Virus Evolution

Here is a short video on virus evolution from the Instituto de Biologia Molecular y Celular de Plantas and the Santa Fe Institute Professor Santiago Elena.

Synopsis

Viruses can evolve fast and sometimes adapt quickly to a new host species. For example, an influenza virus that normally infects birds can become adapted to humans. The tobacco etch virus normally infects tobacco plants. Professor Santiago Elena from Valencia wants to find out what it takes to make the tobacco virus capable of infecting another plant: Arabidopsis. The movie shows how Santiago Elena does the evolutionary experiment and we see that after 30 rounds of experimental evolution the virus is indeed adapted to the new host plant! After the experiment, Elena looks at the genetic code of the adapted virus and finds that there are just three differences between the genetic code of the normal (tobacco loving) virus and the virus that is now adapted to Arabidopsis.

Lawrence Basil Slobodkin (1928-2009)

Larry Slobodkin, eminent ecologist, founding chairman of the Stony Brook University Ecology and Evolution Department, and Fellow of the American Academy of Arts and Sciences passed away last Saturday.

Larry's impact on the science of ecology is immeasurable, particularly with regards to linking population dynamics with ecosystem ecology. A concrete example of this is his famous HSS paper. With coauthors Nelson Hairston Sr. and Jerry Smith, Slobodkin use a simple observation (the world is green) to deduce that predators limit herbivore abundance, thus allow plants to flourish.

Beyond his scientific contributions, Slobodkin is reknown for creating the world's first graduate program in ecology and evolutionary biology (at Stony Brook University). Many of the best and brightest in the field have either taught or schooled in this program.

Larry's (academic) nephew, ecologist Mike Rosenzweig, wrote a great piece about him for Evolutionary Ecology Research. Larry contributed this autobiographical article. More articles in the EER special issue in his honor are available here.

NY Times Obituary

Update: Carol Reid wrote a nice tribute to Larry here.

Update: An obituary was published in PLoS Biology.

Phage Hunters

18 freshmen students have enrolled in my Genomics Research Experience course aka Phage Hunters. This course is supported by the Howard Hughes Medical Institute's Science Education Alliance. My students have begun the process of isolating novel Mycobacteriophages by collecting soil samples from the wild and plating them on lawns of Mycobacterium smegmatis, a M. tuberculosis relative. Unlike M. tuberculosis, M. smegmatis is non-pathogenic and is easier to grow and manipulate under experimental conditions. Nonetheless, by virtue of their close phylogenetic relationship, the two bacteria are quite similar in many respects. Thus, M. smegmatis may be an excellent model for deriving treatments against tuberculosis.

Collecting Mycophage is already paying handsome dividends. Albert Einstein College of Medicine Professor William Jacobs isolated a phage he named the Bronx Bomber from soil from his own backyard in the Bronx. With University of Pittsburgh Professor Graham Hatfull, Jacobs characterized this phage in the laboratory. They found that this phage is able to insert itself into the genome of M. smegmatis at a very specific location in the groEL1 gene, thus disabling the gene. One of groEL1's functions is to facilitate the production of biofilms.

Biofilms are extracellular polymeric substances that aid and protect microbes. They allow bacteria to persist in the face of antibiotics. It's estimated that 80% of infections involve biofilm formation. While biofilm formation in tuberculosis has not yet been uneqivocally confirmed, M. tuberculosis does have a groEL1 gene with 90% similarity to that of M. smegmatis.

If the phage is able to infect M. tuberculosis or is mutated to infect M. tuberculosis, it is possible that some day the phage could be used as therapy against tuberculosis. As one of the three primary diseases of poverty, tuberculosis has a devastating impact in the developing world.

Top Photo: Bxb1 is a mycobacteriophage that was originally isolated from Dr. Jacobs' backyard in the Bronx. It is affectionately called "The Bronx Bomber" as it forms large plaques on a plate with lawn of Mycobacterium smegmatis cells (left panel). The Bxb1 phage plaques are characterized with their clear centers surrounded by turbid rings. The turbid rings represent lysogens (i.e. M. smegmatis bacterial cells into which Bxb1 has integrated) of M. smegmatis that are resistant to superinfection with Bxb1 phage. These lysogens are defective in biofilm formation. A transmission electron micrograph of Bxb1 is shown in the right panel. Courtesy of Jordan Kriakov, William R. Jacobs, Jr.

Middle photo: Image shows Mycobacterium smegmatis growing as a biofilm on a liquid surface, with its characteristically textured folds. Courtesy of Anil Ojha, Tom Harper, Graham Hatfull.

Bigfoot or Mistaken Identity?

Ecological Niche Modeling is a great tool for conservation biology, phylogeography and evolutionary biology. However, as Jeff Lozier and colleagues point out in a paper in Journal of Biogeography, the models are only as good as the data they are based on.

The basic premise of the ENM approach is to predict the occurrence of species on a landscape from georeferenced site locality data and sets of spatially explicit environmental data layers that are assumed to correlate with the species’ range.

This is fine if the researchers themselves collect the data, but many studies rely on publicly available online databases. While no doubt the validity of most of this data is unimpeachable, there can be instances of misidentification or poor taxonomy. These discrepancies have the potential to significantly skew the results. As an extreme example, the authors point to Sasquatch, the North America's purported other large primate. Using data from the Bigfoot Field Researchers Organization, Lozier et al. predict the Sasquatch's range in the Western US (see figure above).

(T)he ENM shows that Bigfoot should be broadly distributed in western North America, with a range comprising western North American mountain ranges such as the Sierra Nevada Mountains, the Cascades, the Blue Mountains, the southern Selkirk Mountains, and the Coastal Range of the Pacific Northwest.

Interestingly, Bigfoot's supposed range overlaps considerably with another large American mammal, Ursus americanus, the Black Bear. Naturally, it is quite possible that the Black Bear and Sasquatch could share similar habitat requirements, but perhaps a more parsimonious hypothesis is that Black Bears are being misidentified as Sasquatch.

Thus, the two ‘species’ do not demonstrate significant niche differentiation with respect to the selected bioclimatic variables. Although it is possible that Sasquatch and U. americanus share such remarkably similar bioclimatic requirements, we nonetheless suspect that many Bigfoot sightings are, in fact, of black bears.

Photo of mangy bear

The take-home message is that scientists should carefully scrutinze literature records and/or public databases. Validate taxonomy. Rely on recognized experts. Don't be afraid to disregard questionable specimens. Ecological Niche Modeling has a bright future, but like any technique it can be properly or improperly applied. The authors should be commended for their clever approach to pointing out the need for scrutiny.

Lozier, J., Aniello, P., & Hickerson, M. (2009). Predicting the distribution of Sasquatch in western North America: anything goes with ecological niche modelling Journal of Biogeography DOI: 10.1111/j.1365-2699.2009.02152.x

Left-handed Snails Beat Snail-eating Snakes

Masaki Hoso reported that the snail-eating snake, Pareas iwasakii, has lopsided jaws to better enable it to tug snails out of their shells. Most snails have shells that whirl clockwise (to the right) so P. iwasakii has evolved an upper jaw with more teeth on the right side than the left. In a sample of 28 snakes, the Hoso found each one had an average of 17.5 teeth on its left jaw and 24.9 teeth on the right.
The lack of symmetry helps the snake pry the snails out of their shells with alternate retractions of their left and right jaws, a technique called "mandible walking".

Here's a video of the snake preying upon a "right-handed" snail.

The snail, Satsuma c. caliginosa, has countered the snake's adaptation by evolving a left-handed swirling pattern.

Hoso et al. write in Biology Letters:

In addition, our experiments demonstrate a defensive function of sinistrality for snails against snake predators. Sinistral variants have been generally considered to suffer selective disadvantages on account of the overwhelming predominance of dextrals (Vermeij 1975, 2002; Johnson 1982; Gould et al. 1985; Asami et al. 1998; but see Dietl & Hendricks 2006). However, sinistrals should enjoy a selective advantage over dextrals under chirally biased predation by snakes. The remarkable diversity of sinistral snails in Southeast Asia (Vermeij 1975; Hoso et al. 2006, unpublished data) may be attributable to ‘right-handed predation’ by the snakes.

In the video below, P. iwasakii attacks but fails to consume the lefty snail.

How cool is that?

Hoso, M., Asami, T., & Hori, M. (2007). Right-handed snakes: convergent evolution of asymmetry for functional specialization Biology Letters, 3 (2), 169-172 DOI: 10.1098/rsbl.2006.0600

Evolution 2009 Moscow, ID

I have finally arrived in Moscow, ID for the the joint annual meeting of the Society for the Study of Evolution (SSE), the Society of Systematic Biologists (SSB), and the American Society of Naturalists (ASN). It was a long and enjoyable drive from Salt Lake City where I met up with Weber State evolutionary biologist and fellow blogger Jon Marshall. Along the way we stopped at Waterfall Canyon and the Hot Pots in Ogden, the Craters of the Moon, Ernest Hemingway's grave, and more hot springs in Stanley.

Several other bloggers are participating in the festivities.

I'll be posting about the scientific content as time permits over the weekend, but now it's time for a few beers at the opening reception and Genie Scott's Stephen Jay Gould Award Lecture "The Public Understanding of Evolution and the KISS Principle."

Roald Dahl on Vaccines

When I was younger, my favorite book was James and the Giant Peach by Roald Dahl (also author of Charlie and the Chocolate Factory and Matilda). Turns out that book was dedicated to his daughter Olivia, who tragically died of measles. In this article, Dahl stresses the importance of vaccinations.

Dahl writes "...there is today something that parents can do to make sure that this sort of tragedy does not happen to a child of theirs. They can insist that their child is immunised against measles. I was unable to do that for Olivia in 1962 because in those days a reliable measles vaccine had not been discovered. Today a good and safe vaccine is available to every family and all you have to do is to ask your doctor to administer it. It is not yet generally accepted that measles can be a dangerous illness. Believe me, it is. In my opinion parents who now refuse to have their children immunised are putting the lives of those children at risk.... It really is almost a crime to allow your child to go unimmunised."