Genetic Diversity and Adaptation

Question

I am somewhat new to evolutionary biology, having studied it on my free time as a computer science student. There is one particular thing that has always bothered me for which I have not seen a good treatment, relating to adaptations to the environment with respect to genetic diversity. If it is possible for a population to adapt to rapid environmental changes, and they don't have an adaptation for dealing with change directly (such as a complex brain), it seems to me that every generation must have present within them almost every possible environmental adaptation that the population is capable of expressing (including many irrelevant ones and a few relevant to the particular environmental challenge). Otherwise, it may take too many generations to deal with a change, which may be disastrous for the population.

So my question would be: how does an evolutionary biologist explain the mechanics behind the ability for a population to adapt quickly? Are most environmental changes slow or gradual enough that the population has a few generations to happen upon the mutations that will allow it to survive, and have generally been successful in this regard for 3.5 billion years? Or, are a large majority of possible adaptations present in almost every generation, and just serve no purpose or advantage for most of the population if the provided "benefit" is unneeded (i.e., are effectively neutral)? Or something in between?

Answer 1

It is a good question. The question is hard to answer though because

• The answer is not completely resolved
• There are many influential parameters hidden behind this question.

Your question, as I understand it, can be formulated as

Do natural populations have enough genetic variance to directly respond to an environmental change or do they have to wait for this variance to be created through mutations?

To address this question, I will have to assume you have some intermediate level of knowledge in evolutionary biology.

How do we call these two alternatives?

Adaptation can occur through selection on:

• Standing genetic variance
• De novo mutations

How can we tell them apart?

This section is mainly inspired from Barrett and Schluter (2008).

Adaptation from standing genetic variance and from de novo mutations tend to yield different genetic signature.

In comparison to de novo mutations, adaptation from standing genetic variation is likely to lead to

• Faster evolution
  • Because there the respond to the new environmental is immediate, there is no need to wait for more mutations.
  • Because the fitness variance associated with the trait under selection is very low even when the first mutation occurs.
• Fixation of more alleles of small effects.
  • Because phenotypic variance is alleles of large effects are likely to be deleterious in the previous environment and would therefore be purged out of the population quite quickly
  • Because, if adaptation occurs from de novo mutation, it is likely that only few mutation would have occurred that would allow adaptation
• Spread of more recessive alleles
  • Because recessive alleles can reach a relatively high frequency in the previous environment even if deleterious in the homozygote mutant.
  • Because recessive alleles represent little to no fitness variance at low frequency and are therefore likely and it would therefore take much time for adaptation to occur from recessive alleles if they just appeared through de novo mutations.

You will note that my explanations are non-exclusive and are overlapping. They all boil down to

• Loci causing high fitness variance in the previous environment are unlikely to be source of adaptation from standing genetic variance
• Loci causing high fitness variance in the new environment are likely to cause adaptation.

If you have a hard time to understand these concepts, then you might want to have a look at Fisher's fundamental theorem, Mutation-selection balance and eventually follow some intermediate level course on the mechanism of natural selection.

Which mechanism is more common?

Do most adaptation occurs through selection on de novo mutations or through selection on standing genetic variance? This question is very hard to answer. It depends on

1. Type of adaptation
2. Population of interest

1. The type of adaptation

The answer is likely to differ depending on whether we are talking about

• adaptation to a changing environment over the whole species range
  • How fast is this environment changing is important too as you noted in your post.
• A single population that detach from the rest of the metapopulation to slowly colonize a new environment
• Adaptation to a universally (independent of the environment) beneficial trait
• Coevolutionary process
• etc...

2. The population of interest

Different populations retain different level of genetic diversity. This level of genetic diversity depends on

• Demographic parameters
  • such as the population size and its variation through time
• Evolutionary history
  • Such as the number of recent selective sweep
• Environment
  • Such as the diversity of environments present over the range of the species
  • Such as temporal variations
• Genomic architecture
  • Such as the presence of strong epistasis that could cause large amount of hidden genetic variation (see for example Hermisson and Wagner, 2004) and the eventual "revelation" of this previously hidden genetic variation through new mutation or a new environment (see for example La Rouzic 2008).

Example

Three-spined sticklebacks are present in salt water and fresh water. They occupy several geographically isolated bodies of fresh water (connected by salt water). All populations present in fresh water environments show similar phenotypic traits. We have first thought that sticklebacks have adapted repeatedly to this freshwater habitats (repeated evolution) through de novo mutations. However, some papers suggest that, as the marine population of sticklebacks is so big, that it is possible that there is standing genetic variation for these traits that are selected for in freshwater habitats. Below are some papers of interest

• Jones et al. 2012, The genomic basis of adaptive evolution in threespine sticklebacks
• Feulner et al. 2012, The genomic basis of adaptive evolution in threespine sticklebacks
• Colosimo et al. 2005, Widespread Parallel Evolution in Sticklebacks by Repeated Fixation of Ectodysplasin Alleles

Answer 2

Great question! A lot of things affect how quickly a population or species can adapt to a new environment, including population size, mutation rate, generation time, standing genetic diversity, and selective pressure.

The diversity of life encompasses practically all combinations of those variables. A bacterial population might very well contain enough diversity to allow a portion of the population to overcome a rapid change. In fact, applying antibiotics to a bacterial population and counting the survivors is a common measure of mutation rates.

On the other hand, organisms with small populations and long generation times will be much less likely to overcome a rapid environmental change. This is why there is so much concern over anthropogenic changes to the environment, including climate change.

It's hard to provide a definitive answer, since "rapid change" is a relative term, and the difficulty of adapting isn't known. Some striking adaptations can be caused by a single base pair mutation, such as in beetles and Monarch butterflies that are insensitive to toxic plant compounds.

It's important to point out that natural selection is based on relative fitness. Therefore, an adaptive mutation will spread because it's likely that carriers will be more fit than all of their neighbors. This does not necessarily mean that individuals without the mutation will die or fail to reproduce, only that those with the mutation will do it better.

Likewise, adaptation is not necessarily caused by the environment changing and wiping out all but a few lucky mutants like in the bacteria example. Instead, the environmental change might make things more difficult, but as long as the population can persist, then mutations will continue to enter the population which could confer a selective advantage against the change. So, no, a population does not (cannot) carry all possible adaptations. A population cannot adapt to an environment it hasn't encountered.

Finally, it's worth pointing out that a species can expand its range through migration. A new, unsuitable environment can act as a migration sink (that is, migrants make it there but fail to establish) for a nearby population. If this happens for long enough, some of the migrants may have a mutation allowing them to establish in the new environment.

Answer 3

Selection and the process of adaptation

The genetic variation for fitness is the determinant of how rapidly adaptation can occur. This is summarised within what is known as Fisher's Fundamental Theorem:

The rate of increase of fitness of any species is equal to its genetic variance in fitness

Adaptation is process resulting from two components, selection and genetic variation. The importance of genetic variation is captured by the breeders equation, where the magnitude of the adaptive response, $\Delta \bar{z}$, is the product of selection, $\beta$, and genetic variance, $G$:

$\Delta \bar{z} = G \beta$

If there is no genetic variance in fitness, there can be no adaptation. This is because adaptive evolution relies on the ever changing genetics of a population. If there is no variance in the parental generation, then reproductive variance (different reproductive success among individuals of the parental generation) will not affect the frequency of alleles. Adaptation occurs because reproductive success is connected to an individual's genotype. Selection can produce a response by acting on standing genetic variation, or by acting on novel genetic variation such as that introduced by mutation.

If an environment changes rapidly, a rapid response can occur, so long as there is enough genetic variance to allow a response. For example, a shift in the environment acted on genetic variance in the Galapagos Finches causing rapid adaptation in to multiple niches. Otherwise, when there is insufficient genetic variance, species will struggle to adapt, as is likely to occur with ongoing rapid climate change, and in the future for species which are going through genetic bottlenecks. Any cases where selection is too strong for prolonged periods will result in extinction of the population by a failure to adapt. For example, by application of antibiotics to bacterial infections, if there are no members of the affected bacterial population which carry resistance genes then the population will be wiped out, but if there are resistant individuals then the population will adapt (only resistant individuals will continue to reproduce).

You may wish to read further on Fisher's Geometric Model of Adaptation, including this paper, and Mutation-Selection(-Drift) Balance. Here's a good paper on the quantitative genetics of adaptation.

It is clear that climate-driven evolution has molded plants in deep time and within extant populations. However, it is less certain whether adaptive evolution can proceed sufficiently rapidly to maintain the fitness and demographic stability of populations subjected to exceptionally rapid contemporary climate change.