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Prioritizing Species for Conservation Efforts Hugh Possingham

Prioritizing Species for Conservation Efforts Hugh Possingham. Con Bio 23:328, TREE 24:183. Genetics 1 Outline. Why do we care about genetic diversity? Genetics 101 terminology Measuring Genetic Diversity Effective population size Genetic drift. Why do we care about genetic diversity?.

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Prioritizing Species for Conservation Efforts Hugh Possingham

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  1. Prioritizing Species for Conservation EffortsHugh Possingham Con Bio 23:328, TREE 24:183

  2. Genetics 1 Outline • Why do we care about genetic diversity? • Genetics 101 terminology • Measuring Genetic Diversity • Effective population size • Genetic drift

  3. Why do we care about genetic diversity?

  4. Important terminology

  5. DNA structure

  6. Proteins DNA Proteins RNA

  7. Nucleus Mitochondrion Two Types of DNA nDNA Biparental Inheritance MtDNA Maternal Inheritance Plants: mtDNA nDNA Chloroplast DNA Animal Cell

  8. Locus A physical location in the genome

  9. Genes: Loci that code for a protein

  10. Neutral Loci vs Loci under selection Genes are loci influenced by natural selection. Other sections of DNA with no known function are neutral.

  11. Genotype - Allelic combination at one locus or multiple loci Father’s Genotype - Aa Allele 1 Allele 2 A a Mother’s Genotype Aa A AA Aa a Aa aa Heterozygote Homozygote

  12. Other Important Terms • Monomorphic locus- • Polymorphic locus • Haploid (1n) • Diploid (2n) • Polyploid

  13. Measuring Genetic Diversity

  14. What is genetic diversity? DNA sequence differences at the same physical location Example: Sample 1 GATCC ATCGA TCTGGC A Sample 2 GATCA ATCGG TCTGAT A

  15. 11.1 A species’ pool of genetic diversity exists at three fundamental levels

  16. Techniques for Detecting Genetic Variation • Allozyme analysis - proteins • Polymerase Chain Reaction (PCR) • DNA sequencing • Microsatellite analysis

  17. DNA Analysis

  18. Polymerase Chain Reaction (PCR) Primer Target Region 1 Copy CYCLE 1 2 Copies CYCLE 2 4 Copies (Mullis 1983)

  19. DNA Sequencing C A G T

  20. Microsatellites - simple sequence repeats of 6 base pairs or less Example: GCTAATC CACACACACACACACACA TACTT GCTAATC CACACACACACA TACTT Process: 1) Amplify microsatellite loci with PCR 2) Determine genotype at each locus by 3) Separate fragments by size on a gel

  21. How do we measure genetic diversity? 3 Main Indicators are used Percent of loci that are polymorphic (P) Allelic diversity (A) or Richness (Ar) 3. Heterozygosity (H)

  22. Heterozygosity: Individual - proportion of loci with two different alleles Population - Proportion of genotypes in the entire population that are heterozygous. Aa AA aa Aa AA aa Aa Aa Aa Aa AA aa AA Aa BB cc Dd Observed Heterozygosity: 0.462 Heterozygosity: 0.50

  23. Discussion Data SetFicetola et al (2007) ME 16:1787-1797 Italian Agile Frog (Rana latastei) • 295 samples • 10 pops • 6 usat loci • Hatch rate Genetic diversity and fitness?

  24. Are all loci polymorphic? • Which population has highest genetic diversity? • Which population has the lowest genetic diversity?

  25. Sustainability Break • High school students use genetics to detect something fishy: • http://consumerist.com/5040548/high-school-students-bust-restaurants-and-grocery-stores-for-selling-mislabeled-fish

  26. Percent of Polymorphic Allozyme Loci Taxa # Species P Vertebrates 551 23% Mammals 184 19% Birds 46 30% Fish 183 21% Invert. 361 38% Gymnosperms 56 58% Monocots 80 40% Dicots 338 29% (Nevo et al 1983, Hamrick and Godt 1990)

  27. Genetic Diversity Brown Bears 8 Nuclear DNA Microsatellite Loci Population (2N) Heterozygosity Kluane NP, Yukon (102) 76% Brooks Range, AK (152) 75% Richardson Mnts, CN (238) 76% Scandinavia (760) 68% S. Canadian Rockies (110) 67% Palatuk, NWT (116) 65% NCD Ecosystem (102) 69% Yellowstone (108) 55% Kodiak Island (68) 27% (from Paekau et al. 1998, and Waits et al. 2000.)

  28. Genetic Diversity 8 Nuclear DNA Microsatellite Loci Population (2N) Heterozygosity American Black Bears S. Canadian Rockies (170) 82% La Mauricie, Quebec (64) 82% Fundy Natl. Park (22) 73% Newfoundland Is. (46) 43% (from Paetkau & Strobeck1998 ) Polar Bears W. Hudson Bay (60) 60% Beaufort Sea (104) 64% (from Paetkau, Stirling, Calvert, Strobeck 1996)

  29. Calculating Diversity - Example Microsatellite locus G1A Genotypes 188/188 188/190 190/190 190/192 Population 1 25 50 25 0 Population 2 100 Population 3 20 45 22 13 Compare Genetic Diversity Levels for 3 populations Is locus G1A polymorphic in all populations? # Alleles ? Observed He?

  30. What 4 processes influence the amount of genetic variation in populations?

  31. What is Genetic Drift? • Changes in allele frequencies caused by sampling error when individuals breed and alleles are passed to the next generation. • The smaller the number of breeders the more likely allele frequencies will change.

  32. Sampling effects = drift Gamete Pool 1 possible F1 * * 6% of F1’s outside 60/40 Gametes Draw 100 50% Small N = Strong Drift 50% * 25% of F1’s outside 6/4 Draw 10

  33. Genetic Drift in the red flour beetle at N=10, N=100 12 replicates Frankham et al 2002

  34. What is Effective Population Size? How is it different than Census Size?

  35. What is effective population size? • Size of the “ideal population” that would lose variation or ‘drift’ at the same rate observed in the real biological population.

  36. How rapidly does variation decline in a population? • Heterozygosity is lost at a rate of 1/(2Ne) per generation. • Ht = H0 [1 – 1/(2Ne)]t Ne=1000 Ne=100 Ne=10

  37. Why do we care? 50/500 rule

  38. Ne and selection: • Selection value of 0.05 is quite high….but at Ne = 10…it becomes selectively neutral

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