population structuring

Question 1

what do adaptive markers tell us

Answer 1

specific processes underlying and driving genetic population structuring

Question 2

abiotic factors that cause genetic structuring

Answer 2

• physical separation by distance or barriers (mountains, rivers) followed by genetic drift
• environmental factors
• environmental change
• habitat fragmentation

Question 3

biotic factors causing genetic structuring

Answer 3

• life history traits (migratory behaviour, fecundity)
• dispersal potential (flight)
• evolutionary pressures: population bottlenecks + expansions (founder effect)

Question 4

what is genetic drift

Answer 4

a mechanism which allele frequencies of a population change over generations due to chance

Question 5

what 2 things can occur to an allele due to genetic drift

Answer 5

extinction of alleles and fixation of others (100% freq)

Question 6

what kind of population experiences genetic drift the greatest

Answer 6

small populations

Question 7

what is the founder effect

Answer 7

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

Question 8

what is a genetic bottleneck

Answer 8

extreme example of genetic drift occurring when pop is severely reduced

Question 9

what happens to allele freq in a genetic bottleneck

Answer 9

can be significantly different from prior population
many alleles extinct

Question 10

what sample size is considered ‘standard’

Answer 10

30

Question 11

what is the Wahlund effect

Answer 11

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

Question 12

what are some things that need to be considered when choosing a genetic marker

Answer 12

neutral or non-neutral
mitochondrial or nuclear
variability - does it need to ID individuals
sequencing technology to be used (Sanger, NGS)
cost

Question 13

HWE dependent genetic analysis methods:

Answer 13

traditional pop structuring (FST)
clustering analysis
detection of markers out of HWE - outliers

Question 14

HWE independent genetic analysis methods:

Answer 14

PCA, DAPC

Question 15

when does linkage disequilibrium occur

Answer 15

if genes don’t assort independently, no recombination during meiosis (genes can’t be inherited independently)

Question 16

when is linkage disequilibrium more likely to occur

Answer 16

if genes are close together on same chromosome or a sex linked

Question 17

what is K

Answer 17

how many genetic groups or clusters are contained in the data

Question 18

what does resolving K ‘with priors’ mean

Answer 18

analysis is run using presumed structure, often using original sample ID

Question 19

what does resolving K ‘without priors’ mean

Answer 19

analysis is run without known sample ID

Question 20

what is Oft and when is it used

Answer 20

adapted version of Fst useful for DNA sequence data

Question 21

what is Rst

Answer 21

modified for stepwise mutation model - microsatellites

Question 22

how are permutations calculated

Answer 22

the expected scenario of panmixia, compare actual Fst with expected panmixia scenario

Question 23

what is global Fst

Answer 23

overall Fst value for all your samples

Question 24

what is the role of Bayesian clustering

Answer 24

is used to test how many population clusters there are, run different K values until units are identified clearly

Question 25

what is PCA

Answer 25

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

Question 26

what is the importance of transforming the data using PCA and then performing discriminant analysis

Answer 26

ensures all variables are non correlated, removing all linkage issues

Question 27

DAPC function constructs synthetic variables, what is the goal of this

Answer 27

maximise variation between groups before placing individuals as coordinates

Question 28

what 3 demographics can be revealed

Answer 28

• population expansion + contraction
• migration / gene flow
• sex ratios