Genetic diversity and Population size

Soldato
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Perhaps a bit heavy for this number of beers and this time of night, but here goes.

I had a bit of a discussion at work after lunch that eneded up with me telling my manager to go back to work. The question we where getting too tetchy about was....

Given a restricted gene pool, will the extra genetic mutaions that will inevitably occur lead to that restricted populations survival - through the dynamics of natural selection and selective mutation, or the populations demisal - through the mechanism of Inbreeding Depression.

My point was that the restricted gene pool would not have suffiecient genetic diversity to survive in the long term...

Your thoughts and comments are welcomed.
 
well, if everyone looks like scandinavians then it's fine by me. just look at iceland, their population is like the size of bristol and it does them no harm
 
Raymond Lin said:
well, if everyone looks like scandinavians then it's fine by me. just look at iceland, their population is like the size of bristol and it does them no harm

Having said that I thought they're having quite a lot of problems with carcinogenic diseases at the moment, apparantly through genetics? Heard about it a while ago on French TV when I used to live in France, can't really remember the details as it was about 2 years ago.
 
A figure I read many years ago is about a thousand: that's the minimum population (of any mammal at least) which would be self-sustaining and not have inbreeding issues. The figure is theoretical only AFAIK. One non-human example: there is genetic data suggesting that at one point there were only about 700 cheetahs in the world - and their current several thousands population has some problems with genetic defects.

But I'm not aware of any proven human examples. For a start, humans tend to migrate when things get bad. Most of the islands with small populations (Pitcairn, Tristan de Cuhna (sp?) etc) were populated after large boats were invented, and usually have small input of outsiders. Pitcairn started with (IIRC) seven men and eleven women, but were only on the second generation when re-discovered, and there has been mixing ever since. There have (I believe) been genetic studies there - try Google.


M
 
Its far, far more complex than what has already been mentioned, I will do my best to explain with some selected text from my studying (As such, I can take no credit for this information). This is very long winded, but if you are generally interested, its a good read.

However, in short, smaller populations are much more likely to go extinct. This is due to increased demographic stochasticity (basically genetic chance and events) affecting populations below an effective size of about 20-50 individuals e.g. the chance production of few female offspring.

And now for the really long answer! ;)
Steve Harris (Professor of Conservation) said:
What is the species' pool of genetic diversity?
One of the most voiced concerns in conservation biology is the threat of loss of genetic variation. A species' pool of genetic diversity consists at three fundamental levels; each level is a genetic resource of importance to conservation:-
1. Variation within individuals is the heritable genetic variation that is the basis for evolutionary change and is essential for natural selection. Whilst we believe that species should be heterozygous, I will show that this is not always the case.
2. Variation within populations is reflected by the types of alleles present and their frequency across all members of the population (the gene pool). The causes of genetic change within populations are of particular importance, since the aim of conservationists is to minimise any major losses or changes in the distribution of the variation. Gene frequencies within a population generally change over time, due either to selection, to random processes such as genetic drift, or gene flow through immigration or emigration.
3. Variation between populations occurs because species rarely exist as single interbreeding or panmictic populations. These geographic genetic differences are an important component of overall genetic diversity.
Thus the total genetic variation of a species is partitioned into within versus between population diversity.

Is heterozygosity important?
Most studies seem to show that heterozygosity and fitness (an individual's fitness is defined by its lifetime reproductive success relative to other individuals in the population) are correlated. However, measured values of heterozygosity for natural populations range from 0 to 30%, with a mean of 7% for plants, 11% for invertebrates and 5% for vertebrates, but with a great deal of variation around these means. We do not know why there are these differences between taxa and whether they are important.
The other problem is that the mechanisms that translate higher levels of heterozygosity into higher levels of fitness, especially in the wild, are unknown. There are a few examples that appear to show a link between low heterozygosity and low levels of fitness in captive populations. The most frequently quoted example is the South African cheetah (note that this does not apply to cheetah populations in east Africa, which are the same species but are thought to be more diverse genetically). A study of fifty-five South African cheetahs from several populations found that the animals were so genetically uniform that skin transplants were routinely accepted between individuals. This was because their immune systems could not distinguish between themselves and other individuals in the population because they were virtually identical genetically. Associated with this it was reported that the animals had difficulty in breeding in captivity, that there were high rates of infant mortality in both wild and captive populations, that males had sperm counts that were ten times lower than in related species of cat, and that the males had 70% abnormal spermatozoa. Also, under zoo conditions, they were very susceptible to a disease called coronavirus. Thus it would appear
that in South African cheetahs at least both genetic diversity and fitness in captivity appear to be linked. However, recent field studies have shown that low population densities and low recruitment are due to heavy predation on juveniles rather than a lack of genetic diversity. So the story is far from clear.
We also know that populations can undergo dramatic increases in size despite low levels of variability between individuals. For instance, the northern elephant seal was nearly hunted to extinction, and the population was down to about 100 individuals in the late 1800s. In 1989 it was estimated that there were 125,000 seals. Allozyme electrophoresis and DNA fingerprinting with microsatellites have both shown very low levels of genetic variability.
Furthermore, low levels of heterozygosity do not necessarily mean that the species has been through a genetic bottleneck - some common species distributed across more than one land mass also have low levels of heterozygosity. However, as a general rule heterozygosity is higher in larger populations. This tends to imply that smaller populations tend to loose heterozygosity over time, and this is a strong argument for the maintenance of larger populations, and/or larger reserves, wherever possible whilst we learn more about the importance of heterozygosity in influencing an organism's fitness.

How is genetic diversity lost?
To maintain heterozygosity, we need to understand how genetic diversity is lost. This is due to four factors, all of which are a function of population size:-
1. Founder effects occur when a few individuals establish a population, and if the number of founders is low or they are not genetically representative of the parent population, then the new population is genetically biased and likely to have an overall lower genetic diversity.
2. Demographic bottlenecks occur when a population experiences a severe, temporary reduction in size. As for the founder effect, the population is then dependent for its genetic variability on a few individuals. Generally, a bottleneck rarely has severe genetic or fitness consequences if the population size recovers quickly.
3. Genetic drift is a random change in gene frequencies that affects populations in the low tens. Basically, the number of alleles at best can only reflect the parent population; it cannot increase, but it can decrease. The smaller the sample and the lower the frequency of an allele the more likely it is to be lost from a population. The rate of allele loss increases with increasing disparity in the sex ratio of the adult population, with deviation from a random mating (especially a problem with polygynous species), and also with disparity in the number of offspring produced by each adult.
4. Inbreeding is mating between close relatives and is manifested by an increase in homozygosity. It is often associated with a phenomenon called inbreeding depression, which is the product of inherited deleterious traits in progeny. Inbreeding depression is usually manifested by a reduction in fecundity, offspring size, growth, survivorship and/or physical deformities. However, concerns about inbreeding depression are based on studies of zoo animals, which are maintained in conditions that do not allow natural selection to occur. As a consequence abnormalities and deleterious alleles that would seldom occur in wild populations accumulate in captive animals.
So conservationists have a quandry. Should small populations be managed to supplement genetic variation by encouraging immigration, e.g. by corridors, or should interpopulation genetic variability be encouraged by maintaining the isolation, thereby encouraging
adaptation to local conditions, and possibly also encouraging speciation? We do not know the answer.

What is an effective population size?
We know that small populations will loose more of their genetic diversity with time. Understanding the role of individuals in the maintenance of population size (and hence heterozygosity) has led to the concept of an effective population size. Not all members of a population breed; this is particularly true for polygynous species. As a general rule the actual population size is two to four times higher than the effective population size for birds and mammals, and by rather more in fish and invertebrates.
The rate of genetic loss is defined by the formula 1/2Ne, where Ne is the effective population size. Thus an effective population of 1000 individuals will retain 99.95% of its genetic diversity (assuming there is no selection) in a generation, while a population of only 50 will retain 99.0%. Such losses are magnified over generations; after twenty generations the population of 1000 will still retain over 99% of its original variation, whereas the population of only 50 will have retained less than 82%.
This has led to a number of general rules for conservation biologists. The most widely applied is the 50/500 rule, and this arose from quantified attempts to put figures to minimum viable population sizes. It is now being used as a paradigm, but it is ill-based. This rule advocates that in the short-term a minimum effective population size of 50 is needed to limit the deleterious consequences on inbreeding, and a longer-term minimum effective population size of 500 is needed to allow the maintenance of genetic variation for adaptive evolution. However, the 50/500 rule was derived largely from considerations of population genetics; due allowance for the non-breeding animals will mean that you need census population sizes of between 100 to 200 and 1000 to 2000 respectively. Obviously, the value of these figures is limited in that they pay undue attention to genetics and do not incorporate environmental and demographic extinction factors, and also widespread generalisations such as this may not apply to many species. This is particularly true because the figure of 500 individuals is largely derived from studies of maize, Drosophila and yeast under captive conditions, hardly good models for endangered species of large mammals. So as far as genetic rules for the conservation of large species, we are still largely operating by guess work.

Steve Harris (Professor of Conservation) said:
We know that once populations become small, they have a much higher, but very variable, risk of extinction. We also know that small population size in itself does not necessarily mean that extinction will occur - there are many examples of bottlenecks in nature. In New Zealand, for instance, an introduced population of 13 Himalayan tahr introduced in the early 1900s had increased to 30,000 to 40,000 animals by 1970. So small population size in itself is not a disaster. Remember also that the other aspect of small population size is speciation, so population declines do play an important part in evolutionary processes.

What is population viability analysis?
As a general rule, the size of isolated populations with little or no immigration affects viability. For example, a study of birds on islands around the British coastline showed that one to two pairs had a mean time to extinction of 1.6 years, three to five pairs had a mean time to extinction of 3.5 years, and populations of six to twelve pairs had a mean time to extinction of 7.5 years. Thus even among very small populations, the time to extinction will increase with very small increases in population size. So conservation biologists used to try to establish minimum viable population sizes for different species. However, intrinsically this is very difficult and fails to take account of population processes.

Clearly many factors can put a species at risk of extinction, and we need to have some means of assessing the magnitude of these risks. Models of the factors contributing to population viability are proving to be an invaluable tool for conservationists in that they provide some basic means of assessing risk by means of a population viability analysis (PVA). There are four issues to consider when compiling a PVA:-

1. Environmental uncertainty or stochasticity
2. Natural catastrophes
3. Demographic uncertainty or stochasticity
4. Genetic uncertainty or stochasticity
Obviously, habitat loss is often also an important factor to consider - is the habitat for the species itself also viable? So now people often talk about a PHVA - a population and habitat viability analysis.

Organisms with low population densities that are restricted to small geographic ranges (i.e. most endangered large vertebrates) require a population viability analysis that concentrates on the genetic and demographic factors that affect small populations, and especially those with less than fifty individuals, although small populations are also at risk from environmental uncertainty and natural catastrophes. Smaller organisms, such as most threatened invertebrates, have a different set of problems. They are frequently restricted to a few habitat patches, but within these patches small organisms can reach high population densities. For these species, population viability analyses will have to concentrate more on environmental uncertainty and catastrophic events.

How do environmental stochasticity and natural catastrophes lead to population declines?
Environmental stochasticity and natural catastrophes used to be considered to be different processes, with catastrophes being more important in leading to population declines than environmental stochasticity. Now it is generally believed that basically they both operate in the same way, and that one is no more important or disrupting than the other.
Unlike demographic stochasticity, the effect of environmental fluctuations and/or catastrophic events is largely independent of population size, and will lead to much the same proportionate effect on numbers irrespective of whether the population is large or small. Thus the impact can be dramatic on large populations, as well as small, and so all populations are susceptible to environmental stochasticity. However, other than that, we know little about the effects on populations.

How does demographic stochasticity lead to population declines?
Demography encompasses the intrinsic factors that contribute to population growth or decline, often referred to as the BIDE factors - birth, immigration, death and emigration. To understand the demographic risks, you need to understand basic population processes and a number of basic population parameters. The first is the carrying capacity of a particular environment for that particular species. In ecological terms, this is the natural limit of the population set by the resources in that environment and populations tend to fluctuate around this equilibrium due to density dependent effects due to lack of food or e.g. nest sites for birds, especially hole nesting species and others with specific requirements. Thus all populations fluctuate, even when at the carrying capacity, and populations are not stable.

How do populations grow?
With density-dependent mortality and birth rates, the rate of population growth follows a sigmoidal curve that is symmetrical around its inflection point. Growth rates are very slow over time at either end of the curve, with maximum rate of recruitment into the population occurring in the middle of the curve. This is because for small populations, the individual reproductive rate is high but numbers are low; for density-dependent populations, crowding lowers both individual and population reproductive rates. In this symmetrical growth curve, the maximum rate of recruitment occurs at the inflection point.
So the theory is simple. If a population has been reduced, so long as the habitat is right i.e. the reasons for its decline have been addressed, initial recovery should be slow, but this will be followed by a period of rapid escalation in numbers before the rate of population growth starts to decline again. The other thing to bear in mind is that populations are best able to sustain losses at the inflection point of the curve - this is at K/2 (K is the carrying capacity). Losses at the start of the curve will be very bad news and are unlikely to be sustainable,
whereas at the top of the curve losses will simply push you back into the period of rapid population growth, so although such losses lead to a population decline they are likely to be sustainable.
However, if you exceed the sustainable level of losses at K/2 - known as the maximum sustained yield - the population will inevitably decline to extinction, even if the mortality rate is only a fraction below the maximum sustained yield.

Predicting rates of population growth is particularly difficult if the population is subject to wide year-to-year variations in numbers. The problem is that the variance in r, the exponential rate of population increase, depends on population size, and a halving in population size leads to a doubling in the variance in r. The variance in r declines with increasing population size, such that by the time that population size exceeds 300, the effects of variance in r is negligible. Thus a small population is likely to suffer erratic swings in size under the influence of demographic stochasticity due e.g. to poor breeding by a number of individuals, or a drift in the sex ratio, and small numbers provide no buffer against a decrease leading to extinction. One of the classic examples is the kakapo, the nocturnal ground parrot found only in New Zealand. There were only two surviving populations. One had 18 individuals - unfortunately all male. They survived for ten years until this population finally disappeared.

The other problem is that many species show age-specific rates of mortality and fecundity. This means that you want to ensure that the population you are trying to conserve has the optimum age distribution i.e. a balance of age classes to ensure a constant rate of population increase. If the population drifts towards a high proportion of young or old animals, age-specific mortality rates exceed fecundity, and so the population inevitably declines to extinction. As an example of the sort of problems that occur with population management, male mortality rates are often greater than those for females, and so if a population crashes due e.g. to lack of food or over-hunting, you end up with a population that is highly skewed towards females. This is good news for polygynous species, where the potential for population increase would then be much higher than if the sex ratio is 50:50, but it is bad news if you are dealing with a monogamous species with pair bonds. However, for many species, an environmental perturbation, such as a drought or food shortage, leads to higher mortality rates for the younger and older age classes, and so the surviving individuals have the greatest potential for increase since they are the individuals with the highest fecundity levels and lowest rates of mortality. So populations can respond positively to bottlenecks.

Part of the reason for sudden population crashes is that populations do not change in a linear fashion. Many show a threshold response, and this makes it very difficult to design a conservation strategy for managing a particular population over time. Such catastrophic population collapses could apply in a variety of situations, including habitat loss, exposure to toxins and habitat fragmentation. For instance, let us assume a hypothetical population of birds that nests in pieces of woodland surrounded by agricultural land where there is a heavy use of pesticides. It is basically a woodland species that is suffering from habitat fragmentation. The birds that nest close to the agricultural land have a low reproductive success due to pesticide poisoning. Consequently, as the area of agricultural land increases, and a greater proportion of the remaining land abuts agricultural land, reproductive success of the whole population declines. When reproductive success declines to the threshold which is necessary to balance mortality, the fraction of the suitable habitat patches that are occupied (and hence the population size) declines abruptly, with the rapidity of the change depending on the dispersal abilities of the species.

Thus it is clear that we need to understand population processes much better, and should not rely simply on simple estimates of minimum viable population sizes.
If anyone has any difficulty understanding any principals stated above, just ask for an explanation :)
 
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aztechnology said:
Perhaps a bit heavy for this number of beers and this time of night, but here goes.

I had a bit of a discussion at work after lunch that eneded up with me telling my manager to go back to work. The question we where getting too tetchy about was....

Given a restricted gene pool, will the extra genetic mutaions that will inevitably occur lead to that restricted populations survival - through the dynamics of natural selection and selective mutation, or the populations demisal - through the mechanism of Inbreeding Depression.

My point was that the restricted gene pool would not have suffiecient genetic diversity to survive in the long term...

Your thoughts and comments are welcomed.

way more complex than that....it depends on the environment (how fast it's changing and how it affects the organisms' fitness (ability to reproduce and survive) in the first place), reproduction rate, mutation rate...the list goes on.
 
Nitefly said:
I don't understand why mutation rate comes into this. Please expand.

Well I'm not very knowledgeable on this subject...I took a few university biology classes after switching from psychology/literature/philosophy but ended up switching to computer science then switched to motorsport engineering. :p

My reasoning was that higher mutation rates would increase the chances of getting a phenotype more suitably adapted to the environment, thus increasing its fitness.
 
gurusan said:
Well I'm not very knowledgeable on this subject...I took a few university biology classes after switching from psychology/literature/philosophy but ended up switching to computer science then switched to motorsport engineering. :p

My reasoning was that higher mutation rates would increase the chances of getting a phenotype more suitably adapted to the environment, thus increasing its fitness.

Now that I think about it a bit more I might have spotted an error in my thinking.

A higher mutation rate would also increase the chances of a phenotype with some kind of inadequacy....

So I suppose it's just reproduction rate as getting as many genetically diverse organisms out there is the important thing...not getting organisms with as many genetic mutations as possible out there....I'd imagine life wouldn't be so successful that way :) am I correct?

In other words....

more offspring, less mutations > fewer offspring, more mutations
 
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gurusan said:
My reasoning was that higher mutation rates would increase the chances of getting a phenotype more suitably adapted to the environment, thus increasing its fitness.
Unless you are talking about animals in woods next to Chernobyl, I don't really think mutation rate is going to be a factor here. Mutation rates are generally conserved amongst higher organisms, and besides, if we are considering that an allele representing a mutation in a population, it will take approximately 500 generations for it to become (somewhat) established if remotely advantagous, I think the fate of a small population will be determined within 500 generations.

What is far more important is the lack of selection that organisms in a small population have :)
 
Nitefly said:
Unless you are talking about animals in woods next to Chernobyl, I don't really think mutation rate is going to be a factor here. Mutation rates are generally conserved amongst higher organisms, and besides, if we are considering that an allele representing a mutation in a population, it will take approximately 500 generations for it to become (somewhat) established if remotely advantagous, I think the fate of a small population will be determined within 500 generations.

What is far more important is the lack of selection that organisms in a small population have :)

gotcha
 
Dogoid said:
don't the royal family have a restricted gene pool ? their bloodline is carefully managed.

The queen and prince Philip come from the same bloodline, the split being just 4 generations back.
 
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