23 Population Sub-Division

Dr. Rajesh Kumar Gautam

 

CONTENTS:

 

Learning outcomes: At the end of the module the reader will know-

  • Population structure
  • Importance of population structure
  • Measuring population subdivision
  • Wahlund Effect
  • Calculation of
  • Migration and subpopulation
  • Population Subdivision in a Number of Sub-Populations or Demes
  • Wright’s “Isolation by Distance Model” of Population Structure
  • Measuring dispersal
  • Genetic Divergence among Subpopulations

 

Introduction

 

All humans around the world today are biologically quite similar despite our superficial differences. In fact, we are 99.9% genetically identical. Most of the differences between us are due to our unique individual traits and being male or female. As compared to many other kinds of animals, it is remarkable how little variation exists within our own species. There is 2-3 times more genetic variation among chimpanzees, 8-10 times more among orangutans, and thousands of times more in many insect species. Most biological anthropologists would agree that human variation is not now sufficient to warrant defining separate biological races, varieties, or sub-species. However, it very likely was in our distant prehistoric past.

 

After being 99.9% genetically identical, the Human population or the population of Homo sapiens sapiens is composed of many thousands of subpopulations, divided by geography, language and religion. Beside culturally defined stereotypes, the human population can be better divided into a number of sub-populations on basis of objective biological criterion.

 

In order to better understand the true patterns of human variation, biological anthropologists have gathered detailed data about genetically inherited traits. Most of this work has been done with blood typing, but DNA sequence comparisons are now providing an even more detailed understanding of human biological diversity.

 

Population division is made on the basis of a number of external and internal physical characteristics. The external physical characteristics are phenotypic characters, which are mostly adaptive in nature, but the internal physical characteristics are genotypic characters, which are strictly hereditary and non-adaptive.

 

A major division of human population is defined as a group of people with certain common inherited features that distinguish them from other groups of people. All men of whatever type or division are currently classified by the anthropologist or biologist as belonging to the one species, Homo sapiens sapiens. This is another way of saying that the differences between human sub-division are not great, even though they may appear. All division of mankind in the world can interbreed because they have so much in common. Earlier workers were divided whole of human population in the following groups:

 

1.      Caucasian,

 

2.      Mongoloid,

 

3.      Negroid, and

 

4.      Australoid.

 

Population Structure

 

In population genetics, usually a population is considered as being composed of several sub populations and can be referred to as local populations, or demes. In many populations, however, there may not be any obvious individual populations or substructure at all, and the populations are continuous. However, even in effectively continuous populations, different areas can have different gene frequencies, because the whole is not panmictic.

 

Population sub-structure is almost universal among organisms. Many organisms naturally form sub-populations in the form of herd, flocks, colonies, or other types of aggregations. Population subdivision is a result of some genetic differentiation, which has resulted from natural selection favoring different genotypes in different subpopulations, but it may also result from random processes in the transmission of alleles from one generation to the next or from chance differences in allele frequency among the initial founders of the sub-populations (Hartl and Clark, 1997).

 

In case of inbreeding or selection or migration or genetic drift the populations have deviations from Hardy-Weinberg proportions, or deviations from panmixia. This dynamics of sub division of populations is also known as population structure.

 

Importance of Population Structure

 

Population structure has profound implications. Subdivision breaks up a population into smaller units that are each genetically independent to some degree. One consequence is that each subpopulation has a smaller effective population size than the effective size of the entire population if there were random mating. The genetic variation found in a single large panmictic population and a population subdivided into many smaller demes is organized in a different manner. Think of the simple case of a diallelic locus. A single large population may take a very long time to experience fixation or loss due to genetic drift and thus maintain both alleles. In a highly subdivided population each deme may quickly reach fixation or loss, but both alleles can be maintained in the overall population since half of the subpopulations are expected to reach fixation and half loss for a given allele (Hamilton 2009). Processes that cause population structure can also be thought of as both creative and constraining in evolutionary change (Slatkin 1987). The genetic isolation among demes caused by subdivision can prevent novel and even advantageous alleles from spreading throughout a population. But, at the same time, genetic isolation allows subpopulations to evolve independent allele frequencies and maintain unique alleles as is required for genetic adaptation to local environments under natural selection.

 

Further, Population structure allows populations to diversify. If populations are subdivided, they can evolve apart, somewhat independently. This is the reason why population structure is a very important part of evolutionary genetics.

 

Population structure and migration interferes with natural selection and drift to allow diversification. In this way a population or meta-population is divided into sub-population because of:

 

·         Natural Selection

 

·         Migration

 

·         Genetic drift, and

 

·         Inbreeding

 

Measuring population subdivision

 

The genetic difference between two populations is measurable. In genetics, the term F generally stands for “inbreeding’’, which tends to reduce genetic variation in the population. Genetic variation can be measured by heterozygosity, and so F generally expresses a reduction in the heterozygosity in the population.  is the reduction in heterozygosity in subpopulations compared to the total population of which they are part.

 

To estimate , following steps are taken:

 

1.      Finding the allele frequencies for each subpopulation.

 

2.      Finding the average allele frequencies for the total population.

 

3.      Calculation of the heterozygosity () for each subpopulation.

 

4.      Calculation of the average of these subpopulation heterozygosities. This is .

 

5.      Calculation of the heterozygosity based on the total population allele frequencies. This is .

 

6.      Finally, the calculation of .

 

This can be further elaborated by Wahlund effect.

 

Wahlund Effect

 

When an organism has two different alleles at a locus is called heterozygosity. This heterozygosity in a population is a cause to divide a population into sub-populations. In this way, the heterozygosity, in a population is caused by sub-population structure. If two or more subpopulations have different allele frequencies then the overall heterozygosity is reduced, even if these subpopulations are in the Hardy-Weinberg equilibrium. The underlying causes of this population subdivision could be geographic barriers to gene flow followed by genetic drift in the subpopulations.

 

In large populations which contain sub-populations there are fewer homozygotes than in the average for the set of subdivided populations. This is a general, and mathematically automatic, result. The increased frequency of homozygotes in subdivided populations was first demonstrated in 1928 by a Swedish geneticist Sten Wahlund and the phenomenon is popularly known as Wahlund effect.

 

It  can   be   further   elaborated   by   an   example: Suppose there is   a opulation P, with allele frequencies of A and a given by p and q respectively (). Suppose this population is split into two equally-sized subpopulations, and , and that all the A alleles are in subpopulation and all the a alleles are in subpopulation (this could occur due to drift). Then, there are no heterozygotes,  even though the subpopulations are in a Hardy-Weinberg equilibrium.

 

To make a slight generalization of the above example, let  and  represent the allele frequencies

of A in  and   respectively (and  and  likewise represent a).

 

Let the allele frequency in each population be different, i.e. .

 

Suppose each population is in an internal Hardy–Weinberg equilibrium, so that the genotype frequencies AA, Aa and aa are p2, 2pq, and q2 respectively for each population.

 

Then the heterozygosity () in the overall population is given by the mean of the two:

 

Figure. Showing Wahlund Effect (After Hamilton, 2009)

 

The Wahlund effect may be generalized to different subpopulations of different sizes. The heterozygosity of the total population is then given by the mean of the heterozygosities of the subpopulations, weighted by the subpopulation size.

 

The Wahlund effect has a number of important consequences:

 

1. We have to know about the structure of a population when applying the Hardy-Weinberg principle to it, otherwise there may seem to be more homozygotes than expected from the Hardy-Weinberg principle. We might then suspect that selection, or some other factor, was favoring homozygotes. In fact both sub-populations are in perfectly good Hardy-Weinberg equilibrium and the deviation is due to the unwitting pooling of the separate populations.

 

2. A second consequence of the Wahlund effect is that when a number of previously subdivided populations merge together, the frequency of homozygotes will decrease. In humans, this can lead to a decrease in the incidence of rare recessive genetic diseases when a previously isolated population comes into contact with a larger population. The recessive disease is only expressed in the homozygous condition, and when the two populations start to interbreed, the frequency of those homozygotes goes down.

 

The calculation of  can be understood by following example:

Fig. Hierarchical nature of heterozygosity among sub-divided population (After Hamilton, 2009)

 

After calculating the different observed and expected heterozygosities. It is apparent that they are not all equivalent. There are differences between the observed and expected heterozygosities at the different hierarchical levels of the population. It should be noticed that the difference between observed and Hardy–Weinberg expected genotype frequencies was used to estimate the fixation index or F. In that case there was only a single population and we were only concerned with how alleles combined into diploid genotypes compared with the expectation under random mating. The fixation index can be extended to accommodate multiple levels of population organization; thereby creating measures of deviation from Hardy–Weinberg expected genotype frequencies caused by two distinct processes. With multiple subpopulations there is a possible excess or deficit of heterozygotes due to non-random mating within subpopulations and a possible deficit of heterozygotes among subpopulations compared to panmixia. In the latter case the fixation index will show how much allele frequencies have diverged among subpopulations due to processes that cause population structure compared with the ideal of uniform allele frequencies among subpopulations expected with panmixia. Accounting for non-random mating and divergence of subpopulation allele frequency necessitates several new versions of the fixation index.

 

It is apparent that the subpopulations on average have a deficit of heterozygosity as expected if there is consanguineous mating taking place. The next level in the hierarchy is the average expected heterozygosity for subpopulations compared with expected heterozygosity for the total population or  (the S stands for subpopulations and the T for the total population). Based on the heterozygosities determined previously,

Migration and Sub-Population

 

Migration is the movement by people from one place to another with the intention of settling temporarily or permanently in the new location. When a group of people migrates to a new location, in many ways, gradually it differs from the parent group and evolves as sub-population. On the other side, when the exchange of genetic information between subpopulations is completely free the two subpopulations will eventually become a single panmictic population within a few generations. However, in most cases the exchange of genetic information between subpopulations happens with low rates of migration of individuals either in one direction or in a bidirectional way. The rate by which new mutations or old variants brought to high frequency or fixation by way of either genetic drift or natural selection combined with the rate of migration between subpopulations determines the degree of differentiation between subpopulations after a number of generations.

 

Migration homogenizes gene frequencies can reduce local adaptation preventing divergence. For example, in a simple model of population structure, the migrant fraction of the island population tends to reduce the difference between the island and the mainland. The amount of difference declines by the migration fraction each generation, as follows:

 

Population Subdivision in a Number of Sub-Populations or Demes

 

Subdivision into populations with distinct gene frequencies creates a heterozygote deficit due to subdivision into subpopulations (this can be considered a sort of inbreeding):

 

One can thus measure a sort of inbreeding coefficient, or heterozygote deficit that is due to population subdivision; it is called  after Fixation index in the Subpopulation relative to the Total population.

Figure. Wright’s “Isolation By Distance Model” of Population Structure

 

Measuring dispersal

 

If the dispersal of an individual between place of birth and breeding site is essentially random, it has the same distribution as passive diffusion, a two-dimensional normal distribution.

 

If this is true, dispersal distance can simply measured as the standard deviation,  of the dispersal distribution.  A population “neighbourhood” can be defined approximately as a group of individuals who come from an area   wide.

 

[Strictly,  is a valid measure of dispersal only if dispersal is exactly normally distributed. Many field

 

studies have shown that dispersal is actually leptokurtic, i.e. most offspring breed very close to their parents, but some breed an enormous distance away. In practice, it doesn’t much matter if dispersal is non-normal, provided it is not too extreme.Neighbourhood population size

 

The  neighbourhood population size was defined by Wright  as the population size  in a  within  a neighourhood of radius where population density is d.      Therefore, the neighbourhood population size, .  The neighbourhood population size plays the same role as the value of Nm in the island model: it determines the amount of variation between populations at equilibrium between gene flow and drift, measured by  .  Like Nm, the neighbourhood size is a product of population number and migration rate. But because the isolation by distance model is more realistic than the island model (at least, for most situations), it is potentially more useful. For isolation by distance, we can estimate population density and dispersal distance, and estimate the value of neighbourhood size, and hence the expected levels of variation from population to population. Many people try to apply the island model to spatially extended, continuous populations, but it wasn’t really designed for such use.

 

Genetic Divergence among Subpopulations

 

The fixation index  serve as a convenient and widely used measure of genetic differences among subpopulations. The identification of the cause underlying a particular value of  observed in a natural population is often difficult. Allele frequencies among subpopulation can become different because of random processes (random genetic drift) as well as by natural selection with complications from migration among the subpopulations. Difficulties in the assignment of cause do not, however, invalidate the usefulness of  as an index of genetic differentiation. The level of genetic divergence among subpopulations of several other species is presented in the following Table:

 

Table: Comparative genetic divergence among Humans and various organism and their groups. (After Hartl and Clark, 1997)

 

 

The value of  observed imply that genetic divergence between human subpopulations is quite small. Of the total genetic divergence found in three major races (Caucasoid, Negroid and Mongoloid) only 7% (0.07) is ascribable to genetic differences among races. About 93% of the total genetic variation found within races. Similarly, of the total genetic variation found in the native Yanomama Indians of Venezuela and Brazil, only 7.7% (0.077) is due to differences in allele frequency among villages. This result implies that 92.3% of the total genetic variation is found within any single village. Value of for other organisms are quite variable, presumably because  is influenced by the size of the subpopulations- which is a major determinant of the magnitude of random changes in allele frequency-by the amount and pattern of migration between subpopulations, and by other factors, including natural selection (Hartl and Clark, 1997).

 

Here, the use of term race is prone to misunderstanding or misuse. In population genetics, a race is a group of organisms in a species that are genetically more similar to each other than they are to the members of other such groups. Populations that have undergone some degree of genetic divergence as measured by, for example,  therefore qualify as races. Each Yanomama village represents, in a certain sense, a separate “race” and the Yanomama as a whole also form a distinct “race” such fine distinction are rarely useful, however. It is usually more convenient to group populations into larger units that still qualify as races in definition given. These larger units often coincide with races based on physical characteristics such as skin colour, hair colour, hair texture, facial features, and body conformation. Contemporary anthropologist tend to avoid “race” as descriptive term for human groups because cultural and linguistic differences, which are also important, are often discordant with genetic differences and sometimes discordant with each other (Hartl and Clark, 1997).

 

Further, it must be pointed out that the data presented in the Table indicate that there is much more genetic variation within than among human races, may be misleading. The conclusion is based on genes determining allozymes, and is certainly is not true for genes influencing skin color, hair color, hair texture, and other traits that most people think of in connection with the word “race”. However, skin color, and other prominent racial characteristics are used to delineate races precisely because racial differences for these traits are rather large, so the genes involved cannot be representative of entire genome. On the other hand, allozymes loci may not be very representative of the either genome (Hartl and Clark, 1997).

 

Epilogue

 

This module has covered the simple ideas about population subdivision, and discussed about population structure, its importance, measurement of population sub-division and heterozygosity, Wahlund effect, calculation of fixation index, migration, genetic divergence and so on Genetic divergence among organism is way of evolution by which gradually a panmictic metapopulation divided into many sub-populations or local populations, or demes. This happens by the process of natural selection; other agents are genetic drift, inbreeding, isolation and migration. In this way the allele frequency within a met population deviate in a group and form subpopulations. Gradually this subpopulation become metapopulation and same process started within it, and again it divided into subpopulation. This is a continuous process.

 

Genetic divergence between human subpopulations is quite small. Of the total genetic divergence found in three major races (Caucasoid, Negroid and Mongoloid) only 7% (0.07) is ascribable to genetic differences among races. About 93% of the total genetic variation found within races.

 

In respect of population sub-division, Indian population is unique in its size and level of subdivision, with 15 major languages and six main religions. Within the Hindu community alone, there are an estimated 3000 major castes, 1055 scheduled castes and 572 schedules tribes (Bhasin et al. 1992), and the Muslim population of over 130 million is similarly subdivided into Sunni, Shia, Ismaili and Dawoodi Bohra communities, and biraderis that are based on traditional social and occupational divisions (Shami et al. 1994). The net result is that the national population of 1296 million (PRB 2014) is composed of some 50,000 to 60,000 essentially endogamous subpopulations (Gadgil et al. 1998).

 

China also may have similar subpopulations. Other countries of the world also have various kinds of dividers which ultimately divide the population into subpopulations. But after being more than 7 billion people on the planet, the amount of genetic variation we carry as a species is much lower than would be expected from a panmictic population of 7 billion people in equilibrium.

 

Still, population structure allows populations to diversify. If populations are subdivided, they can evolve apart, somewhat independently. This is the reason why population structure is a very important part of evolutionary genetics.