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BIOL 479 > Topic 1: Populations and Genetic Variation > Flashcards

Topic 1: Populations and Genetic Variation Flashcards

1
Q

term review:
gene
allele
locus
haploid
diploid
homozygous
heterozygous

A
  • a unit of inheritance (DNA) occupying a fixed position on a chromosome
  • alterative form of a gene at a given locus
  • fixed position on a chromosome where a gene and its alleles are located
  • having one complete set of chromosomes
  • having two complete sets of chromosomes
  • having two copies of the same allele at a locus
  • having two different alleles at a locus
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2
Q

population =?

A

an aggregation of individuals of the same species in same place and time
- a collection of organisms that we have lumped together, bc we think they function as a unit

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3
Q

why are populations hard to define?

A

species exhibit non-random patterns of spatial distribution, or geographic structure, giving rise to population subdivision
- population subdivision arises due to physical barriers, non-random mating from proximity effects, behavioural effects, etc.

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4
Q

what are the factors to an ideal population/deme?

A
  1. non-overlapping generations
  2. diploid
  3. sexual reproduction
  4. random/panmictic mating
  5. large population (no genetic drift)
  6. negligible migration
  7. genetic mutations don’t occur
  8. unaffected by natural selection
    (assumptions of H-W principle)
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5
Q

how does an individual’s phenotype arise?

A

as a result of interactions between its genotype and environment

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6
Q

molecular mark terms
- monomorphic
- polymorphic

A

monomorphic - a locus at which all individuals in a population posses the same allele (no variation)

polymorphic - a locus at which two or more alleles (or haplotypes) are present in a population

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7
Q

how to assess population genetic variation?

A
  • molecular markers: any segment of DNA, or a product of DNA, that can be assayed to determine levels of pop genetic variability
  • common molecular markers: allozymes, microsatellites, nuclear gene seq, mitochondrial DNA seq, chloroplast DNA seq, single nucleotide polymorphisms
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8
Q

2 broad categories of molecular markers, based on mode of inheritance

A

biparental inheritance
- typically applies to the nuclear genome of diploid sexual reproducing organisms (one allele from mom, one from dad)

uniparental inheritance
- important exceptions to biparental inheritance include inheritance of mitochondrial DNA (usu. matrilineally); plastids e.g., chloroplasts (usu. matrilineally); Y chromosome (usu. paternal)

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9
Q

Examples of biparentally inherited marks

A
  • allozymes AKA isozymes
  • microsatellites
  • nuclear DNA
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10
Q

allozymes AKA isozymes

A
  • refer to enzymes
  • allozymes are proteins with diff mobilities in electrical field (electrophoresis)
  • mendelian inheritance
  • codominance (does not mask alleles!)
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11
Q

how to tell heterozygosity vs. homozygosity on allozyme gel?

A

heterozygosity -> multiple bands at a set locus
homozygosity -> one band at a set locus

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12
Q

microsatellites

A
  • AKA Variable Number of Tandem Repeats
  • repetitive short DNA seq
  • assayed w/ PCR, amplification and fluorescence anal
  • codominant
  • mendelian inheritance
  • non-coding, uncertain function
  • dinucleotide repeats most common, tri and tetra exist
  • number of repeats used to distinguish alleles
  • may have null alleles - may not attach to primers used in PCR, can affect data interpret
  • high deg of variability bc rapid rates of evol
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13
Q

nuclear DNA

A
  • generally assayed directly by PCR then sequencing
  • can be assayed indirectly w restriction fragment length polymorphisms (RFLPs), amplified fragment length polymorphisms (AFLPs), and single stranded conformational polymorphisms (SSCP)
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14
Q

short overview steps of sanger DNA sequencing

A
  1. extract DNA
  2. target DNA region in PCR, amplify
  3. add dye to DNA copies (diff for each base)
  4. sequence
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15
Q

next gen sequencing (NGS)

A
  • replaced sanger in many applications
  • DNA first fragmented by sonication or REs, then PCR to make sequencing libraries
  • 50-300 bp fragments in these libraries are simultaneously sequenced with addition of nucleotides to complementary strands
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16
Q

SNPs: Single Nucleotide Polymorphisms (biparental inheritance)

A
  • most abundant polymorphisms in genome
  • consider a single DNA nucleotide position = locus, each locus can have max 4 alleles (AGCT)
  • rate of change at single nucleotide positions are low, most SNPs have 2 alleles
  • most commonly used molecular marker today
17
Q

uniparentally inherited markers list

A
  • mitochondrial DNA
  • chloroplast DNA
  • haploid chromosomes (sex-linked or sex determination chromosomes)
18
Q

mitochondrial DNA (uniparental inheritance)

A
  1. small
  2. circular
  3. haploid
  4. maternal inheritance
    “workhorse” markers, widely used
    (H strand = heavy strand, more G&C)
    (L strand = light strand)
19
Q

chloroplast DNA (uniparental inheritance)

A
  • single circular molecule, larger than mitochondrial DNA
  • maternally inherited
  • paternal in conifers
  • evolves faster than plant mitochondrial DNA
20
Q

3 Disadvantages of mitochondrial DNA and chloroplast DNA

A
  1. pseudogenes
    - sometimes a mitochondrial/chloroplast gene can be integrated into nuclear genome, where it becomes a non-functional pseudogene (can be amplified in PCR accidentally)
  2. all linked and inherited as non-independent units (bc they are circular; if two mitochondrial genes are genes, they do not provide independent data)
  3. heteroplasmy
    - occasionally, paternal “leakage” can occur, and you get two diff copies of mtDNA in one individual (bc they’re supposed to be maternally inherited)
21
Q

haploid chromosomes (uniparental inheritance)
(sex-linked or sex determination chromosomes)

A
  • due to paternal inheritance, can track male descent patterns
  • few genes compared to other chromosomes
    –> little recombination
    – lower mutation rates
    (Genghis Khan lineage detected w this)
22
Q

Assessing population variation, P(L)

A
  • population genetic studies depend on determining amount of genetic variation within and among populations
  • P sub L (P(L)) = proportion of polymorphic loci
23
Q

both allele and genotype freq add up to ___?

A

1!

24
Q

difference between standard deviation and standard error?

A

standard deviation reflects variability within a sample, while standard error estimates variability across samples of a population

25
Q

what is the standard error a measure of?

A

measure of precision, not a measure of accuracy
(possible to be precise without being accurate, not possible to be accurate without being precise)

26
Q

accuracy vs precision?

A

accuracy - how close an estimated value is to the true value in population

precision - measure of repeatability or reproducibility

27
Q

_____ is one of most frequently used measures of variability at biparentally inherited diploid nuclear loci

A

heterozygosity (H)

28
Q

what is the issue with using heterozygosity to measure genetic variability?

A

pop 1: two alleles
- AA, AB, BB
pop 2: three alleles
- AA, BB, CC, AB, AC, BC

does not accurately show that pop 2 is more diverse, if they have same number of heterozygotes

29
Q

what does n/n-1 do in capital pi (correction factor for pop nucleotide diversity), as n gets bigger?

A

it approaches 1
(decreases toward 1)

30
Q

2 hypotheses for how much genetic variability exists within populations?

A
  1. the classical hypothesis:
    - populations contain very little variation, and selection maintains a single best allele at any locus and heterozygotes are rare
    - heterozygotes result from rare deleterious mutations that are quickly eliminated by selection
  2. the balance hypothesis
    - individuals are heterozygous at many loci, and balancing selection maintains lots of genetic variability within pops
    - balancing selection - any type of selection that results in maintenance of genetic variation in pops e.g., heterozygotes superiority
31
Q

summary of genetic variation revealed by allozyme studies

A
  • revealed more genetic variation than classical hypothesis predicted (maybe means balance hypothesis is more supported)
  • DNA seq studies confirmed allozyme results
  • high genetic variation in zebra mussel invasion
32
Q
A

BIOL 479 (6 decks)

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