Using the putative asexual fungus Cenococcum geophilum as a model to test how species concepts influence recombination analyses using sequence data from multiple loci

Current Genetics

Volumn 52, Issue 5-6, 2007, Pages 191-201

  Douhan, Greg W ^a   Martin, Darren P ^b   Rizzo, Dave M ^c  

^a UNIVERSITY OF CALIFORNIA   (United States)

^b UNIVERSITY OF CAPE TOWN   (South Africa)

^c UNIVERSITY OF CALIFORNIA   (United States)

Author keywords

Cenococcum; Fungi; Genealogy; Genetic structure; Mycorrhizae; Phylogeny

Indexed keywords

ACTIN;

ARTICLE; ASEXUAL REPRODUCTION; BIOLOGICAL MODEL; CENOCOCCUM GEOPHILUM; CLADISTICS; CONTROLLED STUDY; FUNGAL GENETICS; FUNGAL REPRODUCTION; FUNGUS ISOLATION; GENE LINKAGE DISEQUILIBRIUM; GENE LOCUS; GENE SEQUENCE; GENETIC ANALYSIS; GENETIC RECOMBINATION; GENETIC VARIABILITY; MOLECULAR EVOLUTION; MYCORRHIZA; NONHUMAN; NUCLEOTIDE SEQUENCE; PHYLOGENETIC TREE; POPULATION STRUCTURE; PRIORITY JOURNAL; SEQUENCE ANALYSIS; SPECIES COEXISTENCE; SPECIES DIVERSITY; SPECIES IDENTIFICATION; TAXONOMIC RANK;

ACTINS; ASCOMYCOTA; BASE SEQUENCE; GENETIC MARKERS; GENETICS, POPULATION; MITOSPORIC FUNGI; MODELS, GENETIC; PHYLOGENY; RECOMBINATION, GENETIC;

CENOCOCCUM; CENOCOCCUM GEOPHILUM; FUNGI; FUNGI IMPERFECTI;

EID: 36048932661     PISSN: 01728083     EISSN: None     Source Type: Journal    
DOI: 10.1007/s00294-007-0150-1     Document Type: Article

References (50)

1. Agapow PM, Burt A (2001) Indices of multilocus linkage disequilibrium. Mol Ecol Notes 1:1001-1002
2. Berbee ML, Pirseyedi M, Hubbard S (1999) Cochliobolus phylogenetics and the origin of known, highly virulent pathogens, inferred from ITS and glyceraldehyde-3-phosphate dehydrogenase gene sequences. Mycologia 91:964-977
3. Birky CW (2004) Bdelloid rotifers revisited. Proc Natl Acad Sci USA 101:2651-2652
4. Brown AHD, Feldman MW, Nevo E (1980) Multilocus structure of natural-populations of hordeum-spontaneum. Genetics 96:523-536
5. Craven KD, Hsiau PTW Leuchtmann A, Hollin W, Schardl CL (2001) Multigene phylogeny of epichloe species, fungal symbionts of grasses. Annals MO Bot Gard 88:14-34
6. Dahlgren RA, Singer MJ, Huang X (1997) Oak tree and grazing impacts on soil properties and nutrients in a California oak woodland. Biogeochem 39:45-64
7. Douhan GW, Rizzo DM (2005) Phylogenetic divergence in a local population of the ectomycorrhizal fungus Cenococcum geophilum. New Phytol 166:263-271
8. Fernández-Toirán LM, Águeda B (2007) Fruitbodies of Cenococcum geophilum. Mycotaxon 100:109-114
9. Gardes M, Bruns TD (1993) ITS primers with enhanced specificity for basidiomycetes-application to the identification of mycorrhizae and rusts. Mol Ecol 2:113-118
10. Gibbs MJ, Armstrong JS, Gibbs AJ (2000) Sister-Scanning: A Monte Carlo procedure for assessing signals in recombinant sequences. Bioinformatics 16:573-582
11. Hudson DH (1998) SplitsTree: Analyzing and visualizing evolutionary data. Bioinformatics 14:68-73
12. Hurst LD, Peck JR (1996) Recent advances in understanding of the evolution and maintenance of sex. TREE 11:A46-A52
13. Jany JL, Garbaye J, Martin F (2002) Cenococcum geophilum populations show a high degree of genetic diversity in beech forests. New Phytol 154:651-659
14. Judson OP, Normark BB (1996) Ancient asexuals: Scandal or artifact? Reply. TREE 11:297-297
15. Kondrashov AS (1993) Classification of hypotheses on the advantage of amphimixis. J Hered 84:372-387
16. Lee SB, Taylor JW (1990) Isolation of DNA from fungal mycelia and single cells In: Innis MA, Gelfand DH, Sninsky JJ, White TJ (eds) PCR protocols, a guide to methods and applications. Academic Press, San Diego, pp 282-287
17. Li K, Rouse DI, German TL (1994) PCR primers that allow intergeneric differentiation of ascomycetes and their application to Verticillium spp Appl Environ Microbiol 60:4324-4331
18. Liu YJ, Whelen S, Hall BD (1999) Phylogenetic relationships among ascomycetes: Evidence from an RNA polymerase II subunit. Mol Biol Evol 16:799-1808
19. LoBuglio KF (1999) Ectomycorrhizal fungi: Key genera in profile. In: Cairney JWG, Chambers SM (eds) Cenococcum. Springer, Berlin, pp 287-309
20. LoBuglio KF, Taylor JW (2002) Recombination and genetic differentiation in the mycorrhizal fungus Cenococcum geophilum Fr. Mycologia 94:772-780
21. Maddison D, Maddison WP (2001) MacClade 4: Analysis of phylogeny and character evolution. Version 4.03. Sinauer Associates, Sunderland, MA, USA
22. Martin DP, Posada D, Crandall KA, Williamson C (2005a) A modified bootscan algorithm for automated identification of recombinant sequences and recombination breakpoints. AIDS Res Hum Retroviruses 21:98-102
23. Martin DP, Williamson C, Posada D (2005b) RDP2: Recombination detection and analysis from sequence alignments. Bioinformatics 21:260-262
24. Marx DH (1969) Influence of Ectotrophic Mycorrhizal fungi on resistance of pine roots to pathogenic infections. I. Antagonism of Mycorrhizal Fungi to root pathogenic fungi and soil bacteria. Phytopathology 59:153
25. Maynard Smith J (1978) Optimization theory in evolution. Annu Rev Ecol Syst 9:31-56
26. Maynard Smith J (1992) Analyzing the mosaic structure of genes. J Mol Evol 34:126-129
27. Muller HJ (1964) The relation of recombination to mutational advance. Mutat Res 1:2-9
28. Normark BB, Judson OP, Moran (2003) Genomic signatures of ancient asexual lineages. Biol J Linn Soc 79:69-84
29. Otto SP, Lenormand T (2002) Resolving the paradox of sex and recombination. Nat Rev Genet 3:252-261
30. Padidam M, Sawyer S, Fauquet CM (1999) Possible emergence of new geminiviruses by frequent recombination. Virology 265:218-225
31. Panaccione DG, Sheets NL, Miller SP, Cumming JR (2001) Diversity of Cenococcum geophilum isolates from serpentine and non-serpentine soils. Mycologia 93:645-652
32. Posada D, Crandall KA (2001) Evaluation of methods for detecting recombination from DNA sequences: Computer simulations. Proc Natl Acad Sci USA 98:13757-13762
33. Schoustra SE, Debets AJM, Slakhorst M, Hoekstra RF (2007) Mitotic recombination accelerates adaptation in the fungus Aspergillus nidulans. PLoS Genet 3(4):ARt No. e68 APR
34. Shinohara ML, LoBuglio KF, Rogers SO (1996) Group-I intron family in the nuclear ribosomal RNA small subunit genes of Cenococcum geophilum isolates. Curr Genet 29:377-387
35. Shinohara ML, LoBuglio KF, Rogers SO (1999) Comparison of ribosomal DNA ITS regions among geographic isolates of Cenococcum geophilum. Curr Genet 35:527-535
36. Swofford DL (2002) PAUP*: Phylogenetic Analysis Using Parsimony (*and other methods). Version 4.0b10. Sinauer Associates, Sunderland, MA, USA
37. Taylor JW, Jacobson DJ, Fisher MC (1999) The evolution of asexual fungi: reproduction, speciation and classification. Annu Rev Phytopathol 37:197-246
38. Thompson JD, Gibson TJ, Plewniak F, Jeanmougin F, Higgins DG (1997) The CLUSTAL_X windows interface: Flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Res 25:4876-4882
39. Trappe JM (1964) Mycorrhizal Hosts + distribution of Cenococcum graniforme. Lloydia 27:100
40. Welch DM, Meselson M (2000) Evidence for the evolution of bdelloid rotifers without sexual reproduction or genetic exchange. Science 288:1211-1215
41. Welch DBM, Cummings MP, Hillis DM, Meselson M (2004a) Divergent gene copies in the asexual class Bdelloidea (Rotifera) separated before the bdelloid radiation or within bdelloid families. Proc Natl Acad Sci USA 101:1622-1625
42. Welch JLM, Welch DBM, Meselson M (2004b) Cytogenetic evidence for asexual evolution of bdelloid rotifers. Proc Natl Acad Sci USA 101:1618-1621
43. White TJ, Bruns T, Lee S, Taylor J (1990) Amplification and direct sequencing of fungal ribosomal RNA genes for phylogenetics. In: Innis MA, Gelfan DH, Sninsky JJ, White J (eds) PCR protocols. Academic Press, San Diego, pp 315-322
44. Worobey M, Rambaut A, Pybus OG, Robertson DL (2002) Questioning the evidence for genetic recombination in the 1918 "Spanish flu" virus. Science 296:211
45. Wu BY, Nara K, Hogetsu T (2005) Genetic structure of Cenococcum geophilum populations in primary successional volcanic deserts on Mount Fuji as revealed by microsatellite markers. New Phytol 165:285-293
46. Xu JP (2002) Estimating the spontaneous mutation rate of loss of sex in the human pathogenic fungus Cryptococcus neoformans. Genetics 162:1157-1167
47. Xu JP (2004) Genotype-environment interactions of spontaneous mutations for vegetative fitness in the human pathogenic fungus Cryptococcus neoformans. Genetics 168:1177-1188
48. Xu JP (2005) Cost of interacting with sexual partners in a facultative sexual microbe. Genetics 171:1597-1604
49. Zeyl C, Bell G (1997) The advantage of sex in evolving yeast populations. Nature 388:465-468
50. Zeyl C, Curtin C, Karnap K, Beauchamp E (2005) Antagonism between sexual and natural selection in experimental populations of Saccharomyces cerevisiae. Evolution 59:2109-2115