The Story of Our Green Anole Story, Part 1

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.

Separate adaptive radiations on separate islands led to the repeated evolution of Anolis ecomorphs, which is one of the most elegant stories in evolutionary biology. The genome will unlock the genetic secrets of this phenomenon. Image from Lizards in an Evolutionary Tree by J. Losos, and adapted from the work of E. WIlliams.

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.

Pretty much what was known about Anolis carolinensis after the invention of PCR and DNA sequencing. Map modified from http://www.terrariet.dk/Anolis_carolinensis_UDB_UK.html

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.

Hey, phylogeographers! Study me!

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.