ODoSE: A Webserver for Genome-Wide Calculation of Adaptive Divergence in Prokaryotes

PLoS ONE

Volumn 8, Issue 5, 2013, Pages

  Vos, Michiel ^a   te Beek, Tim A H ^b,c   van Driel, Marc A ^b   Huynen, Martijn A ^c   Eyre Walker, Adam ^d   van Passel, Mark W J ^e  

^a UNIVERSITY OF EXETER MEDICAL SCHOOL   (United Kingdom)

^b NETHERLANDS BIOINFORMATICS CENTRE   (Netherlands)

^c RADBOUD UNIVERSITY MEDICAL CENTER   (Netherlands)

^d UNIVERSITY OF SUSSEX   (United Kingdom)

^e WAGENINGEN UNIVERSITY   (Netherlands)

Author keywords

[No Author keywords available]

Indexed keywords

ADAPTIVE DIVERGENCE; ARTICLE; CALCULATION; COMPUTER PROGRAM; GENETIC POLYMORPHISM; GENETIC VARIABILITY; GENOME; INTERNET; MOLECULAR EVOLUTION; NONHUMAN; ORTHOLOG DIRECTION OF SELECTION ENGINE; POPULATION GENETICS; PROKARYOTE;

ADAPTATION, BIOLOGICAL; ALGORITHMS; ARCHAEA; BACTERIA; EVOLUTION, MOLECULAR; GENOME, ARCHAEAL; GENOME, BACTERIAL; INTERNET; MODELS, GENETIC; POLYMORPHISM, GENETIC; SEQUENCE ANALYSIS, DNA; SOFTWARE;

PROKARYOTA;

EID: 84877088111     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0062447     Document Type: Article

References (22)

1. van Passel MW, Marri PR, Ochman H, (2008) The emergence and fate of horizontally acquired genes in Escherichia coli. PLoS Comput Biol 4: e1000059.
2. Lefebure T, Stanhope MJ, (2009) Pervasive, genome-wide positive selection leading to functional divergence in the bacterial genus Campylobacter. Genome Res 19: 1224-1232.
3. Lefebure T, Bitar PD, Suzuki H, Stanhope MJ, (2010) Evolutionary dynamics of complete Campylobacter pan-genomes and the bacterial species concept. Genome Biol Evol 2: 646-655.
4. Soyer Y, Orsi RH, Rodriguez-Rivera LD, Sun Q, Wiedmann M, (2009) Genome wide evolutionary analyses reveal serotype specific patterns of positive selection in selected Salmonella serotypes. BMC Evol Biol 9: 264.
5. Xu Z, Chen H, Zhou R, (2011) Genome-wide evidence for positive selection and recombination in Actinobacillus pleuropneumoniae. BMC Evol Biol 11: 203.
6. Joseph B, Schwarz RF, Linke B, Blom J, Becker A, et al. (2011) Virulence evolution of the human pathogen Neisseria meningitidis by recombination in the core and accessory genome. PLoS One 6: e18441.
7. Shapiro BJ, Alm E, (2009) The slow:fast substitution ratio reveals changing patterns of natural selection in gamma-proteobacterial genomes. ISME J 3: 1180-1192.
8. Eyre-Walker A, (2006) The genomic rate of adaptive evolution. Trends Ecol Evol 21: 569-575.
9. Charlesworth J, Eyre-Walker A, (2006) The rate of adaptive evolution in enteric bacteria. Mol Biol Evol 23: 1348-1356.
10. McDonald JH, Kreitman M, (1991) Adaptive protein evolution at the Adh locus in Drosophila. Nature 351: 652-654.
11. Rand DM, Kann LM, (1996) Excess amino acid polymorphism in mitochondrial DNA: contrasts among genes from Drosophila, mice, and humans. Mol Biol Evol 13: 735-748.
12. Presgraves DC, (2005) Recombination enhances protein adaptation in Drosophila melanogaster. Curr Biol 15: 1651-1656.
13. Hughes AL, Friedman R, Rivailler P, French JO, (2008) Synonymous and nonsynonymous polymorphisms versus divergences in bacterial genomes. Mol Biol Evol 25: 2199-2209.
14. Stoletzki N, Eyre-Walker A, (2011) Estimation of the neutrality index. Mol Biol Evol 28: 63-70.
15. Giardine B, Riemer C, Hardison RC, Burhans R, Elnitski L, et al. (2005) Galaxy: a platform for interactive large-scale genome analysis. Genome Res 15: 1451-1455.
16. Li L, Stoeckert CJ, Roos DS, (2003) OrthoMCL: identification of ortholog groups for eukaryotic genomes. Genome Res 13: 2178-2189.
17. Edgar RC, (2004) MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res 32: 1792-1797.
18. Yang Z, (2007) PAML 4: phylogenetic analysis by maximum likelihood. Mol Biol Evol 24: 1586-1591.
19. Bruen TC, Philippe H, Bryant D, (2006) A simple and robust statistical test for detecting the presence of recombination. Genetics 172: 2665-2681.
20. Shapiro BJ, Alm EJ, (2008) Comparing patterns of natural selection across species using selective signatures. PLoS Genet 4: e23.
21. Vos M, (2011) A species concept for bacteria based on adaptive divergence. Trends Microbiol 19: 1-7.
22. Eyre-Walker A, Keightley PD, (2009) Estimating the rate of adaptive molecular evolution in the presence of slightly deleterious mutations and population size change. Mol Biol Evol 26: 2097-2108.