1. Salit Kark Department of Evolution, Systematics and Ecology The Silberman Institute of Life Sciences The Hebrew University of Jerusalem Conservation Biology (Ecology) Lecture 4 November 2009

2. Loss of genetic variability has multiple aspects specific alleles will either be lost or retained (maintained) genetic variance (or heterozygosity) will be lost

3. Probability that alleles are lost in a “founder” population can be described by the following equation:

4. E = m - (1 - Pj) # of alleles left at a locus after foundation 2N # of original alleles at a given locus # of founders frequency of each allele Loss of Alleles

5. 4 E = 4 - (.0081 +.6561 +.6561 +.6561) = 2.0236 alleles left E = m - (1 - Pj) 2N # of original alleles at a given locus # of alleles left at a locus Let m be 4 allele freq =p1= 0.70 p2 = p3 = p4 =0.10 N = 2 (two founders) E = 4 - (1-.10) =.6561 (1-.10) =.6561 (1-.70) =.0081 - little influence - large influence 2N

6. AVERAGE # OF ALLELES RETAINED # INDIVIDUALS IN SAMPLE (N) P1=.70, P1=.94, P2=P3=P4=.10 P2=P3=P4=.02 1 1.48 1.12 2 2.02 1.23 6 3.15 1.64 10 3.63 2.00 50 3.99 3.60 >>50 4.00 4.00

7. Two things are clear from this example: 1. More alleles are lost in populations founded by small numbers of individuals 2. Alleles with a high frequency have relatively little influence, while alleles with low frequencies have considerable influence

8. Heterozygosity (H) Approximation of the proportion of heterozygosity remaining following the sudden reduction of a large population can be described by the following equation:

9. H f = (1 - ) H or 1 2N # founders Heterozygosity remaining Original heterozygosity

10. # % of original percentage founders heterozygosity lost remaining 1 50% 50% 2 75 25 6 91.7 8.3 10 95 5 20 97.5 2.5 50 99 1 100 99.5 0.5 For any size of H Original

11. The expected proportion of variation remaining after t generations can be calculated by: Ht = (1 - ) Hor 1 2N t Heterozygosity retained after t generations # generations # individuals original heterozygosity

12. % Genetic Variance H remaining after t generations Pop Size (N) 1 5 10 100 2 75 24 6 <<<1 6 91.7 65 42 <<1 10 95 77 60 <1 20 97.5 88 78 8 50 99 95 90 36 100 99.5 97.5 95 60

13. So, the following conclusions can be drawn: Small populations of constant size will lose heterozygosity through time The smaller the population is, the more rapidly heterozygosity will decline The higher the number of generations a population of small size is bred the more heterozygosity is lost

14. During Bottlenecks… the loss of alleles, especially rare ones, is much greater than the loss of heterozygosity

15. Rare allele freq. is 10% q 2 =.01 2pq =.18 Rare allele freq. is 1% q 2 =.0001 2pq =.02

16. Changes following the foundation (or reduction in size) When population sizes are low, a population is, in effect, going through a serious bottleneck every generation, and the effects are cumulative…

17. Factors affecting population genetic diversity Population structure, size, sex ratio etc… Dispersal and gene flow in or out of the population Rates of various processes, (e.g., mutation) Recombination (creates new combinations of existing diversity) Selection Genetic Drift more…

18. Various genetic variability estimates and markers can be used, such as: Allozymes Sequencing (genes and others) mDNA, nuclear DNA Microsatellitles and many more… …which show different patterns of diversity…

19. Clegg, S.M., S.M. Degnan, J. Kikkawa, et al. 2002. Genetic consequences of sequential founder events by an island- colonizing bird. PNAS 99:8127-8132 FOUNDER EFFECTS silvereye (Zosterops lateralis)

22. They chose to work with allelic variation at six microsatellite loci They found that allelic diversity gradually declined with repeated colonizations of new islands. The individual reductions are small, but the cumulative changes are large. From first to last in the sequence of recent colonizations, the mean number of alleles per locus dropped by almost half.

23. Because the last population in the sequence is the youngest, one cannot explain this result by long-term genetic drift. Instead, the pattern seems to reflect a small loss of alleles at each colonization, although hardly on the scale envisaged in the original formulation of the founder effects model. More in paper…..

24. Effective Population Size UP to now – we made the assumption that the number of males and females contributing to each subsequent generation is the same

25. If the sex ratio is not 1:1 for each generation then the population loses genetic variability more rapidly This is because the “effective number” of individuals is smaller than the actual number of individuals in the population

26. Effective Number can be calculated as follows: Ne = 4Nm * Nf Nm + Nf Nm + Nf # breeding females females # breeding males Effective Number

27. For a sex ratio of 1 male : 9 females in a population of 100 animals 4(10 X 90) 4(10 X 90) 10 + 90 10 + 90 = 36 Ne =

28. Which means that a population of 100 individuals, consisting of 10 breeding males and 90 breeding females would lose genetic variability as rapidly as a population consisting of only 18 males and 18 females or 36 individuals

29. When do we want to include population genetics in conservation considerations?

30. Many possible inferences from population genetic studies that are important for conservation: Effective population size Inbreeding/selfing Mating success Bottlenecks Time of isolation Migration/dispersal