Plant mating systems

• Plants have a much wider variety of mating patterns than animals

• Markers in population genetics are very useful

Autogamy

• Self-fertilization

• Pollen transfer within or among flowers of same individual

• ~20% of angiosperms are habitual selfers

• ~40% of angiosperms can self-fertilize

Advantages of Autogamy

• Reproductive assurance.

• Selectively advantageous by transmitting both sets of genes to offspring.

• Only single colonizing individual needed.

• Cost-saving on male expenditure.

Disadvantages of Autogamy

• Decreases genetic variability.

• Inability to adapt to changing conditions.

• Increases inbreeding depression.– Reduces heterozygosity and increases

homozygosity of deleterious alleles.– Loss of vigour in offspring!

Aa x Aa

AA Aa

Aa aa

A

A

a

a

Loss of Heterozygosity from Selfing

1/4 AA1/2 Aa1/4 aa

A selfed heterozygote will yield offspring that are 50% heterozygous.

S1: 50% of offspring heterozygous from original parent (Aa).

S2: 25%

S3: 12.5%

S4: 6.2%

S5: 3.1%

S6: 1.5%

Loss of Heterozygosity from Selfing

Proportion of heterozygotes is 1/2 in each successive generation.

Cleistogamy (CL)

• Flowers never open and self-fertilize

• Small, bud-like flowers without petals that form directly into seed capsules

• Common: 488 species, in 212 genera and 49 families

Cleistogamy (CL)

• Mixed mating systems -can produce both CL and chasmogamous (CH) on an individual

• CL fls are a “back-up” in case pollinators scarce

Characteristics of predominantly self-pollinating species

• 1. Reduced "male" investment– fewer pollen (lower pollen/egg ratio)

– smaller/fewer attractive structures (corollas, flowers)

• 2. Phenological changes– more uniform distribution of seed and pollen cones

– simultanous pollen shed and stigma receptivity

• 3. Loss of self-incompatibility (angiosperms)• 4. Reduced inbreeding depression

– self-pollen is vigorous

– adult plants derived from selfing are vigorous

Monkeyflower (Mimulus)

• Stigma and anther (with mature pollen) can be seen to often touch each other within the flower

• If you grow them in the greenhouse without bees, they still set some seed

• Do they self-fertilize in the wild?

Molecular analysis of self-fertilization rates

• Genetic markers (isozymes, microsatellites, AFLPs) can be used to estimate rates of self-fertilization

• Two approaches:– Deviations from Hardy-Weinberg

• Selfing creates excess homozygosity like the Wahlund effect

– Patterns of segregation in progeny arrays• Given maternal genotype, selfing creates excess of

homozygous progeny

Molecular analysis of self-fertilization rates

• Deviations from Hardy-Weinberg– Work with inbreeding coefficient F

• Probability that a locus is homozygous by descent• We estimate it as F=(S-J)/(1-J), just like pairwise relatedness

(S=observed homozygosity, J=expected homozygosity)– Recursion for F with total selfing

• Start with F=0• After one generation of selfing, F=1/2 (example)• Ft+1 = .5(1-Ft) + Ft = (1+Ft)/2

– Recursion for F with partial selfing• Population has a fraction of selfing (s) and outcrossing (1-s)• Ft+1 = s (1+Ft)/2 +(1-s)(0)• At equilibrium, Ft+1 =Ft

• F = s (1+F)/2• s=2F/(1+F)

Mimulus guttatus species complex

• Yellow monkeyflowers• Mostly annual herbs• Selfing evolved several

times• Intercrossible

Estimates of mating system parameters for the four Mimulus taxa.

M. nasutus M. micranthus M. nudatus M. lacinatusF 0.109 (0.055) 0.724 (0.104) 0.219 (0.033) 0.787 (0.053)s 0.642 (0.040) 0.736 (0.140) 0.718 (0.025) 0.916 (0.035)

Estimates of mating system parameters for the four Mimulus taxa.

M. nasutus M. micranthus M. nudatus M. lacinatusF 0.109 (0.055) 0.724 (0.104) 0.219 (0.033) 0.787 (0.053)s 0.642 (0.040) 0.736 (0.140) 0.718 (0.025) 0.916 (0.035)

Are these populations at inbreeding equilibrium? (is s=2F/(1+F))

M. nasutus s=2(0.109)/1.109 =0.196M. micranthis s=2(0.724)/1.724=0.840M. nudatus s=2(0.219)/1.219 = 0.359M. lacinatus s=2(0.787)/1.787 = 0.880

Molecular analysis of self-fertilization rate

– Patterns of segregation in progeny arrays• Given maternal genotype, selfing creates excess of

homozygous progeny

– Consider maternal parent “AA”• Population is a mixture of “A” and “a” alleles, with

frequencies p and q• If the parent outcrosses, expected progeny are:

– p of AA– q of Aa

• If the parent selfs, all progeny are AA• For selfing rate s, the expected frequency of AA progeny

from AA parents is fAA|AA = (1-s)p + s• Solve for s, estimate frequency of selfing as s=(fAA|AA-p)/(1-p)

Progeny array model• Several possible parent genotypes• Probability matrix of progeny conditioned upon

parents:– s=selfing rate; p,q are gene frequencies of A, a

AA Aa aa

AA s+(1-s)p s/4+(1-s)p/2 0

Aa (1-s)q ½ (1-s)p

aa 0 s/4 + (1-s)q/2 s+(1-s)q

Parent genotypes

Progeny genotypes

Progeny array analysis

ij = probability of progeny i, given parent j

– (previous table)

• Xij = observed number of progeny i of parent j– (isozyme or SSR data)

• Likelihood of data is L= ijX

ij

• Use “numerical procedures” to maximize likelihood “L”

Advantages of progeny arrays

• No need to assume equilibrium• Maternal parent doesn’t need to be assayed

(can be inferred from progeny segregation pattern), thus tissue differences are irrelevant

• Separate estimation of pollen gene frequencies (pattern of paternity)

• Family structure also useful for many other population genetic inferences (next week)– Linkage disequilibrium– Haplotype structure– Association genetics

A study of inbreeding depression in monkeyflowers

•Measured as fitness of selfed progeny relative to outcrossed progeny•Large reduction in survival of progeny from selfing compared to outcrossing, in two different populations

Selfing and inbreeding depression

• Self-fertilization causes progeny to exhibit reduced fitness (inbreeding depression)

• Inbreeding depression is a tradeoff with reproductive assurance

• Exposure of recessive deleterious genes tends to remove inbreeding depression over the long term

Genetics of inbreeding depression

• Longer term evolution of inbreeding depression depends upon its genetic expression

• Is it caused by overdominance, or partial dominance? (example)

• Expression of inbreeding depression can depend on the stage of life cycle– early vs. late acting genes (next)

Markers and inbreeding depression

Would to know levels in nature, not greenhouse

Fixation index Level of observed homozygosity Affected by inbreeding depression

Ritland 1990

Inferring inbreeding depression using changes of the inbreeding coefficient

Mimulus guttatus and M. platycalyx

Co-occurring along meadows and streams of North coastal California

M. platycalyx has large flower like guttatus, but is very autofertile

Recently derived from M. guttatus?

Has inbreeding depression been reduced in M. platycalyx?

Dole and Ritland 1993

Paternity analyses methods

• Exclusion

• Likelihood: two methods; both use likelihood in same way– categorical: assigns the entire offspring to a

particular male– fractional: splits an offspring among all

compatible males

Example of paternity analysis (two loci)

• Mother– A1A2, B1B3

• Offspring– A1A3, B1B2

– (father alleles are A3, B2)

• Potential father 1– A2A2, B2B3

• Exclude because father doesn’t have A3

• Just one locus can exclude paternity

Paternity analyses methods

• Exclusion

• Likelihood: two methods; both use likelihood in same way– categorical: assigns the entire offspring to a

particular male– fractional: assigns paternity “in probability”,

allows for all possible males

Summary of likelihood

• Total probability is prior probability (frequency of male parent genotype in populations, maybe other factors) times the transmission probability

• Prior probability = genotype frequencies of alleged male– perhaps multiplied by female frequencies,

mating distance distribution, male fitness, etc.

Problems with using microsatellitesfor paternity analysis

• New mutations– The mutation rate for microsatellites is estimated

to be between 10-2 - 10-4 per generation; new mutations can frequency occur resulting in the true father being excluded.

– This can be overcome operationally by requiring potential fathers to be excluded at least two loci.

• Null alleles– If the offspring inherits a null allele (non-

amplifying allele) at a locus from the father, then the true father may be excluded.