Topic 1: Populations and Genetic Variation Flashcards
term review:
gene
allele
locus
haploid
diploid
homozygous
heterozygous
- 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
population =?
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
why are populations hard to define?
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.
what are the factors to an ideal population/deme?
- non-overlapping generations
- diploid
- sexual reproduction
- random/panmictic mating
- large population (no genetic drift)
- negligible migration
- genetic mutations don’t occur
- unaffected by natural selection
(assumptions of H-W principle)
how does an individual’s phenotype arise?
as a result of interactions between its genotype and environment
molecular mark terms
- monomorphic
- polymorphic
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
how to assess population genetic variation?
- 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
2 broad categories of molecular markers, based on mode of inheritance
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)
Examples of biparentally inherited marks
- allozymes AKA isozymes
- microsatellites
- nuclear DNA
allozymes AKA isozymes
- refer to enzymes
- allozymes are proteins with diff mobilities in electrical field (electrophoresis)
- mendelian inheritance
- codominance (does not mask alleles!)
how to tell heterozygosity vs. homozygosity on allozyme gel?
heterozygosity -> multiple bands at a set locus
homozygosity -> one band at a set locus
microsatellites
- 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
nuclear DNA
- 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)
short overview steps of sanger DNA sequencing
- extract DNA
- target DNA region in PCR, amplify
- add dye to DNA copies (diff for each base)
- sequence
next gen sequencing (NGS)
- 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
SNPs: Single Nucleotide Polymorphisms (biparental inheritance)
- 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
uniparentally inherited markers list
- mitochondrial DNA
- chloroplast DNA
- haploid chromosomes (sex-linked or sex determination chromosomes)
mitochondrial DNA (uniparental inheritance)
- small
- circular
- haploid
- maternal inheritance
“workhorse” markers, widely used
(H strand = heavy strand, more G&C)
(L strand = light strand)
chloroplast DNA (uniparental inheritance)
- single circular molecule, larger than mitochondrial DNA
- maternally inherited
- paternal in conifers
- evolves faster than plant mitochondrial DNA
3 Disadvantages of mitochondrial DNA and chloroplast DNA
- 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) - all linked and inherited as non-independent units (bc they are circular; if two mitochondrial genes are genes, they do not provide independent data)
- 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)
haploid chromosomes (uniparental inheritance)
(sex-linked or sex determination chromosomes)
- 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)
Assessing population variation, P(L)
- population genetic studies depend on determining amount of genetic variation within and among populations
- P sub L (P(L)) = proportion of polymorphic loci
both allele and genotype freq add up to ___?
1!
difference between standard deviation and standard error?
standard deviation reflects variability within a sample, while standard error estimates variability across samples of a population
what is the standard error a measure of?
measure of precision, not a measure of accuracy
(possible to be precise without being accurate, not possible to be accurate without being precise)
accuracy vs precision?
accuracy - how close an estimated value is to the true value in population
precision - measure of repeatability or reproducibility
_____ is one of most frequently used measures of variability at biparentally inherited diploid nuclear loci
heterozygosity (H)
what is the issue with using heterozygosity to measure genetic variability?
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
what does n/n-1 do in capital pi (correction factor for pop nucleotide diversity), as n gets bigger?
it approaches 1
(decreases toward 1)
2 hypotheses for how much genetic variability exists within populations?
- 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 - 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
summary of genetic variation revealed by allozyme studies
- 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
