More Studies on Anole Chromosomes

karyotypes

When it rains, it pours. Research on the immense diversity in anole chromosomes was rampant in the 1970’s and early 1980’s, and then…nothing. Until, that is, the last two months. Not one, but two, papers appeared in Evolution, and now AA has learned of a paper on chromosomal variation in Norops clade anoles, recently published in Zoological Studies (click for a downloadable pdf). The paper, by Castiglia et al., examines karyotypes in Norops anoles and argues that karyological variation is in some cases consistent with our understanding of phylogenetic relationships within the group.

Abstract
Background: Neotropical lizards, genus Anolis (Polychrotidae), with nearly 380 species, are members of one of the most diversified genera among amniotes. Herein, we present an overview of chromosomal evolution in ‘beta’ Anolis (Norops group) as a baseline for future studies of the karyotypic evolution of anoles. We evaluated all available information concerning karyotypes of Norops, including original data on a recently described species, Anolis unilobatus. We used the phylogeny of Norops based on DNA sequence data to infer the main pattern of chromosomal evolution by means of an ancestral state analysis (ASR).

Results: We identified 11 different karyotypes, of which 9 in the species had so far been used in molecular studies. The ASR indicated that a change in the number of microchromosomes was the first evolutionary step, followed by an increase in chromosome numbers, likely due to centric fissions of macrochromosomes. The ASR also showed that in nine species, heteromorphic sex chromosomes most probably originated from six independent events.

Conclusions: We observed an overall good correspondence of some characteristics of karyotypes and species relationships. Moreover, the clade seems prone to sex chromosome diversification, and the origins of five of these heteromorphic sex chromosome variants seem to be recent as they appear at the tip nodes in the ancestral character reconstruction. Karyotypic diversification in Norops provides an opportunity to test the chromosomal speciation models and is expected to be useful in studying relationships among anole species and in identifying cryptic taxa.

Available Now: A New, Large Phylogeny of Anoles

BEAST estimated phylogeny of anoles. Circles on nodes represent posterior probability, black > 0.95, grey > 0.90, white > 0.70.

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.

Anolis stratulus Displaying

Note the arm waving and tongue protrusion!

httpv://www.youtube.com/watch?v=OP3rnPQJT6A

How to Set Up a Lizard Room to House and Breed Anoles

Thinking of setting up a room to maintain and breed lizards for research projects? Back in 2011, the good folks in the Glor Lab–which has done a stupendous job at breeding A. distichus–shared their accumulated knowledge in an 11-part series. Given the fog of memory, it seemed like a good time to remind the world of the existence of this primer, and put the links all together in one place.

So, with no further ado, here are the 11 posts in the “Evolution of a Lizard Room” undecology:

1: Introduction

2: Maintaining humidity

3: The watering wand

4: Crickets

5: The Shopvac

6: Generating food in house

7: Egg-laying

8: Egg inculation

9: Toe clipping

10: Custom cages for breeding experiments

11: Butterfly Cages

For another source of information, check-out the manual put together by the Brodie Lab at the University of Virginia.

Anolis allisoni Featured in Film on Reptile Diversity of Cayos Cochinos, Honduras

httpv://www.youtube.com/watch?v=WyGO_rcVEM0

We’ve had previous posts [1,2] on research on anoles of these islands. Nice footage of ctenosaurs and boas as well.

50% Off Anole Watches for Next 2.5 Hours

What better way to celebrate moving your clock forward than getting that anole watch–available in five ecomorphs–that you’ve been coveting. Pop on over to Zazzle.com now, and don’t delay, because the deal ends at 1 p.m. Eastern Daylight Time. Use code word sundaydeal22.

What Makes Anolis Communities Complete?

One of my favorite graphic representations of a typical anole community is the one where all ecomorphs are hanging out together in a tree and a scrub next to said tree. Each ecomorph has its structural microhabitat place and they are all spaced out evenly across the tree to represent competition. Originally the figure was published by Williams (1983) and then modified later on. Arriving on the Greater Antilles, one thus expects to promptly be able to say hi to all these ecomorphs at the next best tree. Well, from my personal experience, I can tell you that this is unfortunately not the case.

Idealized representation

Localities where all ecomorphs are found together are scarce, and all of them are famous, having served as field sites for the most groundbreaking of anole discoveries. But what about the rest of them? Something must prevent the co-occurrence of ecomorphs in all these other places. This was noted before: Losos (2009) remarked that all utilized structural microhabitats exploited by all ecomorphs are present throughout the islands, so “complete” ecomorph communities should also be able to occur everywhere.

A common explanation for the absence of certain  “functional types” (= Anolis ecomorphs) from local communities is a process that is called “filtering.” Modern community assembly theory distinguishes two such types of filters: 1. Biotic interaction filters and 2. Environmental filters.

 Filters

Biotic filtering involves competitive exclusion: For anoles this phenomenon caused ecological speciation which led to the convergent evolution of the ecomorph communities. But biotic filtering should not be expected to occur at this stage of the radiation: Different ecomorphs are not competing for the same structural microhabitat niche in different localities. This leaves environmental filtering. In our study recently published in Ecology and Evolution, on which I am reporting here, we tested whether environmental filtering could be a possible explanation for the absence of ecomorphs in local communities.

First, we modeled Anolis ecomorph community completeness by constructing environmental niche models for each ecomorph (the sum of species belonging to that ecomorph) on each island. These models were then overlaid for all ecomorphs per island.  ECC map

 The map for ecomorph community completeness shows a very patchy distribution of areas where all ecomorphs are expected to occur. Comparisons of environmental niches among these islands revealed that only Hispaniola and Cuba have their complete Anolis ecomorph communities occurring in a similar bioclimatic parameter space.

This patchiness could be explained by elevation for all islands except Jamaica: the Anolis community completeness map strongly resembles the topographic relief of the Greater Antilles. Looking more closely into the climatic parameters, Jamaica has much lower daily and annual temperature ranges which are also not related to the island’s elevation, whereas in the rest of the Greater Antillean islands, they are. Occurrence probability of ecomorphs seems to be coupled to environmental parameters, which explains why some ecomorphs are “filtered out“ in some locations: they do not encounter a favorable environment there.

Since I mentioned initially that filtering relates to “functional types” (not species), the filtering must be a result of certain functional properties of the Anolis ecomorphs’ phenotype. We wanted to take the study a step further and actually investigate one (among many) possible functional trait: body mass.

Advice Needed: Field Sites for A. sagrei in Florida

Anolis sagrei. Photo by Janson Jones.

I’m planning an in-depth behavioral study of Anolis sagrei for the summer and need your help finding suitable field sites in Florida.

My ideal location would have the following traits:

– Abundant A. sagrei in an area large enough to support at least 50 adult males

– Relatively open understory

– Not heavily trafficked by people (I’d like to minimize the frequency of behavioral trials being disrupted by inquisitive passersby), but still safe to work in

– Management receptive to researchers

Does anyone know of protected areas, biological or agricultural field stations, or other underutilized green spaces that might fit the bill? I’m open to locations throughout the state.

Thanks in advance for any suggestions!

Exploring the Anolis Y Chromosome

Sex chromosomes have historically been identified by inspecting chromosome spreads under a light microscope and looking for a morphologically distinct or heteromorphic pair of chromosomes – typically and X and Y or a Z and W. However, heteromorphic sex chromosomes are absent in many animal groups, particularly fish, amphibians, and lizards, making it difficult to determine whether a species with genetic sex determination has an XY or ZW system. As a consequence, the study by staustinreview.com of sex chromosome evolution in clades in which cryptic or homomorphic sex chromosomes are prevalent has been hampered by a lack of identified sex chromosomes in these groups. New methods are needed to find the sex chromosomes in these species and increase our understanding of homomorphic sex chromosome biology, the evolution of sex determining systems, and patterns of sex chromosome evolution overall.

David Zarkower and I have a paper in press at Molecular Ecology Resources that uses high-throughput DNA sequencing to identify sex-specific genetic markers as a means to reveal sex chromosome systems in species that lack heteromorphic sex chromosomes. We are using a newly developed DNA sequencing technique called restriction site associated DNA sequencing or RAD-seq. RAD-seq sequences the DNA flanking very specific DNA sequences (restriction enzyme recognition sites) scattered throughout the genome, generating tens of thousands of genetic markers. RAD-seq is a powerful technique for exploring genetic variation in ‘nonmodel’ species because it does not require a fully sequenced genome, requires relatively modest sequencing capacity, and can detect even minor genetic differences among individuals. We are using RAD-seq to 1) identify sex-specific molecular markers (i.e., bits of DNA found in individuals from one sex but not the other), and 2) using these markers to determine whether a species has XY or ZW sex chromosomes. Species with male-specific markers will have an XY system while species with female-specific will have a ZW system.

We are interested in using RAD-seq to screen various vertebrate species for sex chromosomes, but first wanted to validate the technique using a species with a known sex-determining mechanism. We chose the green anole (Anolis carolinensis) because its X and Y chromosomes are small and homomorphic. Therefore A. carolinensis sex chromosomes should provide a rigorous test of this technique and success with Anolis suggests there may be broad utility using this technique in other groups with homomorphic sex chromosomes.

We performed RAD-seq on seven male and ten female A. carolinensis and recovered one male-specific molecular marker. We confirmed that the marker was male-specific using PCR and also found that this genetic marker is conserved in some additional Anolis species, confirming homology among the Y chromosomes of these species (Anolis sex chromosome homology has been discussed previously on Anole Annals 1, 2). These results highlight the potential utility of RAD-seq as a tool to discover the sex chromosome systems of large numbers of species in a rapid, cost-effective manner.

PCR validation of the male-specific RAD-seq marker in Anolis carolinensis.

PCR validation of the male-specific RAD-seq marker in Anolis carolinensis.

In addition to learning about Anolis sex chromosomes the male-specific molecular marker we identified can be used to sex individuals of many Anolis species using a simple PCR-based assay, particularly species in the A. carolinensis group and in the Norops clade. This enables identification of an individual’s sex prior to the onset of secondary sexual characteristics, for example in embryos, thereby aiding developmental studies of sexually dimorphic phenotypes. The importance of sexual dimorphism to Anolis ecology and evolution has been examined previously (1, 2, 3, 4), but there is certainly much more to learn, particularly about how sexually dimorphic traits develop and evolve. The ability to sex Anolis embryos is an important step to advance this research.

Phylogenetic relationships among sampled species illustrating the sex-specific amplification of the gene rtdr1y in selected anole species. The autosomal gene kank1 was used as an internal positive control in all reactions. Bands labelled with ‘NS’ are nonspecific PCR products.

Phylogenetic relationships among sampled anoles illustrating the sex-specific amplification of the gene rtdr1y in selected anole species. The autosomal gene kank1 was used as an internal positive control in all PCR reactions. Bands labelled with ‘NS’ are nonspecific PCR products.

Nine Caribbean Skinks Petitioned for Inclusion on Endangered Species List

A while back, we reported on a monograph Hedges and Conn that described an enormous number of new skink species (35) from the Caribbean. Now efforts are being made to prevent some of these species from going extinct. The Center for Biological Diversity has just filed a petition with the U.S. Fish and Wildlife Service asking that nine Caribbean skink species be placed on the Endangered Species List. Those species are: Culebra Skink (Spondylurus culebrae), Mona Skink (Spondylurus monae), Monito Skink (Spondylurus monitae), Lesser Virgin Islands Skink (Spondylurus semitaeniatus), Virgin Islands Bronze Skink (Spondylurus sloanii), Puerto Rican Skink (Spondylurus nitidus), Greater Saint Croix Skink (Spondylurus magnacruzae), Greater Virgin Islands Skink (Spondylurus spilonotus) and Lesser Saint Croix Skink (Capitellum parvicruzae).

A press release from the CBD explains all:

“The Center for Biological Diversity filed a formal petition today seeking Endangered Species Act protection for nine newly identified species of skinks found only in Puerto Rico and the Virgin Islands. These rare lizards with smooth skins are on the knife’s edge of extinction due to introduced predators and habitat destruction. Reptiles around the globe are in the midst of an extinction crisis with roughly 1 in 5 species considered endangered or at risk of disappearing.

Puerto Rican skink
Puerto Rican skink photo © Puerto Rico Wildlife/Alfredo Colón (alfredocolon.zenfolio.com). Photos and maps are available for media use.

“Time is running out for these lizards,” said Collette Adkins Giese, a Center biologist and lawyer focused on protecting reptiles and amphibians. “The Caribbean is home to extremely rare animals found nowhere else in the world, but too many have already gone extinct. To save these skinks, we need to get them protected under the Endangered Species Act.”

Scientists recently recognized the nine petitioned skinks, along with dozens of others on Caribbean islands. The scientists initiated their study after finding unusually large genetic differences among populations of these skinks on different islands in the Caribbean. All of the newly identified endemic Caribbean skinks are near extinction (or already extinct) due to introduced predators like mongooses and cats, as well as large-scale habitat destruction for development and agriculture.

This loss is alarming because reptiles play important roles as predators and prey in their ecosystems and they’re valuable indicators of environmental health. The animals in today’s petition will reap life-saving benefits from the Endangered Species Act, which has a 99 percent success rate at staving off extinction for species under its care.

“Skinks have a slow-moving curiosity and are not adapted to fast predators such as the mongoose, introduced by humans,” said Dr. Blair Hedges of Pennsylvania State University, the lead author of the 2012 study that recognized the petitioned species. “The survival of these skinks depends on the special measures of protection that only the Endangered Species Act can provide.”

Although reptiles have been around for hundreds of millions of years and survived every major extinction period, now, due largely to human impacts, they’re dying off at up to 10,000 times the historic extinction rate. About 20 percent of reptiles in the world are endangered or vulnerable to extinction. Within the Caribbean, scientists estimate that reptiles have levels of endangerment that are at or near the highest levels worldwide.

The Center was joined in its petition for these nine skinks by Dr. Renata Platenberg, an ecologist specializing in Caribbean reptiles.

Background
The petitioned-for Caribbean skinks, which can grow to be about 8 inches long, are unique among reptiles in having reproductive systems most like humans, including a placenta and live birth. They have cylindrical bodies, and most have ill-defined necks that, together with their sinuous movements and smooth, bronze-colored skin, make them look like stubby snakes.

Four of the species for which we petitioned are found within the territory of Puerto Rico: the Culebra skink (Culebra and the adjacent islet of Culebrita), Mona skink (Mona Island), Monito skink (Monito Island) and Puerto Rican skink (Puerto Rico and several of its satellite islands). The remaining five are found in the Virgin Islands: the Greater St. Croix skink (St. Croix and its satellite Green Cay), Lesser St. Croix skink (St. Croix), Greater Virgin Islands skink (St. John and St. Thomas), Lesser Virgin Islands skinks (St. Thomas and two adjacent islets, several British Virgin Islands) and Virgin Islands bronze skink (St. Thomas and several of its islets, several British Virgin Islands).

Eight of the nine petitioned-for species fall within the genus Spondylurus, and one falls within the genus Capitellum. The genus Spondylurusincludes what are now known as the Antillean four-lined skinks because of the four major dark stripes on their back and sides. Skinks in the genus Capitellum are called the Antillean small-headed skinks and have small feet and short heads, lacking dark dorsolateral stripes.”

The entire petition can be downloaded from the CBD’s website.

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