Genomes and Genes
Affiliation: University of South Carolina
- Hughes A. Evolution of the lung surfactant proteins in birds and mammals. Immunogenetics. 2007;59:565-72 pubmed..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. ..
- Hughes A, Friedman R. Amino acid sequence constraint and gene expression pattern across the life history in the malaria parasite Plasmodium falciparum. Mol Biochem Parasitol. 2005;142:170-6 pubmed
- Dudley D, Bailey A, Mehta S, Hughes A, Kirk G, Westergaard R, et al. Cross-clade simultaneous HIV drug resistance genotyping for reverse transcriptase, protease, and integrase inhibitor mutations by Illumina MiSeq. Retrovirology. 2014;11:122 pubmed publisher..This high-throughput and sensitive assay could significantly improve access to drug resistance genotyping worldwide. ..
- 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, 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. 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, 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. Evolutionary diversification of protein-coding genes of hantaviruses. Mol Biol Evol. 2000;17:1558-68 pubmed
- 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. 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. Evolution of the integrin alpha and beta protein families. J Mol Evol. 2001;52:63-72 pubmed
- 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. 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, 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, 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, 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, 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...