Author: Marc Tollis

Postdoc, Arizona State University.

I study comparative genomics of reptiles, birds, and mammals to understand substitution rate variation across lineages, the link between genotypes and phenotypes, and the evolution of cancer suppression.

Hundreds of Genes Help to Resolve Green Anole Evolutionary History in North America

Anolis carolinensis from North Carolina. Photo from Carolina Nature.

One of the most well-known species of anole lizard is Anolis carolinensis, AKA the green anole, which is the only anole native to the continental United States. As a classic model for ecology and behavior, this lizard was the first species of reptile to have a complete genome sequence. Interestingly, only after it became a genomic model, numerous studies (Tollis et al. 2012, Campbell-Staton et al. 2012, Tollis & Boissinot 2014) sought to understand how genetic variation is structured across the geographic range of A. carolinensis,  and to infer historical migration patterns and demographic events to explain the current distribution of green anoles. However, these studies still left many questions unanswered, mostly due to the fact that they were limited in terms of numbers of genetic markers. Now, we have published a new paper in Ecology and Evolution that used a targeted enrichment method to capture more than 500 sequence markers and provide a clearer picture of A. carolinensis historical biogeography.

What we knew about Anolis carolinensis phylogeography

Collecting green anoles for phylogeographic study has been a real hoot, taking us all over the country. Anolis carolinensis ranges across subtropical North America, and consists of five geographically structured genetic clusters supported by both mitochondrial (mtDNA; see Tollis et al. 2012 and Campbell-Staton et al. 2012) and nuclear (nDNA) markers (see Tollis et al. 2012, Tollis & Boissinot 2014). Three of the clusters are found in Florida : one whose distribution primarily hugs the Northwestern coast of the peninsula, another along the Eastern coast of the peninsula, and a third relegated to South Florida. The continental mainland, while making up most of the area of green anole range, harbors only two clusters: one occupying North Carolina and South Carolina, and another from Georgia, west of the Appalachian Mountains and across the Gulf Coastal Plain into Texas.

One confusing result from earlier studies of A. carolinensis molecular phylogeography was the placement of the most basal lineage in NW Florida (Tollis et al. 2012, Campbell-Staton et al. 2012). This didn’t make sense biogeographically, since it is believed that the species dispersed to the continental mainland from western Cuba (Buth et al. 1980, Glor et al. 2005). However, a subsequent nDNA study (Tollis & Boissinot 2014) produced a multi-locus species tree to show that southern Florida harbors the most ancient lineage of A. carolinensis. This discovery of mito-nuclear discordance provided a more satisfying biogeographical explanation that only needs to invoke overwater dispersal to South Florida from Cuba.

(A) Phylogenetic relationships of the major green anole lineages inferred from the ND2 mtDNA locus. (B) Phylogenetic relationships of the major green anole lineages using multi-locus species tree approach (1 mtDNA and 3 nDNA markers).

Different genetic datasets tell different stories about Anolis carolinensis evolutionary history. (A) Phylogenetic relationships of the major green anole lineages inferred from the ND2 mtDNA locus. (B) Phylogenetic relationships of the major green anole lineages using multi-locus species tree approach (1 mtDNA and 3 nDNA markers). Adapted from Manthey et al. 2016.

From there, things remained unresolved even with nDNA. For instance, while the split between South Florida and the rest of the species received full statistical support in Tollis & Boissinot (2014), the relationships between the other clades were less supported, making it difficult to determine if the A. carolinensis mainland clades arose from separate Floridian sources.

The data used in Manthey et al. 2016

To our knowledge, this is the first Anolis phylogeography study to use targeted enrichment, so I thought I would elaborate on the nature of this kind of dataset. Anchored hybrid enrichment (AHE) relies on probes designed from conserved genomic regions ascertained from a panel of vertebrate genomes – including A. carolinensis – which are flanked by non-conserved regions (the level of conservation in determined by PhastCons scores from the UCSC Genome Browser). DNA samples are pooled, and a set containing thousands of probes is used to enrich libraries that get sequenced on an Illumina platform and assembled into contigs, producing hundreds of homologous loci.

Here’s the breakdown of what we ended up with in the new study: our sample contained 42 individual anoles from 26 localities across eight states, and we were able to obtain 487-512 loci per individual, with an average contig length of 629bp, and an average of 17 SNPs per locus including an average of six parsimony-informative SNPS per locus. Roughly speaking, that’s one parsimony-informative SNP every 100bp for 500 loci, so about 3,000 parsimony-informative SNPS  = not bad! For what it’s worth, the 10 nDNA A. carolinensis markers obtained by more traditional PCR/Sanger sequencing contained about one SNP every 100bp as well (see Tollis et al. 2012 and Tollis & Boissinot 2014). Therefore, AHE produced hundreds more informative loci at a fraction of the cost.

New insights into Anolis carolinensis phylogeography using targeted loci

Using different statistical clustering methods (DAPC and Structure), Manthey et al. supports the same five  genetic clusters as previously described. However, there is now a fully resolved species tree – arrived at using multiple methods. First, the South Florida clade is the most ancient lineage of green anoles, likely splitting off from the rest of the species during the Miocene or Pliocene. However, there is now 100% support for a sister-group relationship between the mainland clades, massively simplifying the story of A. carolinensis. Green anoles likely remained in Florida until the Pleistocene, dispersing northward and onto the mainland where two lineages evolved independently- one along the Atlantic coast in the Carolinas, and another dispersing across the Gulf Coastal Plain.

(A) Map showing geographic localities of 42 green anoles selected for targeted enrichment. (B) Results of species tree analyses. Colored symbols correspond to the five geographic and genetic clusters. Adapted from Manthey et al. (2016).

(A) Map showing geographic localities of 42 green anoles selected for targeted enrichment. (B) Results of species tree analyses. Colored symbols correspond to the five geographic and genetic clusters. Adapted from Manthey et al. (2016).

We also found that despite the best resolution to date for the A. carolinensis species tree, incomplete lineage sorting is rampant across these loci, highlighting the need for these kinds of datasets for phylogeographic studies at this evolutionary distance. For instance, the only clade with any gene trees supporting exclusive ancestry was South Florida: meaning on a given gene tree, pre-defined “clades” are often paraphyletic. The reason the species trees agreed in their topologies is due to fact that they probabilistically invoke the coalescent process, which incorporates incomplete lineage sorting. Previous studies, using ≤10 loci, simply lacked enough statistical power to do this confidently.

More work to be done

As with most scientific endeavors, the new study resolves some outstanding questions but also begs new questions. For instance, although we were able to infer gene flow between the Gulf-Atlantic and NW Florida clades, the degree of allele sharing between populations is still not clear. There seems to be some admixture between the Gulf-Atlantic and Carolinas clades south of the Appalachian Mountains in Georgia, suggesting elevational gradients provide a more effective barrier to gene flow in this species than riverine barriers. Also, the divergence times of the green anole clades are still based only on molecular clock models and could benefit greatly from informative fossils calibrations.

The Genetics of Anolis Lizard Tail Regeneration: (Re)generating Major Internet Buzz

Anolis carolinensis duo with regenerated tails. Photo credit: Joel Robertson.

Anolis carolinensis duo with regenerated tails. Photo credit: Joel Robertson.

Readers of this blog are well aware of autotomy in lizards – self-amputation of the tail – that usually occurs as a result of sub-lethal predation. Readers of this blog are also familiar with the fascinating ability of many lizards to regenerate new tails post-autotomy. Lizards are the closest relatives to humans that can regenerate a fully functional appendage in the adult stage, and understanding the molecular basis of this process can shed light on the latent regenerative capacities in mammals. A new paper published this week in PLOS ONE (Hutchins et al. 2014) provides the first insights into the genetic mechanisms of lizard tail regeneration, using Anolis carolinensis as a model. Via the high-throughput sequencing of RNA from regenerating green anole tails, and the mapping of these sequences to the A. carolinensis genome, the authors describe the genes that are expressed during the regeneration process, shedding light on potential targets for future human therapies.

Disclaimer: I am not an author on the paper, although I do work in the Kusumi Lab with the authors.

While the ability to regenerate a fully functional appendage in the adult phase is likely a deeply homologous trait across animals, it is not uniformly conserved across vertebrates. Fish, as in the zebrafish model (Gemberling et al. 2013), and amphibians, as in the salamander models (Knapp et al. 2013) can regenerate both limbs and tails, suggesting that while the ancestral vertebrate was equipped with this ability, it seems mammals have during their evolution somehow lost it. Evolutionary hypotheses explaining exactly why some taxa lose the ability to regenerate adult appendages are far and wide, ranging from the stochastic to ecologically-specific fitness trade-offs (reviewed in Bely and Nyberg 2010).

But what are the proximate (i.e. genetic) reasons as to why lizards remain strong regenerators while mammals are left holding the short end of the regeneration stick?

Green Anoles, Genomic Evolution And Surfing (Wait, What?)

She's looking at me, probably thinking "Will he eat me"? And I'm looking at her, thinking "How many transposable elements are in your genome?"

She’s looking at me, probably thinking “Will he eat me”? And I’m looking at her, thinking “How many transposable elements are in your genome?”

I wanted to bring the attention of the Anolis community to our recent publication in Genome Biology and Evolution (Tollis and Boissinot 2013), where we study the population dynamics of those fascinating features of the green anole genome – transposable elements. Transposable elements (TEs) are important components of vertebrate genomes that may seem a bit esoteric to many readers of this blog, yet the Anolis genome has already yielded great insights into how the vertebrate classes differ in terms of these DNA parasites. In a nutshell, our paper shows how microevolutionary forces such as natural selection and genetic drift account for differences which are most obvious when we make macroevolutionary comparisons (i.e. between mammals and reptiles). Even though I’ve cut to the chase a little early, I thought it might be nice to discuss what we know about the study of genomic evolution, and how the Anolis genome is contributing to the field of comparative genomics.

Actual Anoles at SICB 2012

There’s more than just anole biologists congregating at the SICB 2012 meeting.

To say it’s been cold here in Charleston, SC would be an understatement. Tuesday night, after the conference tipped off, it was 25 degrees Fahrenheit. But today, the temperature picked up a bit and moved into the 50s. Since we know they don’t hibernate in the winter months, I thought it might be possible that the local anoles may take advantage of the sunny afternoon to do a little basking. Just as the poster session was underway at about 3pm, I decided to give it a shot and take a look around what would be prime Anolis carolinensis habitat in the spring and summer: the bushes and a brick wall around the pool.

Sure enough, I spotted one male and two females right away! I texted Bryan Falk immediately, and we set to flexing our off-season collecting muscles. Doing a quick tour around the conference center, we managed to observe 6 and catch 3. No anoles were injured during this brief collecting trip – perhaps only mildly perturbed 🙂

We spotted a female on a sun-drenched black lamp post. Nice warm spot on an otherwise cool day.

Here's a sweet lady I snatched from a vine-laden verandah at the back of the conference center.

Bryan Falk with female green anole. Note the winter plumage on the human.

 

Anolis Transposable Elements and the Evolution of Amniote Genomes

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.

Anoles, American Style

I will admit here that I used to be a little jealous of other anole catchers. This twinge of want was not necessarily due to any perceived greater intellectual merit of the research, nor to collecting successes in terms of sheer numbers of lizards. My envy stemmed from the fact that the stories were exotic, involving international travel to islands in the Caribbean both great and small, where supposedly the anoles practically fall out of the trees and astonish you with their diversity and abundance.

Green anole in Arkansas

I would think to myself how comparatively boring my field work must sound: driving in a blue van with New York plates, weaving across state lines, searching for A. carolinensis, the lone species that lives on the continent —  the Drosophila melanogaster of an otherwise thrillingly diverse genus. Can there be a more boring species than a lizard with the word “green” in its common name? Even the folks I meet while traveling in the field  hint at mundaneness when I tell them what I am looking for: “Where you really need to look is on my aunt’s patio!” Yes sir, I know they often pop up in the begonias, but will they be there when I need them to be (because they never are)? Plus, I have to be in southern Georgia by tomorrow afternoon so I need anoles from this latitude today!

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