population structuring Flashcards
known population structuring example
- European hake (Merluccius merluccius) = commercially important - Widely distributed in northeast Atlantic + Mediterranean Sea
- International Council for the Exploration of the Seas (ICES) considers 2 stocks in the Atlantic:
(1)Northern stock (northern Bay of Biscay, Celtic Sea and all waters west of the British Isles round to western Norway)
(2)Southern stock (southern waters of the Bay of Biscay and around the Iberian peninsula)
(3)Mediterranean?
what areas were sampled and what were the outcome FST values - what can we draw from this
(1)Mediterranean vs Atlantic:
FST = 0.029 (P < 0.001)
(2) Within the Mediterranean Sea:
FST = 0.003 (P > 0.05)
(3) Bay of Biscay vs Portugal (currently managed as one stock)
FST = 0.013 (P < 0.001)
(4) Southern Bay of Biscay vs Celtic Sea samples (managed as separate stocks)
FST = 0.003 (P = 0.2)
- Point = not all parts of the genome are neutral – some are actively selected for in this case
what needs to be considered when looking at Fst values to get an actual differentiation
type of marker
what are the 2 types of markers
Neutral & Non-neutral (often adaptive)
- Neutral markers = important - great at studying demographic processes - FST values often relatively small - subject to genetic drift and mutation but are not directly influenced by natural selection
- Adaptive markers often have very high FST values (0.25 = highest) and can tell us about specific processes underlying and often driving genetic population structuring - directly influenced by natural selection
what is a Genetic Outlier
loci that shows significantly higher or lower genetic differentiation than expected under neutrality
what biotic and abiotic factors make populations exhibit genetic structuring
Abiotic:
- Physical separation - mountains and rivers, followed by genetic drift
- Environmental factors (temperature, weather, salinity etc.)
- Environmental change
- Habitat fragmentation
Biotic:
- Life history traits- e.g. migratory behaviour, fecundity
- Dispersal potential (e.g. Flight)
- Evolutionary pressures: population bottlenecks and expansions, founder effects etc
what is genetic drift
allele frequencies of a population change over generations due to chance (sampling error)
- Primary mechanism for ‘neutral’ evolution
- Can result in extinction of some alleles (could be beneficial) and fixation of others (i.e. 100% freq)
- Effects small populations more
- Fst value represents the change in aleles in two separate populations due to genetic drift
what is the founder effect
Small group of individuals breaks off from a larger population to establish a new colony (extreme example of genetic drift)
- New colony isolated from original
- the ‘new’ gene pool is reflective of the founding individuals
- allele frequencies can be very different from the source populations’ - can lead to a reduction in genetic diversity + increase in the frequency of certain alleles (including rare or recessive ones)
- Prevalence of Huntington’s disease in Afrikaners in humans
explain Genetic bottleneck
- when an event severely reduces the size of a population (another extreme example of genetic drift) e.g natural disasters (earthquakes, floods, fires)
- small, random assortment of survivors
- Allele freq’s in the new pop can be drastically different from prior pop
- Many alleles can go extinct, with alleles continuing to be lost post event
example of a Genetic bottleneck
northern elephant seals
- Huge hunting pressure from humans
- Greatly reduced genetic diversity- approx 20 individuals surviving by 1890s
- Have rebounded to over 30,000 individuals
- BUT their genes still reflect this drastic bottleneck
- More susceptible to Environmental change?
what needs to be considered when sampling population genetics
- Sampling strategy?
- Only breeding individuals?
- Sample size 30 considered ‘standard’ - BUT more is often better
- Conservation concerns and ethics?
- Non-lethal / harmful methodologies?
what is the Wahlund effect
- Wahlund Effect = He (expected heterozygosity) ALWAYS exceeds Ho (observed heterozygosity) when randomly-mating, differentiated subpopulations are merged
- ONLY if merged population is not randomly mating as a whole
- More important: failure to detect the underlying population structure!
- Populations may mix in feeding grounds, but return to their own mating ground - NO random mating
what must be considered when choosing a genetic marker
depends on question asked + cost
- Neutral or non-neutral?
- Mitochondrial vs neutral?
- Variability of the marker - do you need to identify individuals?
- Sequencing technology to be used? Sanger Sequencing, NGS?
- £££ cost is often a deciding factor here
what factors are important regarding bioinformatics
Must be considered and costed into project planning - most population genetic analyses can be considered bioinformatics
- Sanger sequencing results relatively easy to do - BUT complex for thousands of samples
- NGS analysis ‘pipeline’ quality checks, de - barcoding etc
- access to appropriate computing power
- Ensure you have the expertise – workshops - colleagues
different methods used for Population genetic analyses
HWE dependent:
- Traditional population genetics - FST etc - HWE important
- Clustering analyses- STRUCTURE
- Detection of markers out of HWE - outliers
HWE independent:
- Essential methods which do not have the model assumptions of Hardy- Weinberg
- PCA, DAPC.
- Adaptation- gene under study here are not going to be in HWE
