Molecular Evolution
Retroelement insertions are useful for phylogeny reconstruction:
1) It is extremely unlikely that the same element will insert in exactly
the same place more than once.
and
2) Once inserted, it is very unlikely that the element will be deleted.
Thus, when we can use retroelement insertions as our synapomorphies to build a phylogeny, we have very strong confidence in the resulting tree.
This approach has resolved some phylogenetic relationships that had been hard to solve using conventional sequence data.
Example: Tarsiers
There are two main branches of the primate tree, with Lemurs, Lorises, and Galagos on one side, and new- and old-world monkeys and apes on the other.
Tarsiers were hard to place based on morphology and overall DNA sequences.
However: Tarsiers share three SINE insertion sites with monkeys and apes, and none with lemurs and their relatives.
This is strong evidence that tarsiers are on our side of the primate tree.
Multilevel selection
Since TEs can replicate themselves separately from the rest of the
host's genome, selection between elements favors those with high replication
rates.
However, high TE activity may harm the host, by inducing mutations, so selection between organisms favors those with few or inactive TEs.
The behavior of TEs is a consequence of these two different selection processes.
Example: P-elements in Drosophila melanogaster
P-elements are TEs with copies spread throughout the genome.
Can cause Hybrid Dysgenesis (low hybrid fitness).
Non P-element individuals are called type M.
Consider the results of different crosses:
| Parents | P-male P-female | M-male M-female | M-male P-female | P-male M-female |
| Offspring | fertile | fertile | fertile | often infertile |
Thus, when two populations, one P and one M, interbreed, roughly half of the hybrid offspring have low fitness.
Mechanism:
P-elements encode a repressor that inhibits their own transposition
when it is present in the cytoplasm in high concentration.
Since cytoplasm is derived from the mother, P-elements become activated and start transposing themselves when they enter an egg from an M female.
Once a number of copies have been distributed throughout the genome,
transposition stops.
Hybrids have lower fitness since transposition induces mutations.
Note that, for those P male x M female hybrids that are fertile, all
of their offspring will have P-elements because there are copies on all
chromosomes.
Contrast this with the fact that a normal gene that is initially heterozygous
has only a 50% chance of being passed to any given offspring.
Thus, self regulation in P-elements allows them to have a fitness advantage over other genes while reducing the damage that they do to the host.
Note: though they do not replicate themselves directly, P-elements can be replicated by the host genome
Splicing out leaves a double strand break at the original site, which is filled in using the sequence on the homologous chromosome.
If the host was homozygous for a P-element at that site, then another copy is made by the host's DNA repair system.
History of P-elements
Not found in D. melanogaster strains collected before 1950.
Strains collected subsequently have more P-elements as the collection
date gets more recent.
They do not appear to be lost in the lab (since the first strains that had them when collected still have them in the same numbers). So..
It appears that P-elements appeared in wild D. melanogaster populations after 1950 and have been spreading since then.
Horizontal Gene Transfer
Transfer of genes between individuals other than parent-offspring transfer.
Usually refers to transfer between different species.
Sister species to D. melanogaster do not have the same P-elements.
However, a distantly related species, D. willistoni, has nearly
identical P-elements.
These species have overlapping ranges but never interbreed.
One possible mechanism of transfer is via a retrovirus that can infect
both species (common).
In this case, there is a species of mite that lives on both Drosophila
species that could have been an intermediate for such a retrovirus.
Segregation distortion genes
Sometimes referred to as "Meiotic drive" genes.
These are more likely to be transmitted to the next generation than
would be expected from Mendelian genetics.
Thus, an individual with genotype A1A2 might consistently produce more than 50% A1 gametes.
In fact, most segregation distortion "genes" are actually a set of tightly linked genes that work together.
A common pattern is to have two loci, S and R, such that alleles S1 and R1 function normally, but allele S2 produces a compound that kills sperm carrying allele R1 but not those carrying R2. (Note that this only happens in males).
In the figure above, S2 and R2 are each at frequency 0.5.
Note that if the loci are in gametic equilibrium, then the S2 allele kills as many S2 bearing sperm as S1 bearing sperm. It thus gains no advantage over S1.
By contrast, if S and R are in gametic disequilibrium such that S2 and R2 are usually found together, then S2 kills primarily S1 along with R1, so the S2R2 combination increases in frequency.
This process reduces the fitness of the individual organism in which these
alleles are found, since it reduces the number of gametes produced.
This thus represents another example of selection acting directly at the
level of genes, rather than genotypes.
Evolution of Development
Phenotypic traits do not just appear in organisms, they develop through complex interactions between genes, gene products, tissues, and the physical environment.
Development is relevant to evolution because it determines how genetic variation translates into phenotypic variation; and thus determines what selection has to work with.
For example, much evolution within the Arthropods has involved modification
of different segments and the appendages on them.
The genetic control of segment identity in arthropods facilitates this
sort of differentiation.
Homeobox containing genes
Include Hox genes associated with anterior-posterior positional information
in metazoans.
First discovered in insects through mutations that alter the identity of segments.
Examples: