The Genetics of Evolution
We are the Results of Ancient Selection
The discovery of neutral evolution has actually provided a powerful tool for determining whether a particular gene has been under natural selection pressure or not. By comparing the ratio of non-silent to silent mutations in a particular gene, scientists can determine whether that gene has been under selective pressure.
If a gene codes for a protein so vital that even small changes to its function are lethal, then only non-lethal mutations will accumulate.
One might reasonably expect a such a critical protein to have NO non-silent mutations, though it may have some silent ones.
This gene has undergone purifying selection, which has, figuratively "purified" the gene by removing any deleterious variations.
In a gene that has undergone purifying selection, the ratio of nonsilent to silent mutations (NS/S) should be ZERO. (NS, the numerator, is zero)
Neutral Genetic Drift
If a gene is not influenced at all by natural selection, one would expect silent and non-silent mutations to accumulate at an equal rate, since neither kind of mutation matters to the gene's function (or lack thereof).
In a gene changing only due to random chance (genetic drift), the ratio of nonsilent to silent mutations (NS/S) should be ONE (NS = S).
If a gene product's function is a little less rigid, then mutations may be tolerated, resulting in new alleles of that product/protein. Some of the non-silent mutations may result in alleles that function better under certain conditions than other alleles, and these will be naturally selected.
In a gene changing due to natural selection, the ratio of nonsilent to silent mutations (NS/S) should be GREATER THAN ONE (NS > S).
Positive Selection in the Primate Genome: Making us Human?
A study examining entire genomes of monkeys and apes found that of more than 10,000 genes examined, 9.8% of the proteins were conserved, with NO non-silent mutations, and 2.2% of the proteins showed evidence of positive selection.
A protein known as Forkhead box protein P2, or FOXP2 is widely distributed among vertebrates, and existing in various forms in mammals.
In the central nervous system (brain and spinal cord), the FOXP2 protein
Could our species' capacity for language--one of the things that makes it so unique--be due to just two small mutations?
By performing studies like this, and finding genes that show strong evidence of natural selection, we may be able to home in and discover their functions.
But even more interesting to the evolutionary biologist, studying changes in genes can allow us to monitor how they have evolved from ancestral genes through a process of accidental duplication followed by recruitment for a new function
Gene Duplication and Gene Recruitment: Step One
One often hears the anti-evolution claim that "you can't add genetic information" to the genome.
This is entirely wrong.
Just as morphological innovations come from pre-existing structures, new genes also come from pre-existing genes.
Recall that before any cell divides, it must duplicate all its structures to make two new, identical copies of itself during mitosis. This includes the important process of DNA replication.
And as we already know, mistakes can be made during (1) DNA replication or during (2) crossing over at meiosis (unequal crossing over). Possible results:
And any of these mutations can be
Genomes of living species bear copious evidence of permanent inactivation of once-functional genes. These are called pseudogenes. They can be recognized by the presence of the usual "start" and "stop" codons at either end. They are no longer transcribed or translated. Let's focus for a moment on a relatively common phenomenon for which we see evidence in many species' genomes, duplication
This could result in the overproduction of the gene products of the duplicated genes.
But each of these duplicated genes is now subject to mutations that could well leave the original gene intact.
In effect, these "extra" genes become the raw material for new functions that arise via mutation.
Is gene duplication beneficial? Deleterious? Neutral?
The actual identity of the gene products and their functions will determine this.
If the duplication is lethal, then the organism will not pass it on. End of story. But what if the duplication is NOT lethal?
Here are three possible scenarios, post-gene duplication...
GENETIC DUPLICATIONS CAN PROVIDE THE RAW MATERIAL FOR NEW GENETIC FUNCTIONS.
Gene Duplication --> Gene Recruitment --> Evolutionary Innovation
In our own lifetime, we have seen both wild and laboratory incidences of mutations leading to evolutionary innovation and natural selection.
We also can see evidence that similar sequences of gene duplication followed by gene recruitment (i.e., using the duplicate gene for a somewhat changed or entirely new function) has been instrumental in the evolution of such diverse, complex structures as snake venom delivery apparatus and vertebrate eyes.
6. PCP-feeding Sphingobium
Pentachlorophenol (PCP) is a toxic, carcinogenic compound first developed as a fungicide in the 1930s.
It has since contaminated soils and entered water tables, where it can be ingested by living organisms, including humans.
Irreducible Complexity? Not Really
In 1996, Michael Behe, a biochemist from Lehigh University published his contention that many structures found in nature were what he termed "irreducibly complex", and could not be the product of natural processes.
"In crossing a heath, suppose I pitched my foot against a stone, and were asked how the stone came to be there;
I might possibly answer, that, for anything I knew to the contrary, it had lain there forever:
nor would it perhaps be very easy to show the absurdity of this answer.
But suppose I had found a watch upon the ground, and it should be inquired how the watch happened to be in that place;
I should hardly think of the answer I had before given, that for anything I knew, the watch might have always been there. (...)
There must have existed, at some time, and at some place or other, an artificer or artificers, who formed [the watch]
for the purpose which we find it actually to answer; who comprehended its construction, and designed its use. (...)
Every indication of contrivance, every manifestation of design, which existed in the watch, exists in the works of nature;
with the difference, on the side of nature, of being greater or more, and that in a degree which exceeds all computation.
-- William Paley, Natural Theology (1802)
Behe's arguments were similar: that the complexity of living structures could mean only that they had an Intelligent Designer.
Evolutionary biologists have met this contention with many examples of how neutral evolution and natural selection
could quite reasonably have "invented" such complex structures.
Reconstructing the Evolution of a Complex System: Snake Venom
Venom-like proteins first appeared more than 200 million years ago in the common ancestor that gave rise to snakes and their closest saurian (lizard) cousins.
These genes were expressed in mucus-producing glands of the earliest venomous lizards.
Not necessarily fatal. Just enough to slow down the prey, or cause excessive bleeding (anticoagulant venom) and confer a selective advantage on the lizards with early venom.
For example, it's now known that the gene coding for a venom called crotamine (found in rattlesnakes, genus Crotalus) is very closely related to the genes coding for defensins, small proteins found widely in the animal kingdom (and even in plants) that provide anti-bacterial protection. In vertebrates, defensins are found in immune system cells where they help the cells kill bacteria.
These precursor defensin genes appear to have been readily mutable.
There are hundreds of different kinds in the many different species that have them.
By the time the earliest ancestor of snakes appeared (about 60 million years ago), it already had multiple genes coding for venom proteins.
Snake venoms are (molecularly) more similar in related species than in distant species: They have been inherited from common ancestors.
But they do show specialization, even within a lineage, that marks the effects of natural selection:
Green mambas and black mambas have chemically similar venoms. But green mambas hunt in trees, and black mambas hunt on the ground.
Natural selection is no miracle:
...and have evolved from proteins that have different functions in other body organs.
From Simple Beginnings: The Vertebrate Eye
Charles Darwin himself was confounded when he tried to understand how a structure as complex as the vertebrate eye could possibly have evolved by means of natural selection.
Today, however, we have the luxury of a vast trove of molecular and morphological data that make clear how such a progression could have been not only possible, but likely.
All vertebrates have light-sensitive photoreceptor cells (rods and/or cones) comprising the outermost layer of the retina:
When light strikes this molecule, it dissociates into its two components (opsin and retinal), triggering a nervous system stimuls that is eventually perceived by the brain as a spot of light (corresponding to that photoreceptor in the visual field).
The opsin portion of the molecule is variable, and controlled by the genes in the particular species in which it occurs.
Eyes themselves may have evolved from simple patches of light-sensing cells on the skin to the complex structures we see today:
Perhaps the most amazing feature of the vertebrate eye is the light-focusing lens, composed of proteins called crystallins
Modification of Gene Expression Can Change Phenotype
Mutations that change the identity of a protein are not the only way to change phenotype. Sometimes, a mutation can change the timing of gene expression, and/or the degree to which a gene is expressed. This can sometimes have dramatic results.
Recall the Central Dogma of gene expression:
Recall that a transcription factor is a protein that binds to a specific DNA sequence and controls how that segment of DNA is read.
Our Friend the Gene.
Remember that all these stretches are nucleotide sequences, and they can mutate.
Mutations in any of these regions can increase the production of a gene product, decrease it, or shut it off.
As a zygote develops and undergoes its orderly cleavages, the DNA in each new cell is repackaged and modified:
As the genetic instructions guiding a vertebrate embryo's development change in each new cell, the cells themselves follow those instructions, and are modified...
All of this is governed by instructions on the DNA. Each cell has the same genome, but different genes are active and inactive in each type of cell.
Hox Genes and Genetic Toolkits
Every animal embryo has a set of genes that determines its body axes, morphology, segmentation, limbs, and other features. This has been called the Genetic Toolkit.
Among these are the Hox Genes that determine the identity of the body segments in animals as diverse as fruit flies and mammals. How did these toolkits expand to make such different organisms? Duplication and Recruitment, as we have seen before. The Hox genes in fruit flies and mammals are homologous: inherited from a common ancestor.
In the two major lineages of animals, protostomes and deuterostomes, whom we have met before, major organ systems (circulatory, digestive, and nervous) are reversed in body position:
Changing Gene Activity Can Change Phenotype
We've already seen the variety of beak shapes and sizes in Darwin's finches. How can such major differences happen?
The second column shows developing beaks of bird embryos. Dark areas indicate cells expressing a gene product known as BMP4 ("Bone Morphological Protein 4").
The third column shows developing beaks of bird embryos. This time they are stained to show expression of a gene product known as calmodulin.
Red areas show regions of very high levels of expression.
Both bmp4 and calmodulin genes control other embryo development functions.
In some cases, a simple change that changes the activity of a promoter, enhancer or repressor can make a huge difference in a system like this one.
Another example can be seen in the different expression of two proteins--BMP2 and Shh--in disks of skin cells called placodes in embryonic reptiles (including birds).
Different levels of expression of the two proteins in placodes can cause development of scales, tubular feathers, branched feathers, or a feather with a central rachis.
Modern kiwis have simple tubular feathers, and are flightless.
It's possible that the first feathers were tubular structures that aided in insulation, and that small mutations caused them to "feather".
The evolution of two unrelated lineages towards a similar or parallel form is known as convergent evolution. A few examples...
The developmental genetic programming for these convergences must often start with different "raw materials."
New structures and genes must arise from ones that already exist.
There is no end to the grandeur of evolution.