Environment of Earth

May 26, 2008

GENETIC DIVERSITY

Filed under: Diversity,Environment — gargpk @ 2:39 pm
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Biological diversity is usually identified solely with the number of species present i.e the species diversity but the concept can also be applied at intraspecific level. The members of a species show considerable variation, which is partly environmentally induced and partly is of genetic origin. The presence of genetic diversity is a basic characteristic of the species. Phenotypic expression of genetic variation may vary between classical polymorphisms with limited number of distinct phenotypes, and quantitative characters with a continuous distribution. The genetic variation is of fundamental importance from an evolutionary viewpoint. It provides the necessary short-term adaptation to the prevailing abiotic and biotic environmental conditions for the permanence of a species. It also enables long-term changes in the genetic make up to cope up with environmental changes.

Level of genetic diversity

The knowledge of the level of genetic diversity is required for understanding the role of intraspecific variation in the survival and extinction of a species i.e. in changes in biodiversity. Study of the level of genetic diversity includes following aspects of the genetic variants:

  1. determination of polymorphic loci,

  2. the number of alleles,

  3. dominance relationships,

  4. genetic architecture

  5. spatial distribution.

1. GENETIC VARIATION AT INDIVIDUAL LEVEL

The number of different genotypes is potentially tremendous. With x varying loci, each with a alleles, number of genotypes (g) is given by:

g = [a(a+1)/2]^2

2. NUMBER OF VARIABLE LOCI

The number of variable loci is crucial to the discussion of genetic diversity. Two contrasting views have existed on this matter.

  • Classical hypothesis: It assumes that most populations have individuals that are homozygous at nearly all loci because only the ‘best’ genotype for a particular set of environmental variables would be maintained. Therefore, adaptation to the prevailing environment would lead to genetic uniformity. Genetic diversity in a species would be found among populations adapted to different environments.

  • Balance hypothesis: This opposite view assumes that individuals would be heterozygous at many loci and a lot of genetic diversity would be maintained by some kind of balancing selection e.g. heterozygote superiority.

Detection of genetic diversity

Up to two decades ago, it was virtually impossible to decide about the reality of aforementioned two models. Recent techniques like DNA-sequencing, RFLP-assays etc. now provide the means of quantitative screening of genetic diversity. However, the use of these techniques has just started and most of the knowledge up to now has come from the older technique of protein electrophoresis. This method allows detection of genetic variation at molecular level.

  1. After electrophoresis and staining, specific proteins can be identified. Genetic variation at DNA level for a particular protein can be detected by differences in electrophoretic migration distance. This type of genetic variation is called allozyme variation.

  2. Genetic differences at the DNA level, generally caused by single base substitutions, can be detected by electrophoresis. As only those base substitutions which lead to differently charged protein molecules can be detected, the method provides an underestimation of the genetic diversity present at DNA level.

  3. Since individual proteins can be identified by using specific staining techniques, genetic diversity can be detected at separate loci. By sequencing large number of individuals for several loci, estimates of genetic diversity can be obtained.

  4. This method of screening a random sample of structural loci has been extremely helpful in qunatifying genetic variation. Measures generally used are fractions of polymorphic loci (P) and heterozygosity (H). Many species have been surveyed for such allozyme variation. Following table gives a survey of allozyme variation in many species of major groups of living organisms.

GROUP

P

n

H

N

Plants

0.342 (0.012)

468

0.113 (0.005)

468

Invertebrates

0.375 (0.011)

371

0.1 (0.005)

361

Vertebrates

0.226 (0.006)

596

0.054 (0.003)

551

n = Number of species surveyed, standard error in brackets. (From Hamrick and Godt, 1990 and Nevo et al. 1984)

  • Nearly all species have considerable allozyme variation but differences among systematic groups are also present. For example, insects and gymnosperms have high while birds and large carnivores have low levels of allozyme variation. Some species e.g. Mirounga angustirostris (Northern elephant seal), Acinonyx jubalus (Cheetah),Phoca vitulina (Harbour seal) show no allozyme variation despite large number of loci screened. Reasons for this lack of genetic diversity are not clear in these species.

  • Caution should be excersised in equatic allozyme variation with other types of genetic variation e.g. variation for fitness characters. However, allozyme variation is a reliable tool for comparision of the levels of genetic diversity at a random sample of neutral genes.

Factors acting on genetic diversity

Hardy-Weinberg rule formly represnts the phenomenon of preservation of genetic variation in populations when a number of conditions are fulfilled. It also indicates that fixed genotype proportions based on allele frequencies are to be expected. However, one or more conditions most often do not hold and changes in genetic composition do occur. Following table shows the effects of various forces acting in populations on the level of genetic diversity.

Force

Genetic variation

within populations

Genetic variation

between populations

Mutations

Increase

Decrease

Gene flow

Increase

Decrease

Asssortative mating

Increase or decrease

Increase or decrease

Balancing selection

Increase

Decrease

Directional selection

Decrease

Increase or decrease

Genetic drift/inbreeding

Decrease

Increase

  • New genetic variants are introduced through mutations and gene flow from genetically different populations. Assortative mating mainly affects the genotypic proportions.

  • Selection model underlying classical hypothesis discussed above postulates that selection against (partly) rrecessives eliminates alternative alleles and leaves the population monomorphic at a particular locus.

  • Overdominance model, however, postulates that in case of heterozygote being most fit genotype, a stable allele frequency equilibrium is attained. Under this model, as in some other forms of balancing selection (such as in some cases of frequency-dependent selection), genetic diversity is protected. Loss of genetic diversity occurs when genetic drift and inbreeding are predominant.

1. GENETIC DRIFT

Impact of genetic drift is strongly dependent on population size. Genetic drift occurs when population size is small.

Due to genetic drift, allele frequencies fluctuate in the course of generations and finally each subpopulation is fixed by chance for a particular allele and total homozygosity is reduced.Genetic drift thus leads to the loss of genetic diversity in an isolated population.

At genotypic level, an important observation is that the proportion of homozygotes in metapopulation exceeds the expectations based on Hardy-Weinberg proportions associated with particular allele frequencies. In case of very small population, effects of genetic drift are extreme. In larger populations, the effects are moderate in terms of the number of generations needed for complete fixation of subpopulations and the rate of increase in homozygosity of metapopulation.

The chances of loss of an allele through drift are related with its frequency. Rare alleles are lost readily through drift.

Actual population size, as determined in a natural population, is generally not indicative of the level of drift to be expected. Theoretical considerations show that two factors are important in relationship between population size and the level of genetic drift:

(A) Bottlenecks i Bottlenecks in population size: The bottlenecks in population size in past have profound effects on the level of drift to be expected in present population of considerable size. For determination of the level of genetic drift in such situation, estimate of the effective population size (Ne) is required. In case of fluctuations in population size, relation between Ne and population sizes N1, N2, …, Nt in generations 1, 2, …, t respectively is given by:

1/Ne = 1/t [1/N1 + 1/N2 + … + 1/Nt]

This implies that Ne can be much smaller than N measured in a particular generation.

(B) Unequal sex ratio: Another cause of Ne being smaller than N is an unequal ratio of males and females contributing to next the generation. Such a situation generally results in effective population sizes which are much lower than the actual number of individuals.

In such cases of Ne being smaller than N, the effects of genetic drift are stronger than expected from actual population sizes.

2. INBREEDING

Inbreeding is closely related to genetic drift and is predominantly associated with limited population sizes.

  • Inbreeding cofficient (F): It indicates the level of inbreeding and is defined as the probability that two alleles at a locus in a diploid organism are copies of one and same ancestral allele (Wright 1969). Relatedness of inbreeding to genetic drift is shown by the use of F to quantify genetic drift processes.

Level of inbreeding in a population, indicated by F, is strongly determined by N. In a population of constant size, F will increase each generation and following relationship holds:

F = 1/2Ne

In inbreeding populations, fraction of heterozygotes is lower than expected under ideal Hardy-Weinberg conditions i.e. inbreeding results in increase in homozygosity and, therefore, loss of genetic variation.

  • Inbreeding depression: Increase in homozygosity with inbreeding is often accompnied by inbreeding depression i.e. loss of fitness due to inbreeding. Inbred individuals often have lower fitness than outbreds.

Partial dominance theory assumes that heterozygotes are more fit because in populations of sexual outcrossing organisms, recessive deleterious alleles occur at many loci though in low frequency. Due to increased homozygosity accompanying inbreeding, such alleles become homozygous and the fitness of individuals involved is reduced.

  • Niche width hypothesis (Van Valen 1965): The hypothesis proposes that species with greater genetic diversity i.e. with higher level of heterozygosity occupy larger, more variable habitats than the species with low genetic variation i.e. with low levels of heterozygosity.

3. BREEDING SYSTEMS AND DEGREE OF INBREEDING

Breeding system of a species has profound effect on the degree of inbreeding and consequently on the level and organization of genetic diversity.

  • Self-fertilization: Especially in self-fertilizing organisms, inbreeding levels increase very rapidly. Many plant species exhibit high levels of selfing. As predominantly selfing plant species flourish equally well as obligate outbreeders, apparently no or only moderate deleterious effects occur. The probable reason for this is that deleterious alleles in selfing species have been eliminated in the past (Lande and Schemske 1985, Charlesworth et al. 1990). Study of the effects of inbreeding in two populations of Eicchornia paniculata, one predominantly outcrossing and other predominantly selfing has confirmed the above view.

  • Outcrossing: On the other hand, many hermaphrodite plant species possess self-incompatiability systems that prevent selfing. This is commonly viewed as a mechanism to prevent deleterious effects of selfing.

4. GENETIC DIVERSITY AND EXTINCTION OF SPECIES

Species that are exposed to habitat destruction or habitat fragmentation often consist of isolated populations of small population sizes. Such small populations have a relatively high chance of becoming extinct due to purely demographic reasons. Such small populations generally carry high risk of attaining zero population size due to fluctuations in their size than larger populations. The genetic processes described above may also contribute to increased risk of extinction in case of small populations. The lowered individual fitness expected in such populations may increase the vulnerability to current and future environmental stresses. In this respect, following two aspects of genetic drift and inbreeding are highly relevant.

  • Loss of specific alleles at one or restricted number of loci: When such variants provide individuals with tolerance to specific environmental stresses, their loss will lead to deterioration of individual adaptedness. A population consisting of individuals which have lost the potency for adaptation will be more vulnerable to extinction when exposed to a specific stress.

With respect to the relation of particular genetic variants to specific stresses, numerous examples are known where adaptation has been strongly increased in natural populatons e.g. industrial melanism in moths, sickle-cell polymorphism in humans, warfrain resistance in rats, insecticide resistance in insects and heavy-,metal tolerance in plants. It is possible that the gain in individual fitness in a population may also increase the overall population fitness. However, the concept of such increased population fitness is much less well defined than individual fitness and is often disputed.

Short-term population fitness may be defined as the existence of a population over a limited number of generations. Fitness differences among populations are then reflected in differential survival of populations or in differences in population sizes.

Long-term population fitness has been defined by Thoday (1953) as the ‘probability that a contemporary group of individuals will survive for a given long period of time, such as 10^8 years, that is to say, will leave descendents after the lapse of that time’. In this context, Lewontin (1957, 1961) has proposed an all-or-none fitness concept which states that if a population can survive and reproduce in more environments than another population, the fitness of former population is greater than that of the latter population.

It can be argued that a population that survives in a greater number of environments than others also has a greater chance to survive in future environments. This enables an experimental approach to long-term fitness by testing populations in a great number of environments.

The importance of the presence or absence of particular genetic variants is demonstrated by an experiment in which populations of Drosophila melanogaster difffering in genetic composition for alcohol dehydrogenase (Adh) locus were subjected to various types of stresses. Adh locus is polymorphic for two alleles, Fast (F) and Slow (S). The Adh genotypes differ considerably in survival on medium containing toxic concentrations of alcohols. The F-homozygote survives more often than the S-homozygote while heterozygote is intermediate in survival. Survival is positively correlated with ADH-activities of the genotypes. When large numbers of vial populations, either monomorphic for S-allele or for F-allele or popymorphic, were exposed to toxic concentrations of ethanol, some populations did not survive in the course of several generations. However, extinction fractions differred considerably among population types. Monomorphic S-populations had higher extinction rates than the other population types, apparently because they did not have F-allele which gives higher individual fitness to its carriers when exposed to ethanol. Thus, individual fitness differences are transferred to the population level. This results in differential extinction probabilities. In another set of experiments, populations were exposed to varying stress factors in successive generations. The populations were exposed during one generation to one particular stress condition (e.g. high temperature, low humidity, ethanol addition to food etc.) and in the next generation to another factor (randomly chosen from a set of conditions) and so on. The differential extinction was again observed. In this case, however, the polymorphic populations had the lowest extinction rates. This experiment points to the importance of polymorphism in varying environments.

  • General loss of fitness associated with inbreeding depression: In this case, the probability of extinction is not limited to one particular stress factor but will occur generally. However, the effects of inbreeding depression will generally be more severe under harsh conditions.

In this case, the cause for increased rate of extinction is genetic diversity following inbreeding associated with inbreeding depression. For several species of mammals kept in captivity, juvenile mortality is one of the most important traits affected by inbreeding depression. In Drossophila melanogaster, population size and productivity are severely reduced following inbreeding.

Considerable improvement is obtained in such populations when genetic variation is increased artificially by X-irradiation. Merely the reduction in population size will increase the probability of extinction of local, isolated populations.

It is well established that when lines of Drossophila are inbred, a considerable number of lines are lost in the course of generations. Some of these extinctions would occur because of homozygosity for recessive lethals, others will be due to increased chance of extinction associatedwith reduced population size. Similar observations in inbred strains of mice have been made. Litter size decreased with about 0.53 young per 10% increase in F. Only 3 out of 20 lines survived by the time F had increased to 0.76.

5. PROSPECTS FOR NATURAL POPULATIONS

The expectations of the relations between population size, levels of genetic variation and fitness based on theoretical considerations laboratory experiments and data from animal and plant breeding are well established. However, the significance of these results for natural populations is still largely unclear. Studies in this field are comprehensive and time-consuming because information is needed on the demography of populations (both in the present and in the past) as well as on levels of genetic diversity and fitness and fitness. Only few such studies have been undertaken recently.

In the present times, many species in nature are increasingly being faced with destruction of their habitat and consequently in reduction in numbers of individuals together with fragmentation and isolation of the populations. The predicted loss of genetic diversity under such a scenario may have profound effects on biodiversity. Therefore, much interest is being shown for the studies related to relation between population size, genetic diversity and extinction of species. However, much theoretical and experimental work is needed in these areas. More information is needed on the effects of bottlenecks in population size on the genetic variance for quantitative characters. The relation between population extinction, genetic variation and demographic stochasticity also needs to be explored. In addition, important items for serious consideration and further study are the general effects of gene flow and concept of metapopulation levels in relation to demographic and genetic equilibrium.

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