There is not really a good way to get rid of the junk in your genome. Pretty much, once its in there, its in there– there is no organized biochemical system that says “Oy! This ‘eres crap!” and cuts out the useless bits, cleaning up residual transposable elements like a chimney sweep. We just keep accumulating this stuff.
An exception to this is recombination.
Your chromosomes dont always line up just perfectly during meiosis, so when you have lots of repetitive elements (junk DNA– transposable elements, ERVs, etc), you can ‘accidentally’ cut out (or duplicate!) parts of your genome. ERVs accidentally overlap their LTRs and pop out the main ‘retrovirus’ portion of their genome, leaving solo LTRs, all the time (the vast vast vast majority of ‘ERVs’ are solo LTRs).
The thought never even occurred to me that my favorite little oogie woogy junkie wunky ERVs (and their relatives) played/are paying a role in the evolution of sex chromosomes!
Sexual recombination is nothing new, evolutionarily. Is a great way to increase genetic diversity to meet challenges of changing environments, so viruses do it. Bacteria do it. Fungi do it. Tons of organisms increase their genetic diversity by swapping genes/chunks of genes/combinations of genes with each other. But how did we (humans) get to where we are today, with totally different ‘X’ and ‘Y’ sex chromosomes?
I found this cool paper from 2005, hypothesizing on how accumulation of transposable elements in one chromosome could lead to a sex chromosome that looks/is nothing like its ‘partner':
We hypothesize that Y chromosome degeneration is a stepwise evolutionary process:
(1) Massive accumulation of retrotransposons occurs in the non-recombining regions.
(2) Heterochromatic nucleation centers are formed as a consequence of genomic defense against invasive parasitic elements; the established nucleation centers become epigenetically inherited.
(3) Spreading of heterochromatin from the nucleation centers into flanking regions induces in an adaptive process gene silencing of neighbored genes that could either be still intact or in an already eroded condition, e.g., showing point mutations, deletions, insertions; the retroelements should be subjects to the same forces of deterioration as the genes themselves.
(4) Constitutive silenced genes are not committed to the same genetic selection pressure as active genes and therefore more exposed to the decay process.
(5) Gene dosage balance is reestablished by the parallel evolution of dosage compensation mechanisms.
Junk DNA starts accumulating in the new sex chromosome, because the sex chromosome lost its only means of getting rid of it, recombination. The genomes natural defense against mobile elements is epigenetics– shut that shit down. But shutting down all this junk also ends up shutting down some of the normal genes. Normal genes that arent expressed anymore are under different selective pressures, so they start degrading too (mutations/deletions/etc), so the other genes compensate.
But this isnt just a hypothesis or just-so story– we are not left drifting in the breeze, wondering wtf went wrong with guys genetics.
Turns out, plants are just getting the idea to do the ‘sex chromosome’ thing! PERFECT! We can WATCH the evolution of sex chromosomes in another organism to get an idea of how it happened in us!
So, in some plants, they have ‘sex chromosomes’, but they still look the same. Cant tell the difference just by looking at them. But one chromosome has some ‘male’ genes (or ‘female’ genes) compared to its partner.
And in some plants, there are multiple different ‘male’ or ‘female’ sex chromosomes! Like, If male humans could be XYa, or XYb, or XYc (… and the Ys still basically looked like Xs). Or if humans were XYa, and chipanzees were XYb. The sex chromosomes are so new, different species in the same genus made sex chromosomes different ways!
And we can see what mobile DNA is doing in these plants to see if it fits with the hypothesis (points up).
I just think this is just awesome! I just stumbled upon this stuff while PubMedding something totally different. YAY for PubMeds crappy search algorithm!!!
Survey of repetitive sequences in Silene latifolia with respect to their distribution on sex chromosomes
The Y chromosome-specific STS marker MS2 and its peripheral regions on the Y chromosome of the dioecious plant Silene latifolia.