lecture 1-intro to molecular markers Flashcards
How does DNA work as a molecular marker ?
DNA -within recognised location on chromosome used as identification tool
-allow detection of variaitions/polymorphisms that exist between species in populations for specific regions of DNA
-Species identification
-Environmental sampling
-genetic diversity testing
-phylogenetic analysis
-forensic investigations
-Diagnostic testing
-Plant biotechnology
What are some examples of molecular markers in use ?
1.Species Identification:not always easy to identify species
* Minute differences:only few experts can distinguish them on morphology
* Cryptic species:some identical-looking populations inhabiting same area-not actually interbreeding
* Poorly preserved species:identifiying prey in stomach
* environmental DNA :soil,water,moult
Another eg of molecular marker ?
- Tracking Reproductive success :indication of fitness and therefore->long term survival
can identify wildlife corridors between populations that can prevent gentic isolation of endagered populations
2.Tracking while minimising disturbance: only small sample needed
very little tissue-helpfull when species may be harmed by anthropogenic stress
3.Monitoring of pporly documented species: can tell us population size,species,genetic diversity
How much of a genome is used to identify individuals ?
small sections of the genome
same sections from each individuals for comparison
How does a molecular marker work ?
the marker must be appropriate for the evolutionary timescale were interested in
markers that are slow=not goof for close relations -wont change quick enough -so would need a fast one
fast/slow markers
What determines how fast a marker evolves ?
rate of evolution :rate at which mutations accumalate in a DNA sequence across many generations
determined by :
1.the rate at which mutations arise may differ between regions of genome
2.effects of those mutations on the phenotype
The rate of mutation ?
DNA in all cells is under constant attack from mutagens
replication error are main source of mutation in germ line cells
during replication-incorrect nucleotide inserted by DNA polymerase -opposite a damaged base
Repair enzyme usually correct error but approx miss 1 in 10- therefor offspring differs
What determines how fast a marker evolves ?
-rate of evolution: rate at which mutations accumalate in DNA sequence across many generations.
-mutation rate
-effects of mutations
What are the impacts upon phenotypes ?
non-coding DNA-neutral not affected by selection because mutations doesnt affect phenotype:fast evolution
Mutations within protein coding DNA:
synonymous or non-synonymous
S= dont change AA seq
NS=change AA -almost always deleterious (removed by selection)
only few beneficial -so selected for
What are common molecular markers ?
- Population level studies (evolve quickly: VNTRS,microsattelites,mitochondrial d loop
- Species Barcode~(evolve slow): mitochondrial gene COX gene
- 16S rRNA gene)
What are Variable number of Tandem repeats (VNTR) ?
Mini Satelites
tandem meaning 2 or more arranged one by behind the other
originl DNA fingerprints
-highly mutable-germline mutation
unlike single nuceotide polymorphisms (SNP) which most commonly have 2 allles
all VNTS=minisattelites
all minisatelites=not all VNTR
define tandem ?
arrangement one behind the other
How large are VNTRS ?
larger than 5 nucleotides
no of repeats vary ebtween individuals
Wha can VNTRS be ?
both homo or hete
the VNTR at the sam elocus on each chromosme we may have diff number of repeats
What can generate VNTR variability ?
Slipping strand mispairing
How does Original DNA fingerprinting work ?
- cut DNA into fragments with resstriction enzymes
- seperate on a gel and transfer to nitrocellulose filter
- hybriise wit radiolabelled probe sequence homologous to the repated unit
- VNTR stretches in DNA containing the restriction fragment as they differ in size because of variation in no of repeats
PCR?
polymerase chain reaction
amplifying DNA to use in experiments
How does modern DNA fingerprinting use microsatellites ?
microsatellites -STR
shorter than VNTR
MS made up of repeats of a base pair unit that is usually 2,3,5 bp
usually about 10-30 base pairs
What are mitochondrial markers ?
all animals=nuclear DNA and mito DNA
diff properties which determine how quickly they evolve
Nuclear DNA-long strands of double helix
Mitochondrial DNA -forms circular DNA
(only maternally inherited )
What is mtDNA ?
mitochondria have their own DNA
rate of synonymous mutations
10x faster because proofreading is poorer
conserved arrangement of genes
What do we use mtDNA for ?
evolve relatively fast
wouldnt be useful for ancient divergences
some parts good for species level resolution
identify relaives within species
