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
