Download Population Genetics I.

Population Genetics I.
Evolution: process of change in allele
frequencies
Natural Selection: the mechanism
Ecological genetics: study of genes in
natural populations
What are the forces that maintain genetic
diversity? Is that genetic diversity
selectively neutral, or actively
maintained by natural selection?
What IS natural selection, anyway?
•Individuals within a population are different
from each other in various characteristics
•These differences are heritable
•Some individuals survive and reproduce more
successfully than others, based on these
heritable differences
•Over time, this differential survival and
reproduction leads to altered gene
frequencies
An Evolutionary Tree…
Macroevolution:
“Descent with modification”
Example: Galapagos Finches
Micro-evolution:
changes in the genetic
composition of a population
from generation to generation
Another Example of Changing Selection
I’iwi
(Vestiaria coccinea)
Bill shape has changed since the extinction
of several of its original food plants, based on
measurements of museum skins compared
to birds caught recently
(Smith, Freed, Lepson, and Carothers. 1995. Cons. Biol. 9: 107-113)
Population Genetics
•Changes in gene frequency in populations
•Consequences of gene flow
•Consequences of small population size
•Genetic drift, inbreeding, other factors
•Understanding evolutionary relationships
Some Basic Terms and Concepts
•Genes: a sequence of DNA that encodes
for a protein
•Locus: position on a chromosome; may or
may not code for a protein
•Allele: Alternative DNA sequence at a locus
•A locus is monomorphic if there is only one
allele in the population. A locus is
polymorphic if there is more than one allele
Some Basic Terms and Concepts
•Genotype: The overall genetic makeup of an
individual
•Phenotype: The expression of the genotype.
Gene expression influenced by the
environment
•Genetic drift: Changes in allele frequencies
due to chance events
•If the same alleles are present at a locus, the
individual is homozygous. If the alleles are
different, the individual is heterozygous.
Measures of genetic diversity
General diversity, He
He = 1 - Σpi2 where pi is the frequency
of the allele type
Note that when the frequency of pi is
close to or equal to 1, then He is essentially
zero.
This is a measure of locus variability- no
assumptions on mating, etc.
No Selection or Drift?
If population large, randomly mating...
•Offspring gene frequencies depend only
on gene frequencies of parent generation
•Frequencies will be at equilibrium
If this is not the case, the interesting question is:
WHY NOT?
Hardy-Weinberg Equilibrium
Gene frequencies will reach an equilibrium
when the following conditions are met:
•Diploid organism (copy of gene from each parent)
•Sexual reproduction
•Non-overlapping generations
•Random mating
•Large population
•Equal allele frequencies in the sexes
•NO migration, mutation, or selection
Forces that can account for non-HardyWeinberg Equilibrium
Non-random mating
active sexual selection of mates
“isolation by distance”
Geographic structure in population
(can lead to non-random mating throughout)
Natural selection
Some genotypes have better reproductive
success and survival than others
Inbreeding
Plant populations in particular may show a
great deal of inbreeding
Usually not considered advantageous
*leads to a loss of genetic diversity and
*increases expression of deleterious
recessive genes
When inbreeding causes a drop in demographic
rates, it is termed “inbreeding depression”
Measuring the extent of inbreeding
Inbreeding leads to a loss of heterozygosity
The inbreeding coefficient, F, is a measure
measures probability that an individual’s
2 alleles are identical by descent
AA: p2 + Fpq
Aa: 2pq(1-F)
aa: q2 + Fpq
Complete self-fertilization:
F = 1.
Measuring the extent of inbreeding
The coefficient of inbreeding for a selfing
population can be calculated as:
F = S/(2-S)
S is the selfing rate
IF we have information on the frequency of
heterozygous individuals, AND we assume
that the population is in equilibrium,
we can calculate the selfing rate
F-statistics for inbreeding
FIS:
Inbreeding of individuals relative to
their subpopulation
Value is high in inbreeding populations
FST:
Measures whether individuals more similar
to subpopulation than total set of
subpopulations
Increases with increasing isolation
Genetic Drift
•Defined as the random fluctuation in allele
frequencies
•Survival of new mutations can fail due to
chance events
•Particularly important in small populations:
elimination or fixation of alleles possible
solely due to chance
Genetic Drift
•Time needed to fix or eliminate allele a
function of population size
•Effective population size (Ne)
size of idealized popn that loses genetic
diversity at same rate as real population
•Ne almost always smaller than real N
Consequences of population subdivision
and movement of genetic material
•Discrete patches, or demes, of genetic structure
form when populations are isolated
•Associated with limited dispersal capabilities,
even in continuous populations
Isolation by distance
•Movements of individuals or pollen among
populations break down formation of
demes
Gene Flow: animals
•Animals: dispersal is the key;
isolation by distance still applies
•Non-sessile animals: any age or stage could
start new population
•Conservation biology: concerned with popns
either too small, or too isolated,
to maintain gene flow and genetic diversity
Gene Flow: plants
•Genetic mixing occurs through both seed and
pollen dispersal
•Gene flow therefore dependent on dispersal
mechanisms: wind patterns, animal
behavior (both pollination and seed
dispersal)
•Only seeds can start new populations
Those rare events….
What if a few individuals- or even a single
seed- founds a new population far outside the original range, or survives a
catastrophe where all other populations
of the species are lost?
The new population will have greatly reduced
genetic diversity compared to the larger
populations
Bottlenecks and Founder Events
A bottleneck:
population reduced to a tiny fraction
of its former size, thus eliminating
much of its former genetic diversity.
Bottlenecks and Founder Events
A founder event occurs when one or a few
individuals establish an isolated population
This is of particular concern in conservation
biology, and captive breeding programs
British field cricket:
12 individuals
Snow Leopard:
7 individuals
(Frankham et al. 2002)
Puerto Rican Parrot:
13 individuals
frequency
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