Download mean d 2 - Salamander Genome Project

Questions
1. Is there selection for an intermediate level of population
genomic variation in populations?
2. Is heterozygosity the best measure of genomic variation?
3. Do breeding individuals exhibit mate choice to produce
individuals that are intermediate in genomic variation?
Is too little and too much genetic
variation a problem in populations?
Inbreeding Depression: Reduced fitness caused by inbreeding.
e.g. deleterious recessive alleles.
Outbreeding Depression: Reduced fitness caused by out breeding.
e.g. disruption of coadapted gene complexes.
Perhaps an intermediate level is optimal?
1) Inbreeding decreases
heterozygosity.
2) Inbreeding results in inbreeding depression.
measures of heterozygosity should by definition
be good metrics for inbreeding depression.
3) However, notice that the relationship isn’t
exactly linear the deeper the inbreeding.
4) At the other end of the spectrum, too much genomic divergence
might be a bad thing. It might break up combinations of alleles
that allow for local adaptation. (Outbreeding depression).
Heterozygosity as a metric might not perform as well here.
Maybe a better metric than heterozygosity:
mean d2 : it estimates the average divergence time between
an individual’s parents.
Presumably is better when Ne x m > 1
thus, best suited for microsatellite markers
5) Maybe there is an optimum level of population genetic
variation that is selected (stabilizing selection).
Lakes and rivers.
Large population sizes.
Nesting parentals court and spawn
with females and provide care.
Lepomis macrochirus: Blue gill
Cuckolder males mature quickly
and sneak fertilizations.
1) Collected all breeding adults and larvae from nests in L. Opinicon.
2) Genotypes were determined for each adult and a sample of kids.
3) Reproductive success was calculated by weighting each nest by
brood size, which was estimated based on larval dry weight.
4)
Table 1. Summary of the measures for genomic divergence.
1. Genomic divergence and heterozygosity do not differ
among parental males, cuckolder males, females.
2. Heterozygosity and mean d2 are correlated measures.
Cuckolder males
Parental males
females
A quadratic model
provided the best fit
to the data.
Intermediate values of
mean d2 were associated
with higher reproductive
success and less
fluctuating assymetry.
mean d2 based upon 10 loci still yields a dataset that
is best explained by a quadratic model
Mate Choice
1). Offspring of parental had lower values of mean d2
than expected under random mating. They were closer
to the optimum.
2). Offspring of cuckolders had higher values of mean d2
than expected under random mating. They were larger
than the parental offspring values and farther from the
optimum.
3) Across all offspring, mean d2 values were not significantly
different, thus indicating constancy or stability of mean d2 .
Conclusions
1) Stabilizing selection may be operating to maintain
genomic divergence in bluegill.
mean d2 maybe a better metric for detecting both
high and low levels of divergence (especially for deeper
cases of inbreeding).
2) Parental males and females appear to select mates such
that their offspring have intermediate levels of
genomic divergence.
3) Cuckolder’s take what they can get. Their offspring were
further from the optimum than was expected. This would
presumably contribute to the maintenance of genetic variation.
1) What genetically is happening in hybrid populations
of tiger salamander in California?
Ambystoma californiense
Ambystoma tigrinum
Tiger salamanders occur in three different habitats in CA.
The vernal pool habitat is the natural habitat of the CA tiger sal.
A. tigrinum is found in all three types of habitat in the midwest
The different pond types are found in close geographical proximity
Markers used in the Study: Both Nuclear and mtDNA
A greater proportion
of A. tigrinum alleles
There is considerable
variation in allele
frequencies at all
levels of analysis.
Conclusions (without going into all of the stats tests)
1) There is considerable genetic heterogeneity in these
hybrid populations. There does appear to be an association between
perennial ponds and A. tigrinum alleles. Paedomorphosis may be
important.
2) This may reflect a number of things:
endogenous selection: maintenance of different alleles
in different genetic backgrounds due to within-genome
interactions such as heterozygote advantage, disadvantage,
or epistasis.
exogenous selection: maintenance of different alleles in
different environments due to trade-offs in local adaptation.
stochasticity of genetics and demography.