Recent evidence suggests transposons may be critical to tail loss in many apes. Photo credit: Eugene Zhyvchik via Unsplash
In late 1859, just before the first publication of On the Origin of the Species, Charles Darwin circulated the final proofs of his manuscript. Between edits, Darwin’s scientific mentor, Charles Lyell, delighted in his comparison of vestigial structures—features that are retained throughout evolution, but which have lost their ancestral function—to the silent letters in words that persist from bygone pronunciations. Darwin was the first to intuit one of the best-known examples of these structures: the human tailbone (or coccyx) is the evolutionary leftover of a tail.
Around 25 million years ago, the hominoids—humans and the rest of the great apes—split from tailed monkeys and became tailless. What Darwin didn’t know then, and what we are just beginning to understand now, thanks to new research published in February’s Nature, is how we lost our tails.
Dr Bo Xia and colleagues at NYU Langone point to a short stretch of DNA called a transposable element that may have contributed to tail loss. Transposable elements, or transposons, are “jumping genes”: short bits of genetic material that move around the genome throughout evolution, generating both helpful and harmful mutations. Over time, natural selection can encourage the helpful ones to stay put. Some of these sedentary stretches become regulatory elements, controlling when, where, and in what amounts nearby genes are expressed.
…transposons, are “jumping genes”: short bits of genetic material that move around the genome throughout evolution, generating both helpful and harmful mutations.
Comparative genomics has taught us that exons (regions of DNA that encode proteins) are highly conserved, at least amongst mammals. Instead, it’s the regulatory elements that evolution has been tinkering with. It’s not so surprising then that Xia and his team struck out when searching for differences in tailed versus tailless primate exons associated with tail development. But when they widened their search to include neighbouring introns (non-coding regions in between exons where many regulatory elements sit) the authors identified an Alu element, a common kind of transposon, that jumped into a gene only in hominoids.
This variant was intriguing for further study not only because of where it appeared on the tree of life— in us tailless apes, but not in tailed monkeys—but also because of where it was inserted in the genome. Xia and his team report that this Alu element sits in intron 6 of TBXT, a gene required for proper development of the spine. Mutations in TBXT have been linked to shortened tails, kinked tails, and even tail loss in many species, including mice, dogs, zebrafish, fat-rumped sheep, and the famously stubby-tailed Manx cat—making it a prime spot for investigation.
Mutations in TBXT have been linked to shortened tails, kinked tails, and even tail loss…
With these findings in mind, the authors hypothesised that this hominoid-specific TBXT interloper causes apes to make a different form of the TBXT protein than their monkey cousins, which could then contribute to tail loss. Typically, Alu elements act at a splice site, the critical border between introns and exons, to modify protein products. However, this Alu element was not close enough to any splice sites to have such an effect.
Instead of acting alone, the authors thought this hominoid-specific Alu element might enlist a partner. In rare cases, Alu elements oriented just right can pair up like Velcro, trapping whatever lies between and making it impossible for that stretch of RNA to be transcribed into protein. The authors identified a second Alu element in TBXT on the other side of exon 6, which exists in all monkeys and apes. If the authors were correct, and these Alu elements interacted, they would trap exon 6 in a loop of double-stranded RNA. Using computational techniques, the authors modelled the physical structure of the loop. The conformation they predicted brings together exons 5 and 7, which could cause exon 6 to be spliced or “cut” out of the RNA transcript, generating a shortened transcript encoding a TBXT protein only found in hominoids. Skipping this exon could cause the protein to interact differently in the developing posterior spine, maybe even halting tail elongation.
To test whether apes produced TBXT RNA transcripts lacking exon 6, the authors isolated TBXT RNA from mouse and human stem cell models that mimicked cells found in the region of the developing embryo that eventually becomes the tail in mice and the tailbone in humans. The mouse genome does not have Alu elements. Accordingly, mouse cells produced full-length TBXT transcripts. The human cells, however, produced both full-length and shortened TBXT transcripts. Removing either Alu element in the human cells resulted in only full-length transcripts. This experiment hinted that the hominoid-specific Alu element interacts with its partner to delete exon 6 in a portion of TBXT transcripts.
Stem cells in a dish do not grow tails, so to test the effect of losing exon 6 of TXBT on tail phenotype, the authors generated genetically modified mice. These mice had one copy of the TBXT gene without exon 6 and one full-length copy to match the mix of transcripts observed in the human stem cell model. The mice exhibited all sorts of tail lengths, from too-long to tailless. This suggested that the loss of exon 6 in TBXT transcripts influences tail elongation during development but does not fully explain tail loss.
No longer in the era of gentlemen scientists like Darwin and Lyell, today’s researchers post their works-in-progress on pre-print servers like bioRxiv. It was at this stage in the experimental process that Xia and his colleagues first shared their data. They had shown that hominoids produce truncated TBXT transcripts via Alu element interactions and that deleting exon 6 of TBXT had some effect on tail length. But they still needed to show that the hominoid-specific Alu element itself causes the loss of exon 6 and that this modification specifically influences tail length.
Two years later, the team had done the hard work to prove this point. They generated many more strains of genetically modified mice, introducing Alu elements and stretches of DNA that acted like the transposon into intron 6 of mouse TBXT. The researchers collected samples from the embryonic tail bud, a knob of developing tissue at the end of the spine, and quantified the levels of TBXT transcript lacking exon 6. They found that the levels of exon-6-skipped transcript had a dose-dependent effect on tail length. The mice with Alu element insertions, resulting in higher and higher proportions of RNA missing exon 6, had shorter and shorter tails until the mice had no (external) tails at all.
The team’s findings represent a big step forward in the story of how we lost our tails. They identified a single insertion that may play a big part in tail-loss evolution. However, this TBXT variant doesn’t trim our tails down to coccyges in one go. It’s likely one of many evolutionary tweaks to our ape genomes that have led to and stabilised tail loss—the researchers also identified hominoid-specific variants in at least 140 additional tail-development-related genes that haven’t yet been studied. Further research might reveal how exon skipping changes TBXT protein function or whether this protein product interacts with different networks to regulate tail development.
It’s likely one of many evolutionary tweaks to our ape genomes that have led to and stabilised tail loss…
This work also adds to the growing body of evidence that evolution leans on transposons to generate new traits, from pregnancy in mammals to stem formation in trees. It also highlights that transposons don’t always act alone—they may take advantage of all kinds of previously unexplored, complex molecular interactions to introduce mutations, good or bad.
We are still left with the question of why we lost our tails. Darwin suggested it disappeared due to ‘having been injured by friction’ while sitting—surprisingly Lamarckian of him. Most modern theories revolve around the idea that tail loss allowed our ancestors to walk upright. For now, Xia and his team have given us a much better picture of the genetic mechanism driving this change.
