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30 Cards in this Set

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What's the major differences between quantitative genetics and single-locus models?

Quant gen depends on many genes & are affected by the environment. Are more closely linked to fitness, but are harder to estimate the gen var.

Four diffs

What's studied in quant gen? What describes the different 'study subjects'?

1. Continuous traits. Described with mean & variance/standard deviation


2. Meristic traits, integers. Described with the parameter λ (variance=mean)


3. Threshold traits, discrete. The underlying genetic variation is continuously distributed.

Three types of traits

Which are the components of phenotypic variation?

Vp=Vg+Ve

What does Ve include? And Vg?

Ve: The direct effect of environment and developmental noise




Vg=Va+Vd+Vi (additive, dominance, epistasis/interaction var)

What's the formula for broad-sense and narrow-sense heritability?

Hb=Vg/(Vg+Ve)


Hn=Va/Vp (Here Vp=Va+Ve)

What heritability measurement is preferably used to predict response to selection, and why?

Narrow-sense, since broad-sense includes epistasis effects and these can cause gen var to not be expressed in phenotype - phenotype is that which is measured to predict the response.

Can heritability measurement for a trait be generalized to be the same under all conditions? Motivate.

No, since heritability depends on environment, the value depends on the conditions and may differ

What's "additive effect", how is it calculated?


What factor affects the additive effect?

a=The effect of the different alleles in a heterozygote genotype, it equals half the difference between the homozygotes' mean phenotype values
a=(a1-a2)/2
Is affected by dominance, which is calculated by sustracting the observed value of heterozy...

a=The effect of the different alleles in a heterozygote genotype, it equals half the difference between the homozygotes' mean phenotype values


a=(a1-a2)/2


Is affected by dominance, which is calculated by sustracting the observed value of heterozygotes from the expected value of heterozygotes (The expected value of heteroz=(one of the) measured homoz value minus the additive effect)

How can heritability be estimated?

1. Parent offspring regression: the regression slope equals the heritability (Hn). If only one parent is known/measured - Hn=2*the slope


2. Progeny testing "sire model": phenotypic similarity in full- & half-sibs. Vf=pheno. var. AMONG families. For half-sibs Va=4Vf --> Hn=4Vf/Vp


3. Animal model: when it's hard to minimize or measure Ve - use pedigree info and individual phenotypes to estimate Va and Ve with statistical ML model



Three diff methods

What component can be included in Vp apart from the usual two?

V(g*e), there can be interactions between genotype and environment --> different performence of genotypes depending on the environment

What's the definition of local adaptation?

A local population that has greater fitness in their native habitat is locally adapted

What equation can measure directional selection?

"Breeders equation": R=Hn*S


S is the selection differential


R is the response to selection

What factors affects Va (what does Va depend on)?

It depends on Ve, but can also depend on allele frequency ONLY IF there's a dominance effect

What do we need to know to calculate the additive effect for each allele?


Why would we want to calculate this (what can it be used for)?

The fitness of the genotypes (and genotype frequency)


This can be used to calculate the additive effect in the genotypes, i.e. Va

What causes genetic correlation?

Pleiotropy or linkage disequilibrium

How can genetically correlated traits be affected by selection, i.e. what happens if there's selection for only one of the traits?

Two possible outcomes:


1. Both traits will increase in fitness


2. One trait increase in fitness, the other decrease: a trade-off, this constrains selection

How can we find genes affecting quantitative traits?

1. QTL mapping


2. Candidate gene approach


3. Genome-wide association mapping (GWAS)

Three diff methods

What is QTL? How do you identify a QTL?

A region of the genome containing one or more genes that affect variation in a quant trait.


Identified by its linkage to polymorphic marker loci through analysis of phenotypes and marker genotypes in F2 generation (P: homozygous for markers, F1: intermediate, cross F1xF1 or F1xP)

How is GWAS performed?

Genome-wide associations: Very many markers across the genome are genotyped randomly, looking for associations between allelic variation & phenotypic trait of interest.

What makes GWAS so expensive?

Huge sample size is needed since there's lots of variation in a genome and we can't control the environmental effects when not doing experiments (but taking samples from wild pops)

What may cause loss of variation in quant traits?

Genetic drift


or


selection (fixation of beneficial alleles)

Can variation in neutral markers predict quant gen variation?

There's a low correlation between heritability (Hn) and pop size (in the wild), we can't easily use neutral markers for predictions of quant gen var: only general predictions, no clear correlations.

Why can variation persist in highly polygenic traits even under strong selection?

1. Low initial freqs of sel alleles


2. Epistatic effects


3. New mutations (when there's many genes involved, it's more probable a mutation will appear & affect the trait)


4. Change in environment

Four reasons

What's Qst?

A measurement of divergence between pops,


Qst=Va between pops/(2*within pop+between pop)

How do you interpret these results:


Qst>FST


Qst=FST


Qst<FST?

Qst>FST - differential directional selection on quant trait


Qst=FST - Amount of diff at quant trait similar to expected by gen drift


Qst<FST - Natural sel favouring the same phenotype in different pops

For what can quant var be used in a common garden experiment (with plants)?

To identify source pop for restoration & to estimate adaptability to environmental changes

Why is quant variation/genetics useful for conservation of animals?

Progress is likely to come from identification of genes affecting quant traits

Does quantitative traits correlate with variation and pop divergence estimates?

Sometimes they do, sometimes they don't!

What experiment could be performed if we want to study if a antipredator behaviour is inherited or taugth? Motivate.

Cross-fostering (with long-term observations), then do a regression analysis between offspring-biological midparent, and offspring-foster midparent. This type of study allow separation of genetic effects and environmental effects including maternal effects within a natural environment (in naturalpopulations, genetic effects are confounded with environmental effects whenparents raise their own offspring).

The slope of theregression of progeny vertebrae number on maternal vertebrae number in velvetbelly sharks is 0,42. Whatis the estimated narrow-sense heritability for this trait?

HN = 0.84(HN = 2 x slope of regression when phenotype for only one parent isknown)