Evolutionary Genetics Flashcards
What is time to fixation dependent on?
Population size
Define
Genetic load
the presence of unfavourable genetic material in the genes of a population
What is the minimum population size at which an allele with a fitness effect of s = 0.0001 can be acted upon by natural selection
10000
True or False:
Neutral alleles must eventually become fixed or lost
True
What are the important factors when figuring out how long it will take for a beneficial mutation to fix?
Selection coefficient and current frequency in the population
Define
Pseudogenes
segments of DNA that are related to real genes. They have lost at least some functionality, relative to the complete gene, in cellular gene expression or protein-coding ability
Define
Parallel evolution
the similar development of a trait in distinct species which are not not closely related, but share a similar original trait in response to similar evolutionary pressure
Definition
a measure of differences in relative fitness. They are central to the quantitative description of evolution, since fitness differences determine the change in genotype frequencies attributable to selection
Selection co-efficient
Define
Molecular clock
figurative term for a technique that uses the mutation rate of biomolecules to deduce the time in prehistory when two or more life forms diverged. The biomolecular data used for such calculations are usually nucleotide sequences for DNA or amino acid sequences for proteins
How does genome sequence conservation prove that most of the human genome is not functional?
Functionally important DNA sequences are preserved by natural selection. Analysis of 29 Eutherian mammal genomes showed that genome sequences were conserved across only ~4.2% of the human genome
Definition
the expected number of mutations to occur in each new offspring
Genomic mutation rate
Define
Selection co-efficient
a measure of differences in relative fitness. They are central to the quantitative description of evolution, since fitness differences determine the change in genotype frequencies attributable to selection
What is a 2-fold synonymous site?
A synonynous site (the third site of a codon - GAA) where 2/4 possible substitutions at the third site are synonymous
GAA - Glutamate
GAG - Glutamate
GAU - Aspartate
GAC - Aspartate
Definition
the process whereby organisms better adapted to their environment tend to survive and produce more offspring. The theory of its action was first fully expounded by Charles Darwin, and it is now regarded as be the main process that brings about evolution
Natural selection
Definition
the similar development of a trait in distinct species which are not not closely related, but share a similar original trait in response to similar evolutionary pressure
Parallel evolution
How do new genes evolve?
Errors during recombination and DNA repair can lead to genes (i.e. gene A) being duplicated resulting in two copies of that gene (i.e. gene A1 and A2). The duplicated gene can be lost via mutational degradation, retained by natural selection, or develop an entirely new function
How do you work out the chance of a mutation going to fixation?
1/2N
Which population size does genetic drift have a greater effect: 18 or 1800?
18
Define
Wright-Fisher model
a discrete-time Markov chain that describes the evolution of the count of one of two alleles segregating at a locus over time
How can genetic screening stop the spread of deleterious alleles?
Preimplantation genetic screening allows the selective removal of embryo’s that contain disease alleles that have already been identified in the parent and cause disease
What are the assumptions of the Wright-Fisher model?
- Haploid
- Constant population size
- No mating
- Discrete generations (no overlap)
- Genes are transmitted to the next generation by sampling with replacement
- No selection or mutation
True or False:
There is no recombination between cancer cell lineages
True
Cance is a somatic disease
An allele has 100% lethality. What is the predicted equilibrium frequency (fa) of this allele in the population?
μ
What is the probability of fixation of a neutral allele?
It’s current frequency in the population
If N = 100, 1/N = 0.01
Therefore all alleles with a selective effect less than _____ will be seen as neutral by natural selection
0.01
Definition
a discrete-time Markov chain that describes the evolution of the count of one of two alleles segregating at a locus over time
Wright-Fisher model
Definition
variation in the relative frequency of different genotypes in a small population, owing to the chance disappearance of particular genes as individuals die or do not reproduce
Genetic drift
An allele has a selection coefficient of s = 0.04. Approximately how many more generations will this allele take to fix than another allele that has a fitness effect of s = 0.08?
Double
Definition
figurative term for a technique that uses the mutation rate of biomolecules to deduce the time in prehistory when two or more life forms diverged. The biomolecular data used for such calculations are usually nucleotide sequences for DNA or amino acid sequences for proteins
Molecular clock
Define
Divergence
the process in which two or more populations of an ancestral species accumulate independent genetic changes (mutations) through time, often after the populations have become reproductively isolated for some period of time
What are the mutations that drive cancer evolution called?
Driver mutations
Definition
a mutation that increases an organism’s ability to survive
Beneficial mutations
Define
Fixation
the change in a gene pool from a situation where there exists at least two variants of a particular gene (allele) in a given population to a situation where only one of the alleles remains
Definition
a type of hypoxia-inducible factor in humans, a group of transcription factors involved in body response to oxygen levels
EPAS1
What is the only directional force on evolution?
Natural selection
True or False:
The capacity for selection to discern between the fitness effects of alleles do not depend on population size
False
It does
Definition
the change in a gene pool from a situation where there exists at least two variants of a particular gene (allele) in a given population to a situation where only one of the alleles remains
Fixation
A screening procedure can eliminate 20% of all the deleterious allele (with a 1% fitness effect) in the population. How does genetic screening change the equilibrium frequency of the disease?
sd = -0.01
sscreen = -0.21
Results in a 21 fold reduction
How is the selection coefficient (s) calculated?
The starting frequency of a variant, and how its frequency changes over time
Definition
a chromosomal segment that can undergo transposition, especially a segment of bacterial DNA that can be translocated as a whole between chromosomal, phage, and plasmid DNA in the absence of a complementary sequence in the host DNA
Transposon