A L Hughes

Summary

Affiliation: Pennsylvania State University
Country: USA

Publications

  1. ncbi Rapid evolution of immunoglobulin superfamily C2 domains expressed in immune system cells
    A L Hughes
    Department of Biology, Pennsylvania State University, University Park 16802, USA
    Mol Biol Evol 14:1-5. 1997
  2. ncbi A new taxonomy of mammalian MHC class I molecules
    A L Hughes
    Dept of Biology, Pennsylvania State University, University Park 16802, USA
    Immunol Today 20:22-6. 1999
  3. ncbi Natural selection at major histocompatibility complex loci of vertebrates
    A L Hughes
    Department of Biology, Pennsylvania State University, University Park 16802, USA
    Annu Rev Genet 32:415-35. 1998
  4. ncbi Evolutionary diversification of the mammalian defensins
    A L Hughes
    Department of Biology and Institute of Molecular Evolutionary Genetics, The Pennsylvania State University, University Park, 16802, USA
    Cell Mol Life Sci 56:94-103. 1999
  5. ncbi Phylogenetic tests of the hypothesis of block duplication of homologous genes on human chromosomes 6, 9, and 1
    A L Hughes
    Department of Biology, Pennsylvania State University, University Park 16803, USA
    Mol Biol Evol 15:854-70. 1998
  6. ncbi Molecular evolution of the vertebrate immune system
    A L Hughes
    Department of Biology, Pennsylvania State University, University Park 16802, USA
    Bioessays 19:777-86. 1997
  7. ncbi Coordinated amino acid changes in the evolution of mammalian defensins
    A L Hughes
    Department of Biology, 208 Mueller Laboratory, The Pennsylvania State University, University Park, PA 16802, USA
    J Mol Evol 44:675-82. 1997
  8. ncbi Evolution of the arthropod prophenoloxidase/hexamerin protein family
    A L Hughes
    Department of Biology, Institute of Molecular Evolutionary Genetics, The Pennsylvania State University, University Park 16803, USA
    Immunogenetics 49:106-14. 1999
  9. ncbi Phylogenies of developmentally important proteins do not support the hypothesis of two rounds of genome duplication early in vertebrate history
    A L Hughes
    Department of Biology and Institute of Molecular Evolutionary Genetics, The Pennsylvania State University, University Park, PA 16802
    J Mol Evol 48:565-76. 1999
  10. ncbi 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

Collaborators

Detail Information

Publications35

  1. ncbi Rapid evolution of immunoglobulin superfamily C2 domains expressed in immune system cells
    A L Hughes
    Department of Biology, Pennsylvania State University, University Park 16802, USA
    Mol Biol Evol 14:1-5. 1997
    ....
  2. ncbi A new taxonomy of mammalian MHC class I molecules
    A L Hughes
    Dept of Biology, Pennsylvania State University, University Park 16802, USA
    Immunol Today 20:22-6. 1999
  3. ncbi Natural selection at major histocompatibility complex loci of vertebrates
    A L Hughes
    Department of Biology, Pennsylvania State University, University Park 16802, USA
    Annu Rev Genet 32:415-35. 1998
    ..d) Introns have been homogenized relative to exons over evolutionary time, suggesting that balancing selection acts to maintain diversity in the latter, in contrast to the former...
  4. ncbi Evolutionary diversification of the mammalian defensins
    A L Hughes
    Department of Biology and Institute of Molecular Evolutionary Genetics, The Pennsylvania State University, University Park, 16802, USA
    Cell Mol Life Sci 56:94-103. 1999
    ..The resulting rapid evolution explains why it is difficult to reconstruct the evolutionary history of these molecules...
  5. ncbi Phylogenetic tests of the hypothesis of block duplication of homologous genes on human chromosomes 6, 9, and 1
    A L Hughes
    Department of Biology, Pennsylvania State University, University Park 16803, USA
    Mol Biol Evol 15:854-70. 1998
    ..Since the occurrence of these clusters of related genes cannot be explained by block duplication, one alternative explanation is that they cluster together because of shared functional characteristics relating to expression patterns...
  6. ncbi Molecular evolution of the vertebrate immune system
    A L Hughes
    Department of Biology, Pennsylvania State University, University Park 16802, USA
    Bioessays 19:777-86. 1997
    ..Immune system gene families have evolved by gene duplication, interlocus recombination and (in some cases) positive Darwinian selection favoring diversity at the amino acid level...
  7. ncbi Coordinated amino acid changes in the evolution of mammalian defensins
    A L Hughes
    Department of Biology, 208 Mueller Laboratory, The Pennsylvania State University, University Park, PA 16802, USA
    J Mol Evol 44:675-82. 1997
    ..The results support the hypothesis that, in the evolution of these proteins, amino acid changes have occurred in a coordinated fashion so as to preserve an adaptive phenotype...
  8. ncbi Evolution of the arthropod prophenoloxidase/hexamerin protein family
    A L Hughes
    Department of Biology, Institute of Molecular Evolutionary Genetics, The Pennsylvania State University, University Park 16803, USA
    Immunogenetics 49:106-14. 1999
    ....
  9. ncbi Phylogenies of developmentally important proteins do not support the hypothesis of two rounds of genome duplication early in vertebrate history
    A L Hughes
    Department of Biology and Institute of Molecular Evolutionary Genetics, The Pennsylvania State University, University Park, PA 16802
    J Mol Evol 48:565-76. 1999
    ..Taken together with other recently published phylogenies of developmentally important genes, these results provide strong evidence against the 2R hypothesis...
  10. ncbi 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...
  11. pmc Adaptive diversification within a large family of recently duplicated, placentally expressed genes
    A L Hughes
    Department of Biology, Pennsylvania State University, University Park, PA 16808, USA
    Proc Natl Acad Sci U S A 97:3319-23. 2000
    ..Thus, rapid functional diversification of PAG expressed in trophoblast binucleate cells seems to have been associated with the origin of this unique placental adaptation...
  12. ncbi Concerted evolution of exons and introns in the MHC-linked tenascin-X gene of mammals
    A L Hughes
    Department of Biology, Pennsylvania State University, USA
    Mol Biol Evol 16:1558-67. 1999
    ..This is the first known example of concerted evolution of repeated introns within a protein-coding gene...
  13. pmc Evidence that intragenic recombination contributes to allelic diversity of the S-RNase gene at the self-incompatibility (S) locus in Petunia inflata
    X Wang
    Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, Pennsylvania 16802, USA
    Plant Physiol 125:1012-22. 2001
    ..The implications of these findings are discussed...
  14. ncbi Natural selection on apical membrane antigen-1 of Plasmodium falciparum
    F Verra
    Department of Biology, Pennsylvania State University, University Park 16801 5301, USA
    Parassitologia 41:93-5. 1999
    ..These results support the hypothesis that polymorphism at the AMA-1 locus in maintained by balancing selection arising from host immune recognition...
  15. ncbi Phylogeny of the C3/C4/C5 complement-component gene family indicates that C5 diverged first
    A L Hughes
    Department of Biology, Pennsylvania State University, University Park 16802
    Mol Biol Evol 11:417-25. 1994
    ..This phylogeny is most consistent with the hypothesis that the alternative complement pathway was the first to evolve, followed by the terminal pathway and then by the classical pathway...
  16. ncbi Evidence of positive selection at the Lyb-2 locus of the mouse
    A L Hughes
    Department of Biology, Pennsylvania State University, University Park 16802
    Immunogenetics 38:54-6. 1993
  17. ncbi 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...
  18. ncbi Mamu-I: a novel primate MHC class I B-related locus with unusually low variability
    J A Urvater
    Wisconsin Regional Primate Research Center, Department of Genetics, University of Wisconsin, Madison, WI 53715, USA
    J Immunol 164:1386-98. 2000
    ..Additionally, no evidence for positive selection on the peptide binding region was observed. Together, these results suggest that Mamu-I is an MHC class I locus in primates that has features of both classical and nonclassical loci...
  19. pmc Pattern and timing of gene duplication in animal genomes
    R Friedman
    Department of Biological Sciences, University of South Carolina, Columbia, SC 29208, USA
    Genome Res 11:1842-7. 2001
    ..A substantial majority (70.9%) of human four-member families and four-member clusters in larger families showed topologies inconsistent with two rounds of polyploidization in vertebrates...
  20. ncbi Evolution of suiform aromatases: ancestral duplication with conservation of tissue-specific expression in the collared peccary (Pecari tayassu)
    C J Corbin
    Department of Population Health and Reproduction, University of California, Davis, CA, USA
    J Mol Evol 65:403-12. 2007
    ....
  21. ncbi Structure and domain organization of the CD19 antigen of human, mouse, and guinea pig B lymphocytes. Conservation of the extensive cytoplasmic domain
    L J Zhou
    Division of Tumor Immunology, Dana Farber Cancer Institute, Boston, MA 02115 6084
    J Immunol 147:1424-32. 1991
    ..Thus, CD19 appears to be well conserved in structure and expression through recent mammalian evolution and the highly conserved cytoplasmic domains may play a critical role in the transduction of CD19-mediated signals...
  22. ncbi Chimpanzee MHC class I A locus alleles are related to only one of the six families of human A locus alleles
    S N McAdam
    Wisconsin Regional Primate Research Center, Madison, USA
    J Immunol 154:6421-9. 1995
    ..This suggests that the common ancestor of these two species either passed through a genetic bottleneck or that selection has favored the maintenance of the HLA-A1, -A3, -A11 family in chimpanzees...
  23. ncbi The MHC E locus in macaques is polymorphic and is conserved between macaques and humans
    J E Boyson
    Wisconsin Regional Primate Research Center, University of Wisconsin, Madison 53715
    Immunogenetics 41:59-68. 1995
    ....
  24. pmc A uniquely high level of recombination at the HLA-B locus
    S N McAdam
    Wisconsin Regional Primate Research Center, University of Wisconsin, Madison 53715
    Proc Natl Acad Sci U S A 91:5893-7. 1994
    ..This finding suggests that, unlike all other HLA loci, recombination has characterized the HLA-B locus and its homologues for over 5 million years...
  25. ncbi Two more chimpanzee Patr-A locus alleles related to the HLA-A1/A3/A11 family
    Z W Chen
    Harvard Medical School, New England Regional Primate Research Center, Southborough, MA 01772
    Immunogenetics 38:238-40. 1993
  26. ncbi Chemokine PARC gene (SCYA18) generated by fusion of two MIP-1alpha/LD78alpha-like genes
    Y Tasaki
    Department of Biochemistry, Kumamoto University Medical School, Honjo, Japan
    Genomics 55:353-7. 1999
    ..This evidence provides a new model, duplication and fusion, of the molecular basis for diversity within a gene family...
  27. ncbi Placental expression and molecular characterization of aromatase cytochrome P450 in the spotted hyena (Crocuta crocuta)
    A J Conley
    Department of Population Health and Reproduction, School of Veterinary Medicine, University of California, 1 Shields Avenue, Davis, CA 95616, USA
    Placenta 28:668-75. 2007
    ..Other hyaenids and carnivores must be investigated to determine the morphological and functional ancestral state of their placentas, as it relates to evolutionary relationships among species in this important taxonomic group...
  28. ncbi Cloning of rhesus monkey LILRs
    I I Slukvin
    Department of Pathology and Laboratory Medicine, University of Wisconsin, Madison, WI, USA
    Tissue Antigens 67:331-7. 2006
    ..Characterization of rhesus LILRs will facilitate use of this non-human primate model for the study of the functional role(s) of LILRs, including immune regulation through interaction with non-classical MHC class I molecules...
  29. ncbi Comparative genomics: mining the crucial 1%
    A L Hughes
    Heredity (Edinb) 93:5. 2004
  30. ncbi Cloning of rhesus monkey killer-cell Ig-like receptors (KIRs) from early pregnancy decidua
    R L Grendell
    Wisconsin Regional Primate Research Center, University of Wisconsin, Madison, Wisconsin 53715 1299, USA
    Tissue Antigens 58:329-34. 2001
    ..Phylogenetic analysis of the Ig domains supports a D0 - D2 organization of rhesus KIR2DL4.1, similar to human KIR2DL4 and KIR2DL5. The rhesus KIR2DL4.1 transcript contains a long cytoplasmic tail homologous with human KIR2DL4...
  31. ncbi The outcome of hepatitis C virus infection is predicted by escape mutations in epitopes targeted by cytotoxic T lymphocytes
    A L Erickson
    Children's Research Institute, Children's Hospital W503, 700 Children's Drive, Columbus, OH 43205, USA
    Immunity 15:883-95. 2001
    ..We conclude that CTL exert positive selection pressure against the HCV quasispecies and the outcome of infection is predicted by mutations in class I MHC restricted epitopes...
  32. ncbi The MHC class I genes of the rhesus monkey. Different evolutionary histories of MHC class I and II genes in primates
    J E Boyson
    University of Wisconsin, Madison, WI 53715, USA
    J Immunol 156:4656-65. 1996
    ..Although MHC class II allelic lineages are shared between humans and Old World primates, no such trans-species sharing of allelic lineages is seen at the MHC class I loci...
  33. ncbi Molecular evolution of viral fusion and matrix protein genes and phylogenetic relationships among the Paramyxoviridae
    K M Westover
    Department of Biological Sciences, University of South Carolina, Columbia, South Carolina 29208, USA
    Mol Phylogenet Evol 21:128-34. 2001
    ..Rinderpest was most closely related to measles and a more derived virus than to canine distemper virus, phocine distemper virus, or dolphin morbillivirus...
  34. pmc Gene duplication and the structure of eukaryotic genomes
    R Friedman
    Department of Biological Sciences, University of South Carolina, Columbia, South Carolina 29208, USA
    Genome Res 11:373-81. 2001
    ..Thus, duplication of genomic blocks has been an ongoing feature of yeast evolution over the past 200--300 million years...
  35. ncbi Definition of an epitope and MHC class I molecule recognized by gag-specific cytotoxic T lymphocytes in SIVmac-infected rhesus monkeys
    M D Miller
    Harvard Medical School, New England Regional Primate Research Center, Southborough, MA 01772
    J Immunol 147:320-9. 1991
    ..These studies illustrate that AIDS virus-specific CTL can be characterized in detail in the rhesus monkey and lay the foundation for exploring novel approaches to AIDS virus vaccination in this species...