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College of Arts & Sciences
Department of Biological Sciences

Faculty & Staff Directory

Austin Hughes

Department of Biology
University of South Carolina

Office: CLS 501
Phone Number: 777-9186

REFEREED JOURNAL ARTICLES: Hughes, A.L. 1979. Reproductive behavior and sexual dimorphism in the white spotted sawyer Monochamus scutellatus (Say). Coleop. Bull. 33:45-47. Hughes, A.L. 1980. Preferential first-cousin marriage and inclusive fitness. Ethol. So- ciobiol. 1:311-317. Hughes, A.L. 1981. Differential male mating success in the white spotted sawyer Monochamus scutellatus (Coleoptera: Cerambycidae). Ann. Entomol. Soc. Amer. 74:180-184. Hughes, A.L. 1982. Attraction of adult Tribolium confusum to flour conditioned by male conspecifics. Behav. Proc. 7:247-253. Hughes, A.L. 1982. Confidence of paternity and wife-sharing in polygynous and polyandrous systems. Ethol. Sociobiol. 3:125-129. Hughes, A.L. and Hughes, M.K. 1982. Male size, mating success, and breeding habi- tat partitioning in the white spotted sawyer Monochamus scutellatus (Say) (Coleop- tera: Cerambycidae). Oecologia 55:258-263. Hughes, M.K., Hughes, A.L., and Dunning, D.C. 1982a. Stimuli eliciting foodcalling in chickens. Appl. Anim. Ethol. 8:543-550. Hughes, M.K., Hughes, A.L., and Dunning, D.C. 1982b. Frequency and intensity of chick distress calls: effects on maternal foodcalling in chickens. Behav. Proc. 7:335- 340. Hughes, A.L. 1983. Kin selection of complex behavioral strategies. Amer. Nat. 122: 181-190. Hughes, A.L. 1984. Some methods for analyzing the structure and behavior of human kin groups. Ethol. Sociobiol. 5:179-192. Hughes, A.L. 1985. Male size, mating success, and mating strategy in the mosquito- fish Gambusia affinis (Poeciliidae). Behav. Ecol. Sociobiol. 17:271-278. Hughes, A.L. 1985. Seasonal changes in fecundity and size at first reproduction in an Indiana population of the mosquitofish Gambusia affinis. Amer. Midl. Nat. 114:30-36. Hughes, A.L. 1985. Seasonal trends in body size of adult male mosquitofish Gambu- sia affinis with evidence for their social control. Env. Biol. Fishes 14:251-258. Hughes, A.L. and Hughes, M.K. 1985. Female choice of mates in a polygynous insect, the whitespotted sawyer Monochamus scutellatus. Behav. Ecol. Sociobiol. 17:385- 387. Hughes, A.L. 1986. Growth of adult mosquitofish Gambusia affinis in the laboratory. Copeia 1986:534-536. Hughes, A.L. 1986. Seasonal changes in sexual receptivity of female mosquitofish Gambusia affinis. Biol. Behav. 11:3-15. Hughes, A.L. 1986. Biological relatedness and social structure. J. Social Biol. Struct. 9:151-168. Hughes, A.L. 1986. Reproductive success and occupational class in Eighteenth Cen- tury Lancashire, England. Social Biol. 33:109-115. Hughes, A.L. 1986e. Kin coalitions and social dominance. J. Theoret. Biol. 123:55-65. Hughes, A.L., and Hughes, M.K. 1986. Paternal investment and sexual size dimorphism in North American passerines. Oikos 46: 171-175. Hughes, A.L. and Hughes, M.K. 1987. Asymetric contests among sawyer beetles Mo- nochamus notatus and M. scutellatus (Cerambycidae). Can. J. Zool. 65:823-827. Hughes, A.L. 1988. Kin networks and political leadership in a stateless society, the Toda of South India. Ethol. Sociobiol. 9:29-44. Hughes, A.L. and Nei, M. 1988. Pattern of nucleotide substitution at MHC class I loci reveals overdominant selection. Nature 335:167-170. Hughes, A.L. 1989. Interaction between strains in the social relations of inbred mice. Behav. Genet. 19:685-700. Hughes, A.L. and Nei, M. 1989. Nucleotide substitution at major histocompatibility complex class II loci: evidence for overdominant selection. Proc. Natl. Acad. Sci. USA 86:958-962. Hughes, A.L. and Nei, M. 1989. Ancient interlocus exon exchange in the history of the HLA-A locus. Genetics 122:681-686. Hughes, A.L. and Nei, M. 1989. Evolution of the major histocompatibility complex: in- dependent origin of nonclassical class I genes in different groups of mammals. Mol. Biol. Evol. 6:559-579. Hughes, A.L. and Nei, M. 1990. Evolutionary relationships of class II MHC genes in mammals. Mol. Biol. Evol. 7:491-514. Hughes, A.L., Ota, T., and Nei, M. 1990. Positive Darwinian selection promotes charge profile diversity in the antigen binding cleft of class I MHC molecules. Mol. Biol. Evol. 7:515-524. Watkins, D.I., Chen, Z.W., Hughes, A.L., Evans, M.G., Tedder, T.F., and Letvin, N.L. 1990. Evolution of the class I genes of a New World primate from ancestral homo- logues of human non-classical genes. Nature 346:60-63. Watkins, D.I., Chen, Z.W., Hughes, A.L., Hodi, F.S., and Letvin, N.L. 1990. Genetically distinct cell populations in naturally occurring bone marrow-chimeric primates ex- press similar MHC class I gene products. J. Immunol. 144:3726-3735. Watkins D.I., Chen, Z.W., Hughes, A.L., Lagos, A., Lewis, A.M., Jr., Shaddock, J.A., and Letvin, N.L. 1990. Syrian hamsters express diverse MHC class I gene products. J. Immunol. 145:3483-3490. Watkins, D.I., Letvin, N.L., Hughes, A.L., and Tedder, T.F. 1990. Molecular cloning of cDNAs that encode class I molecules from a New World Primate (Saguinis oedi- pus): natural selection acts at positions that may affect peptide presentation to T cells. J. Immunol. 144:1136-1143 Hughes, A.L. 1991. Circumsporozoite protein genes of malaria parasites (Plasmo- dium spp.): evidence for positive selection on immunogenic regions. Genetics 127: 345-353. Hughes, A.L. 1991. Evolutionary origin and diversification of the mammalian CD1 antigen genes. Mol. Biol. Evol. 8:185-201. Hughes, A.L. 1991. Testing for interlocus genetic exchange in the MHC: a reply to Andersson et al. Immunogenetics 33:243-246. Hughes, A.L. 1991. Independent gene duplications, not concerted evolution, explain relationships among class I MHC genes of murine rodents. Immunogenetics 34:367-373. Hughes, A.L. 1991. MHC polymorphism and the design of captive breeding pro- grams. Conserv. Biol. 5:249-251. Miller, M.D., Yamamoto, H., Hughes, A.L., Watkins, D.I., and Letvin, N.L. 1991. Defini- tion of an epitope and MHC class I molecule recognized by gag-specific cytotoxic T lymphocytes in SIVmac-infected rhesus monkeys. J. Immunol. 147:320-329. Watkins, D.I., Chen, Z.W., Garber, T.L., Hughes, A.L., and Letvin, N.L. 1991. Segmental exchange between MHC class I genes in a higher primate: recombination in the go- rilla between the ancestor of a human non-functional gene and an A locus gene. Immunogenetics 34:185-191. Watkins, D.I., Garber, T.L., Chen, Z.W., Toukatly, G., Hughes, A.L., and Letvin, N.L. 1991. Unusually limited nucleotide sequence variation of the expressed major his- tocompatibility complex class I genes of a New World primate species (Saguinus oedipus). Immunogenetics 33:79-89. Zhou, L.-J., Ord, D.C., Hughes, A.L., and Tedder, T.F. 1991. Structure and domain or- ganization of the CD19 antigen of human, mouse, and guinea pig B lymphocytes: conservation of the extensive cytoplasmic domain. J. Immunol. 147:1424-1432. Hughes, A.L. 1992. Coevolution of the vertebrate integrin  and  chain genes. Mol. Biol. Evol. 9:216-234. Hughes, A.L. 1992. 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 Nei, M. 1992. Models of host-parasite interaction and MHC polymor- phism. Genetics 132:863-864. Hughes, A.L. and Nei, M. 1992. Maintenance of MHC polymorphism. Nature 355:402-403. Chen, Z.W., McAdam, S.N., Hughes, A.L., Dogon, A.L., Letvin, N.L., and Watkins, D.I. 1992. Molecular cloning of orangutan and gibbon MHC class I cDNA. J. Immunol. 148:2547-2554. Chen, Z.W., Shen, L., Miller, M.D., Ghim, S.H., Hughes, A.L., and Letvin, N.L. 1992. Cytotoxic T lymphocytes do not appear to select for mutations in an immunodomi- nant epitope of simian immunodeficiency virus gag. J. Immunol. 149:4060-4066. Gaur, L.K., Hughes, A.L., Heise, E.R., and Guttknecht, J. 1992. Maintenance of DQB1 polymorphisms in primates. Mol. Biol. Evol. 9:599-609. Levinson, G., Hughes, A.L., and Letvin, N.L. 1992. Sequence and diversity of rhesus monkey T-cell receptor  chain genes. Immunogenetics 35:75-88. Watkins, D.I., McAdam, S.N., Liu, X., Strang, C.R., Milford, E.L., Levine, C.G., Garber, T.L., Dogon, A.L., Lord, C.I., Ghim, S.H., Troup, G.M., Hughes, A.L., and Letvin, N.L. 1992. New recombinant HLA-B alleles in a tribe of South American Amerindians in- dicate rapid evolution of MHC class I loci. Nature 357:329-333. Hughes, A.L. 1993. Nonlinear relationships among evolutionary rates identify regions of functional divergence in heat-shock protein 70 genes. Mol. Biol. Evol. 10:243-255. Hughes, A.L. 1993. Rates of amino acid evolution in the 26- and 28-kDa glutathione S-transferases of Schistosoma. Mol. Biochem. Parasitol. 58:43-52. Hughes, A.L. 1993. Evidence of positive selection at the Lyb-2 locus of the mouse. Immunogenetics 38:54-56. Hughes, A.L. 1993. Contrasting evolutionary rates in the duplicate chaperonin genes of Mycobacterium tuberculosis and M. leprae. Mol. Biol. Evol. 10:1343-1359. 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 re- combination at the HLA-A and HLA-B loci. Genetics 133:669-680. Hughes, A.L., and Nei, M. 1993. Evolutionary relationships of the classes of major his- tocompatibility complex genes. Immunogenetics 37:337-346. Chen, Z.W., Hughes, A.L., Ghim, S.H., Letvin, N.L., and Watkins, D.I. 1993. Two more chimpanzee Patr-A alleles related to the HLA-A1/A3/A11 family. Immunogenetics 38:238-240. Garber, T.L., Hughes, A.L., Letvin, N.L., Templeton, J.W., and Watkins, D.I. 1993. Se- quence and evolution of cattle MHC class I cDNAs: concerted evolution has not ta- ken place in cattle. Immunogenetics 38:11-20. Hughes, M.K. and Hughes, A.L. 1993. Evolution of duplicate genes in a tetraploid ani- mal, Xenopus laevis. Mol. Biol. Evol. 10:1360-1369. Wagner, A.G., Hughes, A.L., Iandoli, M.L., Stewart, D., Herbert, S., Watkins, D.I., Hur- ley, S., and Rosen-Bronson, S. 1993. HLA-A*8001 is a member of a newly dis- covered ancient family of HLA-A alleles. Tissue Antigens 42:522-529. 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. Evolution of the interleukin-1 gene family in mammals. J. Mol. Evol. 39:6-12. Hughes, A.L. 1994. The evolution of functionally novel proteins after gene duplication. Proc. R. Soc. Lond. B 256:119-124. Hughes, A.L. 1994. Conserved proteins as immunogens: glutathione S-transferase of Schistosoma. Parasitol. Today 10:149-151. Hughes, A.L. 1994. Evolution of ATP-binding-cassette transmembrane transporters of vertebrates. Mol. Biol. Evol. 11:899-910. Hughes, A.L. 1994 Evolution of cysteine proteinases in eukaryotes. Mol. Phylo. Evol. 3:310-321. 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. Garber, T.L., Hughes, A.L., Watkins, D.I., and Templeton, J.W. 1994. Evidence for at least three transcribed BoLA class I loci. Immunogenetics 39:257-265. Jongwutiwes, S., Tanabe, K., Hughes, M.K., Kanbara, H., and Hughes, A.L. 1994.Al- lelic 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. Boyson, J.E., McAdam, S.N., Gallimore, A., Golos, T.G., Li, X., Gotch, F.M., Hughes, A.L., and Watkins, D.I. 1995. The MHC E locus in macaques is polymorphic and is conserved between macaques and humans. Immunogenetics 41:59-68. 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 pro- teins. 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 pro- teins. Mol. Biochem. Parasitol. 71:99-113. Seibert, S.A., Howell, C.Y., Hughes, M.K., and Hughes, A.L. 1995. Natural selection on the gag, pol, and env genes of human immunodeficiency virus 1 (HIV-1).Mol. Biol. Evol. 12:803-813. McAdam, S.N, Boyson, J.E., Liu, X., Garber, T.L., Hughes, A.L., Bontrop, R.E., and Watkins, D.I. 1995. Chimpanzee MHC class I A locus alleles are related to only one of the six families of human A locus alleles. J. Immunol. 154:6421-6429. Weiner, A., Erickson, A.L., Kansopon, J., Crawford, K.,Muchmore, E., Hughes, A.L., Houghton, M., and Walker, C.M. 1995 Persistent hepatitis C virus infection in a chimpanzee is associated with the emergence of a cytotoxic T lymphocyte escape variant. Proc. Natl. Acad. Sci. USA 92:2755-2759. Hughes, A. L. 1996 The evolution of the src -related protein tyrosine kinases. J. Mol. Evol. 42:247-256. Hughes, A.L. 1996. Gene duplication and recombination in the evolution of mammalian Fc receptors. J. Mol. Evol. 43:4-10. Hughes, A.L., Yeager, M., and Carrington, M. 1996. Peptide binding function and the paradox of HLA disease association. Immunol. Cell Biol. 74:444-448.. Allen, T.M., Lanchbury, J.S., Hughes, A.L., and Watkins, D.I. 1996. The T-cell receptor  chain-encoding gene repertoire of a New World primate species, the cotton-top tamarin. Immunogenetics 45:151-160. Boyson, J.E., Shufflebotham, C., Cadavid, L.F., Urvater, J.A., Knapp, L.A., Hughes, A.L., and Watkins, D.I. 1996. The MHC class I genes of the rhesus monkey: different evolutionary histories of MHC class I and class II genes in primates. J. Immunol. 156: 4656-4665. Cadavid, L.F., Hughes, A.L., and Watkins, D.I. 1996. MHC class I-processed pseudogenes in New World primates provide evidence for rapid turnover of MHC class I genes. J. Immunol. 157:2403-2409. Greenberg, A.S., Hughes, A.L.. Guo, J., Avila, D., McKinney, E.C., Flajnik, M.F. 1996. A novel “chimeric” antibody class in cartilaginous fish: IgM may not be the primordial immunoglobulin. Eur. J. Immunol. 26:1123-1129. Milewicz, D.M., Byers, P.H., Reveille, J., Hughes, A.L., Duvic, M. 1996. A dimorphic Alu Sb-like insertion in COL3A1 is ethnic-specific. J. Mol. Evol. 42:117-123. Yeager, M., Hughes, A.L. 1996. Interallelic recombination has not played a major role in the history of the HLA-C locus. Immunogenetics 44:128-133. 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. Coordinated amino acid changes in the evolution of mammalian defensins. J. Mol. Evol. 44:675-682. Hughes, A.L., and Yeager, M. 1997. Comparative evolutionary rates of introns and exons in murine rodents. J. Mol. Evol. 45:125-130. Hughes, A.L., and Yeager, M. 1997. Molecular evolution of the vertebrate immune system. Bioessays 19:777-786. Cadavid, L. F., Shufflebotham, C., Ruiz, F.J., Yeager, M., Hughes, A.L., and Watkins, D.I. 1997. Evolutionary instability of the major histocompatibility complex class I loci in New World primates. Proc. Natl. Acad. Sci. USA 94: 14536-14541 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. Cereb, N., Hughes, A.L., and Yang, S.Y. 1997. Cw*1701, a new HLA-C allelic lineage with an unusual transmembrane domain. Tissue Antigens 49:252-255 Cereb, N., Kim, C., Hughes, A.,L., and Yang, S.Y. 1997. Molecular analysis of HLA-B35 alleles and their relationship to HLA-B15 alleles. Tissue Antigens 49: 389-396 Evans, D.T., Piekarczyk, M.S., Allen, T.M., Boyson, J.E., Yeager, M., Hughes, A.L., Gotch, F.M., Hinshaw, V.S., and Watkins, D.I. 1997. Immunodominance of a single CTL epitope in a primate species with limited MHC class I polymorphism. J Immunol 159:1374-1382. Schweibert, L.M., Hughes, A.L., Monos, D.S., and Ono, S.J. 1997 HLA-DRA promoter polymorphism and diversity generation within the immune system. Human Genetics 99:801-805. Tay, G.K., Leelayuwat, C., Chorney, M.J., Cattley, S.K., Hollingsworth, P.N., Witt, C.S. Daly, L.N., Hughes, A., Dawkins, R.L. 1997. The MHC contains multiple genes potentially relevant to hemochromatosis. Immunogenetics 45:336-340. Yeager, M., Kumar, S., and Hughes, A.L. 1997. Sequence convergence in the peptide-binding region of primate and rodent MHC class Ib molecules. Mol. Biol. Evol. 14:1035-1041 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 and the evolutionary history of major histocompatibility complex loci. Frontiers in Bioscience 3:509-516 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. 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. 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 new taxonomy of mammalian MHC class I molecules. Immunol. Today 20: 22-26. Boyson, J.E., Iwanaga, K.K., Urvater, J.A., Hughes, A.L., Golos, T.G., and Watkins, D.I. 1999. Evolution of a new nonclassical MHC class I locus in two Old World primate species. Immunogenetics 49: 86-98. 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. Tasaki, Y., Fukuda, S., Ito, M., Retsu, M., Imai, T., Sugano, S., Yoshie, O., Hughes, A.L., and Nomiyama, H. 1999. Chemokine PARC gene (SCYA18) generated by fusion of two MIP-1/LD78-like genes. Genomics 55: 353-357. Verra, F., and Hughes, A.L. 1999. Biased amino acid composition in repeat regions of Plasmodium antigens. Mol. Biol. Evol. 16: 627-633. Hughes, A.L. 2000. Modes of evolution in the protease and kringle domains of the plasminogen- prothrombin family. Mol. Phyl. Evol. 14: 469-478. Hughes, A.L. 2000. Evolution of introns and exons of class II MHC genes of vertebrates. Immuno- genetics 51: 473-486. Hughes, A.L., and Friedman, R. 2000. Evolutionary diversification of protein-coding genes of hantaviruses. Mol. Biol. Evol. 17: 1558-1568. 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 Pontarotti, P. 2000. Gene duplication and MHC origins. Immunogenetics 51: 982-983. 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. Mothé, 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. Urvater, J.A., Otting, N., Loerke, J.H., Rudersdorf, R., Slukvin, I.I., Piekarczy, M.S., Golos, T.G., Hughes, A.L., Bontrop, R.E., and Watkins, D.I. 2000. Mamu-I: a novel primate MHC class I B-related locus with unusually low variability. J. Immunol. 164: 1386-1398. 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. Yeager, M., Carrington, M., and Hughes, A.L. 2000. Class I and class II MHC bind peptide sets that are strikingly different in their evolutionary characteristics. Immunogenetics 51:8-15. Hughes, A.L. 2001. Evolution of the integrin α and β protein families. J. Mol. Evol. 52: 63-72. Hughes, A.L. 2001. Evolutionary change of predicted cytotoxic T cell epitopes of dengue virus. Infection, Genetics and Evolution 1: 123-130. 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., and Verra, F. 2001. Very large long-term effective population size in the virulent human malaria parasite Plasmodium falciparum. Proc. R. Soc Lond. B 268: 1855-1860. 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 the tat and vpr genes of simian immunodeficiency virus. J. Virol. 75: 7666-7672. Erickson, A.L., Kimura, Y., Igarashi, S., Eichelberger, J., Houghton, M., Sidney, J., McKinney, D., Sette, A., Hughes, A.L., and Walker, C.M. 2001. The outcome of hepatitis C virus infection is predicted by escape mutations in epitopes targeted by cytotoxic T lymphocytes. Immunity 15: 883-895. Friedman, R., and Hughes, A.L. 2001. Gene duplication and the structure of eukaryotic genomes. Genome Research 11: 373-381. Friedman, R., and Hughes, A.L. 2001. Pattern and timing of gene duplication in animal genomes. Genome Research 11: 1842-1847. Grendell, R.L., Hughes, A.L., and Golos, T.G. 2001. Cloning of rhesus monkey killer-cell Ig-like receptors (KIRs) from early pregnancy decidua. Tissue Antigens 58: 329-334. Wang, X., Hughes, A.L., Tsukamoto, T., Ando, T., and Kao, T.-H. 2001. Evidence 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 proteing enes 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. Hughes, A.L., Friedman, R., and Murray, M. 2002. Genomewide pattern of synonymous nucleotide substitution in two complete genomes of Mycobacterium tuberculosis. Emerg. Infect. Dis. 8: 1342-1346. Bashirova, A.A., Wu, L., Cheng, J., Martin, T.D., Martin, M.P., Benveniste, R.E., Lifson, J.D., KewelRamani, V.N., Hughes, A., and Carrington, M. 2003. Novel member of the CD209 (DC-SIGN) gene family in primates. J. Virol. 77: 217-237. Flugge, P. Zimmermann, E., Hughes, A.L., Günter, E., and Walter, L. 2002. Characterization and phylogenetic relationship of prosimian MHC class I genes. J. Mol. Evol. 55: 768-775. Friedman, R., and Hughes, A.L. 2002. Molecular evolution of the NF-κB 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., Mothé, B., Yamamoto, H., Horton, H., Wilson, N., Hughes, A.L., and Watkins, D.I. 2002. Acute phase cytotoxic T 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 α 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 α-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 β-defensin gene cluster in the chicken: implications for the origin and evolution of mammalian defensins. BMC Genomics 2004, 5:56. Hughes, A.L. 2005. Evidence for abundant slightly deleterious polymorphisms in bacterial populations. Genetics 169: 553-558. Hughes, A.L. 2005. Consistent across-tissue signatures of differential gene expression in Crohn’s Disease. Immunogenetics 57: 709-716. 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 Friedman, R. 2005. Gene duplication and the properties of biological networks. J. Mol. Evol. 61: 758-764. Hughes, A.L., and Hughes, M.A.. 2005. Patterns of nucleotide difference in overlapping and non-overlapping reading frames of papillomavirus genomes. Virus Research 113: 81-88. 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. Hughes, A.L., Packer, B., Welsch, R., Chanock, S.J. and Yeager, M. 2005. High level of functional polymorphism indicates a unique role of natural selection at human immune system loci. Immunogenetics 57: 821-827. Hughes, A.L., Piontkivska, H., Krebs, K.C., O’Connor, D.H., and Watkins D.I. 2005. Within-host evolution of CD8+-TL epitopes encoded by overlapping and non-overlapping reading frames of simian immunodeficiency virus. Bioinformatics 21 Suppl. 3: iii39-iii44. Biron, D.G., Moura, H., Marché, 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. Krebs, K.C., Jin, Z., Rudersdorf, R., Hughes, A.L., and O’Connor, D.H. 2005. Unusually high frequency MHC class I alleles in Mauritian origin cynomolgus macaques. J. Immunol. 175: 5230-5239. Piontkivska, H., and Hughes, A.L. 2005. Environmental kinetoplastid-like 18S rRNA sequences and phylogenetic relationships among Trypanosomatidae: paraphyly of the genus Trypanosoma. Mol. Biochem. Parasitol. 144: 94-99. Hughes, A.L. 2006. Evolutionary relationships of vertebrate NACHT domain-containing proteins. Immunogenetics 58: 785-791. Hughes, A.L., and Friedman, R. 2006. Across-tissue expression and evolution of genes controlled by the aire transcription factor. Genomics 88: 462-467. Hughes, A.L., and Glenn, N.L. 2006. Contrasting patterns of transcript abundance in tumor tissue and cancer cell lines. Applied Bioinformatics 5: 201-210. Hughes, A.L., Friedman, R., and Glenn, N.L. 2006. The future of data analysis in evolutionary genomics. Current Genomics 7: 227-234. Friedman , R., and Hughes, A.L. 2006. Pattern of gene duplication in the Cotesia congregata bracovirus. Infect. Genet. Evol. 6: 315-322. Piontkivska, H., and Hughes, A.L. 2006. Patterns of sequence evolution at epitopes for host antibodies and cytotoxic T-lymphocytes in Human Immunodeficiency Virus Type 1. Virus Research 116: 98-105. Chakrabarty, A., MacLean, J.A. II, Hughes, A.L., Roberts, R.M., and Green, J.A. 2006. Rapid Evolution of the Trophoblast Kunitz Domain Proteins (TKDPs)— a multigene family in ruminant ungulates. J. Mol. Evol. 63: 274-282. Putaporntip, C., Jongwutiwes, S., Iwasaki, T., Kanbara, H., and Hughes, A.L. 2006. Ancient common ancestry of the merozoite surface protein 1 of Plasmodium vivax as inferred from its homologue in Plasmodium knowlesi. Mol. Biochem. Parasitol. 146: 105-108. Slukvin, I.I., Grendell, R.L., Rao, D.S., Hughes, A.L., and Golos, T.G. 2006. Cloning of rhesus monkey LILRs. Tissue Antigens 67: 331-337. Hughes, A.L. 2007. Micro-scale signature of purifying selection in Marburg virus genomes. Gene 392: 266-272. Hughes, A.L. 2007. Evolution of the lung surfactant proteins in birds and mammals. Immunogenetics 59: 565-572. Hughes, A.L. 2007. Looking for Darwin in all the wrong places: the misguided quest for positive selection at the nucleotide sequence level. Heredity 99:364-373. Hughes, A.L., and French, J.O. 2007. Homologous recombination and the pattern of nucleotide substitution in Ehrlichia ruminantium. Gene 387:31-37. Hughes, A.L., and Friedman, R. 2007. Sharing of transcription factors after gene duplication in the yeast Saccharomyces cerevisiae. Genetica 129: 301-308. Hughes, A.L., Friedman, R. 2007. The effect of branch lengths on phylogeny: an empirical study using highly conserved orthologs from mammalian genomes. Mol. Phyl. Evol. 45: 81-88. Hughes, A.L., and Hughes, M.A. 2007. Nucleotide substitution at the highly polymorphic K1 locus of Human herpesvirus 8 (Kaposi’s sarcoma-associated herpesvirus). Infect. Genet. Evol. 7: 110-115. Hughes, A.L., and Hughes, M.A. 2007. More effective purifying selection in RNA viruses than in DNA viruses. Gene 404: 117-125. Hughes, A.L., and Hughes, M.A.. 2007. Coding sequence polymorphism in avian mitochondrial genomes reflects population histories. Mol. Ecol. 16: 1369-1376. Hughes, A.L., and Langley, K.L. 2007. Nucleotide usage, synonymous substitution pattern, and past recombination in genomes of Streptococcus pyogenes. Infect. Genet. Evol. 7: 188-196. Hughes, A.L., and Rivailler, P. 2007. Phylogeny and recombination history of gallid herpesvirus 2 (Marek’s disease virus) genomes. Virus Res. 130: 28-33. Hughes, A.L., Hughes, M.A.K., and Friedman, R. 2007. Variable intensity of purifying selection on cytotoxic T-lymphocyte epitopes in hepatitis C virus. Virus Research 123: 147-153. Hughes, A.L., Piontkivska, H., and Foppa, I. 2007. Rapid fixation of a distinctive sequence motif in the 3’ noncoding region of the clade of West Nile virus invading North America. Gene 399:152-161. Averdam, A., Kuhl, H., Sontag, M., Becker, T., Hughes, A.L., Reinhardt, R., and Walter, L. 2007. Genomics and diversity of the common marmoset monkey NK complex. J. Immunol. 178: 5151-7161. Conley, A.J., Corbin, C.J., Mapes, S.M., Place, N.J., Hughes, A.L., and Glickman, S.E. 2007. Placental expression and molecular characterization of aromatase cytochrome P450 in the spotted hyena (Crocuta crocuta). Placenta 28: 668-675. Corbin, C.J., Hughes, A.L., Hefflefinger, J.R., Berger, T., Waltzek, T.B., Roser, J.F., Santos, T.C., Miglino, M.A., Oliveira, M.F., Braga, F.C., Meirelles, F.V., and Conley, A.J. 2007. Evolution of Suiform aromatases: ancestral duplication with conservation of tissue-specific expression in the collared peccary (Pecari tayassu). J. Mol. Evol. 65: 403-412. Friedman, R., and Hughes, A.L. 2007. Likelihood-ratio tests for positive selection of human and mouse duplicate genes reveal non-conservative and anomalous properties of widely used methods. Mol. Phyl. Evol. 42: 388-397. Loffredo, J.T., Friedrich, T.C., Léon, E.J., Stephany, J.J., Rodrigues, D.S., Spencer, S.P., Bean, A.T., Beal, D.R., Burwitz, B.J., Rudersdorf, R.A., Wallace, L.T., Piaskowski, S.M., May, G.E., Sidney, J., Gostick, E., Wilson, N.A., Price, D.A., Kallas, E.G., Piontkiska, H., Hughes, A.L., Sette, A., and Watkins, D.I. 2007. The MHC class I molecule Mamu-B*08 presents several SIV-derived epitopes to CD8+ T cells that select for widespread viral variation. PloS ONE 2 (11): e1152. Maness, N.J., Valentine, L.E., May, G.E., Reed, J., Piaskowski, S.M., Soma, T., Furlott, J., Rakasz, E.G., Friedrich, T.C., Price, D.A., Gostick, E., Hughes, A.L., Sidney, J., Sette, A., Wilson, N.A., Walkins, D.I. 2007. AIDS virus-specific CD8+ T lymphocytes against an immunodominant cryptic epitope select for viral escape. J. Exp. Med. 204: 2505-2512. O’Connor, S.L., Blasky, A.J., Pendley, C.J., Becker, E.A., Wiseman, R.W., Karl, J.A., Hughes, A.L., and O’Connor, D.H. 2007. Comprehensive characterization of MHC class II haplotypes in Mauritian cynomolgus macaques. Immunogenetics 59: 449-462. Schwartz, R.S., Hodes-Villamar, L., Fitzpatrick, K.A., Fain, M.G., Hughes, A.L., and Cadavid, L.F. 2007. A gene family of putative immune recognition molecules in the hydroid Hydractinia. Immunogenetics 59: 233-246. Westover, K., and Hughes, A.L. 2007. Evolution of cytotoxic T-lymphocyte epitopes in hepatitis B virus. Infect. Genet. Evol. 7: 254-262. Hughes, A.L. 2008. Near neutrality: leading edge of the neutral theory of molecular evolution. Ann. N.Y. Acad. Sci. 1133: 162-179. Hughes, A.L. 2008. The origin of adaptive phenotypes. Proc. Natl. Acad. Sci. USA 105: 13193-19194. Hughes, A.L. 2008. Temporal pattern of vocalization type usage in singing sessions of male tyrant flycatchers. J. Avian Biol. 39: 24-29. Hughes, A.L., and Friedman, R. 2008. Genome size reduction in the chicken has involved massive loss of ancestral protein-coding genes. Mol. Biol. Evol. 25: 2681-2688. Hughes, A.L., and Friedman, R. 2008. Codon-based tests of positive selection, branch lengths, and the evolution of mammalian immune system genes. Immunogenetics 60: 495-506. Hughes, A.L., and Friedman, R. 2008. Alternative splicing, gene duplication and connectivity in the genetic interaction network of the nematode worm Caenorhabditis elegans. Genetica 134: 181-186. Hughes, A.L., Friedman, R., Rivailler, P., and French, J.O. 2008. Synonymous and nonsynonymous polymorphisms and divergences in bacterial genomes. Mol. Biol. Evol. 25: 2199-2209. Hughes, A.L., and Piontkivska, H. 2008. Nucleotide sequence polymorphism in circoviruses. Infection, Genetics, and Evolution 8:130-138. Hughes, A.L., and Piontkivska, H. 2008. Functional diversification of the toll-like receptor gene family. Immunogenetics 60: 249-256. Hughes, A.L., Welch, R., Puri, V., Matthews, C., Haque, K., Chanock, S.J., Yeager, M. 2008. Genome-wide SNP typing reveals signatures of population history. Genomics 92: 1-8. Bimber, B.N., Moreland, A.J., Wiseman, R.W., Hughes, A.L., and O’Connor, D.H. 2008. Complete characterization of killer Ig-like receptor (KIR) haplotypes in Mauritian cynomulgus macaques: novel insights into nonhuman primate KIR gene content and organization. J. Immunol. 181: 6301-6308. Conley, A.J., Corbin, C.J., and Hughes, A.L. 2008. Adaptive evolution of mammalian aromatases: lessons from Suiformes. J. Exp. Zool. Part A. Ecol. Genet. Physiol. 311: 346-357. Grynberg, P., Fontes, C.J.F., Hughes, A.L., Braga, É.M. 2008. Polymorphism at the Apical Membrane Antigen-1 locus reflects the world population history of Plasmodium vivax. BMC Evol. Biol. 2008, 8:123. Irausquin, S.J., and Hughes, A.L. 2008. Distinctive pattern of sequence polymorphism in the NS3 protein of hepatitis C virus type 1b reflects conflicting evolutionary pressures. J. Gen. Virol. 89: 1921-1929. Karl, J.A., Wiseman, R.W., Campbell, K.J., Blasky, A.J., Hughes, A.L., Ferguson, B., Read, D.S., and O’Connor, D.H. 2008. Identification of MHC class I sequences in Chinese-origin rhesus macaques. Immunogenetics 60: 37-46. Maness, N.J., Yant, L.J., Chung, C., Loffredo, J.T., Friedrich, T.C., Piaskowski, S.M., Furlott, J., May, G.E., Soma, T., Léon, E.J., Wilson, N.A., Piontkivska, H., Hughes, A.L., Sidney, J., Sette, A., and Watkins, D.I. 2008. Comprehensive immunological evaluation reveals surprisingly few differences between elite controller and progressor Mamu-B*17-positive Simian immunodeficiency virus-infected rhesus macaques. J. Virol. 82: 5245-5254. Pendley, C.J., Becker, E.A., Karl, J.A., Wiseman, R.W., Hughes, A.L., O’Connor, D.H. 2008. MHC class I characterization of Indonesian cynomulgus macaques. Immunogenetics 60: 339-351. Putaporntip, C., Jongwutiwes, S., and Hughes, A.L. 2008. Differential selectve pressures on the merozoite surface protein 2 locus of Plasmodium falciparum in a low endemic area. Gene 427: 51-57. Hughes, A.L. 2009. Small effective population sizes and rare nonsynonymous variants in potyviruses. Virology 393: 127-134. Hughes, A.L. 2009. Relaxation of purifying selection on live attenuated vaccine strains of the family Paramyxoviridae. Vaccine 27: 1685-1690. Hughes, A.L. 2009. Relaxation of purifying selection on the SAD lineage of live attenuated oral vaccines for rabies virus. Infect. Genet. Evol. 9: 827-831. Hughes, A.L., and Friedman, R. 2009. More radical amino acid replacements in primates than in rodents: support for the evolutionary role of effective population size. Gene 440:50-56. Hughes, A.L., and Friedman, R. 2009. A phylogenetic approach to gene expression data: evidence for the evolutionary origin of mammalian leukocyte phenotypes. Evolution and Development 11: 382-390. Bimber, B.N., Burwitz, B.J., O’Connor, S., Detmer, A., Gostick, E., Lank, S.M., Price, D.A., Hughes, A., O’Connor, D. 2009. Ultradeep pyrosequencing detects complex patterns of CD8+T-lymphocyte escape in simian immunodeficiency virus. J. Virol. 83: 8247-8253. Bondarenko, G.I., Dambaeva, S.V., Grendell, R.L., Hughes, A.L., Durning, M., Garthwaite, M.A., and Golos, T.G. 2009. Characterization of cynomolgus and vervet monkey placental MHC class I expression: diversity of the nonhuman primate AG locus. Immunogenetics 61: 431-442. Campbell, K.J., Detmer, A.M., Karl, J.A., Wiseman, R.W., Blasky, A.J., Hughes, A.L., Bimber, B.N., O’Connor, S.L., and O’Connor, D.H. 2009. Characterization of 47 MHC class I sequences in Filipino cynomolgus macaques. Immunogenetics 61: 177-187. Putaporntip, C., Jongwutiwes, S., and Hughes, A.L. 2009. Natural selection maintains a stable polymorphism at the circumsporozoite protein locus of Plasmodium falciparum in a low endemic area. Infect. Genet. Evol. 9:567-573. Putaporntip, C., Jongwutiwes, S., Grynberg, P., Cui, L., Hughes, A.L. 2009. Nucleotide sequence polymorphism at the apical membrane antigen-1 locus reveals population history of Plasmodium vivax in Thailand. Infect. Genet. Evol. 9: 1295-1300. Hughes, A.L. 2010. Origin and diversification of the L-amino oxidase family in innate immune defenses of animals. Immunogenetics 62: 753-759. Hughes, A.L. 2010. Reduced microsatellite heterozygosity in island endemics supports the role of long-term effective population size in avian microsatellite diversity. Genetica 138: 1271-1276. Hughes, A.L. 2010. Evolutionary conservation of amino acid composition in paralogous insect vitellogenins. Gene 467: 35-40. Hughes, A.L. 2010. Runaway evolution of the male-specific exon of the doublesex gene in Diptera. Gene 472: 1-6. Hughes, A.L., and Buitenhuis, A.J. 2010. Reduced variance of gene expression at numerous loci in a population of chickens selected for high feather pecking. Poultry Sci. 89: 1858-1869. Hughes, A.L., and Verra, F. 2010. Malaria parasite sequences from chimpanzee support the co-speciation hypothesis for the origin of virulent human malaria (Plasmodium falciparum). Mol. Phyl. Evol. 57: 135-143. Hughes, A.L., Irausquin, S.J., and Friedman, R. 2010. Evolutionary biology of poxviruses. Infect. Genet. Evol. 10: 50-59. Hughes, A.L., O’Connor, S., Dudley, D.M., Burwitz, B.J., Bimber, B.N., and O’Connor, D. 2010. Dynamics of haplotype frequency change in a CD8+TL epitope of simian immunodeficiency virus. Infect. Genet. Evol. 10: 555-560. Bimber, B.N., Dudley, D.M., Lauck, M., Becker, E.A., Chin, E.N., Lank, S.M., Grunenwald, H.L., Caruccio, N.C., Maffit, M., Wilson, N.A., Reed, J.S., Sosman, J.M., Tarosso, L.F., Sanabani, S., Kallas, E.G., Hughes, A.L., and O’Connor, D.H. 2010. Whole genome characterization of HIV/SIV intrahost diversity by ultradeep pyrosequencing. J. Virol. 84: 12087-12092. Fuller, M.J., Shoukry, N.H., Bowen, D.G., Callendret, B., Campbell, K., Hasselschwert, D.L., Hughes, A.L., and Walker, C.M. 2010. Selection-driven immune escape is not a significant factor in the failure of CD4 T cell responses in persistent hepatitis C virus infection. Hepatology 51: 378-387. Irausquin, S.J., and Hughes, A.L. 2010. Conflicting selection pressures target the NS3 protein in hepatitis C virus genotypes 1a and 1b. Virus Research 147:202-207. Jongwutiwes, S., Putaporntip, C. and Hughes, A.L. 2010. Bottleneck effects on vaccine-candidate antigen diversity of malaria parasites in Thailand. Vaccine 28: 3112-3117. Luo, H., Tang, J., Friedman, R., and Hughes, A.L. 2010. Ongoing purifying selection on intergenic spacers in group A streptococcus. Infect. Genet. Evol. 11: 343-348. O’Connor, S.L., Lhost, J.J., Becker, E.A., Detmer, A.M., Johnson, R.C., Macnair, C.E., Wiseman, R.W., Karl, J.A., Greene, J.M., Burwitz, B.J., Bimber, B.N., Lank, S.M., Tuscher, J.J., Mee, E.T., Rose, N.J., Desrosiers, R.C., Hughes, A.L., Friedrich, T.C., Carrington, M., and O’Connor, D.H. 2010. MHC heterozygote advantage in simian immunodeficiency cirus-infected Mauritian cynomolgus macaques. Sci. Transl. Med. 2(22):2ra18. Putaporntip, C., Jongwutiwes, S., Thongaree, S., Seethamchai, S., Grynberg, P., and Hughes, A.L. 2010. Ecology of malaria parasites infection Southeast Asian macaques: evidence from cytochrome b sequences. Mol. Ecol. 19: 3466-3476. Hughes, A.L. 2011. Recombinational histories of avian infectious bronchitis virus and turkey coronavirus. Arch. Virol. 156: 1823-1829. Hughes, A.L. 2011. Stereotyped and non-stereotyped features of the temporal patterning of singing sessions in the ovenbird Seiurus auricapillus. Behav. Processes 87: 165-170. Hughes, A.L., and Friedman, R. 2011. A survey of schistosome protein domain types: insights into unique biological properties. Mol. Biochem. Parasitol. 177:100-105. Hughes, A.L., and Friedman, R. 2011. Distinctive amino acid composition profiles in salivary proteins of the tick Ixodes scapularis. Ticks Tick-Bourne Dis. 2: 219-224. Hughes, A.L., and Piontkivska, H. 2011. Evolutionary diversification of the avian fatty acid-binding proteins. Gene 490: 1-5. Callendret, B., Eccleston, H.B., Heksch, R., Hasselschwert, D.L., Purcell, R.H., Hughes, A.L., and Walker, C.M. 2011. Transmission of clonal heoatitis C virus genomes reveals dominant but transitory role for CD8+T cells in early viral evolution. J. Virol. 85: 11833-11845. Creager, H.M., Becker, E.A., Sandman, K.K., Karl, J.A., Lank, S.M., Bimber, B.N., Wiseman, R.W., Hughes, A.L., O’Connor, S.L., and O’Connor, D.H. 2011. Characterization of full-length MHC class II sequences in Indonesian and Vietnamese cynomulgus macaques. Immunogenetics 28: 2751-2760. Irausquin, S.J., and Hughes, A.L. 2011. Conflicting selection pressures on T-cell epitopes in HIV-1 subtype B. Infect. Genet. Evol. 11: 483-488. Knapp, E.W., Irausquin, S.J., Friedman, R., and Hughes, A.L. 2011. PolyAna: analyzing synonymous and nonsynonymous polymorphic sites. Conservation Genet. Resources 3: 429-431. Li, H., Hughes, A.L., Bano, N., McArdle, S., Livingston, S., Deubner, H., McMahon, B.J., Townshend-Bulson, L., McMahan, R., Rosen, H.R., Gretch, D.R. 2011. Genetic diversity of near genome-wide hepatitis C virus sequences during chronic infection: evidence for protein structural conservation over time. PLoS ONE 6(5): e19562. Luo, H., Friedman, R., Tang, J., and Hughes, A.L. 2011. Genome reduction by deletion of paralogs in the marine cyanobacterium Prochlorococcus. Mol. Biol. Evol. 28: 2751-2760. Silva, J., Egan, A., Friedman, R., Munro, J.B., Carlton, J.M., and Hughes, A.L. 2011. Genome sequences reveal divergence times of malaria parasite lineages. Parasitology 138:1737-1749. Hughes, A.L. 2012. Evolution of adaptive phenotypic traits without positive Darwinian selection. Heredity 108: 347-353. Hughes, A.L. 2012. Amino acid sequence coevolution in the insect bursicon ligand-receptor system. Mol. Phyl. Evol. 63: 617-624. Hughes, A.L. 2012. Evolution of the βGRP/GNBP/β-1,3-glucanase family of insects.Immunogenetics 64: 549-558. Becker. E.A., Burns, C.M., Léon, E.J., Rajabojan, S., Friedman, R., Friedrich, T.C., O’Connor, S.L., and Hughes, A.L. 2012. Experimental analysis of sources of error in evolutionary studies based on Roche/454 pyrosequencing of viral genomes. Genome Biol. Evol. 4: 457-464. Boggs, J.M., South, A.H., and Hughes, A.L. 2012. Phylogenetic analysis supports horizontal gene transfer of L-amino acid oxidase gene in Streptococcus oligofermentans. Infect. Genet. Evol. (in press). Lauck, M., Alvarado-Mora, M.V., Becker, E.A., Bhattacharya, D., Striker, R., Hughes, A.L., Carrilho, F.J., O’Connor, D.H., and Rebello Pinho, J.R.2012. Analysis of hepatitis C virus intra-host diversity across the coding region by ultra-deep pyrosequencing. J. Virol. 86: 3952-3960. Mudd PA, Ericsen AJ, Burwitz BJ, Wilson NA, O’Connor DH, Hughes AL, and Watkins DI. 2012. Escape from CD8+ T cell responses in Mamu-B*00801+ macaques differentiates progressors from elite controllers. J. Immunol. 188: 3364-3370. O’Connor, S.L., Weinfurter, J., Chin, E.N., Budde, M.L., Gostick, E., Correll, M., Gleicher, M., Hughes, A.L., Price, D.A., Friedrich, T.C.., and O’Connor, D. H. 2012. Conditional CD8+ T cell escape during simian immunodeficiency virus infection. J. Virol. 85: 605-609.

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