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Population Genetics

Population Genetics. Evolution depends upon mutation to create new alleles. Evolution occurs as a result of population level changes in allele frequencies. What evolutionary forces alter allele frequencies?. How do allele frequencies change in a population from generation

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Population Genetics

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  1. Population Genetics Evolution depends upon mutation to create new alleles. Evolution occurs as a result of population level changes in allele frequencies. What evolutionary forces alter allele frequencies?

  2. How do allele frequencies change in a population from generation to generation?

  3. Hardy-Weinberg Principle When none of the evolutionary forces (selection, mutation, drift, migration, non-random mating) are operative: Allele frequencies in a population will not change, generation after generation. If allele frequencies are given by p and q, the genotype frequencies will be given by p2, 2pq, and q2.

  4. Allele frequencies in the gene pool: A: 12 / 20 = 0.6 a: 8 / 20 = 0.4 Alleles Combine to Yield Genotypic Frequencies

  5. Our mice grow-up and generate gametes for next generations gene pool

  6. Allele frequency across generations: A General Single Locus, 2 Allele Model Freq A1 = p Freq A2 = q

  7. Inbreeding Decreases the Frequency of Heterozygotes

  8. Inbreeding Depression in Humans Inbreeding can reduce mean fitness by “revealing” deleterious recessive alleles.

  9. Probability that two alleles are identical by descent Inbreeding coefficient (F) = What is F for an individual of half sib parents? AB AB 0.5 0.5 0.5 0.5 A A B B 0.5 0.5 0.5 0.5 AA BB (0.5)4 = 0.0625 (0.5)4 = 0.0625 0.0625 + 0.0625 = 0.125

  10. Box 9B, Figure 1(2) Change of Genotype Frequencies by Inbreeding

  11. Heterozygosity and Inbreeding Heterozygosity in an inbred population Heterozygosity in a random mating population Prob. not IBD = x H F = HO (1 - F) Anytime F is greater than 0, the frequency of heterozygotes is lower in an inbred population than in a random mating population.

  12. Box 9B, Figure 2. Change of Genotype Frequencies by Inbreeding

  13. 9.10 Inbreeding depression in humans

  14. 9.11 The golden lion tamarin is a small, highly endangered Brazilian monkey

  15. 9.12 Population decline and increase in an inbred population of adders in Sweden

  16. Inbreeding increases egg failure in Parus major Can organisms avoid inbreeding depression? Mate Choice Genetic Incompatibility Dispersal

  17. Prairie chicken almost went extinct in the 1950’s. Why did fitness decrease after early efforts were implemented to conserve remnant populations?

  18. Average number of nDNA alleles per locus Illinois Illinois Other Pops in pre-bottleneck present Midwest 5.12 3.67 5.33-5.88

  19. Loss of Habitat Extinction or reduced population sizes Gene Flow - reduced / eliminated Genetic Drift and Non-random Mating Loss of heterozygosity Deleterious alleles increase in frequency Inbreeding Depression -- lowered fitness Extinction or reduced population sizes

  20. Measuring Genetic Variation in Natural Populations Historical Method: Examining protein variation via electrophoresis Modern Method: DNA sequencing and typing T T C T T C A G G G G A G G G G G T G G A A N A T A A A A A C A A A A A C C C T A C A A T G T A T A T T C A T C G C C C A T A A T C G G C T A C T T A G A C A

  21. More than one allele at 30-50% of all loci in a population. Such loci are called polymorphic. LDH-B cline in Fundulus

  22. Most populations harbor considerable genetic diversity 0.10 0.20 0.30 Heterozygosity

  23. Heterozygosity has a couple of interpretations: • Average percentage of loci that are heterozygous per individual. or • Average percentage of individuals that are heterozygous per loci.

  24. Polymorphism Polymorphism: when two or more alleles at a locus exist in a population at the same time. Nucleotide diversity: P = xixjpij considers # differences and allele frequency ij Freq (x) 1 2 3 Seq 1 G A G G T G C A A C 0.4 Seq 2 G A G G A C C A A C 0.5 Seq 3 G A G C T G G A A G 0.1 1 p12 p13 2 0.2 p23 3 0.3 0.5 P = (0.4)(0.5)(0.2) + (0.4)(0.1)(0.3) + (0.5)(0.1)(0.5) = 0.077 p12 p13 p23

  25. In Theory: Under infinite-sites model: Expectation (P  4Nem = frequency of heterozygotes per nucleotide site

  26. Nucleotide diversity is low in humans Average nucleotide diversity per site across loci

  27. Polymorphism is also estimated by: ATCCGGCTTTCGA K = 3 for-->ATCCGAATTTCGA ATTCGCCTTTCGA K= Number of segregating (variable) sites in a sample of alleles. In Theory: Expectation (K Where a = 1 + 1/2 + 1/3 +……..1/n-1

  28. Counting alleles or Genotypic frequencies (75 x 2) + (24) / (102 x 2) = 85.3 75/102 + 1/2 (24/102) = 85.3

  29. Sequencing Studies Have Revealed Enormous Genetic Diversity CFTR Locus

  30. Measuring Genetic Variation in Natural Populations Other Methods: EST approach AFLPs Microsatellites

  31. An EST is a tiny portion of an entire gene 3` UTR AAAAAAAA Exon TTTTTTTTT TTTTTTTTT Contextual Region Polymorphic Region

  32. A. t. tig. 6912 A. mex. 7909 2296 523 353 465 X. trop. 34,296 Figure 4. Venn diagram of BLAST comparisons among amphibian EST projects. Values provided are numbers of reciprocal best BLAST hits (E<10-20) among quality masked A. mexicanum and A. t. tigrinum assemblies and a publicly available X. tropicalis EST assembly.

  33. EST Projects: A quick way to obtain complete mtDNA genome sequence. Mt DNA : 22 tRNAs, 2 rRNAs, 13 mRNA Homoplasmic, maternal transmission, evolves quickly Approximately 1-2% sequence divergence / million years

  34. # SNPs per EST A. t. tigrinum A. mexicanum ~ 5% mtDNA sequence divergence

  35. Microsatellites Co-dominant marker type Found in essentially all genomes Evolve at a very high rate (10-3 - 10-4 per locus per gamete per generation) See Figure 3.19 for pict showing gel separation of microsat alleles

  36. Insertion during DNA replication mispairing during replication A G T C T A A A T C T A T A 5’ 3’ T T A G G A T C A T A T A T G T G C T T A A A G T C T A Replication inserting TA A A T C T A T A T AC A C G A A T T 5’ 3’ T T A G G A T C A T A T A T G T G C T T A A A A T C C T A G T A T A T A 5’ 3’ T T A G G A T C A T A T A T G T G C T T A A

  37. Deletion during DNA replication A A T C C T A G T A T A T A 5’ 3’ T T A G A T A TG T G C T T A A G A T A Mispairing of DNA during replication T C T A is excised Replication of DNA A A T C C T A G T A T A C A C G A A T T 5’ 3’ T T A G A T A T G TG C T T A A G A T A T C A A T C C T A G T A T A T A 5’ 3’ T T A G G A T C A T A T A T G T G C T T A A

  38. Insertion in non-replicating DNA Slipped-strand mispairing A G T C T A A A T C T A T A C A C G A A T T 3’ 5’ T T A G G A T C A T A T T T A A A T C G G T A G T C T A Excision and repair inserts TA A A T C T A T A T AC A C G A A T T 5’ 3’ T T A G G A T C A T A T A T G T G C T T A A A A T C C T A G T A T A T A C A C G A A T T 5’ 3’ T T A G G A T C A T A T A T G T G C T T A A

  39. AFLP (Amplified Fragment Length Polymorphisms) E E M M M Allele 1 Allele 2 RD of DNA Ligation of adaptors creates PCR primer recognition sequence Subsequent selective PCR allows sampling of for restriction length polymorphisms

  40. AFLP Gel

  41. Representative Molecular Approaches Genetic/Phylogenetic Resolution vs Appropriateness Clonality Parentage Populations Species Restriction Fragment Analysis * * ** *** DNA sequencing/typing overkill overkill *** *** mt DNA na na ** *** AFLPs * * * * Microsatellites *** *** ** na From Avise’s book

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