- Evolution in Finite Populations
Genetic Drift (random change)
with small sample sizes, observed frequencies will not always be very close to expected frequencies
Wright-Fisher Model
Hardy-Weinberg model for small populations
provides us with a baseline for how genotype frequencies are expected to change in the absence of NS, mutation, migration and nonrandom mating
because population size is small, take into account chance events that influence allele frequencies
How it works?
- Population of N diploid organisms produces a large number of gametes in a gamete pool
- Allele frequencies of large gamete pool exactly reflect those in parental generation
- Draw 2N gametes from the pool by random
- Allele frequencies in this small sample will not be same as parental generation (thus allele frequencies will keep changing due to small population size)
Consequences of Genetic Drift
1. Allele frequencies fluctuate over time, even in absence of NS
-rate at which frequencies fluctuate depends on size of population
-drift causes larger allele frequency fluctuations in small than large populations
-alleles are usually selectively neutral (NS does not act on them)
-in every finite population, there will eventually be fixation of one allele and loss of another
-probability that a neutral allele gets fixed is equal to frequency of that allele in population
2. Causes heterozygosity to decrease within a population
-alleles go to fixation and variation is lost
-inbreeding within small population causes variation to be lost
-use observed & expected heterozygosity to measure amt of variation in population
-Wright-Fisher model: expected heterozygosity decreases
-drift causes heterozygosity to decrease on average, but can increase it in particular instances
3. Causes divergence between populations over time
-since drift is random, different things will happen on different islands
-on some islands, allele A will become fixed while on other islands, B will become fixed. Fixation occurs at different rates too.
-the larger the area of island (aka population size), the greater the amount of genetic diversity --> showing how drift operates more strongly on smaller populations
Coalescent theory and Genealogy of Genes
gene trees: usually all phylogenetic trees that rely on sequence data of a particular gene locus basically are for inferring the patterns of descent with modification at that specific locus. A gene tree tells you the history of that gene.
in a gene tree, gene copies eventually coalesce at the coalescent point, where the same ancestral gene copy is (where 2 or more distinct gene copies descended from)
using mathematical models, can find out the time taken for k lineages to coalesce
coalescent events occur very rapidly earlier in the coalescent process and take a longer time when we get deeper in time
any allelic differences among a set of gene copies (from different species) must have arisen by mutation subsequent to the coalescent point (after the coalescent point)
a deeper coalescent point = greater genetic variation btwn species
small populations have a much more recent coalescent time than larger populations, thus small popns have less variation (consistent with fact that drift reduces heterozygosity in small popns)
NS & Shape of Coalescent trees
a) Neutral drift (neutral genes not under selection)
-new allele replaces ancestral allele slowly by drift
b) Positive selection
-positively selected allele quickly replaces ancestral allele due to NS
c) Balancing selection
-both new allele and ancestral allele persist indefinitely due to balanced polymorphism maintained by selection (overdominance/negative frequency dependence)
Demography, Biogeography & Drift
even a brief reduction in population size can cause effective population size to be drastically reduced, thus causing drift to operate very strongly (below are 2 processes of how population can reduce in size drastically)
1. Population Bottlenecks
-allele frequencies change drastically because (a) sampling effects that occurs during reduction of popn size, (b) accelerated pace of drift after popn reduction
-biggest changes in allele frequency occur during the bottleneck
-bottleneck reduces genetic variation within a popn
-when popn are restored to original size, rate of allele fluctuations slows
-bottleneck causes divergence BTWN populations within a species
2. Founder Effect
-changes in allele frequency that results from sampling effects that occur when small no. of individuals from a large popn colonize a new area and found a new popn
-allele frequencies in founders deviate by chance from those in large popn
-if island popn is smaller than mainland popn, the effect of genetic drift will be greater as well. The probability of an allele going to fixation is equal to its initial frequency on the island
-fixation of particular allele WITHIN popn & high between-popn variation = hallmark of genetic drift
Interplay of Drift, Mutation & NS
if drift were the only evolutionary process occurring, any finite popn will eventually become entirely homozygous. However, in practice, popn do not become homozygous as mutation provides continuous supply of genetic variation.
Selection and drift operate simultaneously on a popn to determine allele frequency change over generations
factors that reduce effective popn size (popn bottlenecks, set ratio biases) reduce the chance that a beneficial mutation will be fixed
Interplay btwn selection and drift depends on the strength of selection and popn size
when selection is strong(as measured by s: fitness advantage) and popn size is large, selection largely determines changes in allele frequencies
when selection is weak and popn size is small, drift mainly determines changes in allele frequencies
EG: in a smaller popn, probability that a selectively favoured allele is fixed is lower than in a larger popn
Neutral Theory of Molecular Evolution
States that:
-Most variation present in population is selectively neutral
-Many of molecular differences btwn species are selectively neutral (not subject to NS)
most substitutions are neutral, NOT most mutations are neutral (mutations are often deleterious)
Why no fitness consequences?
1. Synonymous Substitutions: degeneracy of genetic code (silent mutations which produce same aa)
2. Nonsynonymous Substitutions with little effect on function: change aa sequence, but with minimal fitness effects. Eg. changes away from binding sites have smaller functional consequences
3. Noncoding Regions: mutations in noncoding regions have minor effects on function/fitness. Pseudogenes - nonfunctional & untranslated
4. Effective Neutrality: if mutation has extremely small fitness consequences, random changes due to drift will overwhelm any effects due to NS. Thus the mutation is effectively neutral
Molecular Clock
substitution rate for neutral alleles presents a way to measure time using genetic data
if evolution proceeds at different rates along diff branches on phylogenetic tree, inferences on phylogeny may run into problems like long branch attraction
although substitutions of neutral alleles accumulate in a clocklike fashion, once sequence has become saturated with substitutions, any further substitutions will not be detected (since divergence already accounted for by previous substitutions, thus any further substitutions will be at the same spot)
clocks based on sites that
a) change rapidly: useful to estimate recent evolutionary events since they accumulate changes quickly but also reach saturation quickly
b) change slowly: eg. nonsynonymous sites in highly conserved genes. Slow to saturate and can be used to date ancient evolutionary events
annual rate of molecular change (substitutions) in short-lived and long-lived species are almost equal