I. Molecular Variants address traditional problems of population genetics (e.g., considered in the first half of the course) and allow one to explore various levels of the genome:
II. Phylogenetic relationships as derived by analysis of sequences,
hybridization of DNA (e.g., melting point of hybrid DNA), etc. Because many
molecular changes are close to neutral, they provide just the right kind
of information to address questions of phylogenetic relatedness.
III. The genome as an object of study
Also,
Some of the genes in the mitochondria evolve faster than nuclear genes largely because of the non-proof reading polymerase found in the mitochondria. (Note, however that there are many highly conserved genes in the mitochondria that code for proteins used in the electron transport change -- e.g., cytochromes, etc.).
Neutral Theory of Evolution. The prevalence of "silent" and nearly silent mutations led Kimura (1950) and Ohta and King and Jukes to propose the neutral theory of evolutionary change in which natural selection does not necessarily play the primary role in generating variation at a molecular level, mutations rule.
This is not to say that selection is not important, just that much variation in the genome is neutral and this thry is in keeping with the phenomenal levels of genetic variation researchers have found at the level of moelcules and also protein level differences (electrophoretic morphs). This added an additional richness to the theory of Evolution, which may play a role in subsequent evolution. Perhaps some neutral change can ultimately be co-opted for a functional role (see below).
If mutation rate is relatively constant then we have a useful tool for making phylogenies -- the molecular clock, and we can use sequence variation to construct parsimonious "tress" in which phylogenetic relationship is inversely proportional to the number of mutational differences between members of a clade.
The rate of sequence change is predicted to be linear as long as mutations within a single gene are unique.
As mutations start piling up on top of one another (e.g., a mutation
with a subsequent mutation at the same codon or BASE pair location), the
curve will no longer be linear. As you get more and more mutations (every
gene no matter how large, will get double mutatations at many sites) the
rate of change will assymptote (level off). At that point information on
phylogenetic relatedness from that gene is being wiped out little by little.
Information is being lost as the old mutations are "covered up".
Once this happens, the gene is no longer valid to use as a molecular clock, as time is not directly proportional to number of mutations (e.g., base pair differences) between two taxa that you are comparing.
The solution is to choose a different molecule with a slower mutational rate of change such that you can use it to infer physlogenetic relationship and compute molecular clocks (e.g., time since divergence which is proportional to base pair differences between taxa). For example, microsatellites (Simple sequence repeats) which mutate rapidly are useful in comparing populations of the same species, but to infer evolutionary relationships among eukaryotes, and prokaryotes or types of eukaryotes you need a highly conserved gene such as cytochrome a,b,c or ribosomal DNA. The "deeper" the branches in evolutionary time, the slower the molecule should evolve (e.g., mutation). Thus, the molecule used to infer relationship is crucial depending on the level of phylogenetic analysis being considered:
Psuedogenes discussed above represent one kind of multigene family. The psuedo gene has an an ancestor, a working gene in the genome.
However, many genes in the same organisms are derived from a common ancestor gene in the same way that species are derived from one another. For example the hemoglobins come in two forms, fetal and the normal adult hemoglobin. Whereas these are very similar in form, they are more distantly related (more mutations) compared to another member of the same family, myoglobin, which serves as an oxygen, storage role in the muscle rather than transport in the blood (e.g., hemoglobin).
These are examples of genes in the same family that have evolved different
functions after a tandem duplication. This may be a potent mechanisms for
the evolution of molecular and protein diversity in the workings of a single
organism. See also the Antennapedia/ Bithorax lecture for genes that might
have been tandemly duplicated to produce a different control region over
the development of different tagmata of the body. (e.g., the evolution of
body plans).
There also examples of multigene families in which members are absolutely identical (all 500+ copies of rDNA are largely identical). This is somewhat of a paradox as even small single-base mutations should crop up and yet many multi-copy multi-gene families are carbon copies, counter to mutational expectations.
How do we explain such patterns?
This may be an example of "concerted evolution".
A hypothesis for a homegenizing mechanism is unequal crossing over and change in copy # generation after generation.
There is in fact much variation in copy number, but not much variation in the copies themselves.
Molecular Drive is an extreme case of concerted evolution in which there is biased gene conversion which reflects the propensity for a particular gene to replace its "competitors" during meiosis.
In the case of single genes (e.g., not mulit-gene families), we call this meiotic drive and it reflects genic selection (e.g., the t-allele and sperm production in mice, see lectures on levels of selection.)
Finally, there are other examples from genetics, in which genic selection appears to play a major role. Transposable elements appear to move from one genome to the next (or within the same genome) and the behavior of such genes and the spread of such genes is phenomenal and may reflect an extreme case of genic selection (e.g., transposable elements spread across the laboratory stocks of drosophila within a few decades since there introduction in the 1950's).
A "Byproduct of selfish genes"?
In some interesting case, genes can be transfered between species by either transposable elements (e.g, the transposon carries a host gene with it) or by retroviral mechanisms in the retrovirus takes a host gene with it before it infects a new host. Such "horizantal gene transfers may be important in the evolution of novelties (e.g., hemoglobin transfered to soybean via virus and hemoglobin is used to bind O2, which can poison nitrogen fixing bacteria found in soybean nodules.)
Also superoxide dismutase being transferred from fish to bacteria. SOD is used to wipe out free radicals.
P450 genes were derived from an ancestral cytochrome 2 billion years ago when photosynthesis was producing free oxygen.
The toxic effects of o2 on bacteria created a selective pressure that lead to a novel detoxification enzyme that began evolving and susequently spread to eukaryotes.
We can date their divergence at about 1.45 bya and then backcalculate to 2 by, the origin of the first P450.
A particular family of P450, Family II, began radiating dramatically about 430 to 350 my ago. This event coincided with colonization of the land by herbivores during the Siluro-Devonian explosion. P450 is used by modern insects to detoxify the defensive compounds of plants.
P450 enzyme takes toxic lipophilic compounds and converts them to hydrophilic compounds that can be excreted or further broken down.
P450 is used in other metazoa like mammals. In humans P450 is actively used to breakdown drugs introduced into the body. Some individuals are quite sensitive to drug therapies because they cannot breakdown drugs effectively owing to altered P450 activity.
Gene duplication
Genes that pass down lineages are called orthologous genes. They can be tracked to a common ancestor. (e.g., alpha hemoglobin in verts). This gene can duplicate within a lineage to create new genes that have a different function (e.g., beta, gamma, delta, forms of hemoglobin). The descendants of duplicated genes are known as paralogous genes.
Gene conversion
Portions of the tandemly duplicated genes can recombine in an unequal fashion at meiosis to produced conversion of one gene into another (see figure from lecture). Pieces of genes can recombine to create entirely new P450 proteins, which allows for a novel detoxification function via gene conversion "mutations". This fact is why insects can so rapidly evolve resistance to pesticides.