In the era of Big Data, we can ask questions that would have been inconceivable just a few years ago. Consider the types of questions we can ask using Google’s Ngram Viewer, which uses full-text searches of >4% of all books ever printed to characterize relative word or phrase usage over time (this approach was initially described in a 2011 Science paper about “Quantitative analysis of culture using millions of digitized books“).
Among the most important questions one might ask with the Ngram Viewer is “What is the most written-about lizard genus?” I did some preliminary scouting to assess the relative usage of some of the lizard genera that I guessed would be the most popular. I quickly narrowed my queries to the five taxa – Anolis, Sceloporus, Varanus, Lacerta, and Gekko – that I think give the most interesting graphs for discussion. I excluded other potentially popular genera from my queries for for a few reasons. Iguana is very popular, but I eliminated it because it is often used colloquially to refer to lizards that don’t necessarily belong to the genus Iguana. Eumeces never appears as frequently as the other genera in my searches. Pogona is immensely popular as a pet, but usage of this genus name is still far below the others in my list.
Lacerta jumps out to a big early lead and maintains a strong lead throughout the 19th century, thanks to its widespread use in Latin-language literature from the 19th century and countless books about the European fauna (Ngrams Viewer even provides links to the books or articles containing the phrase of interest!).
In the early 20th century, Anolis joins the competition as one of the most popular lizard genera, and opens up a sizeable lead by the 1980s that it maintains until the turn of the 20th century. Although Anolis is briefly surpassed by Varanus in the 2000s, it nudges back into the lead by the end of 2008!
There you have it folks, quantitative proof of the popularity of Anolis! Have I failed to consider some genera that might be competing with Anolis in the lizard genus popularity contest?
I was hoping to get suggestions from the readers of AA about methods of tissue collection for genetic work other than tail tips. I’ve been working with the agamid lizard Sitana ponticeriana, and my work is now taking decidedly genetic directions. It remains unclear whether or not these lizards regenerate their lost tails–while they seem to lose tails easily, I didn’t see any lizards with noticeably regenerated tails in the field. Given this, I am a little uncomfortable with the idea of taking tail tips as tissue for genetic work. Are there other common and easy options for sampling tissue from lizards? Many thanks in advance for your responses!
(Feel free also to weigh in with whether or not you think it acceptable to collect tail tips in a species that certainly autotomizes its tail but does not grow it back–it seems like a grey area to me).
If you are lucky enough to live in the tropics then you can do away with incubators, endless tinkering with temperature, humidity and light regimes and let nature do it for you. I have been breeding A. apletophallus in Panama for almost two years and thought I should share with you my take on breeding anoles “in situ.”
Left: Mesh cages hanging in the shade house. Right: Newly emerged hatchling.
I use a very basic shade house that is situated on the edge of the forest. The temperature and humidity are similar to the forest where the lizards live. In the shade house, the lizards are housed individually in mesh cages that I constructed from pop-up laundry hampers and mesh bags. Each cage is outfitted with three branches and a plastic leaf. Females have a shallow soil plate to lay eggs in, which they happily do. I feed adult lizards every three days and at the same time check for eggs. All eggs are removed and placed in a plastic cup with water and cotton wool, which is then placed inside a ziplock bag. Eggs are “incubated” at ambient temperature (~45 days). When the eggs hatch the hatchlings are transferred to plastic boxes with a mesh lid. These “baby boxes” also contain three small branches and a plastic leaf. Hatchlings and subadults are feed every other day. All lizards are sprayed daily with water. Although there is probably room for improvement, this has been a successful and economical strategy to breeding anoles in the tropics. For anyone who wants more details I have posted this on my webpage under “animal husbandry.”
Anole biologist Gunther Köhler has produced a handy manual, available from Herpeton publishers, to help describe colors of specimens, especially in field situations. The book’s introduction can explain better than I what it is used for and why it was written:
The accurate description of the coloration in life of organisms represents an important component of the work of any field biologist. Subtle differences in the coloration in life, such as in the color of the iris, the lining of the mouth cavity, or the tongue are diagnostic for certain species and have been used by taxonomists to differentiate among species.
Whereas many aspects of the external morphology of scientific specimens can be preserved with proper fixation methods, there is still no way to assure the long-term conservation of the coloration in life in such specimens. This is especially true for animals traditionally fixed with the help of formalin and ethanol, such as fishes, amphibians, and reptiles, and then stored as a wet collection. Colors such as red, yellow, and orange disappear rapidly once the specimen is placed in the preservative. Green-colored amphibians and reptiles can turn blue, lavender, purple, or black within a short time after preservation.
The Catalogue also provides definitions and examples of different phenotypic characteristics.
Of course, taking photographs of animals helps to document the coloration in life. Possible drawbacks to this technique are incorrectly adjusted white balances, which cause colors not to be reproduced accurately. Also, photographs often do not show coloration of hidden body parts. Therefore, biologists have a long tradition of recording colors by making written descriptions. Since individuals see colors differently and because it not easy to define, for example, different shades of brown or green in words, having a color standard helps to produce more objective and detailed descriptions that also have a greater chance of being reproducible. Such a reference can be used to compare descriptions made by different persons at different times and places. For decades, field biologists have utilized the “Naturalist’s Color Guide” by Frank B. Smithe (1975-1981) as the standard reference for color descriptions. However, for many years now, this important reference has been out of print and is no longer available.
I have used Smithe’s “Naturalist’s Color Guide” (called “Smithe Guide” from here on) extensively during the past 20 years, and my copy now clearly shows signs of this intensive usage under field conditions over the years. With no hope of being able to obtain a copy in good shape to replace my old one, I decided to produce a new reference to fill the gap left by the now unavailable Smithe Guide.
The resulting “Color Catalogue for Field Biologists” you are holding in your hand is not a duplicate of the Smithe Guide.
Most people who have commented on the blog about Nicholson et al. 2012 have focused on whether is it really necessary to name all these inferred clades as genera. I agree with those who state it is completely unnecessary and disruptive, and that there are alternative ways (e.g., assigning names to relevant clades independent of the genus rank) to describe the diversity of Anolis. That said, I would like to direct the discussion towards the methodology used. Yes, there are a lot of missing ND2 data in their dataset (e.g., all of the new data presented in Castañeda and de Queiroz 2011 is missing), but I think it is more relevant to consider how they treated the data they did include. First, the molecular partition of their DNA: the protein coding gene ND2 was not partitioned into codon positions, which has been shown to be the best strategy (e.g., Schulte and de Queiroz, 2008; Torres-Carvajal and de Queiroz, 2009; Castañeda and de Queiroz, 2011), and instead, they chose to set a different partition for each of the tRNAs included (five) and one more for the origin for the light strand replication piece (which is ~30 bases long). As the Bayesian analysis requires a large-enough number of characters to estimate the parameter values for the model selected, I thought it was recommended to have partitions of more than ~300 bases (and I can’t think from the top of my head for a specific citation here). Neither the OL nor any of the tRNAs is close to this size (and the AICc, the corrected Akaike Information Criterion, intended for small sample sizes should have been used to select the best fitting model here instead of the regular AIC).(For more on partition selection and consequences of under– or overparameterization, check Brown and Lemmon, 2007 and Li et al. 2007). This should raise an eyebrow about the thoroughness of the analyses. However, in reality, I think this would have little effect on the actual phylogeny. Those clades that are strongly supported would be robust enough to withstand model and partition misspecifications.
On the other hand, the treatment of the morphological characters might have more serious effects on the resulting topology. Nicholson et al. explain that they used Poe’s 2004 morphological data as is, but without the complex coding system he used for continuous and polymorphic characters, and instead considering all possible characters to be equally weighted. (To be fair, Poe did use equal weighting for characters in his analyses; the cost of changes between states within a single character is what is different). Poe coded continuous characters using a gap-weighting method, which divides the range of a continuous character into discrete segments, maintaining information on the order of the character states and the magnitude of the difference between them, and he coded polymorphic characters using a frequency method, which keeps track of the fraction of individuals within the sample that shows a given state. From what I understood, Nicholson et al. considered all changes to be of equal cost, so transitioning from the smallest head to the largest head, or from having all individuals showing condition x to all individuals showing condition y (where some taxa exhibit both conditions), will cost 26 steps, which is the cost of changing from state a to state z (as recognized by Poe). This means, in the combined parsimony analysis, a transition between the two extreme states in a continuous or polymorphic morphological character is equivalent to [single] DNA substitutions at 26 different positions [characters]. Moreover, changes in those morphological characters that were not continuous or polymorphic would cost only a few steps. This weighting scheme (in the parsimony context) will actually give a higher weight to some morphological characters, which is exactly the opposite of what the authors were aiming for (i.e., equal weights). The effects of this unbalanced weighting on the resulting topology? Not sure, but I’m going to guess not insignificant!
One last thing. Several of their proposed genera (Dactyloa, Deiroptyx, Chamaelinorops and Xiphosurus) are not monophyletic on their combined data tree, the one that supposedly serves as the basis for their taxonomy…
KIRSTEN E. NICHOLSON, BRIAN I. CROTHER, CRAIG GUYER & JAY M. SAVAGE (2012). It is time for a new classification of anoles (Squamata: Dactyloidae) Zootaxa, 3477, 1-108
With only two weeks left in El Yunque, Puerto Rico, the two projects that Travis Ingram and I are doing will soon come to a close. Travis has already written about one project, the enclosure experiment. The second is a diet survey of six species (Anolis evermanni, A. stratulus, A. cristatellus, A. gundlachi, A. pulchellus, and A. krugi) that are sympatric in the area around where we are staying. The goal is to quantify diet overlap between these species. To obtain the stomach contents, we use a nonlethal method known as gastric lavage. I chose this method unsure of how it would turn out because, before this trip, Travis and I had had very little practice performing gastric lavage. My hope was that we could take this technique that we had read about and practiced a few times in the lab and become good enough at it to do it potentially hundreds of times in the field.
From left to right: original image, 8-bit greyscale, threshold image, particle analysis.
Last Fall I worked with Glor Lab graduate student Julienne Ng to develop a method of measuring the number and size of scales on Anolis lizards. We are hoping to determine if a relationship exists between temperature and humidity of a habitat and scale size. Below is the method that we have developed using ImageJ, which approximates both the number of scales and the area of those scales.
An exciting week in the Revell Lab, we received our order of 20 poles from Cabelas, and I picked up our new custom portable x-ray system in Newark yesterday.
The use of x-ray technology has been mentioned previously in AA- here, here , here, here, and here. The Losos Lab has used a similar portable x-ray system for the last several years with great success, and so we have obtained our own unit. One of the great advantages of these systems is that they allow researchers to gather highly detailed morphological data without harming the lizards and without using tedious methods such as dissection. The animals are simply anesthetized, imaged, and released after recovery. The Revell Lab has grand aspirations for our system- our graduate student Kristin Winchell plans to use it this summer in her studies of Anolis urban ecology.
Lacerta jumps out to a big early lead and maintains a strong lead throughout the 19th century, thanks to its widespread use in Latin-language literature from the 19th century and countless books about the European fauna (Ngrams Viewer even provides links to the books or articles containing the phrase of interest!).
In the early 20th century, Anolis joins the competition as one of the most popular lizard genera, and opens up a sizeable lead by the 1980s that it maintains until the turn of the 20th century. Although Anolis is briefly surpassed by Varanus in the 2000s, it nudges back into the lead by the end of 2008!
