We recently published a chromosome-scale assembly of the slender anole (Anolis apletophallus) genome, a species that has been studied for decades at the Smithsonian Tropical Research Institute in Panama.

Here is the abstract: The slender anole, Anolis apletophallus, is a small arboreal lizard of the rainforest understory of central and eastern Panama. This species has been the subject of numerous ecological and evolutionary studies over the past 60 years as a result of attributes that make it especially amenable to field and laboratory science. Slender anoles are highly abundant, short-lived (nearly 100% annual turnover), easy to manipulate in both the lab and field, and are ubiquitous in the forests surrounding the Smithsonian Tropical Research Institute in Panama, where researchers have access to high-quality laboratory facilities. Here, we present a high-quality genome for the slender anole, which is an important new resource for studying this model species. We assembled and annotated the slender anole genome by combining three technologies; Oxford Nanopore, 10X Genomics linked-reads, and Dovetail Omni-C. We compared this genome with the recently published brown anole (Anolis sagrei) and the canonical green anole (Anolis carolinensis) genomes. Our genome is the first assembled for an Anolis lizard from mainland Central or South America, the regions that host the majority of diversity in the genus. This new reference genome is one of the most complete genomes of any anole assembled to date and should facilitate deeper studies of slender anole evolution, as well as broader scale comparative genomic studies of both mainland and island species. In turn, such studies will further our understanding of the well-known adaptive radiation of Anolis lizards.

And here is a slightly longer summary of what we did (and some results): We used a hybrid genome assembly by combining three technologies: Oxford Nanopore, 10X Genomics linked-reads, and Dovetail Omni-C. We annotated our slender anole genome using the Dovetail Genomics annotation pipeline and compared our genome with the recently published brown anole (Anolis sagrei) and the canonical green anole (Anolis carolinensis) genomes. We also estimated the repeat elements composition and repetitive landscape using the RepeatModeler and RepeatMasker pipelines.

After several rounds of improvement, our final genome assembly for the slender anole was ~2.4 Gbp in size with with a scaffold N50 of 154.6 Kbp and a GC content of 43.8%. The slender anole genome was thus substantially larger than both the green anole (1.89 Gbp) and brown anole (1.93 Gbp) genomes. Our annotation using the Dovetail pipeline identified a total of 46,763,836 bp coding regions and a total of 33,912 gene models. The number of gene models identified for the slender anole was higher than that of both the green anole (22,292) and brown anole (20,033).

Authors: Renata M. Pirani^1,2*†, Carlos F. Arias^2,3, Kristin Charles¹, Albert K. Chung^2,4, John David Curlis^2,5, Daniel J. Nicholson^2,6, Marta Vargas², Christian L. Cox^2,7, W. Owen McMillan², Michael L. Logan^1,2

Affiliation:

(1) Department of Biology and program in Ecology, Evolution, and Conservation Biology, University of Nevada, Reno, Reno, 89557, United States

(2) Smithsonian Tropical Research Institute, Panama City, Panama

(3) Data Science Lab, Office of the Chief Information Officer, Smithsonian Institution, Washington, 20013, United States

(4) Department of Ecology and Evolutionary Biology, Princeton University, Princeton, 08544-2016, United States

(5) Department of Ecology and Evolution, University of Michigan, Ann Arbor, 48109-1085, United States

(6) University of Texas, Arlington, Arlington, 76019, United States

(7) Florida International University, Miami, 33199, United States

*Corresponding author: renatampirani@gmail.com

† Present address: Department of Ecology and Evolutionary Biology, University of California, Los Angeles, 90095, USAFigure 1 Figure_2

The Panamanian Anolis apletophallus is the most recent anole reference genome and the first mainland species to have one. Photo credit to agonzalo on iNaturalist (license CC 4.0).

This week, anoles are in the genomic spotlight for three papers– Pirani et al. (2023), Taft et al. (2023), and Farleigh et al. (2023). I’ve briefly highlighted each below, but check em’ all out!

New literature alert!

Pirani et al. (2023) usher in a new age of Anolis lizard biology by publishing the first mainland anole reference genome– a Panamanian species, Anolis apletophallus. It’s a great assembly (scaffold N50 of 154 Mb with an estimated 2.4 Gbp genome), and will be an excellent resource for the community as we continue to expand our genomic stockpile for this group. Give their new paper a read in G3: Genes, Genomes, and Genetics.

Taft et al. (2023) provide the first reference genomes for two species of Bradypodion, the dwarf chameleons. Synteny analysis (looking at gene order conservation across chromosomes) between the two chameleons and Anolis sagrei demonstrates relatively conserved genomic structure across greater than 150 million years of divergence!

Farleigh et al. (2023) investigate the natural hybridization of two Puerto Rican grass anoles–A. pulchellus andA. krugi–using a ddRAD approach (genome-wide SNPs) to understand the directionality of introgression, and how this pattern of introgression is differentially reflected in the genomes of populations across the island.

reprinted with permission

How Do You Create a Book about All the Reptiles of a Mega-diverse Country?

Reptiles of Ecuador | Story of the book

By Alejandro Arteaga. August 2023.

Everyone grasps the fundamental concept of a field guide: a book designed to aid in the identification of species in the wild while offering pertinent information about them. Unlike encyclopedias, field guides strive to provide information about EVERY species within a specific animal or plant group in a given geographical area. Field guides can be comprehensive when the number of species covered is limited. For instance, a field guide centered on the crocodiles of the Americas would include only ten species.

However, how do you create a comprehensive field guide about a species-rich animal group in a mega-diverse country?

To answer this question, I will tell you the story of the Reptiles of Ecuador book, a meticulously created field guide that has gained attention due to its expansive scope, novel photographic style, open-access nature, and funding strategy.

The idea for a Reptiles of Ecuador book emerged in 2010 from a casual conversation with a wildlife photographer friend. I posed a question:

Why are there field guides for birds and mammals of Ecuador, but none dedicated to reptiles?

His response was candid: “I’m not sure… you should consider writing one.”

Andrea Ferrari, editor in chief of Anima Mundi, enjoys reading the Amphibians and Reptiles of Mindo book. Photo by Lucas Bustamante.

His suggestion caught me off guard. I had never contemplated writing a book and, even though I found the concept intriguing, at 18 years old and just commencing my studies in biology, I did not feel qualified for such a task.

Throughout my childhood, I had drawn inspiration from field guides spanning diverse animal groups, ranging from insects to birds, and more recently, amphibians and reptiles. Consequently, I had a general idea of how a field guide about herpetofauna should look like.

But I had no idea how write one.

How could I possibly compile a book encompassing ALL reptile species within a country as biodiverse as Ecuador? The nation boasts a staggering 500 reptile species!

There are 500 species of reptiles in Ecuador, including the Emerald Tree-Boa (Corallus batesii), a snake that lives in the canopy of the Amazon rainforest and is seen no more than once every few years. Photo by Jose Vieira.

Read More

We’ve reported on this a number of times previously. Here are two more examples from Costa Rica.

from the pages of Floridensis:

ANOLIS CAROLINENSIS, 15

MARCH 2018

Anolis carolinensis, the Carolina green anole;
Collier county, Florida (15 March 2018).

In Collier county, Florida, many of the Carolina green anoles sport a fairly grayish dewlap, that fold of skin under the lower jaw. Typically, the dewlap for this species is pinkish. Some consider these regionally-focused “gray-dewlapped” green anoles to be a distinct subspecies (Anolis carolinensis seminolus) separated from the rest of the Carolina green anoles, but I’m not sure there’s much data to back up an actual subspecies distinction. Seem to me to simply be a phenotypic variation in that particular stretch of south Florida. I also find more-standard pink-dewlapped Carolina greens cohabitating in the same areas. Regardless of subspecies designations, I do love coming across these fantastic variants in Collier county.

Want to read more about gray-dewlapped A. carolinensis? Check out previous Anole Annals post (this one, which links to two others).

Green Anole swallowing a Virginia Creeper Sphinx. Photo by Andrei Sourakov.

by ANDREI SOURAKOV
Aug 15, 2023

From the Florida Museum Newsletters

Last week, I was about to go to work, when I spotted a drama unfolding on my window: a green anole had captured a sphinx moth. Of course, I had to stop and investigate.

Moth predation by anoles is not something worth blogging about in its own right, but this sphinx moth was the size of the anole’s entire body and certainly thicker than its head. These moths are very strong fliers, and the fact that this anole could hold on to it seemed quite remarkable. My bets were on the sphinx moth escaping. And if not, I was sure the anole was not going to be able to eat it.

The anole had other plans.

Soon, another green anole approached with the obvious intention of sharing in its conspecific’s success, but the hunter preferred to dine alone, rejecting the invitation to commensalism. It relocated from the window to the table below and then to an even more secluded spot on the back of a patio chair.

My curiosity piqued, I followed.

The moth eventually stopped showing any signs of life. This was interesting, as sphingids are normally very hard to kill by pinching. Perhaps the beta-defensin peptides that green anoles possess, which are similar to reptile venom, played a role in subduing its prey: the lizard had clearly secreted something while chewing on the moth, as it was quite damp by this point.

To my amazement, the moth began to disappear, heading head-first into the anole’s mouth.

Green Anole that just captured a sphinx moth. Photo by Andrei Sourakov.

Green Anole with the sphinx moth inside. Photo by Andrei Sourakov

The anole was doing the trick snakes pull, which I’d had no idea anoles could do: swallowing something larger than its own head, until the entire moth disappeared.

While I ended up being quite late for work that day, I had a most original excuse: “I was watching an anole swallowing a moth.” If you want to watch it too, you can click on the embedded video below.

P.S. There is a detailed page about green anoles (link below):

ADW: Anolis carolinensis: INFORMATION (animaldiversity.org)

P.P.S. Florida Museum’s Blackburn lab created a CT scan model of the green anole’s anatomy, where one can assess the size of its stomach.