Independent mammalian genome contractions following the KT boundary
Tomorrow it is my turn to present a paper at our genome evolution journal club at BiRC, and I have picked this one:
Mina Rho et al. Genome Biology and Evolution, 2009
Although it is generally accepted that major changes in the earth's history are significant drivers of phylogenetic diversification and extinction, such episodes may also have long-lasting effects on genomic architecture. Here we show that widespread reductions in genome size have occurred in multiple lineages of mammals subsequent to the Cretaceous–Tertiary (KT) boundary, whereas there is no evidence for such changes in other vertebrate, invertebrate, or land plant lineages. Although the mechanisms remain unclear, such shifts in mammalian genome evolution may be a consequence of an increase in the efficiency of selection against excess DNA resulting from post-KT population size expansions. Independent historical changes in genome architecture in diverse lineages raise a significant challenge to the idea that genome size is finely tuned to achieve adaptive phenotypic modifications and suggest that attempts to use phylogenetic analysis to infer ancestral genome sizes may be problematical.
We have previously read Michael Lynch's book on genome architecture and evolution and this paper reads a lot like that book in general theme.
Anyway, the paper looks at the age distribution of LTR repetitive elements. These are transposable elements in the genome where when they are inserted they have two long terminal repeat (LTR) strings that are identical. These two identical sequences diverge via mutations over time, and from the divergence between the two you can date the age of the insertion.
If the elements are inserted with a fixed rate B and disappear again with another fixed rate D, we can model this age distribution as a simple birth/death process and the number of elements at time \(t\) is given by \(N_t = B \exp(-Dt)\). For several species this fits quite nicely:
but for mammals there is a strange "bulge" after the KT boundary indicating that either the birth rate has dropped recently or that the death rate has increased:
Since this bulge is after the divergence of these lineages, this change in the process must have occurred independently in all these mammals.
The hypothesis for what has happened given in the paper is this: After the extinction of the dinosaurs the mammals have generally increased in numbers in all lineages with a resulting increase in effective population size. What happens when the effective population size goes up is that selection becomes more efficient compared to genetic drift, so assuming that these elements are slightly deleterious, we would expect that fewer of them gets fixed and more of them gets removed as the effective population size goes up.
That explanation is of course not proven by the data, but it does fit the pattern observed.
In any case, it is clear that we have experienced a decrease in the recent insertions compared to older elements, which means that unless something else is now taking up the space our genomes are shrinking.
Don't worry too much about that, though, it is the junk that is disappearing.
Rho, M., Zhou, M., Gao, X., Kim, S., Tang, H., & Lynch, M. (2009). Independent Mammalian Genome Contractions Following the KT Boundary Genome Biology and Evolution, 2009, 2-12 DOI: 10.1093/gbe/evp007