Austin L. Hughes Professor of Biological Sciences Ph.D., 1984, Indiana University 803-777-9186 austin@biol.sc.edu Director Institute for Biological Research and Technology

The goal of our research is to use statistical analysis of DNA sequence data from a wide variety of systems as a means of understanding the mechanisms of adaptive evolution, with emphasis on genes of the vertebrate immune system. We address the following specific questions:

(1) What is the mechanism maintaining polymorphism at the loci of the vertebrate major histocompatibility complex (MHC)? The MHC is a multigene family that includes a number of loci encoding cell-surface glycoproteins that function to present intracellularly processed foreign peptides to T cells, thereby triggering an appropriate immune response. Some of these loci are among the most polymorphic known, and the evolutionary mechanism that maintains this high level of polymorphism has long been controversial. We have obtained evidence that this polymorphism is maintained by overdominant selection (heterozygote advantage) relating to disease resistance.

(2) What molecular mechanisms have parasites evolved to evade recognition and attack by the vertebrate immune system? The vertebrate immune system consists of many proteins -including MHC molecules, immunoglobulins, T cell receptors, complement components, and so forth-which function to recognize foreign molecules and thus eliminate parasitic organisms. Thus, organisms parasitic on vertebrates are presumably under strong selective pressure to evade host recognition systems and to render the host's immune attack ineffective. By analyzing DNA sequences from genes encoding surface proteins of the malaria parasite Plasmodium falciparum we have provided evidence for one such mechanism: a balanced polymorphism which keeps the host from encountering a single form of the parasite surface protein in every infection.

(3) How do members of multigene families evolve new functions? In eukaryotes, the duplication of genes, leading to the formation of families of related genes sharing similar but not identical functions, plays an important role in adaptive evolution. How this process occurs is not fully understood at present. Now sequence data are available for many different multigene families having a wide variety of functions. Analysis of these data may enable us to devise a realistic model for the evolution of functionally novel genes.

Selected Publications:

Hughes, A.L. 1991. Circumsporozoite protein genes of malaria parasites (Plasmodium spp.): evidence for positive selection on immunogenic regions. Genetics 127: 345-353.

Hughes, A.L. 1991d. Independent gene duplications, not concerted evolution, explain relationships among class I MHC genes of murine rodents. Immunogenetics 34:367-373.

Hughes, A.L. 1991e. MHC polymorphism and the design of captive breeding pro- grams. Conserv. Biol. 5:249-251.

Hughes, A.L. 1992b. Positive selection and interallelic recombination at the merozoite surface antigen-1 (MSA-1) locus of Plasmodium falciparum. Mol. Biol. Evol. 9:381-393.

Hughes, A.L. and Hughes, M.K. 1993. Adaptive evolution in the rat olfactory receptor gene family. J. Mol. Evol. 36:249-254.

Hughes, A.L., Hughes, M.K., and Watkins, D.I. 1993. Contrasting roles of interallelic recombination at the HLA-A and HLA-B loci. Genetics 133:669-680.

Hughes, M.K. and Hughes, A.L. 1993. Evolution of duplicate genes in a tetraploid animal, Xenopus laevis. Mol. Biol. Evol. 10:1360-1369.

Hughes, A.L. 1994. Phylogeny of the C3/C4/C5 complement-component gene family indicates that C5 diverged first. Mol. Biol. Evol. 11:417-425.

Hughes, A.L. 1994. The evolution of functionally novel proteins after gene duplication. Proc. R. Soc. Lond. B 256:119-124.

Hughes, A.L., Hughes, M.K., Howell, C.Y. and Nei, M. 1994. Natural selection at the class II major histocompatibility complex loci of mammals. Phil. Trans. R. Soc. Lond. B. 346:359-367

Jongwutiwes, S., Tanabe, K., Hughes, M.K., Kanbara, H., and Hughes, A.L. 1994. Allelic variation in the circumsporozoite protein of Plasmodium falciparum from Thai field isolates. Amer. J. Trop. Med. Hyg. 51:659-668.

McAdam, S.T., Boyson, J.E., Liu, X., Garber, T.L., Hughes, A.L., Bontrop, R.E., and Watkins, D.I. 1994. A uniquely high level of recombination at the HLA-B locus. Proc. Natl. Acad. Sci. USA 91:5893-5897.

Hughes, A.L. 1995. Origin and evolution of HLA class I pseudogenes. Mol. Biol. Evol. 12:247-258.

Hughes, A.L. 1995. The evolution of the type I interferon gene family in mammals. J. Mol. Evol. 41:539-548.

Hughes, A.L. and Hughes, M.K. 1995. Self peptides bound by HLA class I molecules are derived from highly conserved regions of a set of evolutionarily conserved proteins. Immunogenetics 41:257-262.

Hughes, A.L., and Hughes, M.K. 1995. Natural selection on the peptide-binding regions of major histocompatibility complex molecules. Immunogenetics 42:233-243.

Hughes, A.L. and Hughes, M.K. 1995. Small genomes for better flyers. Nature 377:391.

Greenberg, A.S., Avila, D., Hughes, M.K., Hughes, A.L., McKinney, E.C., and Flajnik, M.F. 1995. A novel antigen receptor gene family that undergoes rearrangement and extensive somatic diversification in sharks. Nature 374:168-173.

Hughes, M.K. and Hughes, A.L. 1995. Natural selection on Plasmodium surface proteins. Mol. Biochem. Parasitol. 71:99-113.

Hughes, A.L. 1996. Gene duplication and recombination in the evolution of mammalian Fc receptors. J. Mol. Evol. 43:4-10.

Hughes, A.L. 1997. Rapid evolution of immunoglobulin superfamily C2 domains expressed in immune system cells. Mol. Biol. Evol. 14:1-5.

Hughes, A.L. 1997. Evolution of the proteasome components. Immunogenetics 46:82- 92.

Hughes, A.L., and Yeager, M. 1997. Molecular evolution of the vertebrate immune system. Bioessays 19:777-786.

Cereb, N., Hughes, A.L., and Yang, S.Y. 1997. Locus-specific conservation of the HLA class I introns by intra-locus homogenization. Immunogenetics 47:30-36.

Hughes, A.L. 1998. Protein phylogenies provide evidence of a radical discontinuity between arthropod and vertebrate immune systems. Immunogenetics 47:283-296.

Hughes, A.L. 1998. Phylogenetic tests of the hypothesis of block duplication of homologous genes on human chromosomes 6, 9, and 1. Mol. Biol. Evol. 15: 854-870.

Hughes, A.L., and Yeager, M. 1998. Natural selection at major histocompatibility complex loci of vertebrates. Annu. Rev. Genet. 32: 415-435.

Hughes, A.L., and Verra, F. 1998. Ancient polymorphism and the hypothesis of a recent bottleneck in the malaria parasite Plasmodium falciparum. Genetics 150: 511-513.

da Silva, J., and Hughes. A.L. 1998. Conservation of host cytotoxic T lymphocyte (CTL) epitopes as a host strategy to constrain parasite adaptation: evidence from the nef gene of human immunodeficiency virus 1 (HIV-1). Mol. Biol. Evol. 15: 1259-1268.

Hughes, A.L. 1999. Evolution of the arthropod prophenoloxidase/hexamerin protein family. Immunogenetics 49: 106-114.

Hughes, A.L. 1999. Differential human impact on genetically distinct avian lineages. Bird Conservation International 9: 147-154.

Hughes A.L. 1999. Phylogenies of developmentally important proteins do not support the hypothesis of two rounds of genome duplication early in vertebrate history. J. Mol. Evol. 48: 565-576.

Hughes, A.L. 1999. Concerted evolution of exons and introns in the MHC-linked tenascin-X gene of mammals. Mol. Biol. Evol. 16: 1558-1567..

Hughes, A.L. 1999. Genomic catastrophism and the origin of vertebrate immunity. Arch. Immunol. Ther. Exper. 47: 347-353.

Hughes, A.L. 1999. Evolutionary diversification of the mammalian defensins. Cell. Mol. Life Sci. 56: 94-103.

Hughes, A.L. 1999. Adaptive Evolution of Genes and Genomes. Oxford University Press, New York

Hughes, A.L. and Yeager, M. 1999. Coevolution of the mammalian chemokines and their receptors. Immunogenetics 49: 115-124.

Hughes, A.L., Yeager, M., Ten Elshoff A., and Chorney, M. 1999. A nex taxonomy of mammalian MHC class I molecules. Immunol. Today 20: 22-26.

da Silva, J., and Hughes, A.L. (1999) Molecular phylogenetic evidence of cytotoxic T lymphocyte CTL) selection on human immunodeficiency virus type 1 (HIV-1). Mol. Biol. Evol. 16: 1420-1422.

Evans, D.T., O'Connor, D.H., Jing, P., Dzuris, J.L., Sidney, J., Da Silva, J., Allen, T.M., Horton, H., Venham, J.E., Rudersdorf, R.A., Vogel, T., Pauza, C.D., Bontrop, R.E., DeMars, R., Sette, A., Hughes, A.L., and Watkins, D.I. (1999) Virus-specific cytotoxic T-lymphocyte responses select for amino-acid variation in simian immunodeficiency virus Env and Nef. Nature Medicine 5: 1270-1276.

Verra, F., and Hughes, A.L. 1999. Biased amino acid composition in repeat regions of Plasmodium antigens. Mol. Biol. Evol. 16: 627-633.

Yeager, M., and Hughes, A.L. 1999. Evolution of the mammalian MHC: natural selection, recombination, and convergent evolution. Immunol. Rev. 167: 45-58.

Hughes, A.L., Green, J.A., Garbayo, J.M., and Roberts, R.M. 2000. Adaptive diversification within a large family of recently duplicated, placentally expressed genes. Proc. Natl. Acad. Sci. USA 97: 3319-3327.

Hughes, A.L., and Roberts, R.M. 2000. Independent origin of IFN-? and IFN-? in birds and mammals. J. Interfer. Cytokine Res. 20: 737-739.

Allen, T.M., O'Connor, D.H., Jing, P. Dzuris, J.L. Moth?, B.R., Vogel, T.U., Dunphy, E. Leibl, M.E., Emerson, C., Wilson, N., Kunstman, K.J., Wang, X., Allison, D.B., Hughes, A.L.Desrosiers, R.C., Altman, J.D., Wolinsky, S.M., Sette, A., and Watkins, D.I. 2000. Tat-specific cytotoxic T lymphocytes select for SIV escape variants during resolution of primary viraemia. Nature 407: 386-390.

Verra, F., and Hughes, A.L. 2000. Evidence for ancient balanced polymorphism at the Apical Membrane Antigen-1 (AMA-1) locus of Plasmodium falciparum. Mol. Biochem. Parasitol. 105: 149-153.

Hughes, A.L. 2001. Evolution of the integrin a and ? protein families. J Mol Evol 52: 63-72.

Hughes, A.L., da Silva, J., and Friedman, R. 2001. Ancient genome duplications did not structure the human Hox-bearing chromosomes. Genome Research 11: 771-780.

Hughes, A.L., Westover, K., da Silva, J., O'Connor, D.H., Watkins, D.I. 2001. Simultaneous positive and purifying selection on overlapping reading frames of thetat and vpr genes of simian immunodeficiency virus. J. Virol. 75: 7666-7672.

Friedman, R., and Hughes, A.L. 2001. Gene duplication and the structure of eukaryotic genomes. Genome Research 11: 373-381.

Wang, X., Hughes, A.L., Tsukamoto, T., Ando, T., and Kao, T.-H. 2001. Evcidence that intragenic recombination contributes to allelic diversity of the S-Rnase gene at the self-incompatibility (S) locus in Petunia inflata. Plant Physiol. 125: 1012-1022.

Westover, K.M., and Hughes, A.L. 2001. Molecular evolution of viral fusion and matrix protein Genes and phylogenetic relationships among the Paramyxoviridae. Mol. Phyl. Evol. 21: 128-134.

Hughes, A.L. 2002. Origin and evolution of viral interleukin-10 and other DNA virus genes with vertebrate homologues. J. Mol. Evol. 54: 90-101.

Hughes, A.L. 2002. Evolution of the human killer cell inhibitory receptor family. Mol. Phyl. Evol. 25: 330-340.

Hughes, A.L. 2002. Evolution of inhibitors of apoptosis in baculoviruses and their insect hosts. Infection, Genetics, and Evolution 2: 3-10.

Hughes, A.L., and Verra, F. 2002. Extensive polymorphism and ancient origin of Plasmodium falciparum. Trends Parasitol. 18: 348-351.

Friedman, R., and Hughes, A.L. 2002. Molecular evolution of the NF-kB signaling system. Immunogenetics 53: 964-974.

Jongwutiwes, S., Putaporntip, C., Friedman, R., and Hughes, A.L. 2002. The extent of nucleotide polymorphism is highly variable across a 3-kb region on Plasmodium falciparum chromosome 2. Mol. Biol. Evol. 19: 1585-1590.

Lipovich, L., Hughes, A.L., King, M.-C., Abkowitz, J.L., and Quigley, J.G. 2002. Genomic structure and evolutionary context of the human feline leukemia virus subgroup C receptor (hFLVCR) gene: evidence for block duplications and de novo gene formation within duplicons of the hFLVCR locus. Gene 286: 203-213.

O?Connor, D.H., Allen, T.M., Vogel, T.U., Jing, P., DeSouza, I.P., Dodds, E., Dunphy, E.J., Melsaether, C., Moth?, B., Yamamoto, H., Horton, H., Wilson, N., Hughes, A.L., and Watkins, D.I. 2002. Acute phase cytotoxic I lymphocyte escape is a hallmark of simian immunodeficiency virus infection. Nature Medicine 8: 493-499.

Vogel, T.U., Friedrich, T.C., O?Connor, D.H., Rehrauer, W., Dodds, E.J., Hickman, H., Hildebrand, W., Sidney, J., Sette, A., Hughes, A., Horton, H., Vielhuber, K., Rudersdorf, R., de Sousa, I.P., Reynolds, M.R., Allem, T.M., Wilson, N., and Watkins, D.I. 2002. Escape in one of two cytotoxic T-lymphocyte epitopes bound by a high-frequency major histocompatibility complex class I molecules, Mamu-A*02: a paradigm for virus evolution and persistence? J. Virol. 76: 11623-11636.

Hughes, A.L., and Friedman, R. 2003. Parallel evolution by gene duplication in the genomes of two unicellular fungi. Genome Research 13: 794-799.

Hughes, A.L., and Friedman, R. 2003. Genome-wide survey for genes horizontally transferred from cellular organisms to baculoviruses. Mol. Biol. Evol. 20: 979-987.

Hughes, A.L., and Friedman, R. 2003. 2R or not 2R: testing hypotheses of genome duplication in early vertebrates. J. Structural and Functional Genomics 3: 85-93.

Hughes, A.L., and Piontkivska, H. 2003. Phylogeny of Trypanosomatidae and Bodonidae (Kinetoplastida) based on 18S rRNA: evidence for paraphyly of Trypanosoma and six other genera. Mol. Biol. Evol. 20: 644-650.

Hughes, A.L., and Piontkivska, H. 2003. Molecular phylogenetics of Trypanosomatidae: contrasting results from 18S rRNA and protein phylogenies. Kinetoplastid Biology and Disease 2003, 2:15.

Hughes, A.L., Packer, B., Welsch, R., Bergen, A.W., Chanock, S.J., and Yeager, M. 2003. Widespread purifying selection at polymorphic sites in human protein-coding loci. Proc. Natl. Acad. Sci. USA 100: 15754-15757.

Hughes, A.L., Friedman, R., Ekollu, V., and Rose, J.R. 2003. Non-random association of transposable elements with duplicated genomic blocks in Arabidopsis thaliana. Mol. Phyl. Evol. 29: 410-416.

Hughes, A.L. Green, J.A., Piontkivska, H., Roberts, R.M. 2003. Aspartic proteinase phylogeny and the origin of pregnancy-associated glycoproteins. Mol. Biol. Evol. 20: 1940-1945.

Friedman, R., and Hughes, A.L. 2003. The temporal distribution of gene duplication events in a set of highly conserved human gene families. Mol. Biol. Evol. 20: 154-161.

O?Connor, D.H., Mother, B.R., Weinfurter,J.T., Fuenger, S., Rehrauer, W.M., Jing, P., Rudersdorf, R.R., Liebl, M.E., Krebs, K., Vasquez, J., Dodds, E., Loffredo, J., Martin, S., McDermott, A.B., Allen, T.M., Wang, C., Doxiadis, G.G., Monefiori, D.C., Hughes, A., Burton, D.R., Allison, D.B., Wolinsky, S.M., Bontrop, R., Picker, L.J., and Watkins, D.I. 2003. Major histocompatibility complex class I alleles associated with slow immunodeficiency virus disease progression bind epitopes recognized by dominant acute-phase acotoxic-T-lymphocyte responses. J. Virol. 77: 9029-9040.

Piontkivska, H., and Hughes, A.L. 2003. Evolution of vertebrate voltage-gated ion channel alpha chains by sequential gene duplication. J. Mol. Evol. 56: 277-285.

Sette, A., Sidney, J., Livingston, B.D., Dzuris, J.L., Crimi, C., Walker, C.M., Southwood, S., Collins, E.J., and Hughes, A.L. 2003. Class I molecules with similar peptide-binding specificities are the result of both common ancestry and convergent evolution. Immunogenetics 54: 830-841.

Hughes, A.L. 2004. The evolution of amino acid repeat arrays in Plasmodium and other organisms. J. Mol. Evol. 59: 528-535.

Hughes, A.L. 2004. Birth-and-death evolution of protein-coding regions and concerted evolution of non-coding regions in multi-component genomes of nanoviruses. Mol. Phyl. Evol. 30: 287-294.

Hughes, A.L. 2004. Phylogeny of the Picornaviridae and differential evolutionary divergence of picornavirus proteins. Infect. Genet. Evol. 4: 143-152.

Hughes, A.L. 2004. Evolutionary origin of the Jiv90 gene of Pestivirus. Infect. Genet. Evol. 4: 329-333.

Hughes, A.L. 2004. A statistical analysis of factors associated with historical extinction and current endangerment of non-passerine birds. Wilson Bull. 116: 330-336.

Hughes, A.L., and Friedman, R. 2004. Differential loss of ancestral gene families as a source of genomic divergence in animals. Proc. R. Soc. Lond. B 271: S107-S109.

Hughes, A.L., and Friedman, R. 2004. Pattern of divergence of amino acid sequences encoded by paralogous genes in human and pufferfish. Mol. Phyl. Evol. 32: 337-343.

Hughes, A.L., and Friedman, R. 2004. Recent mammalian gene duplications: robust search for functionally divergent gene pairs. J. Mol. Evol. 59: 114-120.

Hughes, A.L., and Friedman, R. 2004. Transposable element distribution in the yeast genome reflects a role in repeated genomic rearrangement events on an evolutionary time scale. Genetica 121: 181-185.

Hughes, A.L., and Friedman, R. 2004. Shedding genomic ballast: extensive parallel loss of ancestral gene families in animals. J. Mol. Evol. 59: 837-833.

Hughes, A.L., and Friedman, R. 2004. Patterns of sequence divergence in 5' intergenic spacers and linked coding regions in 10 species of pathogenic Bacteria reveal distinct recombinational histories. Genetics 168: 1795-1803.

Eck, P.J., Erichsen, C., Taylor, J.G., Yeager, M., Hughes, A.L., Levine, M., and Channock, S.J. 2004. Comparison of the genomic structure and variation in the two human sodium-dependent vitamin C transporters, SLC23A1 and SLC23A2. Human Genet. 115: 285-294.

Friedman, R., and Hughes, A.L. 2004. Two patterns of genome organization in mammals: the chromosomal distribution of duplicate genes in human and mouse. Mol. Biol. Evol. 21: 1008-1013.

Friedman, R., and Hughes, A.L. 2004. Codon volatility as an indicator of positive selection: data from eukaryotic genome comparisons. Mol. Biol. Evol. 22: 542-546.

Friedman, R., Drake, J.W., and Hughes, A.L. 2004. Genome-wide patterns of nucleotide substitution reveal stringent functional constraints on the protein sequences of thermophiles. Genetics 167: 1507-1512.

Friedman, R., Ekollu, V., Rose, J.R., and Hughes, A.L. 2004. Dblox: a genome-wide test for ancient segmental duplication. Bioinformatics 14; 2004; 0, 2750-2751.

Friedrich, T.C., Frye, C.A., Yant, L.J., O'Connor, D.H., Kriewaldt, N.A., Benson, M., Vojnov, L., Dodds, E.J., Cullen, C., Rudersdorf, R., Hughes, A.L., Wilson, N., and Watkins, D.I. 2004. Extraepitopic compensatory substitutions partially restore fitness to simian immunodeficiency virus variants that escape from an imunodominant cytotoxic-T-lymphocyte response. J. Virol. 78: 2581-2585.

Friedrich, T.T., Dodds, E.J., Yant, L.J., Vojnov, L., Rudersdorf, R., Cullen, C., Evans, D.T., Desrosiers, R.C., Mothe, B.R., Sidney, J., Sette, A., Kunstman, K., Wolinsky, S., Piatak, M., Lifson, J., Hughes, A.L., Wilson, N., O?Connor, D.H., and Watkins, D.I. 2004. Reversion of CTL escape-variant immunodeficiency viruses in vivo. Nature Med. 10: 275-281.

O'Connor, D.H., McDermott, A.B., Krebs, A.C., Dodds, E.J., Miller, J.E., Gonzalez, E.J., Jacoby, T.J., Yant, L., Piontkivska, H., Pantophlet, R., Burton, D.R., Rehrauer, W.R., Wilson, N., Hughes, A.L., and Watkins, D.I.. 2004. A dominant role for CD8+-T-lymphocyte selection in Simian Immunodeficiency Virus sequence variation. J. Virol. 78: 14012-14022.

Patil, A., Hughes, A.L., and Zhang, G. 2004. Rapid evolution and diversification of mammalian alpha-defensins as revealed by comparative analysis of rodent and primate genes. Physiol. Genomics 20: 1-11.

Piontkivska, H., and Hughes, A.L. 2004. Between-host evolution of CTL epitopes in Human Immunodeficiency Virus Type 1 (HIV-1): an approach based on phylogenetically independent comparisons. J. Virol. 78: 11758-11765.

Pollack, H., Hou, Z., Hughes, A.L., and Borkowsky, W. 2004. Preinatal transmission and viral evolution of Hepatitis C Virus quasispecies in infants coinfected with HIV. J. AIDS 36: 890-899.

Xiao, Y., Hughes, A.L., Ando, J., Matsuda, Y., Cheng, J.-F., Skinner-Noble, D., and Zhang, G. 2004. A genome-wide screen identifies a single beta-defensin gene cluster in the chicken: implications for the origin and evolution of mammalian defensins. BMC Genomics 2004, 5:56.

Hughes, A.L. 2005. Gene duplication and the origin of novel proteins. Proc. Natl. Acad. Sci. USA 102: 8791-8792.

Hughes, A.L., and Friedman, R. 2005. Nucleotide substitution and recombination at orthologous loci in Staphylococcus aureus. J. Bacteriol. 187: 2698-2704.

Hughes, A.L., and Friedman, R. 2005. Expression patterns of duplicate genes in the developing root of Arabidopsis thaliana. J. Mol. Evol. 60: 247-256.

Hughes, A.L., and Friedman, R. 2005. Poxvirus genome evolution by gene gain and loss. Mol. Phyl. Evol. 35: 186-195.

Hughes, A.L., and Friedman, R. 2005. Loss of ancestral genes in the genomic evolution of Ciona intestinalis.Evolution and Development 7: 196-200.

Hughes, A.L., and Friedman, R. 2005. Variation in the pattern of synonymous and nonsynonymous difference between two fungal genomes. Mol. Biol. Evol. 22: 1320-1324.

Hughes, A.L., and Friedman, R. 2005. Amino acid sequence constraint and gene expression pattern across the life history in the malaria parasite Plasmodium falciparum. Mol. Biochem. Parasitol. 142: 170-176.

Hughes, A.L., and Piontkivska, H. 2005. DNA repeat arrays in chicken and human genomes and the adaptive evolution of avian genome size. BMC Evolutionary Biology 2005, 5:12.

Hughes, A.L., Ekollu, V., Friedman, R., and Rose, J.R. 2005. Gene family content-based phylogeny of prokaryotes: the effect of criteria for inferring homology. Syst. Biol. 54: 268-276.

Hughes, A.L., Packer, B., Welsch, R., Bergen, A.W., Chanock, S.J., and Yeager, M. 2005. Effects of natural selection on inter-population divergence at polymorphic sites in human protein-coding loci. Genetics 170:1181-1187.

Biron, D.G., Moura, H., March?, L., Hughes, A.L., and Thomas, F. 2005. Towards a new conceptual approach to 'parasitoproteomics'. Trends Parasitol. 21: 162-168.

Friedman, R., and Hughes, A.L. 2005. The pattern of nucleotide difference at individual codons among mouse, rat, and human. Mol Biol. Evol. 22:1385-1289.

Jongwutiwes, S., Putaporntip, C., Iwasaki, T., Ferreira, M.U., Kanbara, H., and Hughes, A.L. 2005. Mitochondrial genome sequences support ancient population expansion in Plasmodium vivax. Mol. Biol. Evol. 22: 1733-1739.