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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

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population genetics i
Population Genetics I.

Evolution: process of change in allele


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
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


“Descent with modification”

An Evolutionary Tree…
example galapagos finches
Example: Galapagos Finches


changes in the genetic

composition of a population

from generation to generation

another example of changing selection
Another Example of Changing Selection


(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 monomorphicif there is only one
    • allele in the population. A locus is
    • polymorphic if there is more than one allele
some basic terms and concepts
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
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


This is a measure of locus variability- no

assumptions on mating, etc.

no selection or drift
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:


hardy weinberg equilibrium
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 hardy weinberg equilibrium
Forces that can account for non-Hardy-Weinberg 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


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

AA: p2 + Fpq

Aa: 2pq(1-F)

aa: q2 + Fpq

Complete self-fertilization:

F = 1.

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

measuring the extent of inbreeding1
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
F-statistics for inbreeding


Inbreeding of individuals relative to

their subpopulation

Value is high in inbreeding populations


Measures whether individuals more similar

to subpopulation than total set of


Increases with increasing isolation

genetic drift
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 drift1
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
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
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
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
Those rare events….

What if a few individuals- or even a single

seed- founds a new population far out-

side 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


bottlenecks and founder events
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 events1
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

Puerto Rican Parrot:

13 individuals

(Frankham et al. 2002)