Just in case you didn't know...

I saw Ken Miller give a talk today at the BioNES meeting held today at RWU and he showed this bumper sticker (available here) while talking about the downfall of Intelligent Design.

I love this photo

courtesy of the Natural History Museum in London's upcoming exhibit (via Karen at the Beagle Project)

Quick hits

The platypus genome put me in the mood for more evolutionary biology, so here are some interesting recent papers of an evolutionary bend (note: Abstracts available, but subscription or "pay-per-view" needed for full article access. Sorry.):

Amino acid sequence data from collagen extracted from the bones of Tyrannasaurus rex and the mammoth, Mammut americanum, were used to build a phylogeny of these two species. As expected, based on previous phylogenetic work, M. americanum groups with modern elephants and T. rex groups with modern birds (chickens to be exact). This paper builds on earlier success in using protein sequences to elucidate evolutionary history of extinct organisms.

Hermaphoditism evolves when mate-search efficiency is poor. In other words, if ... you ... move ... really ... slowly ... and ... don't come across another individual of your species all that often, it's best to be prepared when you do - it would really suck to look all that time for a mate only to come across an individual of the same sex and have to start the search all over again.

Analysis of oxygen isotope levels in the tooth enamel of extinct relatives of elephants suggest that modern probocidians evolved from aquatic or semi-aquatic forms. This is expected given the close phylogentic relationship between extant elephants and the sirenians (manatees and dugongs) and provides new arguments for the idea that elephant trunks may have originally evolved as a snorkel.

Weird animal, not-so-weird genome

(After reading PZ Myers's post on the matter, I've decided to stop using "weird" to describe the platypus's genome. However, I still think the animal itself can aptly be described as weird.)

Nature reports today that the platypus genome has been sequenced by a large international team (note: subscription needed for full article). Fittingly, it seems that the genome is just as delightfully weird interesting as the platypus itself - a mixture of mammal genes interspersed with ancestral reptilian and avian sequences, with a bit of novelty thrown in, all of which tells us a great deal about mammalian evolutionary history.

Some highlights:

The sequenced genome, with all of its peculiarities details, corroborates the idea that the platypus lineage is the earliest diverging mammalian lineage - diverging from the rest of the mammals over 160 million years ago. Side note: the marsupial-placental split occurred ~150 mya, and all modern placentals orders appeared by ~75 mya.

The genes for caseins, the proteins found in milk, align well with the casein gene families found in other mammals. This suggests, as expected, that milk production evolved before mammals evolved live birthing (or nipples - platypus secrete milk through pores in the skin).

Speaking of birthing, the platypus genome contains sequences that match mammalian genes for the zona pellucida, but also has copies of zona pellucida genes previously only found in amphibians, birds and fish. There is also a gene for the yolk-stored proteins, vitellogenins, that are also found in amphibians, reptiles, and birds, but that have been lost in non-monotreme mammals.

Genes for the proteins found in the platypus' reptilian-like toxins turn out to be novel sequences, independently evolved and are not homologous with reptile toxin genes. Toxin production in reptiles and platypus seems to be a case of convergent evolution. Interestingly though, the same defensin genes were co-opted in each case.

(Note: I was going to strike the word weird from this item, but I've decided that this is indeed weird.) Weirdest of all might be the sex chromosomes. Platypus sex chromosomes are known to be strange structures cytologically speaking, but it turns out that none of their X chromosomes match the X chromosomes of other mammals - they're more like the Z chromosome found in birds. A "normal" autosomal chromosome however matches the mouse X chromosome.

microRNA sequences are all over the place - platypus have both microRNA sequences that are found in birds, but not mammals, as well as microRNA sequences that are found in mammals, but not birds.

Further study of the genome will certainly add to the uniqueness of the platypus and will be helpful in understanding early mammal evolution. I think it's rather poetic that such an odd cool creature has such an odd cool genome. Wouldn't it have been disappointing if it didn't?

Happy Darwin Day!!

Charles Darwin was born this day in 1809 in Shrewsbury, England.

Coincidently, I grew up in Shrewsbury, Massachusetts. I wonder if my home town has a Darwin Day parade? I'll have to look into it for next year's Darwin bicentennial and see if I can't organize a town-wide celebration. Shrewsbury, MA after all is no stranger to revolutionary science - it's home to the Worcester Foundation for Experimental Biology Biomedical Research - birthplace of "the Pill" and early work on in vitro fertilization.

Anyways, go spend part of your Darwin Day over at the Guardian's (UK) online treasure trove of all things Darwinian.

Also, if you don't have enough to read these days, you can check out (almost) all of Darwin's publications online.

(note: the image above is from here)

Half a Billion Year Old Jelly

Researchers report today in PLoS ONE that they have identified fossilized jellyfish that date back to 500 million years. The previous oldest-known cnidarian fossils were "only" 300 million years old. This new find pushes the origin of cnidaria back to at least the middle of the Cambrian. The fact that the fossils show traits that are diagnostic of modern taxa suggest that jelly origin may coincide with (or predate) the Cambrian Explosion (alternatively, modern-looking jellies may have evolved rather quickly during the Cambrian).

This new find should help shed some light on the origin and diversification of a group of critters that are generally not preserved well due to their soft bodies and also adds another piece of the puzzle of rapid diversification during the Cambrian.

No Eugenie for me :(

Well, looks like I've lost my opportunity to meet Eugenie Scott. I was scheduled to meet with her this afternoon before her lecture this evening, but she needed a break from the constant attention from her sycophants admirers, so went back to her hotel room. It's understandable. I guess.

Unfortunately, I also have to miss her lecture this evening to bring my daughter to her Brownie troop meeting. Damn kids.

Attack of the Killer Space Germs (or, Does Evolution Work Differently in Space?)

CNN.com reports that "germs" sent into space return home to Earth more virulent. I can't find the original PNAS article to which it refers, but this seems like a very interesting finding - a strain of Salmonella sent into orbit more easily infected mice and it took 3-times fewer bacteria to kill a host. (update: here's the PNAS paper)

The researchers have a hypothesis for this finding though it is not clear how from the CNN article why. They think that the bacteria evolved in response to the low fluid sheer shear that results from the low gravity environment. I am not able to figure out why the low fluid sheer shear would lead to a more virulent bacterium, but for some reason, the researchers have shown that over 150 genes have changed in the space-traveling Salmonella. Obviously, low gravity (and/or low sheer stress) has applied a strong selective pressure on these little critters. It would be interesting to know more about the genes that were affected.

I have a major issue with the CNN article though (which is one reason I wish I could find the PNAS article). Cheryl Nickerson, a professor at ASU, is quoted as saying:

These bugs can sense where they are by changes in their environment. The minute they sense a different environment, they change their genetic machinery so they can survive

Now, I am no microbiologist, but this statement reeks of an oversimplification of the evolutionary mechanisms at work here. It is this kind of carelessness (or bad reporting?) that helps perpetuate a misunderstanding of evolution in the general public. A scientist should be able to communicate basic evolutionary theory, especially when being quoted in a high-profile media outlet.

BTW, "fluid sheer" is not the same as "fluid shear". My biomechanics professor would be so disappointed (Sorry, Amy!)

Update: Using the correct terminology I was able to find this much more informative National Geographic article. It explains a little more about the possible mechanisms involved here (and doesn't have the same nocuous Nickerson quote)

Friday Science: from Parasite to Mutualist

This is the first in a, hopefully, weekly bi-weekly occasional series of posts in which I will summarize/discuss some new peer-reviewed research that I find interesting. My post on synthetic estrogen and extinction started me thinking that this would be a good addition here. In attempting this, I am in no way suggesting that I am an expert in any of the topics I will be posting, only that I find them interesting and that I hope to be able to present the material in a "chewable" form. I'll also try to restrict my summaries to articles available via open access. Wish me luck.

This week's article that caught my attention is from PLoS Biology and deals with the evolution of parasites into benign or even beneficial organisms. In particular, the researchers show that over approximately 20 years, a particular strain of Wolbachia has evolved in a manner such that it now causes infected female flies (Drosophila simulans) to lay more eggs. Here we have a parasite that used to cause reproductive harm evolving into a "parasite" that helps fly reproduction. Even better, this phenomenon is exactly what evolutionary theory predicts should have happened.

[+/-] Show more/less

Wolbachia is a bacterium that infects all sorts of invertebrates, particularly insects. Individuals that are infected with Wolbachia show decreased reproductive success - partly through a process called cytoplasmic incompatibility (CI). CI basically means that the gametes of an infected individual are incapable of (or less successful in) fusing with the gametes of uninfected individuals. Thus, infected females can only breed with infected males.

Another interesting thing about Wolbachia is that unlike most transmissible parasites, it is passed only from mother to offspring via infected eggs. Such "vertical transmission", combined with CI, can cause a rather rapid spread of the parasite within a population. And this is exactly what has been seen in the population of flies in this study. In the mid-1980s Wolbachia-induced CI was discovered in a population of D. simulans in southern California. Since that time, the Wolbachia infestation has spread north through California and is "now pervasive throughout most North American populations of D. simulans."

Notice though that there are two conflicting aspects of Wolbachia infection: 1) Wolbachia is only passed from mother to egg, yet 2) Wolbachia infections cause females to lay fewer eggs. Evolutionaryly speaking, this set-up is not in the bacteria's (nor the fly's) best interest. Under this type of vertically-transmitted infection scenario, evolutionary theory predicts that the parasite will become less virulent harmful over time. At worst, the parasite should evolve so as to have no affect on female fecundity (just hitching a ride on the eggs). At best, theory predicts that the parasite should come around 180° and become a mutualistic partner by actually increasing female reproduction.

Sure enough, 20 years after the initial "outbreak", Wolbachia infection in D. simulans now has a positive effect on female fecundity. Originally, infected females laid 20% fewer eggs compared to uninfected females. Now infected females lay 10% more eggs than uninfected females. The authors also point out that CI levels and transmission rates have stayed constant, so the fecundity effect is not a result of depressed CI or bacterial transmission.

So, is this change in fecundity an effect of an evolving bacterium or an evolving host (or both)? To test this, the authors essentially infected flies with the old strain of the Wolbachia (that had been kept in culture for the past 20 years?) and found that the fecundity advantage disappeared. Thus, the current fecundity effect appears to be mostly a result of the evolution of the bacteria.

Ah, but what if the current Wolbachia strain that is causing the fecundity advantage is actually a more recently introduced strain and not the direct evolutionary lineage of the old strain? To examine this possibility, the authors tested the CI levels between the current strain and the old strain. If they were two different strains, flies infected with one would be reproductively incompatible with flies infected with the other. This was not the case, supporting the idea that the new Wolbachia strain is an "evolved version" of the old strain.

I found this study fascinating for a number of reasons. First, the design and the thoroughness of the experiments seem flawless to me (given, of course, that I am neither a fly biologist nor a bacteriologist) - the authors seem to have covered all the appropriate ground, showing that indeed the effects they witnessed are the result of bacterial evolution. Secondly, the evolution of this strain of Wolbachia is a great example of how quickly natural selection can work given conducive conditions. Thirdly, this paper shows just how testable (and accurate) predictions from evolutionary theory are.

Based on what is known about evolution by natural selection, coupled with a firm understanding of the biology behind a given natural system, we are able to make hypotheses, design experiments (and/or make the necessary observations to test these hypothesis, and come to scientifically tenable conclusions.

What more could you ask for?

Citation: Weeks AR, Turelli M, Harcombe WR, Reynolds KT, Hoffmann AA (2007) From Parasite to Mutualist: Rapid Evolution of Wolbachia in Natural Populations of Drosophila. PLoS Biol 5(5): e114 doi:10.1371/journal.pbio.0050114

A picture is worth a thousand 150 million words years?

Evolution of Mammals

Galapagos: set your TiVo

On March 18, the National Geographic Channel is premiering a three-part documentary on the Galapagos that looks like it should be excellent. The islands are an amazing place and I'm willing to bet that National Geographic does an incredible job with the show, so I would recommend tuning in for it. (The photo here is a Sally Lightfoot Crab - taken by yours truly)

Added bonus: check out
the show's website and enter to win a 10-day trip to the Galapagos!


UPDATE - 3/20/07: I watched the first two hours and was impressed with the footage and the information. Some of the narration is a bit schlocky, but I guess that can be forgiven. There is one piece that I found humorous in a way - when they speculate on "what might have happened" if Darwin had paid closer attention to the tortoises as if then he REALLY may have come up with some intereting ideas. Cause man, it's a shame that he didn't really notice those tortoises and had to settle for causing a major paradigm shift in modern science and influencing the future of biology, religion, and human culture. Just think what he could have done if he collected some tortoises. Seriously though - it's a well done series and you should definitely check it out if for no other reason than to ooh and aah at the visuals.

Milk: a driving force of evolution?

How many of you are lactose-intolerant? If you are, no need to fret - it's the normal mammalian trait to have.

As you know, lactose is the sugar found in milk, and lactase is the enzyme that helps break it down. Mammals obviously have a need for lactose and the production of lactase - after all, one of the defining mammalian characteristics is that moms produce milk as nourishment for their young. If a mammal is born without the ability to produce lactase, chances are they're going to have a hard time surviving. But, eventually, mammalian babies grow up and wean. For all mammals but us, this is the last time they ever drink milk. Thus, most mammals stop making lactase as they get older - what's the point of spending energy to make an enzyme you don't need anymore. Therefore, most adult mammals are lactose-intolerant.

But a curious thing happened during human history - the domestication of cattle, goats, and sheep. Being able to digest milk became beneficial in adults. So, as you could guess, natural selection has pushed adult humans towards lactose-tolerance. A new study has actually determined that the evolution of adult lactase production in humans happened as recently as 8,000 years ago. This is way after the evolution of Homo sapiens. In fact, by this time most of the globe had been settled by modern humans and various ancient cultures were beginning to establish themselves. Thus, it is likely that lactose-tolerance evolved in only some places, or it evolved multiple times independently. Lactose intolerance is least common in people of Northern European descent, while 80% or more of African-Americans, Asian-Americans, and Native Americans are lactose intolerant - these numbers are probably consistent with if, when, and how much these groups' ancestors utilized domesticated milk sources (though I don't know this for sure).

For some of our ancestors, milk has been a strong evolutionary force - it only took 8,000 years to evolve lactose tolerance (yes, only 8,000 years).

Evolution: It Does a Body Good

Ancient Human Timeline

update on 2/2/07: Just found a blog entry by Carl Zimmer discussing this topic as well.

Happy Birthday!!!!

Charles Darwin was born this day in 1809 in Shrewsbury, England - he would be 198 years old today. Interestingly, in a trivial way, President Abraham Lincoln was also born on this exact day (though not in Shrewsbury, England). For more info about Darwin, check out the following website:

AboutDarwin.com

Happy Darwin's Day everyone!

Blood: It's What's For Dinner

The diversity of life really is amazing. Just about every possible niche you can think of has been exploited at some point - if there is a way to make a living out there, you can bet natural selection has shaped some creature to utilize it. Take sanguinivores for example - better known as "blood-suckers" (Latin: sanguinis = blood; vorare = to eat).

Blood is a protein-rich material so it is not so surprising that some creatures utilize it as a food-source. In fact, sanguinivory is not so uncommon - we all know about mosquitoes, ticks, biting flies (deer/horse flies) and have some exposure to those "mysterious" creatures of the dark - vampire bats (though I bet you'd love to know more). But did you know that there are also vampire birds? Yup, blood-sucking birds.

You know those sweet, helpful, caring birds that eat the awful, ugly ticks and bugs off the backs of rhinos and giraffes, thereby preventing diseases and alleviating discomfort? Well, it turns out that they might not be so sweet and innocent after all. And on our favorite playground of natural selection, the Galapagos Islands, one of 'Darwin's finches' is a blood-sucker - this one doesn't even pretend to be helpful.

I'll let you read the bloody details on your own. Below are some links to some info on sanguinivory, blood-sucking birds, and vampire bats (I've left out mosquitoes, ticks, and flies - they're just too icky). The posts actually follow an order and are from one of the new blogs I am enjoying (yes, I know I'm a geek) - Tetrapod Zoology. There's a lot of info in the following posts, so take them slow. Enjoy!

Check this video out first:

Video: Vampire finches


Then read these in order:

Evolution of vampires

Evolution of vampires, part II

Evolution of vampires, part III

Vampire finches

Vampire Bats

Tree of Life

The Tree of Life Web Project is an amazing database that is attempting to reconstruct the evolutionary history of life on Earth. Essentially, the Project is a database of cladograms. The amount of information there is enormous and the various terms that are used to describe the groups of organisms can be daunting, but it is a fun place to explore (well, I think it's fun anyways). Here are a few links to help you start your exploration (and fun)...

(tip: you can click on the triangle at the base of any cladogram or the "containing group" link to go back in evolutionary time)

Placental Mammals - most "traditional" mammals

Diapsida - not many cladograms here, but follow the links to see the unexpected bird relationships

Animals - from sponges to humans

Eukaryotes

The Tree of Life homepage

Human evolution

Given the fact that we are all Homo sapiens it is not surprising that there was an interest in class about the evolution of humans. There are so many interesting and thought-provoking questions that I thought I would direct you to some websites that discuss our origins:

The Evolution of Man - a site maintained by the BBC that contains a number of good articles

Becoming Human - an online documentary about human evolution

The Genographic Project - National Geographic's project on the geographic expansion of humans out of Africa

there are plenty more sites out there, but this should give you a good start...enjoy

Where do plants come from?

We've been discussing in class a bit how we as a society are able to genetically engineer organisms - a technology that has taken hold over the past 30 years or so. But the natural world has been genetically engineering for millenia - not with anything technological or with that high a success rate, but effective nonetheless. We've mentioned earlier in the year how chloroplasts and mitochondria are believed to have evolved from prokaryotes that were engulfed by larger single-celled organisms - a process called endosymbiosis. Quite an amazing feat - esssentially harnessing the genetic power of one organism to help you survive. It was long believed that the evolution of algae and plants all stemmed from a single endosymbiotic event and that all chloroplasts share a common ancestor some 500 million years ago. But new research has shown that this may not be the case. By sequencing and comparing the genomes (full genetic makeup) of various chloroplasts (remember that chloroplasts and mitochondria have their own DNA) researchers have discovered that there were likely at least two independent endosymiotic events that lead to chloroplasts. This has many implications, including the idea that if this sort of thing can happen twice, why not more. And if it has happened more than once, what does this mean about the origin and evolution of the various photosynthetic organisms around today?


As a side note, this article/research is a good example of a branch of biology that studies the very early branches of the tree of life - basically delving back 100s of millions of years to examine how life emerged. Interesting, but difficult work.


Delving Into Chloroplasts' Past

Lucy's "Baby"

This isn't really relevant to stuff we're talking about in class, but I thought it was an interesting discovery.

Scientists have unearthed the world's oldest human child - an amazingly complete fossil that dates to beyond 3 million years ago. Human evolution is not a topic we will cover much (if at all) in class and is something I wish I knew more about simply because I find it intereting to think about. If anyone is interested in this topic I have a pretty good book you could take a look at and there are a few websites out there I am sure we could dig up.

Anyways, here's the link to the National Geographic story:

World's Oldest Child