Ecological Genetics

1
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

2
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.

3
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

4
Discrete variation between populations
Rat snakes, Elaphe obsoleta
5
Between-population variation
Salmanders, Ensatina eschscholtzii
6
Within-population variationpolymorphism
Hawaiian Happy-face spiders, Theridion grallator
7
Within population sex-linked visible polymorphism
Stag beetles, Lucanus cervus
8
Within-population sex-linked visible polymorphism
Trinidadian guppies, Poecilia reticulata
9
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.

10
Molecular Polymorphism

• Protein variation
• DNA sequence variation

11
Molecular Polymorphism
Protein allozymes electrophoretic variants of
proteins produced by different alleles at
protein-colding genes. Protein
Electrophoresis Gel
12
Protein electrophoresis
13
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

14
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?

15
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?

16
Using protein polymorphism to study population
genetic structure and evolution

• 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.

17
DNA Variation

• RFLP
• RAPD
• AFLP
• VNTR
• Sequencing

18
Restriction Fragment Length Polymorphism (RFLP)

• Enzymes cut DNA at specific sequences
• Restriction sites are often palindromes
• 6-cutter GAATTC 4-cutter TCGA
• CTTAAG AGCT

19
(No Transcript)
20
(No Transcript)
21
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.
22
Can be used for analysis of relatedness
Ladder
23
Using RFLP polymorphism to study population
genetic structure and evolution

• 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

24
PCR based methodsdont need much DNA

• RAPD randomly amplified polymorphic DNA
• AFLP amplified fragment length polymorphism
• VNTR variable number tandem repeats including
  microsatellites

25
PCR polymerase chain reaction
3 5
5 3
26
RAPD randomly amplified polymorphic DNA
Size sorted
27
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--cant tell which. Data analysis more
  complicated.

28
RAPD Analysis

• 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
29
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
30
Sticky ends
31
AFLPs
32
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--cant tell which.

33
RAPDs and AFLPs

• Good for distinguishing between populations
• Often used for trait mapping studies because they
  are variable between the populations that are
  crossed

34
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

35
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

36
(No Transcript)
37
Microsatellites

• Design primers to flanking regions

38
Microsatellite Gels
39
Microsatellites

• Advantages highly variable, fast evolving,
  co-domininant
• Relatively expensive and time consuming to develop

40
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

41
Microsatellites

• Questions
• Is the locus represented by the bands at the
  arrow polymorphic?
• If it is polymorphic, how many individuals are
  heterozygous?
• How many individuals are homozygous for the
  short allele?

42
Sequencing
43
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)

44
Sequencing
Q Whats the DNA sequence?