Genetics of the Evolutionary Process

Groups of organisms change genetically as a result of processes that disrupt Hardy-Weinberg equilibrium.

Charles Darwin

Often thought of as the father of evolutionary biology is Charles Darwin. Charles Darwin was a British naturalist who published a classic book "The Origin of Species by Means of Natural Selection or the Preservation of Favored Races in the Struggle for Life".

Charles Darwin's book was based on his travels aboard the HMS Beagle where he worked as a naturalist. During his travels, he came up with a theory to describe the patterns of variation he observed. The main components of his theory were:

Variation is a characteristic of all organisms.
More offspring are produced than survive.
Of those offspring, the most fit survive and those less fit don't survive.

Darwin's theory suggests that over time the population will be shaped by the environmental forces that define fitness.

The blending of population genetics theory with the views of Darwin is known as neo-Darwinism.

Evolution

Evolution is a change in frequencies of alleles or phenotypes from one generation to the next. This can lead to the formation of new species (speciation). Speciation can occur in 2 ways:

by anagenesis which is a gradual change in the population until it can no longer be considered as belonging to the same species.
by cladogenesis which is the divergence of the original population into 2 distinct forms.

A species can be thought of in different ways.

Early biologists thought of a species as a group of morphologically similar organisms.
Later, a species was thought of as a group of individual organisms capable of interbreeding. This is known as the biological species concept.
- The biological species concept works in defining some groups of organisms (especially higher vertebrates), but is not so effective as defining species with other groups of organisms.
  - One problem with the biological species concept is hybridization. While hybridization is relatively rare in mammals and birds, interspecies (and even intergeneric) hybridization is fairly common in in lower vertebrates, invertebrates and especially plants.
Some biologists have advocated different definitions of a species. The evolutionary species concept does not define a species based on the ability to interbreed, but instead suggests that any group that maintains its own genetic identity should be recognized.
A phylogenetic approach suggests that a taxon (not just a species) should be defined as a monophyletic assemblage of organisms.

Mechanisms of Cladogenesis

The key to the speciation process is reproductive isolation. Reproductive isolation can occur in a number of different ways.

There are pre-zygotic reproductive isolation mechanisms (isolation prior to fertilization).

Residential isolation is when individuals can't interbreed because the live in different locations.
Seasonal or temporal isolation occurs when individuals may live in the same geographic location, but reproduce at different times of the year.
Ethological isolation occurs when individuals don't interbreed because they have different mating behaviors.
Mechanical isolation occurs when individuals can't interbreed because their reproductive structures are not compatible.

There are also post-zygotic isolation mechanisms (isolation after fertilization).

F₁ hybrid breakdown occurs when hybrids don't survive.
Hybrid sterility occurs when hybrids are sterile and can't reproduce.
F₂ breakdown occurs when F₁ hybrids survive and reproduce, but their F₂ offspring are unfit and don't survive.

Reproductive isolation can occur in many ways, but all result in preventing genetic exchange between populations (gene flow).

Modes of Speciation

Allopatric speciation occurs when the original population is split into two separate populations and remain separated by some barrier to gene flow. Genetic differences accumulate between the two populations, until they become distinct species.

If the barrier is removed the two populations (or species) may again be able to interbreed, this can result in a hybrid zone.

Parapatric speciation occurs when a population within the original enters a new niche or habitat. This is different from allopatric speciation in that there is no physical barrier to gene flow.

Sympatric speciation occurs when a new phenotype arises within the population before there is a shift to a new niche.

Phyletic Gradualism vs. Punctuated Equilibrium

We may consider as Darwin did of the process of evolution/speciation as being a gradual process that takes a long time. This concept is referred to as phyletic gradualism.

An alternate view to phyletic gradualism was proposed in 1972 by N. Eldridge and S.J.. Gould. They suggested that speciation occurred rapidly, interspersed by long periods of little change. They termed this concept punctuated equilibrium.

This theory was developed in large part to explain patterns seen in the fossil record. It is likely that this pattern in the fossil record is an artifact of the way that fossils are deposited.

Genetic Variation

The whole process of variation, regardless of how it proceeds, is dependent on the existence of genetic variation (i.e. more than one allele for a gene).

The general belief before the mid-1960's was that there was very little genetic variation in natural populations.

This is because most population genetics models predict a loss of genetic variation.

A landmark paper was published in 1966 by R.C. Lewontin and J.L. Hubby that used electrophoresis of proteins to determine genetic variation in Drosophila.

Surprisingly, Lewontin and Hubby showed that there was much more genetic variation (in Drosophila) than everyone thought existed.

This sparked a very heated debate among evolutionary biologists about the nature of genetic variation of protein polymorphisms. The main points of contention included the following two issues.

Do the proteins revealed by electrophoresis represent the genome as a whole?
Is this variation maintained by natural selection?

Does Electrophoresis Randomly Sample the Genome

There are several generalizations that we can make regarding the nature of protein polymorphisms.

The vast majority of the eukaryotic genome in non-coding.
Most of the mutations occur in the third positions of codons and are thus "silent" (third positions of codons). So many mutations would go undetected by protein electrophoresis.

Recent advances in DNA technology have allowed us to examine the genome at the level of the gene rather than the gene product.

We now know that while protein electrophoresis did not detect silent mutations, it does represent a "random" sample of the genome. Or at least, there is no evidence to indicate otherwise. Furthermore, protein electrophoresis is a gross underestimate of genetic variation at the level of the DNA, especially when non-coding regions of the genome are considered.

Does Natural Selection Maintain Genetic Variation

If you think back to our discussion on population genetics, you should remember that only one type of natural selection actually maintains genetic variation.

This is stabilizing selection or heterozyote advantage.
There are several documented examples of stabilizing selection. Probably the best example of stabilizing selection can be seen in hemoglobin polymorphisms in human populations in Africa.
- In addition to normal hemoglobin (Hb^A), there is another form of hemoglobin (Hb^S) that produces sickle-shaped red blood cells. One might expect natural selection to favor the normal hemoglobin allele because sickle-shaped cells break down more readily than normal red blood cells causing anemia and can clump blocking capillaries causing tissue damage.
In Africa where the sickle-cell allele (HB^S) is found in human populations, the heterozygote Hb^S/Hb^A has a fitness advantage because it increases resistance to malaria.
- Hb^S/Hb^S individuals typically die of anemia at a young age.
- Hb^S/Hb^A individuals are slightly anemic, but have an increased resistance to malaria.
- Hb^A/Hb^A individuals are not anemic, but don't have the malaria resistance of the heterozygous individuals.
One of the consequences of favoring the allele in the heterozygous condition is that there will always be production of lethal homozygotes due to random mating. This is called segregational load.

There are actually several, slightly more complicated models that can be invoked that will also maintain genetic variation in a population.

One is called frequency-dependent selection where selection (S) is dependent of the frequency of the phenotypes.
Another way that genetic variation can be maintained is in heterogeneous or fluctuating environmental conditions.
There is also circumstantial evidence that heterozygosity (in general) can increase an individuals fitness. There have been a number of studies that have found positive correlations between fitness-related characters (such as size, fecundity etc.) and heterozygosity.

Neutral Allele Model

Alternative point of view to idea of natural selection maintaining genetic variation in natural populations was put forth by M. Kimura. Kimura suggested that most alleles are neutral with respect to fitness and selection plays little or no role in maintaining these alleles in the population. Furthermore, Kimura suggested that the occurrence and frequency of polymorphism for most alleles is due to chance or random processes (i.e. mutation and genetic drift).

So with Kimura's model, you might expect populations with large population sizes to harbor greater amounts of genetic variation than small populations.
- Studies have shown this to be largely the case.
It is important to emphasize that Kimura did not mean to imply that selection does not exist, but rather that most alleles are neutral.

Selectionist vs. Neutralist Models

At times the debate among evolutionary biologists has become polarized pitting selectionists versus neutralists. This heated debate has subsided somewhat because of the availability of newer techniques for comparing individuals/populations at the DNA level. Many interesting questions remain, but studies have shed some light on the selectionist-neutralist debate.

DNA studies have shown that most differences among alleles occur in the third position of the codon (neutral mutations).
DNA studies have also shown that there is also a much higher rate of evolutionary change in non-coding regions of DNA (neutral mutations).
- So much of the DNA evidence supports Kimura's view that at least most alleles are neutral.

Even in light of the evidence supporting the neutralist model of evolution, wee must acknowledge that natural selection acts to create organisms that are adapted to their environments. Problems come in trying to design experiments to distinguish between neutral or selection models.