Evolution of endogenous retroviruses in the Suidae: Evidence for different viral subpopulations in African and Eurasian host species

BMC Evolutionary Biology

Volumn 11, Issue 1, 2011, Pages

  Nascimento, Fabrícia F ^a,e   Gongora, Jaime ^a   Charleston, Michael ^b   Tristem, Michael ^c   Lowden, Stewart ^d   Moran, Chris ^a  

^a UNIVERSITY OF SYDNEY   (Australia)

^b UNIVERSITY OF SYDNEY   (Australia)

^c IMPERIAL COLLEGE LONDON   (United Kingdom)

^d Veterinary Health Research Pty Ltd   (Australia)

^e FEDERAL UNIVERSITY OF RIO DE JANEIRO   (Brazil)

Author keywords

[No Author keywords available]

Indexed keywords

COEVOLUTION; COMMON ANCESTRY; COMPARATIVE STUDY; CYTOGENETICS; DOMESTIC SPECIES; EVOLUTIONARY BIOLOGY; GENOME; PHYLOGENETICS; PIG; VIRUS;

AFRICA; EURASIA;

PORCINE ENDOGENOUS RETROVIRUS; SUIDAE; SUS SCROFA; SUS SCROFA DOMESTICA;

AFRICA; ANIMAL; ARTICLE; ASIA; BAYES THEOREM; ENVELOPE GENE; EUROPE; GENETIC RECOMBINATION; GENETICS; HOST PATHOGEN INTERACTION; MOLECULAR GENETICS; PHYLOGENY; PHYSIOLOGY; RETROVIRUS; STRUCTURAL GENE; SWINE; VIROLOGY;

AFRICA; ANIMALS; ASIA; BAYES THEOREM; EUROPE; GAMMARETROVIRUS; GENES, ENV; GENES, GAG; GENES, POL; HOST-PATHOGEN INTERACTIONS; MOLECULAR SEQUENCE DATA; PHYLOGENY; RECOMBINATION, GENETIC; SWINE;

EID: 79956267317     PISSN: None     EISSN: 14712148     Source Type: Journal    
DOI: 10.1186/1471-2148-11-139     Document Type: Article

References (80)

1. The evolution, distribution and diversity of endogenous retroviruses. R Gifford M Tristem, Virus Genes 2003 26 291 315 10.1023/A:1024455415443 12876457
2. Retroviral diversity and distribution in vertebrates. E Herniou J Martin K Miller J Cook M Wilkinson M Tristem, J Virol 1998 72 5955 5966 9621058 (Pubitemid 28283384)
3. The discovery of endogenous retroviruses. RA Weiss, Retrovirology 2006 3 67 10.1186/1742-4690-3-67 17018135
4. Genetics: junk DNA as an evolutionary force. C Biemont C Vieira, Nature 2006 443 521 524 10.1038/443521a 17024082 (Pubitemid 44527281)
5. Multiple groups of novel retroviral genomes in pigs and related species. C Patience WM Switzer Y Takeuchi DJ Griffiths ME Goward W Heneine JP Stoye RA Weiss, J Virol 2001 75 2771 2775 10.1128/JVI.75.6.2771-2775.2001 11222700 (Pubitemid 32185040)
6. Characterization of porcine endogenous retrovirus gamma pro-pol nucleotide sequences. N Klymiuk M Müller G Brem B Aigner, J Virol 2002 76 11738 11743 10.1128/JVI.76.22.11738-11743.2002 12388734 (Pubitemid 35231329)
7. Expression of pig endogenous retrovirus by primary porcine endothelial cells and infection of human cells. U Martin V Kiessig JH Blusch A Haverich K von der Helm T Herden G Steinhoff, Lancet 1998 352 692 694 10.1016/S0140- 6736(98)07144-X 9728985 (Pubitemid 28398704)
8. Host range and interference studies of three classes of pig endogenous retrovirus. Y Takeuchi C Patience S Magre RA Weiss PT Banerjee P Le Tissier JP Stoye, J Virol 1998 72 9986 9991 9811736 (Pubitemid 28520866)
9. Infection of human cells by an endogenous retrovirus of pigs. C Patience Y Takeuchi RA Weiss, Nat Med 1997 3 282 286 10.1038/nm0397-282 9055854 (Pubitemid 27112924)
10. The dangers of xenotransplantation. JP Stoye JM Coffin, Nat Med 1995 1 1100 7584964
11. Xenotransplantation. New risks, new gains. JL Platt, Nature 2000 407 29 30 27
12. Xenotransplantation and risks of zoonotic infections. RS Boneva TM Folks, Ann Med 2004 36 504 517 10.1080/07853890410018826 15513301 (Pubitemid 39490960)
13. The ethics debate in relation to xenotransplantation. C Smetanka DK Cooper, Rev Sci Tech 2005 24 335 342 16110900 (Pubitemid 41112551)
14. Identification of a novel type C porcine endogenous retrovirus: evidence that copy number of endogenous retroviruses increases during host inbreeding. R Mang J Maas X Chen J Goudsmit AC van Der Kuyl, J Gen Virol 2001 82 1829 1834 11457988 (Pubitemid 32707546)
15. Phylogeny, recombination and expression of porcine endogenous retrovirus gamma2 nucleotide sequences. N Klymiuk M Muller G Brem B Aigner, J Gen Virol 2006 87 977 986 10.1099/vir.0.81552-0 16528048
16. Evolutionary spread and recombination of porcine endogenous retroviruses in the Suiformes. M Niebert RR Tönjes, J Virol 2005 79 649 654 10.1128/JVI.79.1.649-654.2005 15596862 (Pubitemid 39648421)
17. High copy number in human endogenous retrovirus families is associated with copying mechanisms in addition to reinfection. R Belshaw A Katzourakis J Paces A Burt M Tristem, Mol Biol Evol 2005 22 814 817 10.1093/molbev/msi088 15659556 (Pubitemid 40471396)
18. Long-term reinfection of the human genome by endogenous retroviruses. R Belshaw V Pereira A Katzourakis G Talbot J Paces A Burt M Tristem, Proc Natl Acad Sci USA 2004 101 4894 4899 10.1073/pnas.0307800101 15044706 (Pubitemid 38469174)
19. The evolutionary dynamics of endogenous retroviruses. A Katzourakis A Rambaut OG Pybus, Trends Microbiol 2005 13 463 468 10.1016/j.tim.2005.08.004 16109487 (Pubitemid 41317523)
20. Transposable elements. DJ Finnegan, Curr Opin Genet Dev 1992 2 861 867 10.1016/S0959-437X(05)80108-X 1335807
21. Effects of retroviruses on host genome function. P Jern JM Coffin, Annu Rev Genet 2008 42 709 732 10.1146/annurev.genet.42.110807.091501 18694346
22. Evolution of the family Suidae and their endogenous retroviruses. FF Nascimento, PhD The University of Sydney 2009
23. Rethinking the evolution of sub-Saharan African suids (Suidae, Artiodactyla). J Gongora RE Cuddahee FF Nascimento CJ Palgrave S Lowden SYW Ho D Simond CS Damayanti DJ White WT Tay E Randi H Klingel CJ Rodrigues-Zarate K Allen C Moran G Larson, Zool Scr 2011
24. RDP2: recombination detection and analysis from sequence alignments. DP Martin C Williamson D Posada, Bioinformatics 2005 21 260 262 10.1093/bioinformatics/bth490 15377507 (Pubitemid 40202028)
25. An exploratory algorithm to identify intra-host recombinant viral sequences. M Salemi RR Gray MM Goodenow, Mol Phylogenet Evol 2008 49 618 628 10.1016/j.ympev.2008.08.017 18801446
26. An index of substitution saturation and its application. X Xia Z Xie M Salemi L Chen Y Wang, Mol Phylogenet Evol 2003 26 1 7 10.1016/S1055-7903(02) 00326-3 12470932 (Pubitemid 36029247)
27. Assessing substitution saturation with DAMBE. X Xia, The phylogenetic handbook : a practical approach to phylogenetic analysis and hypothesis testing Cambridge: Cambridge University Press, Salemi M, Vandamme A-M, Lemey P, 2 2009 615 623
28. Likelihood-mapping: a simple method to visualize phylogenetic content of a sequence alignment. K Strimmer A von Haeseler, Proc Natl Acad Sci USA 1997 94 6815 6819 10.1073/pnas.94.13.6815 9192648 (Pubitemid 27281947)
29. Statistical methods for detecting molecular adaptation. Z Yang JP Bielawski, Trends Ecol Evol 2000 15 496 503 10.1016/S0169-5347(00)01994-7 11114436
30. Likelihood ratio tests for detecting positive selection and application to primate lysozyme evolution. Z Yang, Mol Biol Evol 1998 15 568 573 9580986 (Pubitemid 28194621)
31. Distinctive differences in long terminal repeat sequences between gamma1 endogenous retroviruses of African and Eurasian suid species. FF Nascimento J Gongora M Tristem S Lowden C Moran, Infect Genet Evol 2011 11 686 693 10.1016/j.meegid.2011.01.010 21256982
32. Evolution of the Plio-Pleistocene African Suidae. JM Harris TD White, Trans Am Phil Soc 1979 69 1 128
33. Suid evolution and correlation of African hominid localities. TD White JM Harris, Science 1977 198 13 21 10.1126/science.331477 331477
34. Old world suoid systematics, phylogeny, biogeography and biostratigraphy. M Pickford, Paleontologia i Evoluciá 1993 26-27 237 269
35. Phylogenomics: the beginning of incongruence? O Jeffroy H Brinkmann F Delsuc H Philippe, Trends Genet 2006 22 225 231 10.1016/j.tig.2006.02.003 16490279
36. Phylogenetic inference using whole genomes. B Rannala Z Yang, Annu Rev Genomics Hum Genet 2008 9 217 231 10.1146/annurev.genom.9.081307.164407 18767964
37. Gene tree discordance, phylogenetic inference and the multispecies coalescent. JH Degnan NA Rosenberg, Trends Ecol Evol 2009 24 332 340 10.1016/j.tree.2009.01.009 19307040
38. Relationships of gag-pol diversity between Ty3/Gypsy and Retroviridae LTR retroelements and the three kings hypothesis. C Llorens MA Fares A Moya, BMC Evol Biol 2008 8 276 10.1186/1471-2148-8-276 18842133
39. Molecular and phylogenetic analyses of a new amphotropic murine leukemia virus (MuLV-1313). TM Howard Z Sheng M Wang Y Wu S Rasheed, Virol J 2006 3 101 10.1186/1743-422X-3-101 17147829
40. Functional characterization of a portion of the Moloney murine leukemia virus gag gene by genetic footprinting. MR Auerbach C Shu A Kaplan IR Singh, Proc Natl Acad Sci USA 2003 100 11678 11683 10.1073/pnas.2034020100 14504385 (Pubitemid 37205994)
41. Distribution of endogenous retroviruses in crocodilians. W Jaratlerdsiri CJ Rodriguez-Zarate SR Isberg CS Damayanti LG Miles N Chansue C Moran L Melville J Gongora, J Virol 2009 83 10305 10308 10.1128/JVI.00668-09 19605486
42. Identification and classification of endogenous retroviruses in cattle. R Xiao K Park H Lee J Kim C Park, J Virol 2008 82 582 587 10.1128/JVI.01451-07 17959664 (Pubitemid 350309174)
43. Characterization of a novel murine leukemia virus-related subgroup within mammals. M Tristem P Kabat L Lieberman S Linde A Karpas F Hill, J Virol 1996 70 8241 8246 8892961 (Pubitemid 26339146)
44. Extensive HIV-1 intra-host recombination is common in tissues with abnormal histopathology. SL Lamers M Salemi DC Galligan T de Oliveira GB Fogel SC Granier L Zhao JN Brown A Morris E Masliah MS McGrath, PLoS One 2009 4 5065 10.1371/journal.pone.0005065 19333384
45. Basic concepts of molecular evolution. AM Vandamme, The phylogenetic handbook: a practical approach to phylogenetic analysis and hypothesis testing Cambridge: Cambridge University Press, Salemi M, Vandamme A-M, Lemey P, 2 2009 3 29
46. Cytochrome b sequence data suggest rapid speciation within the Paramecium aurelia species complex. D Barth E Przybos SI Fokin M Schlegel TU Berendonk, Mol Phylogenet Evol 2008 49 669 673 10.1016/j.ympev.2008.08.007 18778782
47. Deciphering ancient rapid radiations. JB Whitfield PJ Lockhart, Trends Ecol Evol 2007 22 258 265 10.1016/j.tree.2007.01.012 17300853 (Pubitemid 46590495)
48. Birds in a bush: five genes indicate explosive evolution of avian orders. S Poe AL Chubb, Evolution 2004 58 404 415 15068356 (Pubitemid 38362384)
49. Analysis of complete mitochondrial genomes from extinct and extant rhinoceroses reveals lack of phylogenetic resolution. E Willerslev MT Gilbert J Binladen SY Ho PF Campos A Ratan LP Tomsho RR da Fonseca A Sher TV Kuznetsova M Nowak-Kemp TL Roth W Miller SC Schuster, BMC Evol Biol 2009 9 95 10.1186/1471-2148-9-95 19432984
50. Bushes in the tree of life. A Rokas SB Carroll, PLoS Biol 2006 4 352 10.1371/journal.pbio.0040352 17105342
51. BioEdit: a user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT. TA Hall, Nucleic Acids Symp Ser 1999 41 95 98
52. MUSCLE: multiple sequence alignment with high accuracy and high throughput. RC Edgar, Nucleic Acids Res 2004 32 1792 1797 10.1093/nar/gkh340 15034147 (Pubitemid 38832724)
53. Z Yang, Computational molecular evolution Oxford: Oxford University Press 2006
54. SEAVIEW and PHYLO-WIN: two graphic tools for sequence alignment and molecular phylogeny. N Galtier M Gouy C Gautier, Comput Appl Biosci 1996 12 543 548 9021275
55. MEGA4: Molecular Evolutionary Genetics Analysis (MEGA) software version 4.0. K Tamura J Dudley M Nei S Kumar, Mol Biol Evol 2007 24 1596 1599 10.1093/molbev/msm092 17488738 (Pubitemid 47236692)
56. Evolutionary distance estimation under heterogeneous substitution pattern among lineages. K Tamura S Kumar, Mol Biol Evol 2002 19 1727 1736 12270899
57. A statistical test for detecting geographic subdivision. RR Hudson DD Boos NL Kaplan, Mol Biol Evol 1992 9 138 151 1552836
58. A robust measure of HIV-1 population turnover within chronically infected individuals. G Achaz S Palmer M Kearney F Maldarelli JW Mellors JM Coffin J Wakeley, Mol Biol Evol 2004 21 1902 1912 10.1093/molbev/msh196 15215321 (Pubitemid 39331637)
59. Phylogenetics by likelihood: evolutionary modeling as a tool for understanding the genome. C Kosiol L Bofkin S Whelan, J Biomed Inform 2006 39 51 61 10.1016/j.jbi.2005.08.003 16226061 (Pubitemid 43140719)
60. Phylogenetic model evaluation. LS Jermiin V Jayaswal F Ababneh J Robinson, Methods Mol Biol 2008 452 331 364 10.1007/978-1-60327-159-2-16 18566772
61. RDP: detection of recombination amongst aligned sequences. D Martin E Rybicki, Bioinformatics 2000 16 562 563 10.1093/bioinformatics/16.6.562 10980155
62. Statistical tests for detecting gene conversion. S Sawyer, Mol Biol Evol 1989 6 526 538 2677599 (Pubitemid 19210235)
63. Possible emergence of new geminiviruses by frequent recombination. M Padidam S Sawyer CM Fauquet, Virology 1999 265 218 225 10.1006/viro.1999.0056 10600594 (Pubitemid 30022217)
64. Analyzing the mosaic structure of genes. JM Smith, J Mol Evol 1992 34 126 129 1556748
65. Evaluation of methods for detecting recombination from DNA sequences: computer simulations. D Posada KA Crandall, Proc Natl Acad Sci USA 2001 98 13757 13762 10.1073/pnas.241370698 11717435 (Pubitemid 33115971)
66. Sister-scanning: a Monte Carlo procedure for assessing signals in recombinant sequences. MJ Gibbs JS Armstrong AJ Gibbs, Bioinformatics 2000 16 573 582 10.1093/bioinformatics/16.7.573 11038328
67. An exact nonparametric method for inferring mosaic structure in sequence triplets. MF Boni D Posada MW Feldman, Genetics 2007 176 1035 1047 17409078 (Pubitemid 46961105)
68. MRBAYES: Bayesian inference of phylogenetic trees. JP Huelsenbeck F Ronquist, Bioinformatics 2001 17 754 755 10.1093/bioinformatics/17.8.754 11524383 (Pubitemid 32851390)
69. MrBayes 3: Bayesian phylogenetic inference under mixed models. F Ronquist JP Huelsenbeck, Bioinformatics 2003 19 1572 1574 10.1093/bioinformatics/btg180 12912839 (Pubitemid 37038874)
70. Assessment of methods for amino acid matrix selection and their use on empirical data shows that ad hoc assumptions for choice of matrix are not justified. TM Keane CJ Creevey MM Pentony TJ Naughton JO McLnerney, BMC Evol Biol 2006 6 29 10.1186/1471-2148-6-29 16563161
71. Bayesian phylogenetic analysis of combined data. JA Nylander F Ronquist JP Huelsenbeck JL Nieves-Aldrey, Syst Biol 2004 53 47 67 10.1080/ 10635150490264699 14965900 (Pubitemid 38370420)
72. Tracer v1.4. http://beast.bio.ed.ac.uk/Tracer
73. An index of substitution saturation and its application. X Xia Z Xie M Salemi L Chen Y Wang, Mol Phylogenet Evol 2003 26 1 7 10.1016/S1055-7903(02) 00326-3 12470932 (Pubitemid 36029247)
74. DAMBE: software package for data analysis in molecular biology and evolution. X Xia Z Xie, J Hered 2001 92 371 373 10.1093/jhered/92.4.371 11535656 (Pubitemid 32848767)
75. TREE-PUZZLE: maximum likelihood phylogenetic analysis using quartets and parallel computing. HA Schmidt K Strimmer M Vingron A von Haeseler, Bioinformatics 2002 18 502 504 10.1093/bioinformatics/18.3.502 11934758 (Pubitemid 34284960)
76. Phylogenetic inference using maximum likelihood methods. HA Schmidt A von Haeseler, The phylogenetic handbook : a practical approach to phylogenetic analysis and hypothesis testing Cambridge: Cambridge University Press, Salemi M, Vandamme A-M, Lemey P, 2 2009 181 198
77. PAML 4: phylogenetic analysis by maximum likelihood. Z Yang, Mol Biol Evol 2007 24 1586 1591 10.1093/molbev/msm088 17483113 (Pubitemid 47236688)
78. Dating of the human-ape splitting by a molecular clock of mitochondrial DNA. M Hasegawa H Kishino T Yano, J Mol Evol 1985 22 160 174 10.1007/BF02101694 3934395 (Pubitemid 16227864)
79. A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences. M Kimura, J Mol Evol 1980 16 111 120 10.1007/BF01731581 7463489 (Pubitemid 11166431)
80. Bayes factors. RE Kass AE Raftery, J Am Stat Assoc 1995 90 773 795 10.2307/2291091