picture of Francisco J. Ayala
Name
   Francisco J. Ayala
     
Position
   Professor
  Ecology & Evolutionary Biology
  School of Biological Sciences
 
Position
   Professor
  Philosophy
  School of Humanities
 
Position
   Professor
  Logic & Philosophy of Science
  School of Social Sciences
 
Degree
  DOCTOR OF PHILOSOPHY Columbia University 1964
 
Phone
  (949) 824-8293
 
Phone
  (949) 824-2474
 
email
  fjayala@uci.edu
 
Interests
  Evolutionary Genetics
 
Abstract
  Some recent research of my group has focused on the origin and evolution of introns, and on the evolution and functional significance of (1) pseudogenes and (2) ectopic expression. We have also dedicated considerable effort to gene organization, gene regulation, and the origin, function, and evolution of small RNAs, particularly in parasitic protozoa. We continue research on questions related to the molecular clock of evolution. DNA and protein sequences can be used for reconstructing evolutionary history and timing events of the past. How good is the clock? We are investigating a number of genes and testing new models of rates of gene evolution. Another major research effort focuses on the origin of malaria and other parasitic diseases, such as leishmaniasis, Chagas and sleeping sickness. We have shown that the four species of Plasmodium that cause human malaria diverged many million years ago; they became human parasites independently, by lateral transfer from other hosts. However, the world populations of P. falciparum, the agent of malignant malaria, originated from a single propagule only a few thousand years ago. We have also shown that the world expansion of P. falciparum parasites is very recent, starting in Africa during the Neolithic, a few thousand years ago. Additionally, I am interested in the philosophy of biology and in bioethics, as well as in the relationships between science and religion, including the teaching of evolution in the schools.
 
Academic Distinctions
  Awarded 2001 National Medal Of Science and 2010 Templeton Prize. Member: National Academy of Sciences; American Academy of Arts & Sciences; American Philosophical Society. Foreign Member: Russian Academy of Sciences, Accademia Nazionale dei Lincei, Rome; Royal Academy of Sciences, Spain; Mexican Academy of Sciences; Serbian Academy of Arts and Sciences. Received: Gold Honorary Gregor Mendel Medal, Czech Academy of Sciences; Gold Medal of the Accademia Nazionale dei Lincei; Gold Medal of the Stazione Zoologica, Naples; President's Award of the American Institute of Biological Sciences; Scientific Freedom and Responsibility Award and 150th Anniversary Leadership Medal, AAAS; Medal of the College of France; UCI Medal, University of California; 1998 Distinguished Scientist Award, SACNAS; Sigma Xi's William Procter Prize for Scientific Achievement, 2000; and numerous other prizes and awards. Honorary Degrees: Universidad de Buenos Aires, Universidad Nacional de La Plata (Argentina); Universidad Nacional de Chile (Santiago, Chile); University of Macau (China); Masaryk University, University of South Bohemia (Czech Republic); University of Athens (Greece); Universities of Bologna and Padua (Italy); University of Warsaw (Poland); Far East National University (Vladivostok, Russia); Universities of Barcelona, Las Islas Baleares, Leon, Madrid, Pais Vasco, Salamanca, Valencia, and Vigo (Spain); Ohio State University (USA).
 
Publications
  Escalante, A.A. and F.J. Ayala. 2012. Malaria: Host Range, diversity, and Speciation. In: L.D. Sibley, B.J. Howlett, and J. Heitman, eds., Evolution of Virulence in Eukaryotic Micorbes, First Edition (John Wiley & Sons: Hoboken, NJ), pp. 93-110.
 
 
  Tibayrenc, M. and F.J. Ayala. 2012. Reproductive clonality of pathogens: A perspective on pathogenic viruses, bacteria, fungi, and parasitic protozoa. PNAS 109 (48): E3305-E3313. Author Summary, PNAS 109 (48): 19523-19524, PNAS 10.1073/pnas.1212452109
 
 
  Balakirev, E.S., T.N. Krupnova, and F.J. Ayala. 2012. Symbiotic Associations in the Phenotypically-Diverse Brown Alga Saccharina japonica. PLoS ONE 7(6): e39587. doi:10.1371/journal.pone.0039587.
 
 
  Ayala, F.J. 2012. The Big Questions. Evolution. Quercus Publishing: London. 208 pp.
 
 
  Wen, Y.-Z., L.-L. Zheng, L.-H. Qu, F.J. Ayala, and Z.-R. Lun. 2012. Pseudogenes are not pseudo any more. RNA Biology 9:1-6.
 
 
  Badaraco, J.L., F.J. Ayala, J.-M. Bart, B. Gottstein, and K.L. Haag. 2008. Using mitochondrial and nuclear markers to evaluate the degree of genetic cohesion among Echinococcus populations. Experimental Parasitology 119:453-459.
 
 
  Ayala, F.J. 2009. Molecular Evolution. In: M. Ruse and J. Travis, eds., Evolution. The First Four Billion Years (Belknap Press: Cambridge, MA), pp. 132-151.
 
 
  Ayala, F.J. 2011. Darwin in the Twenty-First Century: Natural Selection, Molecular Biology, and Species Concepts. In: F.J. de Bruijn, ed., Handbook of Molecular Microbial Ecology, Volume II: Metagenomics in Different Habitats (Wiley-Blackwell: Hoboken, NJ), pp. 589-596.
 
 
  Korený, L., R. Sobotka, J. Kovárová, A. Gnipová, P. Flegontov, A. Horváth, M. Oborník, F.J. Ayala, and J. Lukeš. 2012. The aerobic kinetoplastid flagellate Phytomonas does not require heme for viability. Proc. Natl. Acad. Sci. USA 109:3808-3813.
 
 
  Ayala, F.J. 2011. Philosophical Issues in Biology: Reduction and Emergence; Adaptation and Teleology; Contingency and Determinism. An Introduction. In: B. Brozek, J. Maczka, and W.P. Grygiel, eds., Philosophy in Science. Methods and Applications. (Copernícus Center Press: Kraków), pp. 137-161. Tarrío, R. F.J. Ayala, and F. Rodríguez-Trelles. 2011. The Vein Patterning 1 (VEP1) Gene Family Laterally Spread through an Ecological Network. PLoS ONE 6(7): e22279. doi:10.1371/journal.pone.0022279 Balakirev, E.S., M. Anisimova, and F.J. Ayala. 2011. Complex Interplay of Evolutionary Forces in the ladybird Homeobox Genes of Drosophila melanogaster. PLoS ONE 6(7): e22613. doi:10.1371/journal.pone.0022613 Prugnolle, F., B. Ollomo, P. Durand, E. Yalcindag, C. Arnathau, E. Elguero, A. Berry, X. Pourrut, J.-P. Gonzalez, D. Nkoghe, J. Akiana, D. Verrier, E. Leroy, F.J. Ayala, and F. Renaud. 2011. African monkeys are infected by Plasmodium falciparum non-human primate-specific strains. Proc. Natl. Acad. Sci. USA 108:11948-11953. Wen, Y.-Z., L.-L. Zheng, J.-Y. Liao, M.-H. Wang, Y. Wei, X.-M. Guo, L.-H. Qu, F.J. Ayala, and Z.-R. Lun. 2011. Pseudogene-derived small interference RNAs regulate gene expression in African Trypanosoma brucei. Proc. Natl. Acad. Sci. USA 108:8345-8350. Tazi, L. and F.J. Ayala. 2011. Unresolved direction of host transfer of Plasmodium vivax v. P. simium and P. malariae v. P. brasilianum. Infection, Genetics and Evolution 11:209-221. Ayala, F.J. 2011. Elixir of Life: In vino veritas. Proc. Natl. Acad. Sci. USA 108:3457-3458. Lun, Z.-R., D.-H. Lai, F.-J. Li, J. Lukeš, and F.J. Ayala. 2010. Trypanosoma brucei: two steps to spread out from Africa. Trends in Parasitology 26:424-427. Avise, J.C. and F.J. Ayala, eds. 2010. In the Light of Evolution. Volume IV: The Human Condition (National Academies Press: Washington, DC), xvi + 411 pp. Telleria, J., D.G. Biron, J.-P. Brizard, E. Demettre, M. Séveno, C. Barnabé, F.J. Ayala, and M. Tibayrenc. 2010. Phylogenetic character mapping of proteomic diversity shows high correlation with subspecific phylogenetic diversity in Trypanosoma cruzi. Proc. Natl. Acad. Sci. USA 107:20411-20416. Duval, L., M.Fourment, E. Nerrienet, D. Rousset, S.A. Sadeuh Mba, S.M. Goodman, N.V. Andriaholinirina, M. Randrianarivelojosia, R.E. Paul, V. Robert, F.J. Ayala, and F. Ariey. 2010. African apes as reservoirs of Plasmodium falciparum and the origin and diversification of the Laverania subgenus. Proc. Natl. Acad. Sci. USA 107:10561-10566. Ayala, F.J. 2010. The difference of being human: Morality. Proc. Natl. Acad. Sci. USA 107, suppl. 2:9015-9022. Prugnolle, F., P. Durand, C. Neel, B. Ollomo, F.J. Ayala, C. Arnathau, L. Etienne, E. Mpoudi-Ngole, D. Nkoghe, E. Leroy, E. Delaporte, M. Peeters, and F. Renaud. 2010. African great apes are natural hosts of multiple related malaria species, including Plasmodium falciparum. Proc. Natl. Acad. Sci. USA 107:1458-1463.
 
 
  Ayala, F.J. 2010. Am I A Monkey? Six Big Questions about Evolution. Johns Hopkins University Press: Baltimore. xiii + 83 pp.
 
 
  Ayala, F.J. and R. Arp, eds. 2010. Contemporary Debates in Philosophy of Biology. Wiley-Blackwell: Malden, MA. xii + 426 pp.
 
 
  Rich, S.M., F.H. Leendertz, G. Xu, M. LeBreton, C.F. Djoko, M.N. Aminake, E.E. Takang, J.L.D. Diffo, B.L. Pike, B.M. Rosenthal, P. Formenty, C. Boesch, F.J. Ayala, and N.D. Wolf. 2009. The Origin of Malignant Malaria. Proc. Natl. Acad. Sci. USA 106:14902-14907.
 
 
  Rougeron, V., T. De Meeûs, M. Hide, E. Waleckx, H. Bermudez, J. Arevalo, A. Llanos-Cuentas, J.-C. Dujardin, S. De Doncker, D. Le Ray, F.J. Ayala and A.-L.Bañuls. 2009. Extreme inbreeding in Leishmania braziliensis. Proc. Natl. Acad. Sci. USA 106:10224-10229.
 
 
  Ayala, FJ. 2009. Darwin and the scientific method. Proc. Natl. Acad. Sci. USA 106, suppl. 1:10033-10039.
 
 
  Di Fiore, A., T. Disotell, P. Gagneux, and F.J. Ayala. 2009. Primate malarias: evolution, adaptation, and species jumping. In: Huffman, M.A. and C.A. Chapman, eds., Primate Parasite Ecology. The Dynamics and Study of Host-Parasite Relationships (Cambridge University Press: Cambridge), pp. 141-182.
 
 
  Cela-Conde, C.J., F.J. Ayala, E. Munar, F. Maestú, M. Nadal, M.A. Capó, D. del Río, J.J. López-Ibor, T. Ortiz, C. Mirasso, and G. Marty. 2009. Sex-related similarities and differences in the neural correlates of beauty. Proc. Natl. Acad. Sci. USA 106:3847-3852.
 
 
  Ayala, F.J. 2009. Human Nature: One Evolutionist’s View. In: Pennock, R.T. and M. Ruse, eds., But Is It Science? The Philosophical Question in the Creation/Evolution Controversy (Prometheus Books: Amherst, NY), pp. 136-157.
 
 
  Koffia, M., T. De Meeüs, B. Bucheton, P. Solano, M. Camara, D. Kaba, G. Cuny, F.J. Ayala, and V. Jamonneaua. 2009. Population genetics of Trypanosoma brucei gambiense, the agent of sleeping sickness in Western Africa. Proc. Natl. Acad. Sci. USA 106:209-214.
 
 
  Avise, J.C., S.P. Hubbell, and F.J. Ayala, eds. 2008. In the Light of Evolution. Volume II: Biodiversity and Extinction (National Academies Press: Washington, DC), xvii + 414 pp.
 
 
  Balakirev, E.S., V.A. Pavlyuchkovc, and F.J. Ayala. 2008. DNA variation and endosymbiotic associations in phenotypically-diverse sea urchin Strongylocentrotus intermedius. Natl. Acad. Sci. USA 105:16218-16223.
 
 
  Long, S., M. Jirk?, F.J. Ayala, and J. Lukeš. 2008. Mitochondrial localization of human frataxin is necessary but processing is not for rescuing frataxin deficiency in Trypanosoma brucei. Proc. Natl. Acad. Sci. USA 105:13468-13473.
 
 
  Tarrío, R., F.J. Ayala, and F. Rodríguez-Trelles. 2008. Alternative splicing: A missing piece in the puzzle of intron gain. Proc. Natl. Acad. Sci. USA 105:7223-7228.
 
 
  Lai, D.-H., H. Hashimi, Z.-R. Lun, F.J. Ayala, and J. Lukes. 2008. 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. USA 105:1999-2004.
 
 
  Haag, K.L., B. Gottstein, and F.J. Ayala. 2008. Taeniid history, natural selection and antigenic diversity: evolutionary theory meets helminthology. Trends in Parasitology 24:96-102.
 
 
  Ayala, F.J. 2007. Darwin’s Gift to Science and Religion. Joseph Henry Press: Washington, DC, xi + 237 pp.
 
 
  Cela Conde, C.J. and F.J. Ayala. 2007. Human Evolution. Trails from the Past. Oxford University Press: Oxford, UK, vii + 437 pp.
 
 
  Avise, J.C. and F.J. Ayala, eds. 2007. In the Light of Evolution. Volume I: Adaptation and Complex Design (National Academies Press: Washington, DC), xviii + 360 pp.
 
 
  Ayala, F.J. 2007. Darwin’s greatest discovery: Design without designer. Proc. Natl. Acad. Sci. USA 104:8567-8573.
 
 
  Tatarenkov, A. and F.J. Ayala. 2007. Nucleotide variation at the dopa decarboxylase (Ddc) gene in natural populations of Drosophila melanogaster. Journal of Genetics 86: 125-137.
 
 
  Ayala, F.J. 2007. Human Evolution. The Three Grand Challenges of Human Biology. In: D.L. Hull and M. Ruse, eds., The Cambridge Companion to the Philosophy of Biology (Cambridge University Press: New York), pp. 233-254.
 
 
  Annan, Z., P. Durand, F.J. Ayala, C. Arnathau, P. Awono-Ambene, F. Simard, F.G. Razakandrainibe, J.C. Koella, D. Fontenille, and F. Renaud. 2007. Population genetic structure of Plasmodium falciparum in the two main African vectors, Anopheles gambiae and Anopheles funestus. Proc. Natl. Acad. Sci. USA 104: 7987-7992.
 
 
  Ayala, F.J. 2006. Darwin and Intelligent Design. Fortress Press: Minneapolis, MN, xi + 116 pp.
 
 
  Rodríguez-Trelles, F., R. Tarrío and F.J. Ayala. 2006. Models of spliceosomal intron proliferation in the face of widespread ectopic expression. Gene 366:201-208.
 
 
  Nébavi, F., F.J. Ayala, F. Renaud, S. Bertout, S. Eholié, K. Moussa, M. Mallié and T. de Meeüs. 2006. Clonal population structure and genetic diversity of Candida albicans in AIDS patients from Abidjan (Côte d’Ivoire). Proc. Natl. Acad. Sci. USA 103:3663-3668.
 
 
  Rodríguez-Trelles, F., R. Tarrío and F.J. Ayala. 2006. Origins and Evolution of Spliceosomal Introns. Annu. Rev. Genet. 40:47-76.
 
 
  Hey, J., W.M. Fitch and F.J. Ayala, eds. 2005. Systematics and the Origin of Species. On Ernst Mayr’s 100th Anniversary. National Academies Press: Washington, DC. xiii + 367 pp.
 
 
  Wuketits, F.M. and F.J. Ayala, eds. 2005. Handbook of Evolution: The Evolution of Living Systems (Including Hominids), Volume 2. Wiley-VCH: Weinheim, Germany. 292 pp.
 
 
  Lim, C.S., L. Tazi and F.J. Ayala. 2005. Plasmodium vivax: Recent world expansion and genetic identity to Plasmodium simium. Proc. Natl. Acad. Sci. USA 102:15523-15528.
 
 
  Balakirev, E.S., V.R. Chechetkin, V.V. Lobzin, and F. J. Ayala. 2005. Entropy and GC Content in the ?-esterase Gene Cluster of the Drosophila melanogaster Subgroup. Mol. Biol. Evol. 22:2063-2072.
 
 
  Rodríguez-Trelles, F., R. Tarrío, and F. J. Ayala. 2005. Is ectopic expression caused by deregulatory mutations or due to gene-regulation leaks with evolutionary potential? BioEssays 27:592-601.
 
 
  Ayala, F.J. and M. Coluzzi. 2005. Chromosome speciation: Humans, Drosophila, and mosquitoes. Proc. Natl. Acad. Sci. USA 102:6535-6542.
 
Address
  Department of Ecology & Evolutionary Biology
  321 Steinhaus Hall
  Irvine
  CA
  92697
  2525
   
Grant:
  NIHGMS, Marc U*Star at the University of California, Irvine, 2005-2015
 
 
 
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