The Anolis carolinensis Genome

Today was an important day for natural-, evolution-, and genetic-studies. The first full-scale genetic sequence of a non-avian reptile was published today in Nature. The lucky species to serve as the first reptile to be studied in this way? The Carolina green anole, Anolis carolinensis, of the southeastern United States (yup, the lizard featured on this post).

The article is cited “The genome of the green anole lizard and a comparative analysis with birds and mammals” (http://www.nature.com/doifinder/10.1038/nature10390). From amniotic egg development to convergent evolution in Anolis lizards (a genus with hundreds of independent species), the information, material, and understanding that arises from a study such as this are indeed vast and deep — and not just within the world of lizards. Whereas one might think of publishing an article as an ending, in the scientific community it is merely a new beginning or a next step. This study answers many questions, but it will also provide clear direction for new questions and new inquiry in the immediate years to come.

To read more about this project –or about anoles in general– I highly recommend The Anole Annals (http://anoleannals.wordpress.com), a blog entirely devoted to and focused on All-Things-Anolis. For me, it’s the nexus of Anolis on the web. An amazingly rich and fun resource.

So, congratulations to all those involved in this study, from researchers to writers, from lab-techs to editors.

You might think they’d be collectively sighing and taking a break, but I like to think the energy is fever-high right now and most of them are itching to move forward and to research deeper (not to mention continuing to spread the Gospel of the Anolis Genome right now). Also: teaching classes. And going to meetings.

Personal kudos to Dr. Jonathan Losos of Harvard University for taking the time to answer so many of my questions about anoles and for his obvious delight in his profession. The enthusiasm is contagious!

On my end, my enthusiasm for anoles continues to grow — partially because I’m so damn happy to be back in Anole Country and partially because of everything going on in Anolis studies right now. You can bet I’ll be paying close attention to the Carolina greens in south Georgia (who seem to be hanging out closer to the ground than I’d expect). I’ll also be heading down to Florida from time to time to check out the non-native species and to observe (photograph) their immediate impact/competition with the locals. In fact, I’m heading down to Miami/Coral Gables this weekend. [To those who don't like the snake photos, but don't mind the lizards: next week you should be much, much happier.]

Photographs taken 31 August 2011 at Grand Bay Wildlife Management Area; Lowndes county, Georgia.

~ janson

Videograph: Banks Lake National Wildlife Refuge, Georgia; 29 August 2011

Banks Lake National Wildlife Refuge is on the southern end of Lanier county, not too far from our home in Valdosta. I briefly surveyed the area on the 29th and it looks very, very promising. A beautiful area I’m sure to explore much of in the coming years.

Here’s the first glimpse of Banks Lake National Wildlife Refuge:

Pantherophis alleghaniensis (Yellow Rat Snake), 2007

When I was a kid we simply called the snake featured on this post a “Yellow rat snake.” It made sense, right? It was a snake, it ate rats (sometimes), and it was, you know, sort of yellow. If it had been a purple snake that ate kittens we would have likely called it the “Purple kitten snake.” Seriously.

So, “yellow rat snake” made sense, although some kids called it a “chicken snake.” I didn’t know many of these kids and I never personally saw one of these snakes eating a chicken. In my neighborhood, yellow was the buzz word, regardless of the fact that these snakes were often seen loitering about chicken coups in the south.

Still, some kids I knew weren’t too cool with just going by the common name (you know you who are, Billy). They want to break out their Audubon Field Guide and look up the taxonomic classifications. I was (and still am) one of those kids too, albeit one no longer obsessed with Audubon Field Guides — mainly because they never addressed subspecies classifications, damn it, and were always missing tons of species/subspecies)! Audubon Field Guides were like greatest hits collections, not full-on box set archives. And as a kid I wanted the techie details –minus the technical genetic science, I reckon in hindsight– and that meant I wanted scientific classifications, by god.

Anyhow, for awhile the taxonomic classification of my beloved yellow rat snake was Elaphe obsoleta quadrivittata, a subspecies kin to Elaphe obsoleta obsoleta, the black rat snake, found further to the north. Then, with emerging data and evolving arguments of this snake’s make and model (as well as its relatives the corn and fox snakes), it eventually became known as Elaphe alleghaniensis. This merged Florida’s yellow rat snake population with their Eastern rat snake brethren just to the north as one single species under the genus Elaphe.

Oh good. Glad we cleared that up. Now we can all move on and there can be peace unto science.

Ah, but wait — Yes, there was yet another change.

The Eastern rat snake (including the yellow variant found on the Floridian peninsula) became Pantherophis alleghaniensis. They (being Those Who Know This Stuff for Reals, Yo) split the New World Elaphes into Pantherophis, separating them from the Old World Elaphes because of differences between the two groups. Now not only was there a species play going on here, but also a genus play!  [It's important to iron these things out so that everybody can get on the same page, right? Hey, we're modernists and we demand reliable classifications!] So, at long last we finally had our Pantherophis alleghaniensis classification nailed down. For awhile at least,  I should clarify. It was good while it lasted.

Now the Eastern rat snake is argued to be Scotophis alleghaniensis. Another genus switcheroo. Why this time? Because… well, it’s complicated. It has to do with all the snakes that were included within this Pantherophis mega-genus — the rat snakes, the corn snakes, and the fox snakes. While the corn snakes are still under Pantherophis (lucky for them)fox snakes are now under Mintonius and the rat snakes are now under Scotophis. Three genuses dividing this one group.

At this point –because I am neither a geneticist nor one formally trained in the ways of the Jedi Herpetologist– I have to back up a few steps and admire the rubble of classification piled up at my feet like Paul Klee’s Angelus Novus. I have to just… go with one… And I do it in the name of Progress and of Sanity.

As the title of this post implies, I’m going with Scotophis alleghaniensis. I am going with Scotophis alleghaniensis for no reason other than this: I never thought a yellow rat snake ever looked or acted anything like a damn corn snake. Break ‘em up, I say. Also, I trust the people who actually do this research for a living. If it changes again, so be it. Nobody ever said this was an easy process, for the civilian tourist with a Nikon or for the scientist with mitochondrial DNA in her or his mind.

Regarding the snake in these photos, which I know a little more about than the details of mitochondrial DNA, this is a the “yellow” rat snake (now known as the Eastern rat snake) I found near Little Haw Creek in Volusia county, Florida on 04 January 2007.

I could overcomplicate this post by now describing how I found the snake, but at this point I’m still confused by the first segment of this writing. So I’ll leave it there and break out some techie-eco-tourist talk: this damn snake was fucking awesome!

And that’s something I can understand in its entirety.

UPDATE (September 2012): On Dust Tracks, the yellow rat snake is now listed as Pantherophis alleghaniensis and the gray rat snake is currently listed as Pantherophis spiloides. There is continuing debate about the taxonomic status of the New World rat snakes, including whether or not these are members of the same species, separate and distinct subspecies, or simply different species of the same genus. For the time being I’m listing these as separate species.

~ janson

Videograph: Nerodia clarkii compressicauda, 07 March 2008

Okay, here’s another videograph for today. I love this footage and couldn’t resist posting it now that it’s back online. This is a video of a group of mangrove salt marsh snakes (Nerodia clarkii compressicauda) getting into full-on mating mode. Indeed, baby-making was in the air. Some serious classic ballin’ action going down…

The video was recorded on 07 March 2008 at Matheson Hammock Park in Coral Gables / Miami, Florida. This is the same day I recorded the knight anole and brown basilisk footage. (The brown basilisk video is on my YouTube channel.)

Here ya go:

Videograph: Anolis equestris, 07 March 2008

This is the first in a new series of short videos I’ll be tinkering with and posting from time to time. They’re short (I call them videographs) and tightly focused on specific animals or locales. The new(ish) YouTube channel is located here: http://www.youtube.com/jansonjones.

Here’s the first video — featuring a magnificent knight anole (Anolis equestris)! Let’s hope it doesn’t get scrubbed for the soundtrack

Crocodylus actutus (American Crocodile), 12 May 2006

Here’s a slight shift of gears… These are American crocodiles, Crocodylus acutus, photographed 12 May 2006 at Flamingo, on the edge of Florida Bay in Everglades National Park. I’d wanted to see these amazing saltwater crocs for quite some time. Finally in 2006 I made it down to Flamingo, a strange cluster of buildings drenched in 1960s ethos, at the southern stretch of the Glades, right on Florida Bay. It’s one of the better easier spots to find Crocodylus acutus with a modicum of reliability (and, yes, ease).

These crocs are a bit larger than the more-common freshwater American alligator, Alligator mississippiensis. American crocs can reach lengths upward to twenty feet, but they are usually a bit smaller. Still impressive, right?

As you can see below, they’re often a bit brighter in their body tone than their alligator relatives, almost looking like the Saturday-morning crocs of my childhood cartoon rotation:

The American crocodile’s range is quite expansive. You can find them in Florida Bay, much of the Caribbean, and all the way over toward Central and South America. In U.S. waters, their populations were decimated in years past, but because of successful conservation actions (damn government trying to help nature by taking away are gosh darn freedom; gimme a gun, goshdarnitalready!) their numbers are believed to have increased. They were removed from the endangered species list in the 1990s and are now classified merely as threatened. They’re still protected by law, so put that gun away, Todd Palin. (<– I admit he’s never shot a croc — to the best of my knowledge.)

The individual seen at the top and bottom of this post traced the edge of a concrete dock my friend and I were walking on. The croc was clearly watching us watching it. I have to admit, it was a bit creepy (though not nearly as creepy as the time a one-eyed American alligator traced me on a shoreline in the Glades, stalking me out of curiosity or confusion).

The American crocodile is a large, robust, and gorgeous animal, but not one I would want to tangle with in the water. Me thinks evolution did not prepare me for that particular celebrity death match. I’ll stick to photographing them from above the water. Or from across the water. From a distance, it’s more than just a lyric; it’s a way of life.

~ janson

Storeria (dekayi) victa (Florida Brown Snake), 13 November 2005

Now, here’s a cute one: a Florida brown snake, Storeria dekayi victa, photographed 13 November 2005 at Kanapaha Botanical Gardens in Gainesville, Florida (Alachua county). I should note that the snake’s more recent taxonomic classification appears to be Storeria victa. Regardless of its current classification, this is a tiny (under a foot in length) and non-venomous snake. Cute too!

I didn’t see too many of these itty bitty snakes in central Florida because I was usually too busy trolling the freshwater shore lines for watersnakes and cottonmouths or looking in the bushes for racers and rat snakes. Florida browns, along with their crowned and ringneck cousins, are mainly subterranean — they usually live in the soil, under forest debris, and the like. Sometimes, as was the case on this day, you’ll find them trekking about above ground during the earlier hours of the day (or after a nice, solid rain).

Definitely not a snake I was searching for on this day (that would be the illustrious caramello-phase Florida “banded” watersnake), but one I was pleased to come across with my snake-hiking partner, Erin. We also found a ringneck nearby on the same day. Indeed, it was a day of tiny snakes.

~ janson