Historical contingency in the evolution of E. coli

Blogging on Peer-Reviewed Research

While I was traveling last week, an important paper came out on evolution in E. coli, describing the work of Blount, Borland, and Lenski on the appearance of novel traits in an experimental population of bacteria. I thought everyone would have covered this story by the time I got back, but there hasn’t been a lot of information in the blogosphere yet. Some of the stories get the emphasis wrong, claiming that this is all about the rapid acquisition of complex traits, while the creationists are making a complete hash of the story. Carl Zimmer gets it right, of course, and he has the advantage of having just published a book(amzn/b&n/abe/pwll) on the subject, with some excellent discussion of Lenski’s work.

The key phrase is right there at the beginning of the title: historical contingency. This paper is all about how accidents in the genetics of a population can shape its future evolutionary trajectory. It is describing how a new capability that requires some complex novelties can evolve, and it is saying plainly that in this case it is not by the fortuitous simultaneous appearance of a set of mutations, but is conditional on the genetic background of the population. That is, two populations may be roughly equivalent in fitness and phenotype, but the presence of (probably) neutral mutations in one may enable other changes that predispose it to particular patterns of change.

[Read more…]

IEDG2008: Model systems are dead, long live model systems

I’ve discovered a couple of important things at this meeting.

One, late night sessions at west coast meetings are deadly for any of us coming from more eastern time zones. At least the morning sessions are low stress.

Two, I haven’t heard one Drosophila talk yet, and the message is clear: we’re now in the stage of evo-devo in which everyone is diversifying and chasing down a wide array of species. There was a bit of model-system bashing, but at the same time, everyone is acknowledging the crucial role of those traditional, but weird and derived, lab critters in providing a point of comparison and being the source of many of the tools being used to explore phylogeny now. I thought, though, that the smartest comment of the evening was that now everything is a model system.

I’ve got some dense piles of notes on the evening session, but I’m going to give you the short version of everything, with an emphasis on the novel twists.

Michael Akam talked about segmentation genes, which every developmental zoologist now knows inside and out — trust me, this is a familiar topic with over 25 years of detailed research … in Drosophila. Akam made the point that now it’s looking clear that three of the major segmented phyla, the arthropods, annelids, and chordates, may be using related genes to accomplish segmentation, but they seem to be using different mechanisms — so he considers the question of whether segmentation in these three is homologous is still an open question. He also discussed recent work on the centipede Strigamia (definitely not a lab animal: they can’t breed them in the lab yet, so all the work is done by collecting embryos in the field, in Scotland). They have a dynamic pattern of segment addition that is very different from what you find in flies, and more similar in some ways to chodate segmentation.

Chelsea Specht talked about floral evolution in the Zingiberales. I’m an animal guy, so even the most basic stuff in this talk was entirely new to me. I know the general rules of the spatial development of in the fruit fly of the plant world, Arabidopsis, and she gave us a bit of context there, reminding us of the concentric development of sepals, petals, stamens, and carpels. The Zingiberales are a large and diverse group of plants that includes bananas and ginger, and one characteristic is an extravagant modification of the canonical pattern, with extra stamens, a loss of select stamens, and a fusion of stamens to form a novel structure, the labellum, which in these plants functionally replaces the petals. So of course they’re looking into the genes involved in the patterns, which turn out to be the familiar Arabidopsis genes redeployed in new patterns.

Paul Sereno had a talk that took a very different tack, and was unfortunately giving it at the equivalent of 11:00pm Minnesota time, so I’m sorry to say I didn’t follow it carefully. He was discussing the analysis of morphology, and was advocating the development of tools and techniques to compare data sets in addition to the usual output, phylogenetic trees. He was making the case that a lot of morphological studies are actually very poor (a creationist in the audience would have loved it, largely because he wouldn’t have understood the context) because the input data sets of different studies are not comparable.

And now I have to get back to work and listen to the next set of talks.

Gerobatrachus hottoni

Blogging on Peer-Reviewed Research

It’s another transitional form, this time an amphibian from the Permian that shares characteristics of both frogs and salamanders — in life, it would have looked like a short-tailed, wide-headed salamander with frog-like ears, which is why it’s being called a “frogamander”.

i-3085796f01e5d09425d897b5cd6092e2-gerobatrachus.jpg
Complete specimen in ventral view, photograph (left) and interpretive outline drawing (right). Abbreviations: bc, basale commune; cl, cleithrum; cv, clavicle; dm, digital elements of the manus; dt3, distal tarsal 3; fe, femur; h, humerus; ic, intercentrum; il, ilium; is, ischium; op, olecranon process of ulna; pc, pleurocentrum; r, radius; sr, sacral rib.

[Read more…]

Bat wings and mouse feet

You may recall that a while back I mentioned how Jerry Coyne praised some work on bat evo-devo. I also said that I was going to have to write that paper up sometime. The bad news: I haven’t written it up for the blog. The good news: I did write it up for a future Seed column. The better news: Stephen Matheson has a summary right now, so you don’t have to wait for my column to come out.

You should still subscribe anyway. It’s pretty on shiny paper.

The platypus genome

Blogging on Peer-Reviewed Research

Finals week is upon me, and I should be working on piles of paper work right now, but I need a break … and I have to vent some frustration with the popular press coverage of an important scientific event this week, the publication of a draft of the platypus genome. Over and over again, the newspaper lead is that the platypus is “weird” or “odd” or worse, they imply that the animal is a chimera — “the egg-laying critter is a genetic potpourri — part bird, part reptile and part lactating mammal”. No, no, no, a thousand times no; this is the wrong message. The platypus is not part bird, as birds are an independent and (directly) unrelated lineage; you can say it is part reptile, but that is because it is a member of a great reptilian clade that includes prototherians, marsupials, birds, lizards and snakes, dinosaurs, and us eutherian mammals. We can say with equal justification that we are part reptile, too. What’s interesting about the platypus is that it belongs to a lineage that separated from ours approximately 166 million years ago, deep in the Mesozoic, and it has independently lost different elements of our last common ancestor, and by comparing bits, we can get a clearer picture of what the Jurassic mammals were like, and what we contemporary mammals have gained and lost genetically over the course of evolution.

We can see that the journalistic convention of emphasizing the platypus as an odd duck of a composite creature is missing the whole point if we just look at the title of the paper: “Genome analysis of the platypus reveals unique signatures of evolution.” This is work that is describing the evidence for evolution in a comparative analysis of the genomes of multiple organisms, with emphasis on the newly revealed data from the platypus.

[Read more…]

Evolution, with teeth

My last Seed column is online, which reminds me (as if I weren’t uncomfortably aware already) that I have to finish up the next one today, which actually isn’t the next one, which is already done and submitted, but the one after that. These long leading deadlines force one to live a few months in the future…

You know, if you subscribed to the print magazine, you’d be halfway to my future already instead of living in my distant past.

A single insect can’t demonstrate evolution

I have to criticize the video below. It’s a beautiful piece of work, and the animal it shows is spectacularly well-adapted, but it does not demonstrate the fulfillment of a uniquely Darwinian prediction.

An orchid was found with a nectary that was only accessible by way of a long, narrow tube, and Darwin predicted the existence of an insect pollinator with an almost equivalently long tongue. However, an Owen or a Cuvier, scientists of that century who did not accept evolution, could have easily made the very same prediction, on the basis of created functionality: a god would not have made the flower that way unless he also, in his infallible foresight, also made a complementary pollinator. One could also make an argument based on an orchidized version of the anthropic principle: the flower is there, therefore it must have been produced by a parent flower that had been pollinated, therefore there must exist a long-tongued pollinator.

The special Darwinian character comes from the explanation of how such a phenomenon came to be; not by the fiat of some arbitrary creator, but by a set of processes that must still operate. It is to the advantage of the flower that the pollinator has to struggle a bit to reach the nectar reward, pressing itself against the flower and covering itself with pollen, while the pollinator would prefer to be able to reach in easily and without mess and fuss to get its dinner. This means that there is selection for flowers that have slightly longer nectary tubes than the insect tongues, while there is selection for insects that are able to reach all the pools of sweet nectar — but this is a race in which the insects will always be slightly behind.

What Darwin predicted was not a perfect match between nectary and proboscis, but that the insect proboscis would be slightly shorter than the nectary, and that’s what you find in his work On the Various Contrivances by which British and Foreign Orchids are Fertilised by Insects, and the Good Effects of Intercrossing. Another prediction that I haven’t found that he made explicitly is that there should be a range of heritable variation in nectary length — it could just be that that was so obvious in the collections he examined that it wasn’t necessary to state it.

Anyway, lovely as it is, a video of an insect with a remarkably long proboscis is not confirmation of Darwin’s theory. The key element of that theory is a description of a process which generates diversity over time in populations, which isn’t assessed by examining a single organism at a single moment in time.

(via Atheist Media Blog)

Darwin was a gardener

Maybe you think it’s spring — I don’t, I just looked out through ice-glazed windows at half a foot of new snow — and you’re thinking about the garden. Here’s an idea: you don’t need to take a trip to the Galapagos to study evolution, you can do it right in your backyard. The New York Botanical Garden is opening a new exhibit, called Darwin’s Garden.

In all, the tour is 33 stops, spread throughout about half of the garden’s 250 acres. Visitors who enter the exhibition through the Enid A. Haupt Conservatory will encounter a replica of a room in Darwin’s house, designed so they can look through the window, as he did, to a profusion of plants and bright flowers: hollyhocks, flax and of course primroses, what Todd Forrest, the garden’s vice president for horticulture, calls “a typical British garden.” On a table stands a tray holding quills, brushes, sealing wax and tweezers, the kinds of simple tools Darwin used to conduct his world-shaking research.

Brilliant! Evolution is not something that requires exotic, out of the way locales and weird, obscure organisms to study — it’s everywhere.

Still just a lizard

Blogging on Peer-Reviewed Research

i-fb9fbc1a3a0c689c8eb3f002c9f77335-podarcis.jpg

The title gets the principal objection of any creationist out of the way: yes, this population of Podarcis sicula is still made up of lizards, but they’re a different kind of lizard now. Evolution works.

Here’s the story: in 1971, scientists started an experiment. They took 5 male lizards and 5 female lizards of the species Podarcis sicula from a tiny Adriatic island called Pod Kopiste, 0.09km2, and they placed them on an even tinier island, Pod Mrcaru, 0.03km2, which was also inhabited by another lizard species, Podarcis melisellensis. Then a war broke out, the Croatian War of Independence, which went on and on and meant the little islands were completely neglected for 36 years, and nature took its course. When scientists finally returned to the island and looked around, they discovered that something very interesting had happened.

[Read more…]