMC3490969.
    49. Striedter GF, Avise JC, Ayala F. In the light of evolution VI: brain and behavior. Proc Natl Acad Sci U S A. 2012 Jun 26; 109 Suppl 1:10607-11. PMID: 22723364; PMCID: PMC3386874.
    50. Balakirev ES, Krupnova TN, Ayala F. Symbiotic associations in the phenotypically-diverse brown alga Saccharina japonica. PLoS One. 2012; 7(6):e39587. PMID: 22745792.
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    51. Li Z, Zhao ZJ, Zhu XQ, Ren QS, Nie FF, Gao JM, Gao XJ, Yang TB, Zhou WL, Shen JL, Wang Y, Lu FL, Chen XG, Hide G, Ayala F, Lun ZR. Differences in iNOS and arginase expression and activity in the macrophages of rats are responsible for the resistance against T. gondii infection. PLoS One. 2012; 7(4):e35834. PMID: 22558235; PMCID: PMC3338469.
    52. Wen YZ, Zheng LL, Qu LH, Ayala F, Lun ZR. Pseudogenes are not pseudo any more. RNA Biol. 2012 Jan; 9(1):27-32. PMID: 22258143.
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    53. Yalcindag E, Elguero E, Arnathau C, Durand P, Akiana J, Anderson TJ, Aubouy A, Balloux F, Besnard P, Bogreau H, Carnevale P, D'Alessandro U, Fontenille D, Gamboa D, Jombart T, Le Mire J, Leroy E, Maestre A, Mayxay M, Ménard D, Musset L, Newton PN, Nkoghé D, Noya O, Ollomo B, Rogier C, Veron V, Wide A, Zakeri S, Carme B, Legrand E, Chevillon C, Ayala F, Renaud F, Prugnolle F. Multiple independent introductions of Plasmodium falciparum in South America. Proc Natl Acad Sci U S A. 2012 Jan 10; 109(2):511-6. PMID: 22203975.
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    54. Hall BG, Ayala F, McClure MA. Remembrances of Walter M. Fitch. Mol Biol Evol. 2011 Dec; 28(12):3405-9. PMID: 22084140.
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    55. Prugnolle F, Durand P, Ollomo B, Ayala F, Renauda F. Reply to Sharp et al.: Host species sampling bias and Plasmodium falciparum origin paradigm shifts. Proc Natl Acad Sci U S A. 2011 Oct 25; 108(43):E873. PMID: 22141155; PMCID: PMC3203807.
    56. Tarrío R, Ayala F, Rodríguez-Trelles F. The Vein Patterning 1 (VEP1) gene family laterally spread through an ecological network. PLoS One. 2011; 6(7):e22279. PMID: 21818306; PMCID: PMC3144213.
    57. Balakirev ES, Anisimova M, Ayala F. Complex interplay of evolutionary forces in the ladybird homeobox genes of Drosophila melanogaster. PLoS One. 2011; 6(7):e22613. PMID: 21799919; PMCID: PMC3142176.
    58. Prugnolle F, Ollomo B, Durand P, Yalcindag E, Arnathau C, Elguero E, Berry A, Pourrut X, Gonzalez JP, Nkoghe D, Akiana J, Verrier D, Leroy E, Ayala F, Renaud F. African monkeys are infected by Plasmodium falciparum nonhuman primate-specific strains. Proc Natl Acad Sci U S A. 2011 Jul 19; 108(29):11948-53. PMID: 21730135; PMCID: PMC3141972.
    59. Strassmann JE, Queller DC, Avise JC, Ayala F. In the light of evolution V: cooperation and conflict. Proc Natl Acad Sci U S A. 2011 Jun 28; 108 Suppl 2:10787-91. PMID: 21690379; PMCID: PMC3131816.
    60. Wen YZ, Zheng LL, Liao JY, Wang MH, Wei Y, Guo XM, Qu LH, Ayala F, Lun ZR. Pseudogene-derived small interference RNAs regulate gene expression in African Trypanosoma brucei. Proc Natl Acad Sci U S A. 2011 May 17; 108(20):8345-50. PMID: 21531904; PMCID: PMC3100955.
    61. Ayala F. Elixir of life: In vino veritas. Proc Natl Acad Sci U S A. 2011 Mar 01; 108(9):3457-8. PMID: 21292988; PMCID: PMC3048131.
    62. Wang Y, Kaneko O, Sattabongkot J, Chen JH, Lu F, Chai JY, Takeo S, Tsuboi T, Ayala F, Chen Y, Lim CS, Han ET. Genetic polymorphism of Plasmodium vivax msp1p, a paralog of merozoite surface protein 1, from worldwide isolates. Am J Trop Med Hyg. 2011 Feb; 84(2):292-7. PMID: 21292901; PMCID: PMC3029184.
    63. Prugnolle F, Ayala F, Ollomo B, Arnathau C, Durand P, Renaud F. Plasmodium falciparum is not as lonely as previously considered. Virulence. 2011 Jan-Feb; 2(1):71-6. PMID: 21224722.
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    64. Telleria J, Biron DG, Brizard JP, Demettre E, Séveno M, Barnabé C, Ayala F, Tibayrenc M. Phylogenetic character mapping of proteomic diversity shows high correlation with subspecific phylogenetic diversity in Trypanosoma cruzi. Proc Natl Acad Sci U S A. 2010 Nov 23; 107(47):20411-6. PMID: 21059959; PMCID: PMC2996636.
    65. Tazi L, Ayala F. Unresolved direction of host transfer of Plasmodium vivax v. P. simium and P. malariae v. P. brasilianum. Infect Genet Evol. 2011 Jan; 11(1):209-21. PMID: 20849978.
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    66. Lun ZR, Lai DH, Li FJ, Lukes J, Ayala F. Trypanosoma brucei: two steps to spread out from Africa. Trends Parasitol. 2010 Sep; 26(9):424-7. PMID: 20561822.
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    67. Duval L, Fourment M, Nerrienet E, Rousset D, Sadeuh SA, Goodman SM, Andriaholinirina NV, Randrianarivelojosia M, Paul RE, Robert V, Ayala F, Ariey F. African apes as reservoirs of Plasmodium falciparum and the origin and diversification of the Laverania subgenus. Proc Natl Acad Sci U S A. 2010 Jun 08; 107(23):10561-6. PMID: 20498054; PMCID: PMC2890828.
    68. Avise JC, Ayala F. Colloquium paper: in the light of evolution IV: the human condition. Proc Natl Acad Sci U S A. 2010 May 11; 107 Suppl 2:8897-901. PMID: 20460311; PMCID: PMC3024015.
    69. Ayala F. Colloquium paper: the difference of being human: morality. Proc Natl Acad Sci U S A. 2010 May 11; 107 Suppl 2:9015-22. PMID: 20445091; PMCID: PMC3024030.
    70. Nam DH, Oh JS, Nam MH, Park HC, Lim CS, Lee WJ, Sattabongkot J, Klein TA, Ayala F. Emergence of new alleles of the MSP-3alpha gene in Plasmodium vivax isolates from Korea. Am J Trop Med Hyg. 2010 Apr; 82(4):522-4. PMID: 20348492; PMCID: PMC2844544.
    71. Prugnolle F, Durand P, Neel C, Ollomo B, Ayala F, Arnathau C, Etienne L, Mpoudi-Ngole E, Nkoghe D, Leroy E, Delaporte E, Peeters M, Renaud F. African great apes are natural hosts of multiple related malaria species, including Plasmodium falciparum. Proc Natl Acad Sci U S A. 2010 Jan 26; 107(4):1458-63. PMID: 20133889; PMCID: PMC2824423.
    72. Ayala F. Darwin's explanation of design: from natural theology to natural selection. Infect Genet Evol. 2010 Aug; 10(6):840-3. PMID: 19800418.
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    73. Rich SM, Leendertz FH, Xu G, LeBreton M, Djoko CF, Aminake MN, Takang EE, Diffo JL, Pike BL, Rosenthal BM, Formenty P, Boesch C, Ayala F, Wolfe ND. The origin of malignant malaria. Proc Natl Acad Sci U S A. 2009 Sep 01; 106(35):14902-7. PMID: 19666593.
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    74. Avise JC, Ayala F. In the light of evolution III: two centuries of Darwin. Proc Natl Acad Sci U S A. 2009 Jun 16; 106 Suppl 1:9933-8. PMID: 19528649; PMCID: PMC2702790.
    75. Ayala F. Darwin and the scientific method. Proc Natl Acad Sci U S A. 2009 Jun 16; 106 Suppl 1:10033-9. PMID: 19528662; PMCID: PMC2702794.
    76. Rougeron V, De Meeûs T, Hide M, Waleckx E, Bermudez H, Arevalo J, Llanos-Cuentas A, Dujardin JC, De Doncker S, Le Ray D, Ayala F, Bañuls AL. Extreme inbreeding in Leishmania braziliensis. Proc Natl Acad Sci U S A. 2009 Jun 23; 106(25):10224-9. PMID: 19497885; PMCID: PMC2700931.
    77. Ayala F. One hundred fifty years without Darwin are enough! Genome Res. 2009 May; 19(5):693-9. PMID: 19411593.
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    78. Haag KL, Gottstein B, Ayala F. The EG95 antigen of Echinococcus spp. contains positively selected amino acids, which may influence host specificity and vaccine efficacy. PLoS One. 2009; 4(4):e5362. PMID: 19401778; PMCID: PMC2671473.
    79. Cela-Conde CJ, Ayala F, Munar E, Maestú F, Nadal M, Capó MA, del Río D, López-Ibor JJ, Ortiz T, Mirasso C, Marty G. Sex-related similarities and differences in the neural correlates of beauty. Proc Natl Acad Sci U S A. 2009 Mar 10; 106(10):3847-52. PMID: 19237562; PMCID: PMC2656168.
    80. Ayala F, Avise JC. Darwin at 200. Proc Natl Acad Sci U S A. 2009 Feb 24; 106(8):2475-6. PMID: 19211793; PMCID: PMC2650285.
    81. Koffi M, De Meeûs T, Bucheton B, Solano P, Camara M, Kaba D, Cuny G, Ayala F, Jamonneau V. Population genetics of Trypanosoma brucei gambiense, the agent of sleeping sickness in Western Africa. Proc Natl Acad Sci U S A. 2009 Jan 06; 106(1):209-14. PMID: 19106297; PMCID: PMC2629214.
    82. Ayala F. Where is Darwin 200 years later? J Genet. 2008 Dec; 87(4):321-5. PMID: 19147921.
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    83. Balakirev ES, Pavlyuchkov VA, Ayala F. DNA variation and symbiotic associations in phenotypically diverse sea urchin Strongylocentrotus intermedius. Proc Natl Acad Sci U S A. 2008 Oct 21; 105(42):16218-23. PMID: 18852450; PMCID: PMC2571021.
    84. Avise JC, Hubbell SP, Ayala F. Colloquium paper: in the light of evolution II: biodiversity and extinction. Proc Natl Acad Sci U S A. 2008 Aug 12; 105 Suppl 1:11453-7. PMID: 18695213; PMCID: PMC2556414.
    85. Tarrío R, Ayala F, Rodríguez-Trelles F. Alternative splicing: a missing piece in the puzzle of intron gain. Proc Natl Acad Sci U S A. 2008 May 20; 105(20):7223-8. PMID: 18463286; PMCID: PMC2438231.
    86. Alcaraz LD, Olmedo G, Bonilla G, Cerritos R, Hernández G, Cruz A, Ramírez E, Putonti C, Jiménez B, Martínez E, López V, Arvizu JL, Ayala F, Razo F, Caballero J, Siefert J, Eguiarte L, Vielle JP, Martínez O, Souza V, Herrera-Estrella A, Herrera-Estrella L. The genome of Bacillus coahuilensis reveals adaptations essential for survival in the relic of an ancient marine environment. Proc Natl Acad Sci U S A. 2008 Apr 15; 105(15):5803-8. PMID: 18408155; PMCID: PMC2311347.
    87. Lai DH, Hashimi H, Lun ZR, Ayala F, Lukes J. Adaptations of Trypanosoma brucei to gradual loss of kinetoplast DNA: Trypanosoma equiperdum and Trypanosoma evansi are petite mutants of T. brucei. Proc Natl Acad Sci U S A. 2008 Feb 12; 105(6):1999-2004. PMID: 18245376; PMCID: PMC2538871.
    88. Haag KL, Gottstein B, Ayala F. Taeniid history, natural selection and antigenic diversity: evolutionary theory meets helminthology. Trends Parasitol. 2008 Feb; 24(2):96-102. PMID: 18182327.
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    89. Ayala F. Science, evolution, and creationism. Proc Natl Acad Sci U S A. 2008 Jan 08; 105(1):3-4. PMID: 18178613; PMCID: PMC2224205.
    90. Cachón V, Barahona A, Ayala F. The rhetorical construction of Eldredge and Gould's article on the theory of punctuated equilibria in 1972. Hist Philos Life Sci. 2008; 30(3-4):317-37. PMID: 19579708.
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    91. Tatarenkov A, Ayala F. Nucleotide variation at the dopa decarboxylase (Ddc) gene in natural populations of Drosophila melanogaster. J Genet. 2007 Aug; 86(2):125-37. PMID: 17968140.
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    92. Lukes J, Mauricio IL, Schönian G, Dujardin JC, Soteriadou K, Dedet JP, Kuhls K, Tintaya KW, Jirku M, Chocholová E, Haralambous C, Pratlong F, Oborník M, Horák A, Ayala F, Miles MA. Evolutionary and geographical history of the Leishmania donovani complex with a revision of current taxonomy. Proc Natl Acad Sci U S A. 2007 May 29; 104(22):9375-80. PMID: 17517634; PMCID: PMC1890502.
    93. Ayala F. Darwin's greatest discovery: design without designer. Proc Natl Acad Sci U S A. 2007 May 15; 104 Suppl 1:8567-73. PMID: 17494753; PMCID: PMC1876431.
    94. Avise JC, Ayala F. From the Academy: Colloquium Perspective: In the light of evolution I: Adaptation and complex design. Proc Natl Acad Sci U S A. 2007 May 15; 104 Suppl 1:8563-6. PMID: 17494742; PMCID: PMC1876430.
    95. Annan Z, Durand P, Ayala F, Arnathau C, Awono-Ambene P, Simard F, Razakandrainibe FG, Koella JC, Fontenille D, Renaud F. Population genetic structure of Plasmodium falciparum in the two main African vectors, Anopheles gambiae and Anopheles funestus. Proc Natl Acad Sci U S A. 2007 May 08; 104(19):7987-92. PMID: 17470800; PMCID: PMC1876559.
    96. Ayala F. The Vatican and evolution. Hist Philos Life Sci. 2007; 29(2):225-9. PMID: 18564513.
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    97. Balakirev ES, Anisimova M, Ayala F. Positive and negative selection in the beta-esterase gene cluster of the Drosophila melanogaster subgroup. J Mol Evol. 2006 Apr; 62(4):496-510. PMID: 16547641.
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    98. Nébavi F, Ayala F, Renaud F, Bertout S, Eholié S, Moussa K, Mallié M, de Meeûs T. Clonal population structure and genetic diversity of Candida albicans in AIDS patients from Abidjan (Côte d'Ivoire). Proc Natl Acad Sci U S A. 2006 Mar 07; 103(10):3663-8. PMID: 16501044; PMCID: PMC1450139.
    99. Ayala F. Evolution vs. creationism. Hist Philos Life Sci. 2006; 28(1):71-82. PMID: 17286042.
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    100. Rodríguez-Trelles F, Tarrío R, Ayala F. Origins and evolution of spliceosomal introns. Annu Rev Genet. 2006; 40:47-76. PMID: 17094737.
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    101. Rodríguez-Trelles F, Tarrío R, Ayala F. Models of spliceosomal intron proliferation in the face of widespread ectopic expression. Gene. 2006 Feb 01; 366(2):201-8. PMID: 16288838.
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    102. Lim CS, Tazi L, Ayala F. Plasmodium vivax: recent world expansion and genetic identity to Plasmodium simium. Proc Natl Acad Sci U S A. 2005 Oct 25; 102(43):15523-8. PMID: 16227436; PMCID: PMC1266129.
    103. Barahona A, Ayala F. Theodosius Dobzhansky's role in the emergence and institutionalization of genetics in Mexico. Genetics. 2005 Jul; 170(3):981-7. PMID: 16076938; PMCID: PMC1451177.
    104. Balakirev ES, Chechetkin VR, Lobzin VV, Ayala F. Entropy and GC Content in the beta-esterase gene cluster of the Drosophila melanogaster subgroup. Mol Biol Evol. 2005 Oct; 22(10):2063-72. PMID: 15972847.
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    105. Rodríguez-Trelles F, Tarrío R, Ayala F. Is ectopic expression caused by deregulatory mutations or due to gene-regulation leaks with evolutionary potential? Bioessays. 2005 Jun; 27(6):592-601. PMID: 15892118.
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    106. Ayala F, Coluzzi M. Chromosome speciation: humans, Drosophila, and mosquitoes. Proc Natl Acad Sci U S A. 2005 May 03; 102 Suppl 1:6535-42. PMID: 15851677; PMCID: PMC1131864.
    107. Hey J, Fitch WM, Ayala F. Systematics and the origin of species: an introduction. Proc Natl Acad Sci U S A. 2005 May 03; 102 Suppl 1:6515-9. PMID: 15851660; PMCID: PMC1131868.
    108. Balakirev ES, Ayala F. The beta-esterase gene cluster of drosophila melanogaster: is psiEst-6 a pseudogene, a functional gene, or both? Genetica. 2004 Jun; 121(2):165-79. PMID: 15330116.
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    109. Balakirev ES, Ayala F. Nucleotide variation in the tinman and bagpipe homeobox genes of Drosophila melanogaster. Genetics. 2004 Apr; 166(4):1845-56. PMID: 15126403; PMCID: PMC1470812.
    110. Balakirev ES, Ayala F. Molecular population genetics of the beta-esterase gene cluster of Drosophila melanogaster. J Genet. 2003 Dec; 82(3):115-31. PMID: 15133190.
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    111. Balakirev ES, Ayala F. Nucleotide variation of the Est-6 gene region in natural populations of Drosophila melanogaster. Genetics. 2003 Dec; 165(4):1901-14. PMID: 14704175; PMCID: PMC1462900.
    112. Rodríguez-Trelles F, Tarrío R, Ayala F. Convergent neofunctionalization by positive Darwinian selection after ancient recurrent duplications of the xanthine dehydrogenase gene. Proc Natl Acad Sci U S A. 2003 Nov 11; 100(23):13413-7. PMID: 14576276; PMCID: PMC263828.
    113. Benton MJ, Ayala F. Dating the tree of life. Science. 2003 Jun 13; 300(5626):1698-700. PMID: 12805535.
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    114. Cela-Conde CJ, Ayala F. Genera of the human lineage. Proc Natl Acad Sci U S A. 2003 Jun 24; 100(13):7684-9. PMID: 12794185; PMCID: PMC164648.
    115. Balakirev ES, Chechetkin VR, Lobzin VV, Ayala F. DNA polymorphism in the beta-Esterase gene cluster of Drosophila melanogaster. Genetics. 2003 Jun; 164(2):533-44. PMID: 12807774; PMCID: PMC1462603.
    116. Tarrio R, Rodríguez-Trelles F, Ayala F. A new Drosophila spliceosomal intron position is common in plants. Proc Natl Acad Sci U S A. 2003 May 27; 100(11):6580-3. PMID: 12750476; PMCID: PMC164489.
    117. Sáez AG, Tatarenkov A, Barrio E, Becerra NH, Ayala F. Patterns of DNA sequence polymorphism at Sod vicinities in Drosophila melanogaster: unraveling the footprint of a recent selective sweep. Proc Natl Acad Sci U S A. 2003 Feb 18; 100(4):1793-8. PMID: 12578968; PMCID: PMC149912.
    118. Balakirev ES, Ayala F. Pseudogenes: are they "junk" or functional DNA? Annu Rev Genet. 2003; 37:123-51. PMID: 14616058.
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    119. Rodríguez-Trelles F, Tarrío R, Ayala F. Evolution of cis-regulatory regions versus codifying regions. Int J Dev Biol. 2003; 47(7-8):665-73. PMID: 14756342.
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    120. Rich SM, Ayala F. Progress in malaria research: the case for phylogenetics. Adv Parasitol. 2003; 54:255-80. PMID: 14711087.
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    121. Arhontaki K, Eliopoulos E, Goulielmos G, Kastanis P, Tsakas S, Loukas M, Ayala F. Functional constraints of the Cu,Zn superoxide dismutase in species of the Drosophila melanogaster subgroup and phylogenetic analysis. J Mol Evol. 2002 Dec; 55(6):745-56. PMID: 12486533.
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    122. Ayala F, Balakirev ES, Sáez AG. Genetic polymorphism at two linked loci, Sod and Est-6, in Drosophila melanogaster. Gene. 2002 Oct 30; 300(1-2):19-29. PMID: 12468082.
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    123. DeFilippis VR, Ayala F, Villarreal LP. Evidence of diversifying selection in human papillomavirus type 16 E6 but not E7 oncogenes. J Mol Evol. 2002 Oct; 55(4):491-9. PMID: 12355268.
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    124. Zurovcová M, Ayala F. Polymorphism patterns in two tightly linked developmental genes, Idgf1 and Idgf3, of Drosophila melanogaster. Genetics. 2002 Sep; 162(1):177-88. PMID: 12242232; PMCID: PMC1462240.
    125. Tibayrenc M, Ayala F. The clonal theory of parasitic protozoa: 12 years on. Trends Parasitol. 2002 Sep; 18(9):405-10. PMID: 12377258.
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    126. Rodriguez-Trelles F, Tarrio R, Ayala F. A methodological bias toward overestimation of molecular evolutionary time scales. Proc Natl Acad Sci U S A. 2002 Jun 11; 99(12):8112-5. PMID: 12060757; PMCID: PMC123029.
    127. Ayala F, Lyons E, Michalakis Y, Tibayrenc M. 2002 Neodarwinism and infectious diseases transmission: an e-debate. Infect Genet Evol. 2002 May; 1(3):249-53. PMID: 12798022.
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    128. Machado CA, Ayala F. Sequence variation in the dihydrofolate reductase-thymidylate synthase (DHFR-TS) and trypanothione reductase (TR) genes of Trypanosoma cruzi. Mol Biochem Parasitol. 2002 Apr 30; 121(1):33-47. PMID: 11985861.
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    129. Balakirev ES, Balakirev EI, Ayala F. Molecular evolution of the Est-6 gene in Drosophila melanogaster: contrasting patterns of DNA variability in adjacent functional regions. Gene. 2002 Apr 17; 288(1-2):167-77. PMID: 12034506.
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    130. Ayala F, Rich SM. Genetic variation and the recent worldwide expansion of Plasmodium falciparum. Gene. 2000 Dec 30; 261(1):161-70. PMID: 11164047.
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    131. Ayala F. Neutralism and selectionism: the molecular clock. Gene. 2000 Dec 30; 261(1):27-33. PMID: 11164034.
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    132. Ayala F, Fitch WM, Clegg MT. Variation and evolution in plants and microorganisms: toward a new synthesis 50 years after Stebbins. Proc Natl Acad Sci U S A. 2000 Jun 20; 97(13):6941-4. PMID: 10860953; PMCID: PMC34366.
    133. Ayala F, Escalante AA, Rich SM. Evolution of Plasmodium and the recent origin of the world populations of Plasmodium falciparum. Parassitologia. 1999 Sep; 41(1-3):55-68. PMID: 10697834.
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    134. Ayala F. Molecular clock mirages. Bioessays. 1999 Jan; 21(1):71-5. PMID: 10070256.
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    135. Pascual M, Serra L, Ayala F. INTERSPECIFIC LABORATORY COMPETITION OF THE RECENTLY SYMPATRIC SPECIES DROSOPHILA SUBOBSCURA AND DROSOPHILA PSEUDOOBSCURA. Evolution. 1998 Feb; 52(1):269-274. PMID: 28568145.
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    136. Rodríguez-Trelles F, Weinberg JR, Ayala F. PRESUMPTIVE RAPID SPECIATION AFTER A FOUNDER EVENT IN A LABORATORY POPULATION OF NEREIS: ALLOZYME ELECTROPHORETIC EVIDENCE DOES NOT SUPPORT THE HYPOTHESIS. Evolution. 1996 Feb; 50(1):457-461. PMID: 28568872.
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    137. Galiana A, Moya A, Ayala F. FOUNDER-FLUSH SPECIATION IN DROSOPHILA PSEUDOOBSCURA: A LARGE-SCALE EXPERIMENT. Evolution. 1993 Apr; 47(2):432-444. PMID: 28568735.
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    138. Chang HY, Ayala F. ON THE ORIGIN OF INCIPIENT REPRODUCTIVE ISOLATION: THE CASE OF DROSOPHILA ALBOMICANS AND D. NASUTA. Evolution. 1989 Dec; 43(8):1610-1624. PMID: 28564329.
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    139. Bierbaum TJ, Mueller LD, Ayala F. DENSITY-DEPENDENT EVOLUTION OF LIFE-HISTORY TRAITS IN DROSOPHILA MELANOGASTER. Evolution. 1989 Mar; 43(2):382-392. PMID: 28568549.
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    140. Tibayrenc M, Ayala F. ISOZYME VARIABILITY IN TRYPANOSOMA CRUZI, THE AGENT OF CHAGAS' DISEASE: GENETICAL, TAXONOMICAL, AND EPIDEMIOLOGICAL SIGNIFICANCE. Evolution. 1988 Mar; 42(2):277-292. PMID: 28567853.
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    141. Bruce EJ, Ayala F. PHYLOGENETIC RELATIONSHIPS BETWEEN MAN AND THE APES: ELECTROPHORETIC EVIDENCE. Evolution. 1979 Dec; 33(4):1040-1056. PMID: 28563920.
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    142. Brittnacher JG, Sims SR, Ayala F. GENETIC DIFFERENTIATION BETWEEN SPECIES OF THE GENUS SPEYERIA (LEPIDOPTERA: NYMPHALIDAE). Evolution. 1978 Mar; 32(1):199-210. PMID: 28564085.
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    143. Marinkovic A, Ayala F, Andjelkovic M. GENETIC POLYMORPHISM AND PHYLOGENY OF DROSOPHILA SUBOBSCURA. Evolution. 1978 Mar; 32(1):164-173. PMID: 28564092.
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    144. Avise JC, Ayala F. GENETIC DIFFERENTIATION IN SPECIOSE VERSUS DEPAUPERATE PHYLADS: EVIDENCE FROM THE CALIFORNIA MINNOWS. Evolution. 1976 Mar; 30(1):46-58. PMID: 28565048.
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    145. Avise JC, Smith JJ, Ayala F. ADAPTIVE DIFFERENTIATION WITH LITTLE GENIC CHANGE BETWEEN TWO NATIVE CALIFORNIA MINNOWS. Evolution. 1975 Sep; 29(3):411-426. PMID: 28563177.
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    146. Ayala F, Valentine JW, Hedgecock D, Barr LG. DEEP-SEA ASTEROIDS: HIGH GENETIC VARIABILITY IN A STABLE ENVIRONMENT. Evolution. 1975 Jun; 29(2):203-212. PMID: 28555845.
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    147. Ayala F, Tracey ML, Hedgecock D, Richmond RC. GENETIC DIFFERENTIATION DURING THE SPECIATION PROCESS IN DROSOPHILA. Evolution. 1974 Dec; 28(4):576-592. PMID: 28564832.
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    148. Ayala F, Tracey ML, Barr LG, Ehrenfeld JG. GENETIC AND REPRODUCTIVE DIFFERENTIATION OF THE SUBSPECIES, DROSOPHILA EQUINOXIALIS CARIBBENSIS. Evolution. 1974 Mar; 28(1):24-41. PMID: 28563025.
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    149. Ayala F, Hedgecock D, Zumwalt GS, Valentine JW. GENETIC VARIATION IN TRIDACNA MAXIMA, AN ECOLOGICAL ANALOG OF SOME UNSUCCESSFUL EVOLUTIONARY LINEAGES. Evolution. 1973 Jun; 27(2):177-191. PMID: 28564772.
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    150. Ayala F. POPULATION FITNESS OF GEOGRAPHIC STRAINS OF DROSOPHILA SERRATA AS MEASURED BY INTERSPECIFIC COMPETITION. Evolution. 1970 Sep; 24(3):483-494. PMID: 28562996.
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    151. Ayala F. EVOLUTION OF FITNESS. II. CORRELATED EFFECTS OF NATURAL SELECTION ON THE PRODUCTIVITY AND SIZE OF EXPERIMENTAL POPULATIONS OF DROSOPHILA SERRATA. Evolution. 1968 Mar; 22(1):55-65. PMID: 28564985.
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