RELAX: Detecting relaxed selection in a phylogenetic framework

Molecular Biology and Evolution

Volumn 32, Issue 3, 2015, Pages 820-832

  Wertheim, Joel O ^a   Murrell, Ben ^a   Smith, Martin D ^b   Pond, Sergei L Kosakovsky ^a   Scheffler, Konrad ^a,c  

^a UNIVERSITY OF CALIFORNIA SAN DIEGO   (United States)

^b UNIVERSITY OF CALIFORNIA   (United States)

^c STELLENBOSCH UNIVERSITY   (South Africa)

Author keywords

Bornavirus; Codon models; Daphnia pulex; Echolocation; Endosymbionts; Molecular evolution; Opsin; Phylogenetics; Relaxed selection

Indexed keywords

OPSIN; CODON;

ARTICLE; BAT; BORNAVIRUS; CODON; DAPHNIA PULEX; ECHOLOCATION; ENDOSYMBIONT; GAMMAPROTEOBACTERIA; MOLECULAR EVOLUTION; NATURAL SELECTION; NONHUMAN; PHYLOGENY; RELAXED SELECTION; SIMULATION; VALIDITY; ANIMAL; BIOLOGICAL MODEL; BIOLOGY; BORNAVIRIDAE; COMPUTER SIMULATION; DAPHNIA; DNA SEQUENCE; GENETIC SELECTION; GENETICS; PROCEDURES;

ANIMALS; BORNAVIRIDAE; CHIROPTERA; CODON; COMPUTATIONAL BIOLOGY; COMPUTER SIMULATION; DAPHNIA; EVOLUTION, MOLECULAR; GAMMAPROTEOBACTERIA; MODELS, GENETIC; OPSINS; PHYLOGENY; SELECTION, GENETIC; SEQUENCE ANALYSIS, DNA;

EID: 84982179834     PISSN: 07374038     EISSN: 15371719     Source Type: Journal    
DOI: 10.1093/molbev/msu400     Document Type: Article

References (74)

1. Anisimova M, Kosiol C. 2009. Investigating protein-coding sequence evolution with probabilistic codon substitution models. Mol Biol Evol. 26(2):255-271.
2. Barton NH. 2009. Why sex and recombination? Cold Spring Harb Symp Quant Biol. 74:187-195.
3. Belyi VA, Levine AJ, Skalka AM. 2010. Unexpected inheritance: multiple integrations of ancient bornavirus and ebolavirus/marburgvirus sequences in vertebrate genomes. PLoS Pathog. 6(7):e1001030.
4. Bielawski JP, Yang Z. 2003. Maximum likelihood methods for detecting adaptive evolution after gene duplication. J Struct Funct Genomics. 3(1-4):201-212.
5. Burke G, Fiehn O, Moran N. 2010. Effects of facultative symbionts and heat stress on the metabolome of pea aphids. ISME J. 4(2):242-252.
6. Dainat J, Paganini J, Pontarotti P, Gouret P. 2012. GLADX: an automated approach to analyze the lineage-specific loss and pseudogenization of genes. PLoS One 7(6):e38792.
7. Darwin C. 1859. On the origin of species by means of natural selection. J. Murray London.
8. Degnan PH, Yu Y, Sisneros N, Wing RA, Moran NA. 2009. Hamiltonella defensa, genome evolution of protective bacterial endosymbiont from pathogenic ancestors. Proc Natl Acad Sci U S A. 106(22):9063-9068.
9. Delport W, Poon AFY, Frost SDW, Kosakovsky Pond SL. 2010. Datamonkey. 2010: a suite of phylogenetic analysis tools for evolutionary biology. Bioinformatics 26(19):2455-2457.
10. Delport W, Scheffler K, Seoighe C. 2009. Models of coding sequence evolution. Brief Bioinform. 10(1):97-109.
11. Edgar RC. 2004. MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res. 32(5):1792-1797.
12. Elde NC, Malik HS. 2009. The evolutionary conundrum of pathogen mimicry. Nat Rev Microbiol. 7(11):787-797.
13. Eyre-Walker A. 2006. The genomic rate of adaptive evolution. Trends Ecol Evol. 21(10):569-575.
14. Felsenstein J. 1981. Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol. 17(6):368-376.
15. Feng P, Zheng J, Rossiter SJ, Wang D, Zhao H. 2014. Massive losses of taste receptor genes in toothed and baleen whales. Genome Biol Evol. 6(6):1254-1265.
16. Fenton MB, Faure PA, Ratcliffe JM. 2012. Evolution of high duty cycle echolocation in bats. J Exp Biol. 215(Pt 17):2935-2944.
17. Funk DJ, Wernegreen JJ, Moran NA. 2001. Intraspecific variation in symbiont genomes: bottlenecks and the aphid-buchnera association. Genetics 157(2):477-489.
18. Galtier N, Gouy M. 1995. Inferring phylogenies from DNA sequences of unequal base compositions. Proc Natl Acad Sci U S A. 92(24):11317-11321.
19. Galtier N, Gouy M. 1998. Inferring pattern and process: maximum-likelihood implementation of a nonhomogeneous model of DNA sequence evolution for phylogenetic analysis. Mol Biol Evol. 15(7):871-879.
20. Go Y, Satta Y, Takenaka O, Takahata N. 2005. Lineage-specific loss of function of bitter taste receptor genes in humans and nonhuman primates. Genetics 170(1):313-326.
21. Goldman N, Yang Z. 1994. A codon-based model of nucleotide substitution for protein-coding DNA sequences. Mol Biol Evol. 11(5):725-736.
22. Gouy M, Guindon S, Gascuel O. 2010. SeaView version 4: a multiplatform graphical user interface for sequence alignment and phylogenetic tree building. Mol Biol Evol. 27(2):221-224.
23. Graur D, Zheng Y, Price N, Azevedo RBR, Zufall RA, Elhaik E. 2013. On the immortality of television sets: "function" in the human genome according to the evolution-free gospel of ENCODE. Genome Biol Evol. 5(3):578-590.
24. Guindon S, Dufayard J-F, Lefort V, Anisimova M, Hordijk W, Gascuel O. 2010. New algorithms and methods to estimate maximumlikelihood phylogenies: assessing the performance of PhyML 3.0. Syst Biol. 59(3):307-321.
25. Herbeck JT, Funk DJ, Degnan PH, Wernegreen JJ. 2003. A conservative test of genetic drift in the endosymbiotic bacterium Buchnera: slightly deleterious mutations in the chaperonin groEL. Genetics 165(4):1651-1660.
26. Holmes EC. 2003. Patterns of intra-and interhost nonsynonymous variation reveal strong purifying selection in dengue virus. J Virol. 77(20):11296-11298.
27. Holmes EC, Drummond AJ. 2007. The evolutionary genetics of viral emergence. Curr Top Microbiol Immunol. 315:51-66.
28. Horie M, Honda T, Suzuki Y, Kobayashi Y, Daito T, Oshida T, Ikuta K, Jern P, Gojobori T, Coffin JM, et al. 2010. Endogenous non-retroviral RNA virus elements in mammalian genomes. Nature 463(7277):84-87.
29. Horie M, Kobayashi Y, Suzuki Y, Tomonaga K. 2013. Comprehensive analysis of endogenous bornavirus-like elements in eukaryote genomes. Philos Trans R Soc Lond B Biol Sci. 368(1626):20120499.
30. Hunt BG, Ometto L, Wurm Y, Shoemaker D, Yi SV, Keller L, Goodisman MAD. 2011. Relaxed selection is a precursor to the evolution of phenotypic plasticity. Proc Natl Acad Sci U S A. 108(38):15936-15941.
31. Husník F, Chrudimský T, Hypša V. 2011. Multiple origins of endosymbiosis within the Enterobacteriaceae (Y-Proteobacteria): convergence of complex phylogenetic approaches. BMC Biol. 9:87.
32. Kosakovsky Pond S, Delport W, Muse SV, Scheffler K. 2010. Correcting the bias of empirical frequency parameter estimators in codon models. PLoS One 5(7):e11230.
33. Kosakovsky Pond SL, Murrell B, Fourment M, Frost SDW, Delport W, Scheffler K. 2011. A random effects branch-site model for detecting episodic diversifying selection. Mol Biol Evol. 28(11) 3033-3043.
34. Kosakovsky Pond SL, Scheffler K, Gravenor MB, Poon AFY, Frost SDW. 2010. Evolutionary fingerprinting of genes. Mol Biol Evol. 27(3):520-536.
35. Lahti DC, Johnson NA, Ajie BC, Otto SP, Hendry AP, Blumstein DT, Coss RG, Donohue K, Foster SA. 2009. Relaxed selection in the wild. Trends Ecol Evol. 24(9):487-496.
36. Lenski RE, Ofria C, Pennock RT, Adami C. 2003. The evolutionary origin of complex features. Nature 423(6936):139-144.
37. Lynch M, Conery JS. 2000. The evolutionary fate and consequences of duplicate genes. Science 290(5494):1151-1155.
38. Marková S, Searle JB, Kotlík P. 2014. Relaxed functional constraints on triplicate α-globin gene in the bank vole suggest a different evolutionary history from other rodents. Heredity 113(1):64-73.
39. Maynard Smith J. 1978. The evolution of sex. Cambridge: Cambridge University Press.
40. McCutcheon JP, McDonald BR, Moran NA. 2009. Convergent evolution of metabolic roles in bacterial co-symbionts of insects. Proc Natl Acad Sci U S A. 106(36):15394-15399.
41. McCutcheon JP, Moran NA. 2012. Extreme genome reduction in symbiotic bacteria. Nat Rev Microbiol. 10(1):13-26.
42. Moran NA. 1996. Accelerated evolution and Muller's Rachet in endosymbiotic bacteria. Proc Natl Acad Sci U S A. 93(7):2873-2878.
43. Moran NA, Baumann P. 2000. Bacterial endosymbionts in animals. Curr Opin Microbiol. 3(3):270-275.
44. Muller HJ. 1964. The relation of recombination to mutational advance. Mutat Res. 106:2-9.
45. 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(7):e1002764.
46. Muse SV, Gaut BS. 1994. A likelihood approach for comparing synonymous and nonsynonymous nucleotide substitution rates, with application to the chloroplast genome. Mol Biol Evol. 11(5):715-724.
47. NeiM, Zhang J, Yokoyama S. 1997. Color vision of ancestral organisms of higher primates. Mol Biol Evol. 14(6):611-618.
48. Nemec P, Cveková P, Benada O,Wielkopolska E, Olkowicz S, Turlejski K, Burda H, Bennett NC, Peichl L. 2008. The visual system in subterranean African mole-rats (Rodentia, Bathyergidae): retina, subcortical visual nuclei and primary visual cortex. Brain Res Bull. 75(2-4):356-364.
49. Nielsen R, Yang Z. 1998. Likelihood models for detecting positively selected amino acid sites and applications to the HIV-1 envelope gene. Genetics 148(3):929-936.
50. Ohno S. 1970. Evolution by gene duplication. New York: Allen and Unwin.
51. Oliver KM, Degnan PH, Hunter MS, Moran NA. 2009. Bacteriophages encode factors required for protection in a symbiotic mutualism. Science 325(5943):992-994.
52. Oliver KM, Moran NA, Hunter MS. 2006. Costs and benefits of a superinfection of facultative symbionts in aphids. Proc Biol Sci. 273(1591):1273-1280.
53. Paland S, Lynch M. 2006. Transitions to asexuality result in excess amino acid substitutions. Science 311(5763):990-992.
54. Pond SLK, Frost SDW. 2005. Datamonkey: rapid detection of selective pressure on individual sites of codon alignments. Bioinformatics 21(10):2531-2533.
55. Pond SLK, Frost SDW, Grossman Z, Gravenor MB, Richman DD, Brown AJL. 2006. Adaptation to different human populations by HIV-1 revealed by codon-based analyses. PLoS Comput Biol. 2(6):e62.
56. Pond SLK, Frost SDW, Muse SV. 2005. HyPhy: hypothesis testing using phylogenies. Bioinformatics 21(5):676-679.
57. Pybus OG, Rambaut A, Belshaw R, Freckleton RP, Drummond AJ, Holmes EC. 2007. Phylogenetic evidence for deleterious mutation load in RNA viruses and its contribution to viral evolution. Mol Biol Evol. 24(3):845-852.
58. Scheffler K, Murrell B, Kosakovsky Pond SL. 2014. On the validity of evolutionary models with site-specific parameters. PLoS One 9(4):e94534.
59. Snell-Rood EC, Van Dyken JD, Cruickshank T, Wade MJ, Moczek AP. 2010. Toward a population genetic framework of developmental evolution: the costs, limits, and consequences of phenotypic plasticity. Bioessays 32(1):71-81.
60. Speakman JR. 2001. The evolution of flight and echolocation in bats: another leap in the dark. Mamm Rev. 31(2):111-130.
61. Templeton AR. 2008. The reality and importance of founder speciation in evolution. Bioessays 30(5):470-479.
62. Tucker AE, Ackerman MS, Eads BD, Xu S, Lynch M. 2013. Populationgenomic insights into the evolutionary origin and fate of obligately asexual Daphnia pulex. Proc Natl Acad Sci U S A. 110(39):15740-15745.
63. Veilleux CC, Louis EE Jr, Bolnick DA. 2013. Nocturnal light environments influence color vision and signatures of selection on the OPN1SW opsin gene in nocturnal lemurs. Mol Biol Evol. 30(6):1420-1437.
64. Vogel KJ, Moran NA. 2011. Sources of variation in dietary requirements in an obligate nutritional symbiosis. Proc Biol Sci. 278(1702):115-121.
65. Wernegreen JJ. 2002. Genome evolution in bacterial endosymbionts of insects. Nat Rev Genet. 3(11):850-861.
66. Wernegreen JJ. 2011. Reduced selective constraint in endosymbionts: elevation in radical amino acid replacements occurs genome-wide. PLoS One 6(12):e28905.
67. Wertheim JO, Kosakovsky Pond SL. 2011. Purifying selection can obscure the ancient age of viral lineages. Mol Biol Evol. 28(12):3355-3365.
68. Wertheim JO,Worobey M. 2009. Relaxed selection and the evolution of RNA virus mucin-like pathogenicity factors. J Virol. 83(9):4690-4694.
69. Wicke S, Schäferhoff B, dePamphilis CW, Müller KF. 2014. Disproportional plastome-wide increase of substitution rates and relaxed purifying selection in genes of carnivorous Lentibulariaceae. Mol Biol Evol. 31(3):529-545.
70. Wu CI, Li WH, Shen JJ, Scarpulla RC, Limbach KJ, Wu R. 1986. Evolution of cytochrome c genes and pseudogenes. J Mol Evol. 23(1):61-75.
71. Yang Z, Nielsen R. 2002. Codon-substitution models for detecting molecular adaptation at individual sites along specific lineages. Mol Biol Evol. 19(6):908-917.
72. Yang Z, Nielsen R, Goldman N, Pedersen AM. 2000. Codon-substitution models for heterogeneous selection pressure at amino acid sites. Genetics 155(1):431-449.
73. Zhao H, Rossiter SJ, Teeling EC, Li C, Cotton JA, Zhang S. 2009. The evolution of color vision in nocturnal mammals. Proc Natl Acad Sci U S A. 106(22):8980-8985.
74. Zhao H, Ru B, Teeling EC, Faulkes CG, Zhang S, Rossiter SJ. 2009. Rhodopsin molecular evolution in mammals inhabiting low light environments. PLoS One 4(12):e8326.