population structuring Flashcards
what do adaptive markers tell us
specific processes underlying and driving genetic population structuring
abiotic factors that cause genetic structuring
- physical separation by distance or barriers (mountains, rivers) followed by genetic drift
- environmental factors
- environmental change
- habitat fragmentation
biotic factors causing genetic structuring
- life history traits (migratory behaviour, fecundity)
- dispersal potential (flight)
- evolutionary pressures: population bottlenecks + expansions (founder effect)
what is genetic drift
a mechanism which allele frequencies of a population change over generations due to chance
what 2 things can occur to an allele due to genetic drift
extinction of alleles and fixation of others (100% freq)
what kind of population experiences genetic drift the greatest
small populations
what is the founder effect
a small group of individuals breaks off from larger population, establishing a colony
new colony isolated from original
‘new’ gene pool is reflective of founding individuals
allele frequencies can be drastically different from prior population
what is a genetic bottleneck
extreme example of genetic drift occurring when pop is severely reduced
what happens to allele freq in a genetic bottleneck
can be significantly different from prior population
many alleles extinct
what sample size is considered ‘standard’
30
what is the Wahlund effect
He always exceeds Ho when randomly mating, differentiated subpopulations are merged
e.g. populations may mix in feeding ground but return to own mating ground, populations not actually mixed
what are some things that need to be considered when choosing a genetic marker
neutral or non-neutral
mitochondrial or nuclear
variability - does it need to ID individuals
sequencing technology to be used (Sanger, NGS)
cost
HWE dependent genetic analysis methods:
traditional pop structuring (FST)
clustering analysis
detection of markers out of HWE - outliers
HWE independent genetic analysis methods:
PCA, DAPC
when does linkage disequilibrium occur
if genes don’t assort independently, no recombination during meiosis (genes can’t be inherited independently)
when is linkage disequilibrium more likely to occur
if genes are close together on same chromosome or a sex linked
what is K
how many genetic groups or clusters are contained in the data
what does resolving K ‘with priors’ mean
analysis is run using presumed structure, often using original sample ID
what does resolving K ‘without priors’ mean
analysis is run without known sample ID
what is Oft and when is it used
adapted version of Fst useful for DNA sequence data
what is Rst
modified for stepwise mutation model - microsatellites
how are permutations calculated
the expected scenario of panmixia, compare actual Fst with expected panmixia scenario
what is global Fst
overall Fst value for all your samples
what is the role of Bayesian clustering
is used to test how many population clusters there are, run different K values until units are identified clearly
what is PCA
statistical method for exploring and making sense of datasets with a large number of measurements (dimensions)
reducing number of dimensions to principal components that explain main patterns
what is the importance of transforming the data using PCA and then performing discriminant analysis
ensures all variables are non correlated, removing all linkage issues
DAPC function constructs synthetic variables, what is the goal of this
maximise variation between groups before placing individuals as coordinates
what 3 demographics can be revealed
- population expansion + contraction
- migration / gene flow
- sex ratios
