POPULATION GENETICS

Population

• group of individuals belonging to same species

• live in same geographic area

• actually or potentially interbred

Population genetics

the study of allele frequencies in a population

Gene pool

all of the alleles in a reproducing population

Why measure genetic variation

• determine the potential for adaptation and evolutionary change

• provides evidence about the roles of various evolutionary processes

  • some processes increase variation, others decrease it

• tells us about speciation & extinction

• allows us to predict a population’s chances for long term survival

Genotypic frequency

• the proportion of a specific genotype w/in a population

• ranges from 0 to 1

Allelic frequency

w/in a population, proportion of individuals w/ a specific allele

p + q

= 1… always equal to 1 in case of complete dominance

• p = frequency of dominant allele

• q = frequency of recessive allele

Hardy-Weinberg equation

p²+2pq+q²= 1.0

p

frequency of one allele (dominant)

q

frequency of other allele (recessive)

p²

frequency of homozygous dominant genotype

q²

frequency of homozygous recessive genotype

2pq

frequency of heterozygous genotype

Hardy-Weinberg law

• allows us to calculate allelic and genotypic frequencies in the absence of evolutionary forces

• gives us an idea of genetic variation in a population

• assumptions about the population

  • infinitely large

  • random mating

  • free from mutation

  • no migration

  • no natural selection

• if these conditions are met, the population is in genetic equilibrium

• therefore, the frequency of alleles don’t change over time

Molecular evolution

• changes in allele frequencies is due to mutation followed by natural selection or drift

• most mutations are neutral

• mutations leading to amino acid substitutions are usually deleterious and selected against (not usually favorable) in the environment

• protein variations maintained by adaptation to certain environmental conditions

Population genetics is often used to study evolution

• most populations have a lot of genetic diversity

• genetic diversity allows for adaptation of the population as the environment changes

• microevolution

• macroevolution

Microevolution

change in allele frequencies over time within a population of a species

Macroevolution

• change that results in reproductive isolation between or among populations

• change leading to emergence of new species (speciation) and other taxonomic groups

Reproductive isolating mechanisms

• biological barriers that prevent or reduce interbreeding and therefore exchange of alleles between populations or species

• 2 major types

  • prezygotic isolating mechanism

  • postzygotic isolating mechanism

Prezygotic isolating mechanism

prevents individuals from mating in the first place

• mechanisms could be ecological, behavioral, seasonal, mechanical, physiological

Postzygotic isolating mechanisms

creates reproductive isolation even when members of two populations mate with each other

• the resulting hybrid isn’t viable or is sterile

Natural selection

• individuals with alleles that confer a reproductive advantage in the environment produce more offspring on average than others in the population

  • some phenotypes are more successful at survival and reproduce at higher rates

  • variations are heritable (passed on)

• frequency of alleles that confer increased reproduction (which may or may not also be an increase in survival) increase in the population over time

  • ex: lactose tolerance versus intolerance

• Fitness - the relative reproductive ability of a genotype

  • not the individual’s ability to survive, but the ability to reproduce before death

Types of selection

• directional selection

• stabilizing selection

• disruptive selection

Directional selection

phenotypes at one end of a spectrum become selected for or against

• usually as a result of changes in environment

Stabilizing selection

intermediate types are favored (mean is favored)

• both extreme phenotypes are selected against

• reduces population variance over time but not the mean

Disruptive selection

both phenotypic extremes are selected for at the expense of the mean

• results in population with increasingly bimodal distribution for trait

Geographic-dependent allelic variation

allele frequencies can vary for populations separated by space or across a geographic transect

Cline

gradient for allele frequencies that change in a systematic way according to the physical attributes of an environment

Selective (nonrandom) mating

• most organisms don’t mate randomly

• related to natural selection

Forms of nonrandom mating

• positive assortative mating

• negative assortative mating

• inbreeding

Positive assortative mating

similar genotypes more likely to mate than dissimilar ones

Negative assortative mating

dissimilar genotypes are more likely to mate than similar one

Inbreeding

related individuals mate

• consanguineous mating

• increases proportion of homozygotes in population

• recessive traits are more likely to be observed

• completely inbred population theoretically will consist only of homozygotes

Small effective population size

can decrease genetic variation

Effective population

individuals contributing alleles to the next generation

Bottleneck

• when an effective population is drastically reduced in size and then population size rises again

• selection can be natural or man-made

• can result in inbreeding in a population due to low genetic variation

Migration

• gene flow

• genetic island

• most populations aren’t completely isolated

• immigration can introduce new alleles

• emigration can remove alleles

• alters the frequency of existing alleles

Gene flow

an organism migrates and contributes their alleles to the gene pool of a recipient population or removes alleles from the gene pool if leaving the population

Genetic island

population that breeds within itself and has little gene flow

Founder effect

• when a population is established from a small number of breeding individuals

• later gene pool contains only those alleles from the original population

  • chance can play a significant role in alleles present in founders

Genetic drift

• changes in allele frequencies due to random sampling error

• NOT related to natural selection

• due to chance alone – no selective pressure

• small populations are especially prone to drift

• small effective population, bottleneck, and founder effect can contribute to genetic drift

  • note: these forces can also be related to natural selection

• reduces genetic variation in a population

Phylogeny

genetic differences among present-day species can be used to reconstruct their evolutionary histories

• differences in DNA sequence between species are proportional to evolutionary distance

Phylogenetic trees

branches represent lineages over time

Monophyletic groups

groups consist of an ancestral species an all its descendants

How is genetic variation measured in a laboratory?

• genotype individuals’ DNA from a sample population to measure number of individuals with a specific polymorphism

  • sample population must be random and large enough to accurately represent the entire population

  • similar techniques to genetics testing and diagnosis, but analyzing many samples at the same time

Examples of techniques

• direct DNA sequencing

• qPCR

• look for DNA marker differences on a gel or blot

qPCR to measure amounts of 2 alleles

• amplify locus of interest using primers and primer probes directed against specific polymorphisms (alleles) in your sample population

• probes can be differentially labeled with fluorescence

  • fluorescence from probe would report how much of each allele is present

RFLP analysis

• mutation changes sequence so that a restriction site is added or removed from the locus

• isolate DNA from sample individuals in the population you are studying

• cut with restriction enzyme

• analyze fragments on Southern blot

• could also PCR amplify the locus, cut the fragment, and analyze the fragments on a gel

Biological fitness

measure if the number of offspring a particular individual/phenotype will produce

Speciation

• the process of splitting a genetically homogenous population into 2 or more populations

• become reproductively isolated

• as mutation occurs, barriers of reproduction will form

Founder mutation

first individual in population to acquire a mutation

Founder effect

• one or a few individuals contribute alleles to next generation

• decreases variation