1. Basic premise: genetic variation is valuable for fitness

2. What is variation? described at the individual level as homozygous, heterozygous AA Aa described at the population level as monomorphic, polymorphic

3. Measurement of variation # alleles per locus proportion of loci that are polymorphic in a population (P) = # polymorphic loci number loci examined proportion of loci that are heterozygous among all genes (H) = % of genes at which average individual is heterozygous

4. Measurement of variation P H Aves (birds)0.100.043 Mammalia0.150.036 Teleosts (fishes)0.150.051 Reptilia0.220.047 Plants0.260.071 Insecta0.330.081 Invertebrata0.400.100 from Nevo 1978

5. What is fitness? = relative ability of a genotype, or individual, to survive and reproduce

6. Basic premises more offspring are produced than will survive or reproduce individuals differ in their ability to survive and reproduce some of these differences are genetically based at reproductive age, genotypes that promote survival, or production of more offspring, will be more abundant in the population and will passed on disproportionately It is very difficult to distinguish differences in fitness among genotypes from ‘accident’ or other factors

7. Evidence that variability is important? centuries of breeding studies – hybrid vigor heterosis – enhancement of fitness due to increased heterozygosity

8. Evidence : –growth rate of Coot clam decreased after genetic bottleneck (loss of variation) (Koehn et al. 1988; Meffe and Carroll p.168) –efficiency of oxygen intake in American oyster decreased (Koehn and Shumway 1982) –Florida panther: sperm defects, cowlicks, kinked tails, cryptorchidism – reduced after increasing diversity through outbreeding (Pimm et al. 2006) Evidence that variability is important?

9. Chinook salmon: 82% of outbred salmon resistant to whirling disease - 56% of inbred salmon resistant absence of 3 alleles resulted in complete susceptibility to whirling disease Arkush, D. K., et al. 2002. Can. J. Fish. Aquat. Sci. 59:159-167.

10. MHC (major histocompatibility complex) - immune system protects by recognition of ‘non-self’ proteins (e.g., graft rejection) - most highly variable portion of genome

11. Tasmanian devil (Sarcophilus harrisii) currently ~ 10,000-100,000 Eliminated from mainland Australia ~ 600 yrs ago Protected in Tasmania in 1941

12. Devil facial tumor disease (DFTD) transmissible tumor, spread by biting tumors spread by allografts, genetically identical (clonal) DFTD is recent (~10 yrs) – but not recognized as non-self by MHC Siddle et al. 2007. Transmission of a fatal clonal tumor by biting occurs due to depleted MHC diversity in a threatened carnivorous marsupial. PNAS 104:16221-16226

13. ‘Markers’ of low individual heterozygosity developmental instability fluctuating asymmetry

14. ‘Markers’ of low individual heterozygosity cutthroat trout in hatchery vs. wild ( Leary et al. 1985 ) 57% reduction in # polymorphic loci 29% reduction in average # alleles per locus 21% reduction in average heterozygosity per locus of 51 fish: –10 fish missing one pectoral fin –3 fish missing 2 fins –many had deformed vertebral columns

15. Plants Inverts. Verts. Overall specialists0.04 0.06 0.04 0.05 generalists0.08 0.15 0.07 0.11 Genetic variation present in specialists vs. generalists Heterozygosity as a predictor of adaptability example: zebra musselscounter-example: Asian clam

16. What are the consequences of absence of variation? yellow perch elephant seal David Smith, UCMP

17. What are the sources of variation? mutation – rare!! approx. 10 -6 mutations per gamete per generation > 100 to 1,000 generations to restore variability via mutation

18. What are the sources of variation? mutation – rare!! approx. 10 -6 mutations per gamete per generation sexual reproduction – blending of genes, and rearrangement of genes

19. Distribution of variation : Variation is present within individuals among individuals within populations among populations

20. Source of variation Populations withinbetween AA, AA, AA AA, AA, AA AA, AA, AA nonenone AA, AA, AA BB, BB, BB DD, DD, DD noneall AA, AB, CD AA, AB, CD AA, AB, CD all none AA, AB, AD AB, BC, CC DD, BB, AC presentpresent

21. Factors that reduce variation within populations Short-term small population size –genetic bottleneck – a dramatic collapse in numbers –founder effect – a very small number of colonists that originate a new population

22. Factors that reduce variation within populations Short-term small population size –genetic bottlenecks –founder effect N TIME RECOVERY CRASH bottleneck

23. Factors that reduce variation within populations Short-term small population size –genetic bottlenecks –founder effect TIME POPULATION SIZE

24. Factors that reduce variation within populations Short-term small population size –genetic bottlenecks –founder effect Elephant seals: N = unknown (thousands) 20 30,000 late 1800s 1890 1960s 24 loci examined all monomorphic David Smith, UCMP

25. Factors that reduce variation within populations Short-term small population size –genetic bottlenecks –founder effect Huntington’s chorea - neural function decay, leading to death - frequent in South Africa, and near Lake Maracaibo, Venezuela - single gene, dominant allele - founder effect - weak selection

26. Factors that reduce variation within populations Short-term small population size –genetic bottlenecks –founder effect THE BAD NEWS: Effects of small population size are cumulative – a population is, in effect, going through a serious bottleneck every generation – perennial low numbers erode genetic variation THE GOOD NEWS: A single bottleneck generation will not eliminate most of the genetic variation in a population Crucial issue is whether the population remains small or grows to a relatively large size

27. How to avoid the consequences of bottlenecks: increase population size rapidly Issues with intrinsic rate of increase taxonomic biases age at maturity fecundity

28. Factors that reduce variation within populations Short-term small population size –genetic bottlenecks –founder effect Retention of genetic variation in a small population of constant size: # generations N1510100 27524 6<<1 691.76542<<1 10957760<1 2097.58878 8 5099959036 10099.597.59560

29. Factors that reduce variation within populations Short-term small population size –founder effect –genetic bottlenecks Long-term small population size –genetic drift –inbreeding

30. Factors that reduce variation within populations genetic drift: random loss of variation due to stochastic events

31. Factors that reduce variation within populations genetic drift Qualitatively genetic variance (or heterozygosity) will be lost

32. Factors that reduce variation within populations genetic drift Quantitatively specific alleles will either be lost or retained : Average number out of 4 alleles retained: original allele frequency before founder event N 0.7, 0.1, 0.1, 0.1 0.94, 0.02, 0.02, 0.02 503.993.6 103.632.0 22.021.23 11.481.12

33. Factors that reduce variation within populations genetic drift Loss of alleles is more critical than loss of variation (heterozygosity) WHY?

34. http://darwin.eeb.uconn.edu/simulations/drift.html

35. Small populations of constant size always lose heterozygosity through time More alleles are lost in populations founded by small numbers of individuals –The smaller the population is, the more rapidly heterozygosity is lost Alleles which have low frequencies in the original population tend to be lost much more easily in the founder population than alleles with high frequencies