Austin Hughes

Summary

Affiliation: University of South Carolina
Country: USA

Publications

  1. pmc The origin of adaptive phenotypes
    Austin L Hughes
    Department of Biological Sciences, University of South Carolina, Columbia, SC 29208, USA
    Proc Natl Acad Sci U S A 105:13193-4. 2008
  2. ncbi request reprint Homologous recombination and the pattern of nucleotide substitution in Ehrlichia ruminantium
    Austin L Hughes
    Department of Biological Sciences, University of South Carolina, Coker Life Sciences Bldg, 700 Sumter Street, Columbia, SC 29208, USA
    Gene 387:31-7. 2007
  3. pmc Evolution of adaptive phenotypic traits without positive Darwinian selection
    A L Hughes
    Department of Biological Sciences, University of South Carolina, Columbia, SC 29208, USA
    Heredity (Edinb) 108:347-53. 2012
  4. doi request reprint Evolutionary diversification of insect innexins
    Austin L Hughes
    Department of Biological Sciences, University of South Carolina, Columbia, SC 29208, USA
    J Insect Sci 14:. 2014
  5. pmc Life-history evolution at the molecular level: adaptive amino acid composition of avian vitellogenins
    Austin L Hughes
    Department of Biological Sciences, University of South Carolina, Columbia, SC 29208, USA
    Proc Biol Sci 282:20151105. 2015
  6. doi request reprint Adaptive amino acid composition in collagens of parasitic nematodes
    Austin L Hughes
    Department of Biological Sciences, University of South Carolina, Columbia, SC 29208, USA Electronic address
    Infect Genet Evol 31:277-83. 2015
  7. pmc Evolutionary diversification of the vertebrate transferrin multi-gene family
    Austin L Hughes
    Department of Biological Sciences, Coker Life Sciences Building, University of South Carolina, 715 Sumter St Columbia, Columbia, SC, 29208, USA
    Immunogenetics 66:651-61. 2014
  8. pmc Evolutionary diversification of the avian fatty acid-binding proteins
    Austin L Hughes
    Department of Biological Sciences, University of South Carolina, Columbia, SC 29208, USA
    Gene 490:1-5. 2011
  9. pmc Codon-based tests of positive selection, branch lengths, and the evolution of mammalian immune system genes
    Austin L Hughes
    Department of Biological Sciences, University of South Carolina, Columbia, SC 29208, USA
    Immunogenetics 60:495-506. 2008
  10. ncbi request reprint Aspartic proteinase phylogeny and the origin of pregnancy-associated glycoproteins
    Austin L Hughes
    Department of Biological Sciences, University of South Carolina, USA
    Mol Biol Evol 20:1940-5. 2003

Research Grants

  1. Gene Duplication and Genome Evolution
    Austin Hughes; Fiscal Year: 2004
  2. EVOLUTION OF IMMUNE RECOGNITION AND EVASION
    Austin L Hughes; Fiscal Year: 2010

Detail Information

Publications119 found, 100 shown here

  1. pmc The origin of adaptive phenotypes
    Austin L Hughes
    Department of Biological Sciences, University of South Carolina, Columbia, SC 29208, USA
    Proc Natl Acad Sci U S A 105:13193-4. 2008
  2. ncbi request reprint Homologous recombination and the pattern of nucleotide substitution in Ehrlichia ruminantium
    Austin L Hughes
    Department of Biological Sciences, University of South Carolina, Coker Life Sciences Bldg, 700 Sumter Street, Columbia, SC 29208, USA
    Gene 387:31-7. 2007
    ....
  3. pmc Evolution of adaptive phenotypic traits without positive Darwinian selection
    A L Hughes
    Department of Biological Sciences, University of South Carolina, Columbia, SC 29208, USA
    Heredity (Edinb) 108:347-53. 2012
    ..The PRM mechanism can easily explain cases of explosive adaptive radiation, as well as recently reported cases of apparent adaptive evolution over ecological time...
  4. doi request reprint Evolutionary diversification of insect innexins
    Austin L Hughes
    Department of Biological Sciences, University of South Carolina, Columbia, SC 29208, USA
    J Insect Sci 14:. 2014
    ....
  5. pmc Life-history evolution at the molecular level: adaptive amino acid composition of avian vitellogenins
    Austin L Hughes
    Department of Biological Sciences, University of South Carolina, Columbia, SC 29208, USA
    Proc Biol Sci 282:20151105. 2015
    ....
  6. doi request reprint Adaptive amino acid composition in collagens of parasitic nematodes
    Austin L Hughes
    Department of Biological Sciences, University of South Carolina, Columbia, SC 29208, USA Electronic address
    Infect Genet Evol 31:277-83. 2015
    ....
  7. pmc Evolutionary diversification of the vertebrate transferrin multi-gene family
    Austin L Hughes
    Department of Biological Sciences, Coker Life Sciences Building, University of South Carolina, 715 Sumter St Columbia, Columbia, SC, 29208, USA
    Immunogenetics 66:651-61. 2014
    ....
  8. pmc Evolutionary diversification of the avian fatty acid-binding proteins
    Austin L Hughes
    Department of Biological Sciences, University of South Carolina, Columbia, SC 29208, USA
    Gene 490:1-5. 2011
    ....
  9. pmc Codon-based tests of positive selection, branch lengths, and the evolution of mammalian immune system genes
    Austin L Hughes
    Department of Biological Sciences, University of South Carolina, Columbia, SC 29208, USA
    Immunogenetics 60:495-506. 2008
    ..Our results showed that b (N)/b (S) was consistently elevated in immune system genes, but neither the search for branches with b (N) > b (S) nor the branch-site method revealed this trend...
  10. ncbi request reprint Aspartic proteinase phylogeny and the origin of pregnancy-associated glycoproteins
    Austin L Hughes
    Department of Biological Sciences, University of South Carolina, USA
    Mol Biol Evol 20:1940-5. 2003
    ..The conservation of this ancestral change suggests that it may be important to PAG function, particularly the fact that PAGs lack proteinase activity in spite of the conservation of active site residues in most PAGs...
  11. pmc A survey of schistosome protein domain types: insights into unique biological properties
    Austin L Hughes
    Department of Biological Sciences, University of South Carolina, Columbia, SC 29208, USA
    Mol Biochem Parasitol 177:100-5. 2011
    ..mansoni suggests that this species may be infected by a virus of this group, which might be useful as a biological control agent...
  12. pmc Very large long-term effective population size in the virulent human malaria parasite Plasmodium falciparum
    A L Hughes
    Department of Biological Sciences, University of South Carolina, Columbia, SC 29208, USA
    Proc Biol Sci 268:1855-60. 2001
    ..Both simple methods and phylogenetically based maximum-likelihood methods yielded the conclusion that the effective population size of this species has been of the order of at least 10(5) for the past 300,000-400,000 years...
  13. pmc The effect of branch lengths on phylogeny: an empirical study using highly conserved orthologs from mammalian genomes
    Austin L Hughes
    Department of Biological Sciences, University of South Carolina, Coker Life Sciences Building, 700 Sumter Street, Columbia, SC 29208, USA
    Mol Phylogenet Evol 45:81-8. 2007
    ..Thus, in these data, a tendency of long and short branches to cluster together ("opposite-branch attraction") seemed to be more of a problem than long-branch attraction...
  14. ncbi request reprint Natural selection and the diversification of vertebrate immune effectors
    Austin L Hughes
    Department of Biological Sciences, University of South Carolina, Columbia, SC 29208, USA
    Immunol Rev 190:161-8. 2002
    ..Examples include molecules of the specific immune system (such as immunoglobulin V region genes) and molecules of the innate immune system (such as defensins)...
  15. pmc Evolutionary conservation of amino acid composition in paralogous insect vitellogenins
    Austin L Hughes
    Department of Biological Sciences, University of South Carolina, Coker Life Sciences Bldg, 700 Sumter St, Columbia, SC 29208, USA
    Gene 467:35-40. 2010
    ....
  16. ncbi request reprint Phylogeny of the Picornaviridae and differential evolutionary divergence of picornavirus proteins
    Austin L Hughes
    Department of Biological Sciences, University of South Carolina, Coker Life Sciences Bldg, 700 Sumter Street, Columbia, SC 29208, USA
    Infect Genet Evol 4:143-52. 2004
    ..However, the same pattern was not seen in more distantly related pairs of viruses, which showed a number of distinct patterns with regard to the relative conservation of the 11 proteins...
  17. pmc A phylogenetic approach to gene expression data: evidence for the evolutionary origin of mammalian leukocyte phenotypes
    Austin L Hughes
    Department of Biological Sciences, University of South Carolina, Columbia, SC 29208, USA
    Evol Dev 11:382-90. 2009
    ....
  18. ncbi request reprint Genome-wide survey for genes horizontally transferred from cellular organisms to baculoviruses
    Austin L Hughes
    Department of Biological Sciences, University of South Carolina, Columbia, SC, USA
    Mol Biol Evol 20:979-87. 2003
    ..By contrast, the gene encoding chitinase in these viruses was evidently derived from a group of bacteria (the gamma subdivision of proteobacteria), which use chitinase to break down fungal chitins...
  19. ncbi request reprint Birth-and-death evolution of protein-coding regions and concerted evolution of non-coding regions in the multi-component genomes of nanoviruses
    Austin L Hughes
    Department of Biological Sciences, University of South Carolina, Coker Life Sciences Building, 700 Sumter St, Columbia, SC 29208, USA
    Mol Phylogenet Evol 30:287-94. 2004
    ..Thus, there is a process of concerted evolution of non-coding regions of Nanovirus genome components, which raises the possibility that certain non-coding regions are subject to functional constraint...
  20. doi request reprint Evolution of the βGRP/GNBP/β-1,3-glucanase family of insects
    Austin L Hughes
    Department of Biological Sciences, University of South Carolina, Coker Life Sciences Bldg, 700 Sumter St, Columbia, SC 29208, USA
    Immunogenetics 64:549-58. 2012
    ....
  21. pmc Amino acid sequence coevolution in the insect bursicon ligand-receptor system
    Austin L Hughes
    Department of Biological Sciences, University of South Carolina, Columbia, SC 29205, USA
    Mol Phylogenet Evol 63:617-24. 2012
    ....
  22. ncbi request reprint Transposable element distribution in the yeast genome reflects a role in repeated genomic rearrangement events on an evolutionary time scale
    Austin L Hughes
    Department of Biological Sciences, University of South Carolina, Coker Life Sciences Bldg, Columbia, SC 29205, USA
    Genetica 121:181-5. 2004
    ....
  23. pmc Consistent across-tissue signatures of differential gene expression in Crohn's disease
    Austin L Hughes
    Department of Biological Sciences, University of South Carolina, Coker Life Sciences Bldg, 700 Sumter St, Columbia, SC 29208, USA
    Immunogenetics 57:709-16. 2005
    ..These included a number of genes relevant to the mechanism of pathogenesis of CD and a number of genes mapping to genomic regions that have previously shown linkage to CD in association studies...
  24. ncbi request reprint Pattern of divergence of amino acid sequences encoded by paralogous genes in human and pufferfish
    Austin L Hughes
    Department of Biological Sciences, University of South Carolina, Columbia, SC 29205, USA
    Mol Phylogenet Evol 32:337-43. 2004
    ..On the other hand, the data are easily explained under an alternative model that gene duplications occurred at different times in different vertebrate gene families...
  25. ncbi request reprint Recent mammalian gene duplications: robust search for functionally divergent gene pairs
    Austin L Hughes
    Department of Biological Sciences, University of South Carolina, Coker Life Sciences Building, 700 Sumter Street, Columbia, SC 29208, USA
    J Mol Evol 59:114-20. 2004
    ..This approach identified six duplicate gene pairs that appeared to be candidates for functional differentiation as a result of positive Darwinian selection...
  26. ncbi request reprint Nucleotide substitution at the highly polymorphic K1 locus of human herpesvirus 8 (Kaposi's sarcoma-associated herpesvirus)
    Austin L Hughes
    Department of Biological Sciences, University of South Carolina, Columbia, SC 29208, United States
    Infect Genet Evol 7:110-5. 2007
    ....
  27. pmc Malaria parasite sequences from chimpanzee support the co-speciation hypothesis for the origin of virulent human malaria (Plasmodium falciparum)
    Austin L Hughes
    Department of Biological Sciences, University of South Carolina, Columbia, SC 29208, USA
    Mol Phylogenet Evol 57:135-43. 2010
    ..falciparum mitochondrial genomes. The available data are thus most consistent with the hypothesis that P. reichenowi (in the strict sense) and P. falciparum co-speciated with their hosts about 5-7 million years ago...
  28. ncbi request reprint Evolution of the lung surfactant proteins in birds and mammals
    Austin L Hughes
    Department of Biological Sciences, University of South Carolina, Coker Life Sciences Bldg, 700 Sumter St, Columbia, SC 29208, USA
    Immunogenetics 59:565-72. 2007
    ..Further, they imply that the loss of surfactant protein genes in the avian lineages formed part of major genomic rearrangement events that involved the loss of other genes as well...
  29. ncbi request reprint Nucleotide usage, synonymous substitution pattern, and past recombination in genomes of Streptococcus pyogenes
    Austin L Hughes
    Department of Biological Sciences, University of South Carolina, Columbia, SC 29205, USA
    Infect Genet Evol 7:188-96. 2007
    ..On the other hand, nucleotide content, when suitably measured, can form one of a set of biological indicators that can be used to identify candidate genes for horizontal gene transfer...
  30. pmc Relaxation of purifying selection on live attenuated vaccine strains of the family Paramyxoviridae
    Austin L Hughes
    Department of Biological Sciences, University of South Carolina, Coker Life Sciences Bldg, 700 Sumter St, Columbia, SC 29208, USA
    Vaccine 27:1685-90. 2009
    ....
  31. ncbi request reprint High level of functional polymorphism indicates a unique role of natural selection at human immune system loci
    Austin L Hughes
    Department of Biological Sciences, University of South Carolina, Coker Life Sciences Bldg, Columbia, 29208, USA
    Immunogenetics 57:821-7. 2005
    ..These results identified certain immune system loci that are likely to be subject to balancing selection that acts to maintain polymorphism in either coding or regulatory regions...
  32. ncbi request reprint The evolution of amino acid repeat arrays in Plasmodium and other organisms
    Austin L Hughes
    Department of Biological Sciences, University of South Carolina, Coker Life Sciences Building, Columbia, SC 29208, USA
    J Mol Evol 59:528-35. 2004
    ....
  33. doi request reprint Evolution of the salivary apyrases of blood-feeding arthropods
    Austin L Hughes
    Department of Biological Sciences, University of South Carolina, Columbia, SC 29208, USA
    Gene 527:123-30. 2013
    ....
  34. ncbi request reprint Non-random association of transposable elements with duplicated genomic blocks in Arabidopsis thaliana
    Austin L Hughes
    Department of Biological Sciences, University of South Carolina, Coker Life Sciences Bldg, 700 Sumter St, Columbia, SC 29208, USA
    Mol Phylogenet Evol 29:410-6. 2003
    ....
  35. pmc Nucleotide substitution and recombination at orthologous loci in Staphylococcus aureus
    Austin L Hughes
    Department of Biological Sciences, University of South Carolina, Coker Life Sciences Bldg, 700 Sumter St, Columbia SC 29208, USA
    J Bacteriol 187:2698-704. 2005
    ..Therefore, the results support the hypothesis that exchange of homologous genes among S. aureus genomes can play a role in the evolution of pathogenesis in this species...
  36. pmc Evolutionary diversification of aminopeptidase N in Lepidoptera by conserved clade-specific amino acid residues
    Austin L Hughes
    Department of Biological Sciences, University of South Carolina, Columbia, SC 29208, USA Electronic address
    Mol Phylogenet Evol 76:127-33. 2014
    ....
  37. pmc Reassortment of ancient neuraminidase and recent hemagglutinin in pandemic (H1N1) 2009 virus
    Priyasma Bhoumik
    University of South Carolina, Columbia, South Carolina 29208, USA
    Emerg Infect Dis 16:1748-50. 2010
    ..This pattern implies reassortment and suggests that the novel form of hemagglutinin conferred a selective advantage...
  38. pmc Molecular phylogenetics of Trypanosomatidae: contrasting results from 18S rRNA and protein phylogenies
    Austin L Hughes
    Department of Biological Sciences, University of South Carolina, Columbia SC 29205 USA
    Kinetoplastid Biol Dis 2:15. 2003
    ..One possible explanation for these conflicting results is poor taxon sampling in the case of protein coding genes, most of which have been sequenced for only a few species of Trypanosomatidae...
  39. pmc Genomewide pattern of synonymous nucleotide substitution in two complete genomes of Mycobacterium tuberculosis
    Austin L Hughes
    Department of Biological Sciences, University of South Carolina, Columbia, South Carolina 29208, USA
    Emerg Infect Dis 8:1342-6. 2002
    ..Our results suggest that a large number of loci should be examined for an accurate assessment of the level of nucleotide diversity in natural populations of pathogenic microorganisms...
  40. pmc Experimental analysis of sources of error in evolutionary studies based on Roche/454 pyrosequencing of viral genomes
    Ericka A Becker
    Wisconsin National Primate Research Center, University of Wisconsin, WI, USA
    Genome Biol Evol 4:457-65. 2012
    ..On the other hand, if the goal is to estimate nucleotide diversity, an optimal strategy might be to include all observed variants (even those at less than 1% frequency), while masking out homopolymer runs of four or more nucleotides...
  41. doi request reprint Behavioral correlates of post-breeding weight change in a captive flock of American flamingos (Phoenicopterus ruber ruber)
    Austin L Hughes
    Department of Biological Sciences, University of South Carolina, Columbia, South Carolina 29208, USA
    Zoo Biol 32:204-9. 2013
    ..Intervention to increase the equality of food access in the post-breeding period may not be necessary in captive flamingo flocks, since low social rank in most cases appears not to have harmful long-term consequences...
  42. pmc Accumulation of slightly deleterious mutations in the mitochondrial genome: a hallmark of animal domestication
    Austin L Hughes
    Department of Biological Sciences, University of South Carolina, Coker Life Sciences Bldg, 700 Sumter St, Columbia, SC 29208, USA
    Gene 515:28-33. 2013
    ....
  43. pmc Distinctive amino acid composition profiles in salivary proteins of the tick Ixodes scapularis
    Austin L Hughes
    Department of Biological Sciences, University of South Carolina, Columbia, SC 29208, USA
    Ticks Tick Borne Dis 2:219-24. 2011
    ..scapularis sialome include at least some apparently antigenic proteins that might be tested experimentally to determine whether they would be suitable candidates for anti-tick vaccines...
  44. pmc A genome-wide screen identifies a single beta-defensin gene cluster in the chicken: implications for the origin and evolution of mammalian defensins
    Yanjing Xiao
    Department of Animal Science, Oklahoma State University, Stillwater, OK 74078, USA
    BMC Genomics 5:56. 2004
    ..However, the evolutionary relationships among these five groups of defensins remain controversial...
  45. pmc Polymorphism at the apical membrane antigen 1 locus reflects the world population history of Plasmodium vivax
    Priscila Grynberg
    Departamento de Parasitologia, Instituto de Ciencias Biologicas, Universidade Federal de Minas Gerais, Av Antonio Carlos 6627, 31270 901 Belo Horizonte, MG, Brazil
    BMC Evol Biol 8:123. 2008
    ..In particular, we tested for a signature of the introduction of P. vivax into the New World at the time of the European conquest and African slave trade and subsequent population expansion...
  46. ncbi request reprint Looking for Darwin in all the wrong places: the misguided quest for positive selection at the nucleotide sequence level
    A L Hughes
    Department of Biological Sciences, University of South Carolina, Columbia, SC 29208, USA
    Heredity (Edinb) 99:364-73. 2007
    ..Rather adaptive phenotypes are much more likely to result from other causes, including single amino-acid changes; deletion or silencing of genes or changes in the pattern of gene expression...
  47. pmc Functional diversification of the toll-like receptor gene family
    Austin L Hughes
    Department of Biological Sciences, University of South Carolina, Coker Life Sciences Bldg, 700 Sumter St, Columbia, SC 29208, USA
    Immunogenetics 60:249-56. 2008
    ..Thus, the vertebrate TLRs provide an example of a multi-gene family in which gene duplication has been followed by extensive changes in certain aspects of gene function, while others have been conserved throughout vertebrate history...
  48. pmc Nucleotide sequence polymorphism in circoviruses
    Austin L Hughes
    Department of Biological Sciences, University of South Carolina, Columbia, SC 29208, United States
    Infect Genet Evol 8:130-8. 2008
    ..Such a population history is consistent with the epidemiological evidence of a recent worldwide spread of PCV2...
  49. ncbi request reprint Micro-scale signature of purifying selection in Marburg virus genomes
    Austin L Hughes
    Department of Biological Sciences, University of South Carolina, Coker Life Sciences Bldg, 700 Sumter St, Columbia, SC 29208, USA
    Gene 392:266-72. 2007
    ..The ability of purifying selection to break up linkage between synonymous and nonsynonymous polymorphisms on such a fine scale has not been reported in any other genome...
  50. ncbi request reprint Coding sequence polymorphism in avian mitochondrial genomes reflects population histories
    Austin L Hughes
    Department of Biological Sciences, University of South Carolina, Coker Life Sciences Bldg, 700 Sumter Street, Columbia, SC 29208, USA
    Mol Ecol 16:1369-76. 2007
    ..The reduced genetic diversity of Nearctic migrants provides an additional basis for concern for the survival of these species, which are threatened by loss of habitat in the winter range and by introduced disease...
  51. pmc More effective purifying selection on RNA viruses than in DNA viruses
    Austin L Hughes
    Department of Biological Sciences, University of South Carolina, Columbia, SC 29205, USA
    Gene 404:117-25. 2007
    ..The fact that the negative allometry was more pronounced in RNA viruses than in DNA viruses provided additional evidence that purifying selection is more effective in the former than in the latter...
  52. pmc Phylogeny and recombination history of gallid herpesvirus 2 (Marek's disease virus) genomes
    Austin L Hughes
    Department of Biological Sciences, University of South Carolina, Columbia, SC 29208, USA
    Virus Res 130:28-33. 2007
    ..The two loci (UL49.5 and RLORF12) that were homogenized among the virulent genomes GA, Md5, and Md11 are candidates for contributing to viral virulence...
  53. pmc Rapid fixation of a distinctive sequence motif in the 3' noncoding region of the clade of West Nile virus invading North America
    Austin L Hughes
    Department of Biological Sciences, University of South Carolina, Columbia, SC 29208, United States
    Gene 399:152-61. 2007
    ....
  54. pmc Alternative splicing, gene duplication and connectivity in the genetic interaction network of the nematode worm Caenorhabditis elegans
    Austin L Hughes
    Department of Biological Sciences, University of South Carolina, Coker Life Sciences Bldg, 700 Sumter St, Columbia, SC 29208, USA
    Genetica 134:181-6. 2008
    ..These results support the hypothesis that certain key proteins with high degrees of network connectedness are subject to selection opposing the occurrence of alternatively spliced forms...
  55. pmc Genome-wide SNP typing reveals signatures of population history
    Austin L Hughes
    Department of Biological Sciences, University of South Carolina, Columbia, SC 29208, USA
    Genomics 92:1-8. 2008
    ....
  56. doi request reprint Stereotyped and non-stereotyped features of the temporal patterning of singing sessions in the ovenbird Seiurus auricapillus
    Austin L Hughes
    Department of Biological Sciences, University of South Carolina, Columbia, SC 29208, United States
    Behav Processes 87:165-70. 2011
    ....
  57. pmc Reduced microsatellite heterozygosity in island endemics supports the role of long-term effective population size in avian microsatellite diversity
    Austin L Hughes
    Department of Biological Sciences, University of South Carolina, Coker Life Sciences Bldg, 700 Sumter St, Columbia, SC 29208, USA
    Genetica 138:1271-6. 2010
    ..These results support the hypothesis that long-term effective population size can be an important causative factor behind differences among species with respect to microsatellite heterozygosity...
  58. pmc Runaway evolution of the male-specific exon of the doublesex gene in Diptera
    Austin L Hughes
    Department of Biological Sciences, University of South Carolina, Columbia, 29205, USA
    Gene 472:1-6. 2011
    ....
  59. pmc Origin and diversification of the L-amino oxidase family in innate immune defenses of animals
    Austin L Hughes
    Department of Biological Sciences, University of South Carolina, 700 Sumter Street, Columbia, SC 29208, USA
    Immunogenetics 62:753-9. 2010
    ..It is certain such unique features may be functionally important, especially three unique amino acid replacements in close proximity to the putative active site...
  60. doi request reprint Reduced variance of gene expression at numerous loci in a population of chickens selected for high feather pecking
    A L Hughes
    Department of Biological Sciences, University of South Carolina, Columbia 29208, USA
    Poult Sci 89:1858-69. 2010
    ....
  61. pmc Dynamics of haplotype frequency change in a CD8+TL epitope of simian immunodeficiency virus
    Austin L Hughes
    Department of Biological Sciences, University of South Carolina, Columbia, SC 29208, USA
    Infect Genet Evol 10:555-60. 2010
    ....
  62. pmc The evolutionary biology of poxviruses
    Austin L Hughes
    Department of Biological Sciences, University of South Carolina, Columbia, SC 29208, USA
    Infect Genet Evol 10:50-9. 2010
    ....
  63. pmc Small effective population sizes and rare nonsynonymous variants in potyviruses
    Austin L Hughes
    Department of Biological Sciences, University of South Carolina, Coker Life Sciences Bldg, 715 Sumter St, Columbia SC 29208, USA
    Virology 393:127-34. 2009
    ....
  64. ncbi request reprint Evolution in the post-genome era
    Austin L Hughes
    Department of Biological Sciences, University of South Carolina, Columbia, SC 29208, USA
    Perspect Biol Med 52:332-7. 2009
    ..In new books, Joram Piatigorsky and Michael Lynch provide a corrective to some outdated views and thus provide a glimpse of what the evolutionary biology of the 21th century may look like...
  65. pmc Relaxation of purifying selection on the SAD lineage of live attenuated oral vaccines for rabies virus
    Austin L Hughes
    Department of Biological Sciences, University of South Carolina, Coker Life Sciences Bldg, 700 Sumter St, Columbia, SC 29208, United States
    Infect Genet Evol 9:827-31. 2009
    ..Understanding the biological effects of the unique mutations accumulated in the vaccine lineage is important because of their potential effects on antigenicity and effectiveness of the vaccine...
  66. pmc More radical amino acid replacements in primates than in rodents: support for the evolutionary role of effective population size
    Austin L Hughes
    Department of Biological Sciences, Coker Life Sciences Building, 715 Sumter St, University of South Carolina, Columbia SC 29208, USA
    Gene 440:50-6. 2009
    ....
  67. pmc Genome size reduction in the chicken has involved massive loss of ancestral protein-coding genes
    Austin L Hughes
    Department of Biological Sciences, University of South Carolina, USA
    Mol Biol Evol 25:2681-8. 2008
    ....
  68. pmc Near neutrality: leading edge of the neutral theory of molecular evolution
    Austin L Hughes
    Department of Biological Sciences, University of South Carolina, Coker Life Sciences Bldg, 700 Sumter St, Columbia, South Carolina 29208, USA
    Ann N Y Acad Sci 1133:162-79. 2008
    ..Slightly deleterious variants are a transient feature of evolution in the long term, but they have substantially affected contemporary species, including our own...
  69. doi request reprint Recombinational histories of avian infectious bronchitis virus and turkey coronavirus
    Austin L Hughes
    Department of Biological Sciences, University of South Carolina, Columbia, SC 29208, USA
    Arch Virol 156:1823-9. 2011
    ..The latter hypothesis was supported by a phylogeny of S proteins from representative coronaviruses, in which S proteins of AIBV and TCoV fell in the same clade...
  70. ncbi request reprint Contrasting patterns of transcript abundance in tumour tissue and cancer cell lines
    Austin L Hughes
    Department of Biological Sciences, University of South Carolina, Columbia, South Carolina 29208, USA
    Appl Bioinformatics 5:201-10. 2006
    ..These results imply that data on gene expression in cancer cell lines should be used with caution in inferring gene expression of in vivo tumours...
  71. ncbi request reprint Evolution of introns and exons of class II major histocompatibility complex genes of vertebrates
    A L Hughes
    Department of Biology and Institute of Molecular Evolutionary Genetics, The Pennsylvania State University, University Park 16802, USA
    Immunogenetics 51:473-86. 2000
    ..Thus, the divergence time of DRB1 introns cannot be used to date that of exons in the same alleles, and the hypothesis that most human DRB1 polymorphism is of very recent origin is not supported...
  72. ncbi request reprint Evolutionary origin of the Jiv90 gene of Pestivirus
    Austin L Hughes
    Department of Biological Sciences, University of South Carolina, Coker Life Sciences Bldg, 700 Sumter St, Columbia, SC 29208, USA
    Infect Genet Evol 4:329-33. 2004
    ..This pattern is probably most easily explained on the hypothesis that the insert occurred in the common ancestor of the Type 1 clade and that it has been subsequently lost independently by several members of the clade...
  73. pmc Differential loss of ancestral gene families as a source of genomic divergence in animals
    Austin L Hughes
    Department of Biological Sciences, University of South Carolina, Coker Life Sciences Building, 700 Sumter Street, Columbia, SC 29208, USA
    Proc Biol Sci 271:S107-9. 2004
    ..These results indicate that the differential loss of ancestral gene families can be a significant factor in the evolutionary diversification of organisms...
  74. pmc Widespread purifying selection at polymorphic sites in human protein-coding loci
    Austin L Hughes
    Department of Biological Sciences, University of South Carolina, Columbia, SC 29208, USA
    Proc Natl Acad Sci U S A 100:15754-7. 2003
    ..This, in turn, suggests that slightly deleterious mutations are widespread in the human population and that estimation of gene diversity even in a sample of modest size can help guide the search for disease-associated genes...
  75. ncbi request reprint Parallel evolution by gene duplication in the genomes of two unicellular fungi
    Austin L Hughes
    Department of Biological Sciences, University of South Carolina, Columbia, South Carolina 29208, USA
    Genome Res 13:1259-64. 2003
    ..The results indicate that using phylogenetic analysis to test for parallel gene duplication in different species may help in identifying genes responsible for similar but independently evolved adaptations..
  76. ncbi request reprint Evolutionary change of predicted cytotoxic T cell epitopes of dengue virus
    A L Hughes
    Department of Biological Sciences, Coker Life Sciences Bldg, University of South Carolina, 700 Sumter Street, Columbia, SC 29208, USA
    Infect Genet Evol 1:123-30. 2001
    ..Since dengue is endemic in humans, while WNV and JEV are not, these results are consistent with CTL-driven selection on dengue viruses, particularly, D1V and D3V...
  77. ncbi request reprint Evolution of inhibitors of apoptosis in baculoviruses and their insect hosts
    Austin L Hughes
    Department of Biological Sciences, University of South Carolina, Coker Life Sciences Building, 700 Sumter St, Columbia, SC 29208, USA
    Infect Genet Evol 2:3-10. 2002
    ....
  78. pmc Parallel evolution by gene duplication in the genomes of two unicellular fungi
    Austin L Hughes
    Department of Biological Sciences, University of South Carolina, Columbia, South Carolina 29208, USA
    Genome Res 13:794-9. 2003
    ..The results indicate that using phylogenetic analysis to test for parallel gene duplication in different species may help in identifying genes responsible for similar but independently evolved adaptations...
  79. ncbi request reprint Phylogeny of Trypanosomatidae and Bodonidae (Kinetoplastida) based on 18S rRNA: evidence for paraphyly of Trypanosoma and six other genera
    Austin L Hughes
    Department of Biological Sciences, University of South Carolina, USA
    Mol Biol Evol 20:644-52. 2003
    ..The results suggested that parasitism of vertebrates has probably arisen independently a number of times within the Trypanosomatidae...
  80. ncbi request reprint Extensive polymorphism and ancient origin of Plasmodium falciparum
    Austin L Hughes
    Dept of Biological Sciences, University of South Carolina, Columbia, SC 29208, USA
    Trends Parasitol 18:348-51. 2002
    ..Thus, we can reject the hypothesis that this species underwent a recent extreme bottleneck (i.e. one in which the population was reduced to a single haploid genotype). However, it is possible that less-severe bottlenecks have occurred...
  81. ncbi request reprint Origin and evolution of viral interleukin-10 and other DNA virus genes with vertebrate homologues
    Austin L Hughes
    Department of Biological Sciences, CLS 401, University of South Carolina, Columbia, SC 29208, USA
    J Mol Evol 54:90-101. 2002
    ....
  82. pmc Simultaneous positive and purifying selection on overlapping reading frames of the tat and vpr genes of simian immunodeficiency virus
    A L Hughes
    Department of Biological Sciences, University of South Carolina, Columbia, South Carolina 29208, USA
    J Virol 75:7966-72. 2001
    ....
  83. pmc Ancient genome duplications did not structure the human Hox-bearing chromosomes
    A L Hughes
    Department of Biological Sciences, University of South Carolina, Columbia 29208, USA
    Genome Res 11:771-80. 2001
    ..The results thus indicate that ancient events of genome duplication, if they occurred at all, did not play an important role in structuring the mammalian Hox-bearing chromosomes...
  84. ncbi request reprint 2R or not 2R: testing hypotheses of genome duplication in early vertebrates
    Austin L Hughes
    Department of Biological Sciences, University of South Carolina, Columbia, SC 29208, USA
    J Struct Funct Genomics 3:85-93. 2003
    ..The 2R hypothesis thus can be decisively rejected. Rather, current evidence favors a model of genome evolution in which tandem duplication, whether of genomic segments or of individual genes, predominates...
  85. ncbi request reprint Evolution of the integrin alpha and beta protein families
    A L Hughes
    Department of Biological Sciences, University of South Carolina, Columbia SC 29208, USA
    J Mol Evol 52:63-72. 2001
    ....
  86. ncbi request reprint Evolutionary diversification of protein-coding genes of hantaviruses
    A L Hughes
    Department of Biological Sciences, University of South Carolina, Columbia, SC 29208, USA
    Mol Biol Evol 17:1558-68. 2000
    ....
  87. ncbi request reprint Independent origin of IFN-alpha and IFN-beta in birds and mammals
    A L Hughes
    Department of Biological Sciences, University of South Carolina, Columbia 29208, USA
    J Interferon Cytokine Res 20:737-9. 2000
    ..Therefore, IFN designated alpha and beta in birds are not orthologous to those similarly designated in mammals...
  88. ncbi request reprint Adaptive evolution after gene duplication
    Austin L Hughes
    Depatment of Biological Sciences, University of South Carolina, Columbia, SC 29208, USA
    Trends Genet 18:433-4. 2002
    ..This example is a good illustration of how specialization of protein function after gene duplication can be as source of novel protein functions...
  89. pmc Evidence for abundant slightly deleterious polymorphisms in bacterial populations
    Austin L Hughes
    Department of Biological Sciences, University of South Carolina, Columbia, South Carolina 29208, USA
    Genetics 169:533-8. 2005
    ..The major exceptions to this trend were seen among surface proteins, particularly those of bacteria parasitic on vertebrates, which included a number of cases of polymorphisms apparently maintained by balancing selection...
  90. ncbi request reprint Evolutionary relationships of vertebrate NACHT domain-containing proteins
    Austin L Hughes
    Department of Biological Sciences, University of South Carolina, Coker Life Sciences Bldg, Columbia, SC 29208, USA
    Immunogenetics 58:785-91. 2006
    ....
  91. ncbi request reprint Gene family content-based phylogeny of prokaryotes: the effect of criteria for inferring homology
    Austin L Hughes
    Department of Biological Sciences, University of South Carolina, Columbia, SC 29205, USA
    Syst Biol 54:268-76. 2005
    ....
  92. ncbi request reprint Shedding genomic ballast: extensive parallel loss of ancestral gene families in animals
    Austin L Hughes
    Department of Biological Sciences, University of South Carolina, Coker Life Sciences Building, 700 Sumter Street, Columbia, SC 29205, USA
    J Mol Evol 59:827-33. 2004
    ..This result implies that certain ancestral gene families-and thus the biological functions they encode-have been more expendable than others over the radiation of the animal phyla...
  93. ncbi request reprint Within-host evolution of CD8+-TL epitopes encoded by overlapping and non-overlapping reading frames of simian immunodeficiency virus
    Austin L Hughes
    Department of Biological Sciences, University of South Carolina Columbia, SC 29208, USA
    Bioinformatics 21:iii39-44. 2005
    ....
  94. pmc Gene duplication and the properties of biological networks
    Austin L Hughes
    Department of Biological Sciences, University of South Carolina, Coker Life Sciences Building, 700 Sumter Street, Columbia, SC 29205, USA
    J Mol Evol 61:758-64. 2005
    ..These factors serve to explain well-known general properties of biological networks, including their scale-free and modular nature...
  95. ncbi request reprint Across-tissue expression and evolution of genes controlled by the Aire transcription factor
    Austin L Hughes
    Department of Biological Sciences, University of South Carolina, Columbia, SC 29208, USA
    Genomics 88:462-7. 2006
    ..Thus the set of Aire-activated genes is subject to change over evolutionary time and includes genes of recent origin...
  96. ncbi request reprint Sharing of transcription factors after gene duplication in the yeast Saccharomyces cerevisiae
    Austin L Hughes
    Department of Biological Sciences, University of South Carolina, Coker Life Sciences Bldg 700 Sumter St, Columbia, SC 29208, USA
    Genetica 129:301-8. 2007
    ..These results suggest that functional differentiation of genes after duplication is a multi-dimensional process, with different duplicate pairs differentiating in different ways...
  97. ncbi request reprint Variable intensity of purifying selection on cytotoxic T-lymphocyte epitopes in hepatitis C virus
    Austin L Hughes
    Department of Biological Sciences, University of South Carolina, Columbia, SC 29208, USA
    Virus Res 123:147-53. 2007
    ....
  98. ncbi request reprint Amino acid sequence constraint and gene expression pattern across the life history in the malaria parasite Plasmodium falciparum
    Austin L Hughes
    Department of Biological Sciences, University of South Carolina, Coker Life Sciences Bldg, 700 Sumter St, Columbia, SC 29205, USA
    Mol Biochem Parasitol 142:170-6. 2005
    ....
  99. pmc Gene duplication and the origin of novel proteins
    Austin L Hughes
    Department of Biological Sciences, University of South Carolina, Columbia, SC 29205, USA
    Proc Natl Acad Sci U S A 102:8791-2. 2005
  100. ncbi request reprint Patterns of nucleotide difference in overlapping and non-overlapping reading frames of papillomavirus genomes
    Austin L Hughes
    Department of Biological Sciences, University of South Carolina, Coker Life Sciences Bldg 700 Sumter Street, Columbia, SC 29208, USA
    Virus Res 113:81-8. 2005
    ..Thus, positive diversifying selection on the E2 hinge region appears to coexist with purifying selection on the overlapping region of E4...
  101. pmc Patterns of sequence divergence in 5' intergenic spacers and linked coding regions in 10 species of pathogenic bacteria reveal distinct recombinational histories
    Austin L Hughes
    Department of Biological Sciences, University of South Carolina, Columbia, South Carolina 29205, USA
    Genetics 168:1795-803. 2004
    ..agalactiae...

Research Grants2

  1. Gene Duplication and Genome Evolution
    Austin Hughes; Fiscal Year: 2004
    ..5) Examining the role of transposable elements in duplication of genomic segments by testing for nonrandom association between these elements and putatively duplicated blocks in the yeast genome. ..
  2. EVOLUTION OF IMMUNE RECOGNITION AND EVASION
    Austin L Hughes; Fiscal Year: 2010
    ..In addition, by increasing our understanding of the population diversity and evolutionary history of human immune system genes, this research will enhance our knowledge of human immune function in health and disease. ..