EE Lecture 9: Molecular Ecology and Evolution Flashcards
how can you measure variation among individuals
microsatellites
what are microsatellites
simple sequence repeates of 2-6bp eg.CGTCGTCGTCGT
highly variable due to copying areas
co-dominant: can detect heterozygotes
why are microsatellites highly variable
due to coping errors
what is the method for detecting variation among individuals
- extract DNA
- primers to amplify microsats
- amplify microsat by PCR -mills of copies
- run on gel
on what levels can variation be measured among individuals
through identifying individual
family relationship
genetic variability and inbreeding in pops
what case study has been done to identify individuals
Pyrenean brown bears
what did the brown bear case study involve
used genetic and field data
genetic - SRY gene for sexµsats
field-fur and scat samples
what genetic and field data can be used to identify individuals
genetic: SRY gene for sex + microsats
field: fur and scat samples
why are pyrannean bears problematic
have low genetic variation compared to bears in other pops,this is due to inbreeding
how are people trying to maximise pyrannean bear genetic variation
guid reintroduction of new bears
to identify family groups of cheetahs in algeria, what sequences were used
Cytb and mtDNA
also for 9dinucleotide microsatellite loci
what is kinship analysis based on
the pattern of alleles
what’s the use of microsatellites
identify relationship among individuals-pedigree,genealogy
what can be used to identify relationship among individuals eg.pedigree +genealogy
microsatellites
what can be used to infer popn history
pattern of genetic variation
how can pattern of genetic variation be used to infer popn history
eg.popn bottlenecks,expansion, fragmentation
why might it be useful to analyse popn history
for popn viability analysis
extinction risk
what factors affect genetic variation in pops
pop size mutation rate level inbreeding pop subdivision-gene flow pop history-bottlenecks
what is mtDNA
maternally inherited marker
mitochondrial DNA
how can mtDNA be tested for
- extract DNA
- amplify marker region using primers eg. cytochrome oxidase 1
- clean up the PCR product
- cycle sequencing
what DNA can be used to test variation in humans
mtDNA
what are the results from using mtDNA to test for variation in humans
- other continents nested within African variation
- signature of pop expansion
- lineages coalesce back to SCA:mitochondrial Eve ~200k
what do mitochondrial lineages coalesce back to
a single common ancestor; Mitochondrial Eve ~200kya
what is reverse simulation
reconstructing the past
assuming random sample from a constant pop, random mating, discrete genes, what is the probaiblity that 2 individuals share a mother
[1/Nf] * [1/Nf] * Nf
what is the expected time till coalescence to a single ancestor
2Nf * (1 - 1/k) generations
discuss the popn history of the giant panda
2 pop expansions due to warmer climate
2 pop declines:colder climate
final reduction to extreme low numbers: human cause
subdivision of pops in 3 areas, but with some gene flow
what are alternatives to using the model to explain variation
compare fit of the model to the data (1000s SNPs)
choose the model that best explains the data
what is to blame for endangered giant panda
climate hotter:pop expand twice
climate colder:pop decline twice
final threat:humans
which DNA sequence markers can be used to test species relationships
mtDNA
nuclear
how can you reconstruct a phylogeny
align sequences of species, so comparing homologous sites
how do you get from DNA sequences to a phylogenetic tree (what 2 methods)
- distance methods
- Parsimony methods
- likelihood methods (most likely based on models and data)
what problems do you face when trying to get from sequences to trees
rooted/unrooted?
DNA evoln is not parsimonious
in what way is DNA evoln not parsimonious
multiple subs
transitions vs. transversions
codon positions synonymous/non synonymos
how can you obtain a dated tree
use molecular clock
use fossil/biogeographical calibrations
what is a molecular clock
neutral subs occur @ constant average rate (proportional to the muatoin rate)
what value on tree shows measure of tree support
bootstrap value
what can phylogeny tell us
identification DNA barcoding diet of chamois trnL intron of plastid DNA from faeces history of speciation events leading to a set of species broad history of life
what can neutral markers be used for
to reconstruct individual, popn and species history
for the following level, which markers and analyses can be tested: INDIVIDUAL
microsatellites
SNPs
analyses:pedigree,pop genetics
for the following level, which markers and analyses can be tested:
POPN
mtDNA
SNPs
analyses: phylogeography, coalescence
for the following level, which markers and analyses can be tested:
SPECIES
mtDNA
nuclear DNA
analyses: phylogenies
what markers can be used to test phylogenies
mtDNA
nuclear DNA
what analyses can SNPs be used for
pedigree, pop genetics, phylogeography, coalescence
whar analyses can mtDNA be used for
phylogeography, coalescence, phylogenies
at which levels can SNPs be used to create analyses
individual or species
