Mammalian Population Genetics
Allele Frequencies
The total number of copies of an allele divided by (for mammals) 2N.
Aa
AA
aa
Aa
AA
aa
Aa
Aa
Aa
Aa
AA
aa
AA
p = 14/26 = 0.53; q = 12/26 = 0.47
Heterozygosity – Index of Genetic Diversity
Individual
Population
Aa
AA
aa
Aa
Aa
AA
BB
aa
Aa
cc
Aa
Aa
Dd
Aa
AA
HI – The percentage of loci at
which an individual is
heterozygous
HI = 0.5
HP – The average heterozygosity
in a population.
HP = 0.461
For multiple loci we average across loci .
aa
AA
Several Factors Influence Genetic Diversity
1) Mutation Rate – this is the rate that new variants are generated and
usually is fairly constant.
2) Demographic History – Populations that have recently either expanded or
contracted tend to have low diversity; stable populations tend to have
relatively higher diversity.
3) Genetic Drift – The random sampling of parental alleles can lead to
decreased diversity. This is especially a factor for small populations,
so small populations tend to drift to low diversity.
4) Migration – Populations that receive a lot of immigrants tend to have
high diversity.
Population Differentiation
How strongly differentiated are two (or more) populations?
FST – Fixation index – First developed by Wright decades ago.
1) The correlation of randomly chosen alleles within the same population relative to
the entire set of populations.
2) The proportion of genetic diversity in a sample that’s attributable to allele frequency
differences among or between populations.
The fixation indices (FST and its analogues: RST, GST, fST) are really flexible, in that they
allow us to evaluate several processes relevant to molecular ecology.
An excellent recent overview is provided by Holsinger & Weir (2009. Nat. Rev. Gen. 10:639).
http://digitalcommons.uconn.edu/eeb_articles/22/
Population Differentiation
Example: mule deer (Odocoileus hemionus) subspecies.
O. h. hemionus
Latch et al. (2014. Mol. Ecol. 23:3171) estimated genetic differentiation
among these using microsatellite data.
O. h. columbianus
ΦST = 0.224
There’s strong differentiation among these three subspecies.
O. h. sitkensis
This probably represents Pleistocene refugia.
Applications of Fixation Indices
Migration / Gene Flow
One of the classic equations in population genetics relates gene flow (migration) to FST.
FST ~~ 1/(4Nem +1)
So
Nem »
1- FST
4FST
Ne is the effective population size & m is the fraction of each population that are migrants.
Assumptions:
Infinite number of populations.
Same Ne in each population.
Island model of migration.
Fantasy Island Model
Applications of Fixation Indices
Migration/Gene Flow & Landscape Genetics
What landscape features influence gene flow?
Cervus elephas in Scotland
Most of the variation in FST is
explained by distance between
populations: Isolation-by-Distance.
Some population pairs that don’t fit I-b-D predictions. These are separated by lakes, not roads,
as might be predicted.
Perez-Espona et al., 2008. Mol. Ecol., 17:981
Applications of Fixation Indices
Detecting selection – Outlier FST
FST can be calculated for each locus (just like HP).
We can scan the genome to look for outlier loci that show unusual level of differentiation.
Locus 3 is an outlier.
Applications of Fixation Indices
Detecting selection
Storz, J. 2005. Mol. Ecol. 14:671
Peromyscus maniculatus
The albumin gene is subject of selection in high elevation populations.
Identification of management units and tests of taxonomy.
Preble’s meadow jumping mouse – Zapus hudsonius preblei.
Listed under the ESA.
Z. h. campestris
Z. h. preblei
Z. h. pallidus
Z. h. luteus
Ramey et al. (2005) recommended delisting.
Figure from Ramey et al. (2005).
Identification of management units and tests of taxonomy.
Data from King et al. (2006)
Identification of Mating Systems
Microsats are often variable enough for use
in paternity analysis.
Exclusion Analysis
Locus A
Two loci with multiple alleles
Locus A
100
102
104
106
108
Locus B
230
232
234
236
238
Locus B
Pup: 100 – 106
232 - 234
Male 1: 100 – 108
230 - 236
Male 2: 104 – 106
234 - 236
Male 3: 102 – 108
232 - 234
Male 4: 108 – 108
230 - 234
Male 5: 104 – 108
230 - 238
Identification of Mating Systems
Antilocapra americana
Monestrous: estrus occurs one night per year.
Females wander through
several males' territories and
engage in courtship chases.
Based on observations of behavior, it was
thought that females mated only once.
Females produce twins, so it’s easy enough
to see if the twins have the same fathers.
It turns our that 11 of 25 sets of twins have
different fathers.