1. Biodiversity IV: genetics and conservation

2. Questions
What is heterozygosity, and how does it represent genetic diversity?
What is the 50/500 rule for conserving populations?
What factors influence effective population size?
How is genetic diversity used for descriptive vs. functional goals in conservation?

5. Florida panther Lowest variation of 31 panther spp in N and S America
Allozyme polymorphism
4.9% vs % at 41 loci
Vs. museum specimens of Florida panther
1.2 vs. 2.3 alleles per locus

6. Florida panther
N = ?
Allozyme DNA
He He
Main population
Introgressed population
W’rn US
Other cats
Inbreeding depression: abnormal sperm, cardiac abnormalities, susceptibilty to infectious diseases, cowlicks

7. Florida panther update
35 new kittens, 27 mortalities ( )

8. Heterozygosity
Genes can exist in many forms called alleles (big B, little b; dominant vs. recessive)
Alleles are specific to genetic loci = region of DNA
Heterozygosity is the proportion of diploid genotypes in a population composed of two different alleles
If alleles are identical in an individual, that individual is homozygous

9. How is genetic diversity measured?
At sampled loci (by allozymes, DNA)
Polymorphic vs. fixed (after fixation), Polymorphism
Because of rare mutations, employ arbitrary cut-off (e.g., most dominant allele <99% or <95% frequency)
Heterozygosity, Ho (observed) and He (expected heterozygosity)
Average heterozygosity
Proportion heterozygosity retained
Allelic diversity, Average allelic diversity, Effective number of alleles

10. Genetics are used in two basic ways in conservation biology
Descriptive genetics
A tool for understanding ecological and evolutionary patterns
Functional genetics
Used as a proxy for endangerment (e.g., low heterozygosity is a problem)

11. Descriptive Genetics Resolve taxonomy
Phylogeny in conservation value
Evolutionarily Significant Units (ESUs)
Detect mating systems, parentage, migration, gene flow, hybridization
Understand historic distribution and potential for reintroduction from museum specimens
Choose material for reintroduction, including geographic pattern and genetic diversity
Forensics
Understand pattern: genetic diversity within and between population

12. Functional genetics As Area , spp As N , genetic diversity
Loss on sampling
Ongoing loss (genetic drift)
Function for fitness, evolutionary adaptation

13. Genetic diversity is said to be functional in conservation because:
Genetic diversity is correlated with short-term fitness.
Genetic diversity is correlated with long-term evolutionary potential.
Fitness is defined as the “lifetime reproductive success of a genotype relative to other genotypes”.

14. Effective population size (Ne)
N = number of individuals in a population
Are inds equal in their capacity to increase population size/heterozygosity?
too old to reproduce
can’t find a mate
UNEQUAL GENETIC UNIQUENESS
Ne/N ranges from 0.02 to 0.4 with mean of ~0.1 (Frankham 1995); thus genetic changes are contributed by only about 1/10 of the individuals!

15. What affects Ne?

16. Nf = number of females; Nm = number of males
What affects Ne?
Unequal sex ratio
Ne = 4(Nm)(Nf) / (Nm + Nf)
Nf = number of females; Nm = number of males

17. What affects Ne? Ne = (4N – 2)/(Vk + 2) 2. Variance in family size
Variation in family size occurs when some pairs have no or very few offspring and others have large family sizes.  The formula tells us that the effective population size decreases as the variance in family size increases above 2
Ne = (4N – 2)/(Vk + 2)
Vk = variance in family size
Why does family size variance matter?

18. What affects Ne? Ne = t/Σ (1/Nei)
3. Variance in population size through generations
Ne = t/Σ (1/Nei)
Nei = effective population size for generation I;
t = number of generations

19. Average value = 45 (wrong answer)
What affects Ne?
3. Variance in population size through generations
For example: what is Ne for a population with 10, 100, and 25 individuals over the course of three generations?
Average value = 45 (wrong answer)
Ne = 3 / (1/10 + 1/ /25) = 20

20. Genetic diversity = Ne? Ht/Ho = e-t/2Ne
Because we can estimate how genetic frequencies should change with certain Ne, we can flip the equation around and estimate Ne from the observed change in heterozygosity:
For example, the northern hairy wombat had retained 41% of its original heterozygosity over 12 generations.  From this data, Ne was calculated as 6.7
Ht/Ho = e-t/2Ne
Ht/Ho = ratio of current (Ht) to prior (Ho) heterozygosity
t = number of generations

21. Genetic drift
The genes of one generation are a sample of the genes of the previous generation.  If that sample is small, it will deviate from the previous generation by chance. 
Given time, small populations will become homozygous—fixed for particular alleles. 

22. Genetic drift Rare alleles are more likely to be lost.
If population size is small, drift may play a bigger role than selection in allele frequencies, so that the traits that become fixed are not necessarily the ones that convey highest fitness.

23. 50/500 Rule – Soule and Frankel (1980)
(based on mutation rates in Drosophila)
50 reproductive individuals necessary to prevent losing much genetic variation over the short term
500 necessary to prevent loss over the long term
Lande (1995) suggests that 5000 individuals may be necessary

24. Why is loss of heterozygosity bad?
Inbreeding depression = higher mortality, lower reproduction in individuals sharing alleles by common descent

25. Why is loss of heterozygosity bad?
Inbreeding depression = higher mortality, lower reproduction in individuals sharing alleles by common descent
Deleterious alleles
Florida panther malformities: kinked tail, cowlick, abnormal sperm

26. Johnson et al. 2010

27. Johnson et al. 2010