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What determines the level of genetic variation in a region of the genome?
What determines the level of genetic variation in a region of the genome?
Introduction
Genetic diversity: variation in DNA sequence between genomic regions.
Genetic diversity contributes to the ability of a species to respond to environmental changes, with implications in terms of, for example, human health, breeding strategies in crops and farm animals, management of infectious diseases.
Thesis: (?)
from a theoretical viewpoint, genetic diversity can be thought of as reflecting the balance between appearance and disappearance of alleles.
Observation
It was recognized early that genetic polymorphism varies substantially across loci and chromosomes, as demonstrated in various species of plants, fungi and animals.
variation in diversity within genomes.
variation in diversity between autosomes and sex chromosomes.
Rate of mutation varies across genome
explains part of the observed variation in genetic diversity
rate of allele loss and fixation
from a theoretical viewpoint, genetic diversity can be through of as reflecting the balance between appearance and disappearance of alleles.
new alleles appear by spontaneous mutation due to DNA replication errors or mutagen-induced DNA damage.
loci with neutral alleles are largely influenced by genetic drift, which is the random fluctuation of allele frequency across generations.
effective population size
in an idealized population under WF model, the strength of genetic drift is inversely proportional to the size of the population
Ne: size of an idealized population that would show the same amount of genetic diversity as the population of interest.
neutral theory: genetic diversity should be proportional to Ne. Ne varies over time, with long-term Ne explaining current levels of genetic diversity in populations but contemporary Ne explaining how strong drift currently is
strong population bottleneck, results in a rapid decay of heterozygosity due to enhanced genetic drift. Similar effect in case of a founder event/
drift barrier hypothesis: selection should only be able to reduce the rate of germline mutation to a point at which the selective advantage of further incremental reduction is not higher than the power of genetic drift. selection is more efficient in large populations, negative correlation between mutation rate and Ne.
Life history but not population history predicts genetic diversity.
population history influences but does not predict genetic diversity. demographic history due to environmental changes affect all living species; climate change, pest outbreaks, human activities.
strong correlation was reported between genetic diversity and life history traits: body mass, longevity and reproductive strategy.
Gene density
linked selection strongly affects neutral diversity in large populations
the fate of a mutation is determined not only by its own effect on fitness but also by selection applying to linked loci.
recombination cause chromosomal segments to become shorter, with the haplotypes that contain the selected allele varying in length depending on the particular history of recombination events along each coalescence lineage.
linkage disequilibrium: as long as the selected allele is in linkage disequilibrium with segregating variants at nearby loci, neutral diversity is reduced by linked selection.
selective sweeps
rapid fixation of a beneficial mutation erases preexisting polymorphisms at both the selected locus and nearby loci.
hard sweeps vs soft sweeps, partial sweeps and background selection
Mating system and recombination
Outcrossing
selfing and asexuality