This is the eighth of a series of reviews, looking back at a year of science according to topic and theme. This is about the unexpectedly dynamic world of genes, including some that jump around their host genomes, others that infiltrate new species, and yet others that change in surprisingly constrained ways.
Your genome is full of fossils, the remains of ancient viruses that shoved their genes into those of your ancestors. This year, we learned that this genetic infiltration was far more extensive than anyone had realised. By screening 44 animal genomes of 44 species, Aris Katzourakis and Robert Gifford found fossils representing 11 virus families, including ancient relatives of influenza, Ebola, hepatitis B and rabies. Most of these “endogenous viral elements” or EVEs are broken and fragmented, but some have been domesticated and probably play an active role in their new hosts. The EVEs can tell us about what ancient viruses were like, about which modern animals act as reservoirs for today’s killers, and even about viruses that jumped from one host to another.
Most mammals can trace their origins to a single ancestral species but a Caribbean fruit bat called Artibeus schwartzi has a far more complex family tree. It’s a hybrid of three separate species. Its main genome is a cross between those of two other fruit bats, A. jamaicensis and A. Planirostris. But a third ancestor contributed the genome of its mitochondria (energy-providing structures in the cells of all animals that carry their own accessory genes). This third species has either since gone extinct or hasn’t been discovered yet. Artibeus schwartzi is a fusion bat – a sort of fuzzy, winged spork.
The common fungus Fusarium oxysporum can transform from a harmless Jekyll-like citizen to a murderous Hyde-like killer by trading genes. Individuals can pick up four entire chromosomes from each other just by sharing the same space. These extra genes make up a quarter of the fungus’s entire genome and they act as a mobile armoury, converting harmless strains into ones so dangerous that they have been considered for use as biological weapons. Where did these four chromosomes come from? Their sequences reveal that they are donations from other species of Fusarium, another great example of horizontal gene transfer.
This isn’t a new discovery as such, but a personal account of my own experience with genetic testing, thanks to 23andme. I talk about the psychological issues inherent in finding out about your disease risks, the information provided by the service, and the knowledge that if I could have a baby with Mark Henderson, Science Editor of the Times, that baby would be certain to have wet earwax. Ultimately, I found it a little disappointing. Most of the results are irrelevant to someone of a non-white ethnic group and they provide me with little guidance, save for the ability to play the best version of Top Trumps ever…
Pea aphids come in two colours – red and green. The red ones paint their skins using pigments called carotenoids, and they have stolen the ability to make these pigments from fungi. The pea aphid genome carries seven carotenoid-making genes, but none of these match any known gene in any other animal genome. Their closest relatives are found in fungi. The pea aphid’s story tells us that genetic swaps between complex species like fungi and animals are possible, although probably still rare.
A fifth of our genome consists of L1 sequences – stretches of DNA without any obvious function beyond the ability to copy and paste themselves into new locations. A new study suggests that these selfish jumping genes may be involved in a genetic disease called Rett syndrome, that prevents neurons from developing properly. Rett children typically have a faulty copy of a gene called MECP2, which acts as a warden that restrains the L1 mafia. Without it, the sequences hop about the place, causing genetic havoc when they land. Is this a cause or consequence of Rett syndrome? For now, it’s not clear.
5, 6) Genome infiltrators – Dormant viruses can hide in our DNA and be passed from parent to child; Genes from Chagas parasite can transfer to humans and be passed on to children
T.cruzi is a parasite that causes Chagas disease, potentially fatal illness that affects the heart and digestive system. But Mariana Hecht found that T.cruzi can invade genomes too, by shoving some of its DNA into that of its hosts. These fragments can sustain infections long after the parasite has been cleared from the body. If it manages to get into a sperm or an egg, it can pass from one generation to the next. Among three families that Hecht studied, 29 sons and daughters had trypanosome DNA in their genes, despite never having been infected by the parasite themselves.
A virus called human herpesvirus-6 can do the same, and it’s probably in your genome right now. HHV-6 infects 90% of children in the Western world, causing a near-universal disease called roseola or three-day fever. The signs of infection soon clear out, but the virus stays put, stowing away at the ends of our chromosomes.
2, 3 and 4) Genetic convergence – Two fish families evolved electric powers by tweaking the same gene; Echolocation in bats and whales based on same changes to same gene; ‘Wasabi protein’ responsible for the heat-seeking sixth sense of rattlesnakes
Three separate stories showed how animals often evolve the same abilities by recruiting the same genes. Their bodies arrive at the same forms in parallel, and so do their genomes.
Rattlesnakes and pythons have independently developed the ability to sense the body heat of their prey by recruiting a gene called TRPA1. The gene helps us to sense the pungent whiff of mustard or wasabi, but the snakes have turned their copies into heat sensors. In the rivers of Africa and South America, two groups of electric fish have independently evolved the ability to communicate with electric fields, by recruiting the same gene – Scn4a. The gene controls the flow of ions across muscle cells. By coordinating the timing of these events, the elephantfishes and knifefishes have turned their bodies into living batteries.
Bats and dolphins have independently evolved biological sonar. They can find their way about by making high-pitched calls and timing the rebounding echoes. And both of them have done so using the same gene – Prestin. Their proteins are so similar that if you took them as the basis of a family tree, you’d end up with echolocating bats and toothed whales in the same group, to the exclusion of other bats and whales that don’t use sonar. This was my favourite of the three stories for it was made by two scientists, who independently arrived at the same result and who share virtually identical names (Li and Liu). These are people who take convergence seriously!
Japanese people have special tools that let them get more out of eating sushi than Americans can. These tools are genes that can break down some of the complex carbohydrate molecules in seaweed. They were wielded by the gut bacteria of Japanese people, but not those in American intestines. And most amazingly of all, this genetic cutlery set is a loan, borrowed from other oceanic microbes that ancient Japanese people happened to swallow in the days before seaweed was cooked. Gastronomics, anyone?