Genetic Variation and Evolution
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Questions and Answers

What is a limitation of RFLP?

  • Requires large amounts of high quality DNA (correct)
  • Is a highly efficient technique
  • Requires no special instrumentation
  • Can be automated

    • What is an advantage of RAPD?

  • Requires blotting and hybridization steps
  • Requires sequence information
  • Neither DNA probes nor sequence information is required (correct)
  • Requires DNA probes

    • What is a disadvantage of RAPD?

  • Reproducibility is high
  • It requires large amounts of DNA
  • It is a complex technique
  • Reproducibility is questionable (correct)

    • What is a characteristic of RAPD markers?

    <p>They are dominant markers</p> Signup and view all the answers

    What is a requirement for RFLP?

    <p>Large amounts of high quality DNA</p> Signup and view all the answers

    What is an advantage of RAPD over RFLP?

    <p>RAPD can detect higher levels of polymorphism</p> Signup and view all the answers

    What is a characteristic of RAPD primers?

    <p>They are universal and can be used for any species</p> Signup and view all the answers

    Why is RFLP use limited to specific laboratories?

    <p>It involves radioactive methods</p> Signup and view all the answers

    What is the maximum polymorphic information content for any bi-allelic marker?

    <p>0.5</p> Signup and view all the answers

    What type of repeats are commonly found in SSR markers?

    <p>Di-, tri-, and tetranucleotide repeats</p> Signup and view all the answers

    What is required for AFLP analysis?

    <p>High-quality DNA</p> Signup and view all the answers

    What is a limitation of AFLP markers?

    <p>They cluster densely in centromeric regions</p> Signup and view all the answers

    What is the name of the technique that combines polymorphism at RE sites and hybridization of arbitrary primers?

    <p>AFLP</p> Signup and view all the answers

    What is the size range of fragments amplified in AFLP?

    <p>50-150 bp</p> Signup and view all the answers

    What is necessary to score heterozygotes and homozygotes in AFLP?

    <p>Proprietary technology</p> Signup and view all the answers

    What is a type of variant of SSR markers?

    <p>Microsatellites</p> Signup and view all the answers

    What is the benefit of genetic variation in a population?

    <p>It increases the chance that some individuals will survive.</p> Signup and view all the answers

    What is the gene pool of a population?

    <p>All the alleles in a population.</p> Signup and view all the answers

    What is the result of mutation in a gene?

    <p>A new allele is formed.</p> Signup and view all the answers

    What is the result of recombination?

    <p>New combinations of alleles are formed.</p> Signup and view all the answers

    What is hybridization?

    <p>The crossing of two different species.</p> Signup and view all the answers

    What is the result of natural selection on a population?

    <p>Microevolution occurs.</p> Signup and view all the answers

    What is gene flow?

    <p>The movement of alleles between populations.</p> Signup and view all the answers

    What is the effect of low gene flow on populations?

    <p>It increases the chance that two populations will evolve into different species.</p> Signup and view all the answers

    What is the term used to describe the elimination of a species from Earth?

    <p>Extinction</p> Signup and view all the answers

    What is the primary focus of molecular phylogenetic analysis?

    <p>Analyzing evolutionary relationships between genes or species</p> Signup and view all the answers

    Which of the following DNA markers is used to recognize neutral variation at the DNA level?

    <p>RFLP</p> Signup and view all the answers

    What is the outcome of using RFLP in molecular linkage maps?

    <p>Accelerated the construction of molecular linkage maps</p> Signup and view all the answers

    What is the result of digesting purified DNA using restriction enzymes in RFLP?

    <p>RFLPs – a molecular fingerprint – unique to a particular individual</p> Signup and view all the answers

    Which of the following is an advantage of RFLP?

    <p>Simple methodology</p> Signup and view all the answers

    What is the name of the professor teaching the course 'Genes Evolution and Development'?

    <p>Prof. Dr. Mohamed El-Esawi</p> Signup and view all the answers

    In which year is the course 'Genes Evolution and Development' being taught?

    <p>2023-2024</p> Signup and view all the answers

    What is the characteristic of SSRs in terms of their mutation rate?

    <p>High, around 4x10^4 to 5x10^6 /allele/generation</p> Signup and view all the answers

    What is the mechanism behind SSR mutations?

    <p>Slipped strand miss pairing</p> Signup and view all the answers

    What is the advantage of SSR markers in terms of genotyping?

    <p>They have a high genotyping throughput</p> Signup and view all the answers

    What is the characteristic of SSRs in terms of their allelic variation?

    <p>High level of allelic variation</p> Signup and view all the answers

    What is the characteristic of SSRs in terms of their distribution in genomes?

    <p>Randomly dispersed throughout most genomes</p> Signup and view all the answers

    What is the characteristic of SSRs in terms of their reproducibility?

    <p>Reproducible</p> Signup and view all the answers

    Study Notes

    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

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