Friday, June 19, 2009

Eyes abound

Unraveling and disentangling homology and convergence is one of the most fascinating endeavors in biology. Homology indicates common origin and maintenance, and is often taken as evidence for importance: ancient features are thought to be maintained because they are too useful to dispose of during evolution. In contrast, convergence, is the separate invention of similar features or functions during evolution. Convergence is taken as evidence for an element of predictability in evolution. For a simple example, fish and dolphins are highly convergent, and we can use this knowledge to predict that when vertebrates evolve to live in the ocean, that evolution will produce particular features like flippers/fins.

I recently came across a fascinating paper, arguing that structures that interact with light - either by altering or receiving it - are highly convergent, and may even be homologous at some level. Namely, bird feathers that reflect UV light have some striking similarities with eyes! Furthermore, a paper I am a co-author on just came out in PNAS that further supports this general claim. We found that the light producing structure of a bioluminescent squid shares many features with eyes, including the ability to detect ('see') the light it produces!

First, the feathers. Bleiweiss studied the uv/blue feathers of Tanagers and Bluebirds. In nature, short wavelength colors are often produced by structures, as opposed to pigments which produce longer wave colors like orange and red. Structural colors work by differentially interfering/reflecting different wavelengths of light. A familiar example of structural color is a CD/DVD. These disks contain grooves that are spaced very closely together. Because the spacing is similar to the wavelengths of visible light, interference of certain wavelengths occurs, leaving other specific wavelengths that we see as color. These spaced grooves are called diffraction gratings, and they are known in nature, for example on the antennae of some ostracod crustaceans which reflect blue light. Bluebird and tanager feathers do not use diffraction gratings, but instead a different structural mechanism. In the course of studying these feathers, Bleiweiss found some striking similarities with eyes. Perhaps similar to fins/flippers that push water for locomotion, the physical similarities of feathers and eyes may reflect convergence due to shared physical necessities of interactions with light.

An attractive tanager.  Image from

What are these similarities between eyes and structurally colored feathers? First is a wide, domed surface to receive the light. Second is tissue that is transparent to some light but reflective of other wavelengths. In eyes, this is the cornea and lens, which are transparent to much light, but often reflect UV (human retinas are actually sensitive to UV, except the light never gets there because the cornea and lens reflect it.). Tanager feathers have physically similar tissues with similar properties to reflect UV/blue light and allow other light to pass through. Third, there is a large central space in both eyes and ocular feathers: eyes contain humors and feathers a space filled with gas (air). Finally, at the bottom is a reflective layer. In eyes, this is the tapetum lucidum, which produces eye shine in cats, coons and other night-active animals. Again, optical feathers share a similar pigmented structure also designed to reflect light.

These similarities seem to be a perfect case of convergent evolution: two structures that perform physically similar functions (light gathering, or light reflecting) have converged on similar solutions. However, Bleiweiss also raises the intriguing possibility that eyes and feathers actually share some (partial) homology. Complex traits like eyes and feathers are made of many components, each with a potentially different evolutionary history. Amazingly, some of the genetic components, developmental features, and signal transduction cascades of eyes and feathers are also shared, in addition to their functional similarities. These similarities might be evidence of a deep shared ancestry between multiple organs, including eyes, feathers, and even teeth.

I was particularly struck by Bleiweiss' paper because I've been thinking about similar things in the context of a collaboration studying the light-producing organ of a squid that yielded a PNAS paper this week. Not unlike tanager feathers and eyes, the convergence of squid light-producing organs and eyes has long been noted. Many squid, including Euprymna scolopes, the object of our study, are bioluminescent. Euprymna seems to use its bioluminescence for camouflage. In the ocean, most light comes from straight above, so animals would cast a distinct and conspicuous shadow below them. Instead of eliciting the shadow response of a predator or prey, Euprynma matches downwelling light to make itself more cryptic. The light is produced in a light organ that houses symbiotic bacteria. It is the bacteria that actually generate the light. Consistent with Bleiweiss' general hypotheis, this light organ has many similarities with eyes.

Light organs and eyes both have lenses. Eyes focus incoming light for better visual acuity, and light organs focus outgoing light, similar to a flashlight. Eyes and light organ have an open space below the lens, and a pigmented layer opposite to the lens. In addition to these similarities, we found that the light organ responds physiologically to light using the same genes (opsin and its signaling components) that are used in eyes. Just as with optical feathers, squid light organs are functionally convergent, yet also share structural components in common, indicating some elements of homology.

Euprymna scolopes Hawaiian Bobtail Squid.  Picture by Chris Frazee, image from

These findings indicate an interesting new research program using the tools of phylogenetics. By reconstructing the evolutionary history of multiple components of convergent/partially homologous traits, we can see how and when these components came together, illustrating the pathways by which evolution has produced new features. This will allow a richer, more fundamental understanding of the origins of biodiversity and complexity, topics that intrigue everyone.

Bleiweiss, R. (2009). Feathers with Ocular Architecture: Implications for Functional and Evolutionary Similarities of Visual Signals and Receptors Evolutionary Biology, 36 (2), 171-189 DOI: 10.1007/s11692-009-9059-6

Tong, D., Rozas, N., Oakley, T., Mitchell, J., Colley, N., & McFall-Ngai, M. (2009). From the Cover: Evidence for light perception in a bioluminescent organ Proceedings of the National Academy of Sciences, 106 (24), 9836-9841 DOI: 10.1073/pnas.0904571106

Tuesday, June 16, 2009

Taxi-cab creationism: Idaho style

I have witnessed a thousand evolutionists descend upon Moscow, Idaho. At this conference, I've heard biologists discuss in exquisite detail new research connecting specific genes to specific evolved phenotypes, I've been regaled with stories tracing the pathways of evolution, I've seen tests of explicit historical hypotheses, and I've seen yet more data supporting predictions made by evolutionary science.

I have also been driven to my hotel by a friendly local taxi-cab creationist, something that is not at all unusual. In fact taxi drivers are my main interaction with creationism, in Rhode Island, in Georgia, and now in Idaho. When I teach Macroevolution to biology majors in California, I have come to realize that many of the students are unaware of the evolution denialism that is common in this country. I show them the DVD of the PBS documentary of the Dover trial (Judgment Day), and that is enlightening for many. I also teach them about anti-evolution arguments, and about the evidence against those arguments, and this is quite popular. But I also tell try to begin to relay some of my own experiences with anti-evolutionism, which has usually involved taxi drivers.

"So, what are you in town for", I lecture in my best southern drawl, mimicking some typological taxi driver.

"Well, I'm giving a lecture at the university".

"Aw, so whadya do".

"I'm an evolutionary biologist".

Moment of stunned silence. "Mmmm. I've heard evolution's pretty debatable".

Well, tonight I again entered a taxi, and the conversation started something like the lecture snippet above. But today, since my hotel is out of town I had some time in the cab, and since I was curious, I asked my driver a few questions, and I mostly listened. He was quite friendly, seemed determined to avoid a debate, but also shared many of his beliefs with me. I think he had given this pretty much thought, and he'd argued before about this. He'd always have his caveat, however non-factual.

I didn't ask his name, but he wore a red had, a T-shirt and had several days worth of stubble. He started making small talk about the conference, and said that he had driven someone from the conference recently. I asked him point blank what he thought about evolution - consider it field research for teaching my class, I suppose.

"Well, I'm a creationist, to be quite honest", he said. "But I don't push my beliefs on anyone".

He seemed to value greatly the fact that he wouldn't push his beliefs on anyone. Maybe he just wanted to maintain a chance at a tip.

"I used to be on the opposite side of God", he said. For a brief moment, I thought he meant he was once an evolutionist, but I came to realize he was saying he was once a "sinner". I suppose this means he was once an addict. I've known many people to convert drug or alcohol addiction into an obsession with religion.

"I used to live in New Zealand for 10 years". This seemed important to him, I'm not sure why. "We can debate, but I believe in my faith and my science, and other people believe in their faith and their science, so in the end no one will change their mind. It's fun to debate, but I guess we'll know when we die."

I said it sounds like he is really agnostic, since he says we won't know until we die. He reiterated his faith in God.

At one point I asked him how old he thought the earth is. He said 50,000 years old. "Of course that's debatable, my number comes from scripture. I know there's this carbon dating stuff, and yeah maybe the earth is billions of years old. But carbon dating has been proven to be wrong. Sure, some people argue it's right, but some people argue it's wrong. I'm actually really into collecting fossils", he said, "when I was in New Zealand, I found a turtle egg, a really rare thing, and this had the embryo in it. It was carbon dated, not the whole thing, just a little piece, and the date came back 70,000 years, even though science says these turtles are only 15,000 years old. You can do this carbon dating stuff, but you can't prove it."

I asked him why he required proof of Carbon dating, but didn't require proof in God.

"I just have faith, and I guess we'll see when we die."

At some points it sounded like he accepted some parts of evolution. I said at one point, that an important thing for me is that we share common ancestry with every single other living thing, and that I found that continuity of life beautiful.

"Well, yeah sure, but if we're connected to some green slime and apes and everything, then there is nothing that makes us special", he said. "I believe in the literal word of genesis, and - yeah sure it was translated by man, and humans make mistakes - but genesis and evolution are incompatible".

I asked him if it were possible that God said "let there be evolution". Sometimes he did sound like a deist.

In the end, he said his faith gets him through another day. "Nothing wrong with that", I said, as I got out of the cab, and paid the fare. I did give him a good tip.

Tomorrow I'll go back to the conference. I'm sure I'll see yet more amazing, detailed science, fueled by the predictions of decent with modification. That is what will get me through another day.

Monday, June 15, 2009

Everybody's doin' it

I'm happy to be here at the evolution conference in Idaho. One thing I've noticed is that most everyone I talk to is working to collect data using "next generation" sequencing technology. In my field of macroevolution/phylogenetics, this means 454 sequencing usually, since longer individual reads are possible, good for organisms without genome projects. Most people are working out the protocols, as we are, but one talk I saw yesterday had some great data from 454, which the authors are using to investigate the ancestral land plant genome.

The talk was delivered by Ruth Timme with Chuck Delwiche as a co-author. They sequenced transcriptomes of multiple green algae species, using Sanger and 454. They have a huge data set and will be able to address questions about the ancestral land plant genome. Given the vast amount of data they have, it's early days for the analyses, but already they found some interesting results. For example they found that components of ethylene receptor pathways predate the colonization of land. How aquatic organisms, like green algae, use a gas receptor is pathway is not yet known. I felt this talk was a great glimpse into a rapidly emerging trend in evolutionary biology.... The genomic, or at least transcriptomic age is upon us, even in evolutionarily interesting, non-model organisms.

Friday, June 5, 2009

Who's Afraid of the Big Black Wolf?

Morphological variation within and across species is a subject of great scientific interest. The molecular basis of such variation, including the differences in size, shape, and oftentimes color within a species can be due to numerous factors. Often, random mutations in the melanin biochemical pathway or in the promotor regions of these genes lead to variations in the common agouti phenotype. Occasionally, however, phenotypic variations enter a population as a result of hybridization rather than spontaneous mutation. In wolves, coat color variation probably arose from a surprising pairing…

Fig. 1 - Black wolves may have inheirited their coat color through hybridization with domestic dogs. Photo taken from here

In a recent Science article, Anderson and colleagues attempted to determine the molecular history of the Melanocortin 1 receptor (Mc1r) in North American gray wolves. They studied the melanistic K locus in dogs, coyotes, Italian wolves and North American gray wolves (specifically a small population derived from reintroduced wolves in Yellowstone National Park where genealogy could be easily traced). They noted that the mutation was more frequent in forested areas than on the tundra/taiga, which alone wasn’t exactly earth-shattering news considering a white wolf would stick out like a sore thumb in a dark forest. What was most interesting was that they suspected that the K locus mutation present in the gray wolves in both Italy and from North America as well as coyotes originated from a mutation in domestic dogs. Melanism is very widely distributed in domestic dogs, from Chihuahuas to Great Danes, but is not found in wolves outside of North America who have not been recently hybridized with dogs. It was hybridization between wolves and dogs brought across on the Bering Strait land bridge that allowed wolves the potentially adaptive advantage of having darker coats (or, if it was a trait that was present in ancient Eurasian wolves, it was lost in wolves on that continent after they crossed the bridge).

Interestingly enough, it’s the dog, that animal which has been artificially selected over time to be more suited to life on couches and in cars than one in the wild, which has provided the wolf with a trait so critical to survival. A trait, the paper proposes, that may become even more vital as global warming reduces available tundra territory and prey.

NOTE: This post was written by Lea Mehrkens, an undergraduate in my evolution class. I gave the class the opportunity for extra credit to write a blog-style post on a scientific paper. I think Lea did a nice job on this one... THO

Anderson, T., vonHoldt, B., Candille, S., Musiani, M., Greco, C., Stahler, D., Smith, D., Padhukasahasram, B., Randi, E., Leonard, J., Bustamante, C., Ostrander, E., Tang, H., Wayne, R., & Barsh, G. (2009). Molecular and Evolutionary History of Melanism in North American Gray Wolves Science, 323 (5919), 1339-1343 DOI: 10.1126/science.1165448