What percentage of the fitness variance is explained by the 'n'- most important loci?

Question

Introduction

Standard models in population genetics look up at the evolution of few loci which impact fitness. The variance in fitness is determined by the genetic variance and the environmental variance (and the co-variance between environment and genetics). In this question I am interested only about genetic variance and about what percentage of the total (additive or not) genetic variance in fitness do 'n' loci explain.

Question

In general, in natural populations, what percentage of the total genetic variance is explained by the 'n'- most important loci?

Here, by "most important loci" I mean loci which variance explain much of the total genetic variance.

In other words, the subquestions are of the kind:

• how much of the fitness variance does the most important locus explain?
• How much of the fitness variance do the 3 most important loci explain?
• How much of the fitness variance do the 100 most important loci explain?

Of course, the answer depends on the population under consideration. Factors that might influence the answers are for example

• species
• population size
• environment stability
• …

Beside this question, I also welcome some insights concerning how different factors are likely to influence the answer.

Answer 1

This should be taken less as a holistic answer than as a case study describing an extreme example of very strong selection in a particular environmental context, yielding a particular natural experiment. I suspect that this question may be very difficult to answer in a general case without more work!!

This answer should not be taken to show any general case or reflect anything about the distribution of variant fitness effects of a relatively stable population.

I hope that posting this very partial and contextual answer might inspire other answers to this very interesting question.

In sticklebacks, armor morphology is mostly controlled by a single large-effect variant locus at the Ectodysplasin (Eda) gene, ~85% of phenotypic variance is associated with this locus. It is known that there is a strong fitness relevance of armoring according to environment, wherein freshwater fish are under selection for low armor (due to metabolic cost), and saltwater fish are under selection for high armor (due to predation pressure).

This pattern is highly repeatable across events of colonization by saltwater fish of new freshwater habitats, wherein populations are swept by the low-armored allele of Eda as soon as they become resident freshwater populations.

Recently, Dolph Schluter and colleagues set out to directly quantify the fitness effects of this variant in a newly colonized population of sticklebacks that was undergoing the microevolutionary shift from high to low armor. In this population, the selection coefficient for the lower-armor allele was extremely large ($s = 0.5$).

Schluter and colleagues mapped QTLs for female reproductive fitness in an F2 cross, unsurprisingly yielding the Eda locus. They detected no other loci, though this should not be taken to mean that there are no other loci, due to power issues. They found that Eda explained 8% of the variation in fitness across their F2 panel.

In summary, in this particular case of very strong selection and quite high fitness variation of the population, one locus explains 8% of the fitness variation in an F2 cross (which is likely not completely representative of the population). No other loci have any detectable fitness effects compared to this.

It would be very interesting to see how this is repeated in other case studies, more stable populations, more polygenic cases, or measured at the whole-population (GWAS) level rather than the F2 intercross case.