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Francisco J. Ayala

University Professor and Donald Bren Professor of Biological Sciences
School of Biological Sciences

Professor of Philosophy, Philosophy
School of Humanities

Professor of Logic and the Philosophy of Science, Logic & Philosophy of Science
School of Social Sciences

PH.D., Columbia University, 1964

Phone: (949) 824-8293
Fax: (949) 824-2474
Email: fjayala@uci.edu

University of California, Irvine
Department of Ecology & Evolutionary Biology
353 Steinhaus Hall
Mail Code: 2525
Irvine, CA 92697

picture of Francisco J. Ayala

Research
Interests
Evolutionary Genetics
   
URLs "Am I A Monkey" Johns Hopkins University Press catalog
   
"Darwin's Gift to Science and Religion" National Academies Press catalog
   
The Big Questions: Evolution
   
Essential Readings in Evolutionary Biology
   
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, Internacional Menéndez Pelayo-Santander, Las Islas Baleares, Leon, Madrid, Pais Vasco, Salamanca, Valencia, and Vigo (Spain); Ohio State University (USA).
   
Research
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.
   
Publications Books

Cela-Conde, C.J., R. Gutiérrez Lombardo, J.C. Avise, and F.J. Ayala, eds. 2014. In the Light of Evolution Volume VII: The Human Mental Machinery. National Academies Press: Washington, DC. xvi + 378 pp. ISBN-13: 978-0-309-29640-3.

Ayala, F.J. and J.C. Avise, eds. 2014. Essential Readings in Evolutionary Biology. Johns Hopkins University Press, Baltimore. xiii + 547 pp. ISBN-13:978-1-4214-1305-1.

Striedter, G.F., J.C. Avise and F.J. Ayala, eds. 2013. In the Light of Evolution VI: Brain and Behavior. National Acadmies Press: Washington, DC. xvii + 412 pp.

Ayala, F.J. 2012. The Big Questions. Evolution. Quercus Publishing: London. 208 pp.

Strassmann, J.E., D.C. Queller, J.C. Avise, and F.J. Ayala, eds. 2011. In the Light of Evolution. Volume V: Cooperation and Conflict. National Academies Press: Washington, DC. xvi + 449 pp.

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.

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.

Avise, J.C. and F.J. Ayala, eds. 2009. In the Light of Evolution. Volume III: Two Centuries of Darwin. National Academies Press: Washington, DC. xvi + 414 pp.

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.

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. 2006. Darwin and Intelligent Design. Fortress Press: Minneapolis, MN. xi + 116 pp.

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.

Book Chapters

Balakirev, E.S., V.R. Chechetkin, V.V. Lobzin, and F.J. Ayala. 2014. Computational Methods of Identification of Pseudogenes Based on Functionality: Entropy and GC Content. In: Polisneo, L., ed., Pseudogenes: Functions and Protocols, Methods in Molecular Biology, vol. 1167 (Springer Science+Business Media: New York), pp. 41-62. DOI 10.1007/978-1-4939-0835-6_4.

Ayala, F.J. 2014. Human evolution. Whence and whither? In: Thompson, R.P. and D. Walsh, eds., Evolutionary Biology. Conceptual, Ethical, and Religious Issues (Cambridge University Press: Cambridge, UK), pp. 13-28.

Tibayrenc, M. and F.J. Ayala. 2014. New Insights into Clonality and Panmixia in Plasmodium and Toxoplasma. In: Rollinson, D., ed., Advances in Parasitology, Volume 84 (Elsevier Ltd.), pp. 253-268.

Ayala, F.J. 2014. Evolution and Religion. In Losos, J.B., et al., eds., The Princeton Guide to Evolution (Princeton University Press: Princeton and Oxford), pp.817-824.

Ayala, F.J. 2013. Biology and Religion: The Case for Evolution. In: Kampourakis, K., ed., The Philosophy of Biology: A Companion for Educators (Springer Science + Business Media, Dordrecht), pp. 161-177.

Ayala, F.J. 2012. The Design of Organisms. From Paley to Darwin. In: K.R. Monroe, ed., Science, Ethics, and Politics. Conversations and Investigations (Paradigm Publishers: Boulder and London), pp. 14-36.

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.

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.

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.

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.

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.

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.

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.

Journal Articles

Liao, J.-Y., Y.-H. Guo, L.-L. Zheng, Y. Li, W.-L. Xu, Y.-C. Zhang, H. Zhou, Z.-R. Lun, F.J. Ayala, and L.-H. Qu. 2014. Both endo-siRNAs and tRNA-derived small RNAs are involved in the differentiation of primitive eukaryote Giardia lamblia. PNAS 111(39):14159-14164.

Arnaud-Haond, S., Y. Moalic, C. Barnabé, F.J. Ayala, and M. Tibayrenc. 2014. 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 9(8):e103213. August 22, 2014 (doi:10.1371/journal.pone.0103213).

Skyrms, B., J.C. Avise, and F.J. Ayala. 2014. In the light of evolution VIII: Darwinian thinking in the social sciences. PNAS 111(suppl. 3):10781-10784. www.pnas.org/cgi/doi/10.1073/pnas.1411483111

Tomasini, N., J.J. Lauthier, F.J. Ayala, M. Tibayrenc, and P. Diosque. 2014. How Often Do They Have Sex? A Comparative Analysis of the Population Structure of Seven Eukaryotic Microbial Pathogens. PLOS ONE 9(7):e103131.

Séré, M, J. Kaboré, V. Jamonneau, A.M. Gaston Belem, F.J. Ayala, and T. De Meeûs. 2014. Null allele, allelic dropouts or rare sex detection in clonal organisms: simulations and application to real data sets of pathogenic microbes. Parasites & Vectors 7:333. http://www.parasitesandvectors.com/content/7/1/331.

Cela-Conde, C.J. and F.J. Ayala. 2014. Brain keys in the appreciation of beauty: a tale of two worlds. Rendiconti Lincei DOI 10.1007/s12210-014-0299-8. Published online 14 March 2014.

Machin, A., J. Telleria, J-P Brizard, E. Demettre, M. Séveno, F.J. Ayala, and M. Tibayrenc. 2014. Trypanosoma cruzi: Gene Expression Surveyed by Proteomic Analysis Reveals Interaction between Different Genotypes in Mixed In Vitro Cultures.PLoS ONE 9(4):e95442. doi: 10.1371/journal.pone.0095442

Tibayrenc, M. and F.J. Ayala. 2014. Cryptosporidium, Giardia, Cryptococcus, Pneumocystis Genetic Variability: Cryptic Biological Species or Clonal Near-Clades? PLOS Pathogens 10(4): e1003908. doi:10.1371/journal.ppat. 1003908.

Ayala, F.J. 2013. Scientific Literacy and the Teaching of Evolution. Ludus Vitalis XXI (39):231-237.

Telleria, J., C. Barnabé, F.J. Ayala, and M. Tibayrenc. 2013. Phylogenetic character mapping of RADES Probing, a new marker for exploring the clonal evolution of expressed coding sequences in Trypanosoma cruzi, the agent of Chagas disease. Infection, Genetics and Evolution 19:287-291.

Balakirev, E.S., N.S. Romanov, P.B. Mikheev, and F.J. Ayala. 2013. Mitochondrial DNA Variation and Introgression in Siberian Taimen Hucho taimen. PLoS ONE 8(8):e71147.

Tibayrenc, M. and F.J. Ayala. 2013. How clonal are Trypanosoma and Leishmania? Trends in Parasitology 29:264-269.

Cela-Conde, C.J., R. Gutiérrez Lombardo, J.C. Avise, and F.J. Ayala. 2013. In the light of evolution VII: The human mental machinery. Proc. Natl. Acad. Sci. USA 110 (suppl. 2):10339-10342.

Tibayrenc, M. and F.J. Ayala. 2012. Reproductive clonality of pathogens: A perspective on pathogenic viruses, bacteria, fungi, and parasitic protozoa. Proc. Natl. Acad. Sci. USA 109 (48): E3305-E3313. Author Summary, Proc. Natl. Acad. Sci. USA 109 (48): 19523-19524, Proc. Natl. Acad. Sci. USA 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.

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.

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.

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.

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.

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, F.J. 2009. Darwin and the scientific method. Proc. Natl. Acad. Sci. USA 106, suppl. 1:10033-10039.

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.

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.

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.

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. Jirku, 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. Lukeš. 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 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.

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.

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.

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 ß-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.
   
Grant NIHGMS, Marc U*Star at the University of California, Irvine, 2005-2015
   
Professional
Societies
Genetics Society of America
Society for the Study of Evolution
Sigma Xi, The Scientific Research Society
Society for Molecular Biology and Evolution
American Association for the Advancement of Science
   
   
Link to this profile http://www.faculty.uci.edu/profile.cfm?faculty_id=2134
   
Last updated 10/09/2014