| [1] | Kimura M (1983) The neutral theory of molecular evolution. Cambridge, UK: Cambridge University Press.
|
| [2] | Price DA, Goulder PJ, Klenerman P, Sewell AK, Easterbrook PJ, et al. (1997) Positive selection of HIV-1 cytotoxic T lymphocyte escape variants during primary infection. Proc Natl Acad Sci U S A 94: 1890–1895. doi: 10.1073/pnas.94.5.1890
|
| [3] | Wang P, Wang Q, Sims PF, Hyde JE (2002) Rapid positive selection of stable integrants following transfection of Plasmodium falciparum. Mol Biochem Parasitol 123: 1–10. doi: 10.1016/S0166-6851(02)00105-6
|
| [4] | Escalante AA, Lal AA, Ayala FJ (1998) Genetic polymorphism and natural selection in the malaria parasite Plasmodium falciparum. Genetics 149: 189–202.
|
| [5] | Restrepo A (2003) Paracoccidioidomycosis. In: Dismukes WE, Pappas PG, Sobel JD, editors. Clinical micology. New York, NY: Oxford University Press.
|
| [6] | Brummer E, Castaneda E, Restrepo A (1993) Paracoccidioidomycosis: an update. Clin Microbiol Rev 6: 89–117.
|
| [7] | Matute DR, McEwen JG, Puccia R, Montes BA, San-Blas G, et al. (2006) Cryptic speciation and recombination in the fungus Paracoccidioides brasiliensis as revealed by gene genealogies. Mol Biol Evol 23: 65–73. doi: 10.1093/molbev/msj008
|
| [8] | Carrero LL, Ni？o-Vega G, Teixeira MM, Carvalho MJA, Soares CMA, et al. (2008) New Paracoccidioides brasiliensis isolate reveals unexpected genomic variability in this human pathogen. Fungal Genetics and Biology 45: 605–612. doi: 10.1016/j.fgb.2008.02.002
|
| [9] | Carvalho KC, Ganiko L, Batista WL, Morais FV, Marques ER, et al. (2005) Virulence of Paracoccidioides brasiliensis and gp43 expression in isolates bearing known PbGP43 genotype. Microbes Infect 7: 55–65. doi: 10.1016/j.micinf.2004.09.008
|
| [10] | Goldman GH, dos Reis Marques E, Duarte Ribeiro DC, de Souza Bernardes LA, Quiapin AC, et al. (2003) Expressed sequence tag analysis of the human pathogen Paracoccidioides brasiliensis yeast phase: identification of putative homologues of Candida albicans virulence and pathogenicity genes. Eukaryot Cell 2: 34–48. doi: 10.1128/EC.2.1.34-48.2003
|
| [11] | Felipe MS, Andrade RV, Petrofeza SS, Maranhao AQ, Torres FA, et al. (2003) Transcriptome characterization of the dimorphic and pathogenic fungus Paracoccidioides brasiliensis by EST analysis. Yeast 20: 263–271. doi: 10.1002/yea.964
|
| [12] | Bastos KP, Bailao AM, Borges CL, Faria FP, Felipe MS, et al. (2007) The transcriptome analysis of early morphogenesis in Paracoccidioides brasiliensis mycelium reveals novel and induced genes potentially associated to the dimorphic process. BMC Microbiol 7: 29. doi: 10.1186/1471-2180-7-29
|
| [13] | Nielsen R, Yang Z (1998) Likelihood models for detecting positively selected amino acid sites and applications to the HIV-1 envelope gene. Genetics 148: 929–936.
|
| [14] | Storz JF (2005) Using genome scans of DNA polymorphism to infer adaptive population divergence. Mol Ecol 14: 671–688. doi: 10.1111/j.1365-294X.2005.02437.x
|
| [15] | Vallender EJ, Lahn BT (2004) Positive selection on the human genome. Hum Mol Genet 13 Spec No 2: R245–254. doi: 10.1093/hmg/ddh253
|
| [16] | Nei M (1987) Molecular evolutionary genetics. New York: Columbia University Press.
|
| [17] | Hudson RR, Kreitman M, Aguade M (1987) A test of neutral molecular evolution based on nucleotide data. Genetics 116: 153–159.
|
| [18] | McDonald JH, Kreitman M (1991) Adaptive protein evolution at the Adh locus in Drosophila. Nature 351: 652–654. doi: 10.1038/351652a0
|
| [19] | Yang Z (2007) PAML 4: Phylogenetic Analysis by Maximum Likelihood. Mol Biol Evol 24: 1586–1591. doi: 10.1093/molbev/msm088
|
| [20] | Nielsen R (2005) Molecular signatures of natural selection. Annu Rev Genet 39: 197–218. doi: 10.1146/annurev.genet.39.073003.112420
|
| [21] | Anisimova M, Bielawski JP, Yang Z (2002) Accuracy and power of bayes prediction of amino acid sites under positive selection. Mol Biol Evol 19: 950–958. doi: 10.1093/oxfordjournals.molbev.a004152
|
| [22] | Yang Z (1997) PAML: a program package for phylogenetic analysis by maximum likelihood. Comput Appl Biosci 13: 555–556. doi: 10.1093/bioinformatics/13.5.555
|
| [23] | Hughes AL (2007) Looking at Darwin in all the wrong places: the misguided quest for positive selection at the nucleotide sequence level. Heredity 99: 364–373. doi: 10.1038/sj.hdy.6801031
|
| [24] | Johannesson H, Vidal P, Guarro J, Herr RA, Cole GT, et al. (2004) Positive directional selection in the proline-rich antigen (PRA) gene among the human pathogenic fungi Coccidioides immitis, C. posadasii and their closest relatives. Mol Biol Evol 21: 1134–1145. doi: 10.1093/molbev/msh124
|
| [25] | Liu Z, Bos JI, Armstrong M, Whisson SC, da Cunha L, et al. (2005) Patterns of diversifying selection in the phytotoxin-like scr74 gene family of Phytophthora infestans. Mol Biol Evol 22: 659–672. doi: 10.1093/molbev/msi049
|
| [26] | Stahl EA, Bishop JG (2000) Plant-pathogen arms races at the molecular level. Curr Opin Plant Biol 3: 299–304. doi: 10.1016/S1369-5266(00)00083-2
|
| [27] | Anisimova M BJ, Dunn K, Yang Z (2007) Phylogenomic analysis of natural selection pressure in Streptococcus genomes. BMC Evol Biol 7: 154. doi: 10.1186/1471-2148-7-154
|
| [28] | Ortiz BL, Garcia AM, Restrepo A, McEwen JG (1996) Immunological characterization of a recombinant 27-kilodalton antigenic protein from Paracoccidioides brasiliensis. Clin Diagn Lab Immunol 3: 239–241.
|
| [29] | Nei M, Gojobori T (1986) Simple methods for estimating the numbers of synonymous and nonsynonymous nucleotide substitutions. Mol Biol Evol 3: 418–426. doi: 10.1007/bf00167113
|
| [30] | Yang Z, Bielawski JP (2000) Statistical methods for detecting molecular adaptation. Trends In Ecology And Evolution 15: 496–503. doi: 10.1016/s0169-5347(00)01994-7
|
| [31] | van Burik JA, Schreckhise RW, White TC, Bowden RA, Myerson D (1998) Comparison of six extraction techniques for isolation of DNA from filamentous fungi. Med Mycol 36: 299–303. doi: 10.1080/02681219880000471
|
| [32] | Morais FV, Barros TF, Fukada MK, Cisalpino PS, Puccia R (2000) Polymorphism in the gene coding for the immunodominant antigen gp43 from the pathogenic fungus Paracoccidioides brasiliensis. J Clin Microbiol 38: 3960–3966.
|
| [33] | Rappleye CA, Goldman WE (2006) Defining Virulence Factors in the Dimorphic Fungi. Annual Reviewof Microbiology 60: 281–303. doi: 10.1146/annurev.micro.59.030804.121055
|
| [34] | Edgar RC (2004) MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res 32: 1792–1797. doi: 10.1093/nar/gkh340
|
| [35] | Maddison DR, Maddison WP (2005) MacClade. Sinauer Associates.
|
| [36] | Zhang JaN M (1997) Accuracies of ancestral amino acid sequences inferred by the parsimony, likelihood, and distance methods. J Mol Evol 44: S139–S146. doi: 10.1007/PL00000067
|
| [37] | Pond SL, Frost SD (2005) A simple hierarchical approach to modeling distributions of substitution rates. Mol Biol Evol 22: 223–234. doi: 10.1093/molbev/msi009
|
| [38] | Pond SL, Frost SD, Muse SV (2005) HyPhy: hypothesis testing using phylogenies. Bioinformatics 21: 676–679. doi: 10.1093/bioinformatics/bti079
|
| [39] | Kumar S, Nei M, Dudley J, Tamura K (2008) MEGA: A biologist-centric software for evolutionary analysis of DNA and protein sequences. Brief Bioinform. doi: 10.1093/bib/bbn017
|
| [40] | Tamura K, Dudley J, Nei M, Kumar S (2007) MEGA4: Molecular Evolutionary Genetics Analysis (MEGA) software version 4.0. Mol Biol Evol 24: 1596–1599. doi: 10.1093/molbev/msm092
|
| [41] | Nielsen R (1997) The ratio of replacement to silent divergence and tests of neutrality. J Evol Biol 10: 217–231. doi: 10.1007/s000360050019
|
| [42] | Rozas J, Rozas R (1999) DnaSP version 3: an integrated program for molecular population genetics and molecular evolution analysis. Bioinformatics 15: 174–175. doi: 10.1093/bioinformatics/15.2.174
|
| [43] | Yang Z, Wong WS, Nielsen R (2005) Bayes empirical bayes inference of amino acid sites under positive selection. Mol Biol Evol 22: 1107–1118. doi: 10.1093/molbev/msi097
|
| [44] | Rammensee H, Bachmann J, Emmerich NP, Bachor OA, Stevanovic S (1999) SYFPEITHI: database for MHC ligands and peptide motifs. Immunogenetics 50: 213–219. doi: 10.1007/s002510050595
|
| [45] | Nielsen R (2001) Statistical tests of selective neutrality in the age of genomics. Heredity 86: 641–647. doi: 10.1046/j.1365-2540.2001.00895.x
|
| [46] | Hasegawa M, Cao Y, Yang Z (1998) Preponderance of slightly deleterious polymorphism in mitochondrial DNA: nonsynonymous/synonymous rate ratio is much higher within species than between species. Mol Biol Evol 15: 1499–1505. doi: 10.1093/oxfordjournals.molbev.a025877
|
| [47] | Chen SL, Hung CS, Xu J, Reigstad CS, Magrini V, et al. (2006) Identification of genes subject to positive selection in uropathogenic strains of Escherichia coli: a comparative genomics approach. Proc Natl Acad Sci U S A 103: 5977–5982. doi: 10.1073/pnas.0600938103
|
| [48] | Matute DR, Torres IP, Salgado-Salazar C, Restrepo A, McEwen JG (2007) Background selection at the chitin synthase II (chs2) locus in Paracoccidioides brasiliensis species complex. Fungal Genet Biol 44: 357–367. doi: 10.1016/j.fgb.2007.01.006
|
| [49] | Bamshad M, Wooding SP (2003) Signatures of natural selection in the human genome. Nat Rev Genet 4: 99–111. doi: 10.1038/nrg999
|
| [50] | Kreitman M (2000) Methods to detect selection in populations with applications to the human. Annual Review Of Genomics and Human Genetics 1: 539–559.
|
| [51] | Canino MF, Bentzen P (2004) Evidence for positive selection at the pantophysin (Pan I) locus in walleye pollock, Theragra chalcogramma. Mol Biol Evol 21: 1391–1400. doi: 10.1093/molbev/msh141
|
| [52] | Iwai LK, Yoshida M, Sidney J, Shikanai-Yasuda MA, Goldberg AC, et al. (2003) In silico prediction of peptides binding to multiple HLA-DR molecules accurately identifies immunodominant epitopes from gp43 of Paracoccidioides brasiliensis frequently recognized in primary peripheral blood mononuclear cell responses from sensitized individuals. Mol Med 9: 209–219.
|
| [53] | Coyne J (2004) Jerry Coyne. Curr Biol 14: R825–826. doi: 10.1016/j.cub.2004.09.031
|
