There was a time when the publication of the entire sequence of a genome–any genome–was exciting news. I don’t have any particular passion about Haemophilus influenzae, a microbe that can cause the flu various infections. But in 1997 it was the first species to have its genome sequenced. It became immensely fascinating, simply because we could now, for the first time, scan all of its genes. Now the global genome factory is cranking away so quickly–with over five hundred sequences published and over two thousand in the pipeline–that a new genome is not necessarily news. There has to be something striking, biologically speaking, for it to light up the radar. My personal radar lit up last month, with a monkey genome, because of the clues it offered to our own deep primate history, and to the question of how new genes evolve. And today, the radar lights up again, with the genome of an opossum.
As a kid I always found it strange that along with the raccoons and the squirrels and the deer and the foxes and all the other placental mammals I saw here in the Northeastern U.S., there was a single species of mammal with a pouch. The opossum wandered through our lives, waddling across a road or scurrying along a branch, giving us a blank, primordial glare. It was the lone representative in my own experience of one of the three great lineages of mammal evolution, the marsupials.
The oldest lineage of mammals are the monotremes, which include platypuses. They still lays eggs like reptiles and birds. The ancestors of marsupial and placental mammals split off from monotremes, after which they evolved the ability to develop inside their mothers without an egg. The ancestors of marsupials and placental mammals then diverged. Paleontologists have found fossils of marsupial-related mammals dating back 135 million years; the split between the forerunners of today’s marsupials and placentals must have occurred earlier still, perhaps as long ago as 180 million years. There are many features that separate marsupials and placental mammals, but the most obvious one has to do with how they are born. Placental babies spend a long time developing in the womb before being pushed out by their mother. Marsupial babies squirm out of their mothers much earlier and continue developing in a pouch, where they can nurse.
Today, scientists published the first complete genome of a marsupial. It’s not the skanky prowler of my youth (Didelphis virginiana), but a smaller, cuter relative from South America known as the short-tailed opossum, Monodelphis domestica. Scientists have learned a lot from studying the short-tailed opossum, gaining clues to human disorders such as skin cancer and high cholesterol. Their experience lifted M. domestica to the top of the list of species for genome sequencing.
But the opossum is also interesting for what it tells us about our evolutionary history. If we examine the genome of a monkey or a horse or a dog, we’re still looking relatively close relatives. Like us, each of them is yet another variation on the placental mammal. We all share an ancestor that already had a placenta and a lot of other biological features. Until today, we had to travel very far beyond placental mammals to find another relative whose genome has been sequenced: the chicken. The common ancestor of chickens and us was a cold-blooded reptile-like creature that lived 300 million years ago. So the opossum falls nicely right in the middle of that gap.
Once the opossum team sequenced the raw code of the genome they began to dissect it. They counted up 18,648 genes (remarkably close to our own total at the moment). They matched opossum genes to related versions in placental mammals, and also looked at the parts of the genome that don’t encode proteins. They looked at the chromosomes of opossums as well. Over time, giant chunks of mammal chromosomes also get flipped in reverse, and by comparing the opossum genome to other mammal genomes, scientists can reconstruct the overall look of the chromosomes of our common ancestor some 180 million years ago.
Some of the conclusions the opossum scientists draw have a familiar ring. They’re similar to the ones I wrote about in my post on the monkey genome. They found further evidence that many new genes are produced through the duplication of old ones. As with other species, the genome of opossum has been overrun with genomic parasites, virus-like stretches of DNA that can make new copies of themselves. These genomic parasites have mutated over time, and in some cases they’ve been tamed by our own genes to serve useful functions.
But the opossum genome also has some new lessons of its own, which I’ll explain below…
1. The Shadow Network. Some parts of genomes are very different from species to species, and some parts are nearly identical. The differences arise through mutations, which change the sequence of DNA in an animal. In some cases, a mutation spreads throughout an entire species because it creates a beneficial change that’s favored by natural selection. In other cases, though, the mutation doesn’t cause any noticeable difference to an animal’s well-being, but it spreads anyway thanks to random reproductive luck. Harmful mutations, on the other hand, generally remain rare, because they don’t boost reproductive success. When scientists discover a stretch of DNA that’s very similar from one species to the next, that similarity is a sign that the stretch plays a very important function that cannot be easily altered.
In recent years scientists have been surveying the 98% of the human genome that does not carry genes that encode proteins, comparing it to the non-coding regions of other genomes. There are lots of differences from species to species, which isn’t too surprising. After all, the dead remnant of a virus lodged in our genome can acquire a mutation without having much effect on our well-being. What is surprising is that here and there in this genomic wasteland there are stretches of DNA that are nearly identical from species to species. Scientists suspect that these segments have some important function that lets them resist the eroding winds of mutation.
Pinpointing these conserved regions is tricky business, because they can be so deeply hidden in unconserved expanses of DNA. The more species a scientists can compare, the easier it becomes to pick them out. The opossum offers a crucial point of comparison, situated as it is between us and chickens on the evolutionary tree. The opossum genome team found a vast number of non-coding elements–well over 100,000–that can be found in humans, opossums, and chickens. They’ve stuck around for over 300 million years.
This does not mean that all conserved non-coding elements were plugged into life by some unseen hand billions of years ago. By scanning the opossum genome, scientists discovered that it lacks a number of non-coding elements that are conserved in placental mammals. That means that these elements must have evolved into their essential form after our ancestors split off from the ancestors of opossums. In fact, the scientists estimate that 95% of the innovations in the genomes of placental mammals are of this sort. So how did these new elements come into being? Again, the opossum genome offers clues. It appears that in many cases, conserved non-coding elements evolved from genomic parasites. These useless stretches of DNA mutated in such a way that they began to play a useful function.
Figuring out exactly what these regions do in our bodies will keep many scientists busy for decades. It’s that smelly, dirty business of actually doing experiments, rather than just sweeping through the abstract realm of genome space. But some early experiments indicate that conserved non-coding elements may act like a shadow network of switches, turning protein-coding genes on and off. Making sure the right proteins get made at the right time is very important, particularly for developing bodies from eggs. In fact, one of the fastest-evolving parts of human DNA appears in a non-coding element that influences the development of the brain.
2. Shutting Down the X. Biologists do not study evolution by making up stories about the distant past. They build hypotheses, which they then test against new evidence.
Consider, for example, the X chromosome. If you’re a man, you’ve got one, which you inherited from your mother. If you’re a woman, you got a copy from both mom and dad. That means that women carry twice as many X chromosome genes as men. But women do not churn out twice as many X-chromosome proteins as men. Instead, the cells of woman–and of all female placental mammals–keep most of the genes on one of the X chromosomes shut down.
This shut-down takes place through a baroque process. Dad’s X was shut down in his sperm. After his sperm fertilized one of mom’s eggs, his X switched back on. Only later, as the embryo developed, did most of the genes on one of the X chromosomes shut down. It’s a matter of random chance from cell to cell whether it’s the father’s or mother’s that shuts down. (A digression: this is how female cats get tortoise shell coats: each X chromosome may carry a different fur-color gene.)
Opossums–and all other marsuplials studied so far–also shut down X genes, but through a different, simpler means. As a rule, the father’s X chromosome gets switched off in female embryos. This difference led some scientists to propose that opossums carry the original X-silencing mechanism, and the roundabout off-on-off mechanism evolved later in placental mammals. The opossum genome provides a chance to test this hypothesis. The possum posse looked for the gene that manages the silencing of the placental X chromosome. It’s called XIST, and it turns out that in the opossum, XIST does not exist. They also looked for repeating sequences of DNA on the X chromosomes of placental mammals that XIST somehow uses to spread its silencing. The opossum doesn’t have these repeating sequences either. So it does indeed appear that our peculiar way of silencing the X is a relatively new feature of mammal evolution. This hypothesis also explains why the scientists found that the human X chromosome has been subject to far less chopping and flipping than the opossum’s. These mutations appear to have disrupted the system for silencing genes on the X chromosome in placental mammals. In marsupials, they aren’t so dangerous.
3. Not So Primitive After All. It’s tempting to look at those weird opossums as living fossils, embodying our own distant ancestry. It’s true that in some ways, like the way they silence the X chromosome, they represent the primitive condition of early mammals. But we can’t assume that they’re primitive in all ways. Many scientists, for example, have claimed that marsupials have a primitive immune system. They based their claim on their inability to find a lot of the signaling molecules that placental mammals like ourselves use to create a complex surveillance network against pathogens.
It turns out, however, that marsupials do indeed have quite a sophisticated network of their own. The opossum genome team was able to identify a lot of genes for immune signals, as well as for receptors and other important molecules in the immune system. Previous scientists had suffered from a kind of inadvertent chauvinism. They could not find our own immune system in marsupials, and so they assumed that marsupials didn’t have much of an immune system at all. They do, it turns out–but just not ours. In hindsight, that makes sense. Marsupial babies are exquisitely vulnerable to infection when they creep out of the womb and begin to nurse in their mother’s pouch. It appears that they are protected by their own immune system, and a potent immunological cocktail mixed into their mother’s milk. And while this immune system is different from our own, it’s sophisticated as well.
What’s striking about genome papers is how often they don’t address what seems to be most obvious about the species from which the genome came from. What’s the most obvious difference between opossums and us? That pouch. Yet the new opossum papers (in Nature and in Genome Research) don’t say boo on the evolution of pouches and placentas. Marsupials actually have placentas, but theirs are not as extensive as those of placental mammals. So one has to wonder, did our own ancestors have pouches? Is the opossum in this respect a primitive vestige of our own past, an intermediate on the path from egg-laying? Or does it carry an innovation as new as the placentas that we all depended on in the womb? A few hints come from Eomaia, a 125-million year old mammal whose fossils have been found in China. It branched off early on the lineage leading to living placental mammals, but it still had odd bones projecting from its hips called epipubic bones. There’s been some suggestion that epipubic bones are a sure sign of a pouch. But the link isn’t clear yet. Perhaps there are genetic fossils lurking in our genomes and the genomes of opossums that will someday tell us if our great-great-great (etc.) grandmothers raised their young in pouches.
Source: Mikkelsen, et al, “Genome of the marsupial Monodelphis domestica reveals innovation in non-coding sequences,” Nature, doi:10.1038/nature05805 (Genome Research is also publishing some related papers.)
Photo credit: Paul Samollow, Southwest Foundation for Biomedical Research, San Antonio.