730 likes | 2.16k Views
Ecological Genetics I. Discrete genetic variation: individuals can be categorized into a small number of classesPopulation genetics is the study of the amount, type, and distribution of discrete genetic variation, usually controlled by variation at one or a few genesQuantitative genetics is the study of the genetics of continuous (quantitative) traits, usually controlled by variation an many genes, and by environmental (non-genetic) variation..
E N D
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
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
5: Between-population variation
6: Within-population variation:polymorphism
7: Within population sex-linked visible polymorphism Lucanus cervus 1 (big, middle, small) ,
Lucanus cervus 2 (female) Lucanus cervus 1 (big, middle, small) ,
Lucanus cervus 2 (female)
8: Within-population sex-linked visible polymorphism
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
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: 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
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
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
22: Can be used for analysis of relatedness
23: 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
24: 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
25: PCR: polymerase chain reaction
26: RAPD: randomly amplified polymorphic DNA
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--can’t tell which. Data analysis more complicated.
28: 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”. RAPD Analysis
29: AFLP: amplified fragment length polymorphism
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--can’t 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
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