The Making of the Fittest

"There are a lot of books out there about evolution and extinction. I chose this one because he focusses specifically on what we can learn about evolution by looking at genome sequences, at DNA sequences, which is what I do. There’s a lot of literature that talks about fossils and how we see fossil forms and fossils as evidence for evolution and extinction. But what he goes into tremendously interesting detail on is how the DNA sequences themselves contain the fossil history of evolution. All species share some of the same genes, some of these core processes that are involved with making cells and making proteins. They’re the same in everything that’s alive that does these things. That’s solid evidence that these things have shared a common ancestor in the past. He also shows evidence from fossil genes, that when a gene isn’t needed you see mutations accumulating along that sequence that make the gene non-functional. He talks about converging evolution: the idea that you might get the same mutation arising in different lineages to do the same thing. I just think it’s such a different way of looking at evolution, of understanding evolution, of finding evidence for evolution – just looking at DNA. It means a lot to me. We’re tracing the history of populations: when they were growing, when they were shrinking, when local populations might have gone extinct and been replaced by something else, how different traits evolved that might be adaptive – that might provide an advantage to a species that has them. “Perhaps we will go extinct as well. I think that’s one extinction we can get most people to care about.” In my own work, we’re doing something really similar, except we’re not looking over the deep history of evolution, we’re looking over the last couple hundred thousand years and not trying to understand how different species diverge from each other, but how populations change through time and respond to changes in their environment. So we use the signal of recent evolution past – preserved in DNA sequences of these bones that we dig up from the permafrost – to learn about when populations were getting big or when populations were getting small or when local populations went extinct and might have been replaced by individuals moving in from somewhere else. You wouldn’t see that if you were just counting bones, or looking at the fossil record. But with DNA we can actually translate the amount of diversity we see to how big that population is. It’s a hugely powerful way to learn about how species and populations and communities respond to these short-term evolutionary triggers, like climate change and humans turning up on the landscape, for example. There’s an enormous and growing field of population genetics, or phylogenetics. Phylogenetics is using DNA sequences to try to understand the evolutionary relationships between species. This stuff has been going on for a long time. Before it was DNA, people were hybridising proteins together. It was only in the 80s that it became possible to sequence DNA. Then it was only in the early 2000s that it became possible to sequence a lot of DNA really cheaply and that has really caused this field to take off. We now have hundreds, thousands, of complete genome sequences from humans from across the entire global population, and we can use that to infer the history of the peopling of the world, the spread out of Africa, how the early population that left Africa hybridised with Neanderthals, we see the residuals of that, the traces of that, in our DNA sequences. People of Sub-Saharan-African origin have no Neanderthal DNA in their genomes, but everybody else has something like 1-4% Neanderthal DNA. That’s evidence that when our ancestors left Africa, they mated with Neanderthals and they had offspring. We have grandparents that were Neanderthals. Well, not grandparents, but you know what I mean. All of this stuff is archived in our DNA and this is really what Carroll highlights in this book, but more from a deeper evolutionary perspective. I’m an evolutionary biologist, but it is an incredibly compelling evidence that evolution is fact, that it is something that is definitely real. We have the residuals of this in our genomes, in the genomes of amoebas and in everything else that exists on this planet. All the time. About two years ago the same team that sequenced the Neanderthal genome found a tiny little pinkie bone in a cave in Siberia – Denisova Cave – and sequenced a complete genome from this thing and discovered an entirely new species of homonin that we’re related to, that probably hybridized with human populations and Neanderthal populations as they were spreading around the world. This is from a tiny little fragment of a pinkie bone: a thing that we didn’t know existed prior to that. This kind of discovery happens all the time with DNA. We were shocked to find that we had hybridized with Neanderthals. For a long time, they had said ‘absolutely not’, there’s no evidence of hybridization. And that’s because for a long time in my field – in ancient DNA – we were focussing on something called mitochondrial DNA. Every one of our cells has two types of DNA: the nuclear DNA, stuff that’s in the nucleus that makes us look and act the way we do, and mitochondrial DNA, which has its own genome that lives outside the nucleus of the cell and we inherit only from our mom. You can only tell your mom’s mom’s mom’s mom’s history. But there’s a lot of it in every cell. In ancient DNA, where the amount of DNA that’s preserved deteriorates through time, it was thought for a long time that the only thing we could actually recover was this mitochondrial DNA. They looked at tons of Neanderthal specimens and never found any evidence for human types of mitochondrial DNA in any of these bones and used that to conclude that there had not been hybridization between these two species. It was only when they were able to sequence the rest of the genome, the nuclear data that we inherit from the both of our parents, that they started to see this. Of course, there’s an interesting side story there and that is that all of the bones that we collect for ancient DNA work are contaminated. We touch them and our DNA gets in them, they’re buried in the ground and soil DNA gets in them. We always assume that there’s going to be a little bit of human DNA in everything. So if one were to extract DNA from a Neanderthal bone and see a human mitochondrial sequence, one might just say ‘oh it’s just contamination,’ and throw it out. So who knows?"