Blogs / The Loom

In my last post I wrote about how scientists are learning about the origin of animals by studying their genomes. One of the surprising findings of the latest research is that a group of animals called comb jellies (ctenophores) belong to the oldest lineage of living animals. Comb jellies look a bit like jellyfish–soft, tentacled creatures without brains or eyes but with a nervous system. As I wrote in the Boston Globe Monday, earlier studies had generally pointed to sponges as belonging to the oldest lineage. If comb jellies take their place, that may mean that the ancestors of sponges lost their nerve(s) and became anchored filter-feeders.

David Marjanovic then left this comment:

IMHO the tree is full of long-branch attraction. The position of the ctenophores is probably spurious.

So what’s David talking about? Long-branch attraction refers to a pesky problem that evolutionary biologists face when trying to reconstruct ancient episodes in the history of life. In my article I only referred briefly to these sorts of challenges, but fortunately blogs give me a little room to stretch out.

Long-branch attraction is a new twist on a classic phenenomon in evolution called convergence. This happens when two lineages evolve into very similar forms. Legless lizards and snakes, for example, independently evolved a serpent body shape. The octopus eye forms images like a camera, just as ours do. Several strains of E. coli have evolved into disease-causing bacteria that invade intestinal cells. On the surface, two convergent species may look as if they share a close common ancestry. It can take some close scrutiny to discover that they are not.

A segment of DNA can also evolve convergenty in two lineages. Imagine that a particular segment of DNA in the ancestors of insects had a sequence, AAATAAA. Imagine that vertebrates had a sequence AATTGAA. It takes only one mutation in each lineage for them to both evolve into AAATGAA. Now they have an identical segment that they did not inherit through common ancestry.

This sort of convergence is unlikely to happen soon after two lineages split apart. But as more time passes–as branches get longer–it becomes more likely. Branches that are not in fact closely related get attracted to each other when scientists study their DNA. Hence, long-branch attraction. In the case of this new study, David is suggesting that sponges ended up looking more closely related to us than comb jellies because the DNA the scientists studied happened to evolve convergently.

I dropped a note to Casey Dunn, the lead author of the new study in Nature, and he fired back some enlightening comments…

Long branch attraction is one of the most common types of systematic error encountered in phylogenetic inference…It is the primary reason we say in the paper that the ctenophore result “should be viewed as provisional”. Unfortunately, the Nature format is very restrictive in its length so we did not have room to explicitly discuss this issue, though we were very mindful of it and much of the experimental design was structured specifically to address it.

That design included finding lots of weird animals. Adding branches to an evolutionary tree essentially chops down long branches to shorter lengths, because the new species are more closely related to some of the animals than to others. That’s why one of Dunn’s colleagues fished up a second species of comb jelly when the startling results first emerged. The long branch of the original comb jelly now became split in two, reducing the amount of long-branch attraction.

Another possibility might be that the ancestors of comb jellies have evolved faster than other animals. Their rapid evolution would give rise to more differences between their DNA and the DNA of other animals. As a result, the more slowly-evolving animals, including sponges and us, would appear more similar. But when they measured the rate of change on each branch, the comb jellies didn’t appear at all peculiar.

By taking these extra steps (and others), Dunn and his colleagues felt confident enough to go into print with their results. Fortunately, scientists can continue to test for the possibility of long-branch attraction by adding more species to the tree. Animals that belong to deep lineages are the best. The bizarre, balloon-bodied Trichoplax would be a good place to start, since its genome is already sequenced. Science, thankfully, marches on.

Comb jelly photo from bzibble

Today in the Boston Globe, I write about how scientists are revising their understanding of the evolution of animals, thanks to more DNA and more weird animals. My favorite quote comes from biologist Mark Pallen, who says that the human genome would have been worthless without understanding how humans are related to other animals.

Unfortunately, this research has been subject to some poor reporting, and to some distortions from creationists. Ryan Gregory and Troy Britain set them straight, respectively.

Click here to watch it on blip.tv (you can even watch in full screen, if you dare…)

NOTE: I’VE SET UP A FLASH VERSION OF THIS TALK HERE. DON’T BOTHER TRYING TO DOWNLOAD THE QUICKTIME VERSION I DESCRIBED IN THIS POST.

Recently I gave the Discovery Lecture at Carleton University in Ottawa, in which I talked about new developments in evolutionary biology. They sent me a DVD of the talk, and I got a lunatic notion in my head that I would figure out how to get all Web Two-Point-O-Ee and post the lecture online. They told me to go ahead as long as I put a watermark on. Ever eager to waste time, I slowly figured out how to do that on QuickTime. Then I uploaded it to blip.tv, because they let you post big files. But that’s where my superduper tech acumen falls apart, because for some mysterious reason the site won’t convert it into a sleek, embeddable Flash format. If you don’t mind the somewhat less sleek QuickTime, here’s the talk.

(If anybody wants to teach this tech cub a lesson or two on how to do this sort of thing, I’m all ears.)

Radiolab is a show about science that briliantly uses radio’s greatest strength–sound–to bring stories to life in ways we print goons can only dream about. I wrote a story about how animals sleep. The Radiolab folks played the sound of brain waves from a sleeping cat. And so on.

I’m particularly fond of their latest podcast, which you can listen to below. It’s about chimeras, synthetic biology, and other threats to our conventional notions of life.

Full disclosure: I am acquainted with Robert Krulwich, one of the hosts, and in recent months he and I have spent a fair amount of time talking about the brave new world of synthetic biology. He is freaked out in many ways, some legitimate, and some, I think, not so much. (I recently wrote about why I can’t summon up a good freak-out in Wired.) Bascially, I think ordinary biology like foul drinking water and drug-resistant bacteria is more frightening than a microbe that smells like wintergreen. But you can listen to Krulwich get disturbed and judge for yourself.

These biologists are holding out on me.

I’ve been writing about biology for quite some time now, and sometimes I think I’ve got a pretty good sense of the scope of life. Neurosurgeon wasps–got it. Eels with alien jaws–check. And then I stumble across something new, or should I say, new to me.

This week’s revelation is androgenesis. Androgenesis is what happens when kids get all their genes from their father. Normally humans and other animals produce offspring by combining DNA from both mother and father, an arrangement that’s often the case in plants as well. Both sperm and eggs only get one of the two copies of each chromosome in the genome. When male and female gametes combine, they have enough DNA together to make a new organism. There are exceptions. Hermaphrodites can be fathers or mothers. Then there’s parthenogensis, in which a female animal’s eggs begin developing into embryos without any sperm carrying Dad’s genetic delivery. I thought that this represented the outer edge of strange kinds of reproduction. And then I came across androgenesis.

At first I couldn’t even imagine how androgensis can work. How can you start growing an embryo from a sperm, I wondered? And while I could at least imagine that a man might bear a child if an embryo was implanted in his gut, I could not understand how this could happen in any animal naturally. But of course, I should know never to rely on my feeble powers of imagination to guess at the maximal weirdness nature can deploy. (I probably shouldn’t have posted this on April 1, because people may think I’m joking. I’m not.)

Androgenesis, it turns out, transforms fatherhood into a parasitic invasion. It begins like normal fertilization, with a sperm fusing to an egg. But then the egg’s DNA gets hurled out of its nucleus, so that the sperm’s genes are the only ones left in the egg. The egg begins to develop into an embryo, but only after it has lost the mother’s DNA.

Androgenesis is rare in the natural world, but it’s not obscure. Asian clams (Corbicula) came to the United States several decades ago, possibly by Chinese immigrants for food. Today they’re a major pest. And two of the species that have come to our shores use androgenesis to reproduce. These particular Asian clams are hermaphrodites. Along with eggs, they also make sperm–but these are odd sperm, with a full supply of DNA. Once their sperm has fertilized the egg of another clam, the female DNA is ejected, and the clam embryo starts to develop. The mother clam broods father’s clones in her gills, where they can probably thrive on the food that gets trapped there.

To be precise, the eggs of Asian clams don’t lose all their DNA. Most of the DNA in animal cells is in the nucleus, but there are also dozens of little energy-generating factories in the cell called mitochondria that carry their own bits of DNA as well. Fathers evict the maternal DNA from the nucleus, but the mitochrondial DNA stays behind. This only makes sense (insofar as androgenesis makes much sense at all), because a cell without a way to generate energy would have a hard time growing into an embryo.

Scientists can build evolutionary trees from DNA, using it to determine how individual animals are related to one another. But when they build the tree of invasive Asian clams, the mitochondrial and nuclear DNA reveal different genealogies. It looks as if the two invasive species have been carrying out androgenesis on each other.

The ability Asian clams have to use other species to make near-clones of themselves may help resolve one of the paradoxes of androgenesis. Once androgenesis arises in a species, it should be able to spread quickly because the fathers can reproduce so much faster than more conventional clams. Taking the female side of this deal is a losing proposition, because females can’t pass their DNA down to the next generation. So androgenesis ought to lead to swift extinction, like some sort of paternal plague. Even if androgenetic animals could somehow avoid this doom, they would bear another burden: mutations. Without the benefit of sex to mix up their DNA, they would accumulate harmful mutations over the generations that could threaten the survival of the entire population.

The huge success of Asian clams in the US is proof that androgenesis is not a one-way ticket to oblivion. Androgenesis may survive in part because the fathers can make other species their victims, too. Another species can offer an extra supply of eggs, as well as an extra supply of DNA. Studies on the DNA of Asian clams in the US suggest that on rare occasion, some of the mother’s DNA stays behind in the egg. This fresh influx of genes may rescue androgenetic clams from some of their harmful mutations.

For more information on androgenesis, check out this new paper in the journal Evolution. And if any biologists are holding out on any other bizarre biology, it’s time to come forward.

Science writer Edmund Blair Bolles is in Barcelona at the Evolution of Language conference, and he’s live-blogging like crazy. Fascinating stuff well worth checking out. [Link fixed-cz]

Hyenas are fascinating in many ways, such as the way female spotted hyenas are equipped with a penis of sorts (pdf). In tomorrow’s New York Times, I look at a new kind of fascination: hyena brains. Hyenas have a remarkably complex social life, and it appears to have altered the shape and size of their brains. The same social forces were at work in our own ancestors. Humans and hyenas, in other words, have been rolling on parallel evolutionary tracks.

For further details, check out the densely packed web site of Kay Holekamp, the biologist who has been investigating the social hyena brain. And don’t miss the slide show the Times has put together for my article.

The Encyclopedia of Life, about which I blogged and wrote about in the New York Times, has gone live earlier than previously scheduled. So go check it out. A few people have left comments here, and others are blogging too. I’m very curious to see what hard-core bioinformatics folks think as they take this baby out for a ride. Deepak Singh at business bytes genes molecules has some complaints, and Rod Page has a lot of them. It will take a little time to sort out these comments into the constructive criticisms and the outright dismissals. For example, I’m sure that it wouldn’t take too long for EoL to get a decent search engine. Rod points out that ultimately, every page will be authenticated by an expert. Are there enough experts out there to authenticate 1.8 million species? That was a point that I raised in my article. Taxonomy is not a boom industry. If species were nothing more than bits of DNA, this would be a slam dunk. But real species are DNA and bodies and ecologies and lots more. I would not be surprised that the interests of communities within biology drive a lot of the growth of the encyclopedia. If the kinks are worked out, it could be a tool that a group of people interested in, say, orchids, could use to store and study their data. Seen that way, it wouldn’t have to hit all 1.8 million species pages to achieve something important.

Update: I just discovered that the news of EoL triggered a tidal wave of traffic–11.5 million visitors Tuesday morning! (I hope I played some part in the chaos.) This brings up an important aspect of EoL–it’s not just for scientists. This could potentially be a place where millions of people can learn about cuttlefish, mushrooms, slime molds, and all the rest. That strength should not be forgotten in the discussion of genome access and the like.

Update, Wed. 2/27 8 am: Henk Poley informs us that the EoL web site has reverted to the demo version. Hmm…

Kim writes:

“This is my tattoo of Darwin. It’s from a political cartoon published in the late 1800’s. As I’m an anthropologist studying human evolution, it felt appropriate.” The original cartoon appeared in Hornet magazine in 1871, in the wake of Darwin’s publication of The Descent of Man. Here is the magazine editor’s note; if you then press “next” you can see the original. Wikipedia has a cleaner copy of the original.

Click here to go to the full Science Tattoo Emporium.

“This is another Haeckel- a brittle star. I am a physical chemist, but I’ve always admired Haeckel’s obsessive use of visual and design analogy to bolster his (useful, but not entirely correct) ideas about evolution. ” -Aurelia Honerkamp-Smith, PhD student, University of Washington.

Click here to go to the full Science Tattoo Emporium.

Click here to go to the full Science Tattoo Emporium.