ASYNCHRONOUS EVOLUTION OF PHYSIOLOGY AND MORPHOLOGY INANOLISLIZARDS

Predictability of the community-function landscape in wine yeast ecosystems

Predictively linking taxonomic composition and quantitative ecosystem functions is a major aspiration in microbial ecology, which must be resolved if we wish to engineer microbial consortia. Here, we have addressed this open question for an ecological function of major biotechnological relevance: alcoholic fermentation in wine yeast communities. By exhaustively phenotyping an extensive collection of naturally occurring wine yeast strains, we find that most ecologically and industrially relevant traits exhibit phylogenetic signal, allowing functional traits in wine yeast communities to be predicted from taxonomy. Furthermore, we demonstrate that the quantitative contributions of individual wine yeast strains to the function of complex communities followed simple quantitative rules. These regularities can be integrated to quantitatively predict the function of newly assembled consortia. Besides addressing theoretical questions in functional ecology, our results and methodologies can provide a blueprint for rationally managing microbial processes of biotechnological relevance.

Draft genome of six Cuban Anolis lizards and insights into genetic changes during their diversification

Background

Detecting genomic variants and their accumulation processes during species diversification and adaptive radiation is important for understanding the molecular and genetic basis of evolution. Anolis lizards in the West Indies are good models for studying evolutionary mechanisms because of the repeated evolution of their morphology and the ecology. We performed de novo genome assembly of six Cuban Anolis lizards with different ecomorphs and thermal habitats (Anolis isolepis, Anolis allisoni, Anolis porcatus, Anolis allogus, Anolis homolechis, and Anolis sagrei). We carried out a comparative analysis of these genome assemblies to investigate the genetic changes that occurred during their diversification.

Results

We reconstructed novel draft genomes with relatively long scaffolds and high gene completeness, with the scaffold N50 ranging from 5.56 to 39.79 Mb and vertebrate Benchmarking Universal Single-Copy Orthologs completeness ranging from 77.5% to 86.9%. Comparing the repeat element compositions and landscapes revealed differences in the accumulation process between Cuban trunk-crown and trunk-ground species and separate expansions of several families of LINE in each Cuban trunk-ground species. Duplicated gene analysis suggested that the proportional differences in duplicated gene numbers among Cuban Anolis lizards may be associated with differences in their habitat ranges. Additionally, Pairwise Sequentially Markovian Coalescent analysis suggested that the effective population sizes of each species may have been affected by Cuba’s geohistory.

Conclusions

We provide draft genomes of six Cuban Anolis lizards and detected species and lineage-specific transposon accumulation and gene copy number changes that may be involved in adaptive evolution. The change processes in the past effective population size was also estimated, and the factors involved were inferred. These results provide new insights into the genetic basis of Anolis lizard diversification and are expected to serve as a stepping stone for the further elucidation of their diversification mechanisms.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12862-022-02086-7.

Relationship between gene expression networks and muscle contractile physiology differences in Anolis lizards

Muscles facilitate most animal behavior, from eating to fleeing. However, to generate the variation in behavior necessary for survival, different muscles must perform differently; for instance, sprinting requires multiple rapid muscle contractions, whereas biting may require fewer contractions but greater force. Here, we use a transcriptomic approach to identify genes associated with variation in muscle contractile physiology among different muscles from the same individual. We measured differential gene expression between a leg and jaw muscle of Anolis lizards known to differ in muscle contractile physiology and performance. For each individual, one muscle was used to measure muscle contractile physiology, including contractile velocity (V_max and V₄₀), specific tension, power ratio, and twitch time, whereas the contralateral muscle was used to extract RNA for transcriptomic sequencing. Using the transcriptomic data, we found clear clustering of muscle type. Expression of genes clustered in gene ontology (GO) terms related to muscle contraction and extracellular matrix was, on average, negatively correlated with V_max and slower twitch times but positively correlated to power ratio and V₄₀. Conversely, genes related to the GO terms related to aerobic respiration were downregulated in muscles with higher power ratio and V₄₀, and over-expressed as twitch time decreased. Determining the molecular mechanisms that underlie variation in muscle contractile physiology can begin to explain how organisms are able to optimize behavior under variable conditions. Future studies pursuing the effects of differential gene expression across muscle types in different environments might inform researchers about how differences develop across species, populations, and individuals varying in ecological history.

Phylogenetic analysis of adaptation in comparative physiology and biomechanics: overview and a case study of thermal physiology in treefrogs

Comparative phylogenetic studies of adaptation are uncommon in biomechanics and physiology. Such studies require data collection from many species, a challenge when this is experimentally intensive. Moreover, researchers struggle to employ the most biologically appropriate phylogenetic tools for identifying adaptive evolution. Here, we detail an established but greatly underutilized phylogenetic comparative framework - the Ornstein-Uhlenbeck process - that explicitly models long-term adaptation. We discuss challenges in implementing and interpreting the model, and we outline potential solutions. We demonstrate use of the model through studying the evolution of thermal physiology in treefrogs. Frogs of the family Hylidae have twice colonized the temperate zone from the tropics, and such colonization likely involved a fundamental change in physiology due to colder and more seasonal temperatures. However, which traits changed to allow colonization is unclear. We measured cold tolerance and characterized thermal performance curves in jumping for 12 species of treefrogs distributed from the Neotropics to temperate North America. We then conducted phylogenetic comparative analyses to examine how tolerances and performance curves evolved and to test whether that evolution was adaptive. We found that tolerance to low temperatures increased with the transition to the temperate zone. In contrast, jumping well at colder temperatures was unrelated to biogeography and thus did not adapt during dispersal. Overall, our study shows how comparative phylogenetic methods can be leveraged in biomechanics and physiology to test the evolutionary drivers of variation among species.

Thermal Sensitivity of Heat Sensor TRPA1 Correlates With Temperatures Inducing Heat Avoidance Behavior in Terrestrial Ectotherms

Temperature is an essential environmental factor that controls an organism’s performances. As ectothermic animals largely rely on external heat sources for adjusting their body temperature, thermal perception is a primary process of behavioral thermoregulation. Transient receptor potential ankyrin 1 (TRPA1) is a heat sensitive ion channel in most non-mammalian species, and its heat activation has been suggested to induce heat avoidance behaviors in ectothermic animals. However, associations between TRPA1 and ecologically relevant temperatures have not been investigated, and the analyses including diverse taxa will provide robust support for understanding the associations. Here, I conducted extensive literature review, and assembled published data on thermal threshold of TRPA1 and three physiological parameters: the experimental voluntary maximum (EVM), which is body temperatures when heat avoidance behaviors are induced; the critical thermal maximum (CTmax), which is a point in temperature beyond which an organism becomes incapacitated; and average body temperature (Tmean) recorded in the field. Then, I examined the relationships between thermal threshold of TRPA1 and each of the three physiological parameters. As phylogenetically closely related species tend to show similar trait values among species, I conducted the regression analyses by accounting for phylogenetic distances among species. This study supports previous research by affirming that thermal threshold of TRPA1 is substantially correlated with body temperature that the animals escaped from the heat source, represented here as EVM. Nevertheless, thermal threshold of TRPA1 showed a statistically insignificant correlation with CTmax and Tmean. The results suggest that although thermal threshold of TRPA1 is evolutionarily labile, its associations with EVM is highly conserved among diverse terrestrial ectotherms. Therefore, thermal threshold of TRPA1 could be a useful parameter to evaluate species vulnerability to thermal stress particularly in the recent climate warming scenario.

Ecological Opportunity from Innovation, not Islands, Drove the Anole Lizard Adaptive Radiation

Islands are thought to facilitate adaptive radiation by providing release from competition and predation. Anole lizards are considered a classic example of this phenomenon: different ecological specialists ('ecomorphs') evolved in the Caribbean Greater Antilles (Cuba, Hispaniola, Jamaica, and Puerto Rico), resulting in convergent assemblages that are not observed in mainland Latin America. Yet, the role of islands in facilitating adaptive radiation is more often implied than directly tested, leaving uncertain the role of biogeography in stimulating diversification. Here, we assess the proposed "island effect" on anole diversification using Bayesian phylogenetic comparative methods that explicitly incorporate rate heterogeneity across the tree and demonstrate two cases of would-be false positives. We discovered that rates of speciation and morphological evolution of island and mainland anoles are equivalent, implying that islands provide no special context for exceptionally rapid diversification. Likewise, rates of evolution were equivalent between island anoles that arose via in situ versus dispersal-based mechanisms, and we found no evidence for island-specific rates of speciation or morphological evolution. Nonetheless, the origin of Anolis is characterized by a speciation pulse that slowed over time - a classic signature of waning ecological opportunity. Our findings cast doubt on the notion that islands catalyzed the anole adaptive radiation and instead point to a key innovation, adhesive toe pads, which facilitated the exploitation of many arboreal niches sparsely utilized by other iguanian lizards. The selective pressures responsible for arboreal niche diversification differ between islands and the mainland, but the tempo of diversification driven by these discordant processes is indistinguishable.

Ecological Memory of Historical Contamination Influences the Response of Phytoplankton Communities

Ecological memory (EM) recognizes the importance of previous stress encounters in promoting community tolerance and thereby enhances ecosystem stability, provided that gained tolerances are preserved during non-stress periods. Drawing from this concept, we hypothesized that the recruitment of tolerant species can be facilitated by imposing an initial sorting process (conditioning) during the early stages of community assembly, which should result in higher production (biomass development and photosynthetic efficiency) and stable community composition. To test this, phytoplankton resting stages were germinated from lake sediments originating from two catchments that differed in contamination history: one impacted by long-term herbicides and pesticides exposures (historically contaminated lake) from an agricultural catchment compared to a low-impacted one (near-pristine lake) from a forested catchment. Conditioning was achieved by adding an herbicide (Isoproturon, which was commonly used in the catchment of the historically contaminated lake) during germination. Afterward, the communities obtained from germination were exposed to an increasing gradient of Isoproturon. As hypothesized, upon conditioning, the phytoplankton assemblages from the historically contaminated lake were able to rapidly restore photosynthetic efficiency (p > 0.01) and became structurally (community composition) more resistant to Isoproturon. The communities of the near-pristine lake did not yield these positive effects regardless of conditioning, supporting that EM was a unique attribute of the historically stressed ecosystem. Moreover, assemblages that displayed higher structural resistance concurrently yielded lower biomass, indicating that benefits of EM in increasing structural stability may trade-off with production. Our results clearly indicate that EM can foster ecosystem stability to a recurring stressor.

The highest kingdom of Anolis: Thermal biology of the Andean lizard Anolis heterodermus (Squamata: Dactyloidae) over an elevational gradient in the Eastern Cordillera of Colombia

Vertebrate ectotherms may deal with changes of environmental temperatures by behavioral and/or physiological mechanisms. Reptiles inhabiting tropical highlands face extreme fluctuating daily temperatures, and extreme values and intervals of fluctuations vary with altitude. Anolis heterodermus occurs between 1800 m to 3750 m elevation in the tropical Andes, and is the Anolis species found at the highest altitude known. We evaluated which strategies populations from elevations of 2200 m, 2650 m and 3400 m use to cope with environmental temperatures. We measured body, preferred, critical maximum and minimum temperatures, and sprint speed at different body temperatures of individuals, as well as operative temperatures. Anolis heterodermus exhibits behavioral adjustments in response to changes in environmental temperatures across altitudes. Likewise, physiological traits exhibit intrapopulation variations, but they are similar among populations, tended to the "static" side of the evolution of thermal traits spectrum. The thermoregulatory behavioral strategy in this species is extremely plastic, and lizards adjust even to fluctuating environmental conditions from day to day. Unlike other Anolis species, at low thermal quality of the habitat, lizards are thermoconformers, particularly at the highest altitudes, where cloudy days can intensify this strategy even more. Our study reveals that the pattern of strategies for dealing with thermal ambient variations and their relation to extinction risks in the tropics that are caused by global warming is perhaps more complex for lizards than previously thought.

The need for speed: functional specializations of locomotor and feeding muscles in Anolis lizards

Muscles often perform diverse mechanical roles within an organism. Tuning of contractile properties may therefore provide an opportunity for muscles to better perform their different roles and impact their associated whole-organism performance. Here, we examined the muscle contractile physiology of a jaw and a leg muscle in five Anolis species to determine whether consistent physiological differences are found in these muscles. We found that these jaw and leg muscles exhibited consistent patterns of variation across species, which may be related to the functional use of each muscle. In particular, we found that each muscle had differentially increased different measures of muscle speed. Although the jaw muscles had faster peak contractile velocities than the leg muscles, the leg muscles had faster twitch times and faster contractile velocities under intermediate loads. We also found that the jaw muscles exerted higher specific tensions and had a greater curvature to their force-velocity relationship. The consistent patterns across five species suggest that these jaw and leg muscles have specialized in different ways. Examination of these contractile property variations may help illuminate important features relating to performing their individual functional roles.

Physiological evolution during adaptive radiation: A test of the island effect in Anolis lizards

Phenotypic evolution is often exceptionally rapid on islands, resulting in numerous, ecologically diverse species. Although adaptive radiation proceeds along various phenotypic axes, the island effect of faster evolution has been mostly tested with regard to morphology. Here, we leveraged the physiological diversity and species richness of Anolis lizards to examine the evolutionary dynamics of three key traits: heat tolerance, body temperature, and cold tolerance. Contrary to expectation, we discovered slower heat tolerance evolution on islands. Additionally, island species evolve toward higher optimal body temperatures than mainland species. Higher optima and slower evolution in upper physiological limits are consistent with the Bogert effect, or evolutionary inertia due to thermoregulation. Correspondingly, body temperature is higher and more stable on islands than on the American mainland, despite similarity in thermal environments. Greater thermoregulation on islands may occur due to ecological release from competitors and predators compared to mainland environments. By reducing the costs of thermoregulation, ecological opportunity on islands may actually stymie, rather than hasten, physiological evolution. Our results emphasize that physiological diversity is an important axis of ecological differentiation in the adaptive radiation of anoles, and that behavior can impart distinct macroevolutionary footprints on physiological diversity on islands and continents.

Combining molecular and landscape tools for targeting evolutionary processes in reserve design: An approach for islands

The importance of targeting ecological and evolutionary processes in reserve design has been widely acknowledged in the literature but rarely implemented on islands. Using Socotran reptiles as models, we aim to relate richness of widespread and restricted-range species directly with landscape variables and to compare the impact of setting conservation targets for lineages versus species. Socotra Island is a UNESCO Natural World Heritage Site, containing high levels of endemism in relation to its area, especially of reptiles, the vertebrates with the most comprehensive available genetic data. We predicted the occurrences of reptile species using distribution models and used a novel approach to interpolate maps of spatial phylogenetic patterns. Patterns of intra and interspecifc diversity and differences between spatial outputs of lineage and species richness were related to eco-geographic variables. We evaluated differences in target achievement for each conservation unit within protected areas (PAs) under the current Zoning Plan (ZP) using gap and reserve design analyses. Although intraspecific richness was strongly correlated with interspecific richness, differences in their spatial distribution reached ~30% in some areas. Differences were more pronounced for wide-ranging than restricted-range taxa. Gap analysis indicates that most conservation units are under-represented in sanctuaries and that intra and interspecific richness were significantly higher outside PAs. This work will guide local-scale conservation planning as the ZP is due to be re-evaluated. This is one of the few studies on islands using genetic data from an entire class of vertebrates to incorporate lineage diversity in reserve design. This study provides an alternative methodological framework for supporting the use of landscape and genetic tools in reserve design, circumventing the use of phylogenetic distances and deterministic spatial interpolation of lineage diversity that can be widely applied to other systems.

Thermal niche evolution across replicated Anolis lizard adaptive radiations

Elucidating how ecological and evolutionary mechanisms interact to produce and maintain biodiversity is a fundamental problem in evolutionary ecology. Here, we focus on how physiological evolution affects performance and species coexistence along the thermal niche axis in replicated radiations of Anolis lizards best known for resource partitioning based on morphological divergence. We find repeated divergence in thermal physiology within these radiations, and that this divergence significantly affects performance within natural thermal environments. Morphologically similar species that co-occur invariably differ in their thermal physiology, providing evidence that physiological divergence facilitates species coexistence within anole communities. Despite repeated divergence, phylogenetic comparative analyses indicate that physiological traits have evolved more slowly than key morphological traits related to the structural niche. Phylogenetic analyses also reveal that physiological divergence is correlated with divergence in broad-scale habitat climatic features commonly used to estimate thermal niche evolution, but that the latter incompletely predicts variation in the former. We provide comprehensive evidence for repeated adaptive evolution of physiological divergence within Anolis adaptive radiations, including the complementary roles of physiological and morphological divergence in promoting community-level diversity. We recommend greater integration of performance-based traits into analyses of climatic niche evolution, as they facilitate a more complete understanding of the phenotypic and ecological consequences of climatic divergence.

Thermoregulatory Behavior Simultaneously Promotes and Forestalls Evolution in a Tropical Lizard

The role of behavior in evolution has long been discussed, with some arguing that behavior promotes evolution by exposing organisms to selection (behavioral drive) and others proposing that it inhibits evolution by shielding organisms from environmental variation (behavioral inertia). However, this discussion has generally focused on the effects of behavior along a single axis without considering that behavior simultaneously influences selection in various niche dimensions. By examining evolutionary change along two distinct niche axes-structural and thermal-we propose that behavior simultaneously drives and impedes evolution in a group of Anolis lizards from the Caribbean island of Hispaniola. Specifically, a behavioral shift in microhabitat to boulders at high altitude enables thermoregulation, thus forestalling physiological evolution in spite of colder environments. This same behavioral shift drives skull and limb evolution to boulder use. Our results emphasize the multidimensional effects of behavior in evolution. These findings reveal how, rather than being diametrically opposed, niche conservatism and niche lability can occur simultaneously. Furthermore, patterns of niche evolution may vary at different geographic scales: because of thermoregulatory behavior, lizards at high and low elevation share similar microclimatic niches (consistent with niche conservatism) while inhabiting distinct macroclimatic environments (consistent with niche divergence). Together, our results suggest that behavior can connect patterns of niche divergence and conservatism at different geographic scales and among traits.

Thermal ecology of three coexistent desert lizards: Implications for habitat divergence and thermal vulnerability

How ectotherms exploit thermal resources has important implications for their habitat utilization and thermal vulnerability to climate warming. To address this issue, we investigated thermal relations of three sympatric lizard species (Eremias argus, Eremias multiocellata, and Phrynocephalus przewalskii) in the desert steppe of Inner Mongolia, China. We determined the thermoregulatory behavior, body temperature (T _b), operative temperature (T _e), selected body temperature (T _sel), and critical thermal maximum (CT_max) of adult lizards. Based on these physiological parameters, we quantified the accuracy and effectiveness of thermoregulation as well as thermal-safety margin for these species. The three species were accurate and effective thermoregulators. The P. przewalskii preferred open habitats, and had a higher T _b than the two Eremias lizards, which preferred shade habitats and shuttled more frequently between the shade and sun. This indicated that the three sympatric lizards have different thermoregulatory behavior and thermal physiology, which might facilitate their coexistence in the desert steppe ecosystem. In addition, the P. przewalskii had higher T _sel and CT_max, and a wider thermal-safety margin than the two Eremias lizards, suggesting that the two Eremias lizards would be more vulnerable to climate warming than P. przewalskii.

Immunocytological analysis of meiotic recombination in two anole lizards (Squamata, Dactyloidae)

Although the evolutionary importance of meiotic recombination is not disputed, the significance of interspecies differences in the recombination rates and recombination landscapes remains under-appreciated. Recombination rates and distribution of chiasmata have been examined cytologically in many mammalian species, whereas data on other vertebrates are scarce. Immunolocalization of the protein of the synaptonemal complex (SYCP3), centromere proteins and the mismatch-repair protein MLH1 was used, which is associated with the most common type of recombination nodules, to analyze the pattern of meiotic recombination in the male of two species of iguanian lizards, Anolis carolinensis Voigt, 1832 and Deiroptyx coelestinus (Cope, 1862). These species are separated by a relatively long evolutionary history although they retain the ancestral iguanian karyotype. In both species similar and extremely uneven distributions of MLH1 foci along the macrochromosome bivalents were detected: approximately 90% of crossovers were located at the distal 20% of the chromosome arm length. Almost total suppression of recombination in the intermediate and proximal regions of the chromosome arms contradicts the hypothesis that "homogenous recombination" is responsible for the low variation in GC content across the anole genome. It also leads to strong linkage disequilibrium between the genes located in these regions, which may benefit conservation of co-adaptive gene arrays responsible for the ecological adaptations of the anoles.

An ecophysiological background for biogeographic patterns of two island lizards?

Distributions of sedentary ectotherms are dependent on temperature and humidity due to their low homeostatic and dispersal abilities. Lizards are strongly conditioned by temperature, but hydric environment may be also important, at least in arid environments. Biotic interactions may also play a role in range patterns, but they are of minor importance in islands where native species monopolize well-delimited niche spaces. On the arid island of São Vicente (Cabo Verde), two endemic lizards display different spatial patterns. While the gecko Tarentola substituta is widely distributed across the island, the skink Chioninia stangeri is restricted to the NE, which is cooler, more humid, and vegetated. We hypothesized that this is due to differences in the fundamental niche, specifically in ecophysiology. We predict that C. stangeri should select for lower temperatures and lose more water by evaporation than T. substituta. We submitted adults of each species to standard experiments to assess preferred body temperatures (T_p) and evaporative water loss (EWL) rates, and examined the variation between species and through time using repeated-measures AN(C)OVAs. Results only partially supported our expectations. Contrary to the prediction, skinks attained higher Tp than geckos but in the long term showed a trend for higher EWL as predicted. Thus, while ecophysiology certainly contributes to functional interpretation of species distributions, it needs to be combined with other evidence such as habitat use and evolutionary history. These findings will be useful to perform mechanistic models to better understand the impact of climate change and habitat disturbance on these endemic species.

Do ectotherms partition thermal resources? We still do not know

Partitioning of the niche space is a mechanism used to explain the coexistence of similar species. Ectotherms have variable body temperatures and their body temperatures influence performance and, ultimately, fitness. Therefore, many ectotherms use behavioral thermoregulation to avoid reduced capacities associated with body temperatures far from the optimal temperature for performance. Several authors have proposed that thermal niche partitioning in response to interspecific competition is a mechanism that allows the coexistence of similar species of ectotherms. We reviewed studies on thermal resource partitioning to evaluate the evidence for this hypothesis. In almost all studies, there was insufficient evidence to conclude unequivocally that thermal resource partitioning allowed species coexistence. Future studies should include sites where species are sympatric and sites where they are allopatric to rule out alternative mechanisms that cause differences in thermal traits between coexisting species. There is evidence of conservatism in the evolution of most thermal traits across a wide range of taxa, but thermal performance curves and preferred temperatures do respond to strong selection under laboratory conditions. Thus, there is potential for selection to act on thermal traits in response to interspecific competition. Nevertheless, more stringent tests of the thermal resource partitioning hypothesis are required before we can assess whether it is widespread in communities of ectotherms in nature.

Habitat use in eight populations of Sceloporus grammicus (Squamata: Phrynosomatidae) from the Mexican Plateau

Studies on habitat use have often helped explain observed variation in morphology, behavior and reproductive characteristics among populations within a single species. Here we analyze morphological and ecological characteristics of individuals from the Sceloporus grammicus species complex from 7 different localities (CER, El Cerezo; PAC, Pachuca; HUI, Huichapan; EZA, Emiliano Zapata; SMR, San Miguel Regla; LMJ, La Mojonera; and LMZ, La Manzana) in the state of Hidalgo, and one locality (Cahuacán) in the State of Mexico. A canonical correspondence analysis (CCA) showed that females from PAC, EZA, LMZ, HUI, SMR and CAH populations use similar microhabitats characterized mostly by bare soil, in females from LMJ and CER use microhabitats characterized primarily by vegetation and rocks. Females were observed using 12 different types of perches. With regard to perch height use, the CCA showed that females from PAC, LMJ, LMZ, SMR, CER and CAH populations were correlated with height to nearest perch (HNP), in the rest of the females were not related to any perch use variable. In contrast, the CCA showed that males from PAC, LMJ and CAH were characterized by microhabitats with higher vegetal coverage, while males from LMZ and CER used microhabitats composed of bare soil, but males from HUI and SMR populations used microhabitats composed chiefly of bare soil and rocks. With respect to perch height use, the CCA showed that males from PAC, LMJ, EZA and LMZ were correlated with distance to the nearest perch, but the rest of the males were not correlated with any perch use variables. Males were observed in 9 different perch types. The males were larger than the females in all morphological variables analyzed. Moreover, in both sexes the snout-vent length is positively correlated with all morphological variables, and although both the slope and ordinate of the origin of all morphological variables were larger in males than females, the analysis of covariance indicated that there is no increase in the morphological variables with increasing SVL between sexes. Our results suggest that variation in habitat use and morphology among populations is an adaptive response (phenotypic plasticity) to the environmental conditions where these populations of Sceloporus grammicus occur.

Differentially expressed genes associated with adaptation to different thermal environments in three sympatric Cuban Anolis lizards

How animals achieve evolutionary adaptation to different thermal environments is an important issue for evolutionary biology as well as for biodiversity conservation in the context of recent global warming. In Cuba, three sympatric species of Anolis lizards (Anolis allogus, A. homolechis and A. sagrei) inhabit different thermal microhabitats, thereby providing an excellent opportunity to examine how they have adapted to different environmental temperatures. Here, we performed RNA-seq on the brain, liver and skin tissues from these three species to analyse their transcriptional responses at two different temperatures. In total, we identified 400, 816 and 781 differentially expressed genes (DEGs) between the two temperatures in A. allogus, A. homolechis and A. sagrei, respectively. Only 62 of these DEGs were shared across the three species, indicating that global transcriptional responses have diverged among these species. Gene ontology (GO) analysis showed that large numbers of ribosomal protein genes were DEGs in the warm-adapted A. homolechis, suggesting that the upregulation of protein synthesis is an important physiological mechanism in the adaptation of this species to hotter environments. GO analysis also showed that GO terms associated with circadian regulation were enriched in all three species. A gene associated with circadian regulation, Nr1d1, was detected as a DEG with opposite expression patterns between the cool-adapted A. allogus and the hot-adapted A. sagrei. Because the environmental temperature fluctuates more widely in open habitats than in forests throughout the day, the circadian thermoregulation could also be important for adaptation to distinct thermal habitats.

Decoupled evolution of floral traits and climatic preferences in a clade of Neotropical Gesneriaceae

Background

Major factors influencing the phenotypic diversity of a lineage can be recognized by characterizing the extent and mode of trait evolution between related species. Here, we compared the evolutionary dynamics of traits associated with floral morphology and climatic preferences in a clade composed of the genera Codonanthopsis, Codonanthe and Nematanthus (Gesneriaceae). To test the mode and specific components that lead to phenotypic diversity in this group, we performed a Bayesian phylogenetic analysis of combined nuclear and plastid DNA sequences and modeled the evolution of quantitative traits related to flower shape and size and to climatic preferences. We propose an alternative approach to display graphically the complex dynamics of trait evolution along a phylogenetic tree using a wide range of evolutionary scenarios.

Results

Our results demonstrated heterogeneous trait evolution. Floral shapes displaced into separate regimes selected by the different pollinator types (hummingbirds versus insects), while floral size underwent a clade-specific evolution. Rates of evolution were higher for the clade that is hummingbird pollinated and experienced flower resupination, compared with species pollinated by bees, suggesting a relevant role of plant-pollinator interactions in lowland rainforest. The evolution of temperature preferences is best explained by a model with distinct selective regimes between the Brazilian Atlantic Forest and the other biomes, whereas differentiation along the precipitation axis was characterized by higher rates, compared with temperature, and no regime or clade-specific patterns.

Conclusions

Our study shows different selective regimes and clade-specific patterns in the evolution of morphological and climatic components during the diversification of Neotropical species. Our new graphical visualization tool allows the representation of trait trajectories under parameter-rich models, thus contributing to a better understanding of complex evolutionary dynamics.

Electronic supplementary material

The online version of this article (doi:10.1186/s12862-015-0527-6) contains supplementary material, which is available to authorized users.

Thermal niche predicts tolerance to habitat conversion in tropical amphibians and reptiles

Habitat conversion is a major driver of the biodiversity crisis, yet why some species undergo local extinction while others thrive under novel conditions remains unclear. We suggest that focusing on species' niches, rather than traits, may provide the predictive power needed to forecast biodiversity change. We first examine two Neotropical frog congeners with drastically different affinities to deforestation and document how thermal niche explains deforestation tolerance. The more deforestation-tolerant species is associated with warmer macroclimates across Costa Rica, and warmer microclimates within landscapes. Further, in laboratory experiments, the more deforestation-tolerant species has critical thermal limits, and a jumping performance optimum, shifted ~2 °C warmer than those of the more forest-affiliated species, corresponding to the ~3 °C difference in daytime maximum temperature that these species experience between habitats. Crucially, neither species strictly specializes on either habitat - instead habitat use is governed by regional environmental temperature. Both species track temperature along an elevational gradient, and shift their habitat use from cooler forest at lower elevations to warmer deforested pastures upslope. To generalize these conclusions, we expand our analysis to the entire mid-elevational herpetological community of southern Costa Rica. We assess the climatological affinities of 33 amphibian and reptile species, showing that across both taxonomic classes, thermal niche predicts presence in deforested habitat as well as or better than many commonly used traits. These data suggest that warm-adapted species carry a significant survival advantage amidst the synergistic impacts of land-use conversion and climate change.

Common Ancestry Is a Poor Predictor of Competitive Traits in Freshwater Green Algae

Phytoplankton species traits have been used to successfully predict the outcome of competition, but these traits are notoriously laborious to measure. If these traits display a phylogenetic signal, phylogenetic distance (PD) can be used as a proxy for trait variation. We provide the first investigation of the degree of phylogenetic signal in traits related to competition in freshwater green phytoplankton. We measured 17 traits related to competition and tested whether they displayed a phylogenetic signal across a molecular phylogeny of 59 species of green algae. We also assessed the fit of five models of trait evolution to trait variation across the phylogeny. There was no significant phylogenetic signal for 13 out of 17 ecological traits. For 7 traits, a non-phylogenetic model provided the best fit. For another 7 traits, a phylogenetic model was selected, but parameter values indicated that trait variation evolved recently, diminishing the importance of common ancestry. This study suggests that traits related to competition in freshwater green algae are not generally well-predicted by patterns of common ancestry. We discuss the mechanisms by which the link between phylogenetic distance and phenotypic differentiation may be broken.

Amber fossils demonstrate deep-time stability of Caribbean lizard communities

Whether the structure of ecological communities can exhibit stability over macroevolutionary timescales has long been debated. The similarity of independently evolved Anolis lizard communities on environmentally similar Greater Antillean islands supports the notion that community evolution is deterministic. However, a dearth of Caribbean Anolis fossils--only three have been described to date--has precluded direct investigation of the stability of anole communities through time. Here we report on an additional 17 fossil anoles in Dominican amber dating to 15-20 My before the present. Using data collected primarily by X-ray microcomputed tomography (X-ray micro-CT), we demonstrate that the main elements of Hispaniolan anole ecomorphological diversity were in place in the Miocene. Phylogenetic analysis yields results consistent with the hypothesis that the ecomorphs that evolved in the Miocene are members of the same ecomorph clades extant today. The primary axes of ecomorphological diversity in the Hispaniolan anole fauna appear to have changed little between the Miocene and the present, providing evidence for the stability of ecological communities over macroevolutionary timescales.

Ecophysiology Tracks Phylogeny and Meets Ecological Models in an Iberian Gecko

Because fitness of ectotherms, including reptiles, is highly dependent on temperature and water availability, the study of ecophysiological traits, such as preferred temperature (T p) and water loss rates (WLRs), may provide mechanistic evidence on the restricting factors to the species ranges. The Moorish gecko, Tarentola mauritanica, is a species complex with a circum-Mediterranean distribution. In the Iberian Peninsula, two sister parapatric forms of the complex, known as the Iberian and the European clades, are found. Ecological models previously performed using presence records and bioclimatic variables suggest niche divergence between both lineages correlated with precipitation rather than with temperature. In this study, we test this correlative hypothesis using ecophysiological evidence. In the laboratory, we analyzed the T p and WLRs for 84 adult males from seven distinct populations ascribed to one of the two lineages present in Iberia. Specifically, we evaluated the existence of trait conservatism versus adaptation among populations, lineages, or both. In addition, we tested for a trade-off between water and thermal traits and assessed whether climate regime of sampling localities had any influence on the ecophysiological patterns found. We found that T p is quite conserved at both the population and lineage levels and independent from body size. In contrast, water loss experiments revealed some variation among populations, but the regression analysis failed to detect correlation between T p and WLR at any level. Overall, the European lineage displayed a trend for higher water loss and was more diverse among populations when compared with the Iberian lineage. The lack of correspondence between ecophysiological traits and local climatic conditions favors phylogenetic signal versus adaptation. This suggests divergent evolutionary responses to the environment, mainly acting on water ecology, in both lineages, which may account for the differences in their range expansion.

Developmental stages for the divergence of relative limb length between a twig and a trunk-ground Anolis lizard species

The divergent evolution of niche-related traits can facilitate adaptive radiation, yet identification of the genetic or molecular mechanisms underlying such trait changes remains a major challenge in evolutionary biology. Conducting a detailed morphological comparison along growth trajectories is a powerful method for observing the formation of differences in niche-related traits. Here, we focused on hindlimb length of Anolis lizards, differences in which are related to adaptation for use of different microhabitats. We measured the length of hindlimb skeletons in different ecomorphs of anole lizards (A. sagrei, a trunk-ground ecomorph with long hindlimbs, and A. angusticeps, a twig ecomorph with short hindlimbs) from early embryonic stages to adulthood, to determine which hindlimb elements mainly differentiate the species and the timing of the formation of these differences. With respect to the digit, differences between the species mainly occurred during the embryonic stages of interdigit reduction, when the cartilage of the distal phalanges was simultaneously forming. In addition, we compared the relative length of developing autopods in early embryonic stages using whole-mount in situ hybridization before the formation of the cartilaginous bones, and the results showed that the relative growth rate of the Hoxa11-negative distal region in A. sagrei was greater than that in A. angusticeps. Our results show that there are several important developmental stages for hindlimb length differentiation between A. angusticeps and A. sagrei, depending on which hindlimb element is considered. In particular, the species differences were largely due to variations in digit length, which arose at early embryonic stages.

Untangling intra- and interspecific effects on body size clines reveals divergent processes structuring convergent patterns in Anolis lizards

Bergmann's rule-the tendency for body size to increase in colder environments-remains controversial today, despite 150 years of research. Considerable debate has revolved around whether the rule applies within or among species. However, this debate has generally not considered that clade-level relationships are caused by both intra- and interspecific effects. In this article, we implement a novel approach that allows for the separation of intra- and interspecific components of trait-environment relationships. We apply this approach to body size clines in two Caribbean clades of Anolis lizards and discover that their similar body size gradients are constructed in very different ways. We find inverse Bergmann's clines-high-elevation lizards are smaller bodied-for both the cybotes clade on Hispaniola and the sagrei clade on Cuba. However, on Hispaniola, the inverse cline is driven by interspecific differences, whereas intraspecific variation is responsible for the inverse cline on Cuba. Our results suggest that similar body size clines can be constructed through differing evolutionary and ecological processes, namely, through local adaptation or phenotypic plasticity (intraspecific clines) and/or size-ordered spatial sorting (interspecific clines). We propose that our approach can help integrate a divided research program by focusing on how the combined effects of intra- and interspecific processes can enhance or erode clade-level relationships at large biogeographic scales.

Evolutionary stasis and lability in thermal physiology in a group of tropical lizards

Understanding how quickly physiological traits evolve is a topic of great interest, particularly in the context of how organisms can adapt in response to climate warming. Adjustment to novel thermal habitats may occur either through behavioural adjustments, physiological adaptation or both. Here, we test whether rates of evolution differ among physiological traits in the cybotoids, a clade of tropical Anolis lizards distributed in markedly different thermal environments on the Caribbean island of Hispaniola. We find that cold tolerance evolves considerably faster than heat tolerance, a difference that results because behavioural thermoregulation more effectively shields these organisms from selection on upper than lower temperature tolerances. Specifically, because lizards in very different environments behaviourally thermoregulate during the day to similar body temperatures, divergent selection on body temperature and heat tolerance is precluded, whereas night-time temperatures can only be partially buffered by behaviour, thereby exposing organisms to selection on cold tolerance. We discuss how exposure to selection on physiology influences divergence among tropical organisms and its implications for adaptive evolutionary response to climate warming.