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My last phrasing of this question did not go down well, so I will try again.

The genotype of species is not always the same. If you ask yourself why not all of these possible expressions except one have died out, a natural answer is each genotype occupies a specific niche: For example, different eye colors might be found attractive by different kinds of people. If the the genotype for one eye color became more rare for some reason, other individuals with this genotype had a higher mating chance; the frequency of that genotype would get pushed back up.

But there seem to be genotypes (for example, having zits) that don't occupy any niche at all. Why didn't they die out?

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I'm still not convinced we are quite 'there' with this question to be honest. Firstly I don't think acne can be considered a genotype (although there may be genetic factors). Are you talking about adult persistent acne or transient teenage acne (which 80% of 11-30 year olds are affected by)? Similarly I don't really understand your example with eye colour. –  Rory M Feb 6 '12 at 10:37
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Agreed, acne is a phenotype, not a genotype. Also it's possible that, in some cases, acne is an effect of Antagonistic pleiotropy, and as such, would have no need to occupy any particular acne-related niche to propagate well.. –  naught101 Feb 6 '12 at 12:51
    
variation generally is proportional to the number of individuals in the species and how quickly it has been increasing in number over time. so some species, with small numbers in recent history have relatively little variation. in that light the question doesn't make as much sense. –  shigeta Nov 1 '12 at 11:31
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3 Answers

First of all, your assumption is incorrect: those are not genotypes and they do not occupy specific niches. You are talking about phenotypes (eye colour) or in the case of acne, not a trait at all.

I'll answer the question I think you're asking: why does biological variation exist?

Variation is constantly being generated by mutation, errors in the replication of the genome of an individual. If a mutation occurs in the gametic cells, it affects the genotype of the offspring. By affecting the genotype, it may or may not have a discernable effect on the phenotype. Where a gametic mutation isn't fatal, it has a chance of becoming established in the population when that mutant individual breeds. That chance is increased the further along the gradient from harmful to beneficial that effect of that mutation is.

Variation also exists because development responds to environmental factors, not just genetics. Different individuals grow in different environments, and have unique combinations of factors influencing many traits.

The reason variation persists is because, except under conditions of extreme selective pressure or genetic bottlenecks, many traits have no impact on survival or fecundity (reproductive success) or are determined only partly by genetics. Height, for example, only has a very slight impact on fecundity within quite a broad range of heights. It is partly genetically determined, and partly determined by environmental factors such as diet (Eckhardt et al. 2005), exposure to toxins during development, muscular development etc.

If height were the key factor in human mate selection, we might see a gradual reduction in the range of heights, and a gradual increase in average height. However, what we see in reality is that height has changed through human history in concordance with economic factors like social status, inflation and war (e.g. Steckel, 2001), suggesting that nutrition is a major determinant.

I know it wasn't your choice of example, but for more detail on the effects of natural selection on human height, see this question.

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It sounds like you're also trying to ask the question, "how can non-adaptive or maladaptive traits evolve?" and that you're not necessarily interested in acne specifically. The following are just a few examples.

It is possible that a gene that contributes to an undesirable trait, might also play a role in a strongly desirable trait. The classic textbook example of this is the gene involved in sickle-cell anemia, which causes the disease in homozygous individuals and is almost asymptomatic in heterozygous individuals. Since the gene helps with resistance to malaria, heterozygous individuals are actually better of than those with no mutation of this gene in areas where malaria is prevalent.

However, this is not the only way a less than optimal genotype can persist. A gene may only produce an undesirable trait in combination with certain other genes, and there may not be enough selective pressure for it to be eliminated form a population.

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I think there are two elements to this answer. To cut to the short answer skip to the bold summary at the bottom...

Firstly, genetic variation exists because of mutation. Genes get mutated every generation, the . Larger populations will have more mutants within them because: more individuals = more nucleotide base pairs (C's G's A's and T's) = more potential sites of mutation. However mutation is not likely to explain the persistence of variation because mutation rates are very low (1 in 100,000 to 1,000,000 gametes have a newly mutated loci at any individual locus) and singleton alleles have only a 50% chance of reproduction (assuming no selection) so are likely to be lost by drift (Falconer & Mackay, Intro to Quantitative Genetics 1996).

You also talk about acne, which is likely to have a large component of environmental variance. Therefore you should remember that not all phenotypic variance is genetic its source and it is highly likely that an individual trait has some degree of environmental variance component. Simplistically:

Phenotypic variance = genotypic variance + environmental variance

So the bigger question is why does variation persist? There are many potential causes of this which continue to be widely debated. Essentially it seems paradoxical because selection should reduce variation as it drives the fixation of all loci to the fittest allele. However, selection is transient, both spatially and temporally, and is not efficient against rare alleles (especially recessive alleles because they are hidden by dominant traits - e.g. disease "carriers"). Another important point is that some mutations will be neutral, therefore remain unaffected by selection.

In the spatial context, this means that selection is not always favouring the same allele in all places a species inhabits. Selection might be different based on the where it is occurring (within a species, traits like fur would be beneficial to populations in cold climates but not to those in warmer climates - here I am assuming that the sole effect of fur is to improve the ability of retaining heat).

Temporally there are also key elements. Principally, over time selection changes. Again sticking with my fur example, climates change. Ice ages come and go bringing with them different selection coefficients for fur growth.

Another variance in selection can be sexually antagonistic selection, where different alleles are favoured in either sex. In this case selection does not deplete variation but instead maintains it. It has recently been shown that sexual antagonism is prevalent throughout the genome.

the divergent reproductive strategies of the sexes could promote the maintenance of sexually-antagonistic variation (Sharp & Agrawal 2012... yesterday!)

Other hypotheses suggest mechanisms by with selection can maintain variation such as assortative mating.

Long story short, you stated that you expect variation to reduce as a consequence of selection. However genetic variation persists for many reasons, and can even be maintained by selection in several ways. Furthermore, phenotypic variation which is what you actually describe with your acne example (and I with my fur example) can be caused by non-genetic components of variation.

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Suggested reading:

Cox & Calsbeek 2009, Sexually Antagonistic Selection, Sexual Dimorphism, and the Resolution of Intralocus Sexual Conflict.

Falconer & Mackay 1996, Introduction to Quantitative Genetics.

Singh & Krimbas 2000, Evolutionary Genetics: from molecules to morphology.

Sharp & Agrawal 2012 (in press, accepted on-line version released yesterday, print may be 2013) Male-biased fitness effects of spontaneous mutations in Drosophila melanogaster, Evolution.

Innocenti & Morrow 2011, The Sexually Antagonistic Genes of Drosophila melanogaster, PLoS Biology.

Arnqvist 2011 Assortative mating by fitness and sexually antagonistic genetic variation, Evolution. (also see his book sexual conflict).

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