Author: Ivan Prates

Peter Buck Postdoctoral Fellow at Smithsonian's National Museum of Natural History. I study mainland anole evolution, biogeography, and comparative genomics.

Dr. Aaron Reedy presenting at Evolution 2019.

Aging theory predicts that organisms will age faster when the probability of survival to old age is low. As a result, males and females of a species may age at distinct rates if they experience different rates of mortality due to environmental factors. Postdoctoral researcher Dr. Aaron Reedy (Auburn University) and colleagues tested this idea by performing a mark-recapture study of introduced Anolis sagrei in the small Island H in Florida, an island that is approximately the size of a baseball field.

The team tracked 6,591 individuals of A. sagrei from hatchling to death through a near-complete sampling of the population four times a year between 2015 and 2019 (!!). The research group measured the body condition of individuals based on the residuals of mass on body length and estimated the rate of aging based on chromosomal telomere length from real-time qPCR.

The results suggest that males have higher mortality and shorter lifespans than females; most males die within two years, while females can live up to three and even four years. The study also found that males suffer a decline in body condition with age that females don’t seem to – Aaron even mentioned that he is often capable of predicting how old a male individual is based on how haggard it looks! Preliminary data suggests no statistical differences in telomere length between males and females, although there seems to be a trend of decreasing telomere length with age in males only.

In conclusion, Dr. Reedy and colleagues found that males have increased mortality and shorter lifespans than females, but it is unclear whether males senesce more rapidly. The next steps of this investigation will include longitudinal studies in both the field and lab to follow how fast single individuals age over their lifetimes.

You can check his poster on Aaron’s website.

Local Adaptation in Mainland Anole Lizards: Integrating Population History and Genome-Environment Associations

By Ivan Prates

On November 9, 2018

In Anole Genome Research, New Research

Figure 1. Anolis punctatus, South America’s coolest lowland anole – literally. Picture by Renato Recoder.

In ectothermic organisms, environmental factors such as temperature and water availability constrain physiological and behavioral performance. Therefore, the occurrence of species in varied environments may be associated with local adaptation. On the other hand, experimental studies have shown that physiological function can be highly conserved within species over broad environmental gradients, which may be associated with the homogenizing effects of population gene flow. In a recently published study, we focus on widespread South American anoles to investigate whether the occurrence of species in distinct environments is linked to local adaptation and whether population structure and history have constrained adaptive differentiation.

Based on molecular data, my collaborators and I have previously found that arboreal lizard species have independently colonized the Atlantic Forest from Amazonia, subsequently expanding southward towards subtropical regions. This is the case of Anolis ortonii and Anolis punctatus (Fig. 1), whose ranges now encompass a climatic gradient from warm and wet conditions in Amazonia to cooler and less rainy settings in the Atlantic Forest. Our new study investigates whether species establishment in distinct climates is associated with potentially adaptive genetic differentiation between populations. To this purpose, we implement genome-environment association analyses on the basis of thousands of restriction site-associated DNA markers. Moreover, to estimate levels of gene flow – a force that could oppose adaptive differentiation – we perform historical demographic inference under a genetic coalescent framework. Lastly, to characterize the climatic gradients presently occupied by A. ortonii and A. punctatus, we estimate climatic space occupancy over their ranges.

Analyses of genetic structure inferred distinct populations in Amazonia and the Atlantic Forest in both anole species (Fig. 2), suggesting that separation of these forests following a period of contact in the past has favored genetic divergence. In the two species, historical demographic analyses inferred large effective population sizes, mid-Pleistocene colonizations of the Atlantic Forest from Amazonia, and post-divergence population gene flow (Fig. 3). These results support the hypothesis of recurrent rainforest expansions that connected presently disjunct biomes in northern South America.

Figure 2. Genetic clustering based on all SNPs from Anolis ortonii (A) as well as all SNPs (B) and candidate SNPs only (C) from A. punctatus. Proportions in pie charts on maps correspond to ancestry coefficients estimated by genetic clustering analyses. Grey areas on map indicate South American rainforests. Red arrows indicate A. punctatus sample MTR 20798 from Pacaraima on the Brazil-Venezuela border in the Guiana Shield region, a locality that is climatically similar to Atlantic Forest sites (see Fig. 4); this sample is genetically more similar to eastern Amazonian samples based in the entire SNP dataset, yet more similar to Atlantic Forest samples based on the candidate SNPs only.

Figure 3. Population history (from SNAPP) and historical demographic parameters (from G-PhoCS) inferred for Anolis ortonii (A) and A. punctatus (B). Parameters are the time of coalescence between populations (in millions of years, Mya), effective population sizes (in millions of individuals, M), and migration rates (in migrants per generation, m/g). Colors of terminals correspond to genetic clusters in Fig. 2.

Genome-environment association analyses found allele frequencies of 86 SNPs in 39 loci to be significantly associated with climatic gradients in A. punctatus. Among the candidate loci, eleven uniquely mapped to known protein-coding genes in the reference genome of Anolis carolinensis; two mapped non-specifically to more than four genes; and the remaining mapped against non-coding regions, which may correspond to regions that regulate gene expression or that are physically linked to genes that underwent selection. In the case of A. ortonii, no SNPs were associated with temperature and precipitation variation across space. Constraints related to population structure and history do not seem sufficient to explain discrepant signatures of adaptation between the two anole species; instead, this discrepancy may be related to species differences in climatic space occupancy over their ranges (Fig. 4).

Figure 4. Environmental space occupancy along latitude based on climatic PC1 for Anolis ortonii and A. punctatus. Samples used in genetic analyses are indicated with a black dot. Higher PC scores correspond to drier and colder sites. Dashed line indicates the approximate region of a pronounced north-south climatic turnover in the Atlantic Forest identified by previous studies. Red arrow indicates A. punctatus sample MTR 20798 from Pacaraima, a mid-elevation site (820 m above sea level) in the Guiana Shield region that overlaps climatically with Atlantic Forest sites (horizontal axis). Note that the two species experience largely similar climates in Amazonia and the northern Atlantic Forest, yet A. punctatus occupies cooler and less humid localities that are not occupied by A. ortonii in the southern Atlantic Forest.

The candidate genes identified in A. punctatus play essential roles in energy metabolism, immunity, development, and cell signaling, providing insights about the physiological processes that may have experienced selection in response to climatic regimes. Similar to our study, other investigations of anole lizards found differences in the frequency of alleles that underlie ecologically relevant physiological processes between populations that inhabit contrasting habitats. These examples support the hypothesis that adaptation to colder climates has played an essential role in range expansions across anole taxa, including mainland and Caribbean forms that span altitudinal and latitudinal gradients.

Anolis ortonii. Spotting this cryptically colored rainforest anole is quite challenging indeed. Picture by Miguel T. Rodrigues.

This investigation illustrates how studies of adaptation on the basis of genome-environment association analyses can benefit from knowledge about the history of landscape occupation by the species under investigation. Data on population structure and history can provide insight into how gene flow and natural selection interact and shape population genetic differentiation. Moreover, information about the direction and routes of colonization of new habitats can support spatial sampling design, help to characterize landscape gradients, and support the formulation of hypotheses about how organisms have responded to environmental variation in space.

To know more:

Prates I., Penna A., Rodrigues M. T., Carnaval A. C. (2018). Local adaptation in mainland anole lizards: Integrating population history and genome-environment associations. Ecology and Evolution, early view online.

A Second Caribbean Anole Species Introduced to Brazil

By Ivan Prates

On September 7, 2018

In Introduced Anoles, New Research, Notes from the Field

The brown or festive anole, Anolis sagrei, is an invasive species in several countries in the Americas and Asia. This species is native to Cuba, the Bahamas, and the Cayman islands. Following introductions, A. sagrei can reach high population densities and undergo rapid range expansion. In a recently published contribution, we provide the first record of this aggressive invasive lizard in Brazil.

In 2017, we recorded specimens of A. sagrei within the limits of an International Airport in the metropolitan area of the city of Rio de Janeiro, southeastern Brazil. The observation of juveniles and mating couples suggests that the species is established locally.

The origin, geographic extent, and potential for spread of A. sagrei in Rio de Janeiro and Brazil are currently unclear. It is also unclear whether this species will be able to colonize natural habitats, such as the surrounding Atlantic Rainforest.

The establishment of brown anole populations elsewhere has led to shifts in substrate use by native anoles and promoted major shifts in the structure of local insect assemblages. As such, this species has the potential of affecting local ecological communities in Brazil. However, the effects of A. sagrei on the local fauna – including native lizards that we sampled in the area – are difficult to predict.

This is the second case of an established exotic anole species in Brazil. Populations of the Cuban green anole, Anolis porcatus, were recently detected in several sites in the Baixada Santista coastal region, state of São Paulo.

To know more:

Oliveira J.C.F., Castro T.M., Drago M.C., Vrcibradic D., Prates I. (2018). A second Caribbean anole lizard species introduced to Brazil. Herpetology Notes, 11: 761-764.

PDF available here (at the bottom of the webpage).

Notes on the Neblina tepui Anole (Anolis neblininus), Discovered in Brazil

By Ivan Prates

On December 11, 2017

In Natural History Observations, Notes from the Field

Female Anolis neblininus .

In November 2017, I had the opportunity to join a team of scientists led by herpetologist Miguel T. Rodrigues (University of São Paulo) in an extraordinary expedition to the Serra da Neblina, a very remote tepui (sandstone table-top mountain) on the Brazil-Venezuela border. The expedition involved the Brazilian Army, several Yanomami guides, and a team of BBC journalists. We collected around 2,500 samples of amphibians, reptiles, birds, small mammals, and plants between 80 and 2,995 m of altitude – among them, at least 10 frog and lizard species new to science!

Neblina peak (2,995 m) as seen from our camp at the Bacia do Gelo ("ice bowl", 1,997 m).

Neblina peak (2,995 m), Brazil’s highest mountain, as seen from our camp in the Bacia do Gelo (“ice basin”) at 1,997 m.

As soon as we got to an elevation of around 2,000 m, we started looking for Anolis neblininus, the Neblina anole. This mysterious lizard was described based on six individuals collected on the Venezuelan portion of the mountain in the 80’s by a team of AMNH-Smithsonian scientists. To our surprise, it took us only a few hours to find one, two, several individuals – the first records of A. neblininus in Brazil!

The Neblina anole seems to be locally abundant, with more than 30 individuals found over a week. Because of their slow movements and cryptic coloration, these lizards are really hard to spot during the day. All but two individuals were found at night, sleeping on thin branches and leaves on the edge of forest patches, at a height of 1-4 meters above the ground. Although we set up 100 pitfall traps in the area to sample herps and small mammals, all of the anoles were found through active search.

Neblina anoles really like to sleep on fern leaves – most individuals were found this way.

To learn a bit about how much Neblina anoles move during the day, we experimented with spooling a few individuals. Based on how much thread they left along their way, it seems that A. neblininus does not move much in a day. Individuals go up and down short trees and bushes, but do not seem to walk on exposed ground. However, the spools that we had – leftovers from a study of larger Enyalius lizards – may have been too awkward for such small anoles to carry.

Spooling lizards is an effective way to learn how much they move and what type of substrate they use. Unfortunately the spools that we had were rather big for these anoles.

Spooling lizards is a simple yet effective way to learn how much they move and what type of substrate they use. Unfortunately, the spools that we had were probably too big for these anoles!

Follow the thread to find the lizard!

These montane lizards experience remarkably low temperatures. At night, when temperatures were as low as 6^oC, the anoles were unresponsive for long periods after captured, apparently because they were too cold. On consecutive mornings, we followed individuals (spotted on the night before) to check at what time they would become active. To our surprise, the anoles started moving at different times in each day, between 6 and 9:30 am, in an apparent association with how cold it was. It is therefore possible that the onset of activity is given mostly by temperature, as opposed to when the sun comes out.

Male Anolis neblininus. Too cold to go anywhere.

One interesting feature of A. neblininus is how variable their coloration is. Some individuals have gray bodies, others green or brown; some have yellow heads. They are also capable of changing their colors a bit. The dewlap is well developed in females, with dark spots on an orange or brown background. Male dewlaps are white, bluish, or yellowish. Neblina anoles have a very cool-looking dorsal crest, more developed in males.

Male (left, center) and female dewlaps.

Our recent studies of mainland anole lizard evolution and biogeography have found that A. neblininus is closely related to species from montane Atlantic Forest, Andes, and Andean foothills. This pattern may result from a history of cool habitats connecting South American mountains in the past, followed by habitat retraction and extinction in intervening areas. Our expedition to the Neblina revealed additional species that seem to be related with taxa from distant mountains. We are now examining their history based on genetic data to help shed light on the history of the mysterious tepui fauna.

Legendary Brazilian Anoles Rediscovered

By Ivan Prates

On May 14, 2017

In New Research

Several anole species are known from a single remote locality or only a few individuals, sometimes collected long ago. Because sampling these species is hard, we have a limited understanding about their biology and evolution. In a recent paper, we report on the rediscovery of Anolis nasofrontalis and Anolis pseudotigrinus, two mainland species from the Brazilian Atlantic Forest that were not reported for more than 40 years. Based on DNA sequence data, we examine their placement in the Anolis tree of life and estimate divergence times from their closest relatives. Moreover, based on the morphological attributes of newly and previously collected specimens (some of which were overlooked due to misidentification), we provide much needed taxonomic re-descriptions.

Fig. 1. Coloration in life of Anolis nasofrontalis (A, B) and A. pseudotigrinus (C, D). In A, inset shows the black throat lining of A. nasofrontalis, an uncommon trait that may be indicative of close relationships with Andean anoles (such as A. williamsmittermeierorum). Photographed specimens are females.

Coloration in life of Anolis nasofrontalis (A, B) and A. pseudotigrinus (C, D). In A, inset shows the black throat lining of A. nasofrontalis. Photographed specimens are females.

This study starts with efforts by collaborator Dr. Miguel T. Rodrigues (Universidade de São Paulo) to investigate reptiles and amphibians that have been undetected for years – a gap that could indicate human-driven extinctions. On late 2014, Dr. Rodrigues and his students (including co-author Mauro Teixeira Jr.) launched an expedition to the mountains of Santa Teresa (state of Espírito Santo, Brazil), the type locality of both A. nasofrontalis and A. pseudotigrinus. After a few days (and nights) of search, the team spotted the first A. pseudotigrinus in decades. The adult female was found sleeping on a narrow branch, (probably) unaware of its significance for South American biogeography (so were we). No signs, however, of A. nasofrontalis.

Shortly after, PhD students Paulo R. Melo-Sampaio (Museu Nacional) and Leandro O. Drummond (Universidade Federal do Rio de Janeiro) decided to visit Santa Teresa, inspired by conversations with Dr. Rodrigues. At this point, Dr. Rodrigues, my supervisor Dr. Ana C. Carnaval (City University of New York), and I had agreed that a phylogenetic study of A. pseudotigrinus would fit my PhD research well. Then, on early 2016, we got an unexpected email from Paulo and Leandro, with the first picture ever taken of an A. nasofrontalis in life. Both legendary anoles were real!

Back to the lab, we generated DNA sequence data and performed phylogenetic analyses, with completely unexpected results. First, A. nasofrontalis and A. pseudotigrinus are not closely related to the other (confirmed) Atlantic Forest species (A. fuscoauratus, A. ortonii, and A. punctatus); instead, they are close relatives of a species from western Amazonia, the “odd anole” Anolis dissimilis. These three species were found to compose a clade with A. calimae from the western cordillera of the Colombian Andes, A. neblininus from a Guiana Shield tepui on the Brazil-Venezuela border, and two undescribed Andean species (Anolis sp. R and Anolis sp. W from Poe et al. 2015 Copeia). This clade falls outside of the five major clades previously recovered within the Dactyloa radiation of Anolis, which have been referred to as species series (aequatorialis, heterodermus, latifrons, punctatus, roquet). Based on these results, we define the neblininus species series of Anolis.

Fig. 2. Phylogenetic relationships and divergence times between species in the Dactyloa clade of Anolis inferred using BEAST. Asterisks denote posterior probabilities > 0.95.

Phylogenetic relationships and divergence times between species in the Dactyloa clade of Anolis inferred using BEAST. Asterisks denote posterior probabilities > 0.95.

The neblininus series is composed of narrowly-distributed species that occur in mid-elevation sites (or adjacent habitats in the case of A. dissimilis) separated by large geographic distances. This pattern suggests a complex biogeographic history involving former patches of suitable habitat between regions, followed by habitat retraction and extinction in the intervening areas. In the case of A. nasofrontalis and A. pseudotigrinus, for instance, past forest corridors may explain a close relationship with the western Amazonian A. dissimilis. Atlantic and Amazonian rainforests are presently separated by open savannas and shrublands, yet geochemical records suggest that former pulses of increased precipitation and wet forest expansion have favored intermittent connections between them. These connections may have also been favored by major landscape shifts as a result of Andean orogeny, such as the establishment of the Chapare buttress, a land bridge that connected the central Andes to the western edge of the Brazilian Shield during the Miocene.

Fig. 3. Geographic distribution of confirmed and purported members of the neblininus species series. The inset presents a schematic map of South America around 10-12 mya, when the ancestor of A. nasofrontalis and A. pseudotigrinus diverged from its sister, the western Amazonian A. dissimilis. The approximate locality of the Chapare buttress, a land bridge that connected the central Andes to the western edge of the Brazilian Shield, is indicated.

Geographic distribution of confirmed and purported members of the neblininus species series. The inset presents a schematic map of South America around 10-12 mya, when the ancestor of A. nasofrontalis and A. pseudotigrinus diverged from its sister, the western Amazonian A. dissimilis. The approximate locality of the Chapare buttress, a land bridge that connected the central Andes to the western edge of the Brazilian Shield, is indicated.

During our morphological examinations of A. nasofrontalis and A. pseudotigrinus, it became apparent that these two species are not very different from Caribbean twig anoles, with whom they share short limbs and cryptic coloration. We learned that these features are also present in other, distantly-related mainland anoles, such as A. euskalerriari, A. orcesi, A. proboscis, and A. tigrinus. Phylogenetic relationships support that a twig anole-like phenotype was acquired (or lost) independently within Dactyloa, perhaps as a result of adaptive convergence. Alternatively, this pattern may reflect the conservation of an ancestral phenotype. In the former case, an apparent association with South American mountains is intriguing.

Unfortunately, natural history data from A. nasofrontalis and A. pseudotigrinus are lacking. It is currently unclear whether they exhibit the typical ecological and behavioral traits that characterize the Caribbean twig anole ecomorph, such as active foraging, slow movements, infrequent running or jumping, and preference for narrow perching surfaces.

Anolis dissimilis, the ‘odd anole’.

It has become increasingly clear that broader sampling of genetic variation is key to advance studies of mainland anole taxonomy and evolution. This significant challenge also provides exciting opportunities for complementary sampling efforts, exchange of information, and new collaborations between research groups working in different South American countries.

To learn more:

Prates I, Melo-Sampaio PR, Drummond LO, Teixeira Jr M, Rodrigues MT, Carnaval AC. 2017. Biogeographic links between southern Atlantic Forest and western South America: rediscovery, re-description, and phylogenetic relationships of two rare montane anole lizards from Brazil. Molecular Phylogenetics and Evolution, available online 11 May 2017.

Cuban Anolis porcatus introduced to Brazil (perhaps through Florida?)

By Ivan Prates

On February 9, 2017

In Introduced Anoles, New Research

Several anole species have become established outside of their native ranges as a result of human-mediated transportation, being introduced to Japan, Singapore, Taiwan, Hawaii, the continental U.S., and beyond. Alien anoles can have major impacts on the ecological communities that they invade, for instance leading to local extinction of arthropod taxa and displacing native anole species. It is therefore key to detect and report instances of introduction by these potentially aggressive invaders, as well as to document their geographic spread in colonized regions. In a recent paper, we report on the presence of Anolis porcatus, a species native from Cuba, in coastal southeastern Brazil, using DNA sequence data to support species identification and examine the geographic source of introduction.

Anolis porcatus collected in Brazil, and comparison with the native anole A. punctatus. A, male A. porcatus showing green coloration. B, male A. porcatus showing brown coloration. C, the pink dewlap of male A. porcatus. D, female A. porcatus. E, male A. punctatus, a native anole species. F, the yellow dewlap of male A. punctatus. Picture credits: A–D, Mauro Teixeira Jr.; E, Renato Recoder.

Perhaps embarrassingly, this study started with Facebook. On August 2015, Ricardo Samelo, an undergraduate Biology student at the Universidade Paulista in Santos, posted a few pictures of an unknown green lizard in the group ‘Herpetologia Brasileira.’ A heated debate about the animal’s identity took place, with people eventually agreeing on Anolis carolinensis. On my way to Brazil to join the Brazilian Congress of Herpetology, I contacted Ricardo (but only after properly hitting the ‘like’ button) and proposed to examine whether the exotic anole was established more broadly in the Baixada Santista region.

To our surprise, local residents knew the lizards well, with some people quite fond of the ‘lagartixas’ due to their pink dewlap displays. People could often tell when the anoles were first noticed in the vicinities – ‘six months’, ‘nine months’, ‘one year ago’ –, suggesting a rather recent presence. Guided by these informal reports, we sampled sites in the municipalities of Santos, São Vicente and Guarujá, where we found dozens of lizards occupying building walls, light posts, fences, debris, trees, shrubs, and lawn in residential yards, abandoned lots, and alongside streets and sewage canals. It was clear that the alien anoles are doing great in human-modified areas; the high density of individuals across multiple sites, as well as the presence of juveniles with various body sizes, seem to suggest a well-established reproductive population.

Sites in the Baixada Santista in southeastern coastal Brazil where introduced A. porcatus were detected. 1, Guarujá. 2, Santos. 3, São Vicente. Green indicates Atlantic Forest cover; gray indicates urban areas; black indicates water bodies.

By reading and bugging experienced anole researchers about the Anolis carolinensis species group, I learned about paraphyly among species, hybridization, and unclear species diagnosis based on external morphology. As a result, my PhD supervisor, Dr. Ana Carnaval, and I decided to recruit Leyla Hernandez, by the time an undergraduate student in the Carnaval Lab at the City University of New York, to help generate DNA sequences to clarify the species identity, and perhaps track the geographic source of introduction in Brazil. To our surprise, a phylogenetic analysis found Brazilian samples to nest within Anolis porcatus, a Cuban species that has also been introduced to Florida and the Dominican Republic. Brazilian A. porcatus clustered with samples from La Habana, Matanzas, and Pinar del Río, which may suggest a western Cuban source of colonization. Nevertheless, Brazilian specimens are also closely related to a sample from Coral Gables in Florida, which may suggest that the Brazilian population originated from lizards that are exotic elsewhere.

Phylogenetic relationships of A. porcatus introduced into Brazil (indicated in red), inferred using MrBayes based on a mitochondrial DNA locus. Purple indicates samples of A. porcatus invasive elsewhere (Florida and the Dominican Republic). Blue indicates native Atlantic Forest anole species. Asterisks indicate posterior probability >0.95. Picture depicts a male A. porcatus collected in São Vicente, Brazil.

The presence of A. porcatus in the Baixada Santista may be related to the country’s largest seaport complex, the Porto de Santos, in this region. Numerous storage lots for intermodal shipping containers were situated near sites where the lizards were detected, and in one instance we found the animals sheltered inside an open container. An exotic green anole (identified as A. carolinensis) was previously found in Salvador in Brazil’s northeast; like Santos, Salvador hosts a major seaport complex, which may indicate that the exotic anoles reached Brazil after being unintentionally transported by ships bringing goods from overseas – perhaps twice independently.

It is currently unclear whether A. porcatus will be able to expand into the surrounding coastal Atlantic Rainforest, or into more open natural settings such as shrublands in the Cerrado domain. It is also unknown whether this species will have negative impacts on the local ecological communities. In Brazil, introduced A. porcatus may potentially compete with other diurnal arboreal lizards, such as Enyalius, Polychrus, Urostrophus, and the native Anolis. Five native anoles inhabit the Atlantic Forest (for sure): A. fuscoauratus, A. nasofrontalis, A. ortonii, A. pseudotigrinus, and A. punctatus. While none of them is currently known to occur in sympatry with A. porcatus, the worryingly similar A. punctatus has been reported for a site in Bertioga located only 50 kilometers from the site in Guarujá where we found the exotic anoles.

To properly evaluate the potentially invasive status of A. porcatus in Brazil, we hope to continue assessing the extent of its distribution and potential for future spread, as well as to gather data about whether and how A. porcatus will interact with the local species – especially native Brazilian anoles. This seemingly recent, currently expanding colonization also represents an exciting opportunity for comparisons with other instances of introduction of A. porcatus, as well as the closely-related A. carolinensis, based on ecological and phenotypic data.