All posts by Anthony Geneva

About Anthony Geneva

Postdoctoral Fellow at Harvard University. I use a variety of evolutionary genetic approaches to ask questions about gene flow, adaptation and speciation.

Panfish Pole Alternatives

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

Happy Birthday, ANSP!

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!

Anoles on HerpNet

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.

Anole AFLP Protocol

The core of my dissertation involves assessing genome-wide patterns of gene flow during anole speciation. For a variety of reasons, I ultimately want to acquire DNA sequences from throughout the genome.  As a first pass, however, I’ve been using Amplified Fragment Length Polumorphisms (AFLPs).  As a molecular technique, AFLPs are experiencing a comeback of sorts [1] [2].  Popular in the early 2000’s, AFLPs went out of favor as Sanger sequencing became cheaper and easier.  The resurgence AFLPs has largely been due to the realization that evolutionary patterns often vary throughout genomes and therefore methods that survey as much of the genome as possible are preferable to those that look at one or a few regions.

Continue reading Anole AFLP Protocol

Animal, Vegetal, and Mechanical Perils of Fieldwork

Dan Scantlebury recently recently posted a pair of success stories [1] [2] from the field.  This post focuses on a darker side, the perils of field work.  I’ve highlighted three stories below, one animal, one vegetal and one mechanical.

Mechanical Perils
No trip to the Dominican Republic is complete without transportation issues; we generally lose about a day every two weeks to dealing with vehicles.  In our last few trips we discovered in the middle of a river that our supposedly 4WD truck was in fact FWD, had a Dominican gomero refuse to fix a flat because the tire was too worn (remarkable because nobody has lower standards for what qualifies as a functional tire than a gomero), and realized our rental truck had one tire that was significantly smaller than the other three only after driving from Santo Domingo to Barahona.  Pictured above is my “favorite” vehicular mishap. Continue reading Animal, Vegetal, and Mechanical Perils of Fieldwork

Anoles on Genbank

With the recent sequencing of the Anolis carolinensis genome and Thom’s recent post on resources for other anole species I got to wondering how many DNA sequences are available for anoles?  In an effort to answer this question, I searched for DNA sequence data from Anolis and other genera now considered part of Anolis (Norops, Chamaeleolis, Chamaelinorops, and Phenacosaurus) on the NCBI’s popular GenBank database.  I found that Genbank‘s nucleotide database contains over 29,ooo unique anole sequences. Not surprisingly, the most sequence (25,973) are from A. carolinensis.  Remaining sequences are divided among 216 anole species. The top species after carolinensis are: krugi (433), distichus (378), sagrei (351) and cristatellus (328).  Is anyone else surprised by these totals?  I would have guessed sagrei would be second.  I think A. distichus will at least double in the next few years, partly because I’m doing lots of sequencing from this species myself.

Only 29 species are represented by more than 10 sequences and half of the 216 species represented in GenBank are represented by a single (usually mitochondrial) sequence. The availability of this data highlights our prospects for asking evolutionary and ecological questions across the rest of anoline diversity, but also highlights the huge amount of work ahead if we are interested in making broad genus-wide comparisons. Admittedly, Genebank lags behind current research as most of us only post sequences at the time of publication (we have hundreds of sequences to be added in the next few years).

Scantlebags: A New Innovation for Anole Field Work

Scantlebags being used in the field.

When in the field, we often need to temporarily house many animals from multiple localities for a short period of time.  While doing this, we need to keep animals healthy and track collection sites during transportation.  Anole researchers have used a variety of techniques to bag and sort captured anoles and often  rely on commercial reptile bags, pillow cases or plastic bags.

Thanks to the ingenuity of Dan Scantlebury and his mother, the Glor Lab has another solution: Scantlebags.  Scantlebags are individually manufactured in Stone Mountain, GA to our precise specifications.  They are made from white ripstop cloth material that is machine washable.  By making our bags from white fabric we can also write specimen data directly on the bag with a sharpie.  Each Scantlebag has a zipper closure, allowing easy access to captured animals without completely opening the bag.  You’ll have to trust us when we say that dealing with zippers is much easier than trying to constantly tie and untie pillow cases.  Scantlebags come in sizes ranging from a few square inches (for small anoles and Sphaeros), up to bags that are about the size of a typical pillowcase (which can temporarily accomodate ~20 small anoles). Finally, each bag has a webbing strap in one corner which allows Scantlebags to be tied to a belt, where they are easily accessible but secure from accidental loss.  The strap is at the opposite end of the bag from the zipper opening because the anoles we work with tend to aggregate at the top of the bag and are less likely to escape when the bag is opened from the bottom.

How does everyone else secure animals in the field? Any ideas for Scantlebag improvements?  Let us know in the comments.

Anolis Flickr Pool – Anolis Decorus

the altercation by Flickr user Dixie Native

I recently stumbled across a Flickr pool dedicated to beautiful images of anoles – Anolis Decorus.  From the pool’s description:

Photographs of anole lizards. This group is open to all, but a very high standard will be maintained so please submit only your best photographs. No photographs of dead or dying lizards please. The emphasis of the photograph should be on the lizard (ergo: please post photographs of Anole lizards, not photographs with lizards in them).

Some AA bloggers (and I assume readers) have contributed images. The pool includes a diverse array of Anolis species and includes some stunning photography. The picture above is yet another example of carolinensis/sagrei encounters like that posted previously here.  Overall there are some really high quality images, check them out.

NSF DDIGs anoles

With the the deadline quickly approaching, the National Science Foundation‘s Doctoral Dissertation Improvement Grant (NSF DDIG) program is on the mind on many graduate student anologists (myself included).  These grants provide significant funding (up to $15,000 this year) to graduate students allowing them to expand upon their existing dissertation research. A large part of my preparation has been reading the successful proposals of other students.  That got me to wondering how many other anole-centric proposals have been funded recently.  Luckily, the NSF has a handy search function for just such a question.

I found 16 funded projects since 1987 coming from the labs of 9 PIs (8 of whom have a single funded student each – the 9th PI and most of his 8 funded students post here often).  In total, students of anole science have been awarded $167,306 with a substantial uptick in the last few years. Here’s hoping this trend continues.  Good luck to all applying this year.

The Anole Phylogeny at JMIH

In addition to a number of Anole posters yesterday, the Joint Meeting of Icthyologists and Herpetologists featured a talk by Rich Glor entitled “Phylogenetics and Diversification of Anolis Lizards.” In his 12 minutes Rich covered a lot of material. He described: the key components in diagnosing an adaptive radiation (speciation, adaptation and the more controversial extraordinary diversification), how the properties of adaptive radiations result in problems resolving their phylogenies (particularly when diversification rates are extraordinary), leveraging the anole genome project to generate and analyze new, informative loci for anole phylogenetics, the impact of incomplete data matrices on the ability to accurately infer phylogenies, and closed with a presentation of the latest, greatest genus-wide phylogeny of Anoles.

The Knight and the anole

Although it was filmed a few years ago, I just recently got around to watching the BBC documentary series Life in Cold Blood written and narrated by Sir David Attenborough.  In the third episode of the series “Dragons of the Dry” there is a brief segment on anole display behavior.  Attenborough aggravates a male A. sagrei with a mirror and is rewarded with “the full works”: erect dorsal and nuchal crests, tail wags, push-ups and dewlaping.

Measuring the Light on High

Last summer the Glor lab began collecting light data to supplement ongoing research into the speciation of distichoid Anolis lizards.  Following methods developed by Leo Fleishman and Manuel Leal, our aim was to measure light levels at the exact location where a lizard had displayed.  Doing so involves holding a small sensor to the spot of the display and measuring the average light intensity for 15 seconds. That’s easy enough when the animal was 7 or 8 feet high, but most of our observations were substantially out of arms reach.

Necessity being the mother of invention (Plato, 360 B.C.), we rigged together our very own collapsible light meter pole using a broken panfish rod, utility cord and athletic tape.  This rig, pictured at right, has served us well, including our current trip to the Dominican Republic (for updates on the the trip see the Glor Lab Page).  It is our hope that by accurately measuring light at the site of displays we get a better handle on where males choose to display in their environment and how those sites differ between populations.