Genetic Variation in Populations

Study Notes

Genetic variation in a population increases the chance of some individuals surviving
Genetic variation leads to phenotypic variation, which is necessary for natural selection
Genetic variation is stored in a population's gene pool, made up of all alleles in a population
Allele frequencies measure genetic variation and can be calculated for each allele in the gene pool

Mutation: a random change in the DNA of a gene that can form a new allele and be passed on to offspring
Recombination: forms new combinations of alleles, usually occurring during meiosis, and rearranges parents' alleles in new ways in gametes
Hybridization: the crossing of two different species, which can lead to new genetic variation

Microevolution is evolution within a population, resulting in observable changes in allele frequencies
Natural selection can change the distribution of a trait in a population in one of three ways
Gene flow is the movement of alleles between populations, keeping neighboring populations similar

Species can become extinct, which is the elimination of a species from Earth
Background extinctions occur continuously at a low rate, usually affecting a few species in a small area due to local environmental changes

Molecular phylogenetic analysis is the study of evolutionary relationships between genes or species
DNA markers used for measuring genetic variation include:
- RFLP (Restriction Fragment Length Polymorphism)
- RAPD (Randomly Amplified Polymorphic DNA)
- AFLP (Amplified Fragment Length Polymorphism)
- SSR (Simple Sequence Repeat)

First used by Botstein et al. in 1980
Recognizes neutral variation at the DNA level, SNPs within a gene or between genes, and variable number of tandem repeats present between genes
Outcome: accelerated construction of molecular linkage maps, improved accuracy of gene location, and reduced time required to establish a complete linkage map
Technique: digestion of purified DNA using restriction enzymes, leading to the formation of RFLPs, a molecular fingerprint unique to a particular individual
Advantages: co-dominant, reproducible, simple methodology, and requires no special instrumentation
Limitations: requires large amounts of high-quality DNA, low genotyping throughput, difficult to automate, and involves radioactive methods

A single, random-sequence oligonucleotide primer in a low stringency PCR simultaneously amplifies several discrete DNA fragments
Outcome: several discrete DNA products up to 3 kb are amplified (amplicons), considered to originate from different genetic loci
Advantages: no DNA probes or sequence information required, no blotting or hybridization steps, small amounts of DNA required, can be automated, and detects higher levels of polymorphism than RFLP
Limitations: reproducibility is questionable due to factors such as PCR buffer, deoxynucleotide triphosphates (dNTPs), Mg2+ concentration, cycling parameters, source of Taq polymerase, and condition and concentration of template DNA primer concentration

Amplified fragment length polymorphism (Zabeau and Voss, 1993; Vos et al., 1995)
The selective PCR amplification of restriction fragments from a gDNA double-digest under high stringency conditions
Combination of polymorphism at RE sites and hybridization of arbitrary primers
50 to 150 bp are amplified and polymorphism detected
Small DNA samples (1-100 ng) only required
Relatively reproducible across laboratories
Limitations:
- Maximum polymorphic information content for any bi-allelic marker is 0.5
- High-quality DNA is needed
- Proprietary technology is needed to score heterozygotes and ++ homozygotes
- AFLP markers cluster densely in centromeric regions in species with large genomes

Variants: microsatellites, short tandem repeats (STRs), and sequence-tagged microsatellite sites (STMS)
Repeat Units 1-6 bp long
Di-, tri-, and tetranucleotide repeats – (CA)n, (AAT)n, and (GATA)n
Widely distributed in genomes (plants & animals)
Advantages:
- High level of allelic variation
- Flanks of SSR motifs-templates for specific primers to amplify the SSR alleles via PCR
- Referred to as simple sequence length polymorphisms (SSLPs)
- Mutation rates of SSR are about 4x10^4 – 5x10^6 /allele/generation
SSRs are characterized by:
- Hypervariability
- Reproducibility
- Codominant nature
- Locus specificity
- Random dispersion throughout most genomes
- More variable than RFLPs or RAPDs