The Atavism

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This a PhD student in evolutionary genetics who very occasionally thinks he has something that the internet simply needs to know

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  • September 18, 2010
  • 11:52 PM

Sunday Spinelessness - Throwing pesky males off the scent

by David in The Atavism

We often think about evolution as a competition, but it's not always clear who the competitors are. Popular accounts of evolution often talk about species competing for survival, Darwin saw evolutionary change as the result of individual's struggle for existence and Richard Dawkins recast individuals as proxies in a battle between genes. A new paper form Kerstin Johannesson and her colleagues at the University of Gothenburg highlights another ongoing competition which explains a good deal of biology: the battle of the sexes.In sexually reproducing species, the costs of making the next generation often fall unevenly on males and females. Take the rough periwinkle, Littorina saxatilis for an example.

Periwinkles are snails that live in the harsh zone between the sea and the shore on rocky beaches. Life in the inter-tidal means a perwinkle can expect to spent some if its day underwater, some high and dry, and be buffeted by waves the rest of the time. Female L. saxatilis have tweaked the typical marine snail lifecycle in response to their harsh habitats. Instead of laying a lot of eggs which hatch as tiny swimming plankton, L. saxatilis females retain a relatively few eggs within their shells. Safely stowed by their mothers, the young snails can develop to such a size that they are able to look after themselves once they hatch. Which is all well and good, but the maternal care displayed by these periwinkles means and females have very different interests than females when it comes to mating. From a male's point of view more is better, since every mating will increase the number of offspring he will sire. For females it's a different, they can only retain so many eggs so only need so many matings to maximise the number of offspring they will produce.

In my little sketch of this sexual conflict I've suggested females actually decrease the number of offspring they produce with each mating after some optimal point. That's with good reason, mating almost always comes at some cost. The examples from species with sexual conflicts can be gruesome; male bedbugs exclusively inseminate females by puncturing their abdomen with hyperemic penis, some male water striders will attract the attention of predators unitll would-be mates yield to their advances, and ducks, well, Carl Zimmer has said enough about the ducks. There doesn't seem to be anything quite as unsavory going on with these snails, but Joannesson and colleagues were able to show mating still comes at a cost. Inter-tidal creatures are always at risk of being washed off their rocks. Enough rough periwinkle lives have been lost to the waves that all around the world L. saxatilis populations have evolved into two distinct morphological types, a form with a large muscular foot capable of tightly gripping rocks dominates low on the shore while a less muscular form lives higher on the beach. Since a mating couple presents twice as much surface area to an incoming wave, you might expect mating increases the chance a periwinkle gets swept from the rocks. To test this idea researchers got crafty. Literally, they broke out the hot glue guns and stuck empty shells on to females and saw what happened. They showed that periwinkles sporting an extra shell were more likely to fall off a platform dragged underwater in a laboratory tank and less likely to survive in the wild. L. saxatilis populations are often very dense (around 200 snails per square metre in this study) so females don't have to go out of their way to provision their eggs with sperm and, given the cost of mating, it's in their interest to dissuade males as much as possible. So how do they do it? In general, snails seek out other snails by following chemical cues in the trail of mucous they leave behind them. Periwinkles males in particular have been shown to follow female trails when they are on the lookout for a mate, so there must be some clue in that mucous that marks it as belonging to a female. To see how L. saxatilis males do at finding females the researchers collected populations of this species, and three other periwinkle species that live in much sparser populations on Swedish beaches They then filmed these captive snails moving about in the laboratory and totaled up this distance each male covered in following female and male trails. By comparing L. saxatilis male's tracking ability with males from these other species the researcher's could isolate the effects of the sexual conflict in L. saxatilis . These other species have sparser populations and different mating systems, which means females are less likely to achieve the optimal number of matings and sexual conflict is less likely to arise. Heres what they found.

Each point in these charts is the result recorded from one male, the position of the point depends on this distance he covered following male trails (the y- or vertical axis) and the distance covered following female trails (the x- or horizontal axis). So, in the first chart the majority of males spend the majority of their time following female trails while one crawled to the beat of his own drum an followed male trails to the tune of 400 millimeter without showing the slightest interest in females at all. The same overall patter, males following female trails significantly more often than male trails, is repeated in each of the other species (charts 'a' through 'c') but not in L. saxatilis. Male L. saxatilis don't seem to be able to pick male and female trails, even when a different population was subjected to the test (so it's not a local effect in the Swedish snails) and when they were given an hour to get sniffing. So what's going on? Are females deliberately putting pesky males of their scent, or do males in such a densely packed species just not have to bother with tracking females? As the authors point out, the latter seems unlikely since the male's inability to pick females trails leads to an unusually large number of male-male couplings in the wild. Time spend tracking and mounting a male is time that could be spend in search of a female. So, even in a dense population, it's in a male's interest to be able to tell the difference between male and female trails. To put it to the test, the researchers ran one more test. This time the L. saxatilis males were observed among females from another species (the flat periwinkle L . fabalis). This time, even with the species gap, the L. saxatilis males have not trouble picking out females:

So, given the chance, L. saxatilis males can find female trails but it seems female L. saxatilis aren't giving them the chance. So, by smelling like males these females reduce the burden of unwanted matings and frequently set males up on accidental male-male couplings

Johannesson, K., Saltin, S., Duranovic, I., Havenhand, J., & Jonsson, P. (2010). Indiscriminate Males: Mating Behaviour of a Marine Snail Compromised by a Sexual Conflict? PLoS ONE, 5 (8) DOI: 10.1371/journal.pone.0012005... Read more »

  • August 28, 2010
  • 04:21 PM

Sunday Spinelessness - New Zealand's GIANT Sprintgtails

by David in The Atavism

I know, a couple of week it was multiple exclamation points, then a reference to lyrics from a band anyone who is remotely cool is trying to forget they ever liked and this week it's all caps all the way. Hopefully, by the end of this post you'll agree that, this time at least, the subject left me with no option. I missed out a little fact about peripatus when I wrote about them the other day: Dunedin is full of them. There is even a local endemic species which appears to be restricted to one patch of "bush" which is little more than a road-side paddock. So, before I wrote that post I went on a little excursion to another reserve that I know has peripatus in the hope I'd find something to illustrate my ravings. I didn't uncover any of those wonderful animals, but what I did find was every bit as cool:The little grey-blue thing with the bright yellow spikes is Holacanthella paucispinosa, one of New Zealand's giant springtails. Are you amazed yet? Perhaps you need to know a little more about normal springails before you can appreciate the quite grandeur of the giants. I've writen about springtails (also known as Collembola) before, but they're animals that are worth two takes. Springtails are small, six legged arthropods which live mainly in the soil and leaf litter and such moist habitats. This might be the first time you've heard of them, but they've around you for your whole life. They live on every continent (including Antarctica) and there are as many as 100 000 of them in your average square metre of soil. If you were to go outisde now and pick up a clump of soil from your garden or your lawn you'd almost certainly see a bunch of tiny elongate or globular creatures crawling around and, a few seconds later, vaulting off into the air. That bouncy behavior is achieved with an organ that is neither a spring nor a tail. It's called the furcula (meaning "little fork") an it is held under tension under the abdomen. When a springtail senses danger it can release the furcula, driving it into the ground and flinging the animal away from the threat.Drawing of a springtail from a British National History Museum display, the furcula is the fork-like organ on the underside of the animalWhen they aren't flinging themselves around at random, springtails are playing an important role in the health of the soil. They contribute to the breaking down of organic matter themselves, and, at least as importantly, they move spores from mycorrhizal fungi from plant to plant. Mycorrhza are among the most important organisms on earth. They live on the roots of plants, where they help process soil minerals for their host in exchange for a more or less constant flow of sugars for the plant's photosysthesis. Almost all plant species have Mycorrhzal relationships, and the fungi are key players of the productivity of ecological and agricultural plantations. These two important jobs make springtails a major contributor to nutrient cycling in the soil. Given their enormous abundance and important jobs you might wonder why you don't hear a bit more about springtails. Well, most springtails are really, really small. To prove the point, I've just popped outside and pulled a brick from a retaining wall in our garden (it's OK, the giant clay back stayed up):

The tiny white thing in the upper left is a pretty big springtail (for North American readers, a New Zealand 50 cent coin is almost exactly the same size as a quarter). I didn't think to add something to provide scale in the H. paucispinosa photos, but that springtail would happily cover the "50" on the coin. H. paucispinosa's big cousin from up north, H. duospinosa would cover a good deal more than half diameter of the coin. New Zealand has a fair few giant invertebrates. Every time I introduce myself as someone who studies snails I get asked about the giant carnivorous Powelliphanta (I study small snails that eat biofilms and are generally considered less cool). To those you can add the flax snails, weta, the glorious giant bush dragonfly (kapokapowai) and a one and a half metre long long earthworm. The Holacanthella usually get missed off the list of New Zealand giant invertebrates, even though they are many times larger than most of their relatives. I've done my bit in trying to fix that. These are the springtails I mentioned spending a summer looking for in my previous post. I did a summer studentship with Mark Stevens from Allan Wlison Centre in which we collected new samples from all over the country to get a gauge on just where they live and how they are doing. We published some of our results in the New Zealand Journal of Zoology .
As you might have guessed for our paper's venue it we didn't present any earth shattering new results, instead we focuses on laying the ground work for anyone that wanted to do some more detailed studies of these creatures. We looked at all the currently described species in museum collections (Te Papa has pictures of two of the type specimens online) and in our new specimens and found that the existing key, the algorithm by which someone can identify a specimen to a species, didn't quite work. Some of the characters that were meant to diagnose species polymorphic and spread across all species So we updated the keys, and presented updated data on the distribution of each species whcih might form the basis of further studiesThe distirbution of giant springtail species and populations might be particularly interesting, since they are reliant on rotting hardwood logs for life and don't appear to able to disperse over any great distance. This lack of dispersal ability might mean that genetic relationships between Holacanthella populations might bare the mark of ancient geological and climatic events which have been overwritten in more dispersive animals. The Holacanthella's Australian cousin, the Acanthanura (which it's my patriotic duty to point our aren't quite as big as our giants...) have been used to infer small patches of forest that survived the last ice age. Their reliance on hardwood also makes the New Zealand's giant springtails interesting from a conservation point of view. We spent a lot of the summer in Wellington's hills looking for H. spinosa which was recorded all around the city at the turn of the 20th century. Most of those forests have been logged, and, though there is plenty of regenerating native bush around Wellington, H. spinosa didn't seem to survive the logging. By contrast, managed forests around Nelson and the Tongariro National Park had species-rich and dense population. It seems the giant springtails are particularly susceptible to changes in their forests. In fact, we even suggested that the presence of giant sprintails in a forest patch can be used as a marker for forest health ("canaries in the undergrowth"), in which case the City Council should be pleased to learn they are living in the little forest fragment I found these guys in!
... Read more »

  • July 28, 2010
  • 09:42 PM

The First New Zealanders and their rats

by David in The Atavism

Crispin Jago has made a very cool thing, a periodic table of irrational nonsense. Rolling my eyes over the groups, wondering how people can believe some of these things, made me think about New Zealand's unique ecosystem of kooky ideas. We don't have to suffer creationists in any organised sense and I don't think anyone is too into ear candelling, but those TV psychics have found themselves a niche to exploit and most people seem think chiropratric and homeopathy are normal parts of medicine. Then I was reminded about our very own, home grown cranks. There are people who believe that New Zealand was settled by Celts several hundred years before it was discovered by the ancestors of modern Māori. It probably goes without saying that these people are nuts, but the idea of a pre-Māori civilization in New Zealand is one of our culture's enduring myths. It's worth talking about why people who are serious about studying our country's prehistory have discarded it.People coming to this question for the first time my want a little bit of background. The settlement of the Pacific is one of the most interesting stories in our species' history. I did the field work for my PhD (on landsnails, and not people) in the Cook Islands and you get a feel for the enormity of that achievement when you travel around that group. To fly from one island to another you walk out across the tarmac and meet your pilot, who is almost invariably sitting on the steps to his 12 seater plane, reading the paper through massive aviator glasses. Once you're safetly stowed you get your safety briefing ("it's gonna be pretty fine all the way, should be a good flight") and you take off. The pilots don't close the door to the cockpit, so you can see out the windscreen, but all you see is ocean and sky. You can fly for an hour without seeing land in front of you or out your window. Then an island looms. A few minutes later you land, and, even among the Cook Islands, you're in a new culture. The Polynesian people who discovered and settled these tiny islands separated by such vast distances were master navigators. Without metal tools or written records, let alone maps and compasses, they very deliberately settled islands (taking livestock and crops with them), maintained trading relationships between island groups and almost certainly made it to South America (very likely beating Columbus in the process).Schematic of the settlement of the Pacfic (this one is taken from a study of the evolution of Austronesian languages)The "mainstream" view on the settlement of New Zealand fits nicely into what's known about the settlement of the Pacific. There is good evidence that the bulk of Polynesia was settled in a stepwise fashion, moving west to east with the prevailing winds. Eastern Polynesia was settled by about 800 AD. The far reaches reaches of Polynesian - Hawai'i, Rapanui and New Zealand would require a different pattern of migration (upwind, or over vast distances) and remained, with Antartica, as the last uninhabited lands on earth for hundreds of years.The first evidence for humanity in the New Zealand archeological record comes from the Wairau bar, where artifacts similar to those from contemporaneous sites in the Society Islands and the Southern Cooks have been dated to about 1280 AD. At the same time the pollen record shows New Zealand's first wide scale deforestation, trees being replaced by bracken, scrub and charcoal. A few hundred years later the much sparser record of sub-fossil animals shows its first mega-faunal extinctions. Combined with evidence for "sattelite" settlements in the Kermadec islands (on the edge of the tropical Pacfic) you have exactly the pattern of evidence you'd expect to see with the settlement of islands as remote as Te Wai Pounamu and Te Ika a Māui - settlement as an extension of an ongoing process with clear evidence for human impacts starting from a date that makes sense in that frameworkCompare that with the Celtic NZ people. The idea of Celts arriving in New Zealand without leaving any real evidence of their presence anywhere else outside of Europe hardly needs talking about. When we look within New Zealand, almost all the evidence supposed to support a pre-Maori celtic civilization amounts to big rocks that form, if you just imagine they used to be arranged slightly differently, a giant surveying network. Or astronomical observatories. Proponents of the Celtic NZ hypothesis spend very little time trying to find any evidence for the populations that must have lived, died, eaten, built, dug, farmed, and buried their dead in New Zealand to support these mad priests' plans to move megaliths across the country. And when they do the results are less are less than convincing By all accounts they treat the historical method with about as much respect as the scientific one, so academics don't take them very seriously. In fact, you'd think these claims are so kooky that there was really no need to rebut them. Sadly, the Celtic NZ people seem to have convinced at least a few people that they are on to something. I'm sure part of the reason for that is New Zealanders were once taught that the ancestors of modern Māori did meet another people when they came to New Zealand.Up untill about the 1960s school textbooks said the Moriori were a Melanesian people that were driven off the New Zealand mainland by Māori, with a few survivors taking refuge on the Chatham Islands (called Rekohu in their language). That idea had been rejected by every scholar who's addressed it since the 1920s because it's clear that the Moriori descended from mainland Māori and the unique aspects of their culture were acquired during their subsequent isolation. Part of the reason the Moriori myth came about in the first place is that it fitted into a Victorian narritive view of history - a chain of never ending progress It was only right that Moriori hunter-gatherers were replaced my the adventurous and noble Māori, just as the advanced British settlers would in turn assimilate the Māori. We might have given up that story, but the Moriori myth is still tied to politics in New Zealand. For people who think the New Zealand government shouldn't make reparations for its breaches of the Treaty of Waitangi the idea that Maori themselves were once colonisers looks like a get out of jail free card. Russel Brown quoted one example in 2004:Leaders and academics that hark back to the pre-European days of Maori domination of New Zealand have driven this opportunism. They appear to conveniently forget that Maori violently conquered the Moriori, the original settlers, and their claims of tangata whenua status and demands for compensation for historical grievances appear to many to be ill informed.Ignoring the gaps in the logic (the Treaty is between Maori and the crown, and is not contingent on Maori being the original inhabitants of New Zealand) such claims also face a pretty big evidence gap. The piece Brown picked up was from then Member of Parliament Muriel Newman. Dr Newman is no longer and MP, but she has set up a think tank (which shows about as much evidence for thought as any group with that name) and it seems she hasn't given up on her politically motivated brand of crypto-history. Here's her latest, in which she tries to argue New Zealand has no indigenous people: Archaeologists agree that humans first settled in New Zealand well over 1,000 years before the main Maori migration, which is estimated to have arrived around 1200 AD. Their evidence is based on the exhaustive forensic examination of historic plant and animal remains. They believe that the settlement of New Zealand was most likely a continuous process, a view that is certainly consistent with early settler journal accounts (from the proceedings of the Royal Society of New Zealand) which indicate that not only did Moriori precede Maori, but that when they arrived in the... Read more »

Holdaway, R. (1996) Arrival of rats in New Zealand. Nature, 384(6606), 225-226. DOI: 10.1038/384225b0  

  • June 7, 2010
  • 10:12 PM

If some of us have Neanderthal genes, are Neanderthals us?

by David in The Atavism

I got a little bit starry eyed writing about the Neanderthal genome the other day. I chose to retrace the arc of scientific progress that links the initial description of Neanderthal man as something different than modern humans to the point reached last month, where we are able to tag some of those differences to a single gene. Most of the news stories about the Neanderthal genome focused not on the genes that made us different from them, but a small percentage of the genome that reinforced the continuity been them and us. Genetic evidence that Neanderthals interbred with the ancestors of some modern humans. The revelation of these ancient assignations has caused some quite sensible people to say some quite silly things about what species are and what Neanderthals were. So, perhaps I can compliment my slightly hazy earlier piece with a more hardheaded take on why Neanderthals remain a species unto themselves.

Let's start with the evidence that Neanderthals interbred with the ancestors of modern humans. Modern humans (Homo sapiens) arose in Africa about two hundred thousand years ago, all modern human populations outside of Africa descend from a relatively small number of migrants who left that continent between eighty and fifty thousand years ago. When those migrants first left Africa and entered the Middle East they would have met other humans. The ancestors of the Neanderthal had moved out of Africa and established themselves in Europe and Central Asia thousands of years before. Until now we haven't known which of the four 'F's (fighting, fleeing, feeding or reproduction) followed that first contact, the Neanderthal genome has given us a clue.

When you compare individual DNA bases that are variable within modern human genomes to the corresponding sequences in the Neanderthal genome you find that non-African sequences match the Neanderthal sequence slightly (but significantly) more often than African sequences do. It's possible that this pattern is an artifact of our poor sampling of African genomic diversity (that observant nerd Christie does a good job of explaining how here) but for the sake of argument let's take it for granted that his pattern is the result of ancient interbreeding. The authors of the paper describing the Neanderthal genome estimate people with no recent African ancestry inherited between one and four percent of their genome from Neanderthals. That number is the same for Papuan and East Asian populations as it is for Europeans despite Neanderthals having lived alongside Europeans for thousands of years, suggesting any interbreeding that contributed to modern human genomes was limited to that first period of contact.

This is where the problems start. Having heard the news that Neanderthals and some of our ancestors might have once swapped genes some people remember that nice easy test of species-status from high-school biology. Something like "if two animals can interbreed then they're part the same species." So, are we Neanderthals; or are Neanderthals us? No. In fact, the Neanderthal genome serves to highlight some the mistakes we commonly make when start trying to define species.

Biologists have spent a lot of time arguing about just what a species is and how can delimit species from the creatures that we study, too often we've forgotten that those are two different arguments. DeLene from Wild Muse has a thoughtful overview of some of the factors that contribute to the "species problem" in her review of Jody Hey's book on the same topic. You should read her piece because the species problem really is a fascinating philosophical question, but I think most of the fights that erupt around competing definitions of species come from a failure to understand that defining species and organising critters into species are two different tasks. We've been studying speciation, the process by which new species arise, for a while now and we've developed a pretty good idea of how it works. Two populations stop interbreeding with each other, during that period of "reproductive isolation" genetic changes in one population can't effect the other so natural selection and random changes (called genetic drift) change each population independently. Species are populations which are on independent evolutionary trajectories. Reproductive isolation drives the independence that is at the heart of what species are, but it's not the sine qua non of a species. James Mallet from University College London has made a special study of hybridisation, and he reckons 10% of animal species and a whopping 25% of plants interbreed with other species from time to time. As molecular tools have been applied to non-model organisms it's become increasingly clear that the "species barrier" is more porous than we'd thought, and species can maintain their independence even in the face of the occasional injection of genes from other species.(If you're interested in the wider question, I've written a bit on the species problem here. The short version is we should see competing "species concepts" as operational tools that might be used to help delimit species, but not as definitions).

Now, think about the results from Neanderthal genome. Most sequences in that genome are separated from their human counterpart by a split that happened over five hundred thousand years ago. There is pretty good evidence that Neanderthals and the ancestors of non-Africans interbred when they met each other in the Middle East about four hundred and fifty thousand years after that initial split. That gene flow had the potential to homogenise the two populations into one, but it didn't. Each lineage maintained its identity. For the twenty or so thousand years that Neanderthals continued to exist they retained identifiable morphological traits. There are fossils in Europe that some argue show a mixture of characters, but any interbreeding in that continent left no mark on modern European genomes, which have no more Neanderthal DNA than Papuan and Chinese genomes do. At the same time, the authors didn't detect any flow of modern human genes into Neanderthal genomes (so it's not a case of of modern humans swamping Neanderthal populations and erasing any trace of genetic admixture in the process). The available evidence seems to point o Neanderthals and modern humans as separately evolving populations, and a little bit of gene flow between them wasn't enough to upset that pattern.

I should stress, by saying H. neanderthalensis and H. sapiens are different species we aren't saying very much about how different Neanderthals were from us. Species are not defined by a degree of difference, or an essence that was missing in Neanderthals but is present in us, they're just another human population that was moving in a different direction (and eventually extinction). If some of us do have Neanderthal genes, then it only goes to show how fuzzy the line between our species and the rest of the biological world is.

Green RE, and many, many others (2010). A draft sequence of the Neandertal genome. Science (New York, N.Y.), 328 (5979), 710-22 PMID: 20448178

James Mallet's bit on the frequency of hybridisation is taken form here:

... Read more »

Green RE, Krause J, Briggs AW, Maricic T, Stenzel U, Kircher M, Patterson N, Li H, Zhai W, Fritz MH.... (2010) A draft sequence of the Neandertal genome. Science (New York, N.Y.), 328(5979), 710-22. PMID: 20448178  

  • May 22, 2010
  • 04:22 PM

Sunday Spinelessness - Attack of the Killer Sponge!

by David in The Atavism

Chondrocladia turbiformis, a ruthless carnivore hauled from bottom of the sea off new New Zealand by NIWA scientists, has been named among the top ten new species described last year. This abyssal predator isn't a kraken, a plesiosaur that time forgot or even an improbable (but awesome) hybrid. It's a sponge.
It may come as some surprise that a sponge can be a carnivore, or even that sponges are animals. Sedentary as they are, sponges tick all the boxes for inclusion in the kingdom Anamalia. They eat other organisms to make energy and build their body (differentiating them form plants and algae), they have cells enclosed by membranes (not cell walls like plants and fungi) and they are truly multi-cellular, with specialised cell-types (which sets them apart from protists). On the other hand, sponges are pretty unusual animals. Sponges have no nervous system, no gut, not circulatory system and their cells don't form tissues. The relative simplicity of sponges helps us to understand the evolutionary history of animals, by plotting some of the characteristics of modern animals onto a phylogeny we can see what order those characters evolved in:

How the sponges relate to other animals. The protostomes and deuterostomes differ from each other in in fate of the blastopore, the first opening to form during embryonic development. In protostomes it becomes the mouth, indeuterostomes it becomes the anus.
So, sponges are useful in trying to understand the evolution of animals. But we shouldn't view modern species as steps along a path toward more complex animals. Sponges are amazing creatures in their own right, for a start they're the only animals that don't have a mouth. Most sponges feed by drawing water into the their body through pores and absorbing bacteria and small algae from that water with specialized cells on the inner surface of their bodies. The cells of the inner surface have two sets of projections to help them with this task. The tail-like flagella which beat together to get water flowing over the absorbing cells and the hair-like micro-villi which increase the cells surface area and make them more efficient absorbers (the guts of more complex animals play the same trick on a larger scale). Most sponges further increase the efficiency of this process by taking the form, and the function, of a chimney. The tubular forms are help together by a mesh of small calcium carbonate structures called spicules.
Filter feeding works well in relatively nutrient-rich shallow waters, but scientists have pulled odd looking sponges up from the bottom of the ocean. Some of those sponges still had the characteristic sponge filter feeding system, but others had lost it all together. Quite how these strange sponges were getting by in the dark and unproductive abyss without even the normal sponge feeding system remained a mystery until 1995 when French researchers found a relative of the deep sea sponges in a relatively shallow submarine cave. Abestopluma hypoa gave scientists their first chance to observe these sponges, and what they saw was amazing: it was a carnivore. In life A. hypoa projects a set of filaments into the water. Those filaments are covered in tiny spicules which act like Velcro (that's the author's own simile) grabbing passing crustaceans and holding them in place. It takes a while for the sponge to get its meal, cells make contact with prey within an hour but the actual ingestion follows a period of cell growth and movement which completely covers the animal after a day. It takes another couple of days to completely digest the crustacean. Since that first discovery scientists have discovered many more carnivorous sponges, with a surprisingly large number coming from sea mounts off New Zealand and in the Southern Ocean. The topic of today's post (I knew I'd get to it eventually...), Chondrocladia turbiformis, is one of the newest killer sponges, and it looks a bit like a mushroom:

The Chondrocladia are a bit of a special case among the carinovore-sponges because they have retained the rudiments of their filter feeding system. They don't appear to use it to supplement their diet, rather it's been re-purposed to inflate a balloon like structure the sponge uses to help capture prey. (For a stunning example of this structure in a live sponge see the photo that illustrates Olivia Judson's article here.). But the thing that really distinguishes C. turbiformis from the already amazing carnivorous sponges are its spicules:

Beautiful as they are, those symmetrical curved claws in D and E are run of the mill for Chondrocladia. The spinning top spicules in G and H are something quite different. It was only through the description of C. turbiformis and a related species C. tasminae that it became apparent these spicules, with have been named trochirhabds, are present in some modern Chondrocladia species. It's not extactly clear what these cool little spiclues are doing in modern Chondrocladia but they give us a clue to the history of carnivorous sponges. Spicules just like the trochirhabds described from C. turbiformis have been found in marine sediments from the Jurassic period. It appears the carnivorous sponges that it took us until 1995 to learn about have been living in the oceans for at least 150 million years.
The rest of the this years top ten - including bombardier worms, amphibious sea slugs and giant web building spiders - can be found here.

Vacelet, J., Boury-Esnault, N., Fiala-Medioni, A., & Fisher, C. (1995). A methanotrophic carnivorous sponge Nature, 377 (6547), 296-296 DOI: 10.1038/377296a0

Jean Vacelet,, Michelle Kelly, & Monika Schlacher-Hoenlinger (2009). Two new species of Chondrocladia (Demospongiae: Cladorhizidae) with a new spicule type from the deep south Pacific, and a discussion of the genus Meliiderma Zootaxa (2073), 57-68... Read more »

Vacelet, J., Boury-Esnault, N., Fiala-Medioni, A., & Fisher, C. (1995) A methanotrophic carnivorous sponge. Nature, 377(6547), 296-296. DOI: 10.1038/377296a0  

Jean Vacelet,, Michelle Kelly, & Monika Schlacher-Hoenlinger. (2009) Two new species of Chondrocladia (Demospongiae: Cladorhizidae) with a new spicule type from the deep south Pacific, and a discussion of the genus Meliiderma. Zootaxa, 57-68. info:/

  • March 26, 2010
  • 12:33 AM

Does a forty thousand year old finger point to another human species?

by David in The Atavism

DNA extracted from a 40 000 year old finger bone found in a cave in Siberia might be evidence for a previously unrecognized human species. Or it might not be. The bone, which comes from what New Zealanders call a "little finger", Americans call a"pinky" and paleo-anthropologists call the "distal manual phalanx of the fifth digit", was found in the Denisova cave, in a region of Siberia from which remains of members of both our own species (Homo sapiens) and Neanderthals (H. neanderthalensis) have previously been found. The mitochondrial DNA (mtDNA) sequences generated from the finger bone are distinct from both modern human sequences and from previously published neanderthal sequences, but inferring species boundaries is a tricky business and the mtDNA sequences are not, in and of themselves, proof that the finger belonged to a member of a third human species.
Here's the big figure from the paper, which was presented by Johannes Krause and colleagues in Nature yesterday. It's a phylogenetic tree which relates the little finger's mtDNA to H. sapiens and H. neanderthalensis sequences (click to see a high-resolution version):

The Denisnova sequence is red, Neanderthal sequences are in blue and modern humans are grey. So, the Denisova mtDNA forms a distinct lineage that isn't represented in modern humans or in previously published Neanderthal sequences. By using the tree as the basis for molecular dating the researchers where able to estimate that Denisova lineage separated from other human mitochondrial lineages between 0.78 and 1.3 million years ago. The temporal context the molecular dating adds to the phylogenetic tree helps to us understand where this new mitochondrial lineage might fit into humanity's family tree.I've said before that most of our species' history was played out in Africa, and, in fact, the same is true when we step up a taxonomic level and look at our genus. All the human species that have been found outside of Africa descend from migrants that moved out of that continent at some stage. Here's a schematic representing some of the species in the wider human family tree and the timing of the migrations that moved them out of Africa.

How does the new evidence presented by Krausse et al. fit into that scheme? Perhaps the simplest interpretation is the the Denisova lineage represents a new species. The estimated age of the Denisova lineage makes it too young to have been carried out of Africa by the first wave of H. erectus migrants to leave Africa and apparently too old to have been inherited from the migrants that went on to form the Neanderthal lineage. If the Denisova sequence is something new then we'll have to update our family tree, adding a new branch and a fourth migration out of Africa.

John Hawkes thinks we should hold off on updating the family tree too qucikly. The Desinova specimen might be a Neanderthal. At first glance the tree presented by Krausse et al. seems to dispel that possibility since previously identified Neanderthal sequences are more closely related to modern human sequences than the new linaeage, but that tree is based entirely on mtDNA. The mitochondrial genome is inherited as if it was a single gene. We can often use trees estimated from a single gene ("gene trees") as a proxy for species-level relationships ("species trees") but, in fact, every gene in a population has its own history and there there are scenarios that can push a given gene tree away from underlying species tree. Perhaps the easiest way to visualise how you'd end up with mitochondrial lineages that diverged millions of years ago within a single species is to think about genetic lineages moving through a population while speciation happens. Rember, speciation is a process, not an event, when new species form when populations stop sharing genes with each other. What happens if multiple different gene lineages are present in the ancestral population at the time that this gene flow stops? Usually, given enough time, each species will "sort" into specific gene lineages that descend from just one of the lineages in the ancestral population, but it's also possible for one (or both) species to maintain multiple lineages for some time. Such "incomplete lineage sorting" makes gene trees bad proxies for species trees and it's just possible that something like this has happened in Neanderthals:

Perhaps by moving to the very Easterm edge of the Neanderthals range we've sampled for the first time a lineage that existed in that species for the whole time it was in Europe. Maybe, and Hawkes surely knows a lot more about paleobiology than I do, but I don't really buy it. It's certainly possible for a species to harbour deeply divergent mitochondrial lineages, but the time it takes for gene-lineages to sort within a species is relative to the effect population size of that species. Neanderthals probably had a relatively small effective population size (and mtDNA definitely does, since only females pass it on and then in only one copy) making the retention of multiple lineages over hundreds of thousands of years seem like a long shot. As Hawkes argues, strong geographic structure in Neanderthal populations might have aided the retention of divergent genetic lineages against those odds, maybe the Denisova mitochondrial lineage was extinct in Western Europe but common in Central Asia? It's possible, but I wouldn't bet on it.Finally, the Denisova sample might be our first look at H. erectus DNA. H. erectus remains have been recovered from China so it seems possible they where in Siberia too. As I've said, the molecular dating of the Denisova lineage probably makes it too young to be a descendant of the first wave of migration form Afirca (though, of course, there is some uncertainty associated with that dating), but it might be evidence of genetic exchange between African and Central Asian populations of H. erectus. As we've come to understand the origin of our species we've realised that the simple "Out of Africa" model is just that, a model, and the true pattern is more complex. H. sapiens really did have its start in Africa and it really did push out into the rest of the world in the last 50 000 years but during that expansion populations have continued to exchange genes. There's no reason to believe that that H. erectus would not have done the same, perhaps the main thrust of the H. erectus expansion was 1.6-2 million years ago but genes continued to flow in and out of African for sometime after that. So, there are three possibilities for the Denisova sample:

It could be a new species,
It could be an ancient mitochondrial lineage retained in eastern Neanderthal populations but lost elsewhere
It could be the first H. erectus sequence.

We'll need more genes (Krausse et al. report they are working on the nuclear genome) or more complete specimens to know for sure but I'll throw caution to the wind and say I think the first scenario to be the most likely and the second the least probable (remembering of course, that I'm not an anthropologist and these are pretty subjective estimates!). Perhaps I'm displaying some biases because I aslo think numbers one and three would be the cooler results. In either of those scenarios are true then we can add a third human species (alongside the Neanderthals and the 'Hobbit' H. floresiensis) that modern humans might have interacted with - it's just so fascinating to imagine our ancestors living alongside other human species and how differently the world might have turned out if those other species had survived the few thousand years that separate us. You should read Carl Zimmer's post on the paper, he's compiling expert opinions as they come to him. There's also some more qualified comments via The Independant who made up for their poor news article on the story by having Chris Stringer from t... Read more »

  • February 25, 2010
  • 11:41 PM

Nucleotide diversity - what two new African genomes mean

by David in The Atavism

If you wanted evidence that we live in a post-genomic age you would need to look no further than the headlines in the science section of the newspaper last week. A man dubbed Inuk who lived and died in Greenland 4 000 years ago had dry earwax and might have gone bald if he lived long enough, Tutankhamun was inbred and had a cleft palate and Desmond Tutu has had his whole genome sequenced. What about the science behind the hook? Ed Yong has the the story of Inuk (whose genes tell us about migrations into and out of North America). I'll leave it the reader to imagine what the broader significance of Titankhamun's illnesses might be but the publication by Stephan Schuster and colleagues of complete genomes from Desmond Tutu and !Gubi, a Khoisan tribal elder, is an important step in our understanding of human genomic diversity.

As I've said before there really is no such thing as the human genome. There are millions of differences between individual genomes and we are each born with about 150 new muations. In an age in which we can sequence assemble and analyse entire genomes in two years understanding the breadth of human genetic diversity is at last an achievable goal and if you want to understand human diversity then you need to look to where we came from. Trace any family tree back far enough and you will end up in Africa and, in fact, most of human history was played out entirely in that continent. Modern humans arose in Africa about 250 000 years ago and only spread out to Europe and the rest of the world in the last 60 000 years, displacing Homo erectus in the process. The migrants that founded the modern European, Asian and American populations would have carried with them only fraction of humanity's genetic diversity when they left Africa but untill recently genomics has focused on those populations. Until last week the two African genome sequences available to researchers were both from Yoruban volunteers to the hapmap project. Although those sequences are very useful they represent only one tip in the deeply branching tree of humanity
Summary of human genetic diversity redrawn from Campbell and Tishkoff (2008) doi:10.1146/annurev.genom.9.081307.164258 . Numbers in brackets are the number of complete genome sequences from each region available before last week.

To broaden our understanding of African genomes Schuster et al looked to the South of the continent and at two people in particular. !Gubi is a Khoisan (or bushman), a member of a one of the earliest diverging groups within the humanity while Desmond Tutu hails for various Bantu peoples. The results taken from theses genomes along with lower density sequencing and genotyping of other Bantu and Khoisan volunteers reinforces just how much genetic diversity exists within Afirca. By using a method called principle component analysis to reduce a the correlations among millions of single base pair differences (single nucleotide polymorphisms of SNPs) to a smaller set of uncorrelated vectors you can see patterns in the genetic diversity of groups. Applying this method to West African (Bantu and Yoruba), Khoisan and European populations reveals the comparative genetic homogeneity within Europeans and that the difference between the two African groups is comparable to that between either of them an Europeans.

All in all Schuster et al found 3 million SNPs that hadn't been previously identified. Those new polymorphisms will be a boon to researchers searching for a genetic basis to, for instance, HIV restiance in Africa or African-American's increased risk to type 2 diabetes. Just as interesting as the new SNPs is the discovery of others that have already been associated with diseases even though Desmond Tutu and !Gubi are healthy 80 year olds. A couple of scientists quoted in dispatches seem to think these genomes will act as quality control, allowing researchers to 'clean up' polymorphisms incorrectly associated with dieseases in other studies but it seems at least as likely that something more complex is going on. The selective, or health, value of a gene can only be measured against the environment it is expressed in and the rest of the genome is absolutely part of that environment. It's entirely possible for a gene to be associated with Wolman disease amongst Europeans but to be of no consequence to busman thanks to the different genetic background against which it expressed.
Uncovering the genetic basis of these diseases and untangling the complex genetic interactions that underly populations' risk to disease still lies in the future but this study also tells us something about our past. Most Khoisan are nomadic hunter-gathers and their ancestors have been for thousands of years, by comparing their sequences to those of agricultural from societies you can see the evolutionary impacts of that switch. Malaria resistance genes, scars from humanities long battle with that disease, are absent from the Khoisan sequences as are genes for digesting lactose as adults. Though those primitive characters have been retained by the Khoisan they are no more an 'ancient' or primitive people than the tuatara is a 'living fossil'. In fact, there are a large number of bases in which European sequences are identical to the corresponding chimpanzee sequence while the Khoisan sequences diverge - lots of those changes will have been fixed at random but the fact some of them are in genes that are likely target of selection (especially perception of taste and smells and immune responses) suggests they may also have adaptive consequences.

The paper is available to under a creative commons license here and if you feel suitably qualified you can play with their data which has been released on the Galaxy framework.

Schuster SC, Miller W, Ratan A, Tomsho LP, Giardine B, Kasson LR, Harris RS, Petersen DC, Zhao F, Qi J, Alkan C, Kidd JM, Sun Y, Drautz DI, Bouffard P, Muzny DM, Reid JG, Nazareth LV, Wang Q, Burhans R, Riemer C, Wittekindt NE, Moorjani P, Tindall EA, Danko CG, Teo WS, Buboltz AM, Zhang Z, Ma Q, Oosthuysen A, Steenkamp AW, Oostuisen H, Venter P, Gajewski J, Zhang Y, Pugh BF, Makova KD, Nekrutenko A, Mardis ER, Patterson N, Pringle TH, Chiaromonte F, Mullikin JC, Eichler EE,... Read more »

Schuster SC, Miller W, Ratan A, Tomsho LP, Giardine B, Kasson LR, Harris RS, Petersen DC, Zhao F, Qi J.... (2010) Complete Khoisan and Bantu genomes from southern Africa. Nature, 463(7283), 943-7. PMID: 20164927  

  • February 4, 2010
  • 01:47 AM

Did the Moa's ancestor fly to New Zealand?

by David in The Atavism

Unlikely cousins? Tinamou from brunorigin @ flickr (CC BY-SA 2.0| Moa from PLoS Biology

New Zealanders often think of our unique biota as a sort of time capsule - a glimpse at lifeforms that have long since been extinguished in other parts of the world. New Zealand has been apart from the rest of the world for 85 million years. At that time the land that makes up our mini-continent split from the super-continent Gondwana, opening up the Tasman Sea and moving northward . A land apart from the rest of the world. Until recently most scientists have thought that the subset of the Gondwanan flora and fauna that set sail on that proto-New Zealand was likewise on its own evolutionary trajectory -insulated from biological happenings in the rest of the world. The idea of the New Zealand biota as a group of refugees from an ancient ecosystem hanging onto "Moa's Ark" has become part of the New Zealand psyche.

In recent years Moa's Ark has sprung more than a few leaks. Icons of our Gondwanan heritage like Nothofagus beech trees have been shown to be recent arrivals. Geologists have suggested the whole continent submerged 20 million years ago, drowning any refugees still on board, and now new research suggests even the most unlikely of immigrants - the giant, flightless moa - may have arrived in New Zealand well after we left Gondwana.

The group of birds to which the moa belonged, the ratites, have long fascinated evolutionary biologists. All the ratites are flightless (though, as we'll see they are related to the quail-like tinamous which can fly passably well) and all the major landmasses that had their start in Gondwana had at least one ratite species before humans arrived on the scene. Africa has ostriches, South America the rhea, Australians have emus and cassowary, Madagascar had the Elepahant bird and New Zealand lost the moa but retains the kiwi. The far flung distribution of the ratites and their apparent lack of ability to disperse between continents has led to them being put forward as a classic example of an idea called vicariance biogeography in which the evolutionary history of a group is driven by the geological history of the land on which they live.

For vicariance biogeographers the evolution of the ratites was driven by the movement of the continents. The ancestor of all modern ratites was a flightless bird living in Gondwana and as each new continent split and rifted away from the super continent it took with it a population of ratites which adapted to the ecological changes brought on by their continent's journey: cassowaries in the Wet Tropics of Australia, ostriches on the African Savannah, rhea on the Pampas. It's certainly a nice story, but science has a way of ruining nice stories. The role of vicariance of evolution in the ratites was put to the test once we became able to use molecular evidence to reconstruct the relationships between species. If the geologically driven sketch of ratite evolution I presented above is right then the pattern of branching we find among ratites from different continents should match the order in which we know the continents broke up, something like this:

In 2001 Alan Cooper and colleagues sequenced the entire mitochondrial genome (some 12 000 bases of DNA) from representatives of each of the extant ratites and, remarkably, two species of moa. The long, careful process of retrieving DNA sequences from sub-fossil bones deserves a post of its own but for the sake of this article we only need to know what Cooper et al found when they used that DNA to recover the the relationships between ratite species.

The species in bold text above don't fit the pattern that we'd expect from geology alone. If ratite relationships simply reflected the Gondwanan breakup we'd expect to see ostriches grouping with rheas (and apart from the other ratites). New Zealand's two ratite orders are even more surprising, the kiwi lineage is more closely related to the Australian ratites than it is to the moa species. When combined with a molecular clock analysis Cooper et al. concluded that modern kiwis are the descendants of ancient immigrants hailing from either Australia or islands in the Lord Howe Rise (which have since submerged). In order to explain that trans-tasman dispersal the authors reached for the last resort of the desperate biogeographer and invoked a land bridge for which there is little geological evidence. In fact, as we'll see it now seems more likely that the ancestors of the kiwi and the moa flew to New Zealand.

Even with the mitochondrial phylogeny of the group published there was considerable room for uncertainty in how the ratites related to each other. The underlying shape of ratite tree makes it particularly difficult to accurately recover with phylogenetic methods. When we use DNA sequences to estimate a phylogenetic tree we need to find species that share mutations that have accrued during the evolution of the group we're looking at. The branches that relate the different ratite species are relatively short, so there was little time for mutations that set related groups apart from more distantly related ones to accrue. Even worse, the branches that reach to the modern species (the tips of the tree) are very long meaning there has been a lot of time to any mutations that did accrue in those critical short branches to be overwritten*. There are three approaches to dealing with this problem - sequence more genes (since each unlinked gene acts as a separate witness to the evolution of the group), sequence more samples (especially if doing so breaks up a long branch) or use a better model for the way mutations accrue in the genes you are studying. People have tried all three methods to get a better look at ratite evolution. Last year a group centred around the Field Museum in Chicago published a mutli-gene phylogeny of all birds that contained a big surprise for ratite evolution- the most recent common ancestor of all ratites flew.

As long as the ratites grouped together in a phylogeny it was reasonable to assume that they all inherited their flightlessness from the common ancestor of the group. The Field Museum study found that, in fact, the flying tinomous fit right in the middle of the flightless ratites. So, either the most recent common ancestor of the ratites and the tinamous flew and ratite lineages have subsequently lost that ability at least three times or that ancestor was grounded and the tinamous have rediscovered flight. In vertebrates the evolution of true flight has happened three times (in bats, pterosaurs and birds) while there are hundreds of examples of birds that have given up on flying. Moreover, a group of flying birds that are prone to flightlessness is hardly anything new - at least 30 species of rail (including our own weka and takahe) have taken to life on the ground. Given the ways the odds are stacked towards losing flight it seems probable the common ancestor that relates tinamous and ratites flew. The Field Museum study didn't include any moa species and didn't attempt any molecular dating so it's hard to see just how the ancestors of the kiwi and the moa made it to New Zealand

A new study (I knew I'd get to it eventually) published in Systematic Biology throws some light on the New Zealand ratite story. Matt Philips and a team of researchers from the Alan Wilson Centre at Massey University took another look at the mitochondrial dataset used in Cooper et al's 2001 study by adding more kiwi species and using models of DNA evolution that avoid some of the pitfalls of the ratite phylogeny's difficult shape. The new ratite tree and a molecular clock analysis based on that tree confirm the idea of multiple loses of flight in the ratites and add a new finding - the closest living relatives of our giant moa are the quail-like tinamous:
... Read more »

  • January 14, 2010
  • 08:22 PM

The why of the Y-Chromosome's amazing evolutionary rate

by David in The Atavism

There is something faintly pathetic about the Y-chromosome when its lined up with its peers in a karyotype. Each of the 22 numbered chromosomes pair off with a near identical partner just their size while the Y has to shape up to the X which has more than twice as much DNA and 25 times as many functional genes.

The puny Y-chromosome only looks worse when you realise that mammalian sex chromosomes weren't always so mismatched. 160 million years ago the X and Y were just another pair of chromosomes, albeit the pair that the carried the sex determining gene SRY. Over time the chromosome that went on to become the Y stopped swapping genes with its partner, allowing it to maintain a suite of genes that are beneficial in male bodies but not in females. It's the lack of genetic recombination that sent the Y into its decline. Genes on any other chromosome can be swaped between pairs, meaning over many generations individual gene copies (called alleles) are exposed to natural selection independently of alleles either side of them. The same process doesn't apply to alleles on the Y-chromosome. Since the Y is always passed on as a single unit natural selection acts on the whole thing - a broken gene might make it into the next generation because it is attached to beneficial mutations. The efficiency of natural selection is further reduced in the Y-chromosome because it has a relatively small effective population size (less that one quarter of that for normal chromosomes since only males carry the Y and then in only one copy and even then a larger number of males than females don't contribute to the next generation) which makes genetic drift a strong force.

What we've known about the Y-chromosome's past has has shaped out ideas about what it is now and what it will become. Until quite recently the Y was seen as more or less a derelict chromosome, a few broken remnants of the genes still found on the X and a couple of male-specific genes hanging on the the sex determining gene SRY. People have even go so far as to extrapolate the Y's long slow decline to a future time at which the Y will simply disappear. The first clue that the Y-chromosome might be a little more resilient than that came in 2003. The publication of the complete sequence of the human Y-chromosome revealed more than fossils from the Y's more substantial ancestor. There are plenty of those so called "X-degenerate" segments but most of the active genes in the Y are in large repetitive runs of DNA called the "ampliconic regions". The genes in these regions are mainly made of DNA sequences unique to the Y chromosome and are expressed only in the testes - suggesting the Y has been making its own genes at the same time that its been losing the X-degenerate ones.

Untill this week it has been hard to test the idea of a regenerating Y-chromosome in an evolutionary framework. Those large repeated runs of DNA are very hard to sequence (the standard metaphor is putting together a jigsaw puzzle made entirely of sky) so we haven't had another Y-chromosome sequence to compare ours with. Now, thanks to Jeniffer Hughes and colleagues, we do and the result it stunning. Not only has the Y-chromosome been making genes, it's been making them at an outrageous rate. Thirty percent of our Y-chromosome sequences have no counterpart in the chimpanzee. As the authors say that's the sort of divergence you'd expect to see between humans and chickens, which are separated by 310 million years of evolution not humans and chimps which only split 6 million years ago!
It's evident that, far from being in the tail end of an inexorable decline, the Y-chromosome is evolving a good deal more quickly than the rest of the genome. So, the burning question is what is behind that evolutionary rate? There is probably no single answer to that question but it's safe to assume it results from some of the unique features of the Y-chromosome; a lack of genetic recombination, the presence of those large repetitive sections of DNA and the preponderance of male specific genes.
It's usually a good idea when trying to explain an evolutionary phenomenon to think of explanations that don't invoke natural selection as the main driver as a sort of null hypothesis against which to test other ideas. In this case the increased fixation of new genes on the Y-chromosome might simply reflect an increased rate of production of new genes. Those highly repetitive sections of the Y-chromosome are the perfect substrate for a process called ectopic gene conversion in which a Y-chromosome can recombine with itself and as a result duplicate streches of DNA. We know from human studies that a process like this has made wide scale structural changes in the last 100 000 years and it might be enough to explain the Y's unusual gene production.I think it's very likely that natural selection also plays a role in the number of of those new genes that become fixed in the human and especially the chimp lineage. Most of the active genes on the Y-chromosome are expressed in the testes and involved in sperm production. Chimpanzees are highly polygynous, in most cases a female will mate with each of several dominant males in a troop, and a result sperm competition is an important level of selection. . Although humans aren't as polygynous as chimps (and likely haven't been in our recent history) it's clear that fertility selection is still an important force and we know for sure that mutations in the Y-chromosome can lead to infertility so, again, the fate of new genes on the Y-chromosome are likely to be driven by selection.Both the adaptive and non-adaptive explanations above might will be influenced by the lack of recombination in the Y-chromosome. The reduction in the efficiency of natural selection described above will stop very slightly deleterious mutations from being driven to extinction which might mean new genes that would be selected against on any other chromosome become fixed on the Y. This phenomenon can be enhanced when it is coupled with selection producing a 'selective sweep'. If a new beneficial mutation, perhaps associated with sperm competition or fertitily selection, pops up in on a chromosome with a bunch of other mutations that whole thing will be selected for and driven to fixation which has the potential to make for large scale changes quickly.It is likely that the amazing evolutionary rate of the Y-chromosome is a result of some combination of all these factors but it should be possible to disentangle at least some of their contributions. If sperm competition is a major driver of Y-chromosome evolution then it follows that animals that go in for purely monogamous relationships will have comparatively low rates. Evolution has furnished us a natural experiment to test this idea, all gibbon species form pair bonds and are highly monogamous. We could test the sperm production hypothesis by sequencing the Y-chromosome of two gibbon species and calculating the rate of evolution of a Y-chromosome in a monogamous species. .Although I'm happy to present the test of this idea I'm not going to line up to do it, those repetitive sections of DNA make sequencing Y-chromosome so hard that it took 13 years to do the human one and 8 to finish the chimp one.

Hughes, J., Skaletsky, H., Pyntikova, T., Graves, T., van Daalen, S., Minx, P., Fulton, R., McGrath, S., Locke, D., Friedman, C., Trask, B., Mardis, E., Warren, W., Repping, S., Rozen, S., Wilson, R., & Page, D. (2010). Chimpanzee and human Y chromosomes are remarkably divergent in structure and gene content Nature DOI: 10.1038/nature08700... Read more »

Hughes, J., Skaletsky, H., Pyntikova, T., Graves, T., van Daalen, S., Minx, P., Fulton, R., McGrath, S., Locke, D., Friedman, C.... (2010) Chimpanzee and human Y chromosomes are remarkably divergent in structure and gene content. Nature. DOI: 10.1038/nature08700  

  • September 28, 2009
  • 04:41 PM

Where did you get that preposterous hypothesis

by David in The Atavism

From time to time you find youself disagreeing with something you read in a scientific paper. Perhaps you don't think the authors have applied a method correctly or ,more often, you don't think that the results they present are enough to justify the claims made in the their discussion or their university PR department's breathless press release. You don't often end up wondering if the third most prestigious journal in the world might have an April Fool's day issue. But what else is one to think when confronted with an opening paragraph like this one from a recent paper [1]:

I reject the Darwinian assumption that larvae and their adults evolved from a single common ancestor. Rather I posit that, in animals that metamorphose, the basic types of larvae originated as adults of different lineages, i.e., larvae were transferred when, through hybridization, their genomes were acquired by distantly related animals.

Got that? The author thinks that animals with distinctly different larval forms (caterpillars and butterflies, tadpoles and frogs, veligers and marine snails...) don't descend from a single ancestor that had a simple life history and later developed a two-stage strategy. Rather, Donald Williamson thinks that metamorphosing organisms are chimeras - hybrids between two distinct lineages in which the two parental genomes have reached a compromise such that one parent gets to run what we call the larval form and the other oversees the adult.

This is certainly not a mainstream idea, but the paper I'm talking about was published in the Proceedings on the National Academy of Science (PNAS), one of the most prestigious scientific journals that there is, Williamson must have some good data to support his idea right? Well, no. Williamson's entire case appears is that he finds it really really hard to imagine metamorphosis evolving in gradual steps and, besides, some larval forms look quite a lot some other organisms. Williamson does distinguish himself from other pedlars of what Richard Dawkins has named the "argument from personal incredulity" by at least providing a specific hypothesis to test: modern insects with 'caterpillar' larvae (butterflies, beetles, ants, wasps, bees, files...) descend from an 'accidental' mating between a flying insect and an onychophran (no illustration of this process is provided).

Peripatoides novaezealandiae, a wide spread New Zealand endemic onychophoran and young, photo © Te Ara

Onychophorans (which we usually call 'peripatus' in New Zealand) are part of that admittedly large list of creatures that can be called "David's favourite animals" so before we hang Williamson's preposterous hypothesis out to dry I'm going to have to subject you to a little bit of cheer-leading. This is not the first time that onychophorans have been the subject of woolly evolutionary thinking. Since they are likely related to some of the most spectacular cambrian fossils people have called them "living fossils" and you'll even sometimes hear it proposed they represent a *shudder* "missing link" between arthropods (insects, crustaceans, spiders...) and annelids (earthworms and their kin). Which is all a great shame because it diverts attention from the fact the onychophorans are nocturnal hunters which crawl through the leaf litter on hydro-statically inflated legs in pursuit of small invertebrates which they immobilise with a sticky glue they spray from their mouths in order to let them inject digestive enzymes into their stricken prey and suck the resulting soup from its lifeless body. That's the sort of thing people ought to know about it.

What about Williamson's "larval transfer" idea? Is this a case, like Wegner and continental drift or Bretz on ice ages, in which science needs some outré thinking to get itself out of a rut that is holding it back? Hardly.

Insect metamorphisms isn't that hard a problem

An adult cicada emerging from its last nymphal molt © Te Ara

Just how complete metamorphosis of the sort you see in butterflies evolved is a genuinely difficult and, as such, interesting question. But it's one that Williamson clearly hasn't bothered to read about. If he had he would've found a lovely review from Deniz Ereyilmaz2 who traces the history of the problem and makes a case that larvae are effectively free living embryos (an idea that was articulated by Harvey (of the circulatory system) and later used by Darwin in the 6th edition of The Origin to reply to contemporary criticism that his theory couldn't explain metamorphosis). Specifically, the idea is that the holometabolous insects (the ones that undergo complete metamorphosis) evolved from direct developing insects like cicadas and grasshoppers. In these insects the final stage of embryonic development is called a pronymph, in most species the pronymph molts into a mini-adult (called a nymph) before it hatches but a few species actually hatch as pronymphs. Ereyilmaz and the few entomologists that have tackled this question in recent years think holometabolous insects descend from species in which the pronymph hatched and then became able to feed. From there the development of the pronymph stage was extended while nymphal development (which usually proceeds as small changes accrued in each of several molts) was progressively squeezed into one step, which we now call pupation (like a caterpillar's cocoon).

There is some nice genetic evidence that something like that process has happened. One of the genes required to start the metamorphosis process is called broad, mutants that can't produce functional broad protein fail to pupate. Insects like cicadas and grasshopers that don't undergo complete metamorphosis also have copies of broad but in these insects broad is expressed at each nymphal molt - consistent with the idea pupation in holometabolic insects corresponds to nymphal molt in direct developing insects.

The evolution of complete metamorphosis remains an interesting question (if you are want to learn more Christopher Taylor has deeper look at it than I've given here) but the sort of path laid out above - the gradual addition of multiple, relatively small changes to the existing insect life cycle is surely orders of magnitude more likely than two genomes being thrown together and, somehow, deciding to regulate two complete separate developmental programmes as well as the entirely new process of breaking down the first genomes animal before development of the second one can begin?

Complete metamorphosis doesn't use two sets of genes

Williamson also asks 'genomocists' to search for distinct genomes within the DNA sequence of holometabolous insects. We don't need a complete genome to know that the same genes are being used in the development of adults and larvae. People have been studying the genetic basis of development in Drosophila (which my taxonomic pedantry won't allow me to call fruit-flies) for at least 20 years - all Williamson needed to do to check his hypothesis against the evidence was open an undergraduate textbook. Had he done that he would have seen, in one tirivial example, that the that patterning of the adult wing in Drosphila requires the genes hedgehog and wingless (geneticists usually name genes after what loss of function mutants look like ) both of which are also vital to defining the polarity of the segments formed in embryonic development. We've also know since at 1997 [3] than oncychophorans and insects inherited their hox genes, (the genes that lay out the basic body plan in animals) from a common ancestor that lived before the two groups split up - and the holometabolic insects we've looked at only have one set of hox genes.

So why is this in PNAS?
OK, so Williamson has his answer to the problem of metamorphosis and no evidence is about to sway him from it. But he's not asking for his nonsense to be taught in public schools or anything - he's just a harmless crank. The question is why was his idea afforded space in one of the most prominent scientific journals instead of being expressed in the standard media for cranks - self published pamphlets or a huge single page website made with Mircrosoft FrontPage and featuring five different colours of text interspersed with clip-art and presented on a yellow background. Well, until very recently there where two ways to be published in PNAS, you could submit an article to the editorial office in the normal way or you could have a member of the ... Read more »

  • September 6, 2009
  • 07:09 PM

I TOLD you you're all mutants

by David in The Atavism

Recently I tried to make this case that a mutation in my mitochondrial DNA
didn't make me so very different than the rest of you:

Our typical conception of mutation is drawn from the tragic effects of those
relatively rare mutations, induced in our bodies or passed on through germ
cells, that lead to diseases (or, in movies to super powers). In fact, we
are, each of us, mutants. DNA replication is not perfect, we are born with about
6 or 7 new mutations...

Well, a paper published last week[1] proved my general point while proving me wrong
on the detail by a factor of 20 or so. A team of British and Chinese
researchers that work with a family that has a unique Y-chromosome linked
hearing disorder sequenced the entire sequence of the Y-chromosome from two
men and found four mutations. Scaling up from the Y-chromosome to the whole
genome then dividing by the combined 13 generations that separate the two men
they arrived a mutation rate of 3 x 10-8 changes per nucleotide per
generation. That would give us between one and two hundred new mutations.

This finding isn't actually a revelation. We had an idea of the rate of
mutation in the human genome before we even knew what a gene was made of. JBS
Haldane, one of the founders of evolutionary genetics and perhaps the only
person to have enjoyed the First World War, used his theory of mutation
selection balance to estimate new haemophilia causing mutations occur about
once in every 105 generations.[2] When you consider that the gene
responsible for Haemophilia A contains about 7 x 103 nucleotides
and changes to many of those won't cause Haemophilia Haldane's estimate looks
pretty good.

In fact, the Cool New Stuff in this paper isn't really the number that
they've produced - that number is similar Haldane's esimate and to the
measurble error rate of the enzymes that replicate our DNA and to the
rate inferred by comparing our genome to that of the cimpanzee *. What's really neat is the fact they directly measured the rate by resequencing the whole Y-chromosome - that's more than 10 million bases to sequence, 35 at a time, and put together to check for mutations. The sort of project that would only have been possible as part dedicated genome sequencing projects a couple of years ago. With only two people and four mutations the estimate has
wide error bars but it does pave the way to more accurate estimates for
particular areas of the genome (including those underlying for diseases) and
particular lineages of organisms (which is important for us evolutionary

I can't revel in my earlier post being confirmed in the broad sense without
apologising for misleading you in the details. I was just flat out wrong when I
claimed we all have 6 or 7 new mutations - I used a number that I had in my
head and didn't bother to look it up. You can see where my number came from
once you consider that only about 4% of the genome is functional DNA - 150
mutations in your genome will lead to about 6 mutations in functional regions.
Still, the original is (about to be) modified and I am suitably shamed.

* As Larry Moran points out taken together these studies tell us something
about the way evolution works. If the observed rate of mutation in DNA
replication is not wildly different than the inferred rate of mutation in a
pedigree or between closely related species most mutations aren't being
selected against - more evidence for the importance of neutral theory in
molecular evolution. back to the story ^

[1] Xue, Y., Wang, Q., Long, Q., Ng, B., Swerdlow, H., Burton, J., Skuce, C., Taylor, R., Abdellah, Z., & Zhao, Y. (2009). Human Y Chromosome Base-Substitution Mutation Rate Measured by Direct Sequencing in a Deep-Rooting Pedigree Current Biology DOI: 10.1016/j.cub.2009.07.032

[2]J. B. S. Haldane (1935). The rate of spontaneous mutation of a human gene Journal Of Genetics DOI: 10.1007/BF02717892... Read more »

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