All posts by Jonathan Losos

About Jonathan Losos

Professor and Curator of Herpetology at the Museum of Comparative Zoology at Harvard University. I've spent my entire professional career studying anoles and have discovered that the more I learn about anoles, the more I realize I don't know.

Placing Extinct Species in a Molecular Phylogeny Using Quantitative Characters: A Case Study Using Anolis roosevelti

Liam Revell writes:

My co-authors (Luke Mahler, Graham Reynolds, & Graham Slater) and I recently presented a ‘new’ method for placing recently extinct taxa into a backbone molecular phylogeny on the basis of quantitative trait data. I say ‘new’ with quotes, because our methods derives closely, with full credit given where due, from a Maximum Likelihood phylogeny inference approach presented originally by Felsenstein (1981, 2002).

The idea is basically as follows. We start with a time-calibrated molecular phylogeny containing N – 1 species, and a single taxon of interest (the Nth taxon) whose placement in the tree is of interest, but for which molecular characters are missing. If we have quantitative trait data from one or more characters for all N species in the tree, we can use an approach based on Felsenstein (1981) to add this taxon to our base phylogeny using the statistical criterion of Maximum Likelihood.Revell_etal.Figure3_1In our article (Revell et al. 2015), we demonstrate that the method works pretty well in theory. In fact, for more than a few quantitative characters & particularly for trees of large size, the method often places the missing taxon in our dataset in a topological position that is identical to its true position. (See figure below, reproduced from our article.) In the figure, white bars show the performance of our method (compared to grey bars which represent placement at random). In all cases, lower values indicate that the estimated tree is closer to the generating tree.

The question you’re probably asking yourself (and quite rightly so) is: what could this possibly have to do with anoles? The answer is that we applied the method to the unusual case of Anolis roosevelti. Anolis roosevelti, as many readers of this blog likely already know, is a mysterious crown-giant anole from Culebra and (probably) the Spanish, U.S., and British Virgin Islands, excluding St. Croix. It is only known from a few specimens and was last collected in 1932. Aside from some unconfirmed reports, it has neither been seen nor heard from since. Unfortunately – and tragically given the impressive nature of this creature – all but the most optimistic anole biologists agree that this species is most likely extinct. (Many of us, the author included, still holds out hope, of course.) The figure below shows the type specimen of this impressive creature. (Figure from our article and image courtesy of the Museum of Comparative Zoology at Harvard.)

figure2Since no prior investigator has collected molecular characters from this species, and the prospects for so doing in the future are somewhat mixed (for reasons that we explain in the article), we thought Anolis roosevelti would represent an interesting test case for our method. Would A. roosevelti, we asked ourselves, fall out as sister to the Puerto Rican crown-giant, Anolis cuvieri, as sister-to or nested-within the rest of Puerto Rican anoles, or in another part of the tree entirely? Continue reading

Identify These Puerto Rican Anoles

Bill Schlesinger, one of the world’s most eminent biogeochemists and President Emeritus of the Cary Institute of Ecosystems Studies, turns out to have an eagle eye for anoles. While on a birding trip to Puerto Rico, his wife, writer Lisa Dellwo, snapped the photos below in the rainforest in the west central part of the island. Which species are they?

Lizards Falling out of the Trees in the Rainforest


Piero Angeli Ruschi from the Ornithology Department in the National Museum in Rio de Janeiro sent the pictures of Anolis punctatus shown here. His story:


It’s raining lizards!

“These are the pictures that I took of one of the Anolis specimens that had fallen that day. They fell from the canopy straight to open ground over an area of ~70 squared meters. About 10 specimens fell within ~3 min. It happened in Santa Lucia Ecological Station, at Santa Teresa, ES, Brazil in late september 2007 during the afternoom while I monitored a woodpecker nest.

The individuals were all the same as the one in that picture…green with a yellow circle around the eye…Those pictures might even include more than one individual—I am not sure if the one photographed on the ground was the same I captured (they stayed knocked out for a minute or so before running from where they landed).


I wish I had more data to publish a communication about it, as well as more evidence to explain the cause of it. My ornithological background leads me to the alternative hypothesis of some sort of “arena,” but I have no idea if such thing can be expected for these lizards.”

Piero Angeli Ruschi in his day jobobserving birds

Piero Angeli Ruschi in his day job observing birds


The Social Life of Lizards Revealed: Lizard Social Behavior Research in Gainesville

If you’re in Gainesville and come across a site like this, odds are you’re not at a crime scene, but rather Ambika Kamath’s study site, where she’s investigating the social organization of brown anoles. The standard view of anole social structure is that a male brown anole defends a large territory, excluding all other males and courting the several females that reside therein. Ambika’s work to date suggests that reality is a lot more complicated. Ambika provides an in-depth discussion of what she’s doing and why on her blog .

Cellular Mechanism of Tail Regeneration in Anolis carolinensis

Green anole with a regrowing tail. Photo from Daffodil’s Photo Blog.

Lorenzo Alibardi is conducting detailed studies of what the cells are doing as the tail regenerates. His latest work is now available online in the Journal of Morphology. Here’s the abstract:

Using an antibody against a lizard telomerase-1 component the presence of telomerase has been detected in regenerating lizard tails where numerous cells are proliferating. Immunoblots showed telomerase positive bands at 75–80 kDa in normal tissues and at 50, 75, and 90 kDa in those regenerating. Immunofluorescence and ultrastructural immunolocalization showed telomerase-immunoreactivity in sparCe (few/diluted) mesenchymal cells of the blastema, early regenerating muscles, perichondrium of the cartilaginous tube, ependyma of the spinal cord, and in the regenerating epidermis. Clusters of gold particles were detected in condensing chromosomes of few mesenchymal and epithelial cells in the regenerating tail, but a low to undetectable labeling in interphase cells. Telomeraseimmunoreactivity was intense in the nucleus and sparCe (few/diluted) in the cytoplasm of spermatogonia and spermatocytes and drastically decreased in early spermatids where some nuclear labeling remains. Some intense immunoreactivity was seen in few cells near the basal membrane of intestinal enterocytes or in leukocytes (likely lymphocytes) of the intestine mucosa. In spermatogonia, spermatids and in enterocytes part of the nuclear labeling formed cluster of gold particles in dense areas identified as Cajal Bodies, suggesting that telomerase is a marker for these stem cells. This therefore suggests that all of the sparCe (few/diluted) telomerase positive cells detected in the regenerating tail may represent sparCe (few/diluted) stem cells localized in regenerating tissues where transit amplifying cells are instead preponderant to allow for tail growth. This observation supports previous studies indicating that few stem cells are present in the stump after tail amputation and give rise to transit amplifying cells for tail regeneration.

A Four-Tailed Brown Anole

Four-tailed Anolis sagrei. Photo by Lynne Carpenter Ingram.

Four-tailed Anolis sagrei. Photo by Lynne Carpenter Ingram.

Photo by Lynne Carpenter Ingram

Photo by Lynne Carpenter Ingram

Lynne Carpenter Ingram took this photo of a quadricolous (I made that word up) brown anole. Here’s what she had to say on her Facebook page: “Last Sept I posted some pictures of a lizard I have living in my backyard, that had grown three tails, or partial tails. I have an update. Not only is he still alive, he now has a fourth piece growing. I noticed he had an injury to his tail about a month or so ago, and now a new piece is growing out of that spot. i remember a lot of people asked to permission to share the last photos i took. Please feel free to share. Taken in Broward County, FL, with a Nikon D7000 and a Tamron 90mm SP Di lens.”

Anybody ever seen anything like this?


Great Lizard-Watching Binos on Sale


My favorite brand of binos for lizard watching are steeply discounted right now. In optics–binoculars, cameras, etc.–you get what you pay for: more expensive units are generally of higher quality. Nevertheless, there’s a sweet spot that maximizes your bang for the buck, and that sweet spot in binos, I contend, is Eagle optics 8×32. Normally retailing at $380 or so, these have high quality lens and a good feel in the hand. And, most importantly, they can focus on lizards three feet away! Many binoculars are made for bird watchers and can’t focus anywhere near that close, making them not useful for looking at small objects such as lizards. And now the good news: the glasses are currently discounted to $239. Get ‘em while the supplies last! You might also consider the 10×32’s. They don’t focus as close–a respectable 8′ according to the specs–but they do give greater magnification. And they’re more than half off.


High Population Density Estimate of the Crested Anole in Puerto Rico


Photo by Jim Ackerman

AA correspondent Liam Revell reports from Puerto Rico:

For the past three weeks I have been running an activity with Jim Ackerman’s integrative ecology laboratory students that Jim has dubbed (perhaps with a touch of irony) the Great Anole Survey. The objective of this survey is to measure the species richness of anoles (three, it turns out) and the population density of the most common species (the Puerto Rican crested anole, Anolis cristatellus) in a small urban forest called Bosque Centenario on the Río Piedras campus of the University of Puerto Rico here in San Juan, Puerto Rico.

Over three capture sessions, with groups of students ranging between from about three to ten, we made 99 captures of 80 different adult male A. cristatellus in the 1.5 hectare area of Bosque Centenario. Bosque Centenario, as far as I can tell, is an abandoned, highly disturbed, open area or old sports field that consists of grassy area, some wetland, and patches of trees. Lizards were found mostly on trees, but were also observed using concrete and various PVC pipes as perches.

Our data collection ended last Friday, but we finally ran the numbers today. We used two methods to estimate the population size within this open forest patch. Due to variability in our collection effort by day, we first pooled sessions 1 & 2 into a single “marking” session in which 53 distinct animals were marked. We then treated the 3rd session, with 40 captures including 13 marked animals, as the “recapture” session and estimated the population size of adult males from these two numbers with the Petersen method (analysis 1). We also used only sessions 2 & 3 with the Petersen method (analysis 2), and finally the Schnabel method with all three mark and capture sessions (analysis 3).

By the Petersen method in analysis 1, we obtained a population size estimate of 157.1 (95% CI: 111.6, 235.6). In analysis 2, also using the Petersen method but with only data from mark & recapture sessions 2 & 3, we obtained a highly similar estimate, but with broader confidence limits, of N = 163.0 (114.7, 286.7). Finally, by the Schnabel method and using data from all three sampling sessions, we obtained an estimate of N = 147.8 (100.3, 255.3).

Given that this population estimate is from an area that Google Maps area calculator’s suggests is no more than about 1.5 hectares in size, this is quite an impressive number. The only prior study to quantitatively estimate population density of Anolis cristatellus in its native range is Genet (2002), and they found maximum densities of 68.0 male Anolis cristatellus per hectare – well below our lowest estimate of 147 individuals in 1.5 hectares, or about 98 adult males per hectare. That study also obtained population density estimates for juveniles and females, which they found to be significantly more dense than males – and I would guess that this is also true of our site (although we didn’t measure it).

Finally, some potential limitations include the fact that the Schnabel & Petersen estimators both assume a closed population. Our population is technically ‘open’ – but anyone that has studied adult male A. cristatellus knows that in the span of a few weeks, adult males are not going very far! We no doubt violated other assumptions of the method with our sampling protocol, but I will note that we marked 80 unique adult males in 1.5 hectares, and plenty of unmarked animals remained – so 150 in the whole plot seems more than reasonable, if not conservative.

For the record, the other two anoles we found in Bosque Centenario were Anolis pulchellus and the adaptable generalist A. stratulus.

New Video Game Uses Anoles to Teach Ecological Principles

Way cool. Check out it her. Based on actual research by Louie Yang and colleagues at UC-Davis.

Here’s the press release about it:

Budding Biologist™’s Lizard Island™ is a fun and scientifically accurate video game for K-5 players to teach observation, measurement and reasoning skills. Lizard Island™ teaches students about ecology by allowing them to catch and tag lizards as they explore multiple islands in the Bahamas.  Kayaking from one island to the next, players must capture, mark and measure all the lizards on the island. As players search for lizards, they see the rich biodiversity on each island and can click on plants and animals for more information.  Advancing through the levels leads to larger, more complex islands to explore and glean data from.

 Based on 30 years of scientific data collected from microislands in the Bahamas the game draws upon research and photographs from scientists at the University of California-Davis. Katy Castronovo, the artist, has combined island photographs with her own artwork to create plant and animal life on the island, including hermit crabs, buttonwood plants, pearl necklace plants, and joewoods.  Programmer Walter Hsiao portrays the lizards as realistically as possible in terms of breathing and movement.  Lizards have subtle size and pattern changes to help players understand differences among animals of the same species.

Players have three choices for catching lizards.  They can use one finger to draw a complete circle around the lizard, they can use a lasso, which works by tilting the tablet in order to get the loop of the lasso around the lizard or they can use their limited number of photos to grab a picture of a sly lizard that is hard to catch.  Players must be careful not to scare the lizard with movements that are either too fast or too slow, and the more time a player spends trying to catch an individual lizard, the more the lizard become skittish. Lizards can only be caught if the player is zoomed all the way in, accomplished by using two fingers and spreading them apart.  To have a view of the island as a whole, players can use two fingers to pinch together and zoom out.  Zooming out gives players a sense of the size of the island and gives clues for where the lizards may be hiding, since they are often found under plants.

A bar along the bottom of the screen fills with color as a player catches more lizards, so players can guess how far along they are for their level.  The number of lizards increases as players reach higher levels.  Once a lizard is caught, the player discovers information about the lizard, such as sex and health.   Players measure the lizard themselves so they can compare sizes of lizards on different islands. Players then tag the lizard by selecting a paint color that appears on the lizard’s back. Players will have the ability to view statistics about the lizards they have caught: how many on each island, the sex of the lizards, lizard sizes, and lizard territories. They record this data in their field notebook, as well as facts and observations about the lizards.  Players can also observe and learn about the other plants, animals and insects. They can record these observations and the facts they learn about the other organisms in their field notebook. For added fun, the longer the player spends on the island, the more likely they are to get pooped on by a bird flying overhead!

A Treasure Trove of Fossil Geckos

fossil gecko

amber geckosWho knew there were so many fossil geckoes? In the first review of fossil geckodom in more than three decades, Juan Daza, Aaron Bauer, and Eric Snively examine 28 fossil geckos, providing new insights into whether the specimens can be confidently attributed to taxa. Some times, they can placed into extant genera, other times, especially for the older ones, it’s hard to say for sure just where the belong.

If nothing else, the fossils are cool and sometimes quite old, the most ancient, Cretaceogecko, dating back to the early Cretaceous.

This paper was part of a special of the Anatomical Record published last year, “New Advances In Morphology and Evolution of Living and Extinct Squamates,” which was previously discussed in these pages.

Here’s the abstract:

Gekkota is often interpreted as sister to all remaining squamates, exclusive of dibamids, or as sister to Autarchoglossa. It is the only diverse lineage of primarily nocturnal lizards and includes some of the smallest amniotes. The skeleton of geckos has often been interpreted as paedomorphic and/or “primitive” but these lizards also display a wide range of structural specializations of the postcranium, including modifications associated with both scansorial locomotion and limb reduction. Although the concept of “Gekkota” has been variously applied by different authors, we here apply a rigorous apomorphy based definition, recent advances in gekkotan morphology and phylogenetics, and diverse comparative material to provide a comprehensive assessment of 28 known pre-Quaternary geckos, updating the last such review, published three decades ago. Fossils evaluated include both sedimentary fossils and amber-embedded specimens. Known Cretaceous geckos are exclusively Asian and exhibit character combinations not seen in any living forms. Cenozoic gekkotans derive from sites around the world, although Europe is especially well represented. Paleogene geckos are largely known from disarticulated remains and show similarities to Sphaerodactylidae and Diplodactylidae, although resemblances may be plesiomorphic in some cases. Many Neogene gekkotans are referable to living families or even genera, but their geographic occurrences are often extralimital to those of modern groups, as is consistent with paleoclimatic conditions. The phylogenetic placement of fossil gekkotans has important repercussions for timetree calibration, but at present only a small number of fossils can be confidently assigned to even family level groupings, limiting their utility in this regard.

More Examples of Different Dewlap Colors in Males and Females

dewlap dimorphism

In a recent post, we discussed the description of two new Costa Rican anoles, but didn’t draw attention to the fact that all members of the A. pachypus species complex exhibit dewlap dichromatism, with the dewlaps of males and females differing within a species. Shown here are differences in A. tropidolepis (top) and A. pachypus (bottom). The images on the right are females and the left and center are males.

In a previous post, we discussed this phenomenon, but its explanation still escapes us. Interestingly, it occurs almost exclusively in mainland anoles.

Which Anole Is That in the Addams Family Dollhouse?


anole skeletonJoe Martinez of the Museum of Comparative Zoology writes in: “I was recently contacted by Samantha Grantham, the collections manager of the Wenham Museum in Wenham Massachusetts, who would appreciate learning the identification of a lizard skeleton that resides in the Coffin Room of their Addams Family dollhouse. The dollhouse was constructed locally, presumably with artifacts that were readily available.

It appears to be an anole and Anolis carolinensis would have been available through the pet trade at that time. Anolis sagrei may have begun showing up in the pet trade as well by then. Can anyone give an authoritative identification?”

And want to learn more about the Addams Family Dollhouse? There’s a whole blog devoted to it!


New Book on the Anoles of Honduras


johnsmeyersiMcCranie and Köhler have just published an authoritative account of the 39 species of Honduran anoles. Rich in detail and thorough in coverage, this volume will be of interest to anyone interested in neotropical herpetology.

Harvard University Press’s description says it all: Caribbean members of this group have been intensively studied and have become a model system for the study of ecology, evolution, and biogeography, but knowledge of the anoles of Central and South America has lagged behind. In this landmark volume, veteran herpetologists James R. McCranie and Gunther Köhler take a step toward rectifying this shortcoming by providing a detailed account of the rich anole fauna of Honduras. Generously illustrated with 157 photos and drawings, The Anoles of Honduras includes information on the evolutionary relationships, natural history, distribution, and conservation of all 39 Honduran anole species. The work is the result of decades of study both in the field and in museums and is the first synthetic discussion of the complete anole fauna of any Central or South American country. Each species is described in great detail with locality maps. Bilingual (English and Spanish), extensively illustrated identification keys are also included.

Distribution maps are provided for all species.

Distribution maps are provided for all species.

Like all publications of the Bulletin of the MCZ and Breviora, the book is freely available as a pdf on the journal’s website. But a pdf just doesn’t look right on a bookshelf, not to mention getting soggy in the field. For those who really  want to get the most out of this volume, why not consider purchasing it from Harvard University Press for only $24.95 (not bad for a 280 page volume jam-packed with color photos!)? And it’s even cheaper on Amazon (currently $20.48).


Help Identify Anole from Guyana

Photo by Thadaigh Baggallay

Thadaigh Baggallay writes: “I took this picture in Kaieteur National Park, Guyana. Anolis chrysolepis perhaps?”

Looks to me like whichever chrysolepis-type anole occurs in Guyana. Exactly a year ago today, we had a post on a new field guide to Guyanan herps by Cole et al. which probably would help. According to that guide, I believe the species would be A. planiceps. Any thoughts any one?


Video of Anolis pentaprion Displaying

Little is known about the Central American twig anole, but it does have a beautiful dewlap! In recent years, what used to be known as A. pentaprion has been split into a large number of species, the most recently described of which is A. triumphalis. (Editor’s note: Gunther Kohler points out that this is one of the newly named species, A. charlesmyersi).

Here’s the backstory from the videographer who posted this on Youtube: Greetings Casa Alta Vista, Costa Rica. That video was shot about 15 feet above ground, on the guava wood handrail that goes up my stairs. Our house is a rustic style “pole” house, constructed from plantation grown gmelina and teak woods. We are located about 2 miles inland of the shores of Golfo Dulce , Costa Rica, at about 600 feet elev. in a mostly second growth seasonally dry rainforest. Dry season from Dec to April, then usually 300 inches of rain , a lot of which is in September-October usually. We are across the gulf from Corcovado National Park . Maybe 15 miles as the toucan flies. The area around the house was pasture up until about 20 years ago, but now pretty lush with second growth. Fairly undeveloped, and there is some primary growth surrounding us down in the “quebradas” or streams that are all around here. Down there we have stream anoles, and lots of snakes and critters. Saw a bushmaster down there once . Yikes. We also see slender anoles (I think) but they aren’t very “brown” and the yellow spot on the dewlap isn’t as prominent as the picture in my book . We also sometimes see the dry forest anole, which seems to trade off the territory of my deck railing system with the lichen anoles. We see green anoles down on some of the fruit trees we have planted as well. Amazing creatures all, they don’t seem fearful of us, and maintain eye contact . And will bite of course if they are provoked and can catch hold of you. I once had a full grown basilisk lizard that I was rescuing from some dogs bite me nicely on the hand. We have really a lot of all kinds of wildlife here. The birding is great, and we have a large troop of mono titi’s (squirrel monkeys) that occasionally traverse our back deck, peek in the windows, and move on to eat guabo beans in the trees surrounding our house. We’re built about 4 meters off the ground, not a treehouse , but kind of up in the trees .
My camera is new, and I will be posting other animal videos soon. And will try to get more anole videos.

Editor’s Update, 2/23/2015:

Here’s another clip of the same animal: