Tag: genomics

Anoles are models for studying evolution in the wild. Not only do anoles have a history of repeatedly diversifying to specialize in the same types of microhabitats in the same ways across the Greater Antilles, these lizards also have a tendency to adapt on rapid timescales to environmental change — be it the addition or subtraction of a predator or competitor, a polar vortex, a change to the structural environment, or a hurricane.

Anoles are also models for urban evolution. Why? Anoles are found abundantly across the Caribbean in urban and forest environments where they specialize in divergent microenvironments characterized by shifts in climate and physical structure. Urban habitats tend to be warmer, drier, more open, and dominated by buildings and impervious surfaces instead of vegetation — providing the perfect opportunity for repeated adaptation to a novel combination of environmental conditions. In other words, Caribbean cities provide a replicated natural laboratory to study adaptation as it happens when these lizards colonize and thrive in urbanizing areas. And there is no shortage of urban-tolerant and urbanophilic anole species to choose from!

Species of Anolis lizards are found in urban environments across the Caribbean (photos CC-BY K. Winchell; Earth at night by NASA).

Urban Lizards Like It Hot (and Their Genes May Tell Us Why)

By Kristin Winchell

On February 26, 2021

In New Research

Anolis allisoni, Photo by breslauer iNaturalist

Cities are hot. Because of the urban heat island effect, urban environments tend to be significantly warmer than nearby non-urban environments. For ectothermic organisms, like lizards and insects, elevated urban temperatures create thermally stressful conditions. It might be unsurprising then that researchers have documented an increase in thermal tolerance in urban animals (e.g., City Ants Adapt to Hotter Environment). These studies point to the ability to cope with elevated urban temperatures as a critical aspect of persisting in urban environments.

Although there is evidence that the urban environment shapes adaptive thermal tolerance in Anolis lizards at the genomic level, it is also possible that anole species that thrive in hot urban environments have an innate ability to do so due to local adaptation in their ancestral habitat (i.e., forests). In fact, an analysis of patterns of urban tolerance across Caribbean anoles found that species that experience hotter and drier temperatures in their native ranges and those that maintain higher field body temperatures tended to be the ones that do well in urban environments (Winchell et al. 2020). And when researchers looked at genomic variation in Cuban species not found in urban areas, they identified genes associated with thermal sensitivity (Akashi et al. 2016), suggesting tolerance of different thermal environments may be encoded at the genomic level. But does this mean that some anoles are predisposed to tolerate hot urban temperatures based on the climate of their ancestral forest homes?

Kanamori et al. (2021) — “Detection of genes positively selected in Cuban Anolis lizards that naturally inhabit hot and open areas and currently thrive in urban areas” — set out to answer this question by examining the transcriptome of nine species of Cuban anoles that occupy different thermal microhabitats. Cuba is home to the largest number of anole species, with species diversifying to occupy distinct thermal and structural microhabitats. In their study, the researchers attempted to identify genomic signatures of selection in non-urban populations of species that thrive in urban environments in order to understand if there was something unique about the genetic background related to thermal tolerance in these species that enables urban colonization.

Of the nine species Kanamori and colleagues studied, three are found in naturally hot and open environments: A. allisoni, A. porcatus, and A. sagrei, representing two different branches of the Cuban anole radiation. These three species (and several of their close relatives) also thrive in urban environments both in Cuba (e.g., Havana) and in their non-native range (e.g., Miami, Florida).

Anolis sagrei, Photo by Jody Shugart iNaturalist

Anolis porcatus, Photo by James Telford iNaturalist

Anolis allisoni, Photo by Juan Rafael Rodríguez iNaturalist

Five other species are found in cool and deeply shaded forests: A. alutaceus, A. isolepis, A. garridoi, A. allogus, and A. mestrei. The last species, A. homolechis, is common in the shaded areas of forest margins.

Anolis mestrei, Photo by Alex Alfil iNaturalist

Anolis isolepis, Photo by Yasel U. Alfonso iNaturalist

Anolis homolechis, Photo by Alex Alfil iNaturalist

Anolis allogus, Photo by Alex Alfil iNaturalist

Anolis alutaceus, Photo by Yasel U. Alfonso iNaturalist

Kanamori and colleagues examined a total of 5,962 genes and found genomic signatures of selection in 21 genes in the two main branches of species that contain urbanophilic species (A. porcatus & A. allisoni, and A. sagrei), but did not identify selection in the same genes across the two lineages. In other words, these closely related species have found unique genomic pathways to deal with the hot and dry forest environments in which they thrive. This finding suggests that the predisposition to tolerate hot urban environments is determined by different genes in different anole species, and raises the possibility that further local adaptation to urban thermal environments may also be lineage specific.

When the researchers looked at the functional associations of the genes under selection in each species, they found that they were related to stress responses, epidermal tolerance to desiccation, and cardiac function. All three of these biological functions are implicated in maintaining appropriate acclimation responses to thermal stress in anoles. These findings implicate ancestral selection on stress responses, perhaps in response to thermal or ultraviolet radiation, as potential factors influencing tolerance of anoles in urban environments. Further exploring the importance of these functions will shed light on their role in the initial tolerance of urban environments upon urban colonization and adaptive modification as urban lineages persist.

Read the full paper here:

Kanamori, S., Cádiz, A., Díaz, L.M., Ishii, Y., Nakayama, T. and Kawata, M., 2021. Detection of genes positively selected in Cuban Anolis lizards that naturally inhabit hot and open areas and currently thrive in urban areas. Ecology and Evolution, 11(4), pp.1719-1728.

This post was cross-posted on the blog “Life in the City” — check it out if you want to learn more about urban evolution!

Parallel Selection on Thermal Physiology Facilitates Repeated Adaptation of City Lizards to Urban Heat Islands

By Kristin Winchell

On March 11, 2020

In New Lit Abstracts

New literature alert!

In Nature Ecology and Evolution

Campbell-Staton, Winchell, Rochette, Fredette, Maayan, Schweizer, and Catchen

Abstract

Only recently have we begun to understand the ecological and evolutionary effects of urbanization on species, with studies revealing drastic impacts on community composition, gene flow, behaviour, morphology and physiology. However, our understanding of how adaptive evolution allows species to persist, and even thrive, in urban landscapes is still nascent. Here, we examine phenotypic, genomic and regulatory impacts of urbanization on a widespread lizard, the Puerto Rican crested anole (Anolis cristatellus). We find that urban lizards endure higher environmental temperatures and display greater heat tolerance than their forest counterparts. A single non-synonymous polymorphism within a protein synthesis gene (RARS) is associated with heat tolerance plasticity within urban heat islands and displays parallel signatures of selection in cities. Additionally, we identify groups of differentially expressed genes between habitats showing elevated genetic divergence in multiple urban–forest comparisons. These genes display evidence of adaptive regulatory evolution within cities and disproportionately cluster within regulatory modules associated with heat tolerance. This study provides evidence of temperature-mediated selection in urban heat islands with repeatable impacts on physiological evolution at multiple levels of biological hierarchy.

Campbell-Staton, S. C., Winchell, K. M., Rochette, N. C., Fredette, J., Maayan, I., Schweizer, R. M., & Catchen, J. (2020). Parallel selection on thermal physiology facilitates repeated adaptation of city lizards to urban heat islands. Nature Ecology & Evolution, 4(4), 652-658.

SICB 2020: Gene Expression Can Lead to Size Dimorphism in Anole Lizards

By Anthony Gilbert

On January 8, 2020

In All Posts, New Research

The Panamanian slender anole (Anolis apletophallus).

In keeping with the previous year, Albert Chung (now a Ph.D. student at UCLA with Shane Campbell-Staton), presented in the prestigious Division of Ecology and Evolution Raymond B. Huey best student paper session of SICB2020. Albert’s work encompasses a very old, enduring, and important question in biology: how males and females of the same species exhibit differences in so many traits, despite the fact that males and females share a common genome.

A male brown anole from the island of Great Exuma, in The Bahamas.

This dynamic is called sexual conflict: when what is best for one sex might not be the best for the other sex, and has challenged biologists for decades to study a multitude of incredible organisms to answer this question, including anoles! Albert and his collaborators addressed this question by studying two species of anole, the brown anole (Anolis sagrei) and the Panamanian slender anole (Anolis apletophallus). Brown anoles are one species where males are super large compared to females, whereas in the slender anole, males and females are relatively the same size.

Albert et al. described differences in the genes expressed in both males and females to understand what factors promote the development of male-biased size dimorphism. They found that differences in gene expression between males and females was highest in gonad tissue compared to liver and brain tissue, and that when female lizards are supplemented with additional testosterone (traditionally viewed as a hormone more highly concentrated in males of a given species), their gene expression profiles look like those of male lizards. They also found that liver tissue exhibits the greatest differences in sex-biased gene expression, because the liver is one organ responsible for supplying the body with the energy and molecules needed for growth. They suggest that differences in gene expression between males and females might be one factor promoting the evolution of size differences between the sexes, and that physiological controls on these genes could play prominent roles in having males and females exhibit huge differences in traits despite sharing a similar genetic makeup.

Evolution 2019: Comparative Landscape Genetics and Epigenetics in Anolis Lizards

By Sofia Prado-Irwin

On June 27, 2019

In New Research

The field of landscape genetics seeks to understand how patterns of genetic diversity vary across a landscape. But an organism’s traits are not just determined by their genome – they are also impacted by processes that affect the way the genome is expressed. The study of such mechanisms (i.e. heritable non-genetically based gene expression) is known as epigenetics, and has become a topic of great interested to evolutionary biologists who aim to understand the processes by which phenotypes change over time and space. Non-genetically based phenotypes can be the targets of selection, can impact the plasticity of traits in different environments, and more.

Understanding the impact of epigenetics on evolutionary processes is difficult, because it is hard to disentangle the genetic and epigenetic effects on phenotypes. Of course, epigenetics are not independent from the underlying genetic code – the genes that are expressed are a part of the genome after all. Thus because populations differ in genetic structure, it is difficult to determine whether differences in phenotypes across populations are driven by genetic changes, or epigenetic changes. To understand the influence of epigenetic changes on phenotypes, it is necessary to “subtract” the effects of the underlying genetic variation.

Ian Wang decided to tackle this problem using a well-studied Anolis species, A. cristatellus. Wang is interested in understanding what factors drive epigenetic patterns; but before understanding the factors involved, it is first necessary to describe the patterns. Wang chose to focus on A. cristatellus because it is distributed widely and throughout various environments on the island of Puerto Rico, and is therefore a good candidate for understanding how populations diverge across geographic regions (i.e. isolation by distance) and in different habitats (i.e. isolation by environment).

Wang and colleagues collected tissues from 8 localities, some of which were located in the xeric southwest, and some of which were located in the mesic interior. He performed RRBS sequencing, which captures information about methylated regions of DNA, and therefore provides information on variation in gene expression across populations (i.e. epigenetic variation). He also performed ddRAD sequencing, which captures information about genetic differences across populations (i.e. genetic variation).

In analyzing these two complementary datasets, Wang found that epigenetic and genetic distances were correlated between populations – that is to say, populations with high genetic divergence also had high epigenetic divergence. Recall that epigenetics are to not wholly independent from genetics, so this result is expected. However, each of these two types of variation – genetic and epigenetic – were also influenced by other factors.

In terms of genetic divergence, geographic distance was the strongest correlate – populations that were close to one another were more similar than populations that were further away. Interestingly, temperature and vegetation also appeared to play a role as well. In terms of epigenetic divergence, genetic distance (as represented by Fst) was the strongest predictor. Interestingly, however, vegetation was also a strong predictor as well. This suggests that on top of the genetic changes that accumulate when populations diverge, additional epigenetic shifts have also occurred, and are likely impacting the populations’ fitness in their respective environments.

These results highlight the importance of considering both genetic and epigenetic changes in studies of adaptive variation. Genomes alone may not explain the whole story! Wang is continuing this research in multiple avenues, including comparing results across species (e.g. comparing results from A. cristatellus to another trunk ground anole, A. cybotes on Hispaniola), and digging deeper into the functions of individual outlier loci from the RRBS sequencing. Looking forward to hearing more about this emerging perspective on adaptation in anoles!

Evolution 2016: Using Anoles to Understand Shifts in Forests

By Kristin Winchell

On June 20, 2016

In New Research

Ivan Prates presents his poster at Evolution 2016.

Here at Evolution 2016 there have been a lot of anole talks and posters. In fact, there have even been several that pretend to not actually be about anoles. Ivan Prates presented a poster which he insisted, despite multiple pictures of anoles and the use of anole DNA, was not actually about anoles… Instead, this poster was actually about the historical extent of Brazilian forest cover (or so he says).

In short, Ivan used genomic data to understand historical patterns of dispersion and distribution of South American anoles in order to infer patterns of rainforest expansion and contraction. He suspected that the geological data gave a false interpretation of rainforest patterns in Amazonia and the Atlantic Forest in Brazil, and that anoles could help tell the true story of how the forests have changed over time. By looking at species with strong genetic signals associated with forest shifts he hypothesized that true forest patterns could be elucidated based on the historical demography of these species.

Ivan and coauthors looked at three species of lizards: Anolis punctatus, Anolis ortonii, and Polychrus marmoratus. They used the next-generation sequencing technique Genome by Sequencing (GBS) to answer three main questions: (1) Did all 3 species experience range expansions simultaneously? (2) Did populations expand and contract at similar points in time? (3) How did population sizes vary over time? While all three of these questions are about anoles, don’t forget that this poster was actually about the forest.

Ivan found that the Atlantic Forest individuals composed a monophyletic group nested within the Amazonian lineage. This suggests that the anoles of the Atlantic Forest on the coast actually arose from a single colonization event from Amazonia. The land between Amazonia and the Atlantic forest is presently quite arid compared to the rainforest – more like grassland. This presumably forms a barrier to contemporary dispersal, which implies that historical dispersal must have involved greater habitat connectivity. So Ivan’s results support the hypothesis that the forests experienced a drastic historical expansion creating a contiguous habitat that enabled dispersal around 1 million years ago. Interestingly, the timing for the dispersal of all 3 species was approximately the same. A million years ago seems to have been the ideal time to move to the coast for Brazilian anoles.

Ivan and his colleagues also looked at how populations size changed over time. He found that whereas Anolis punctatus experienced a trend of population expansion, Anolis ortonii and Polychrus marmoratus experienced population contractions. It was surprising to the authors that these species did not respond the same – why did only one of the species experience population expansions? They suspected that the expansion of one species might be related to the population contractions of the others, perhaps because of competition. However, their analysis on synchrony of population trends proved otherwise. They found that although trends within species were synchronized across populations, between species the shifts in demography were asynchronous. In other words, when one species expanded or contracted in population size, the others were stable. Ivan concluded that this was support for the idea that these populations were not influencing each other and that instead there was some other factor independently controlling population size fluctuations – perhaps precipitation patterns.

In conclusion, Ivan told me a lot about the demography of anoles during the Quaternary, and a little about the forest. I look forward to hearing more about his “forest” research on these understudied mainland anoles!