F J Ayala

Summary

Affiliation: University of California
Country: USA

Publications

  1. ncbi request reprint Genetic variation and the recent worldwide expansion of Plasmodium falciparum
    F J Ayala
    Department of Ecology and Evolutionary Biology, University of California, Irvine, CA 92697 2525, USA
    Gene 261:161-70. 2000
  2. pmc Patterns of DNA sequence polymorphism at Sod vicinities in Drosophila melanogaster: unraveling the footprint of a recent selective sweep
    Alberto G Saez
    Department of Ecology and Evolutionary Biology, University of California, Irvine, CA 92697, USA
    Proc Natl Acad Sci U S A 100:1793-8. 2003
  3. ncbi request reprint Models of spliceosomal intron proliferation in the face of widespread ectopic expression
    Francisco Rodriguez-Trelles
    Department of Ecology and Evolutionary Biology, University of California, Irvine, California 92697 2525, USA
    Gene 366:201-8. 2006
  4. pmc DNA variation in the phenotypically-diverse brown alga Saccharina japonica
    Evgeniy S Balakirev
    Department of Ecology and Evolutionary Biology, University of California, Irvine, CA 92697 2525, USA
    BMC Plant Biol 12:108. 2012
  5. ncbi request reprint Molecular clock mirages
    F J Ayala
    Department of Ecology and Evolutionary Biology, University of California, Irvine 92697 2525, USA
    Bioessays 21:71-5. 1999
  6. pmc Darwin and the scientific method
    Francisco J Ayala
    Department of Ecology and Evolutionary Biology, University of California, Irvine, CA 92697, USA
    Proc Natl Acad Sci U S A 106:10033-9. 2009
  7. pmc Colloquium paper: the difference of being human: morality
    Francisco J Ayala
    Department of Ecology and Evolutionary Biology, University of California, Irvine, CA 92697, USA
    Proc Natl Acad Sci U S A 107:9015-22. 2010
  8. ncbi request reprint Neutralism and selectionism: the molecular clock
    F J Ayala
    Department of Ecology and Evolutionary Biology, University of California, Irvine, CA 92697 2525, USA
    Gene 261:27-33. 2000
  9. ncbi request reprint Where is Darwin 200 years later?
    Francisco J Ayala
    Department of Ecology and Evolutionary Biology, University of California, Irvine, CA 92697, USA
    J Genet 87:321-5. 2008
  10. ncbi request reprint Evolution of Plasmodium and the recent origin of the world populations of Plasmodium falciparum
    F J Ayala
    Department of Ecology and Evolutionary Biology, University of California, Irvine 92697 2525, USA
    Parassitologia 41:55-68. 1999

Research Grants

  1. MARC U*STAR at the University of California, Irvine
    Francisco Ayala; Fiscal Year: 2007

Collaborators

Detail Information

Publications86

  1. ncbi request reprint Genetic variation and the recent worldwide expansion of Plasmodium falciparum
    F J Ayala
    Department of Ecology and Evolutionary Biology, University of California, Irvine, CA 92697 2525, USA
    Gene 261:161-70. 2000
    ..We conclude that the antigenic polymorphisms of P. falciparum are consistent with a recent expansion of the world populations of the parasite from a cenancestor that lived in tropical Africa a few thousand years ago...
  2. pmc Patterns of DNA sequence polymorphism at Sod vicinities in Drosophila melanogaster: unraveling the footprint of a recent selective sweep
    Alberto G Saez
    Department of Ecology and Evolutionary Biology, University of California, Irvine, CA 92697, USA
    Proc Natl Acad Sci U S A 100:1793-8. 2003
    ..We estimate that the length of the chromosomal segment impacted by the selective sweep is 41-54 kb, the age of the selective sweep is 2,600-22,000 years, and the selective advantage is 0.020 < s < 0.103...
  3. ncbi request reprint Models of spliceosomal intron proliferation in the face of widespread ectopic expression
    Francisco Rodriguez-Trelles
    Department of Ecology and Evolutionary Biology, University of California, Irvine, California 92697 2525, USA
    Gene 366:201-8. 2006
    ..We conclude with a speculation on a possible interplay between spliceosomal introns and ectopic expression at the origin of multicellularity...
  4. pmc DNA variation in the phenotypically-diverse brown alga Saccharina japonica
    Evgeniy S Balakirev
    Department of Ecology and Evolutionary Biology, University of California, Irvine, CA 92697 2525, USA
    BMC Plant Biol 12:108. 2012
    ..japonica...
  5. ncbi request reprint Molecular clock mirages
    F J Ayala
    Department of Ecology and Evolutionary Biology, University of California, Irvine 92697 2525, USA
    Bioessays 21:71-5. 1999
    ..But it is a time-dependent process, so that accumulation of empirical data often yields an approximate clock, as a consequence of the expected convergence of large numbers...
  6. pmc Darwin and the scientific method
    Francisco J Ayala
    Department of Ecology and Evolutionary Biology, University of California, Irvine, CA 92697, USA
    Proc Natl Acad Sci U S A 106:10033-9. 2009
    ..Darwin advanced hypotheses in multiple fields, including geology, plant morphology and physiology, psychology, and evolution, and subjected them to severe empirical tests...
  7. pmc Colloquium paper: the difference of being human: morality
    Francisco J Ayala
    Department of Ecology and Evolutionary Biology, University of California, Irvine, CA 92697, USA
    Proc Natl Acad Sci U S A 107:9015-22. 2010
    ..That is, morality evolved as an exaptation, not as an adaptation. Moral codes, however, are outcomes of cultural evolution, which accounts for the diversity of cultural norms among populations and for their evolution through time...
  8. ncbi request reprint Neutralism and selectionism: the molecular clock
    F J Ayala
    Department of Ecology and Evolutionary Biology, University of California, Irvine, CA 92697 2525, USA
    Gene 261:27-33. 2000
    ..SOD evolves very fast in Drosophila species and also in mammals, but much more slowly in other animals and still slower when plants and fungi are compared to one another, or to animals...
  9. ncbi request reprint Where is Darwin 200 years later?
    Francisco J Ayala
    Department of Ecology and Evolutionary Biology, University of California, Irvine, CA 92697, USA
    J Genet 87:321-5. 2008
    ..At that point, science came into maturity, because all natural phenomena in the universe, living as well as nonliving, could be investigated scientifically, and explained as matter in motion governed by natural laws...
  10. ncbi request reprint Evolution of Plasmodium and the recent origin of the world populations of Plasmodium falciparum
    F J Ayala
    Department of Ecology and Evolutionary Biology, University of California, Irvine 92697 2525, USA
    Parassitologia 41:55-68. 1999
    ..The extensive polymorphisms observed in the highly repetitive central region of the Csp gene, as well as the apparently very divergent two classes of alleles at the Msa-1 gene, are consistent with this conclusion...
  11. pmc Chromosome speciation: humans, Drosophila, and mosquitoes
    Francisco J Ayala
    Department of Ecology and Evolutionary Biology, University of California, Irvine, 92697, USA
    Proc Natl Acad Sci U S A 102:6535-42. 2005
    ....
  12. pmc Darwin's greatest discovery: design without designer
    Francisco J Ayala
    Department of Ecology and Evolutionary Biology, University of California, 321 Steinhaus Hall, Irvine, CA 92697, USA
    Proc Natl Acad Sci U S A 104:8567-73. 2007
    ..The theory of evolution conveys chance and necessity, randomness and determinism, jointly enmeshed in the stuff of life. This was Darwin's fundamental discovery, that there is a process that is creative, although not conscious...
  13. ncbi request reprint Genetic polymorphism at two linked loci, Sod and Est-6, in Drosophila melanogaster
    Francisco J Ayala
    Department of Ecology and Evolutionary Biology, University of California, 321 Steinhaus Hall, Irvine, CA 92697 2525, USA
    Gene 300:19-29. 2002
    ..Some linkage disequilibrium also exists between the two genes...
  14. ncbi request reprint Shared nucleotide composition biases among species and their impact on phylogenetic reconstructions of the Drosophilidae
    R Tarrio
    Department of Ecology and Evolutionary Biology, University of California at Irvine, 92697 2525, USA
    Mol Biol Evol 18:1464-73. 2001
    ..Our analyses confidently place the Chymomyza genus as an outgroup closer than the genus Scaptodrosophila to the Drosophila genus and conclusively support the monophyly of the Sophophora subgenus...
  15. pmc Molecular evolution of two linked genes, Est-6 and Sod, in Drosophila melanogaster
    E S Balakirev
    Department of Ecology and Evolutionary Biology, University of California, Irvine, California 92697 2525, USA
    Genetics 153:1357-69. 1999
    ..There are traces of statistically significant linkage disequilibrium between the two genes that, we suggest, may have arisen as a consequence of selection favoring one particular sequence at each locus...
  16. ncbi request reprint On the evolution of Dopa decarboxylase (Ddc) and Drosophila systematics
    A Tatarenkov
    Department of Ecology and Evolutionary Biology, 321 Steinhaus Hall, University of California, Irvine, CA 92697 2525, USA
    J Mol Evol 48:445-62. 1999
    ..Molecular evolution is erratic. The rates of nucleotide substitution in 3rd codon position relative to positions 1 + 2 vary from one species lineage to another and from gene to gene...
  17. ncbi request reprint Fluctuating mutation bias and the evolution of base composition in Drosophila
    F Rodriguez-Trelles
    Department of Ecology and Evolutionary Biology, University of California, Irvine 92697 2525, USA
    J Mol Evol 50:1-10. 2000
    ..The shift in mutation bias has affected the extent of the rate variation among sites in Xdh...
  18. pmc Switch in codon bias and increased rates of amino acid substitution in the Drosophila saltans species group
    F Rodriguez-Trelles
    Department of Ecology and Evolutionary Biology, University of California, Irvine, California 92697 2525, USA
    Genetics 153:339-50. 1999
    ..Previous observations suggesting that GC content evolution is very limited in Drosophila may have been distorted due to the restricted number of genes and species (mostly D. melanogaster) investigated...
  19. ncbi request reprint Disparate evolution of paralogous introns in the Xdh gene of Drosophila
    F Rodriguez-Trelles
    Department of Ecology and Evolutionary Biology, 321 Steinhaus Hall, University of California, Irvine, CA 92697 2525, USA
    J Mol Evol 50:123-30. 2000
    ..The observed differences cannot be attributed to selection acting differently at the level of the secondary structure of the pre-mRNA. Rather, they are better accounted for by locally heterogeneous patterns of mutation...
  20. ncbi request reprint Xanthine dehydrogenase (XDH): episodic evolution of a "neutral" protein
    F Rodriguez-Trelles
    Department of Ecology and Evolutionary Biology, 321 Steinhaus Hall, University of California, Irvine, CA 92697 2525, USA
    J Mol Evol 53:485-95. 2001
    ..Spastic evolution of Xdh appears to be related to the particularities of the genomes in which the locus is embedded...
  21. pmc Erratic overdispersion of three molecular clocks: GPDH, SOD, and XDH
    F Rodriguez-Trelles
    Department of Ecology and Evolutionary Biology, University of California, Irvine, CA 92697 2525, USA
    Proc Natl Acad Sci U S A 98:11405-10. 2001
    ..The observations are inconsistent with the predictions made by various subsidiary hypotheses proposed to account for the overdispersion of the molecular clock...
  22. ncbi request reprint Erratic evolution of glycerol-3-phosphate dehydrogenase in Drosophila, Chymomyza, and Ceratitis
    J Kwiatowski
    Department of Ecology and Evolutionary Biology, University of California, Irvine, CA 92717 2525, USA
    J Mol Evol 44:9-22. 1997
    ..At the nucleotide level, however, Gpdh evolves in a fairly clockwise fashion...
  23. pmc DNA polymorphism in the beta-Esterase gene cluster of Drosophila melanogaster
    Evgeniy S Balakirev
    Department of Ecology and Evolutionary Biology, University of California, Irvine 92697 2525, USA
    Genetics 164:533-44. 2003
    ..Brosius and S. J. Gould, we suggest that the term "potogene" may be appropriate for psiEst-6, indicating that it is a potential gene that may have acquired some distinctive but unknown function...
  24. ncbi request reprint The effect of superoxide dismutase alleles on aging in Drosophila
    R H Tyler
    Department of Ecology and Evolutionary Biology, University of California, Irvine 92717
    Genetica 91:143-9. 1993
    ..To detect the effects of SOD genotypes on longevity with high probability would require a ten-fold increase in the number of families used...
  25. ncbi request reprint Evidence for a high ancestral GC content in Drosophila
    F Rodriguez-Trelles
    Department of Ecology and Evolutionary Biology, University of California at Irvine, Irvine, CA 92697 2525, USA
    Mol Biol Evol 17:1710-7. 2000
    ..The analysis of eight nuclear genes unambiguously corroborates that the common ancestor of Sophophora had an elevated GC content...
  26. ncbi request reprint Phylogeny of Drosophila and related genera inferred from the nucleotide sequence of the Cu,Zn Sod gene
    J Kwiatowski
    Department of Ecology and Evolutionary Biology, University of California, Irvine 92717
    J Mol Evol 38:443-54. 1994
    ..The Sod results manifest how, in addition to the information derived from nucleotide sequences, structural features (i.e., the deletion of an intron) can help resolve phylogenetic issues...
  27. pmc Evidence for positive selection in the superoxide dismutase (Sod) region of Drosophila melanogaster
    R R Hudson
    Department of Ecology and Evolutionary Biology, University of California, Irvine 92717
    Genetics 136:1329-40. 1994
    ..We suggest that the high frequency of some haplotypes is due to natural selection at the Sod locus or at a tightly linked locus...
  28. ncbi request reprint Molecular evolution of the Est-6 gene in Drosophila melanogaster: contrasting patterns of DNA variability in adjacent functional regions
    Evgeniy S Balakirev
    Department of Ecology and Evolutionary Biology, 321 Steinhaus Hall, University of California, Irvine 92697 2525, USA
    Gene 288:167-77. 2002
    ..The previously reported Est-6 allozyme latitudinal clines may be accounted for by the interaction between selective processes in the promoter and coding regions...
  29. ncbi request reprint A compact gene cluster in Drosophila: the unrelated Cs gene is compressed between duplicated amd and Ddc
    A Tatarenkov
    Department of Ecology and Evolutionary Biology, University of California, Irvine, CA 92697 2525, USA
    Gene 231:111-20. 1999
    ..melanogaster. The function of Cs remains to be identified, but a high degree of similarity indicates that it is homologous to genes coding for a corticosteroid-binding protein in yeast and a polyamine oxidase in maize...
  30. ncbi request reprint Characterization of a Cu/Zn superoxide dismutase-encoding gene region in Drosophila willistoni
    J Kwiatowski
    Department of Ecology and Evolutionary Biology, University of California, Irvine 92717
    Gene 147:295-6. 1994
    ..The polyadenylation signals of the two genes are separated by only 61 bp in D. willistoni, conforming to the common picture of compact dipteran genomes...
  31. pmc Molecular clock or erratic evolution? A tale of two genes
    F J Ayala
    Department of Ecology and Evolutionary Biology, University of California, Irvine 92697, USA
    Proc Natl Acad Sci U S A 93:11729-34. 1996
    ..However, we know of no model consistent with the molecular clock hypothesis that would account for the increase in the rate of GPDH evolution as the divergence between species increases...
  32. pmc Multiple paternity in two natural populations (orchard and vineyard) of Drosophila
    M D Ochando
    Department of Ecology and Evolutionary Biology, University of California, Irvine 92697 2525, USA
    Proc Natl Acad Sci U S A 93:11769-73. 1996
    ..Population density had been thought to be an important determinant of CMP incidence. We have used four gene loci coding for enzymes as independent markers for detecting CMP...
  33. pmc New Drosophila introns originate by duplication
    R Tarrio
    Department of Ecology and Evolutionary Biology, University of California, Irvine, CA 92697 2525, USA
    Proc Natl Acad Sci U S A 95:1658-62. 1998
    ....
  34. ncbi request reprint Evolution of the Drosophila obscura species group inferred from the Gpdh and Sod genes
    E Barrio
    Department of Ecology and Evolutionary Biology, University of California, Irvine 92717, USA
    Mol Phylogenet Evol 7:79-93. 1997
    ..A second radiation occurred during the colonization of the deciduous forests of the New World by the descendants of a single lineage that soon split into the affinis and pseudoobscura subgroups...
  35. ncbi request reprint Tree rooting with outgroups when they differ in their nucleotide composition from the ingroup: the Drosophila saltans and willistoni groups, a case study
    R Tarrio
    Department of Ecology and Evolutionary Biology, University of California, Irvine, California 92697 2525, USA
    Mol Phylogenet Evol 16:344-9. 2000
    ....
  36. pmc DNA variation at the Sod locus of Drosophila melanogaster: an unfolding story of natural selection
    R R Hudson
    Department of Ecology and Evolutionary Biology, University of California, Irvine, CA 92697, USA
    Proc Natl Acad Sci U S A 94:7725-9. 1997
    ..01) and that the sweep occurred more than 25,000 generations ago. In addition, there are striking similarities to patterns of variation observed at the Est6 and Est-P loci, which are located approximately 1,000 kb from Sod...
  37. pmc Nucleotide variation of the Est-6 gene region in natural populations of Drosophila melanogaster
    Evgeniy S Balakirev
    Department of Ecology and Evolutionary Biology, University of California, Irvine, California 92697 2525, USA
    Genetics 165:1901-14. 2003
    ..melanogaster, creates an excess of very similar sequences (RsaI- and S allelic lineages, in the promoter and coding regions, respectively) in the non-African samples...
  38. pmc Vagaries of the molecular clock
    F J Ayala
    Department of Ecology and Evolutionary Biology, University of California, Irvine, CA 92697 2525, USA
    Proc Natl Acad Sci U S A 94:7776-83. 1997
    ..At the other extreme, SOD yields divergence times of 211 My and 224 My for the animal phyla and the kingdoms, respectively. It remains unsettled how often proteins evolve in such erratic fashion as GPDH and SOD...
  39. ncbi request reprint The beta-esterase gene cluster of drosophila melanogaster: is psiEst-6 a pseudogene, a functional gene, or both?
    Evgeniy S Balakirev
    Department of Ecology and Evolutionary Biology, University of California, Irvine, CA 92697 2525, USA
    Genetica 121:165-79. 2004
    ..The Est-6 gene cluster of D. melanogaster represents an example of a functionally interacting complex ('intergene') in which two components (Est-6 and psiEst-6) or more are required to perform the final function...
  40. ncbi request reprint Evolution vs. creationism
    Francisco J Ayala
    Department of Ecology and Evolutionary Biology, University of California, Irvine, CA 92697, USA
    Hist Philos Life Sci 28:71-82. 2006
  41. pmc Drosophila virilis Cu-Zn superoxide dismutase gene sequence
    J Kwiatowski
    Department of Ecology and Evolutionary Biology, University of California, Irvine 92717
    Nucleic Acids Res 17:2133. 1989
  42. pmc Drosophila simulans Cu-Zn superoxide dismutase gene sequence
    J Kwiatowski
    Department of Ecology and Evolutionary Biology, University of California, Irvine 92717
    Nucleic Acids Res 17:6735. 1989
  43. pmc Drosophila melanogaster Cu, Zn superoxide dismutase gene sequence
    J Kwiatowski
    Department of Ecology and Evolutionary Biology, University of California, Irvine 92717
    Nucleic Acids Res 17:1264. 1989
  44. pmc Evolutionary changes in the expression pattern of a developmentally essential gene in three Drosophila species
    D Wang
    Developmental Biology Center, University of California, Irvine, CA 92717, USA
    Proc Natl Acad Sci U S A 93:7103-7. 1996
    ..The "sudden" appearance of a completely new and robust domain of expression provides a glimpse of evolutionary variation resulting from changes in regulation of structural gene expression...
  45. ncbi request reprint Complex evolution of orthologous and paralogous decarboxylase genes
    L E Sáenz-de-Miera
    Department of Ecology and Evolutionary Biology, University of California, Irvine, CA, USA
    J Evol Biol 17:55-66. 2004
    ..62 in dipteran Ddc vs. 4.13 in mammalian Ddc; and very large temporal variations in some lineages, from 3.7 up to 54.9 in the Drosophila Ddc lineage. Our results are inconsistent with the molecular clock hypothesis...
  46. pmc Nucleotide variation in the tinman and bagpipe homeobox genes of Drosophila melanogaster
    Evgeniy S Balakirev
    Department of Ecology and Evolutionary Biology, University of California, Irvine, California 92697 2525, USA
    Genetics 166:1845-56. 2004
    ..We suggest that negative selection and demographic history are the major factors shaping the pattern of nucleotide polymorphism in the tin and bap genes; moreover, there are clear indications of positive selection in the bap gene...
  47. pmc Two modes of balancing selection in Drosophila melanogaster: overcompensation and overdominance
    T X Peng
    Department of Ecology and Evolutionary Biology, University of California, Irvine 92717
    Genetics 128:381-91. 1991
    ..Moreover, our results indicate that the significance of overcompensation as a mechanism to account for polymorphism in natural populations deserves further investigation...
  48. ncbi request reprint Fertility and viability at the Sod locus in Drosophila melanogaster: non-additive and asymmetric selection
    M Milosevic
    Department of Ecology and Evolutionary Biology, University of California, Irvine 92717
    Genet Res 57:267-72. 1991
    ..Selection at the Sod locus yields stable polymorphic equilibria, with the frequency of the F allele predicted at P = 0.641 or 0.695, respectively for low and high larval density...
  49. pmc Is esterase-P encoded by a cryptic pseudogene in Drosophila melanogaster?
    E S Balakirev
    Department of Ecology and Evolutionary Biology, University of California, Irvine 92697 2525, USA
    Genetics 144:1511-8. 1996
    ..We also conjecture that the rarity of detected pseudogenes in Drosophila may be due to the difficulty of discovering them, because most of them are cryptic...
  50. ncbi request reprint A truncated P element is inserted in the transcribed region of the Cu,Zn SOD gene of an SOD "null" strain of Drosophila melanogaster
    J Kwiatowski
    Department of Ecology and Evolutionary Biology, University of California, Irvine 92717
    Free Radic Res Commun 12:429-35. 1991
    ..The diminished expression of SODCA1 allele is most possibly due to a reduction of the rate of transcription attributable to the insertion of the P element...
  51. ncbi request reprint Molecular population genetics of the beta-esterase gene cluster of Drosophila melanogaster
    Evgeniy S Balakirev
    Department of Ecology and Evolutionary Biology, University of California, Irvine, CA 92697 2525, USA
    J Genet 82:115-31. 2003
    ..Est-6 and psiEst-6 may represent an indivisible intergenic complex ('intergene') in which each single component (Est-6 or psiEst-6) cannot separately carry out the full functional role...
  52. ncbi request reprint Positive and negative selection in the beta-esterase gene cluster of the Drosophila melanogaster subgroup
    Evgeniy S Balakirev
    Department of Ecology and Evolutionary Biology, University of California, 321 Steinhaus Hall, Irvine, CA 92697 2525, USA
    J Mol Evol 62:496-510. 2006
    ....
  53. ncbi request reprint Nucleotide variation at the dopa decarboxylase (Ddc) gene in natural populations of Drosophila melanogaster
    Andrey Tatarenkov
    Department of Ecology and Evolutionary Biology, University of California, Irvine, CA 92697 2525, USA
    J Genet 86:125-37. 2007
    ..Altogether, the Ddc locus exhibits a complicated pattern of variation apparently due to several evolutionary forces. Such a complex pattern may be a result of an unusually high density of functionally important genes...
  54. pmc Polymorphism patterns in two tightly linked developmental genes, Idgf1 and Idgf3, of Drosophila melanogaster
    Martina Zurovcová
    Department of Ecology and Evolutionary Biology, University of California, Irvine, California 92697 2525, USA
    Genetics 162:177-88. 2002
    ..The rate of recombination between the two loci is high enough to uncouple any linkage disequilibrium arising between Idgf1 and Idgf3, despite their close physical proximity...
  55. pmc The superoxide dismutase molecular clock revisited
    W M Fitch
    Department of Ecology and Evolutionary Biology, University of California, Irvine 92717
    Proc Natl Acad Sci U S A 91:6802-7. 1994
    ....
  56. ncbi request reprint Pseudogenes: are they "junk" or functional DNA?
    Evgeniy S Balakirev
    Department of Ecology and Evolutionary Biology, University of California, Irvine, California 92697 2525, USA
    Annu Rev Genet 37:123-51. 2003
    ..We agree with the proposal that pseudogenes be considered as potogenes, i.e., DNA sequences with a potentiality for becoming new genes...
  57. pmc Nucleotide sequences provide evidence of genetic exchange among distantly related lineages of Trypanosoma cruzi
    C A Machado
    Department of Ecology and Evolutionary Biology, University of California, Irvine, CA 92697, USA
    Proc Natl Acad Sci U S A 98:7396-401. 2001
    ..We estimate that the major extant lineages of T. cruzi have diverged during the Miocene or early Pliocene (3-16 million years ago)...
  58. pmc From the Academy: Colloquium Perspective: In the light of evolution I: Adaptation and complex design
    John C Avise
    Department of Ecology and Evolutionary Biology, University of California, Irvine, CA 92697
    Proc Natl Acad Sci U S A 104:8563-6. 2007
  59. ncbi request reprint Entropy and GC Content in the beta-esterase gene cluster of the Drosophila melanogaster subgroup
    Evgeniy S Balakirev
    Department of Ecology and Evolutionary Biology, University of California, Irvine, CA, USA
    Mol Biol Evol 22:2063-72. 2005
    ..The observed differences in entropy and GC content reflect an evolutionary shift associated with the process of pseudogenization and subsequent functional divergence of psiEst-6 and Est-6 after the duplication event...
  60. pmc DNA variation and symbiotic associations in phenotypically diverse sea urchin Strongylocentrotus intermedius
    Evgeniy S Balakirev
    Department of Ecology and Evolutionary Biology, University of California, Irvine, CA 92697 2525, USA
    Proc Natl Acad Sci U S A 105:16218-23. 2008
    ..We also propose that the symbiotic bacteria likely play an important role in the evolution of morphological divergence of S. intermedius...
  61. ncbi request reprint Sequence variation in the dihydrofolate reductase-thymidylate synthase (DHFR-TS) and trypanothione reductase (TR) genes of Trypanosoma cruzi
    Carlos A Machado
    Department of Ecology and Evolutionary Biology, University of California, Irvine, CA 92697 2525, USA
    Mol Biochem Parasitol 121:33-47. 2002
    ..cruzi. However, one nearly significant reduction of variation in the TR sequences from one sequence group suggests a recent selective event at, or close to, that locus...
  62. ncbi request reprint Origins and evolution of spliceosomal introns
    Francisco Rodriguez-Trelles
    Department of Ecology and Evolutionary Biology, University of California, Irvine, California 92697 2525, USA
    Annu Rev Genet 40:47-76. 2006
    ..quot; Here we review seminal and recent ideas about intron origins. Recent discoveries about the patterns and causes of intron evolution make this one of the most hotly debated and exciting topics in molecular evolutionary biology today...
  63. pmc Colloquium paper: in the light of evolution II: biodiversity and extinction
    John C Avise
    Department of Ecology and Evolutionary Biology, University of California, Irvine, CA 92697, USA
    Proc Natl Acad Sci U S A 105:11453-7. 2008
  64. ncbi request reprint Is ectopic expression caused by deregulatory mutations or due to gene-regulation leaks with evolutionary potential?
    Francisco Rodriguez-Trelles
    Department of Ecology and Evolutionary Biology, University of California, Irvine, CA 92697 2525, USA
    Bioessays 27:592-601. 2005
    ..It seems likely that ectopic expression represents a leak in the evolution of regulatory systems, but one that is endowed with considerable evolutionary possibilities...
  65. ncbi request reprint Evolution of cis-regulatory regions versus codifying regions
    Francisco Rodriguez-Trelles
    Department of Ecology and Evolutionary Biology, University of California, Irvine, California 92697 2525, USA
    Int J Dev Biol 47:665-73. 2003
    ..We bring into this emerging scenario several recent findings pointing to different ways in which spliceosomal introns, pseudogenes and patterns of point mutation can be active players for the evolution of novel transcriptional profiles...
  66. pmc Convergent neofunctionalization by positive Darwinian selection after ancient recurrent duplications of the xanthine dehydrogenase gene
    Francisco Rodriguez-Trelles
    Department of Ecology and Evolutionary Biology, University of California, Irvine, CA 92697 2525, USA
    Proc Natl Acad Sci U S A 100:13413-7. 2003
    ..Caution is appropriate in structural genomics when using sequence similarity for assigning protein function...
  67. ncbi request reprint The Vatican and evolution
    Francisco J Ayala
    Department of Ecology and Evolutionary Biology, University of California, Irvine, CA 92697, USA
    Hist Philos Life Sci 29:225-9. 2007
  68. ncbi request reprint 2002 Neodarwinism and infectious diseases transmission: an e-debate
    Francisco J Ayala
    Department of Ecology and Evolutionary Biology, University of California, Irvine, CA 92697, USA
    Infect Genet Evol 1:249-53. 2002
  69. ncbi request reprint Evidence of diversifying selection in human papillomavirus type 16 E6 but not E7 oncogenes
    Victor R DeFilippis
    Department of Ecology and Evolutionary Biology, University of California Irvine, Irvine, CA 92697, USA
    J Mol Evol 55:491-9. 2002
    ..The amino acid compositions and locations of selected sites are described. Possible sources of natural selection including antiviral immune pressure and polymorphism of host cellular proteins are discussed...
  70. pmc A new Drosophila spliceosomal intron position is common in plants
    Rosa Tarrio
    Department of Ecology and Evolutionary Biology, University of California, Irvine 92697 2525, USA
    Proc Natl Acad Sci U S A 100:6580-3. 2003
    ..If the observed phylogenetic pattern had resulted from recurrent loss, all observational support previously gathered for the introns-late theory of intron origins based on the phylogenetic distribution of introns would be invalidated...
  71. pmc Plasmodium vivax: recent world expansion and genetic identity to Plasmodium simium
    Chae Seung Lim
    Department of Ecology and Evolutionary Biology, University of California, Irvine, CA 92697, USA
    Proc Natl Acad Sci U S A 102:15523-8. 2005
    ..There are reasons favoring each of the two possible directions of host transfer between humans and monkeys...
  72. pmc A methodological bias toward overestimation of molecular evolutionary time scales
    Francisco Rodriguez-Trelles
    Department of Ecology and Evolutionary Biology, 321 Steinhaus Hall, University of California, Irvine, CA 92697 2525, USA
    Proc Natl Acad Sci U S A 99:8112-5. 2002
    ..This introduces a bias toward an overestimation of time since divergence, which becomes greater as the length of the molecular sequence and the rate of evolution decrease...
  73. ncbi request reprint Dating the tree of life
    Michael J Benton
    Department of Earth Sciences, University of Bristol, Bristol BS8 1RJ, UK
    Science 300:1698-700. 2003
    ..Intense study of the dating of major splits in the tree of mammals has shown rapprochement as fossil dates become older and molecular dates become younger...
  74. ncbi request reprint Progress in malaria research: the case for phylogenetics
    Stephen M Rich
    Division of Infectious Disease, Tufts University School of Veterinary Medicine, 200 Westboro Road, North Grafton, MA 01536, USA
    Adv Parasitol 54:255-80. 2003
    ..Lastly, we present a detailed account of our current understanding of the evolutionary past of the most deadly of the human malaria species--P. falciparum...
  75. pmc Theodosius Dobzhansky's role in the emergence and institutionalization of genetics in Mexico
    Ana Barahona
    Departamento de Biologia Evolutiva, Facultad de Ciencias, UNAM, Coyoacan 04510, Mexico
    Genetics 170:981-7. 2005
  76. pmc Population genetic structure of Plasmodium falciparum in the two main African vectors, Anopheles gambiae and Anopheles funestus
    Zeinab Annan
    Génétique et Evolution des Maladies Infectieuses, Unité Mixte de Recherche Institut de Recherche pour le Développement Centre National de la Recherche Scientifique 2724, B P 64501, 34394 Montpellier Cedex 5, France
    Proc Natl Acad Sci U S A 104:7987-92. 2007
    ....
  77. ncbi request reprint The emergence and development of genetics in Mexico
    Ana Barahona
    Departamento de Biologia Evolutiva, Facultad de Ciencias, UNAM, Zapata 6 9, Col Miguel Hidalgo, Tlalpan 14410, Mexico
    Nat Rev Genet 6:860-6. 2005
    ....
  78. pmc Clonal population structure and genetic diversity of Candida albicans in AIDS patients from Abidjan (Côte d'Ivoire)
    François Nébavi
    Laboratoire de parasitologie et mycologie médicale, EA 2413, Faculte de Pharmacie, 34060 Montpellier Cedex 1, France
    Proc Natl Acad Sci U S A 103:3663-8. 2006
    ..albicans between human adults is very low. Most important is the inference that the prevailing mode of reproduction of C. albicans in natural populations is clonal, so that sexual reproduction is extremely rare, if it occurs at all...
  79. ncbi request reprint The clonal theory of parasitic protozoa: 12 years on
    Michel Tibayrenc
    UR Génétique des Maladies Infectieuses, UMR Centre National de la Recherche Scientifique Institut de Recherche pour le Développement 9926, IRD, BP 64501, 34393 Montpellier Cedex 5, France
    Trends Parasitol 18:405-10. 2002
    ..The proposals that initiated this debate are reviewed here and the subsequent developments of the clonal theory, in light of recent contributions, are examined...
  80. ncbi request reprint John C. Avise--recipient of 2006 Molecular Ecology prize
    Francisco J Ayala
    Mol Ecol 16:15-6. 2007
  81. pmc Genera of the human lineage
    Camilo J Cela-Conde
    Departamento de Filosofia, Universitat de las Islas Baleares, E 07071 Palma Baleares, Spain
    Proc Natl Acad Sci U S A 100:7684-9. 2003
    ..We propose a classification that includes four well defined genera: Praeanthropus, Ardipithecus, Australopithecus, and Homo, plus one tentative incertae sedis genus: Sahelanthropus...
  82. pmc Systematics and the origin of species: an introduction
    Jody Hey
    Department of Genetics, Rutgers, The State University of New Jersey, Piscataway, 08854, USA
    Proc Natl Acad Sci U S A 102:6515-9. 2005
  83. pmc Alternative splicing: a missing piece in the puzzle of intron gain
    Rosa Tarrio
    Grupo de Medicina Xenómica Centro de Investigación Biomédica en Red de Enfermedades Raras, Hospital Clinico Universitario, Universidade de Santiago de Compostela, 15706 Santiago, Spain
    Proc Natl Acad Sci U S A 105:7223-8. 2008
    ..We posit that intron positional diversity is driven by two overlapping processes: (i) background process of continuous relocation of preexisting introns by sliding and (ii) spurts of extensive gain/loss of new intron sequences...
  84. doi request reprint Taeniid history, natural selection and antigenic diversity: evolutionary theory meets helminthology
    Karen L Haag
    Departamento de Genetica, Instituto de Biociencias, Universidade Federal do Rio Grande do Sul, Porto Alegre, 91501 970 RS, Brazil
    Trends Parasitol 24:96-102. 2008
    ..This review focuses on the study of adaptive evolution as the cause of antigenic diversity in tapeworms and its potential applications...
  85. pmc Science, evolution, and creationism
    Francisco J Ayala
    Proc Natl Acad Sci U S A 105:3-4. 2008
  86. pmc Evolutionary and geographical history of the Leishmania donovani complex with a revision of current taxonomy
    Julius Lukes
    Biology Centre, Institute of Parasitology, Czech Academy of Sciences, and Faculty of Biology, University of South Bohemia, 370 05 Ceske Budejovice, Czech Republic
    Proc Natl Acad Sci U S A 104:9375-80. 2007
    ..4 and 0.8 Mya. The prevailing mode of reproduction is clonal, but there is evidence of genetic exchange between strains, particularly in Africa...

Research Grants2

  1. MARC U*STAR at the University of California, Irvine
    Francisco Ayala; Fiscal Year: 2007
    ..abstract_text> ..