Chapter 15. Population Genetics
Population Genetics is the study of the distribution of genes in a population and of how the frequencies of genes and genotypes are maintained or changed.
A population is a localized group of individuals belonging to the same species. A species is a group of organisms capable of in- terbreeding and producing fertile offspring, and separated from other such groups with which interbreeding does not (normally) happen.
Human Genetic Variation
Although the human chromosomes and loci they contain are identical in all members of the human species, allele frequen- cies at many loci vary widely among population groups.
Within each population there is extensive variation, greater on the average than the mean differences between groups.
Hardy-Weinberg Law
The Hardy-Weinberg principle is a general rule for allelic behavior in a large population with random mating. It states that in an infinitely large, randomly mating population in which selection, migration, and mutation do not occur, the frequencies of alleles and genotypes do not change (that is, they are at equilibrium) from generation to generation.
In the simplest case of a single locus with two alleles: the dominant allele is denoted A and the recessive a and their frequencies are denoted by p and q; freq(A)=p; freq(a)=q; p+q=1. If the population is in equilibrium, then we will have freq(AA) = p2 for the AA homozygotes in the population, freq(aa) = q2 for the aa homozygotes, and freq(Aa) = 2pq for the heterozygotes.
A better, but equivalent, probabilistic description for the HWP is that the alleles for the next generation for any given individual are chosen randomly and independent
of each other. Consider two alleles, A and a, with frequencies p and q, repectively, in the population. The different ways to form new genotypes can be derived using a Punnett square, where the fraction in each is equal to the product of the row and column probabilities.
These frequencies are called Hardy–Weinberg frequencies (or Hardy–Weinberg proportions). This is achieved in one generation, and only requires the assumption of random mating with an infinite population size.
It is important to understand that the infinite population size is a theoretical category and the Hardy-Weinberg principle is a theoretical model. That is, the Hardy–Weinberg equilibrium is impos- sible in nature. Genetic equilibrium is an ideal state that provides a baseline against which to measure change.
The following factors affect the Hardy-Weinberg equilibrium:
Small population size
Non-random mating (assortative mating, inbreeding) Selection
Mutation
Migration, gene flow
Small population size can cause a random change in allele frequencies. This is due to a sampling effect, and is called genetic drift. Sampling effects are most important when population sizes are small or the allele is rare.
Random mating in human populations
In human populations, mating can be random with respect to some traits, and nonrandom for others. Mating seems to be random for such characteristics as blood type groups (not observable). Mating may be nonrandom (assortative) for traits such as skin color and height (observable).
Non-Random Mating: the Dutch’ story
(Adapted from By Richard Ingham, AFP, 2015)
The Netherlands is the land of giants: on average, its women stand almost 1.71 meters (5 feet 7 inches) tall, and its men 1.84 meters. But how the Dutch became the world’s tallest people has been somewhat of a mystery. After all, two centuries ago they were renowned for being among the shortest. What happened since then?
A popular explanation is nutrition — a calorie-stuffed diet rich in meat and dairy products. But that can’t be the whole story, experts say. Other European countries, too, have enjoyed similar prosperity and a rise in living standards, yet their citizens have not shot skywards as much.
The average male height in the Netherlands has gained 20 cm (eight inches) in the last 150 years, according to military records. By comparison, the height of the average American man has risen a mere six cm over the same period.
Researchers led by Gert Stulp, a specialist in population health at the London School of Hygiene and Tropical Medicine, combed a Dutch database for clues. Called LifeLines, the record contains exhaustive detail about the lives and health of more than 94,500 people who lived in the northern the Netherlands from 1935 to 1967. In this three-decade snapshot, the people who had the most children were tall men, and women of average height, the team found. For example, the most fertile men were 7 cm above the average height. Statistically, they had 0.24 more children on average than the least fertile men, who were about 14 cm below the average height.
Compared to counterparts in other countries where they often tended to have fewer children, taller women also reproduced more in the Netherlands. Many postponed having children until after their studies, but once they forged a successful relationship, often had a large family. The study did not involve genetic testing, but concluded from the observations that natural selection must have played a part: with time, more and more Dutch started sporting tall genes.
“Natural selection in addition to good environmental conditions may help explain why the Dutch are so tall,” said the study published in the Royal Society journal Proceedings B (Stulp et al., 2015).
“Height is very heritable — taller parents tend to have somewhat taller children than shorter parents,” Stulp told AFP by email. “Because taller individuals would have more offspring in the next generation who would be taller, the average height in that generation would a bit taller on average than the preceding generation, if all else is equal.”
There seems to be a cultural preference as well. Stulp pointed to figures showing that, in the United States, shorter women and men of average height have the most reproductive success. “There is much variation in what men and women want,” he said.
“When it comes to choosing a mate, height tends to have (only) a small effect, which is not very surprising given the many other, more important, traits people value in their mate.”
Inbreeding and the frequency of rare traits
Inbreeding describes matings between individuals who are related by descent from a common ancestor. Both assortative mating and inbreeding can bring about an increase in the frequency of both homozygous genotypes and a decrease in the corresponding heterozygous form.
Selection
Selection, in general, causes allele frequencies to change, often quite rapidly. While directional selection (a mode of natural selection in which a single phenotype is favored, causing the allele frequency to continuously shift in one direction) eventually leads to the loss of all alleles except the favored one, some forms of selection, such as balancing selection, lead to equilibrium without loss of alleles.
Mutation
Mutation will have a very subtle effect on allele frequencies. Mutation rates are of the order 10−4 to 10−8, and the change in allele frequency will be, at most, the same order. Recurrent muta- tion will maintain alleles in the population, even if there is strong selection against them.
Migration genetically links two or more populations together. In general, allele frequencies will become more homogeneous among the populations. Some models for migration inherently include nonrandom mating (Wahlund effect, for example). For those models, the Hardy–Weinberg proportions will normally not be valid.
Gene Flow
Defined as gradual diffusion of genes from one population to another by migration and mating. The process involves large population and gradual change in gene frequencies.
Classic example: transfer of genes between ethnic groups.
Ethnic Groups and Human Races
From a biological prospective, race is a synonym to population and is defined as a group of organisms that can interbreed and differs from other groups in the frequency of certain hereditary traits.
The nineteenth-century idea that there are only three human races — Caucasoid, Mongoloid, and Negroid — emerged from European folk concepts of the Middle Ages about the significance of physical differences like skin color, head shape, or type of hair. All people were thought to belong to one of these races and most authorities believed that these physical differences also implied differences in intelligence, abilities, and general merit as human beings. Some believed that such “racial” differences justified social inferiority, colonial control, and even slavery.
Louis Agassiz, a 19th-century Harvard professor of zoology and geology, is the father of scientific racism. The foundation of his racial distinction was the concept of polygenism, which assumes that different races have separate geographic and biological origins, essentially designating different races as different species. This pattern of thinking led some US politicians of the early 20th century to argue that multiracial marriages would be childless, due to biological incompatibility among human races, and those children that do get born would be a danger to society. These ideas led the Commonwealth of Virginia to outlaw marriages between “whites” and any other race, where the latter was defined as having even one drop of “non-white blood” (Virginia’s 1924 Racial Integrity Act).
The concept of race in humans is socio-political and biologically non-applicable. Genetic research has shown that human populations cannot be divided into clearly defined, biologically distinct groups. In the last 200+ years, genetic flow among different formerly isolated human populations increased and frequencies of many genetic traits became indistinguishable between individuals from different populations. Phenotypic differences began to disappear as well.
All modern humans are related to a common ancestral group that lived in Africa 100,000 years ago. We know about the latter through the research on mtDNA. Most humans who live outside of Africa today also have a small amount of genetic ancestry from our extinct biological cousins, Neanderthals and Denisovans, with whom we share common ancestry. Human evolutionary genetics is the subject of Chapter 16.
Key Takeaways
- In a large population with no external sources influencing the allelic and genotypic frequency, these frequencies remain constant from generation to generation.
- Allelic and phenotypic frequencies are affected the population size, the mating strategy, as well as on the incidence of positive or negative selection and the influx of new mutations.
