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Volume 22, Number 6—June 2016
Research

Use of Population Genetics to Assess the Ecology, Evolution, and Population Structure of Coccidioides

Marcus M. Teixeira and Bridget M. BarkerComments to Author 
Author affiliations: Translational Genomics Research Institute, Flagstaff, Arizona, USA (M.M. Teixeira, B.M. Barker); Northern Arizona University, Flagstaff (B.M. Barker); University of Arizona, Tucson, Arizona, USA (B.M. Barker)

Main Article

Figure 1

Results of principal coordinate analysis and STRUCTURE analyses of Coccidioides spp. populations. A) Principal coordinate analysis using Nei’s unbiased genetic distance estimates supports 3 main groupings: C. immitis, C. posadasii TX/SA/MX, and C. posadasii Arizona (see also Technical Appendix 3 Figure 2). The greatest separation occurs between species and is reflected in principal coordinate 1 (93.92% of variance). Color-coding for populations: lime green, San Joaquin Valley (SJV); aqua, San Di

Figure 1. Results of principal coordinate analysis and STRUCTURE analyses of Coccidioides spp. populations. A) Principal coordinate analysis using Nei’s unbiased genetic distance estimates supports 3 main groupings: C. immitis, C. posadasii TX/SA/MX, and C. posadasii Arizona (see also Technical Appendix 3 Figure 2). The greatest separation occurs between species and is reflected in principal coordinate 1 (93.92% of variance). Color-coding for populations: lime green, San Joaquin Valley (SJV); aqua, San Diego/Mexico (SDMX); pink, Texas/South America (TXSA); purple, Mexico (MEXICO); red, Tucson (TUCSON); yellow, Phoenix/Yuma (PHOENIX); orange, soil (AZSOIL). B) STRUCTURE analysis. Microsatellite matrices were analyzed with STRUCTURE 2.3.4 to determine population structure within Coccidioides populations (30). The running length of burn-in period was 100,000 repetitions with 1 million Markov chain Monte Carlo repetitions. Default settings in STRUCTURE 2.3.4 were as follows: the admixture model was used to infer α along with the previous sampling location information model (LOCPRIOR) (30). We used CLUMPP, a cluster matching and permutation program (https://web.stanford.edu/group/rosenberglab/clumpp.html), to define populations within the STRUCTURE algorithm. K is the number of significant populations in each main group. A consensual STRUCTURE plot was generated from the admixture values by using the Clustering Markov Packager Across K (CLUMPAK) server, and final plots were built with STRUCTURE PLOT (32,33).

Main Article

References
  1. Fisher  MC, Koenig  GL, White  TJ, Taylor  JW. Molecular and phenotypic description of Coccidioides posadasii sp. nov., previously recognized as the non-California population of Coccidioides immitis. Mycologia. 2002;94:73–84. DOIPubMedGoogle Scholar
  2. Cairns  L, Blythe  D, Kao  A, Pappagianis  D, Kaufman  L, Kobayashi  J, Outbreak of coccidioidomycosis in Washington state residents returning from Mexico. Clin Infect Dis. 2000;30:61–4. DOIPubMedGoogle Scholar
  3. Nguyen  C, Barker  BM, Hoover  S, Nix  DE, Ampel  NM, Frelinger  JA, Recent advances in our understanding of the environmental, epidemiological, immunological, and clinical dimensions of coccidioidomycosis. Clin Microbiol Rev. 2013;26:505–25. DOIPubMedGoogle Scholar
  4. Lewis  ER, Bowers  JR, Barker  BM. Dust devil: the life and times of the fungus that causes Valley fever. PLoS Pathog. 2015;11:e1004762. DOIPubMedGoogle Scholar
  5. Huppert  M, Sun  SH, Harrison  JL. Morphogenesis throughout saprobic and parasitic cycles of Coccidioides immitis. Mycopathologia. 1982;78:107–22. DOIPubMedGoogle Scholar
  6. Chiller  TM, Galgiani  JN, Stevens  DA. Coccidioidomycosis. [viii. ]. Infect Dis Clin North Am. 2003;17:41–57. DOIPubMedGoogle Scholar
  7. Fisher  MC, Koenig  GL, White  TJ, San-Blas  G, Negroni  R, Alvarez  IG, Biogeographic range expansion into South America by Coccidioides immitis mirrors New World patterns of human migration. Proc Natl Acad Sci U S A. 2001;98:4558–62. DOIPubMedGoogle Scholar
  8. Marsden-Haug  N, Hill  H, Litvintseva  AP, Engelthaler  DM, Driebe  EM, Roe  CC, Coccidioides immitis identified in soil outside of its known range—Washington, 2013. MMWR Morb Mortal Wkly Rep. 2014;63:450 .PubMedGoogle Scholar
  9. Litvintseva  AP, Marsden-Haug  N, Hurst  S, Hill  H, Gade  L, Driebe  EM, Valley fever: finding new places for an old disease: Coccidioides immitis found in Washington State soil associated with recent human infection. Clin Infect Dis. 2015;60:e1–3. DOIPubMedGoogle Scholar
  10. Johnson  SM, Carlson  EL, Fisher  FS, Pappagianis  D. Demonstration of Coccidioides immitis and Coccidioides posadasii DNA in soil samples collected from Dinosaur National Monument, Utah. Med Mycol. 2014;52:610–7 and. DOIPubMedGoogle Scholar
  11. Canteros  CE, Vélez  HA, Toranzo  AI, Suárez-Alvarez  R, Tobón  OÁ, Jimenez  AMP, Molecular identification of Coccidioides immitis in formalin-fixed, paraffin-embedded (FFPE) tissues from a Colombian patient. Med Mycol. 2015;53:520–7. DOIPubMedGoogle Scholar
  12. Whiston  E, Taylor  JW. Genomics in Coccidioides: insights into evolution, ecology, and pathogenesis. Med Mycol. 2014;52:149–55. DOIPubMedGoogle Scholar
  13. Duarte-Escalante  E, Zúñiga  G, Frías-De-León  MG, Canteros  C, Castañón-Olivares  LR, Reyes-Montes  MR. AFLP analysis reveals high genetic diversity but low population structure in Coccidioides posadasii isolates from Mexico and Argentina. BMC Infect Dis. 2013;13:411. DOIPubMedGoogle Scholar
  14. Brilhante  RS, de Lima  RA, Ribeiro  JF, de Camargo  ZP, Castelo-Branco  DS, Grangeiro  TB, Genetic diversity of Coccidioides posadasii from Brazil. Med Mycol. 2013;51:432–7. DOIPubMedGoogle Scholar
  15. Campins  H. Coccidioidomycosis in South America. A review of its epidemiology and geographic distribution. Mycopathol Mycol Appl. 1970;41:25–34. DOIPubMedGoogle Scholar
  16. Neafsey  DE, Barker  BM, Sharpton  TJ, Stajich  JE, Park  DJ, Whiston  E, Population genomic sequencing of Coccidioides fungi reveals recent hybridization and transposon control. Genome Res. 2010;20:938–46. DOIPubMedGoogle Scholar
  17. Fisher  MC, Koenig  G, White  TJ, Taylor  JW. A test for concordance between the multilocus genealogies of genes and microsatellites in the pathogenic fungus Coccidioides immitis. Mol Biol Evol. 2000;17:1164–74. DOIPubMedGoogle Scholar
  18. Fisher  MC, White  TJ, Taylor  JW. Primers for genotyping single nucleotide polymorphisms and microsatellites in the pathogenic fungus Coccidioides immitis. Mol Ecol. 1999;8:1082–4. DOIPubMedGoogle Scholar
  19. Lim  S, Notley-McRobb  L, Lim  M, Carter  DA. A comparison of the nature and abundance of microsatellites in 14 fungal genomes. Fungal Genet Biol. 2004;41:1025–36. DOIPubMedGoogle Scholar
  20. Fisher  MC. DE Hoog S, Akom NV. A highly discriminatory multilocus microsatellite typing (MLMT) system for Penicillium marneffei. Mol Ecol Notes. 2004;4:515–8. DOIPubMedGoogle Scholar
  21. Fisher  MC, Aanensen  D, de Hoog  S, Vanittanakom  N. Multilocus microsatellite typing system for Penicillium marneffei reveals spatially structured populations. J Clin Microbiol. 2004;42:5065–9. DOIPubMedGoogle Scholar
  22. Taylor  ML, Hernández-García  L, Estrada-Bárcenas  D, Salas-Lizana  R, Zancopé-Oliveira  RM, García de la Cruz  S, Genetic diversity of Histoplasma capsulatum isolated from infected bats randomly captured in Mexico, Brazil, and Argentina, using the polymorphism of (GA)(n) microsatellite and its flanking regions. Fungal Biol. 2012;116:308–17.
  23. Matute  DR, Sepulveda  VE, Quesada  LM, Goldman  GH, Taylor  JW, Restrepo  A, Microsatellite analysis of three phylogenetic species of Paracoccidioides brasiliensis. J Clin Microbiol. 2006;44:2153–7. DOIPubMedGoogle Scholar
  24. Barker  BM, Jewell  KA, Kroken  S, Orbach  MJ. The population biology of coccidioides: epidemiologic implications for disease outbreaks. Ann N Y Acad Sci. 2007;1111:147–63. DOIPubMedGoogle Scholar
  25. Jewell  K, Cheshier  R, Cage  GD. Genetic diversity among clinical Coccidioides spp. isolates in Arizona. Med Mycol. 2008;46:449–55. DOIPubMedGoogle Scholar
  26. Hector  RF, Rutherford  GW, Tsang  CA, Erhart  LM, McCotter  O, Anderson  SM, The public health impact of coccidioidomycosis in Arizona and California. Int J Environ Res Public Health. 2011;8:1150–73. DOIPubMedGoogle Scholar
  27. Fisher  MC, Koenig  GL, White  TJ, Taylor  JW. Pathogenic clones versus environmentally driven population increase: analysis of an epidemic of the human fungal pathogen Coccidioides immitis. J Clin Microbiol. 2000;38:807–13 .PubMedGoogle Scholar
  28. Barker  BM, Tabor  JA, Shubitz  LF, Perrill  R, Orbach  MJ. Detection and phylogenetic analysis of Coccidioides posadasii in Arizona soil samples. Fungal Ecol. 2012;5:163–76. DOIGoogle Scholar
  29. Peakall  R, Smouse  PE. GenAlEx 6.5: genetic analysis in Excel. Population genetic software for teaching and research—an update. Bioinformatics. 2012;28:2537–9. DOIPubMedGoogle Scholar
  30. Hubisz  MJ, Falush  D, Stephens  M, Pritchard  JK. Inferring weak population structure with the assistance of sample group information. Mol Ecol Resour. 2009;9:1322–32.
  31. Earl  D, vonHoldt  B. STRUCTURE HARVESTER: a website and program for visualizing STRUCTURE output and implementing the Evanno method. Conserv Genet Resour. 2012;4:359–61.
  32. Kopelman  NM, Mayzel  J, Jakobsson  M, Rosenberg  NA, Mayrose  I. Clumpak: a program for identifying clustering modes and packaging population structure inferences across K. Mol Ecol Resour. 2015;15:1179–91.
  33. Ramasamy  RK, Ramasamy  S, Bindroo  BB, Naik  VG. STRUCTURE PLOT: a program for drawing elegant STRUCTURE bar plots in user friendly interface. Springerplus. 2014;3:431.
  34. Pickrell  JK, Pritchard  JK. Inference of population splits and mixtures from genome-wide allele frequency data. PLoS Genet. 2012;8:e1002967. DOIPubMedGoogle Scholar
  35. Baptista-Rosas  RC, Hinojosa  A, Riquelme  M. Ecological niche modeling of Coccidioides spp. in western North American deserts. Ann N Y Acad Sci. 2007;1111:35–46. DOIPubMedGoogle Scholar
  36. Fisher  FS, Bultman  MW, Johnson  SM, Pappagianis  D, Zaborsky  E. Coccidioides niches and habitat parameters in the southwestern United States: a matter of scale. Ann N Y Acad Sci. 2007;1111:47–72. DOIPubMedGoogle Scholar
  37. Litvintseva  AP, Brandt  ME, Mody  RK, Lockhart  SR. Investigating fungal outbreaks in the 21st century. PLoS Pathog. 2015;11:e1004804. DOIPubMedGoogle Scholar
  38. Muller  LA, Lucas  JE, Georgianna  DR, McCusker  JH. Genome-wide association analysis of clinical vs. nonclinical origin provides insights into Saccharomyces cerevisiae pathogenesis. Mol Ecol. 2011;20:4085–97. DOIPubMedGoogle Scholar
  39. Thompson  GR III, Stevens  DA, Clemons  KV, Fierer  J, Johnson  RH, Sykes  J, Call for a California coccidioidomycosis consortium to face the top ten challenges posed by a recalcitrant regional disease. Mycopathologia. 2015;179:1–9. DOIPubMedGoogle Scholar

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Page created: May 16, 2016
Page updated: May 16, 2016
Page reviewed: May 16, 2016
The conclusions, findings, and opinions expressed by authors contributing to this journal do not necessarily reflect the official position of the U.S. Department of Health and Human Services, the Public Health Service, the Centers for Disease Control and Prevention, or the authors' affiliated institutions. Use of trade names is for identification only and does not imply endorsement by any of the groups named above.
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