1. Genomic Conflict and DNA Sequence Variation
Marcy K. Uyenoyama
Department of Biology
Duke University

2. Overview Population genetics Self-incompatibility systems in plants
Historically model-rich
Present need: model-based interpretation of observed patterns of genomic variation
What are hallmarks of each model?
Self-incompatibility systems in plants
Recognizing genomic conflict due to sexual antagonism

3. Canonical models Neutral evolution Selection
Pure neutrality: distribution of offspring number is independent of any trait in parent
Demographic history: deme founding, gene flow
Purifying selection: maintain functioning state against random deleterious mutations
Selection
Balancing selection: maintenance of different forms
Selective sweeps: substitution of most fit for less fit

4. Hallmarks of evolution
How do we know it when we see it?
Patterns evident in genome variation
Model selection
Choosing among a small number of canonical models for any particular system

5. A random sample of genes
Observed
Sample
Ancestral sequence

6. Allele and mutation spectra
Site frequency spectrum
Number of mutations
Multiplicity
a = {a1 = 6, a3 = 1, a5 = 1, a6 = 1}, for ai the number of alleles with multiplicity i

7. The neutral coalescent
Sample root from stationary distribution of P, mutation transition matrix and bifurcate
After an interval choose a lineage at random
Replace it by two identical copies with probability
Mutate it according to P with probability

8. Evolutionary rates Events on level k
Bifurcation at rate Mutation at rate
Population parameters: ratios of rates
Next event is a bifurcation/coalescence with probability

9. Allele and mutation spectra
Site frequency spectrum
Number of mutations
Multiplicity
a = {a1 = 6, a3 = 1, a5 = 1, a6 = 1}, for ai the number of alleles with multiplicity i

10. Infinite-alleles model
Mutation
Novel allelic types formed at rate u per gene per generation
Reproduction
Frequency of allele i in the parental population: pi
Multinomial sampling of N genes to form the offspring
To find: probability of the sample of n genes (n1, n2, …, nk) or (a1, a2, …, an)
for k the number of distinct haplotypes (alleles) ni the number of replicates of allele i ai the number of alleles with i replicates

11. Ewens sampling formula
a = (a1, a2, …, an), for ai the number of alleles represented by i replicates in a sample of size n
θ = 2Nu, for N the effective number of genes and u the per-locus, per-generation rate of mutation
Ewens (1972, Theoretical Population Biology)

12. Allele and mutation spectra
Site frequency spectrum
Number of mutations
Multiplicity
a = {a1 = 6, a3 = 1, a5 = 1, a6 = 1}, for ai the number of alleles with multiplicity i

13. Population genomics
About 750 accessions isolated from natural populations worldwide
Summary statistics for sample of 19 entire genomes

14. Arabidopsis SNP spectra
Minor allele counts 2 3 4 5 6 7 8
Site frequency spectra differ among functional classes
Kim et al. (2008 Nature Genetics. 39: 1151)

15. ESF conditioned on two alleles
Biallelic sample of size m
Multiplicities i and (m – i )
independent of θ!

16. Ewens sampling formula
a = (a1, a2, …, an), for ai the number of alleles represented by i replicates in a sample of size n
θ = 2Nu, for N the effective number of genes and u the per-locus, per-generation rate of mutation
Ewens (1972, Theoretical Population Biology)

17. Actual site frequency spectra
Excess of rare and common types, deficiency of intermediate types
Data from NIEHS Environmental Genome Project
Direct resequencing of loci considered environmentally-sensitive
Global representation of ethnicities
Hernandez, Williamson, and Bustamante (2007)

18. Spectrum shape Signature of expansion? Signature of selective sweep?
Expansions maintain more rare mutations
Signature of selective sweep?
Neutral variants experience selection as a population bottleneck
Braverman et al. (1995)
Black: constant population size
Grey: recent expansion from small population size

19. Arabidopsis SNP spectra
Minor allele counts 2 3 4 5 6 7 8
Site frequency spectra differ among functional classes
Kim et al. (2008 Nature Genetics. 39: 1151)

20. Modelling a SNP data set
Nordborg (2001 Handbook of Statistical Genetics)
Single segregating mutation in the sample genealogy
Conditional on exactly one segregating site, determine the distribution of the size (number of descendants) of the branch on which the mutation occurs
Exactly two alleles in the sample
Conditional on two haplotypes, bearing any number of segregating sites, determine the distribution of numbers of the two alleles

21. Conditioning
Two alleles
One segregating site

22. Multiplicity conditioned on a SNP
Single segregating site in a sample of size m
Multiplicity i
dependent on θ !
Ganapathy and Uyenoyama (2009 Theoretical Population Biology)

23. Arabidopsis SNP spectra
Minor allele counts 2 3 4 5 6 7 8
Site frequency spectra differ among functional classes
Kim et al. (2008 Nature Genetics. 39: 1151)

24. Overview Population genetics Self-incompatibility systems in plants
Historically model-rich
Present need: model-based interpretation of observed patterns of genomic variation
What are hallmarks of each model?
Self-incompatibility systems in plants
Recognizing genomic conflict due to sexual antagonism

25. Genomic conflict Phenotypes Conflict
Multiple genes generally influence a given phenotype
Conflict
Target trait value differs among genes that control phenotype
Sexual antagonism
Male and female function collaborate in reproduction
Genes influencing each function may come into conflict

26. Conflict and genomic variation
Mating type regions as a battleground
S-locus controls self-incompatibility in flowering plants
How does sexual antagonism affect the pattern of molecular-level variation within the S-locus?
What are hallmarks of conflict?
Develop a basis for inference
Model-based approach to the analysis of genetic variation

27. Flower development Fertilization
Basic perfect flower includes both male and female components
Fertilization
Pollen grains deposited on stigma germinate and pollen tubes grow down style to the ovary
Mariana Ruiz

28. Gametophytic SI (GSI) Pollen rejection
Mariana Ruiz
Gametophytic SI (GSI)
Specificity expressed by individual pollen grain or tube determined by own S-allele
Pollen rejection
Growth of pollen tube arrested in style
Norbert Holstein

29. Sporophytic SI (SSI) Pollen rejection
Mariana Ruiz
Sporophytic SI (SSI)
Specificity expressed by individual pollen grain or tube determined by the S-locus genotype of its parent
Pollen rejection
Germination of pollen grain may be arrested at stigma surface
Norbert Holstein

30. Sn An Bn Pistil (A) component: rejection of recognized specificities
Mariana Ruiz
Norbert Holstein
Pistil (A) component: rejection of recognized specificities
Pollen (B) component: declaration of specificity An Bn Sn
Norbert Holstein

31. Mating type regions
Uyenoyama (2005)

32. Human Y chromosome Non-recombining male-specific Y (MSY)
Skaletsky et al. (2003 Nature 423: 825)
Non-recombining male-specific Y (MSY)
Euchromatic region ~ 23 MB
Differences between two random Ys every 3 – 4 KB
Mammalian sex determinant SRY
Y-linked regulator of transcription of many male-specific Y-linked genes

33. Mating type regions
Linkage between pistil (A) and pollen (B) components is essential to SI function
Pollen: declaration of specificity
Pistil: rejection of recognized specificities
Uyenoyama (2005)

34. Brassica S-locus Natural populations often contain 30 – 50 S-alleles
Pollen component
Pistil component
Natural populations often contain 30 – 50 S-alleles
Nasrallah (2000 Curr. Opin. Plant Biol.)

35. Ubiquitin tags proteins for degradation
Style: S-RNase disrupts pollen tube growth
Upon entering a pollen tube, S-RNases initially sequestered in a vacuole
In incompatible crosses, vacuole breaks down, releasing S-RNases into cytoplasm of pollen tube
Pollen: SLF (S-locus F-box)
Mediator of ubiquitinylation (attachment of ubiquitin)
Disables all S-RNases except those of the same specificity
Vierstra (2009, Nature Reviews Molecular Cell Biology)

36. Sexual antagonism Pistil: why reject fertilization?
Screening of potential mates may improve offspring quality
Cost under incomplete reproductive compensation: ovules may go unfertilized
Pollen: why provoke rejection?
Self-rejection may improve quality of own ovules
Rejection by other plants reduces siring success
Hide behind another S-specificity in sporophytic SI?
Decline to declare S-specificity altogether?

37. GSI model Basic discrete time recursion
Symmetries in genotype and allele frequencies
Model change in frequency of focal allele i, assuming all other alleles in equal frequency
Wright (1937, Genetics)

38. Diffusion approximation
Change in allele frequency
Diffusion equation coefficients
holds for large population size (N) and u (rate of mutation to new S-alleles) of order 1/N
Wright (1937, Genetics)

39. Wright’s diffusion model
Diffusion with jumps
Turnover rate
Number of S-alleles
Frequency in population

40. Expansion of time scale under balancing selection
High rate of invasion of rare alleles
Promotes invasion of new and retention of rare types
Maintains high numbers of alleles
Genealogical relationships
Tree shape similar under symmetric balancing selection and neutrality
Greatly expanded time scale
Takahata (1993, Mechanisms of Molecular Evolution)

41. S-allele turnover Quasi-equilibrium of S-alleles
Invasion of new, rare S-alleles balanced by extinction of common S-alleles
Expansion of time scale
Rate of divergence among S-allele classes similar to rate among neutral lineages, but in a population of size fN:

42. Gametophytic SI models
Basic discrete time recursion
Diffusion approximation
Parameters:
Effective population size (N)
Rate of mutation to new S-specificities (u)

43. Simulation results Stationary distribution of allele frequency
Most time spent close to deterministic equilibrium (1/n) or in boundary layer close to extinction
Number of S-alleles
Analytical expectation for number of common S-alleles
Vallejo-Marín and Uyenoyama (2008)

44. Sn An Bn Pistil (A) component: rejection of recognized specificities
Mariana Ruiz
Norbert Holstein
Pistil (A) component: rejection of recognized specificities
Pollen (B) component: declaration of specificity An Bn Sn
Norbert Holstein

45. Pollen specificity in GSI
Each pollen expresses its own specificity
Rarer specificities are incompatible with fewer plants
Incompatible matings
For n S-alleles in equal frequencies, a pollen type is incompatible with a proportion 2/n of all plants
Norbert Holstein

46. Sexual antagonism Pistil: why reject fertilization?
Screening of potential mates may improve offspring quality
Cost under incomplete reproductive compensation: ovules may go unfertilized
Pollen: why provoke rejection?
Self-rejection may improve quality of own ovules
Rejection by other plants reduces siring success
Hide behind another S-specificity in sporophytic SI?
Decline to declare S-specificity altogether?

47. Fate of style-part mutant
Self-pollen fraction (s)
Relative viability of inbred offspring (s )
An+1 Bn Sa
Full SC
Polymorphism
Full SI

48. Fate of pollen-part mutant
Bn+1 Sb
Full SC
Relative viability of inbred offspring (s )
Disruption
Polymorphism
Full SI
Self-pollen fraction (s)
Uyenoyama, Zhang, and Newbigin (2001)

49. Sn Sb Sa Sn+1 An Bn An Bn+1 An+1 Bn An+1 Bn+1 Direction of pollen flow
Uyenoyama, Zhang, and Newbigin (2001)

50. Sn Sb Sa Sn+1 An Bn An Bn+1 An+1 Bn An+1 Bn+1 TURN OFF
Partial breakdown of SI by pollen disablement Sn
Evolutionarily unlikely An
Bn+1
An+1 Bn Sb Sa
TURN ON
Restoration of SI by stylar recognition
Evolutionarily unlikely
An+1
Bn+1
Sn+1
Uyenoyama, Zhang, and Newbigin (2001)

51. Joint genealogies Unlike S-RNase genes, SLF genes show
Solanaceae and Plantaginaceae
Rosaceae
Unlike S-RNase genes, SLF genes show
Low divergence between allelic types
No trans-specific sharing of lineages
Newbigin, Paape, and Kohn (2008)

52. Cycles of loss/restoration of SI?
Family-specific genealogies
Rosaceae: do highly-diverged, ancient SFB lineages reflect continuous operation or restoration of same F-box genes?
Solanaceae, Plantaginaceae: Recruitment of new F-box genes?
Turnover of pollen-specificity loci
Expression and recognition of a paralogue of the former pollen specificity gene?
Can homologues be distinguished from paralogues with new function?

53. Brassica S-locus Natural populations often contain 30 – 50 S-alleles
Pollen component
Pistil component
Natural populations often contain 30 – 50 S-alleles
Nasrallah (2000 Curr. Opin. Plant Biol.)

54. An appeal for inference methods
Sexual antagonism in mating type regions
Neutral variation in linked regions
Rates of substitution at determinants of mating type
Inference
Goal: use the pattern of variation in population samples of genomic regions as a basis for inference about the evolutionary process
Detection
genomic conflict and other forms of selection
mating systems and population structure

55. Pollen specificity in SSI
Codominance
Both specificities expressed
Almost twice as many incompatible styles under SSI than GSI for same number of S-alleles
Complete dominance
One specificity expressed
Norbert Holstein

56. SRK genealogies Sporophytic SI Class II: pollen-recessive
Diploid genotype of pollen parent determines S-specificity of each pollen grain
Class I is dominant over Class II, with codominance within class
Class II: pollen-recessive
Lower number of segregating alleles, each with relatively higher frequency in population
Greater genealogical relationship within class?
Edh, Widén and Ceplitis (2009)

57. Is class II younger than class I?
MRCA ages
Class I: 25.5 ± 8.1 MY
Class II: 3.1 ± 0.9 MY
I/II: 41.4 ± 12.7 MY
Origin of SLG/SRK system
42.1 ± 9.0 MY
Uyenoyama (1995)