Population Genetics

This is a term paper on Population Genetics submitted by the author to his course coordinator of Advanced Silviculture as per the fulfillment of assignment assign to him. This is not an accepted article from any renowned institution however, it can be an important piece of literature for the learner and reader.

Author: Ashok Bhandari

M.Sc. Forestry, IOF, Pokhara Campus, TU, Nepal.

Email: [email protected]

Evolution of Population Genetics 

Theory of Natural Selection: 

Darwin's Origin of Species, published in 1859, proposed two main ideas: first, that modern species were derived from common ancestors, and next to that the process of natural selection was the major mechanism of evolutionary change. However, Darwin could not describe the mechanism of inheritance and the transfer of fitness-enhancing traits among different generations of an organism. Darwin did later put forward a theory of inheritance, based on hypothetical entities called ‘gemmules’, but it turned out to have no basis in fact. 

Blending Theory of Inheritance: 

For a population to evolve by natural selection, the members of the population must vary. If all organisms are identical, no selection can occur. So, for selection to gradually modify a population over a long period of time, in the manner suggested by Darwin, a continual supply of variation is needed. This was the basis for Fleeming Jenkin's objection to Darwin. Jenkins' ‘blending’ theory of inheritance proposed that an offspring's phenotypic traits are a ‘blend’ of those of its parents. For example, if a short and a tall organism mate, the height of the offspring will be intermediate between the two. 

Mendel's Law of Segregation: 

Inheritance is ‘particulate’ rather than ‘blending’. Gregor Mendel experimented on two pure breeding lines of pea plants, one producing plants with round seeds, the other wrinkled seeds. Based on the findings of the experiment, he postulated that offspring inherit discrete hereditary particles (genes) from their parents, which means that sexual reproduction does not diminish the heritable variation present in the population. 

Mendel crossed the pure lines to produce F1, the first daughter generation. All the plants of F1 generation had round seeds. Mendel then crossed the F1 plants with each other to produce the F2 generation. Amazingly, about one-quarter of the F2 plants had wrinkled seeds. So the wrinkled trait had made a comeback, skipping a generation. 

Therefore, the synthesis of Darwinism & Mendelism marked the birth of modern population genetics.  

Population Genetics:  

A group of individuals of a species that can interbreed is called population. The collection of all the alleles of all of the genes found within a freely interbreeding population is known as the gene pool of the population. A gene occurring at the same place on a chromosome in two or more alternative forms is known as an allele. Every individual of the population gets their alleles from its parents and passes them on to its offspring. The genetic composition of biological populations is changed from the operation of various factors, including natural selection. The study of genetic variation within populations, which involves the study of changes in the frequencies of genes and alleles in populations over space and time is known as population genetics. 

Population genetics is the study of the variation in alleles and genotypes within the gene pool, and how this variation changes from one generation to the next. In other words, population genetics can be defined as the study of the variation in alleles and genotypes within the gene pool, and how this variation changes from one generation to the next. 

Factors Influencing Genetic Diversity (Allele Frequency):  

1. Natural Selection: Alleles for fitter organisms become more frequent. In many cases, the effects of natural selection on a given allele are directional. The allele either confers a selective advantage, or spreads throughout the gene pool, or it confers a selective disadvantage and disappears from it. 
2. Non-random Mating Patterns (Sexual selection): Alleles for more sexually attractive organisms become more frequent. 
3. Mutation: New alleles pop up due to mistakes in DNA. It is a primary source of new alleles in a gene pool, but the other factors act to increase or decrease the occurrence of alleles.  
4. Genetic Drift: Changes in allele frequency due to random chance. Migration and the population size are often responsible for genetic drift. Genetic drift occurs as the result of random fluctuations in the transfer of alleles from one generation to the next, especially in small populations formed, say, as the result adverse environmental conditions (the bottleneck effect) or the geographical separation of a subset of the population (the founder effect). The result of genetic drift tends to be a reduction in the variation within the population and an increase in the divergence between populations. If two populations of a given species become genetically distinct enough that they can no longer interbreed, they are regarded as new species (a process called speciation). 
5. Gene Flow: Changes in allele frequency due to mixing with new genetically different populations. 

Hardy-Weinberg Principle:  

G.H. Hardy and Wilhelm Weinberg independently worked & proposed this principle in 1908. This principle is regarded as the foundation of population genetics and demonstrates that Mendelian genetics works at the scale of the whole population. 

"Frequencies of alleles and genotypes in a population will remain constant over time in absence of other evolutionary influences." 

Or, the genetic variation in a population will remain constant from one generation to the next in the absence of disturbing factors. 

Assumptions: 

• No natural selection occurs and individuals reproduce at an equal rate. 
• No sexual selection.  
• No mutation in the gene of interest. 
• The population must be large. 
• No migration (no gene flow between populations and no genetic drift). 

NO SELECTION	SELECTION
In an environment without herbicide, both herbicide-resistant weeds and herbicide sensitive weeds can live and reproduce.	In an environment containing herbicide, weeds that are sensitive to herbicide die and this does not pass their genes. Weeds with the allele for herbicide resistance are selected for.

NO MUTATIONS	MUTATIONS
With no mutations, the comparison of the gene pool remains the same generation after generation, if the other conditions for Hardy-Weinberg equilibrium are also met.	Mutations change the composition of the gene pool. New alleles are introduced, and allelic frequencies change.

NO MIGRATION	MIGRATION
Isolation of a population of trees prevents changes in the gene pool due to immigration and emigration.	Immigration of alleles' pollen from a neighboring population of trees can cause a change in the composition of gene pool.

LARGE BREEDING POPULATION	SMALL BREEDING POPULATION
An earthquake that kills three people out of a population of 10 million has little effect on the composition of the gene pool.	An earthquake that kills three people out of a band of 20 individuals has a significant effect on the composition of the gene pool.

RANDOM MATING	ASSORTATIVE MATING
Coral Polyps disperse their sperm into ocean currents. Contact with an egg in another coral is completely up to chance.	Blister beetles are most likely to mate with partners of the same size.

Assumptions of Hardy-Weinberg Equilibrium

Hardy Weinberg Equation:  

Hardy-Weinberg equation can be used to estimate the frequency of alleles in a population. According to this equation, p = the frequency of the dominant allele A q = the frequency of the recessive allele a For a population in genetic equilibrium:  p + q = 1.0 (The sum of the frequencies of both alleles is 100%.) 

(p + q)2 = 1                 

So, p2 + 2pq + q2 = 1 

	Female Gamete A (p)	Female Gamete a (q)
Male Gamete A (p)	AA (p2)	Aa (pq)
Male Gamete a (q)	Aa (pq)	aa (q2)

The three terms of this binomial expansion indicate the frequencies of the three genotypes: 

p2 = frequency of AA (homozygous dominant) 

2pq = frequency of Aa (heterozygous)                

q2 = frequency of aa (homozygous recessive)     

Problem: The allele for the black coat is recessive. Determine the percent of the pig population that is heterozygous for the white coat. 

Heterozygous population

• Individuals, that are homozygous recessive, q2=?  

Four of the sixteen individuals show the recessive phenotype, so the correct answer is 25% or 0.25.  

• The frequency of recessive allele is the square root of q2. So, q= 0.5 

• The frequency of dominant allele= 1-q = 0.5 

• The frequency of heterozygotes = 2pq = 2* 0.5* 0.5 = 0.5  

i.e. 50% of the population is heterozygous. 

References: 

• Okasha, Samir. “Population Genetics.” Stanford Encyclopedia of Philosophy, Stanford University, 22 Sept. 2006, https://stanford.library.sydney.edu.au/archives/spr2009/entries/population-genetics/. 
• “Population Genetics.” University of Leicester, 1 Aug. 2017, https://www2.le.ac.uk/projects/vgec/highereducation/topics/population-genetics. 
• “The Hardy-Weinberg Equation.” Pearson - The Biology Place, http://www.phschool.com/science/biology_place/labbench/lab8/hardwein.html. 
• Wright, J. (2012). Introduction to Forest Genetics. Elsevier Science, Amsterdam.