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Population genetics.pptx

  1. Population “to a group of organisms of the same species living within a sufficiently restricted geographical area so that any member can potentially mate with any other member of the opposite sex” “refer to a group of organisms belonging to the same species” Vs World Population In population gentics
  2. The fundamental importance of population genetics is the basic insights it provides into the mechanisms of evolution, some of which are far from intuitively obvious. Many of these insights came from the work of the first generation of population geneticists, notably Fisher, Haldane, and Wright. Their mathematical models showed that, contrary to what was believed by the majority of biologists in the 1920s, natural selection operating on Mendelian variation can cause evolutionary change at rates sufficient to explain historical patterns of evolution. This led to the modern synthesis of evolution (Provine 1971). Brian Charlesworth
  3. Population Genetics When Mendel met Darwin
  4. Population Genetics Population genetics is the study of genetic differences within and among populations of individuals, and how these differences change across generations. Why study genes in populations? In natural populations: Adaptation – the ability to survive and exploit an environmental niche – involves the response of populations, not individuals In breeding populations: Genetic gain – improving the average performance of populations for desired breeding objectives – depends on selecting and breeding parents with the best genetic potential
  5. Phenotype is… The description of all traits of an individual as they concern its morphology, physiology and behaviour Phenotypic variation
  6. Gene and allele • A gene is the basic physical and functional unit of heredity, passing information from one generation to the next • An allele is any of the alternative forms of a gene that can exist at a single locus
  7. Genotype is… • The description of the complete set of genes that an individual inherits from its parents • The genotype of an individual remains unchanged throughout its life, regardless of the environment surrounding and affecting it
  8. Allele frequency • Allele frequency is the concept used to quantify genetic variation • It is defined as a measure of the commonness of a given allele in a population, that is, the proportion of all alleles of that gene in the population that are specifically this type
  9. Calculating the allele frequency • Twice the number of homozygous genotypes with that allele (because homozygotes carry two copies each of the same allele), • plus the number of heterozygous genotypes with that allele (because heterozygotes carry only one copy of a particular allele), • divided by two times the total number of individuals in the sample (because each individual carries two alleles per locus) P(A) = [2(AA) + (Aa)]/2n
  10. Calculating the genotypic frequency • This is the frequency of a given genotype in a population • The frequencies of various types of breeding systems determine the mathematical relationship between the allele and genotype frequencies AA Aa aa 200 300 500 0.20 0.30 0.50 N=1000 Genotypic frequency
  11. The Hardy-Weinberg principle • A population with random mating results in an equilibrium distribution of genotypes after only one generation, so that the genetic variation is maintained • When the assumptions are met, the frequency of a genotype is equal to the product of the allele frequencies AA Aa aa p2 2pq q2
  12. • The organism is diploid • Reproduction is sexual • Generations are not overlapping • Mating is random • Population size is very large • Migration is negligible • Mutations can be ignored • Natural selection does not affect the alleles Assumptions: Hardy-Weinberg principle
  13. Generations are not overlapping
  14. Mating is random
  15. Demonstrating the H-W principle
  16. Application of population genetics in genomic era
  17. Calculating allele frequencies: Examples • Calculating allele frequencies with a codominant marker • Calculating allele frequencies with a dominant marker • Calculating the allele frequencies with a codominant gene having multiple alleles
  18. …With a codominant marker
  19. …expected and observed genotype frequencies
  20. … with a codominant marker (>1loci)
  21. …expected and observed genotype frequencies
  22. … with a dominant marker
  23. …expected and observed genotype frequencies
  24. … with a dominant marker (>1loci)
  25. …expected and observed genotype frequencies
  26. ... with a codominant gene having multiple alleles
  27. 1966–2016: 50 Years of Molecular Population Genetics
  28. H Prashanth Babu, Scientist (SS), Genetics 1966–2016: 50 Years of Molecular Population Genetics
  29. Drosophila: Model Organism for Population Genetics • First introduced as a research tool in the early 20th century (Morgan et al. 1915; Muller 1927) • Played a crucial role in all fields of genetic analysis, including ecology, speciation, development, and also population genetics (Powell 1997) • >1000 complete genomes are available for D. melanogaster (Lack et al. 2015, 2016) • Population genomic resources are available for • 27 lines of D. simulans • 21 lines of D. yakuba • 117 pooled samples of D. mauritiana H Prashanth Babu, Scientist (SS), Genetics
  30. Population genomics resources available for four Drosophila species Sònia Casillas, and Antonio Barbadilla Genetics 2017;205:1003-1035 H Prashanth Babu, Scientist (SS), Genetics
  31. The Data: From Empirical Insufficiency to the Present Flood of Genome Variation • A primary concept of the modern evolutionary synthesis period (1930s–1960s) was the primary role of natural selection to explain evolution • Classical hypothesis: supported the role of natural selection in purging the population of most genetic variation, predicting that most loci are homozygous for the wild-type allele • Balance hypothesis: postulated that natural selection actively maintained high levels of genetic diversity in populations, and that a large proportion of loci are therefore polymorphic 1930 to 1960
  32. The allozyme era: setting the stage for the neutralist – selectionist debate Population genetics entered the molecular age with the publication of seminal articles describing electrophoretically detectable variation or allozymes i.e., proteins differing in electrophoretic mobility as a result of allelic differences in the protein sequence, which ultimately result from the existence of variation in the corresponding DNA sequence 1966
  33. The nucleotide sequence era • Before the invention of PCR amplification the first surveys of DNA sequence variation were done using restriction enzymes to detect variation at restriction sites • Restriction mapping was the starting point for the development of new summary statistics to represent genetic diversity on DNA sequences, including the nucleotide site diversity 1980
  34. The current population genomics era • First large-scale population genomics studies in D. simulans (Begun et al. 2007) • the development of next generation sequencing (NGS) technologies: deciphering of complete genome sequences of 100s of individuals • Data coming from these massive parallel sequencing methods differ from all previous variation data obtained by allozymes and Sanger sequences 2000 onwa rds
  35. The (nearly) neutral theory
  36. Thank you