1. Microbial
Reproductive
Modes
Fungal Reproduction
Week 12, PMB 220
J. Taylor

2. The cost of sex is two-fold.
Clonal progeny have twice
as many parental genes.

3. The Value of Sex? The Red Queen Hypothesis.
"Now, here, you see, it takes all the running
you can do, to keep in the same place."
Lewis Carroll
John Tenniel (illus)
1872.

4. The Value of Sex?
Muller’s Ratchet
H. Muller, 1964

5. Goddard,
Godfray
Burt. 2005
Nature
434:

6. Goddard,
Godfray
Burt
Nature
434:636-40
2005

7. Harsh
environment
Goddard,
Godfray
Burt
Nature
434:636-40
2005
Benign
environment

8. Sex is nearly ubiquitous. Only the bdelloid rotifers have been
claimed to be an old asexual group.
Aydin Örstan

9. Numbers of Species of Fungi
Ascomycota 32, %
Lichenized fungi 13, %
Basidiomycota 22, %
Chytridiomycota %
Zygomycota 1, %
Mitosporic fungi 14, %
Dictionary of the Fungi, Hawksworth et al. 1996

10. What is a
species?
How do they
reproduce?

11. Determining the reproductive mode of Microbes:
Recombination v. clonality

12. Clonal:
Association
of Alleles.

13. Recombining: Lack of Association

14. Testing for reproductive mode.

15. Tree Length Test

16. Compter sex: Resampling
without replacement.

17. Tree
Length
Test

18. Index of Association

19. Distance
matrix

20. IA

21. Gene
Genealogy
Concordance

22. Computer sex:
Shuffling variable nucleotides
among genes.

23. Aspergillus flavus

24. You have to know the species before you can study reproductive mode.

25. Example:
Coccidioides immitis
Vasso Koufopanou
Austin Burt
Mat Fisher

26. Distribution of
Coccidioides
immitis
Rippon, 1988

27. Phylogenetic Species in C. immitis

28. Finding Single Nucleotide Polymorphisms
Agarose and SSCP gels of PCR products

29. Coccidioides immitis: multilocus genotypes
as single nucleotide polymorphisms (SNPs)

30. Parsimony analysis:
Consensus of 62 most parsimonious trees.

32. Test of association of alleles: Index of Association

33. Phylogenetic Species in C. immitis

34. California
Coccidioides
Fisher et al. 2000

35. Likelihood ratio tests Kishino-Hasegawa Two different topologies
Shimodaira-Hasagawa
Multiple topologies

36. Trebouxia and Letharia
Lichens
Scott Kroken
Trebouxia and Letharia

37. Letharia columbiana
Question: Are there two species of Letharia, one sexual and the other not?
Letharia vulpina

38. Letharia vulpina Letharia columbiana always produces soredia
apothecia are rare
Letharia columbiana
always produces apothecia
sometimes produces isidia
Are they a “species pair” and how do they reproduce?

39. Distribution of Letharia species
Xerox
PARC
map

40. Apothecia, filled with meiotic ascospores
Asexual
Sexual
Thomas Nash
Apothecia, filled with meiotic ascospores
Soredia, algal cells wrapped in hyphae

41. Kroken and Taylor. 2000. Mycologia 93:38-53
6 species
suggested
Kroken and Taylor Mycologia 93:38-53

42. Question: does the lichen outbreed or inbreed?

43. Paternity analysis of lichen apothecia
Fertilization
Spermagonium--
produces spermatia
Trichogyne--
fuses with spermatium
Paternity analysis of lichen apothecia

44. Parent and progeny

45. Kroken and Taylor 2001 Fungal Genetics & Biology 34:83-92
Letharia “lupina” paternity analysis
‘lupina’ locus CS EarI
‘lupina’ ITS 1F/ 2 SacI
Mom1 and 7 kids
Mom2 and 6 kids
Mom1 and 7 kids
Mom2 and 6 kids
All 36 apothecia in both species
are the result of outcrossing
Kroken and Taylor 2001 Fungal Genetics & Biology 34:83-92

46. Outbreeding and separate fertilizations

47. Högberg et al. 2002. Molecular Ecology 11:1191-1196
Dispersal of Letharia vulpina with its alga
Xerox
PARC
map
Högberg et al Molecular Ecology 11:

48. Recombining and Clonal in Letharia
North American
sorediate
Recombining:
North American
apotheciate
Clonal: European and North African sorediate Letharia species

50. Daubin et al Science 301:

51. More polymorphism?
Microsatellites or
Short Tandem Repeats

52. Molecular markers- Microsatellites
Dinucleotide repeats randomly dispersed through the genome
ctgcgtgtgacatACACACACACACACActgtatgtgatc
Highly polymorphic and multialleleic due to polymerase
slippage during strand replication
Cocci_1 ctgcgtgtgacatACACACACACACACA ctgtatgt
Cocci_2 ctgcgtgtgacatACACACACACACACACA------ctgtatgt
Cocci_3 ctgcgtgtgacatACACACACACACACACACA----ctgtatgt
Cocci_4 ctgcgtgtgacatACACACACACACACACACACACActgtatgt

53. Microsatellites

54. Microsatellite distance Flanking-sequence distance
These trees have the same topology (Kishino-Hasegawa test non-significant)
THE MICROSATELLITE MARKERS ARE GOOD
(Fisher et al. Mol. Biol. Evol. 2000)

55. Renaming the species California
- Coccidioides immitis Rixford and Gilchrist 1896
non-California
- Coccidioides posadasii after Alejandro Posadas

56. All populations

57. Arizona

58. Texas/
South America

59. North America/ Mexico C. immitis ( ) and C. posadasii ( )
show isolation by distance...
r = 0.694**
r = 0.905

60. ...but NOT if South American isolates (all C. posadasii)
are included…
r = 0.023
r = 0.694**

61. S. American isolates contain 6% of the variation found in N. America
28% of loci are in linkage disequlibrium (7% in N. America)
This is a bottlenecked population
…and is descended from
the TEXAS population of
Coccidioides posadasii

62. Genetic dating show that South American
populations were founded from those in
North America between 9, ,000 BP
(the Pleistocene)

63. Migration of Homo sapiens into South America by 10,000 BC
Jared Diamond ‘Guns, Germs and Steel’, 1997

64. How did non-CA C. immitis arrive in South America?
Host-pathogen dispersal:
9,000 year old bones of Bison antiquus from Nebraska
contain C. immitis spherules. Demonstrates potential for
long-distance dispersal with a host
Human infections are viable for more than 12 years
Ancient Amerindian middens contain high concentrations of
C. immitis
Documented invasion of South America by the Amerindians
12,500 yrs bp.

65. Does the present distribution of C. posadasii reflect the
co-dispersal of a host and its pathogen?

66. Recombining and Clonal in Coccidioides
Clonal (C. posadasii in Latin Amer?)

68. Daubin et al. 2003. Science 301:829-832 Fig 1

69. Daubin et al.
2003. Science
301:
Fig 2

70. Daubin et al.
2003. Science
301:
Fig 3