Genomes and Genes
Affiliation: University of South Carolina
- Hughes A, Green J, Piontkivska H, Roberts R. Aspartic proteinase phylogeny and the origin of pregnancy-associated glycoproteins. Mol Biol Evol. 2003;20:1940-5 pubmed..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. ..
- Hughes A. Near neutrality: leading edge of the neutral theory of molecular evolution. Ann N Y Acad Sci. 2008;1133:162-79 pubmed publisher..Slightly deleterious variants are a transient feature of evolution in the long term, but they have substantially affected contemporary species, including our own. ..
- Hughes A, Verra F. Malaria parasite sequences from chimpanzee support the co-speciation hypothesis for the origin of virulent human malaria (Plasmodium falciparum). Mol Phylogenet Evol. 2010;57:135-43 pubmed publisher..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. ..
- Hughes A, Westover K, da Silva J, O connor D, Watkins D. Simultaneous positive and purifying selection on overlapping reading frames of the tat and vpr genes of simian immunodeficiency virus. J Virol. 2001;75:7966-72 pubmed
- Hughes A, Piontkivska H. DNA repeat arrays in chicken and human genomes and the adaptive evolution of avian genome size. BMC Evol Biol. 2005;5:12 pubmed
- Hughes A. Origin and diversification of the L-amino oxidase family in innate immune defenses of animals. Immunogenetics. 2010;62:753-9 pubmed publisher..It is certain such unique features may be functionally important, especially three unique amino acid replacements in close proximity to the putative active site. ..
- Xiao Y, Hughes A, Ando J, Matsuda Y, Cheng J, Skinner Noble D, et al. A genome-wide screen identifies a single beta-defensin gene cluster in the chicken: implications for the origin and evolution of mammalian defensins. BMC Genomics. 2004;5:56 pubmed..Further analysis of these defensins in different vertebrate lineages will shed light on the mechanisms of host defense and evolution of innate immunity. ..
- Hughes A, Friedman R. Codon-based tests of positive selection, branch lengths, and the evolution of mammalian immune system genes. Immunogenetics. 2008;60:495-506 pubmed publisher..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. ..
- Hughes A, Friedman R. Differential loss of ancestral gene families as a source of genomic divergence in animals. Proc Biol Sci. 2004;271 Suppl 3:S107-9 pubmed..These results indicate that the differential loss of ancestral gene families can be a significant factor in the evolutionary diversification of organisms. ..
- Hughes A, Friedman R. Pattern of divergence of amino acid sequences encoded by paralogous genes in human and pufferfish. Mol Phylogenet Evol. 2004;32:337-43 pubmed..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. ..
- Hughes A, Friedman R. Evolutionary diversification of protein-coding genes of hantaviruses. Mol Biol Evol. 2000;17:1558-68 pubmed
- Hughes A, Friedman R. Poxvirus genome evolution by gene gain and loss. Mol Phylogenet Evol. 2005;35:186-95 pubmed..Thus "capture" of host genes by HGT has been a recurrent feature of poxvirus evolution and has played an important role in adapting the virus to survive host antiviral defense mechanisms...
- Hughes A, Hughes M. More effective purifying selection on RNA viruses than in DNA viruses. Gene. 2007;404:117-25 pubmed..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...
- Hughes A, Rivailler P. Phylogeny and recombination history of gallid herpesvirus 2 (Marek's disease virus) genomes. Virus Res. 2007;130:28-33 pubmed..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...
- Hughes A. Birth-and-death evolution of protein-coding regions and concerted evolution of non-coding regions in the multi-component genomes of nanoviruses. Mol Phylogenet Evol. 2004;30:287-94 pubmed..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...
- Hughes A. Adaptive evolution after gene duplication. Trends Genet. 2002;18:433-4 pubmed..This example is a good illustration of how specialization of protein function after gene duplication can be as source of novel protein functions...
- Hughes A. Evolution of the integrin alpha and beta protein families. J Mol Evol. 2001;52:63-72 pubmed
- Hughes A, Piontkivska H. Phylogeny of Trypanosomatidae and Bodonidae (Kinetoplastida) based on 18S rRNA: evidence for paraphyly of Trypanosoma and six other genera. Mol Biol Evol. 2003;20:644-52 pubmed..The results suggested that parasitism of vertebrates has probably arisen independently a number of times within the Trypanosomatidae...