Genetic Variation in Populations

Genetic Variation

• 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

Sources of Genetic Variation

• 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

• 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

Extinction

• 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 Phylogeny and Markers Used for Measuring Genetic Variation

• 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)

RFLP

• 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

RAPD

• 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

AFLP

• 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

SSR

• 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