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Evolution Midterm II 09/11/19 (Genomic evolution (Organismal Diversity…
Evolution Midterm II
09/11/19
Quantitative Genetics 1
Genetics of Multiple Loci
Why does selection on one trait change other traits?
Pleiotropy
One locus affects multiple traits
A single position affects multiple traits
ex. size and number of eggs, flower spot (pollinator behavior) and concentration of leaf tennis (resistance to herbivores)... change to one affects the other
Linkage Disequilibrium
Alleles at different loci are statistically associated
What are the consequences of LD?
LD can cause allele frequency to move in the "wrong" direction
Genetic hitchhiking
Deleterious mutations can fix
The fate of a new mutation depends on the background in which they occur (Genetic Draft)
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reduce genetic diversity
selective sweeps
reduce diversity
LD can slow the rate of adaptation
clonal interference
ex. HIV antiviral
Occurs in an asexual lineage ("clone") with a beneficial mutation. This mutation would be likely to get fixed if it occurred alone, but it may fail to be fixed, or even be lost, if another beneficial-mutation lineage arises in the same population; the multiple clones interfere with each other.
How do we calculate this?
D = p (AB) - p (A) p (B)
D < 0 = AB less than expected
D = 0 AB as much as expected
D > 0 AB more than expected
ex. D = p (AC) - p (A) p(C) = 0.5 - (0.5)(0.5)
What causes LD?
Physical proximity in genome
Evolutionary forces can generate correlation
NOT ALWAYS
occuring
Mutation... may cause statistical relation between two alleles
Selection
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Non-random mating
Migration
Drift
Recombination breaks LD
Delta D = - rD
Evolution can CAUSE LD, recombination BREAKS it
Why are some traits more variable?
Genotype depends on alleles at many loci
Phenotype influenced by environment
Each gene -> phenotype
number of phenotypes increases number of loci
increasing loci increases phenotypes
increasing number of environments increases number of phenotypes
describing quantitative traits
mean
Variance
influenced by genotype and environment
P = G + E
How much variation in a trait is determined by genes?
H^2 = Vg / Vp
This is
broad sense herritability
How heritable is a trait?
Additive Genetic Variance
Portion of genetic variation transmitted from parents to offspring
phenotype is determined by the average of the two parent
Non additive offspring equal one parents trait
ex. dominant traits
Narrow sense heritability
The proportion of the phenotypic variance that is due to additive genetic differences among individuals
if narrow sense heritability (h^2) = 1, the offspring's traits are perfectly heritable from the parents
values are between 0 - 1
Properties
h^2 is not
h^2 is
h^2 is dependent on
h^2 = V a / V p
heritability allows us to predict response to selection
R = h^2 S
S = selection differential
S = avg. of selected individuals - avg. of population of all individuals
Evolution changes mean and heritability of trait
*is not dependent on if a trait is beneficial for fitness
How to calculate:
Slope of regression of mid-parent v. offspring
Selection response/selection differential
Fitness Landscapes (
Adaptive landscapes
)
Build intuition about evolutionary change
natural selection keeps population from traversing fitness valleys
Population can get stuck on local peak if landscape is rugged
in genotype space can predict the order of adaptive mutations
such that this is the most fit route
Conceptual cartoon to inform intuition
The genetic mechanisms of some traits cause "teleporting" in phenotype space
Why are some traits continuous?
Genomic evolution
Genome sequencing
Organismal Diversity
Phenotypes
Genomes
The GC content of genomes varies
The remains unclear why
2) Codon usage bias
3) Stability of DNA or RNA
1) There is a mutational bias toward GC
Selection for compact genomes in viruses
can go from 1 to 10^13 individuals within an hour
~ 10 min duplication time
How does overlapping genes affect evolution?
A single mutation gives you changes in 2 different genes
allows for quicker adaptation
more deleterious mutations
Less specificity
Are BIG genomes also caused by selection?
size =/= organismal complexity
Little variation in gene number
Bigger genomes do not have more genes
Phenotypic complexity is not correlated with more genes
Gene regulation is important!
Big genomes tend to be seen in small populations
A function of drift
Why is there so much DNA?
Genetic duplication
Selection at the level of the gene
Genomes full of DNA with foreign origin
horizontal from infected person to uninfected person
vertical transfer from mother to child
Also in bacterial genomes with bacteriophage
most diseases are caused by lysogenic conversion: Botulism, Cholera, Dysentery, Diphtheria, etc.
Gene loss is common in bacteria
Genomes suggest most bacteria lack some essential biosynthetic pathways
Metabolite exchange suggested as one reason <1% of bacteria can be isolated
Also have mechanism that allow them to acquire new DNA
Conjugatoin
Transformation
Transduction
uses bacteriophage to donate DNA