The effect of species representation on the detection of positive selection in primate gene data sets

Molecular Biology and Evolution

Volumn 32, Issue 4, 2015, Pages 1091-1096

  McBee, Ross M ^a   Rozmiarek, Shea A ^b   Meyerson, Nicholas R ^a   Rowley, Paul A ^a   Sawyer, Sara L ^a  

^a UNIVERSITY OF TEXAS AT AUSTIN   (United States)

^b Liberty Hill High School   (United States)

Author keywords

HIV; host virus arms race; host virus coevolution; positive selection; simian primates

Indexed keywords

EXPORTIN 5; NIBRIN; NUCLEOPORIN 98; POL PROTEIN; PROTEIN KINASE WNK1; XRCC4 PROTEIN; VIRAL PROTEIN;

APE; ARTICLE; CALLITRICHINAE; CERCOPITHECIDAE; CHIMPANZEE; CODON; COEVOLUTION; CONTROLLED STUDY; DNA REPAIR; GENE NUMBER; GENE SEQUENCE; GENETIC ANALYSIS; GENETIC VARIABILITY; GENOME; NATURAL SELECTION; NONHUMAN; NULL HYPOTHESIS; PLATYRRHINI; PRIMATE; RHESUS MONKEY; SIMIAN; VIRUS CELL INTERACTION; ANIMAL; GENE; GENETIC SELECTION; GENETICS; HOST PATHOGEN INTERACTION; METABOLISM; MOLECULAR EVOLUTION; VIROLOGY; VIRUS;

PRIMATES; SIMIAE;

ANIMALS; EVOLUTION, MOLECULAR; GENES; HOST-PATHOGEN INTERACTIONS; PRIMATES; SELECTION, GENETIC; VIRAL PROTEINS; VIRUSES;

EID: 84926677816     PISSN: 07374038     EISSN: 15371719     Source Type: Journal    
DOI: 10.1093/molbev/msu399     Document Type: Article

References (36)

1. Clark AG, Glanowski S, Nielsen R, Thomas PD, Kejariwal A, Todd MA, Tanenbaum DM, Civello D, Lu F, Murphy B, et al.(2003).Inferring nonneutral evolution from human-chimp-mouse orthologous gene trios.Science 302:1960-1963
2. Compton AA, Emerman M.(2013).Convergence and divergence in the evolution of the APOBEC3G-vif interaction reveal ancient origins of simian immunodeficiency viruses.PLoS Pathog.9:e1003135
3. Delport W, Poon AFY, Frost SDW, Kosakovsky Pond SL.(2010).Datamonkey 2010: a suite of phylogenetic analysis tools for evolutionary biology.Bioinformatics 26:2455-2457
4. Demogines A, Abraham J, Choe H, Farzan M, Sawyer SL.(2013).Dual hostvirus arms races shape an essential housekeeping protein.PLoS Biol.11:e1001571
5. Demogines A, East AM, Lee J-H, Grossman SR, Sabeti PC, Paull TT, Sawyer SL.(2010).Ancient and recent adaptive evolution of primate non-homologous end joining genes.PLoS Genet.6:e1001169
6. Demogines A, Farzan M, Sawyer SL.(2012).Evidence for ACE2-utilizing coronaviruses (CoVs) related to severe acute respiratory syndrome CoV in bats.J Virol.86:6350-6353
7. Demogines A, Truong KA, Sawyer SL.(2012).Species-specific features of DARC, the primate receptor for Plasmodium vivax and Plasmodium knowlesi.Mol Biol Evol.29:445-449
8. Duggal NK, Malik HS, Emerman M.(2011).The breadth of antiviral activity of Apobec3DE in chimpanzees has been driven by positive selection.J Virol.85:11361-11371
9. Elde NC, Child SJ, Geballe AP, Malik HS.(2009).Protein kinase R reveals an evolutionary model for defeating viral mimicry.Nature 457: 485-489
10. Gupta RK, Hué S, Schaller T, Verschoor E, Pillay D, Towers GJ.(2009).Mutation of a single residue renders human tetherin resistant to HIV-1 Vpu-mediated depletion.PLoS Pathog.5:e1000443
11. Hurst LD.(2002).The Ka/Ks ratio: diagnosing the form of sequence evolution.Trends Genet.18:486
12. Kaelber JT, Demogines A, Harbison CE, Allison AB, Goodman LB, Ortega AN, Sawyer SL, Parrish CR.(2012).Evolutionary reconstructions of the transferrin receptor of Caniforms supports canine parvovirus being a re-emerged and not a novel pathogen in dogs.PLoS Pathog.8: e1002666
13. Kelley JL, Swanson WJ.(2008).Positive selection in the human genome: from genome scans to biological significance.Annu Rev Genomics Hum Genet.9:143-160
14. Kerns JA, Emerman M, Malik HS.(2008).Positive selection and increased antiviral activity associated with the PARP-containing isoform of human zinc-finger antiviral protein.PLoS Genet.4:e21
15. Laguette N, Rahm N, Sobhian B, Chable-Bessia C, Munch J, Snoeck J, Sauter D, Switzer WM, Heneine W, Kirchhoff F, et al.(2012).Evolutionary and functional analyses of the interaction between the myeloid restriction factor SAMHD1 and the lentiviral Vpx protein.Cell Host Microbe.11:205-217
16. Lim ES, Fregoso OI, McCoy CO, Matsen FA, Malik HS, Emerman M.(2012).The ability of primate lentiviruses to degrade the monocyte restriction factor SAMHD1 preceded the birth of the viral accessory protein Vpx.Cell Host Microbe.11:194-204
17. Lim ES, Malik HS, Emerman M.(2010).Ancient adaptive evolution of tetherin shaped the functions of Vpu and Nef in human immunodeficiency virus and primate lentiviruses.J Virol.84: 7124-7134
18. Locke DP, Hillier LW, Warren WC, Worley KC, Nazareth LV, Muzny DM, Yang SP, Wang Z, Chinwalla AT, Minx P, et al.(2011).Comparative and demographic analysis of orang-utan genomes.Nature 469: 529-533
19. McNatt MW, Zang T, Hatziioannou T, Bartlett M, Fofana IB, Johnson WE, Neil SJD, Bieniasz PD.(2009).Species-specific activity of HIV-1 Vpu and positive selection of tetherin transmembrane domain variants.PLoS Pathog.5:e1000300
20. Meyerson NR, Rowley PA, Swan CH, Le DT, Wilkerson GK, Sawyer SL.(2014).Positive selection of primate genes that promote HIV-1 replication.Virology 454-455:291-298
21. Mikkelsen TS, Hillier LW, Eichler EE, Zody MC, Jaffe DB, Yang S-P, Enard W, Hellmann I, Lindblad-Toh K, Altheide TK, et al.(2005).Initial sequence of the chimpanzee genome and comparison with the human genome.Nature 437:69-87
22. Mitchell PS, Patzina C, Emerman M, Haller O, Malik HS, Kochs G.(2012).Evolution-guided identification of antiviral specificity determinants in the broadly acting interferon-induced innate immunity factor MxA.Cell Host Microbe.12:598-604
23. Murrell B, Wertheim JO, Moola S, Weighill T, Scheffler K, Kosakovsky Pond SL.(2012).Detecting individual sites subject to episodic diversifying selection.PLoS Genet.8:e1002764
24. Nielsen R.(2005).Molecular signatures of natural selection.Annu Rev Genet.39:197-218
25. Nielsen R, Bustamante C, Clark AG, Glanowski S, Sackton TB, Hubisz MJ, Fledel-Alon A, Tanenbaum DM, Civello D, White TJ, et al.(2005).A scan for positively selected genes in the genomes of humans and chimpanzees.PLoS Biol.3:e170
26. Ortiz M, Guex N, Patin E, Martin O, Xenarios I, Ciuffi A, Quintana-Murci L, Telenti A.(2009).Evolutionary trajectories of primate genes involved in HIV pathogenesis.Mol Biol Evol.26:2865-2875
27. Patel MR, Loo Y-M, Horner SM, Gale M, Malik HS.(2012).Convergent evolution of escape from hepaciviral antagonism in primates.PLoS Biol.10:e1001282
28. Gibbs RA, Rogers J, Katze MG, Bumgarner R, Weinstock GM, Mardis ER, Remington KA, Strausberg RL, Venter JC Rhesus Macaque Genome Sequencing and Analysis Consortium, et al.(2007).Evolutionary and biomedical insights from the rhesus macaque genome.Science 316: 222-234
29. Sawyer SL, Wu LI, Emerman M, Malik HS.(2005).Positive selection of primate TRIM5alpha identifies a critical species-specific retroviral restriction domain.Proc Natl Acad Sci U S A.102:2832-2837
30. Scally A, Dutheil JY, Hillier LW, Jordan GE, Goodhead I, Herrero J, Hobolth A, Lappalainen T, Mailund T, Marques-Bonet T, et al.(2012).Insights into hominid evolution from the gorilla genome sequence.Nature 483:169-175
31. Schaller T, Ocwieja KE, Rasaiyaah J, Price AJ, Brady TL, Roth SL, Hué S, Fletcher AJ, Lee K, KewalRamani VN, et al.(2011).HIV-1 capsidcyclophilin interactions determine nuclear import pathway, integration targeting and replication efficiency.PLoS Pathog.7: e1002439
32. Swanson WJ, Nielsen R, Yang Q.(2003).Pervasive adaptive evolution in mammalian fertilization proteins.Mol Biol Evol.20:18-20
33. Vitti JJ, Grossman SR, Sabeti PC.(2013).Detecting natural selection in genomic data.Annu Rev Genet.47:97-120
34. Yang Z.(1997).PAML: a program package for phylogenetic analysis by maximum likelihood.Comput Appl Biosci.13:555-556
35. Yang Z.(2007).PAML 4: phylogenetic analysis by maximum likelihood.Mol Biol Evol.24:1586-1591
36. Yang Z, Wong WSW, Nielsen R.(2005).Bayes empirical bayes inference of amino acid sites under positive selection.Mol Biol Evol.22: 1107-1118