davegodfrey: Coelacanth (Science)
There's a new paper on the origin of primates. Now I've not looked into primate evolution much (other than criticising the hype around some recent discoveries). But this seemed interesting. In a "Yer what?" way.

Michael Heads has calibrated the origin of the various primate groups to several tectonic events involved in the breakup of Pangaea.

New and Old World Monkeys diverged 120 million years ago when the Atlantic opened. Lemurs diverged from their closest relatives when the Mozambique Channel opened 160 million years ago, and the deepest split in the primate tree, between the haplorhines (monkey, apes, and tarsiers) and strepsirrhines (lemurs and lorises) is 180 million years ago in the Early Jurassic.

This is a problem. The earliest known primate fossil is Purgatorius from the Upper Cretaceous of the USA. (Well maybe. A recent paper in Nature indicates that it isn't a primate but the sister group to placentals as a whole.) Other than that the earliest primates turn up in the Eocene, about 56 million years ago. Molecular divergence times however put the split between primates and their closest living relatives the Dermopterans (the Colugos or "flying lemurs") at about 80 million years.

He is right in pointing out that the previously accepted dates are indeed the minimum dates. Any new fossil discovery could shift them by several million years. Just a week or so ago some tetrapod footprints were found that indicated that tetrapod evolution occurred about 10-20 million years earlier than we thought, creating "ghost lineages", spans of time where no fossils are known, but are expected.

If Heads' model of primate evolution is correct then it creates ghost lineages of 100 million years. This, to me, seems rather excessive. Defending this he points out that several groups do not have a fossil record, yet must be very old, while other modern groups are only known from a few very early fossils (he mentions proscopiid grasshoppers from 110 million years ago). Fair enough, but the molecular dates indicate a ghost lineage of about 25-30 million years from the earliest fossils to the latest divergence times. Increasing this by four times really needs rather more support than he gives it. A new fossil would be enough to make people think.

He is correct in his statements that molecular dates (however they are calibrated) are generally minimum dates, but he repeatedly states that they are "transmogrified" into maximum dates. I can't find any detailed criticism from this paper as to how this is done (do the authors just swap words around? Or are there mathematical tricks that can get you this result?)

Moreover where Heads' paper also falls down is in his refusal to accept that rafting can play a part in evolution and dispersal. It is generally accepted that chameleons originated on Madagascar and then spread. Frogs have made it to Madagascar from Indonesia, and this week a paper was published in Nature showing how ocean currents in the Eocene would have allowed lemurs to raft across the Mozambique Channel, but would prevent them doing so today. He also fails to take into account that the separation of continents is not a simple matter. The North Atlantic began to appear in the Cretaceous, but there were extensive connections between Europe and North America throughout the Eocene, allowing animals to island hop across. I see no reason why South America and Africa would be different.

He doesn't address the issue of why we have a nice transitional sequence of various primate groups in the Eocene, but that isn't necessarily a problem- the footprint paper in Nature gave us the same problem to deal with. However the footprints are evidence for the existence of tetrapods at a particular time period. Heads has not presented any physical evidence to back up his claims, rather he's taken the current distribution of primate groups as evidence that they always lived in these areas, and matched them up with past events. Would he have got the same results if he had used a different group? And if not what does that say about his methods?

Finally, other than ascribing a date of 185 million years to the split at the base of the Archonta (the larger group uniting Primates, Tree Shrews, and Colugos) he says nothing about what this data means for the diversification of other placentals, marsupials or indeed the origin of mammals as a whole. Without running the mathematics I can't help get the feeling that were this paper correct it would push the origin of mammals somewhere into the Permian. Which seems, shall we say, extremely unlikely given the fossil record we have there.

As they say, extraordinary claims require extraordinary evidence.

Michael Heads: Evolution and biogeography of primates: a new model based on molecular phylogenetics, vicariance and plate tectonics, Zoologica Scripta, Published Online: Nov 10 2009 4:44AM DOI: 10.1111/j.1463-6409.2009.00411.

J. R. Wible, G. W. Rougier, M. J. Novacek & R. J. Asher: Cretaceous eutherians and Laurasian origin for placental mammals near the K/T boundary, Nature 447, 1003 - 1006 (21 June 2007)
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davegodfrey: Coelacanth (Science)
Remember Ida? (or Darwinius massillae to give her full name)? Remember how six months ago she was unveiled to the world in a whirlwind of hype? Remember how the blogging community despaired of this, while noting what a lovely fossil she was?

This week more research has been published, after the discovery of Afradapis, a related species from the Late Eocene of Egypt. Not nearly as nice as Ida its a jaw and teeth. This is not unusual- most of our ideas about mammalian evolution were based on teeth until genetics came along and morphology had to play catch-up. And when dealing with extinct groups such as adapids its the best thing we have going- teeth are the most robust parts of your body, and withstand the processes of decay and weathering the best. The fossils shows some features present in the catarrhine primates (the group that include apes and Old-World monkeys). Which is very interesting. However...

...all is not as it seems. The team did a phylogenetic analysis, of 117 living and extinct species, using 360 characters. This is only about 3 characters per taxa, and I'm sure more would be nice- but you can guarantee that not all characters will be preserved in each group (its rather hard to say what features are present in the ankle of a genus only known from its teeth for example), and its the first phylogenetic analysis I'm aware of that includes Darwinius which is a very Good Thing. Sadly for most people, its published in Nature, which means anyone who doesn't have a subscription only gets the abstract and whatever mangling the newspapers put this and the press release through.

This analysis shows that Ida, Afradapis and the other Adapoids are not stem anthropoids, and are not even haplorhines (the group that includes monkeys [and apes] and tarsiers). In fact they fall out as the sister group to the living strepsirrhines (lemurs, lorises, and bushbabies). To me thats far more interesting than if the adapids were on the line to humans, because it means the features they share with us either evolved twice (once in anthropoids and once in adapids- the position the paper's authors take) or are primitive to a wider group of primates. Without having read the paper I can't say why the author's favour one over the other.

ETA: Brian Switek over on Laelaps has a very nice post, (with a lovely drawing of Afradapis' jaw). The features that link adapids and anthropoids (but are not present in the earliest anthropoids) are details of the mandibular symphysis (the joint between the two halves of the lower jaw) and the loss of the second premolar. Neither of these features are likely to be lost and re-evolved, when evolution discards things they tend to stay discarded, and when they come back, they're usually subtley different.

Before we start questioning how effective the analysis was- and believe me scientists will, plugging more species in, pulling others out, re-examining specimens, poking holes everywhere they can to see how good this tree really is, taking the analysis at face value raises a whole series of interesting questions. If we're seeing convergence between anthropoids and adapids, then what were these two different groups doing that was similar, and if the features we are seeing are primitive, then why did lemurs and other groups lose them.

And this to me is the beauty of science. When scientists are wrong it is very often for interesting reasons- lack of data, working within a theory that could not account for new observations, etc. And when they are shown to be wrong, a whole vista of new questions open up, new ways to be interestingly wrong, but at the same time inch closer to a greater understanding of the universe. And people wonder why I love science so damn much.

Seiffert, E., Perry, J., Simons, E., & Boyer, D. (2009). Convergent evolution of anthropoid-like adaptations in Eocene adapiform primates Nature, 461 (7267), 1118-1121

I recommend reading this interview with Seiffert.

davegodfrey: Coelacanth (Science)
The entire world seems to have gone utterly insane over this fossil, known colloquially as "Ida", but officially as Darwinius masillae. And it is a lovely fossil. It is also important because it will, I'm sure, tell us lots about what was going on in primate evolution 47 million years ago. I'm not going to go through the reports because there are too bloody many of them, but I will point out that while many have fallen for the "Missing Link" Found! angle plenty of others- especially the bloggers writing opinion pieces are being rather more restrained.

However utterly revolutionary it is not. At best it means a group of animals a bit like lemurs (Adapids) are more closely related to apes and monkeys than a group of animals a bit like Tarsiers (Omomyids). Be honest had you heard of either?

I quite like it because its another species published in PLoSOne (The Public Library of Science). This is an open access journal, so anyone can download and read a copy of the paper for free. There's a lovely long description of the fossil- it is young (under a year old), female (it lacks a baculum [penis bone] which you'd expect to see in male primates like this), and very nicely preserved (the body outline, hair and stomach contents are all preserved).

Its from the Messel deposits, which have yielded beautiful fossils of fishes, early horses, ants, weird mammals like Leptictidium, and all sorts of other things. Messel was covered in one episode of David Attenborough's 1980s series on fossils Lost Worlds, Vanished Lives, and also in the first episode of Walking With Beasts- though proto-whales aren't known from the area. I can't believe someone thought it was a good idea to turn the site into a rubbish dump. Fortunately they haven't, and it is now a World Heritage Site.

I am not qualified to say how much this fossil supports the conclusions that the authors are trying to draw- that the group to which Ida belongs are more closely related to monkeys and apes than tarsiers and their relatives are.  However the paper lacks a phylogenetic analysis and as Laelaps and The Open Source Paleontologist points out this is something one expects to see when claims for moving large groups around are made. Hopefully one will be done soon, and the question of whether Adapids (the group to which Darwinius belongs) is closer to lemurs or monkeys and apes will be better resolved.

I don't really have much to add to the criticism of the hype either. Both Ed Yong and Carl Zimmer have covered it far better than I could hope to. Especially Ed's post.

Personally the part that really annoys me- I wouldn't be at all surprised if the view of the Adapids in the paper turned out to be wrong. You just know that the creationists will have a field day because while I'm sure most of you know that the great strength of science is that whenever new information appears which contradicts its conclusions we change our minds- something the creationists seem incapable of appreciating as being A Good Thing. I just hope I am pleasantly surprised.
davegodfrey: Coelacanth (Science)
So the beeb is going all out with the marking of Darwin's 200th birthday and the 150th anniversary of the publication of "On the Origin of Species". As part of this they have several TV programmes. Including "What Darwin Didn't Know" a 90 minute documentary by the biologist Armand Leroi, discussing the various problems that Darwin foresaw in his theory, and how these gaps have been filled.

(This programme should not be confused with Geoffrey Simmons book of the same title about ID, by a guy who thinks whales are evidence against evolution, but knows nothing about their fossil record).

It deals with the fact that Darwin didn't have a workable theory of inheritance, plumping for a blending hypothesis, which clearly has problems- novel traits will be quickly diluted, so can never spread. One thing it covers in a good degree of detail is the "Eclipse of Darwinism" that happenned soon after his death. Scientists discovered mutations, and came up with ideas about "orthogenesis" species passing along defined evolutionary paths, like those of a developing embryo. Natural selection was pretty much ignored. Even when Mendelian genetics was rediscovered it took until the 1920s and 30s to really get to grips with what was going on. Leroi largely skips over this, concentration on one of the competing theories (Hugo de Vries' model that suggested that all evolution needed was mutations to occur). If he'd have gone into any more detail he;'d probably have filled the entire programme, which is a pity, because the rest of the show was also extremely good.

One of the most interesting fields to have developed since Darwin is that of "evo-devo", the examination of shared genetic and developmental pathways across groups. For instance the gene Pax-6 is responsible for initiating eye development in both humans and insects. Alter it in a fruit fly and you get an eyeless fly (which is what it sounds like). In humans the same kinds of mutations exist, and the condition aniridia results- children are born without an iris, and thus have trouble seeing.

Similarly a characteristic shared across animals is the presence of a particular group of genes called Hox genes. These control development, and like Pax-6 operate as switches turning other genes on and off in different parts of the genome. When these genes are expressed incorrectly we can see what they do. We have, it seems come full circle and are back to de Vries' cataloguing and examination of mutants, albeit using techniques that he and Darwin would be astounded by.

Its available on BBC iPlayer (for the UK residents) until the 4th of February, but I'm sure its crept onto the filesharing websites by now.
davegodfrey: Coelacanth (Science)

Oh dear. What starts off as a musing on a small part of Wagner, rapidly turns into a discussion of evolution. Jerry Fordor (who?) wants to know why pigs don't have wings. He doesn't like natural selection. Which is a pity because while adaptationism is sometimes taken too far it still works and is still the most important driving force in nature.

Fodor doesn't like evolutionary psychology much. Fair enough, I'm not too keen on its excesses (like the recent non-study suggesting that girls prefer pink and boys blue). However it is not unreasonable to suppose that our behavioural patterns evolved in response to living on the savannah. As the majority of humans don't live in hunter-gather groups it isn't much of a stretch to suggest that some of the problems we have with modern life are because the behavioural modules that worked then don't work now.

Fodor distinguishes the two parts of "Darwinism", phylogeny and natural selection. (You can always tell if the essayist is going to get it badly wrong when they use the term "Darwinism" to describe modern evolutionary theory. I'd like to see a ban on the word outside of its historical context.) He then introduces the idea that adaptationism cannot explain everything, bringing up Sephen Jay Gould's analogy of the spandrels of San Marco. A spandrel is a triangular space which you get in the corners of arches when they are supporting a dome. They are often highly decorative.  If you support a dome with arches you automatically get spandrels. Similarly in biology there is debate about how significant natural selection is in producing a particular phenotype. Some people, like Larry Moran and the late Stephen Jay Gould see a greater role for mechanisms other than natural selection. Others such as Richard Dawkins and Simon Conway Morris don't think these ideas are useful. Nobody contends that natural selection is the be-all and end-all.

Except it seems Mr Fodor. Fodor also doesn't like the fact that artificial selection is a good analogy for natural selection because nature isn't conscious. 

               "How could a studied decision to breed for one trait or another be ‘the very same thing’ as the adventitious culling of a population?" 

Fodor asks. Well, because NS doesn't necessarily proceed by culling. All you need is for the organisms with that trait to have a couple more children in order for the trait to spread. As far as evolution is concerned having no kids is the same as being dead. Fodor has got rather too wrapped up in the "survival of the fittest" analogy to see that it isn't always like this.

              "The crucial test is whether one’s pet theory can distinguish between selection for trait A and selection for trait B when A and B are coextensive: were polar bears selected for being white or for matching their environment? Search me; and search any kind of adaptationism I’ve heard of. Nor am I holding my breath till one comes along."

Um, polar bears live in a predominately white environment. If they didn't maybe they wouldn't be white? Why bears might be white in a non-white environment is an interesting question however. (But not relevant to Fodor's thesis).

Fodor seems to think that evolutionary development is a far more important part of evolution than natural selection is, discussing why pigs don't have wings, and correctly surmising that they are constrained by their embryology. There's nowhere to grow them without radically redesigning the tetrapod body-plan. Organisms have all sorts of constraints placed upon them by their biology, and it makes it very interesting to see how they solve particular problems, or failed to develop particular solutions. Bats pterosaurs and birds sacrificed a pair of limbs to fly. Insects used a different solution and still retain all their original legs.

However this harks back to the old orthogenetic arguments of biologists like Cope, and others Wiliam Patten wrote that "Natural Selection cannot create it can only sift". Natural selection plus mutation can do all sorts of things.

The traits we see are the result of pre-existing constraints, fiddly bits that come along for the ride and are kept because they aren't harmful, all mediated through natural selection. If an evolutionary spandrel was harmful it wouldn't hang around very long. One of the most important parts of evolution is "stabilising selection"- keeping things the same because they work, and penalising deviations from the norm because they don't. This works in artificial selection too.

So, in all a mixed bag. It had the potential to be a good essay, but as so often happens the "Darwinism in crisis!!" angle has been massively overplayed, and Fodor seems to have thrown the baby out with the bathwater in his realisation that things are a littl emore ocmplex than they appear at first.

davegodfrey: Coelacanth (Science)

Yet another aberrant theropod from China. Called Gansus yumenensis, after the area it was found its 100 million years young. It looks a lot like the modern diver (or Hesperornis a large flightless toothed bird.) Feathers and the webbing between the toes is preserved. Sadly its missing a skull. But its still pretty. And ist shows the kind of diversity of bird species and ecotypes during the Early Cretaceous. The sad thing is that you won't see some of the variety of birds that probably existed because they lived on land, and never got fossilised. Our history of bird evolution is largely known from seabirds.

Its from another deposit in China with soft-tissue preservation, but not one I'd heard of before.  Still in a country that big I'm not suprised there are so many.

Metro thinks this is important. So important that it shows that birds evolved from fish! ARRRGH!!! I'm going to have to give up reading it. Its bad for my blood pressure.

davegodfrey: South Park Me. (Default)

Further to yesterday's post regarding the Kansas School Board, it would appear that they have redefined science so that it is "no longer limited to natural explanations for phenomena".

They also say that the fossil record is inconsistent with evolution. *headdesk* NO IT FUCKING ISN'T!!!!! It never ceases to amaze me that Kansas can be home to such idiots on school boards, and yet the university and palaeontologists there produce websites like Mike's Oceans of Kansas site.

[livejournal.com profile] innerbrat , next time your off to the states d'y'think you could pop down Kansas way and "lay some smack down" as they say?

 The New Scientist regarding this is here.


davegodfrey: South Park Me. (Default)
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