e1003766. https://doi.org/10.1371/jour
nal.ppat.1003766
88. Xu Z, Chen H, Zhou R (2011) Genome-wide
evidence for positive selection and recombination in Actinobacillus pleuropneumoniae.
BMC Evol Biol 11:203
89. Cao P, Guo D, Liu J, Jiang Q, Xu Z, Qu L
(2017) Genome-wide analyses reveal genes
subject to positive selection in Pasteurella
multocida. Front Microbiol 8:961. https://
doi.org/10.3389/fmicb.2017.00961
90. Petersen L, Bollback JP, Dimmic M,
Hubisz M, Nielsen R (2007) Genes under
positive selection in Escherichia coli. Genome
Res 17:1336–1343
91. Nandi T, Ong C, Singh AP et al (2010) A
genomic survey of positive selection in Burkholderia pseudomallei provides insights into
the evolution of accidental virulence. PLoS
Pathog 6:e1000845
92. O’Connor DH, McDermott AB, Krebs KC
et al (2004) A dominant role for CD8+-Tlymphocyte selection in simian immunodeficiency virus sequence variation. J Virol
78:14012–14022
93. de Oliveira T, Salemi M, Gordon M, Vandamme
A-M,
van
Rensburg
EJ,
Engelbrecht S, Coovadia HM, Cassol S
(2004) Mapping sites of positive selection
and amino acid diversification in the HIV
genome: an alternative approach to vaccine
design? Genetics 167:1047–1058
94. Yang Z (1997) PAML: a program package for
phylogenetic analysis by maximum likelihood.
Comput Appl Biosci 13:555–556
95. Kosakovsky Pon S, Poon A, Frost S (2009)
Estimating selection pressures on alignments
of coding sequences. In: The phylogenetic
handbook: a practical approach to phylogenetic analysis and hypothesis testing, 2nd
edn. Cambridge University Press, New York,
NY, pp 419–452
96. Anisimova M, Nielsen R, Yang Z (2003)
Effect of recombination on the accuracy of
the likelihood method for detecting positive
selection at amino acid sites. Genetics
164:1229–1236
97. Kosakovsky Pond SL, Posada D, Gravenor
MB, Woelk CH, Frost SDW (2006) GARD:
a genetic algorithm for recombination detection. Bioinformatics 22:3096–3098
98. Dobson R, Stockdale C, Lapsley C, Wilkes J,
McCulloch R (2011) Interactions among Trypanosoma brucei RAD51 paralogues in DNA
repair and antigenic variation. Mol Microbiol
81:434–456
99. Holden NJ, Uhlin BE, Gally DL (2001) PapB
paralogues and their effect on the phase variation of type 1 fimbriae in Escherichia coli. Mol
Microbiol 42:319–330
100. Tsuru T, Kobayashi I (2008) Multiple
genome comparison within a bacterial species
reveals a unit of evolution spanning two adjacent genes in a tandem paralog cluster. Mol
Biol Evol 25:2457–2473
101. Rappuoli R (2011) The challenge of developing universal vaccines. F1000 Med Rep 3:16.
https://doi.org/10.3410/M3-16
102. Bambini S, Piet J, Muzzi A et al (2013) An
analysis of the sequence variability of meningococcal fHbp, NadA and NHBA over a
50-year period in the Netherlands. PLoS
One 8:e65043
103. Wachter J, Hill S (2016) Positive selection
pressure drives variation on the surfaceexposed variable proteins of the pathogenic
neisseria. PLoS One 11:e0161348. https://
doi.org/10.1371/journal.pone.0161348
104. Counoupas C, Pinto R, Nagalingam G, HillCawthorne GA, Feng CG, Britton WJ, Triccas JA (2016) Mycobacterium tuberculosis
components expressed during chronic infection of the lung contribute to long-term control of pulmonary tuberculosis in mice. NPJ
Vaccines 1:16012
62
Daniel Yero et al.
nal.ppat.1003766
88. Xu Z, Chen H, Zhou R (2011) Genome-wide
evidence for positive selection and recombination in Actinobacillus pleuropneumoniae.
BMC Evol Biol 11:203
89. Cao P, Guo D, Liu J, Jiang Q, Xu Z, Qu L
(2017) Genome-wide analyses reveal genes
subject to positive selection in Pasteurella
multocida. Front Microbiol 8:961. https://
doi.org/10.3389/fmicb.2017.00961
90. Petersen L, Bollback JP, Dimmic M,
Hubisz M, Nielsen R (2007) Genes under
positive selection in Escherichia coli. Genome
Res 17:1336–1343
91. Nandi T, Ong C, Singh AP et al (2010) A
genomic survey of positive selection in Burkholderia pseudomallei provides insights into
the evolution of accidental virulence. PLoS
Pathog 6:e1000845
92. O’Connor DH, McDermott AB, Krebs KC
et al (2004) A dominant role for CD8+-Tlymphocyte selection in simian immunodeficiency virus sequence variation. J Virol
78:14012–14022
93. de Oliveira T, Salemi M, Gordon M, Vandamme
A-M,
van
Rensburg
EJ,
Engelbrecht S, Coovadia HM, Cassol S
(2004) Mapping sites of positive selection
and amino acid diversification in the HIV
genome: an alternative approach to vaccine
design? Genetics 167:1047–1058
94. Yang Z (1997) PAML: a program package for
phylogenetic analysis by maximum likelihood.
Comput Appl Biosci 13:555–556
95. Kosakovsky Pon S, Poon A, Frost S (2009)
Estimating selection pressures on alignments
of coding sequences. In: The phylogenetic
handbook: a practical approach to phylogenetic analysis and hypothesis testing, 2nd
edn. Cambridge University Press, New York,
NY, pp 419–452
96. Anisimova M, Nielsen R, Yang Z (2003)
Effect of recombination on the accuracy of
the likelihood method for detecting positive
selection at amino acid sites. Genetics
164:1229–1236
97. Kosakovsky Pond SL, Posada D, Gravenor
MB, Woelk CH, Frost SDW (2006) GARD:
a genetic algorithm for recombination detection. Bioinformatics 22:3096–3098
98. Dobson R, Stockdale C, Lapsley C, Wilkes J,
McCulloch R (2011) Interactions among Trypanosoma brucei RAD51 paralogues in DNA
repair and antigenic variation. Mol Microbiol
81:434–456
99. Holden NJ, Uhlin BE, Gally DL (2001) PapB
paralogues and their effect on the phase variation of type 1 fimbriae in Escherichia coli. Mol
Microbiol 42:319–330
100. Tsuru T, Kobayashi I (2008) Multiple
genome comparison within a bacterial species
reveals a unit of evolution spanning two adjacent genes in a tandem paralog cluster. Mol
Biol Evol 25:2457–2473
101. Rappuoli R (2011) The challenge of developing universal vaccines. F1000 Med Rep 3:16.
https://doi.org/10.3410/M3-16
102. Bambini S, Piet J, Muzzi A et al (2013) An
analysis of the sequence variability of meningococcal fHbp, NadA and NHBA over a
50-year period in the Netherlands. PLoS
One 8:e65043
103. Wachter J, Hill S (2016) Positive selection
pressure drives variation on the surfaceexposed variable proteins of the pathogenic
neisseria. PLoS One 11:e0161348. https://
doi.org/10.1371/journal.pone.0161348
104. Counoupas C, Pinto R, Nagalingam G, HillCawthorne GA, Feng CG, Britton WJ, Triccas JA (2016) Mycobacterium tuberculosis
components expressed during chronic infection of the lung contribute to long-term control of pulmonary tuberculosis in mice. NPJ
Vaccines 1:16012
62
Daniel Yero et al.