I find Transposable Elements (TEs) to be some of the most fascinating features of genomes. Also known as selfish genetic elements, these sequences contain the genetic machinery to create copies of themselves and insert these new copies in locations throughout the genome. The genomes of different organisms vary widely in their degree TE abundance. For example, 20% of the human genome is composed of just one kind of TE!
This morning Robert Ruggiero, a Postdoctoral Fellow in the lab of Stephane Boissinot at NYU Abu Dhabi, presented his work on the population genomics of TEs in the genomes of Anolis carolinensis populations. Robert employed a clever approach that uses a feature of next-generation sequence data to identify TE insertions. In this way, he can characterize all of the TE insertions in an individual’s genome and determine what portion of a population contains any particular insertion.
It’s easy to see how Transposable Elements could be bad for an organism. If a TE inserts itself into the middle of an important gene, the function of that gene could be interrupted, and render the bearer of that insertion less evolutionarily fit. The ability of natural selection to purge this type of deleterious insertion is governed in part by the effective population size of the group where that insertion arises. In essence, natural selection is more effective in larger populations.
Using the information he collected on TE insertions in anole populations, Ruggiero created a population genetic summary called an Allele Frequency Spectrum, the count of insertions that exist at a particular frequency in a population. This distribution can then be used to infer how well populations control the frequency of TE insertions, and in addition, estimate the effective size of those populations. Robert found TE insertions in Floridian populations of Anolis carolinensis were maintained at lower frequencies than other populations suggesting that selection is better able to purge deleterious insertions in the Florida population. He also found that different families of TEs appear to employ strategies that mirror ecological r/K theory. Some TEs create insertions frequently but few of these insertions get to high frequency, whereas other TEs insert infrequently, but those insertions that do occur are more likely to reach high frequency. Moving forward, using this line of inquiry in anoles will be an excellent opportunity to understand the control and evolutionary consequences of TEs, particularly as more Anolis genomes come online allowing comparative analyses.
On each of the Greater Antillean islands, habitat-specialist Anolis ecomorphs have independently evolved complex suites of shared phenotypes and behaviors. This remarkable convergence has motivated the work of generations of anolologists. With anoles entering the once-exclusive club of genome-enabled organisms, a new line of investigation has become possible: Is the convergence observed in anole ecomorphs caused by molecular convergence? Such convergence can take many forms, including shared changed at individuals sites, or shared changes in the rates of protein evolution of individual genes.
Russ Corbett-Detig of UCSC sought to answer this question using whole-genome sequence data from 12 species – four from each of the Trunk-Ground, Trunk-Crown, and Grass-Bush ecomorphs drawn from different islands and different evolutionary lineages. Accurately detecting molecular convergence is fraught and much recent research has focused on avoiding pitfalls that could lead to a positively misleading inference of convergence where none actually exists. Previous studies have trumpeted amazing cases of molecular convergence in a variety of animals, only to be later shown to be artifacts of data analysis.
Corbett-Detig did everything right. He used null models that account for the expected background levels of convergence caused by processes other than natural selection. He found no evidence of extra shared non-synonymous mutations in any of the three ecomorph groups. Similarly, he found no signal of shared changed in protein evolution in Trunk-Ground or Trunk-Crown but Grass-Bush anoles seemed to share elevated rates of changes in many genes. This result was exciting, but Corbett-Detig dug deeper and discovered a new way this type of analysis could be mislead – two of the four Grass-Bush anoles exhibited accelerated evolution across their entire genomes and, as a result, seemed to share faster rates at more genes than expected by chance. When Corbett-Detig corrected for this bias, the signal of convergence disappeared.
While this result was in one sense disappointing, it is also fascinating and suggests the evolutionary pathways to shared ecomorphological traits are numerous and strongly influenced by contingency. Furthermore, anole ecomorphs have evolved such a stunning set of similarities that other forms of convergence like genome structure, gene family expansion, or convergence in gene regulation may still hold the key to understanding the genetic basis the remarkable convergence of Anolis ecomorph classes.
We anolologists (and herpetologists generally) are a devoted bunch, particularly when it comes to our field equipment. It is therefore very troubling to learn that an essential component of our field kit is being discontinued. Perhaps most chilling is the thought losing access to our beloved   Cabela’s Panfish Poles. A recent series of tweets between AA stalwart James Stroud and Cabela’s customer service revealed noose poles are currently out of stock and may not return:
We have experienced the disappearance and return    of these poles before and, despite our best efforts, have not found a good alternative. With this essential tool at risk, I am taking up the effort to convince Cabela’s it is worthwhile to continue producing panfish poles. I would like to present them with the economic argument that many herpetologists use, and will continue to buy, this product. I created a Twitter poll below and will present the results to Cabela’s customer service in making our case. Please take a moment to share your thoughts using the poll and in the comments. Thanks!
Green Fruit Loop, the salad anole of Princeton, NJ
We’ve previously reported on anoles finding their way into commercial produce, with happy and not so happy outcomes. Count this story from Princeton, New Jersey as one of the happy ones…
A kindergartener at Riverside Elementary found this juvenile Anolis carolinensis in a bundle of lettuce that had been stored in the family refrigerator for three days. Although initially listless, the animal recovered quickly and now seems to be doing just fine living with her reptile enthusiast science teacher. The new class pet was named Green Fruit Loop and will hopefully serve as an anole ambassador at Riverside for years to come.
Wooden anole tile from http://bythesycamoretree.blogspot.com/2014/10/enthusiasm-with-experience.html
Last week marked the fifth anniversary of the first Anole Annals post. Back on November 21, 2009 Jonathan Losos shared three anole haikus by Yoel Stuart. Since then there have been over 1,500 posts and 37,000 comments, both truly remarkable achievements for the anole community. Contributors, commenters and readers alike are all responsible for the success of Anole Annals. Here’s to many more years for the online home of all things Anolis. Finally, if you happen to be looking for the appropriate anniversary gift for your local anole blogger the traditional gift is wood (example above), and the modern is silver  .
The annual meeting of the Society for Molecular Biology and Evolution meetings start this weekend in San Juan, PR and there are a number of talks and posters to appeal to the squamatophile.
There are three presentations from AA contributors (Marc Tollis and Tony Gamble) using anole genomic data, as well as posters and talks on phylogeography of Puerto Rican Sphaerodactylus, and genome-scale studies of Sceloporus, skinks, and snakes. You can see the full list after the jump.
Continue reading Anoles (and Other Lizards) at SMBE 2014
BEAST estimated phylogeny of anoles. Circles on nodes represent posterior probability, black > 0.95, grey > 0.90, white > 0.70.
In the course of our recent study on sex chromosome evolution in anoles (Gamble et al. in press) [AA post] we assembled a 216-species mitochondrial DNA phylogeny of anoles, the largest published to date (at least that we know of), yet containing only a little more than half of all recognized species. Although we collected new sequences for some species, our dataset is largely built on the hard work of others who collected and published on sequences from across the genus, such as Jackman et al. 1999, Poe 2004, Nicholson et al. 2005, Mahler et al. 2010 [AA post], and Castañeda & de Quieroz 2011 [AA post]. Without access to data from these and other studies, we would have had a far less complete and robust tree for our comparative analyses.
There is a big debate going on now regarding what, where and how much data should be shared in association with publishing academically. I personally feel that providing easy access to those data used and generated during a study serves to accelerate the rate and increase the quality of scientific discovery. I am heartened that more and more journals are making data deposition a requirement for publication, although often this means little more than dumping sequence data to GenBank. Sites like Dryad, Figshare, and GitHub now provide open, permanent, and citable access to raw data, figures and, most importantly in my view, research products like alignments, code and analysis logs. In an effort to make our data as accessible and useful as possible we have archived our alignment, MrBayes and BEAST consensus trees as well as as the BEAST posterior distribution on the digital data repository Dryad [doi link]. It is our hope that other anolologists can use and improve upon these data to ask new, interesting questions and to build a larger, more complete view of the evolution of anoles.
George Gorman in Dominica
In the 1960s and 70’s evolutionary cytogenetics experienced a remarkable burst of interest and scholarship. Thanks largely to the efforts of George Gorman (at right) and others working at the Museum of Comparative Zoology, anoles played a central role in this research (some historical detail has previously been posted on AA). Among their findings was the occurrence of heteromorphic sex chromosomes, sex chromosomes that are visibly distinguishable from each other under a microscope, in several Anolis species but not others. Furthermore, Gorman and colleagues discovered that those Anolis species with heteromorphic sex chromosomes all had male heterogamety, with some having an XX/XY system while others had an XXXX/XXY system. Chromosomes from nearly 100 Anolis species were examined during this period and about 1/3 of those species had heteromorphic sex chromosomes. Interest in chromosome evolution waned in the 1980’s as DNA sequence data became increasing accessible, but there has been a recent resurgence thanks, in part, to sex chromosomes.
Continue reading Reconstructing the History of Anole Sex Chromosomes
Is this an embarrassment of anoles? Image from petparadise.info.
For natural history students, professionals and enthusiasts some of the most entertaining, albeit fairly useless, facts are the collective nouns used to describe a group of organisms. From taxon to taxon, collective nouns are literary (a murder of crows), descriptive (a prickle of porcupines or a sneak of weasels), mundane (a shoal of sticklebacks), and even absurd (an aurora of polar bears).
When I first read the headline of Jonathan’s latest dispatch to the New York Times Scientist at Work blog, An Embarrassment of Anoles, I briefly thought that anoles had their very own collective noun. But alas, I was wrong and a group of anoles isn’t (yet) referred to as an embarrassment.
In a quick flurry of googling I found words for groups of various amphibians and reptiles: crocodiles (bask), cobras (quiver), iguanas (mess), frogs (knot), toads (knot), salamanders (congress) and lizards (lounge), to name a few. But nothing for anoles!
Does anyone know of a collective noun for anoles or, failing that, have a suggestion?
A portion of our current collection. Each cup contains a single incubating egg.
Our group has posted frequently about our anole breeding work. Now many years of fine-tuning our methods has resulted in a very efficient and high yield colony, but has generated an unforeseen, but welcome problem… too many eggs. We currently have 260 eggs incubating and are getting 50-70 new eggs laid a week (in addition to the ~2700 eggs and ~1500 hatchlings that this experiment has already produced). All of these eggs are the results of a cross involving members of the A. distichus species complex from Hispaniola. This quantity of eggs is more than we need for our current experiments and more than we can house, so we are wondering if folks in the AA community can help us figure out how to put them to good use. These eggs are from a research colony and can only be used for research purposes at an accredited research institution; we cannot provide eggs or hatchlings to be kept as pets*.
Do you have a need for, or ideas for the use of, a large number of eggs, embryos or recent hatchlings? We are looking for suggestions that might help us use these eggs to learn something about anole biology that we may not have thought of, or don’t have the expertise to do. For example, if there is anybody out there who wants to create a developmental series for A. distichus, we can provide you with the required samples. Perhaps someone could make use of a large sample of egg yolk or other egg components for their work on anole reproduction? We are also hoping for some creative suggestions; see, for example, a recent study on explosive hatching in response to predator presence.
Drop us a line in the comments or contact me directly if you are interested or have ideas.
* To be clear, we are not against keeping anoles as pets but our university committee on animal resources stipulates that animals from our colony must be used for addressing specific projects or questions. Indeed, any potential uses would need to be approved by the approproate institutional review committee(s).
As we have posted previously, the Glor lab has been breeding anoles to assess the degree of reproductive isolation between A. distichus-clade lineages. Most eggs we collect fall into two easily separated categories: white, calcified, viable eggs; and yellow, uncalcified, inviable eggs. On occasion we get a third type: white, seemingly viable, yet uncalcified eggs. These represent only about 1% of the eggs in our current experiment. We always incubate these, in the hopes that they will develop, but typically they mold early in incubation and, upon dissection, show no signs of fertilization or development. The egg above is our first exception which, when incubated for about 3 weeks, was clearly developing (it has, sadly, since died).
So, AA community, has anyone else seen anything like this? I would very much like to hear your thoughts, interpretations and comments.
Ventral and dorsal view of polydactyl anole, click to enlarge.
As Rich Glor mentioned recently, we are in the second year of an experimental hybrid cross between two bark anole species. Although we are still early in this year’s experiment, we have had about 50 eggs hatch and, surprisingly, two have had malformed forelimb digits. The first was missing two toes on one of its forelimbs and died a few days after hatching. The second (pictured above) hatched with six toes, but has been otherwise healthy. Each of these toes has an intact claw, and at least one has lamellae. The fourth digit (from closest to the body counting outwards) seems to lack the (expected) scansor and is permanently bent upwards.
Mats Olsson and colleagues (2004) found malformations in the limbs and jaws and kinked backbones in crosses between populations of Lacerta agilis. Of the over 800 hatchlings in last year’s F1 experiment, we found a few animals with malformed spines, but not a single animal with digit or jaw issues. It’s particularly interesting (to me at least) that these issues have manifested in the backcross generation, an issue I hope to investigate further as more animals hatch.
Polydactyly has been reported in captive-bred crested geckos (Correlophus ciliatus), but I couldn’t find anything about anoles. Has anyone else seen something similar in anoles? If so, please let us know in the comments.
Turns out today is Reptile Awareness Day. The reptile channel has some suggestions of things to do to in honor of the day and Audubon has put their Reptile and Amphibian Field Guide iOS app on sale for $0.99. So is anybody doing anything special to celebrate?
BBC host Michael Mosley with a Jamaican anole he captured
Our local PBS station has been airing episodes of the entertaining 2010 BBC series The Story of Science: Power, Proof, and Passion, hosted by medical journalist and doctor Micheal Mosley. The program recounts the history of major advances in science by focusing on the individuals responsible for them.
Episode Three, “How did we get here?”, tracks Evolutionary theory, from the development of geology, through Cuvier’s advances in comparative morphology and on to the field work that kickstarted Darwin and Wallace’s thought processes. In this episode Mosley follows in the footsteps of early collector Hans Sloane. Sloane, as you will recall from a previous post, assembled an expansive collection of Jamaican flora and fauna including anoles.
There is a brief segment where Mosley and his botanist guide construct small nooses and capture an anole, pictured above. I don’t know the Jamaican fauna well, but my guess is that he’s got A. lineatopus. Unfortunately I can’t find any video clips and the only picture available (above) is pretty grainy. If you’ve seen the episode or if you can make out the species from the picture above, let me know if I’m close in the comments.
UPDATE: The anole segment is online! Thanks to Jonathan for sleuthing this out.
My brother just sent me the Spring 2012 issue of the Temple University magazine, a quarterly publication the university sends to alumni and donors. The cover story features the biomechanics research of Dr. Tonia Hsieh and describes the various animal taxa her lab uses to ask questions about animal locomotion in challenging environments. This work, also featured in a January article in the Philadelphia Inquirer, has a wide variety of potential applications ranging from the development of nimble robots to suggestions for how to prevent slips and falls among the elderly.
The article and some accompanying online material are a quick, interesting read and contain some great images and videos. Although other taxa get all the glamor shots, the article does describe how a lab colony of Anolis carolinensis is used study how animals recover and maintain their balance when navigating slippery surfaces.
A 'slug' next to a healthy, freshly laid egg. The scale bars in millimeters.
In December, Rich posted on infertile eggs occasionally produced by anoles, also known as slugs. These eggs are small, yellow, and uncalcified. We have found that females typically lay slugs in different locations than fertile eggs. In our breeding colony, nearly every viable egg is deposited in egg laying substrate (moistened vermiculite in a plastic yogurt container), whereas slugs are found on nearly any surface but these cups, as described in a previous comment by William Baugher.
As our hybridization experiment in distichoids proceeds, it has become clear that these inviable eggs may be an important measure of the success of hybrid matings. There are some really great studies on viable anole eggs in the reproductive biology literature (1, 2, and 3, to name a few), but I have had no luck in finding papers that discuss, or even mention the production of, these inviable eggs. Since the last post on this subject AA readership has gone up and I am hoping that someone out there has some additional information on the phenomenon.
Continue reading Help With Yellow Eggs
All things 8-bit are making a comeback. The worlds of art, technology, fashion and music all have (re)embraced the format, and I, for one, don’t want anoles to be left behind. Here’s my 8-bit take on a member of the disticus clade (bonus points on guessing which one). Drawn in Adobe Illustrator following these instructions, you can also roll your own with a free webapp here.
Comparison of panfish poles, click for larger image
In a comment a few months ago I promised a review of alternatives to the beloved but
discontinued long-backordered, Cabela’s Telescopic Panfish pole. As of Monday, Cabela’s claims that the panfish poles we have grown to love will be available again on May 6th. With any luck they will be back to stay and the review that follows will be moot, but after being fooled by two previous restock dates that came and went, we set out to evaluate alternatives. Read on for a review of each.
Continue reading Panfish Pole Alternatives
The Centenary celebration at the Academy of Natural Sciences... The bicentenary will be a far less formal affair.
Two hundred years ago today a group of seven prominent Philadelphians: two physicians, a dentist, an apothecary, a manufacturing chemist, a distiller and naturalist Thomas Say formally founded the Academy of Natural Sciences of Philadelphia, the first natural history museum in North American. Today and for the next year the Academy will hold events celebrating its long history of contribution to natural history research.
Over the past 200 years the Academy has played a continuing role in advancing natural history research from the myriad contributions of entomologist/malacologist/ herpetologist Thomas Say, to Ruth Patrick‘s work testing the predictions MacArthur and Wilson‘s theory of island biogeography, and Ted Daeschler’s co-discovery and analysis of transitional fish-tetrapod fossils. This being Anole Annals, read on for a summary of the Academy’s contributions to the anole world…
Continue reading Happy Birthday, ANSP!
Anolis species in HerpNet wordcloud, name size is plotted to be proportional to the number of records on HerpNet for that species
Because I’m a big fan of obtaining data from public databases I’m writing another post on availability of anole data from huge bioinformatic databases. This time, I’ll discuss the NSF-funded database of amphibian and reptile museum records known as HerpNet. I found an astonishing 142,225 unique Anolis specimen records on HerpNet, including 602 unique binomials. The over-abundance of names relative to recognized species is due largely to lots of misspellings (I found five different spellings for vermiculatus and four for valencienni). An interesting side note on how errors in electronic databases can propagate themselves: One individual of Anolis sagifer appears in the MCZ (catalog #45484). You can see the original catalog entry here. This entry was mis-transcribed, likely when the database was digitized. That in term led to it’s presence on the MVZ website and HerpNet, and also spawned search pages on GBIF and ITIS.
Many of the five most common species on HerpNet are also among the most common on GenBank; A. sagrei (13040), distichus (8944), carolinensis (8270), cristatellus (7126), cybotes (7106). A. krugi (number 2 in terms of sequences on Genbank) falls to #22 on the HerpNet list. Lots of interesting questions could be addressed using these HerpNet records. For example, we could use these records to thoroughly investigate how new anole names have accumulated and been used over time. Has species discovery/description been leveling off? HerpNet records could also be used to consider how the anole research community’s interests have changed over time and how specific policies have impacted anole collecting? How, for example, has the US embargo of Cuba impacted collection of Cuban specimens?
The more interesting applications of the HerpNet database will come from a careful consideration of the data associated with individual specimen records. A number of efforts, for example, are already underway to use the thousands of georeferenced locality records for anoles included in the HerpNet database to address questions about geographic range and community evolution.