Lecture 5: Inbreeding and Allozymes. Sept 1, 2006

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1 Lecture 5: Inbreeding and Allozymes Sept 1, 2006

2 Last Time Tandem repeats and recombination Organellar DNA Introduction to DNA in populations

3 Organelle Inheritance Organelles can be excluded from one parent's gametes during gametogenesis, fertilization, or post-fertilization (Birky 2001: Annu. Rev. Genet. 35: 125) Sutovsky et al, Biol Reprod Aug;63(2): Mammals: postfertilization. Mitochondria labeled with ubiquitin, targeted by lysozymes in oocyte cytoplasm

4 Today More DNA in populations Allozymes!

5 Expected Heterozygosity Expected Heterozygosity (H E ): a measure of the diversity of a population, assuming H-W 2pq for 2-allele, 1 locus system OR 1-(p 2 + q 2 ) or 1-Σ(expected homozygosity) more general: what s left over after calculating expected homozygosity

6 Partitioning of Diversity H E depends on how you define populations Separate Subpopulations: H S = 2pq = 2(1)(0) 2(0.5)(0.5) = 0 = 0.5 Merged Merged Subpopulations: Subpopulations: H T = T 2pq 2pq = 2(0.5)(0.5) 2(0.5)(0.5) = H T ALWAYS increases when randomlymating subpopulations are merged: Wahlund Effect This effect is quantified by the Fixation Index of Subpopulations: (F ST ) F ST = (H T -H S )/H T =(0.5-0)/0.5 =( )/0.5 = 1= 0

7 What Controls Differentiation of Populations? Mutation + Drift + +/- Selection F ST - Migration BALANCE among 4 major evolutionary forces

8 Inbreeding Coefficient Measure of Hardy-Weinberg deviations at the level of individuals Inbreeding: the fractional reduction of heterozygosity relative to a randommating population with the same allele frequencies F = (H E -H O )/H E where H O is observed Heterozygosity Question: When would F be negative?

9 Indentity by State vs Identity by Descent Alternative interpretation of inbreeding coefficient is probability that two alleles at a locus of an individual are identical by descent Alleles that look the same but have different evolutionary history are Identical by State: Homoplasy

10 Inbreeding Depression Reduced fitness of inbred offspring in normally outbred organisms Exposure of recessive deleterious alleles: example of Scandinavian Wolves Aa AA Inbreeding depression in Scandinavian wolves Liberg et al. 2005: Biology Letters 1:17-20 AA Aa Aa aa

11 Heterosis and Overdominance Flip side of inbreeding depression: heterosis: superior fitness of heterozygous individuals Overdominance is possible explanation Enhanced fitness of heterozygote due to pleiotropy (one gene affects multiple traits): differentiation of allele functions Bypass homeostasis/regulation Overdominance

12 Linkage Disequilibrium Tendency for physically linked loci to be inherited together Calculated from covariance between alleles at different loci Phenotypes will also co-vary in populations LD can be caused by inbreeding, bottlenecks, drift, suppressed recombination Are effects of heterozygous loci due to the loci themselves, or linked loci? Ldh

13 Allozymes

14 Primary Protein Structure Composed of chains of amino acids Basic and acid amino acids lend positive or negative charge to proteins Charge depends on ph of solution: low ph means positive charge for basic groups, no charge for acidic groups Lodish et al. 2004

15 Lodish et al Secondary and Tertiary Protein Structure Proteins fold into complex threedimensional secondary and tertiary structures Proteins often comprise multimeric units (quaternary structure) consisting of identical or different component polypeptides Lactate Dehydrogenase Dym et al 2000: PNAS 97:

16 Isozymes and Allozymes Mutations can cause differences in basic and acidic amino acid composition, but no change in enzyme function Small changes in primary structure can alter secondary and quaternary structure Isozymes: different forms of an enzyme Sometimes specifically refers to enzymes coded by different loci: not here! Allozymes: Allelic isozymes: different forms of an enzyme that are coded at the same locus

17 Electrophoresis Create a gel: matrix with pores through which electrolyte solution and molecules can flow Anode and cathode creates electric field Molecules move according to amount of charge and size Hydrolyzed potato starch most common for isozymes

18 Detection Isozymes dected based on enzyme action Stain contains substrate for enzyme, cofactors, and oxidized salt (dye) Lactate Dehydrogenase: Lactic Acid (substrate) NADH (cofactor) phenazine methosulfate (catalyst) Nitro-blue tetrazolium (NBT: dye) Lactic Acid -> Pyruvic Acid + e - NBT + e - -> blue precipitate Resulting pattern is zymogram

19 Zymogram Interpretation Complicated by quaternary structures of proteins Predictable banding patterns for single loci: intensity proportional to number of combinations Multiple interacting loci more complex Murphy, R.W., J.W. Sites, Jr., D.G. Buth, and C.H. Haufler Proteins: Isozyme electrophoresis. Chapter 4, pp , in: D.M. Hillis C. Moritz and B. K. Mable (eds.). Molecular Systematics, 2nd ed. Sinauer Assoc. Inc., Sunderland, Mass

20 Typical Allozyme Characteristics Allozymes are usually codominant: readily distinguish heterozygotes from homozygotes "Null alleles" do occur Moderate to low levels of polymorphism 2 to 5 alleles per locus, with one dominant allele Low H E Commonly fixed (monomorphic) within species, polymorphic between species

21 Advantages of Allozymes Cheap and relatively easy Readily interpreted Direct link to genes and genome locations Simple to extend to uncharacterized species: 'Anonymous' marker

22 Disadvantages of Allozymes Low polymorphism, much hidden genetic variation Limited numbers of loci: ~100 is maximum; usually Evolutionary relationships among alleles unclear: uncoupled from genetic mutations Selection?

23 Allozyme Applications Excellent for studies of genetic structure of populations: F ST Studies of hybridization: fixed differences between species common Polyploidy: easier to deconvolute genotypes than for other markers Heterosis and inbreeding depression

24 Example: Detection of Hybridization by Allozymes Hybridization in Crysopteris ferns TxF T F Allozymes (PGI2) confirm hybrid origin of Crysopteris fragilis x tenuis

25 Next Time Literature Discussion: Allozymes, neutrality, and heterozygosity-fitness correlations (Rachel and John)