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

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