It’s hard not to feel sorry for the naked mole rat. No fur, enormous teeth and beady eyes: I suppose it’s a blessing that it relies on a keen sense of touch to navigate the system of dark subterranean tunnels it calls home.
But you can’t judge a book by its cover: and thanks to the recently released genome sequence, we can now read the genetic book of the naked mole rat (NMR hereafter). This DNA recipe (not blueprint) is made up of 22,561 genes, and has the potential to inform studies of cancer, pain, and ageing (see here and here for summaries of the implications for these areas).
The genome has also produced two points of interest to evolutionary biology in general: 244 more examples of pseudogenes; and the genetic mutations underlying the loss of a major morphological trait (eyes in the NMR’s case).
A pseudogene is created when a replication error or mutation occurs in a gene no longer important to the organism, disrupting the sequence as a whole and abolishing its function but leaving the sequence either side of the mutation unaffected. It is analogous to inserting the word “badger” into the middle of a copy of the Queen’s speech, or changing one letter to make “ration” from “nation”: anyone comparing the original and copy could tell they came from the same speech, but the copy has lost the meaning of the original. It should be stressed that, like all mutation, this is in no way a directed process, to prune the genome of useless genes: organisms with mutations in genes they no longer use simply survive just as well as those without mutations (and hence pass on these mutated copies to their offspring), whereas those with mutated useful genes are selected against (and their mutated copies are not passed on). As well as being a great argument for evolution and against intelligent design (why would a designer programme in useless or redundant genes?), we can read an organism’s pseudogenes to trace the habits, environments and specialisations of its ancestors.
The pseudogenes found in the NMR genome reveal a history of evolutionary specialisation from a surface-dwelling ancestor: genes involved in olfaction, vision and spermatogenesis were all still present, but no longer functioning. The authors also traced the split of the NMR ancestor from other rodents to 73 million years ago: since then smelling, seeing and being able to outcompete mates has become less important, as the NMR moved underground and developed a colonial mating system with one queen.
This study has also spelt out for the first time the genetic basis for the loss of vision in NMR evolutionary history. A key gene family in vertebrate vision is the opsins: most vertebrates have four opsin genes, but NMR has lost two of these (OPN1LW and OPN1MW). These missing two are key in colour vision; however, they only work in bright light, so NMR had little use for them in their dark tunnels, and any individual carrying a mutated copy was not selected against. This makes further sense when we consider the NMR eye: whereas the normal vertebrate eye has both rod and cone cells (providing poor vision under all light conditions and acute colour vision in poor light respectively) in the retina, the NMR retina is dominated by rods, just as its opsin gene family is dominated by the rod-associated genes (RHO and OPN1SW). As well as the opsins, inactivation was also found in CRYBA4 (possibly associated with small eyes) and CRYGS (possibly associated with abnormal eye morphology).
This paper paints a revealing portrait of the nature of evolutionary specialization: as well as beneficial mutations being preserved and creating complex new adaptations, natural selection disposes of redundant traits through pseudogenization of the genes encoding them. While the genes may be useless to the organism, they are invaluable to us when reconstructing its evolutionary history.
Kim et al (2011) Genome sequencing reveals insights into physiology and longevity of the naked mole rat. Nature 000:1-5