Evolution of phenotypic traits
Quantitative genetics
Very few phenotypic traits are controlled by one locus, as in our previous discussion of genetics and evolution
Quantitative genetics considers characters that are controlled by more than one locus
Multilocus systems
Definitions
In “multilocus systems,” a phenotypic trait is influenced by more than one locus
Each locus might have alternative alleles
Diverse alleles and loci produce phenotypic “polymorphism”
Different loci can be on one chromosome (“linked”) or scattered
Quantitative genetics
The study of traits affected by many genes and the environment
Polygenic traits show continuous variation
Most phenotypes lack clear categories
Living histogram
Living histogram
Swallowtail polymorphism
Heliconius mimicry
Multiple loci
H. erato (15) and H. melpomene (12)
Loci are scattered on different chromosomes – not linked
Mating between forms produces diverse (and unsuccessful) intermediates
What are quantitative traits (QT)?
Continuous variation (lack of discrete categories)
Influenced by:
genotype at many different loci
environmental (developmental) influences
gene-environment interactions
What does this experiment tell us?
Evolution occurs in quantitative traits..
Examples
Behavioral
Physiological
Morphological
Evolution in behavior
Critical photoperiod for entering diapause has changed in introduced populations
Evolution in physiology
Metal tolerant plants
Cost of tolerance detected
Evolution in morphology
Soapberry bugs
How do we add this complexity to models of population genetics?
It depends
How many loci are involved?
Do the loci assort independently, or as a group?
How are genes influencing quantitative traits identified?
QTL mapping
More complex than “on-off” or “single-gene” approach
Measures association between variation in a phenotype and a genetic marker
Reveals
Number of loci influencing a quantitative trait
Magnitude of their effects on the quantitative trait
Location in the genome
Juenger et al., 2005. Quantitative trait loci mapping of floral and leaf morphology traits in Arabidopsis thaliana . . .. Evolution & Development 7:259-271.
Genomic positions of QTL for floral and leaf characters – Juenger et al. 2005
General conclusions about QTL
Variation may be influenced by dozens of loci
53 QTL for Drosophila bristle number
Loci vary in intensity of effect
Diverse genetic mechanisms for affecting variation
Additive effects
Epistatic effects
Gene-environment interactions
Linkage disequilibrium
What is linkage disequilibrium?
Why is this phenomenon important?
How is linkage disequilibrium measured?
What factors influence change in linkage disequilibrium?
How are linkage disequilibrium and natural selection related?
What is linkage disequilibrium?
Addresses relations among different genes (loci)
Genomes are organized by chromosome structure
Law of Independent Assortment
of alleles from different loci
does not apply to different loci physically linked by proximity on the same chromosome
Linkage disequilibrium defined
What is linkage equilibrium?
When genotypes of one locus are distributed independently of genotypes at another locus, the two loci are in linkage equilibrium
A “null model” for whether gametes tend to have similar combinations of alleles (compared to random combinations)
What is linkage disequilibrium
anything else
Haplotype: the arrangement of alleles along a chromosome
How is linkage disequilibrium measured?
Count each haplotype in the population
e.g., AB Ab aB ab
Calculate frequencies (the proportion of all chromosomes represented by each haplotype)
gAB gAb gaBgab
Coefficient of Linkage Disequilibrium = D
D = gAB*gab – gAb* gaB
Linkage disequilibrium tends to decline
What reduces physical linkage?
Crossing over during meiosis
Sexual reproduction is required
Genetic recombination results from
shuffling of chromosomes
crossing over within chromosomes
Recombination rates affect LD breakdown
An experimental test of L.-D. theory
Why is L.-D. observed in nature?
Nonrandom mating
New mutations arising
Recent population formation
Low recombination
Genetic drift
Selection on multilocus genotypes
How does L.-D. influence selection?
What if . . . a new, beneficial mutation is linked with a deleterious allele?
What if . . . a new, nasty mutation is linked with a beneficial allele?
Can single-locus models predict evolutionary change?
Measuring variation
A review and revision
Measure of variation
Variance is measure of variation in natural populations
Average of squared deviations from the mean of a sample
Standard deviation is the square root of the variance
If a variable has a normal distribution, 68% of the observations will be within 1 SD, 96% in 2 SD and 99.7 in 3 SD
Variation in phenotype is due to genes AND environment:
For one locus,
Midpoint between two homozygotes as a point of reference
Mean phenotype of A1A1 individuals is A+a, and mean phenotype of A2A2 individuals is A–a.
a is the additive effect of an allele
If the inheritance of the phenotype is completely additive, then the heterozygote is exactly in between that of the two homozygotes
Phenotypic variance within populations is the environmental variance, VE
Additive genetic variance
Component of genetic variance denoted VA
Genetic variance includes other variance as well, but we will not discuss here
VA depends on magnitude of a and genotype frequencies
Variance is lower if one genotype is most common
At one locus, VA = 2pqa2
At several loci,
Average phenotype of any particular genotype is the sum of the phenotypic values of each loci
VA is the sum of the additive genetic variance contributed by each of the loci
Additive genetic variance
The additive effects of alleles are responsible for the degree of similarity between parents and offspring
Therefore, are the basis for response to selection within populations
Expected average phenotype of a brood of offspring equals the average of their parents’ phenotypes
Additive genetic inheritance allows a response to selection
Heritability in the narrow sense
Heritability is determined by the additive genetic variance (depends on allele frequencies) and environmental variance (depends on environment)
hN2 = VA /(VG + VE)
Compare to heritability in the broad sense we learned earlier
h2 = VG /(VG + VE)
hN2
hN2 is the slope of the regression of offspring phenotypes on the average of the parents of each brood of offspring
Heritability
Narrow sense heritability = h2 = VA/VP
= VA
(VA + VD + VI + VE)
VP = variation in phenotype
VA = additive effects of genes
VD = dominance effects
VI = interaction between genes (epistasis)
VE = environment effects
Heritability
Broad sense heritability = H = VG/VP
Variation due to dominance and interactions not truly heritable
H is seldom used, ‘heritability’ is usually heritability in the narrow sense (h2)