Variability and its measurements - Molecular variability

19 important questions on Variability and its measurements - Molecular variability

The technique of gel electrophoresis....

Was used to screen populations for variants affecting protein migration rates in an electric current
  • Enzyme loci detected by this method are knows are allozyme loci

How does electrophoresis work?

Some amino acid differences involve residues whose electric charges differ, causing different mobilities in gels exposed to electric currents, resulting in detectable differences in band positions

What are codominant variants?

When two alleles in heterozygotes are detectable, usually the case for allozyme variants
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What is the most commonly used method for surveying DNA sequencing variation?

DNA sequencing of multiple copies of the same region of the genome, sampled from a population or set of populations

Studies of further loci and species show that...

As well as containing many SNPs, noncoding sequences also include indel variants:
  • Indels are much less common in protein-coding sequences, where they may alter the reading frame, causing loss of protein's function

Repeat number polymorphisms and copy number polymorphisms

In addition to variability arising from "point mutations", many organisms also have loci with highly variable numbers of copies of members of tandem arrays or repeated sequences

When comparing estimates of genome-wild diversity in different populations or species...

It is best to use data on synonymous or silent site variability because such variants are less affected by selection than nonsynonymous variants

The number of distinct alleles possible at a given locus (a defined region of the genome) depends on....

The number of variants at each nucleotide site in the stretch of the genome that has been sequenced multiple times, and on the number of combinations of these different variants

What is a haplotype?

A sequence that carries a particular set of variants
  • Two haplotypes from a population will usually differ at multiple sites, unless only a short length of sequence is studies 

What is the effect of recombination on haplotype variability?

Recombination does not affect diversity per nucleotide site, but merely distributes variants differently among haplotypes

With mendelian inheritance in a sexual population...

Variants present in a very large parental population without selection and mutations will be present in their progeny at the same frequencies as in the parents: 
  • variation is therefore preserved
  • The same holds for asexual reproduction, since each different genotype reproduces itself exactly 

What is coefficient of kinship?

If we take two individuals C and D from a pedigree, we can calculate the probability Fcd, that an allele at an autosomal locus, chosen randomly from individual C is IBD with an allele chosen randomly from D

What is the inbreeding coefficient?

The probability that two alleles at a locus in E are IDB

What is the fixation index (F)?

Can be viewed as a measure of departure from random mating, which can take values from -1 to +1
  • Positive F = excess of homozygotes
  • Negative F = excess of heterozygotes 

Positive assortative mating also....

Generates homozygote excess, but this is caused by identity in sate of alleles, and not directly by identity in descent.
- Negative assortative mating has the opposite effect

Assortative mating can affect...

The fertilities of different genotypes, and may thus act as a form of selection that changes allele frequencies

What are the different mutational changes?

Genome organization
  • Polyploidy -> Multiple complete sets of chromosomes
Chromosome rearrangements

  • Deletions
  • Duplications
  • Inversions
  • Translocations

Point mutations -> most frequent

What are the mutation rares of most DNA-based genomes?

They are low because there are elaborate molecular mechanisms for correcting errors in DNA replication and repairing DNA damage
- Mutation rates are greatly increased by mutations in the genes controlling them

In multicellular organisms with a germline...

Mutations can arise in germ-line cell lineages before meiosis. A cluster of identical mutations may therefore appear in a brood of offspring, rather than just a single mutation

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