population genetics

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