Why study population genetic structure?In general, provides perspective on adaptation and speciation.

Can reveal the recent demographic history of a population and the role of:

Gene flowGenetic driftInbreedingNatural selectionPopulation size

Can reveal the history of population structuring over deeper time.

e.g. Phylogeography

Why do we expect population genetic structures to vary within

and among organisms?1) Differences in mobility/dispersal ability

2) Differences in reproductive attributes/system

3) Differences in life history attributes

4) Differences in behavioral attributes

5) Differences in geographic distribution

6) Habitat patchiness or variability

7) Historical reasons

e.g. See Table 6.3 and 6.4

One of the first idealized models of a population

From J. Hey, 2003, Nature Reviews Genetics, 4:535-544.

a. Island model

b. Stepping stone

c. Isolation by distance

d. Metapopulation

Idealized Population Models

Models of population structure that allow for migration (Gene Flow)

Statistical Description of Population Structure

Wright’s F statistics. A method to summarize how geneticvariation is partitioned among different hierarchical levels.

Among population level:

FST = Vp / p (1 - p)

This is a measure of the observed variation in allele frequencies among populations (regardless of how the variation arose).

Another way from Avise: FST = (ht - hs) / ht

hs = mean expected heterozygosity at a locus within subpops under H/Wht = overall expected heterozygosity in total population (given allele freq & H/W)

FST :Ranges from 1.0 to 0.0

subpopulations fixed foralternate alleles

subpopulations have samealleles frequencies

“structured” “not structured”

From Selander (1970): An analysis of mouse population structure within and among barns in Texas.

Estimated Number of Mean Allele Variance ofPopulation Size Pops Sampled Frequency Allele Frequency

Small ~10 29 0.418 0.849 0.0506 0.1883Large ~200 13 0.372 0.843 0.0125 0.0083

Es-3b Hbb Es-3b Hbb

FST = Vp / p (1 - p)

FST = 0.0506/(0.418)(0.582) = 0.208 for small pops

FST = 0.0125/(0.372)(0.628) = 0.054 for large pops

Consider the joint effects of genetic drift and gene flow on population structure

In the absence of migration, finite populations become more inbred and diverge from one another at random (with respect to allele frequencies) as a result of drift.

The probability of autozygosity (that an individual carries IBD allelesat a locus) increases faster, the smaller the population.

FST provides a measure of divergence under drift. At some pointin time, as a population approaches FST = 1, the increase inautozygosity will be balanced by the rate of migration (and/or mutation also, in reality). An equilibrium is struck.

Migration rates (Gene Flow) can be estimated assumingan equilibrium FST has been reached:

FST = 1 / 1 + 4Nm~

For neutral alleles in an island model, the equilibrium value of FST :

or, Nm = (1 - FST ) / 4FST

~

This is interpreted as the absolute number of individuals exchanged between populations.

As Nm increases, FSTdecreases.

If Nm = 1,

Subpopulations are 20% more structured (inbred) than if all subpopulations essentiallycomprised a single, randomly mating population

Gene Flow is a powerful thing

FST = 0.20.

FST

Nm

1.0

0.8

06.

0.4

0.2

0.0

However, FST is not a very precise measure. At best it can onlyprovide qualitative perspective.

More recently, there has been development of DNA sequence variation approaches to characterize population structure.

However, all summarystatistic approaches liveand die by the assumeddemographic model.

The model specifies meaningto the parameters and theassumptions that underliethem.

A summary statistic doesn’tnecessarily provide insight.