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Ecological Genetics
Study of the process of evolution
occurring in present-day natural
populations
Evolution occurs primarily by changing
the amount, type, and distribution of
genetic variation
Ecological Genetics I
Discrete genetic variation: individuals can be
categorized into a small number of classes
Population genetics is the study of the
amount, type, and distribution of discrete
genetic variation, usually controlled by
variation at one or a few genes
Quantitative genetics is the study of the
genetics of continuous (quantitative) traits,
usually controlled by variation an many
genes, and by environmental (non-genetic)
variation.
Population genetic variation
Between-population variation
Within-population variation
Variation in gross phenotype (visible)
Variation in cellular or physiological traits
(blood groups, MHC antigen-presenting
molecules)
Molecular variation
Discrete variation between
populations
Rat snakes, Elaphe obsoleta
Between-population variation
Salmanders, Ensatina eschscholtzii
Within-population variation:
polymorphism
Hawaiian Happy-face spiders, Theridion grallator
Within population sex-linked
visible polymorphism
Stag beetles, Lucanus cervus
Within-population sex-linked
visible polymorphism
Trinidadian guppies, Poecilia reticulata
Using visible polymorphisms to study
population genetic structure and evolution
Advantages: inexpensive to
score, amenable to
experiments in natural
populations
Disadvantages: Visible
polymorphisms relatively
rare. Most genetic
variation not so easily
observed. Genetic basis of
variation can be complex,
and is not necessarily easy
to determine.
Molecular Polymorphism
Protein variation
DNA sequence variation
Protein allozymes: electrophoretic variants of
proteins produced by different alleles at
protein-colding genes.
Protein Electrophoresis Gel
Molecular Polymorphism
negative
anode
positive
anode
Well
s
Protein
migrates
Protein electrophoresis
How variable are proteins?
Polymorphism = proportion of
proteins that are polymorphic
(i.e., the most common allele is <
99%):
Polymorphism
Mammals 15%
Birds 22%
Insects 33%
Plants 25%
Polymorphism
Of 71 allozyme loci surveyed in humans, 51 had
only one electrophoretic allele,the other had
two or more alleles. What is the
polymorphism of this population?
Heterozygosity
H = Proportion of individuals that are
heterozygotes at a particular locus.
At 20 different loci, the heterozygosity of a
human population ranged from 0.05 to 0.53
Q: 50 people are sampled at the PGI locus; 35
of them have two different alleles, and 15 of
them have only one allele. What is the
heterozygosity of this locus?
Advantages: inexpensive;
markers are co-dominant.
Disadvantages: Only
reveals small proportion of
DNA variation. Many DNA
variants do not result in
changes in amino acid
sequence (e.g.,
synonymous substitutions).
Some changes in amino
acid sequence do not
result in changes in
mobility on the gel.
Using protein polymorphism to study
population genetic structure and evolution
DNA Variation
RFLP
RAPD
AFLP
VNTR
Sequencing
Restriction Fragment Length
Polymorphism (RFLP)
Enzymes cut DNA at specific sequences
Restriction sites are often palindromes:
6-cutter GAATTC 4-cutter TCGA
CTTAAG AGCT
Can be used for species or
population identification
• Human mt DNA has 2 EcoR1 restriction
sites
• Honey bee mt DNA has 5 restriction
sites
Q: How many bands would you see on a gel after
digesting human and honey bee mtDNA with the
EcoR1 restriction enzyme? Hint: mtDNA is
circular in both humans and honey bees.
Can be used for analysis of
relatedness
“Ladder”
Advantages: variants are co-dominant;
measures variation at the level of DNA
sequence, not protein sequence.
Disadvantages: labor intensive; requires
relatively large amounts of DNA
Using RFLP polymorphism to study
population genetic structure and evolution
PCR based methods:
don’t need much DNA
• RAPD: randomly amplified polymorphic
DNA
• AFLP: amplified fragment length
polymorphism
• VNTR: variable number tandem
repeats; including microsatellites
PCR: polymerase chain
reaction
3’
5’
5’
3’
RAPD: randomly amplified
polymorphic DNA
Size sorted
RAPDs
Advantages: fast, relatively inexpensive,
highly variable.
Disadvantages: markers are dominant.
Presence of a band could mean the
individual is either heterozygous or
homozygous for the sequence--can’t tell
which. Data analysis more complicated.
Questions:
1. Is the locus represented by
band “B” polymorphic?
Band A?
2. Is individual 232 a
homozygote or
heterozygote for alleles
represented by band “B”?
What about individual
236?
3. Does band “B” represent a
longer or shorter DNA
fragment than band “A”.
B
RAPD Analysis
AFLP: amplified fragment
length polymorphism
Digestion of DNA with
two enzymes
Ligation of adapters
to fragment ends
Primers
complementary to
adapters and to 3’
region of some of the
fragments
Sticky ends
AFLPs
AFLPs
Advantages: fast, relatively inexpensive,
highly variable.
Disadvantages: markers are dominant.
Presence of a band could mean the
individual is either heterozygous or
homozygous for the sequence--can’t tell
which.
RAPDs and AFLPs
Good for distinguishing between
populations
Often used for trait mapping studies
because they are variable between the
populations that are crossed
VNTR: variable number
tandem repeats
• Non-coding regions
• Several to many copies of the same
sequence
• Large amount of variation among
individuals in the number of copies
Microsatellites
• Not a tiny orbiting space craft
• Most useful VNTRs
• 2, 3, or 4 base-pair repeats
• A few to 100 tandem copies
• Highly variable
• Many different microsatellite loci
(1000s) in any species
Microsatellites
• Design primers to flanking regions
Microsatellite Gels
Microsatellites
Advantages: highly variable, fast evolving,
co-domininant
Relatively expensive and time consuming
to develop
Microsatellites
Used for within-
population studies;
not as much for
between-
population studies
b/c they evolve too
fast
Paternity analysis
and other studies
of kinship
Microsatellites
Questions:
1. Is the locus
represented by the
bands at the arrow
polymorphic?
2. If it is polymorphic, how
many individuals are
heterozygous?
3. How many individuals
are homozygous for
the “short” allele?
Sequencing
Sequencing
Often used for phylogenetics (especially
sequences of mitochondrial genes).
Also used for studies of molecular
evolution (e.g., compare rates of
synonymous vs. non-synonymous
substitution)
Sequencing
Q: What’s the DNA sequence?

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