Image copyright Andrew M. Shedlock.
The anole genome paper is out in Nature today (although links on Nature’s own page only take you to a list of authors at the present time, I’m assuming this glitch will be fixed shortly). Nature also published a brief commentary highlighting some of the most interesting discoveries from this work. For more coverage of work related to the genome, check out this post and stay tuned to Anole Annals – we’ll have a bunch more genome posts over the next few days.
As the publication of the anole genome approaches, one might ask: “Just how was Anolis carolinensis selected to be the first non-avian reptile to have its genome sequenced?” Turns out that it’s a long and convoluted story, and this is one man’s first-hand account.
To set the stage, we have to go back to the early days of genome sequencing, all the way back to 2005. This was a time when to sequence a genome was a really big, time-consuming, extremely expensive affair (the human genome had cost ca. $2 billion; by 2005, the price had dropped to ca. $20 million per genome). Such a big deal, in fact, that there was an NIH committee that decided which species would be sequenced, and assigned them to one of the three genome sequencing centers (Baylor University, Washington University in Saint Louis and the Broad Institute in Cambridge) that had been created as part of the human genome sequencing initiative. The first few species selected were chosen exclusively with regard to their potential relevance to human health. They were the laboratory model systems, the workhorses of biomedical research, such as the mouse, chimp, Xenopus, chicken, Drosophila and C. elegans.
By 2005, a couple of mammals had been sequenced and representatives of all classes of vertebrates except one: reptiles.
Interested in transposable elements in the Anolis genome? You should be!
As DNA sequences that can move about the genome, transposable elements – or TEs – are also called “jumping genes”. These are some of the most important components of genomes, accounting for much of the variation in genome size and structure across vertebrates. The activity of TEs add to the genetic variation of populations in neutral, deleterious, and sometimes adaptive ways. In the human genome, TEs can insert into genes and cause numerous genetic diseases such as muscular dystrophy (Cannilan and Batzer 2006).
We published a review in last month’s issue of Mobile Genetic Elements (Tollis & Boissinot 2011) describing the diversity and abundance of TEs found so far in the Anolis genome, and how they impact our understanding of genome evolution in reptiles and mammals. The Anolis genome contains an extraordinary diversity of TEs, including DNA transposons (“cut and paste” elements) and long terminal repeat (LTR) and non-LTR retrotransposons (“copy and paste” elements). Even though there are many different kinds of TEs in Anolis, within most TE families there are low copy numbers relative to the human genome, suggesting that purifying selection keeps tight control.
Fig. 1: Figures illustrating Cuban origins of A. carolinensis from our 2005 paper in Molecular Ecology. Green shading indicates the range and phylogenetic position of A. carolinensis, blue shading indicates Cuban populations related to A. carolinensis. The arrows indicate possible dispersals from Cuba, some of which are supported by phylogenies (including the dispersal from Cuba to the continental United States indicated by the bold arrow).
With all this discussion of the green anole’s genome, it seems like a good time to remind everyone of how Anolis carolinesis came to be the model organism that it is today. The simple answer, of course, is that A. carolinensis is the only species of anole endemic to the continental United States. As such, its always been the anole species most accessible to the broadest range of researchers. The deeper answer – and the focus of this post – concerns how A. carolinesis happened to become the continental United States’s only native anole in the first place.
For information on why the anole genome is useful for evolutionary studies, go here.
For information on how the genome is already being used in research, try here, here, here, here and here.
For the history of discovery and study of anoles, go here.
For the evolutionary history of the green anole, check this one out.
For a great story, don’t miss this one.
For great pictures of anoles and their dewlaps, try here, here, and here (among others).
For many other topics in anole ecology, behavior, and diversity, try looking up terms in the blog’s search window.
One of these species has had its genome sequenced, and the other has independently evolved to look very similar and live in the same environment. The anole genome will make anoles an even more powerful group in which to study evolutionary convergence. Photos by Melissa Losos (left) and Pete Humphrey (right).
When the genome of Anolis carolinensis is finally published, most attention will focus on how this genome, the first reptile to be sequenced (not including birds), differs from other vertebrate genomes, and what these differences may tell us about genome evolution. No doubt this will be interesting, but the real value of this genome–in my unbiased opinion–resides in the questions we finally will be able to address about the evolutionary process, particularly in one model system of evolutionary study, Anolis lizards. Chris Schneider published a perceptive article, “Exploiting genomic resources in studies of speciation and adaptive radiation of lizards in the genus Anolis,” on this topic three years ago, and I will briefly expand on his points here.
An anole genome will be useful for evolutionary studies in two ways. First, a long-standing question in evolutionary biology concerns the genetic basis of convergent evolution (i.e., when two or more evolutionary lineages independently evolve similar features). Do convergent phenotypes arise by convergent evolution of the same genetic changes, or do different lineages utilize different mutations to produce the same phenotype? In other words, does convergence at the phenotypic level result from convergent change at the genetic level, or can different genetic changes produce the same phenotypic response? In the last few years, molecular evolutionary biologists have produced a wealth of studies investigating whether convergent changes in coat color in rodents, eye and spine loss in fish, bristle loss in fruit flies and many other changes are the result of changes in the same gene, even some times by the very same genetic mutation. Underlying these questions are more fundamental questions about constraints and the predictability of evolution (these topics have been reviewed a number of times in the last couple of years, most recently in a paper by me, in a paper which refers to other recent reviews).
The anole ecomorphs, habitat specialists behaviorally and morphologically adapted to use different parts of the environment. The same set of ecomorphs (with several exceptions) have evolved independently on each island in the Greater Antilles. Figure from "Lizards in an Evolutionary Tree," based on earlier figures in Ernest Williams' work.
Anolis lizards are, of course, the poster child for evolutionary studies of convergent evolution. Indeed, convergence has run rampant in this clade. AA has prattled on endlessly about the famous anole ecomorphs, a set of habitat specialist types that have evolved repeatedly on each island in the Greater Antilles to occupy different habitat niches. This convergence is usually studied in terms of limb length, tail length, and toepad dimensions: arboreal species have big toepads, twig species short legs, grass species long tails, and so on, with these traits independently evolving many times. But the ecomorphs are convergent in many other traits that have received less attention: head and pelvis dimensions, sexual dimorphism in both size and shape, territorial and foraging behavior, to name a few, and the more closely we look, the more convergent traits we find. And, further, anole convergence is not entirely an ecomorph phenomenon; some traits vary within an ecomorph class, but are convergent among species in different ecomorph classes, for example, thermal physiology and dewlap color.
In other words, there’s more convergence in Anolis than you can shake a stick at, and the availability of the anole genome sequence will provide the tools to investigate its underlying genetic basis.
Figures from Fujita et al. illustrating relative homogeneity of GC content across the anole genome (left) and shifts in GC3 along branches in the vertebrate tree, with black branches indicating descreases of GC3 and gray branches indicating increases of GC3 (right).
Genomes are rarely homogeneous aggregations of Gs, As, Ts, and Cs. Indeed, variation in basepair frequency can have important implications for how genomes, and the organisms they generate, evolve. Regions with relatively homogenous GC content that extend for more than 300 kb known as isochores are prominent features of previously sequenced amniote genomes. Isochores are associated with a range of important variables, including gene density, intron length, DNA replication timing, and gene expression. GC-rich isochores also tend to experience high rates of recombination, resulting in elevated effective population sizes and increased efficiency of purifying selection relative to drift.
Table from Portik et al.'s Conservation Genetics paper reporting new primer pairs for amplification of nuclear loci (left side) and a phylogeny generated using some of these loci from Stanley et al.s' 2011 MPE paper on cordylids (right panel).
A new study by Portik et al. used the anole genome to develop more than 100 new primer pairs for the amplification of nuclear-encoded DNA from squamates, some of which have already proven useful for inferring relationships within and among species. Portik et al.’s carefully thought out strategy for marker development – which focused on rapidly evolving protein-coding loci – ensures that their loci will be particularly useful for phylogenetic analyses. First, Portik et al. focused on intronless protein-coding genes, with the goal of limiting length variation and simplifying alignment. Second, recognizing low variability relative to non-coding regions as a potential limitation of protein-coding loci, Portik et al. focused exclusively on developing markers from loci that are more variable than the first third of RAG-1 (one of the most useful and widely-used of the nuclear genes used previous phylogenetic studies of squamates). This strategy yielded 104 genes and led to development of primers for 170 gene fragments ranging from 407-2,492 bp. Portik et al. conducted limited PCR testing on 70 of these loci and found varying degrees of success across five squamate families, including Scincidae, Varanidae, Agamidae, Cordylidae, and Gekkonidae. More importantly, some of the loci have already proven useful for phylogenetic studies of skinks (Portik et al. 2010 , Portik et al. 2011), cordylids (Stanley et al. 2011) and iguanids (anole genome paper, which is currently in press at Nature).
While high throughput sequencing technology will eventually render PCR primers and Sanger sequencing nothing more than curiosities from a previous generation, this time is at least a few years away. In the meantime, Portik et al. have given the herpetological community some very useful new tools to play with.
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