Population Genetics I.

1. Population Genetics I. Evolution: process of change in allele frequencies Natural Selection: the mechanism Ecological genetics: study of genes in natural populations What are the forces that maintain genetic diversity? Is that genetic diversity selectively neutral, or actively maintained by natural selection?

2. What IS natural selection, anyway? • Individuals within a population are different • from each other in various characteristics • These differences are heritable • Some individuals survive and reproduce more • successfully than others, based on these • heritable differences • Over time, this differential survival and • reproduction leads to altered gene • frequencies

3. Macroevolution: “Descent with modification” An Evolutionary Tree…

4. Example: Galapagos Finches Micro-evolution: changes in the genetic composition of a population from generation to generation

5. Another Example of Changing Selection I’iwi (Vestiaria coccinea) Bill shape has changed since the extinction of several of its original food plants, based on measurements of museum skins compared to birds caught recently (Smith, Freed, Lepson, and Carothers. 1995. Cons. Biol. 9: 107-113)

6. Population Genetics • Changes in gene frequency in populations • Consequences of gene flow • Consequences of small population size • Genetic drift, inbreeding, other factors • Understanding evolutionary relationships

7. Some Basic Terms and Concepts • Genes: a sequence of DNA that encodes • for a protein • Locus: position on a chromosome; may or • may not code for a protein • Allele: Alternative DNA sequence at a locus • A locus is monomorphicif there is only one • allele in the population. A locus is • polymorphic if there is more than one allele

8. Some Basic Terms and Concepts • Genotype: The overall genetic makeup of an • individual • Phenotype:The expression of the genotype. • Gene expression influenced by the • environment • Genetic drift:Changes in allele frequencies • due to chance events • If the same alleles are present at a locus, the • individual is homozygous. If the alleles are • different, the individual is heterozygous.

9. Measures of genetic diversity General diversity, He He = 1 - Σpi2 where pi is the frequency of the allele type Note that when the frequency of pi is close to or equal to 1, then He is essentially zero. This is a measure of locus variability- no assumptions on mating, etc.

10. No Selection or Drift? If population large, randomly mating... • Offspring gene frequencies depend only • on gene frequencies of parent generation • Frequencies will be at equilibrium If this is not the case, the interesting question is: WHY NOT?

11. Hardy-Weinberg Equilibrium Gene frequencies will reach an equilibrium when the following conditions are met: • Diploid organism (copy of gene from each parent) • Sexual reproduction • Non-overlapping generations • Random mating • Large population • Equal allele frequencies in the sexes • NO migration, mutation, or selection

12. Forces that can account for non-Hardy-Weinberg Equilibrium Non-random mating active sexual selection of mates “isolation by distance” Geographic structure in population (can lead to non-random mating throughout) Natural selection Some genotypes have better reproductive success and survival than others

13. Inbreeding Plant populations in particular may show a great deal of inbreeding Usually not considered advantageous *leads to a loss of genetic diversity and *increases expression of deleterious recessive genes When inbreeding causes a drop in demographic rates, it is termed “inbreeding depression”

14. AA: p2 + Fpq Aa: 2pq(1-F) aa: q2 + Fpq Complete self-fertilization: F = 1. Measuring the extent of inbreeding Inbreeding leads to a loss of heterozygosity The inbreeding coefficient, F, is a measure measures probability that an individual’s 2 alleles are identical by descent

15. Measuring the extent of inbreeding The coefficient of inbreeding for a selfing population can be calculated as: F = S/(2-S) S is the selfing rate IF we have information on the frequency of heterozygous individuals, AND we assume that the population is in equilibrium, we can calculate the selfing rate

16. F-statistics for inbreeding FIS: Inbreeding of individuals relative to their subpopulation Value is high in inbreeding populations FST: Measures whether individuals more similar to subpopulation than total set of subpopulations Increases with increasing isolation

17. Genetic Drift • Defined as the random fluctuation in allele • frequencies • Survival of new mutations can fail due to • chance events • Particularly important in small populations: • elimination or fixation of alleles possible • solely due to chance

18. Genetic Drift • Time needed to fix or eliminate allele a • function of population size • Effective population size (Ne) • size of idealized popn that loses genetic • diversity at same rate as real population • Ne almost always smaller than real N

19. Consequences of population subdivision and movement of genetic material • Discrete patches, or demes, of genetic structure • form when populations are isolated • Associated with limited dispersal capabilities, • even in continuous populations • Isolation by distance • Movements of individuals or pollen among • populations break down formation of • demes

20. Gene Flow: animals • Animals: dispersal is the key; • isolation by distance still applies • Non-sessile animals: any age or stage could • start new population • Conservation biology: concerned with popns • either too small, or too isolated, • to maintain gene flow and genetic diversity

21. Gene Flow: plants • Genetic mixing occurs through both seed and • pollen dispersal • Gene flow therefore dependent on dispersal • mechanisms: wind patterns, animal • behavior (both pollination and seed • dispersal) • Only seeds can start new populations

22. Those rare events…. What if a few individuals- or even a single seed- founds a new population far out- side the original range, or survives a catastrophe where all other populations of the species are lost? The new population will have greatly reduced genetic diversity compared to the larger populations

23. Bottlenecks and Founder Events A bottleneck: population reduced to a tiny fraction of its former size, thus eliminating much of its former genetic diversity.

24. Bottlenecks and Founder Events A founder event occurs when one or a few individuals establish an isolated population This is of particular concern in conservation biology, and captive breeding programs British field cricket: 12 individuals Snow Leopard: 7 individuals Puerto Rican Parrot: 13 individuals (Frankham et al. 2002)