Two Snake Genomes Equals a Good Reading Day

It’s a good week for snake genomics, because PNAS has published both the Burmese python genome (Castoe et al. 2013) and the king cobra genome (Vonk et al. 2013). The related papers come from separate research teams (the python people mostly from Colorado and the cobra cabal the Netherlands), albeit with significant overlap between them. The world of snake molecular biology is a small one, after all.

The python group planted its snake genome flag in the ground more than two years ago with a paper describing their first draft assembly, and I have been eagerly awaiting the  results of their full-blown analysis. It was well worth the wait. As the python is known for its feast-or-famine metabolism (the small intestine can grow up to three times in size after gulping a meal half the python’s body mass), the researchers provided a very elegant analysis of the differential expression of genes in digestive organs before and after a meal and show, basically, that different genes are turned on or off either pre- or post-feeding. Very cool.

Figure 3B from Castoe et al. (2013), showing genes that have undergone positive selection on the vertebrate lineage leading to snakes.

Figure 3B from Castoe et al. (2013), showing genes that have undergone positive selection on the vertebrate lineage leading to snakes.

The authors of the python paper also investigated how snakes evolved their iconic and constrained morphology – because, after all, snakes lack legs and are equipped with a feeding apparatus equivalent to a human being swallowing a 16lb Thanksgiving turkey whole, and the molecular bases of these adaptations are unresolved. They analyzed a large number of genes shared across vertebrates – called orthologs – and found that during the evolution of the vertebrate lineage leading to snakes, many genes associated with skull and spinal development, metabolism and other functions experienced a faster rate of evolution than in other lineages. Also very cool.

Next up: king cobra. Why do we need both a python AND a cobra genome? The answer lies in the difference between these two snakes. One of them – and I hope you guessed cobra – is venomous. So it is no surprise that much of the justification for sequencing the king cobra genome included a need to understand the evolutionary origins and maintenance of the genes that control venom production. The cobra genome contains a multitude of protein families that underwent a significant expansion during cobra evolution that resulted in what we see today – a highly potent mixture of toxins designed to ensure certain death to a chosen prey item.

The two genomes differ vastly in their qualities of assembly. Through a mixture of various sequencing methods, the python team was able to get an N50 value of 207kb, meaning 50% of the assembled chunks of contiguous sequence were at least 207,000 base pairs of DNA in length. That assures that the research team would be able to recover the majority of genes – exons and introns and all. The cobra genome by contrast has an N50 value of only 3,982 base pairs, meaning that some of the genes may be fragmentary and the length of many introns will remain unresolved. However, I think that using N50 as a the gold standard of genome assembly “quality” is misleading. Sequencing strategies that significantly raise N50 values cost more money. In this day and age of modern biology, where small labs or groups of researchers conjure up whatever resources they can for an in-house genome sequencing project, the most affordable strategy for however you wish to address your biological questions will probably suffice. Both of these snake genome papers make the cut in that regard, and they are a significant contribution to the field of reptilian genomics.

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iPhone Herpetology: Among the Many Joys of Living in the Desert…

…is that occasionally, wild geckos wander into our home.

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The Rattlers of Suizo, AZ

Last weekend I took a night trip out with the Suizo Project. The project’s hard working leaders use radio telemetry to record the movements and key life history traits of rattlesnakes living in the Suizo Mountains in Pinal County, Arizona, which is in the heart of the Sonoran Desert. You can view their Facebook page for project updates here. This was beautiful country and the time of year couldn’t be more perfect: the hot and humid monsoon which plagues the region every summer has officially ended (and so have the days which reach 100 degrees Fahrenheit by 10am and 108 by 3pm). While it still gets hot  in the Valley of the Sun near Phoenix (100+, occasionally but not for long), down south in the mountainous Suizo area closer to Tucson (close to 3000 feet at the site I was told) it is simply lovely. The moon was a few days after full, and through the clear and dry desert sky the landscape glowed in a cool blue nightlight. Throughout the evening the temperatures stayed in the 70s and it was the type of night you spend on top of, but not inside, your sleeping bag.

After sundown we embarked on a five hour trek, meaning I followed the knowledgable and experienced guys around the desert and completely took advantage of their skill and expertise in order to learn a lot of things and take a few pictures (I’m not ashamed). Let me just say that in academia, I meet a lot of folks who know a lot about a lot of things but these. Guys. Know. Rattlesnakes. They are experts who can school anyone in the natural history of these incredibly fascinating species – the seasonality of their movements, their food preferences, their mating strategies, their evolution and the environment in which they live.

Some gratuitous musing:

Throughout the 20th century and into today, biology has evolved into ever more specific sub-disciplines, each noble in their own right yet many increasingly cordoned into a sterile laboratory or anonymous computer server, removed from the true natural world. I think the subject of natural history still has its place as a philosophy, a method and appreciation of understanding how the world works. It was after all what inspired me to become an evolutionary biologist.

Anyway, here are some great rattlesnake pictures:

Black-tailed rattlesnake (Crotalus molossus)

Black-tailed rattlesnake (Crotalus molossus). Very docile creature distinguishable by its relatively large, roundish triangular-shaped head.

Longhorn cactus beetle

Here’s a nice closeup of a  longhorn cactus beetle.

Funnel web spider

A nocturnal funnel web spider, waiting for its next meal.

Tiger rattlesnake (Crotalus tigris)

A female tiger rattlesnake (Crotalus tigris). Note the cactus spines lodged into the scales on her face and torso (yes, snakes have a torso, there’s more to them than a head and a tail). Despite these difficulties, she was in a rather accommodating mood.

Nice shot of the same tiger rattler from above, to highlight its beautiful markings

Nice shot of the same tiger rattler from above, to highlight its beautiful markings

Western Diamond-backed Rattlesnake (Crotalus atrox). I crossed the continent hoping to see these guys in their natural habitat, and I was ecstatic to find him. While beautiful and wary of humans, it is extremely venomous (even more so than the other rattlers).

Western Diamond-backed Rattlesnake (Crotalus atrox). I crossed the continent hoping to see these guys in their natural habitat, and I was ecstatic to see this one. While beautiful and wary of humans, it is extremely venomous (even more so than the other rattlers).

UPDATE [9/27/2013]: I received a response from Marty of the Suizo Project team, who corrected my summation of the relative potencies of rattlesnake venom:

…”extremely venomous, (even more so than other rattlers)” wouldn’t be how I’d describe their venom. They are more venomous, which can be measured in toxicity or volume, than many species of rattlesnakes in terms of volume but few when using LD50 values as a proxy of toxicity. Tiger rattlesnakes, on the other hand, have the most toxic rattlesnake venom but have a small venom yield. Tigers don’t bite people due to their habits and habitat, and relatively small geographic range, while diamondbacks have a comparatively large geographic range, often in close association with people, and are responsible for more human deaths in the U.S. than any other rattlesnake species. It could be said diamondbacks are ‘more deadly’ than other U.S. rattlesnakes…not as in ‘deadly’ in a comparison of toxicity but literally are more deadly because they bite and kill more people – the true measure of deadly!

Thanks for the important distinction, Marty. I wouldn’t want to give diamondbacks a bad name, although we must admit that sadly it is a lost cause…


A Desert Tortoise Field Trip

It’s the hottest time of year in the Valley of the Sun, and the unavoidable and unrelenting desert summer heat prevents newcomers such as me and my family from fully exploring our new beautiful surroundings. This is a sad fact, although the reality is that our lives are so upended by the move that we have little room for field trips – it will be better come springtime when (1) we are more settled and (2) daily temperatures will be cooler and the desert will be blooming and full of life. My wife and daughter escaped the heat this week to visit family in Portland, OR – a place with almost opposite climatic conditions from here. The brief northwestern Oregonian summer with its dry warm days and blue blue skies are hard to beat. So I am glad they have a chance to have some fun in the sun without having to worry about their health, like they would here.

Meanwhile, in the Phoenix area I have been relegated to air-conditioned indoor activities at the lab, office and home. Pleasingly, I received an invitation from one of my new colleagues who studies tortoises to join the Arizona Fish and Wildlife Turtle Management Team as a volunteer on a tortoise-monitoring trip. Since I am part of a group that is planning on sequencing the Desert Tortoise genome for its conservation, I thought it was a serendipitous opportunity to actually meet one of our possible study organisms. We were to meet the team at the Sugarloaf Mountain Area in the Tonto National Forest, about one hour northeast of downtown Phoenix. In the summer, these excursion need to start early – both humans and animals need to avoid the midday heat – so I picked my colleague up at 4:30am. The habitat was beautiful. It’s amazing that these sprawling desert landscapes contain large desert reptiles!

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The Sugarloaf Mountain area in Tonto National Forest. There are tortoises wandering around this landscape, and we were searching for both tagged and un-tagged individuals.

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Here comes one now!

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Close-up of a desert tortoise (Gopherus morafkai)

The team did manage to find tortoises but I forget the exact number. I was much more of a spectator on this trip, as it was my first excursion into the desert since we moved our here, and my field search image is not attuned to tortoises. So while these photos are my own, I had to rely on other more experienced folks to actually find the animals. They really just look like desert rocks, and they freeze when they see a person.

The extremely competent members of the turtle team were taking vital measurements of each tortoise as part of a long-term study tracking the growth and movements of desert tortoises that live in this part of the Sonoran Desert.ImageBeing out in the desert afforded an opportunity to see other reptiles, of course. Here are some pictures of an earless lizard (genus Holbrookia). During one rest point for the team, this individual was perched on a nearby rock giving us the business – which in lizard language consists of nasty looks and push-ups.Image

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You think you can take me?

Out of all the reptiles, you have to admire the chutzpah of some lizards. Upon being approached by humans, tortoises hide in their shells, snakes slither silently away, alligators dash messily to the water’s safety… but many species of lizards give humans displays of dominance almost right up until the last minute. Then they run away of course. But for the first few seconds it always seems like the little lizards really are sizing you up and thinking they can take you on.

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Believe it or not, the tortoises love this rocky terrain!

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Breaking Up (Anolis) Is Hard to Do

The “Anolisphere” is all abuzz with a recent paper by Nicholson et al. published in the journal Zootaxa with the inviting title, “It is Time for a New Classification of Anoles”. The authors propose two important and potentially disruptive changes to some widely-accepted features of the study of Anolis lizards:

1) The currently recognized genus Anolis is actually comprised of eight ancient lineages that are so divergent it is justified to break Anolis into eight genera (DactyloaDeiroptyx, Chamaelinorops, AnolisXiphosurus, Ctenonotus, Audantia, and Norops).

2) The widely accepted “ecomorph” hypothesis, which states that several independent lineages of Anolis lizards underwent convergent adaptive radiations on Caribbean islands (I wrote about this in a previous post), is not supported by the evidence.  The authors therefore suggest a looser-fitting “ecomode”model, which simply describes similar ecological adaptations without having to invoke any deterministic process.

The phylogenetic tree from the Anolis genome paper (Alfoldi et al. 2011). Nicholson et al. (2012) suggest that the eight lineages on this tree are so divergent they merit separate generic status.

Jonathan Losos of Harvard University has referred to this paper as “undoubtedly the most important paper on anoles to be published in the last several years”. Nonetheless, these intriguing ideas will require long and heated debate before they are to be accepted by the scientific community as a whole.  The editors of the anole-themed blog Anole Annals have already staked out a position as being strongly opposed to the changes. It has already been suggested that the Anolis community need not be compelled to formally adopt the new classification, and that it would be disruptive and confusing for future researchers, given the long body of work in which Anolis is referred to as a single large genus. There are also mounted defenses of the new paper as well. Check out what’s happening on the blog this week.

In my opinion, we should keep the single-genus status of Anolis, and here’s why. Pretty much everyone in evolutionary biology agrees that Linnean classifications (the binomial system which assigns genus and species names, as well as higher order classifications such as family, class, phylum, etc.) should reflect the monophyly of groups. This means that if you are describing a new genus, or family, or class, the number of lineages nested within the new group is largely subjective and the only real criterion is that all the lineages have descended from a common ancestor.

When basing taxonomy on the estimation of phylogenetic trees (which is pretty much how it’s done these days since tree building is how one establishes monophyly), your taxonomies are only going to be as good as the trees you use. Granted, the tree in the Nicholson et al. paper has strong statistical support, but that only really means that it does a good job of describing the data used to construct it in the first place. If down the line there is more or better data, a new tree may have better support, and then new taxonomies will have to be proposed. Since our understanding of taxonomy is dependent on phylogenetic information that is subject to change, and since we can say with certainty that Anolis in the broad sense represents a monphyletic group, AND much of the research out there treats it as such, I think we’re better off just keeping Anolis the way it is. But up to this point, I’m a consumer of systematics and not an authority on this by any means.

You’re staying put, honey! Whatever happens, Anolis carolinensis will remain in the genus Anolis.

The question remains, can a single genus be ~130 million years old? And the answer is absolutely yes. While our genus, Homo, is only just over 2 million years old, Ginkgo is probably about 200 million years old. And they’re both considered genera! My point is that Linnean classification, while useful, really serves a purpose in the sense that someone knows what museum drawer to put these things in. And I think Anolis should be one drawer (with almost 400 species, that’s a big drawer!).

In any case, under the newly proposed taxonomy, the species I study, A. carolinensis, will remain in Anolis. So I have little to lose, other than a divorce from hundreds of other fascinating possibly former congeners.


iPhone Herpetology: Winter Anoles

The SICB 2012 meeting in Charleston, South Carolina has been an eye opener, for sure, in many ways. First, the breadth of talks is staggering, ranging from biomechanics to comparative genomics. Second, many anole biologists have attended and it is exciting to mingle and share ideas with people who work on the same organism.

Finally, during a brief excursion outside yesterday, I opened my eyes to find quite a few anoles basking. This was surprising because it was following two days where the daytime temperatures were in the 30s and overnight dipped into the 20s. Freezing! Nonetheless, our favorite green guys were taking advantage of the comparatively warmer 50 degrees and sunny day to do some basking.

On a cold yet sunny day, a black lamp post can actually be a warm place for an anole to bask. The dark color of this female indicates that she is in quite a torpid state, which is expected considering it was January 5th, and she's cold-blooded!

Actually, seeing the anoles outside was not completely surprising. Anolis carolinensis occurs at higher latitudes than any other Anolis species (out of ~380 overall), and have conserved the non-hibernating tendencies of their tropical progenitors. For green anoles, the northern range limit is at about the 35th parallel in eastern Tennessee, where it snows and freezes often, and here in South Carolina the winters can be cold as well (as the last few days have demonstrated to us conference-goers). Sandy Echternacht at the University of Tennessee (who helped guide me in my collecting activities in that state) has made a career out out of studying the thermal ecology of these lizards, and has demonstrated that on a wintry yet sunny day an anole can clamber out of its hiding place and bask on a rock to achieve the same body temperature it would if it was summertime (obviously the time it takes to attain thermal optimum – the temperature at which the lizard is most comfortable – takes much longer).

Here's a pretty lady I snatched from a vine-laden verandah near the back of the conference center. Note the dorsal stripe, hallmark of her gender.

In the spring and summer, basking anoles attain a bright green color, sometimes with striking shoulder patterns of blue. All the anoles I observed yesterday were brown and olive-green in color, indicative of torpor. Since the temperatures have been so cold the past week, these anoles have had a rough time getting out of bed.


iPhone Herpetology: Poison Dart Frog

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I was at the American Museum of Natural History yesterday with family and took what I thought was a nice photo of this Dendrobates auratus. It’s a bluish morph of a Green and Black Poison Dart Frog.