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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.

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.

Reconstructing the History of Anole Sex Chromosomes

Gorman_Dominica_1965_Anolis_oculatus

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.

Display Behaviour in Anolis sagrei: Deterring Predators, Daunting Opponents or Drawing Partners?

A.sagrei_M&F_Sorao

Male and female A. sagrei at the famous Soroa, Cuba locality.

Anole displays consist of conspicuous behaviors that are known to be used in multiple contexts, such as exhibiting territory ownership and territory defense, mate attraction and female receptivity, species recognition, and even predator deterrence. As most of you know, the display repertoire typically involves three major signal types: “dewlap extensions” (DE, pulsing of the throat fan or dewlap), “push-ups” (PU, up and down movement of the body and tail), and “head-nods” (HN, up and down movement of the head only). Although the visual display behavior in anoles has been extensively studied, the function of these three major signal types (DE, PU and HN) remains highly equivocal, and especially in the brown anole. Therefore, we decided to set up a behavioral experiment addressing DE, PU and HN signaling rates across diverse contexts, using the brown anole as study species.

Our study differed from previous ones in two main aspects. Whereas most other studies have focused on male signaling only, we looked to the three separate signal types in both male and female lizards. Secondly, our study is the first one to compare display rates across a wide range of contexts using the same individuals over again (repeated-measures design). This design could, however, only work under fully-controlled laboratory testing conditions. The diverse contexts we tested included predator, non-predator and several social interactions (i.e., mirror, male-male, male-female and female-male). For the predator and non-predator interactions, we used a living curly-tailed and equally-sized ocellated spiny-tailed lizard, respectively; the social context involved only conspecific interactions. Rather than examining display structure, we focused on the frequency with which each individual signal type was performed.

What did our results show? We found that brown anoles of both sexes exhibited higher display rates in the presence of conspecifics than when confronted with a predator or non-predator. DE, PU, and HN seem to be of main importance during brown anole social interactions, and thus not in predator deterrence. Whereas the females did not significantly raise display rates in response to a mirror or during intersexual interactions compared to a control situation, males did. The PU signal type only appears to play a major role for brown anole males during aggressive encounters. On the other hand, increased frequencies of all signal types during male-female interactions suggest that DE, PU, and HN are all essential for male courtship.

Staged intersexual interactions in the brown anole

Staged intersexual interactions in the brown anole

Finally, we suggest that intersexual selection is probably a driving force for frequency-related dewlap use in both sexes (we found a very strong, but not significant, trend that females increased their DE frequency only during female-male interactions). In contrast, pronounced intersexual differences were detected for PU and HN rates within a social context. I would like to mention once more that all our behavioral experiments were conducted under controlled laboratory conditions and that caution is needed on the general interpretation of our findings.

To end, I would like to say that we did experience some difficulties in comparing our PU and HN results with results from previous studies on brown anole display behavior, due to an inconsistent terminology found in the literature. Authors have variously used the terms “nod,” “headnod,” “bob,” “headbob” and “pushup” to refer to the stereotyped bobbing display and it is not always clear which movements correspond exactly to which terms (e.g., only head movement, only front legs, whole body movement including/excluding tail). Partan et al. (2011) did a very nice job by discussing several bobbing display terms in her paper, but still we think there is need for a more consistent and defined “bobbing” terminology. In this way, pooling display datasets and comparing display results will become more efficient and accurate, which in turn may lead to better “anole science”!

Driessens, T., Vanhooydonck, B., Van Damme, R. 2014. Deterring predators, daunting opponents or drawing partners? Signaling rates across diverse contexts in the lizard Anolis sagrei. Behav Ecol Sociobiol 68:173–184.

Measuring Maximal Performance In Animals: The Cautionary Story From The Calaveras County Frog Jumping Contest

For more than three decades, since the seminal work of Ray Huey, Al Bennett, and Steve Arnold, biologists have measured whole animal performance–how fast they run, how far they jump, how well they can swim–to understand how species are adapted to their environment.  Work on anoles has been a prime example of how we can study differences among individuals and species to understand how natural selection works and why species living in different environments possess different morphologies (several AA posts have discussed this sort of work [e.g., 1, 2, 3]).

But a critical assumption of all of this research is that we can get animals to perform maximally. Otherwise, it’s tough to study what causes variation in maximal capabilities if animals aren’t performing maximally. The catch is: how do you tell if an animal is going all out? Sure, it’s easy to weed out the slackers, but distinguishing a lizard giving it his all from one going at, say, 90% of max…hard to tell.

In an important and entertaining paper, Henry Astley and colleagues provide some sobering information. The short story goes as follows, and you really should watch the video below for more details and some great images: biomechanicians have studied frog jumping for decades to understand how muscles work. Bullfrogs are known not to jump very well. The maximum jump ever recorded in the lab was only 1.3 m, whereas the much smaller Cuban treefrog can bound 1.7 m. The proffered explanation was that bullfrogs live on land and in the water, and so their morphology must be a compromise.

But…the Guinness Book of World Records claims that a bullfrog–Rosie the Ribeter, to be exact–once jumped 2.18 meters at the Calaveras County Fair. That’s  68% farther than any scientist had ever recorded in the lab. Sounds like a bunch of hooey, right? Well, just to debunk this nonsense, a bunch of Brown University biologists headed to sunny California to visit the County Fair, eat some cotton candy, and check out the frogs. And, lo and behold, it’s true–bullfrogs there regularly far exceed the lab record.

The story’s a lot more complicated–it turns out that there are “pro” frog jumpers–and I won’t go into the details; the paper is well worth a read, very entertaining and sobering for lab performance types (abstract here). But the short story is this: it seems that lab studies had massively underestimated how far bullfrogs can jump, calling into question many of the conclusions that had been reached about their physiology. Moreover, records for the maximum jump distance at the fair showed a steady increase for the first 50 years before levelling off for the last 30. This suggests that the people who jump the frogs (and some families have been doing this for generations) have only gradually learned exactly what conditions and behaviors maximally stimulate the frogs. And this suggests that lab scientists, who just guess at what may work best and tinker a little bit, may not have much of a chance of hitting on the right stimuli.

There’s been lots of great press coverage, too–just google “calaveras frog astley” or something like that. But, first, watch the video and go read the paper (I can email you a copy if you can’t access it online).

httpv://www.youtube.com/watch?v=QKFpvoez7_M

Are Bark Anoles (Anolis distichus) Native to Abaco Island, Bahamas?

Bark anole, A. distichus

Bark anole, A. distichus

I’ve been working on Abaco, in The Bahamas for several years now. The Bahamas, Abaco in particular, is famous for the abundance of terrific science that originates there. Currently, Abaco has three species of anole: A. sagrei, A. smaragdinus, and A. distichus. However, only A. sagrei has been considered native to the island, the others likely introduced relatively recently from islands of the Great Bahama bank such as New Providence or Bimini. However, a recent study reports fossil evidence of A. distichus in peat deposits from about 950 YBP supporting a long history of A. distichus on Abaco.

One interesting aspect of this find is that the contemporary distribution of A. distichus on Abaco appears to be limited to the main port town of Marsh Harbour. I always suspected that this limited distribution suggested that A. distichus was not native to the island, but rather came in on landscaping plants over the last several decades.

So why are there conflicting observations here? Is it possible that A. distichus was extirpated on Abaco due to settlement by indigenous peoples (seems to be contemporaneous with the fossil sediment formation)?  While it might seems rather hard to extirpate such a small, abundant animal, there is growing evidence that the Bahamas were reptile-dominated ecosystems at the time of human arrival. Therefore, the coincident extirpation of tortoises, Cuban crocodiles, and rock iguanas places the modern hiatus of A. distichus in a different light. I am guessing that the altered (intensified) fire regimes initiated by ancient human civilizations may have contributed to the absence (rarity) of A. distichus from contemporary, natural ecosystems. This is admittedly, a lot of conjecture, but how else might one explain their ancient presence, yet contemporary confinement to a human-dominated habitat?

I look forward to hearing more from the interesting work that Dave Steadman, Janet Franklin and Nancy Albury are doing on these ancient Bahamas communities. And it looks like there is a lot more to come! Also, the name of the journal is The Holocene. How cool is that?!

Steadman DW, NA Albury, P Maillis, JI Mead, J Slapcinsky, KL Krysko, HM Singleton, and J Franklin. 2014. Late-Holocene faunal and landscape change in the Bahamas. The Holocene. DOI: 10.1177/0959683613516819.

 

 

 

 

Genetic Differentiation in the Beach Anole, Anolis onca, in Venezuela

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Everyone’s favorite beach anole, A. onca. Photo by J. Losos

Anolis onca, the only padless anole, occurs in sandy habitats in Venezuela. Little is known about the evolutionary history of this quite distinctive species (we had a discussion of its natural history last year [1,2]).

Now a recent paper appears in the journal Saber  in which a team of Venezuelan scientists led by Alejandra Tejada used starch gel electrophoresis methods to measure the degree of genetic differentiation among populations. The paper can be downloaded, albeit a bit slowly, and is in Spanish, but here’s the English summary:

Anolis onca is a lizard species located in the Araya peninsula, in northern Venezuela. Populations of this species may have been isolated in the late Cretaceous and later recombined during the Quaternary through a new isthmus by sedimentary processes. To test this assumption, in five populations of A. onca, starch gel electrophoresis was used to estimate genetic variability within populations, interpopulation differentiation (FST), and gene flow (Nem). Additionally, under the premise of genetic differentiation between subpopulations under the isolation by distance (IBD) model, we conducted a phylogenetic analysis for five subpopulations of this lizard. Increases of genetic distance values (D) between subpopulations arranged consecutively between the Chacopata and Guayacán locations and a clear structuration as estimated by the FST parameter, evidence isolation by distance as indicated by the IBD model. However, Nem values did not conform to this model, suggesting that the subpopulations, although actually connected, may have been shaped by independent evolutionary processes. The two clades resulting from the phylogenetic analysis do not group populations closer geographically since clade B (Chacopata+Istmo Sur) lies in areas geologically ancient whereas clade A [(Istmo Centro+Istmo Norte)+Guayacán)] occupies areas of recent sedimentary origin. It is thus reasonable to infer that other factors besides the geographical distance between subpopulations may have also conditioned the structure found.

 

SICB 2014: Testosterone Regulation of Multiple Traits


Anolis sagrei has impressive sexual size dimorphism, but what causes it? (Photo by Bob Reed)

Sexual dimorphism is always a hot topic at SICB, and this year it was no exception for anoles (1, 2). Christian Cox, a postdoc in the laboratory of Bob Cox (no relation) at the University of Virginia, sought to explain how testosterone might lead to phenotypic divergence in a number of sexually dimorphic traits. As many of us are aware, sexual dimorphism varies widely among lizard species, and evolutionary shifts to and away from dimorphism are common, including in anoles. Testosterone has been shown to be an important regulator of growth in several lizard species, so Cox experimentally tested this effect in Anolis sagrei.

Both males and females were given a testosterone or blank implant and allowed to grow to maturation. One group was manipulated as juveniles, just as phenotypic divergence was beginning, and the other group was manipulated as subadults after divergence. Testosterone addition increased growth in body size and mass, increased metabolic rate, increased dewlap size, and changed dewlap coloration in both sexes and both juveniles and subadults. Fat storage was reduced as expected, in both sexes and age classes. These results are intriguing, because a sex difference in testosterone production may play a role in the degradation of between-sex genetic correlations. The next question is how that happens, as both sexes produce testosterone, just to different extents.

SICB 2014: Phenotypic Selection in Anolis sagrei

Numerous variables can affect an organism’s survival, including its age and sex, the demographics of the population in which it resides, and environmental conditions like climate, and habitat. However, the relative importance of these factors is poorly understood. Dan Warner described his investigation into factors affecting natural selection in wild populations of anoles in his talk titled, “Spatial and temporal variation in phenotypic selection in the lizard Anolis sagrei.”

A sagreiWarner measured directional selection on A. sagrei on six islands in the Matanzas National Estuarine Reserve in Florida. These islands were intentionally founded with populations having unequal adult sex ratios. Half of the islands were founded with more males than females (male-biased), and the other islands received more females than males (female-biased). This manipulation was done to strengthen the effects of male-male competition on the male-biased islands. Warner measured survival selection on adult and juvenile body size by marking and recapturing individuals over the last three years.

Warner found a lot of variation in the strength of directional selection on adult and juvenile body size both across islands and within each island in different years. However, there was no relationship between the strength of selection on each island and either habitat structure (represented by canopy openness) or island size. Thus, the probability of survival at a particular body size does not seem to depend on environment.

However, population demographics did seem to affect survival at different body sizes. There was a negative correlation between the strength of selection on body size and the density of adult lizards, indicating that smaller body sizes are favored at high population densities (and vice versa). This trend was observed in both adults and juveniles, but was more pronounced in juveniles. Warner hypothesized that it was the density of adult males in particular, rather than the total density of adults, that was driving the observed trend. To test this idea, he tested for a correlation between the strength of selection on juvenile body size and the adult sex ratio. He found a negative correlation, indicating that large juveniles are favored in more female-biased populations while small juveniles do better in male-biased populations. One possible explanation is that on islands with male-biased sex ratios, large juveniles are more likely to come into contact with territorial adult males, are more likely to be perceived by these males as a possible competitor, and are therefore more likely to be harassed by these males. The presence of adult males might even reduce recruitment, as evidenced by slower population growth rates on male-biased versus female-biased islands.

These results suggest that patterns of natural selection on individuals can depend on characteristics of the population. Only with long-term field studies such as this one can we begin to unravel the many factors affecting selection in wild populations.

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