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 (Dactyloa, Deiroptyx, Chamaelinorops, Anolis, Xiphosurus, 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.
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.
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.
I recently learned I won’t be offered a postdoc I really wanted. There are other pending and as yet unrealized opportunities. Rejection is always a risk in science (papers, fellowships, grants, and now jobs), and everybody gets a lot of it. I knew these things going into the postdoc job market.
But sometimes when you come so close to something you can almost taste it, and you start to imagine yourself living in that not-yet-happened situation, working in that very lab with those very people, moving your family to the region – what neighborhood would we move to? Where are the nearest daycares? Oh, it’s so much better than Brooklyn, because we can afford a backyard… Reality can really smack you right in the face, and it’s a huge letdown.
But it’s not over. Other opportunities abound. I have skills, publications, and darn it, people like me!
I’ll get back up. I am still filled with resolve. The future is going to happen, anyway, right? Sigh…. Sometimes, resolve is so much work, you kind of want to just sleep in and drink a little coffee while reading The New Yorker for a while. Reminds me of these guys:
I am the battle-worn king inspiring my army, which is also me (and my wife and child) into the battle of our lives – THE FUTURE!!! Which will be sometime in the morning, just after some odds and ends we have to do, and maybe a little me time, perhaps?
Our paper on green anole phylolgeography has been published, so I thought I would justify the study in the first place and briefly synopsize our major findings and their implications. There’s a lot to talk about, so it will be completed across two posts.
First, some background….
As you may know, Anolis carolinensis is the scientific name for the green anole, which is a smallish lizard that lives in the southeastern United States. Last year, its complete genome sequence was published. At the time, it was the only reptile to have a fully sequenced genome (although this list is ever growing) and the phylogenetic gap it filled among sequenced vertebrates created a real demand. In addition, Anolis carolinensis is the lone species — out of a genus of around 400 — which occurs naturally in North America, with the bulk of Anolis biodiversity situated in South America and the islands of the Caribbean. On these islands, several independent yet convergent adaptive radiations led to the evolution of the same “ecomorphs” on different islands (a nice blog-post-sized review can be found on this Map of Life page). It’s a lovely story.
What does the Anolis genome offer? The chance to understand the genetic basis of adaptation (discussed by the eminent evolutionary biologist Jonathan Losos in this blog post on the Anole Annals), which is a very exciting prospect indeed. Using the genome as a resource, biologists may be able to pinpoint exactly which parts of the genome are affected by natural selection as new species form, or as different populations adapt to new surroundings. On another note, our lab wanted to look at how natural selection shapes the structure of a genome by limiting the activity of transposable elements, and the Anolis genome offered a unique opportunity to address this important question in comparative genomics. With regard to A. carolinensis specifically, it lives in a wide variety of habitats from subtropical Florida (FL) to more temperate Tennessee (TN), where anoles are subjected to freezing winters. The genome opens considerable opportunities for investigators to learn the genetic basis of each population’s unique set of adaptations across this landscape.
There was one problem, and it is familiar to anyone who studies population genetics (an esoteric bunch, indeed, however this is a major field in biology): if you want to know how much of the genetic variation in a population is affected by natural selection, you have to first have an estimate of the total amount of expected genetic variation (a parameter known as θ, or Theta). One thing that significantly affects θ is population size (usually denoted as N; the other thing affecting θ is the mutation rate u, so that θ=4Nu): a large population will have more genetic variation. But in order to measure the size of the population, you need to know its structure. What does that mean? Well, in a wide-ranging species (like A. carolinensis), it is very unlikely that individuals living in, say North Carolina are able to mate and share genes with those from Texas. Through a process called genetic drift (which is the random changing of gene frequencies due to finite numbers), these separated populations will resemble each other less and less over time. Understanding structure allows biologists to measure the amount of gene flow across landscapes, which can significantly alter local population sizes. Once you have an idea of the population structure, only then can you estimate the population size and measure natural selection at the genetic level.
In addition to estimating population sizes, looking at how genetic variation is distributed geographically allows researchers to make inferences about the evolutionary history of a species. For instance, if you were to observe that certain fixed genetic differences occur on either side of a large river, it may be due to the fact that the river provides a dispersal barrier. If you know how old the river is, you may be able to estimate how long the populations have been separated. Applying these methods to the understanding of the history and formation of species is a field in biology known as phylogeography. Phylogeography had its origins in the late 1970s, and as it became more practical to study genetic variation (especially after the advent of PCR and DNA sequencing), it exploded in the 1990s and 2000s, and now has at least one technical journal (aptly titled Molecular Ecology) solely dedicated to publishing studies using its methods. The phylogeography of a species is of special importance with regard to θ, because if the history of the population includes exponential growth (as it would when a receding glacier reveals virgin habitat) it will skew the θ estimates downward.
What was known about the phylogeography of green anoles? Well, not much. It was established that A. carolinensis arrived from Cuba sometime near the Pliocene-Pleistocene boundary about ~3 million years ago — an “Out of Cuba” hypothesis. The last study that looked at genetic variation in the species was Wade and Echternacht (1983), which relied on the differential electrophoretic movements of proteins called allozymes from anoles collected at seven localities. The major findings were: (1) 17 out of 25 allozymes completely lacked variation and (2) South FL was the home of the most divergent anole population. I like this paper, but it didn’t delve deep enough to make any robust inferences about green anole evolutionary history. This is nothing against the authors, it’s just that the methodology and technology weren’t strong enough yet.
Since then, as major advancements were made in the application of robust evolutionary models to more easily attainable DNA sequences for phylogeographic inference, the green anole escaped the scrutiny of phylogeographers, even as more and more co-distributed taxa were looked upon. It seems as if this widespread, abundant and even iconic lizard had become completely overlooked. It wasn’t as if samples were hard to come by. In fact, if you were to search HerpNet for museum samples of green anoles, you would receive 9,548 records! We had done our own fieldwork as well, and several questions were left wide open for us to address: (1) what is the structure of green anole populations across its range and just how divergent are the major lineages; (2) are the often-cited common dispersal barriers associated with co-distributed taxa also correlated with the distribution of genetic variation in green anoles; and (3) how did the glacial history during the most recent ice ages effect green anoles living at higher latitudes? So we decided to give it a try.
I’ll talk about the paper in Part 2.
A very interesting study published in PLoS ONE turned up in my RSS feed this week. It looks at how graduate students in the sciences change their outlooks on careers in academia as they progress. PhD students in the life sciences, chemistry, and physics were asked to rate the attractiveness of various careers. The researchers wanted to see if the answers given depended on how long the student had been in grad school. The results, especially for the life sciences, were striking. The later the stage of program progress for the student, the less likely he or she was going to find a faculty-teaching or faculty-research position as “extremely attractive”. In all fields, careers in “other” or “startup firm” become much more attractive to grad students as they near graduation.
Two other things to take home from the results of this study that the authors point to: (1) it is right to be concerned that there are far fewer tenure track faculty positions in academia than the market of graduating students will demand, and (2) the fact that PhD advisors strongly encourage academic career paths to their students reflects a growing disconnect with what actually may be attainable.
The state of Tennessee has not exactly racked up its pro-science credentials over the last 90 years. To start off, in 1925 the Butler Act was passed, which banned the teaching of evolution in Tennessee public schools, leading to the Scopes Trial (one of last century’s many “trials of the century”). It wasn’t until 1967 when Tennessee repealed the Butler Act, and in 1968 the SCOTUS declared in Epperson versus Arkansas that these types of laws violated the Establishment Clause of the U.S. Constitution which mandates the separation of church and state. That was 40 years ago, yet the saga of teaching evolution in Tennessee schools continues, as last month the governor of Tennessee allowed to pass a “Monkey Bill” law that lets teachers present evolution and global warming as controversial topics (even though they are based on scientifically sound principles). Boo!
Tennessee is not alone, and we know about the anti-intellectualism that occupies the current political zeitgeist, which also has roots further back in time. In the 1960s Wisconsin Senator William Proxmire was famous for handing out the Golden Fleece Award in his monthly press releases, which documented what he considered to be reckless government spending on silly scientific pursuits. This was echoed recently when last year Senator Tom Coburn of Oklahoma made a big deal about what he thought to be dumb scientific mental masturbation wasting taxpayer money, such as the now famous “shrimp on a treadmill” which was funded by a $500,000 NSF grant. Never mind the treadmill itself was hand-built by the P.I. for $1,000, a small part of his study of commercially important species and how they are affected by water quality. But why would a politician actually want to learn about the science he is lambasting, when he could just gorge on the political points scored when the media dives for his soundbite? The senator’s side of the story was taken up without scrutiny by major news outlets such as here, here, and here. Boo!
Although politically there seems to be some anti-science sentiment in the city halls, legislatures and governors mansion of Tennessee, the state’s Wildlife Resources Agency and Game and Fish Commission are unequivocally dedicated to scientific research. The folks working in those offices were extremely helpful when I had to acquire the proper scientific collecting permits for my field work. I knew these scientists and administrators were not the only reasonable Tennesseans.
You can count congressman Jim Cooper (D-TN) as one of them. His idea, announced this week with an alliance of congressional representatives, universities, and science and policy organizations, is the Golden Goose Award, which will honor obscure yet federally-funded research that leads to important breakthroughs.
Here are some rare reasonable soundbites to gorge on.
Jim Cooper on his Golden Goose Award:
It recognizes that a valuable federally funded research project may sound funny, but its purpose is no laughing matter.
Federal support for basic scientific research creates jobs, fosters innovation, and improves the American people’s quality of life.
Research supported by the federal government has led to remarkable breakthroughs and valuable scientific developments that affect our lives on a daily basis.
Science plays an important role in our economy, as many jobs in this field go unfilled. We must continue to invest in this field and similar fields so that more people have the resources they need to find a job.
Nice words, Congressman. Tennessee should be proud to have you.
Cooper may be my favorite Tennessean, after Aretha Franklin, B.B. King, Booker T. Jones, Elvis Presley, Carl Perkins, Chet Atkins, Cormac McCarthy, Dolly Parton, George Hamilton, Isaac Hayes, Jack Daniel (yes THAT Jack Daniel), Oscar Robertson, Quentin Tarantino, Rufus Thomas, Samuel Jackson, Sam Phillips, Sonny Boy Williamson, and Tina Turner (I picked these from here). Sorry, Jim Cooper. You’re tops with me, but you have to get in line.
- Who Will Win First Golden Goose Award? (news.sciencemag.org)
- Surprise! Congressmen Support Science with the Golden Goose Award (motherboard.vice.com)
Thanks to science.memebase.com for embedding this terrific segment in which astrophysicist Neil deGrasse Tyson argues Bill O’Reilly’s assertion that proof of God exists where scientists are ignorant. The examples of scientific ignorance O’Reilly uses (I paraphrase: “tide comes in, tide goes out – how do you explain that?”) are QUITE EXPLAINABLE.
Listen to deGrasse Tyson’s extremely convincing counter, and you be the judge:
Well put, Neil.
Here’s a video of O’Reilly explaining his reasoning. The utter lack of logic is stupefying.
Tennessee Governor Bill Haslam (R) recently failed to block a law passed by his state legislature that provides legal protections for science teachers who criticize scientifically tested principles such as evolution and global warming in their classrooms. I’m sure there exists across the internet numerous angry rants about this as an assault against scientific reasoning and the proper education of our citizenry, and I fall heavily on the side of that argument, but I won’t get into it here.
I will chime in with one thing, however.
The bill states “some scientific subjects, including, but not limited to, biological evolution, the chemical origins of life, global warming, and human cloning, can cause controversy”. What this “teach the controversy” argument really means is “create controversy”, because the scientific subjects listed above are like comparing apples and oranges. Evolution and global warming are hypotheses that have not yet been falsified and thus are considered theories. This means that for both, there has to date been almost no evidence leading the scientific community to believe an alternative explanation. The consensus among scientists is: life evolves and the Earth’s climate is getting warmer. There really is no controversy, unless you ask certain non-scientists who argue against these theories on moral grounds.
That is like taking your car to the mechanic, and he/she says: “I looked at your car and determined that the reason your steering wheel is drifting is because your tires are unevenly worn”. Then, you take your car to your uncle and he says “ah, the roads are just crooked”. Who would you believe: the person with the expertise and training to examine the situation and make a determination as to the cause of his/her observations, or the non-expert who is just telling you what he thinks?
Furthermore, one may believe that the act of cloning a human is immoral. Fine. But human cloning is not a theory, it is an act, so one is allowed to make a logical argument against its practice. To argue that scientific theory is immoral just doesn’t make any sense. Are Tennessee teachers going to tell students that it’s okay to think that scientists should maybe “lay off the evolution thing”, as in “HEY, STOP DOING EVOLUTION”? Scientists would respond, “uh, we’re not doing anything, as far as we can tell the things are just evolving on their own, we are just watching”.
The reasoning behind it is suspect. Which makes me worry that powers greater than you or me or the average Tennessee parent were at hand. Which, in turn, makes me fear for the future of our republic.
- Anti-Evolution ‘Monkey Bill’ In Tennessee (1oneday.wordpress.com)
- Tennessee Passes ‘Monkey Bill’ To Teach The ‘Controversy’ On Evolution And Climate Science – Brad Johnson – ThinkProgress (richarddawkins.net)
- A Question for Education ‘Reformers’ About Tennessee’s “Monkey Bill” (mikethemadbiologist.com)