Molecular Biology and Evolution 17:1164-1174 (2000)
© 2000 Society for Molecular Biology and Evolution
Regular Article |
A Test for Concordance Between the Multilocus Genealogies of Genes and Microsatellites in the Pathogenic Fungus Coccidioides immitis
*Department of Plant and Microbial Biology, University of California at Berkeley;
and
Roche Molecular Systems, Alameda, California
Abstract
Uncovering the correct phylogeny of closely related species requires analysis of multiple gene genealogies or, alternatively, genealogies inferred from the multiple alleles found at highly polymorphic loci, such as microsatellites. However, a concern in using microsatellites is that constraints on allele sizes may occur, resulting in homoplasious distributions of alleles, leading to incorrect phylogenies. Seven microsatellites from the pathogenic fungus Coccidioides immitis were sequenced for 20 clinical isolates chosen to represent the known genetic diversity of the pathogen. An organismal phylogeny for C. immitis was inferred from microsatellite-flanking sequence polymorphisms and other restriction fragment length polymorphism–containing loci. Two microsatellite genetic distances were then used to determine phylogenies for C. immitis, and the trees found by these three methods were compared. Congruence between the organismal and microsatellite phylogenies occurred when microsatellite distances were based on simple allele frequency data. However, complex mutation events at some loci made distances based on stepwise mutation models unreliable. Estimates of times of divergence for the two species of C. immitis based on microsatellites were significantly lower than those calculated from flanking sequence, most likely due to constraints on microsatellite allele sizes. Flanking-sequence insertions/deletions significantly decreased the accuracy of genealogical information inferred from microsatellite loci and caused interspecific length homoplasies at one of the seven loci. Our analysis shows that microsatellites are useful phylogenetic markers, although care should be taken to choose loci with appropriate flanking sequences when they are intended for use in evolutionary studies.
CiteULike 
Connotea 
Del.icio.us What's this?
This article has been cited by other articles:
|
|
 |
|
  T. J. Sharpton, J. E. Stajich, S. D. Rounsley, M. J. Gardner, J. R. Wortman, V. S. Jordar, R. Maiti, C. D. Kodira, D. E. Neafsey, Q. Zeng, et al. Comparative genomic analyses of the human fungal pathogens Coccidioides and their relatives Genome Res., October 1, 2009; 19(10): 1722 - 1731. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 N. Gauthier, C. Dalleau-Clouet, J. Fargues, and M.-C. Bon Microsatellite variability in the entomopathogenic fungus Paecilomyces fumosoroseus: genetic diversity and population structure. Mycologia, September 1, 2007; 99(5): 693 - 704. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 B. A. Lasker, G. Butler, and T. J. Lott Molecular Genotyping of Candida parapsilosis Group I Clinical Isolates by Analysis of Polymorphic Microsatellite Markers. J. Clin. Microbiol., March 1, 2006; 44(3): 750 - 759. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
S. Ochsenreither, K. Kuhls, M. Schaar, W. Presber, and G. Schonian Multilocus Microsatellite Typing as a New Tool for Discrimination of Leishmania infantum MON-1 Strains J. Clin. Microbiol., February 1, 2006; 44(2): 495 - 503. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 N. Vanittanakom, C. R. Cooper Jr., M. C. Fisher, and T. Sirisanthana Penicillium marneffei Infection and Recent Advances in the Epidemiology and Molecular Biology Aspects Clin. Microbiol. Rev., January 1, 2006; 19(1): 95 - 110. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
E. Fournier, T. Giraud, C. Albertini, and Y. Brygoo Partition of the Botrytis cinerea complex in France using multiple gene genealogies. Mycologia, November 1, 2005; 97(6): 1251 - 1267. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 H. Johannesson, J. P. Townsend, C.-Y. Hung, G. T. Cole, and J. W. Taylor Concerted Evolution in the Repeats of an Immunomodulating Cell Surface Protein, SOWgp, of the Human Pathogenic Fungi Coccidioides immitis and C. posadasii Genetics, September 1, 2005; 171(1): 109 - 117. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
E. Nascimento, R. Martinez, A. Rodrigues Lopes, L. A. de Souza Bernardes, C. Pomponio Barco, M. H. S. Goldman, J. W. Taylor, J. G. McEwen, M. Pasetto Nobrega, F. G. Nobrega, et al. Detection and Selection of Microsatellites in the Genome of Paracoccidioides brasiliensis as Molecular Markers for Clinical and Epidemiological Studies J. Clin. Microbiol., November 1, 2004; 42(11): 5007 - 5014. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
M. C. Fisher, D. Aanensen, S. de Hoog, and N. Vanittanakom Multilocus Microsatellite Typing System for Penicillium marneffei Reveals Spatially Structured Populations J. Clin. Microbiol., November 1, 2004; 42(11): 5065 - 5069. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
J. R. Dettman and J. W. Taylor Mutation and Evolution of Microsatellite Loci in Neurospora Genetics, November 1, 2004; 168(3): 1231 - 1248. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
R. A. Cox and D. M. Magee Coccidioidomycosis: Host Response and Vaccine Development Clin. Microbiol. Rev., October 1, 2004; 17(4): 804 - 839. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
B. A. Lasker and Y. Ran Analysis of Polymorphic Microsatellite Markers for Typing Penicillium marneffei Isolates J. Clin. Microbiol., April 1, 2004; 42(4): 1483 - 1490. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
B. Slippers, P. W. Crous, S. Denman, T. A. Coutinho, B. D. Wingfield, and M. J. Wingfield Combined multiple gene genealogies and phenotypic characters differentiate several species previously identified as Botryosphaeria dothidea Mycologia, January 1, 2004; 96(1): 83 - 101. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 Increase in Coccidioidomycosis--Arizona, 1998-2001 JAMA, March 26, 2003; 289(12): 1500 - 1502. [Full Text] [PDF]
|
|
|
|
|
|
M. C. Fisher, G. L. Koenig, T. J. White, and J. W. Taylor Molecular and phenotypic description of Coccidioides posadasii sp. nov., previously recognized as the non-California population of Coccidioides immitis Mycologia, January 1, 2002; 94(1): 73 - 84. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 V. Koufopanou, A. Burt, T. Szaro, and J. W. Taylor Gene Genealogies, Cryptic Species, and Molecular Evolution in the Human Pathogen Coccidioides immitis and Relatives (Ascomycota, Onygenales) Mol. Biol. Evol., July 1, 2001; 18(7): 1246 - 1258. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 M. C. Fisher, G. L. Koenig, T. J. White, G. San-Blas, R. Negroni, I. G. Alvarez, B. Wanke, and J. W. Taylor Biogeographic range expansion into South America by Coccidioides immitis mirrors New World patterns of human migration PNAS, March 29, 2001; (2001) 71406098. [Abstract] [Full Text]
|
|
|
|
|
|
M. C. Fisher, G. L. Koenig, T. J. White, G. San-Blas, R. Negroni, I. G. Alvarez, B. Wanke, and J. W. Taylor From the Cover: Biogeographic range expansion into South America by Coccidioides immitis mirrors New World patterns of human migration PNAS, April 10, 2001; 98(8): 4558 - 4562. [Abstract] [Full Text] [PDF]
|
|