Genomic and phenotypic signatures of climate adaptation in an Anolis lizard

Integrated knowledge on phenotype, physiology, and genomic adaptations is required to understand the effects of climate on evolution. The functional genomic basis of organismal adaptation to changes in the abiotic environment, its phenotypic consequences, and its possible convergence across vertebrates are still understudied. In this study, we use a comparative approach to verify predicted gene functions for vertebrate thermal adaptation with observed functions underlying repeated genomic adaptations in response to elevation in the lizard Anolis cybotes. We establish a direct link between recurrently evolved phenotypes and functional genomics of altitude‐related climate adaptation in three highland and lowland populations in the Dominican Republic. We show that across vertebrates, genes contained in this interactome are expressed within the brain, the endocrine system, and during development. These results are relevant to elucidate the effect of global climate change across vertebrates and might aid in furthering insight into gene–environment relationships under disturbances to homeostasis.     

Unique evolutionary trajectories in repeated adaptation to hydrogen sulphide‐toxic habitats of a neotropical fish (Poecilia mexicana)

Replicated ecological gradients are prime systems to study processes of molecular evolution underlying ecological divergence. Here, we investigated the repeated adaptation of the neotropical fish Poecilia mexicana to habitats containing toxic hydrogen sulphide (H₂S) and compared two population pairs of sulphide‐adapted and ancestral fish by sequencing population pools of >200 individuals (Pool‐Seq). We inferred the evolutionary processes shaping divergence and tested the hypothesis of increase of parallelism from SNPs to molecular pathways. Coalescence analyses showed that the divergence occurred in the face of substantial bidirectional gene flow. Population divergence involved many short, widely dispersed regions across the genome. Analyses of allele frequency spectra suggest that differentiation at most loci was driven by divergent selection, followed by a selection‐mediated reduction of gene flow. Reconstructing allelic state changes suggested that selection acted mainly upon de novo mutations in the sulphide‐adapted populations. Using a corrected Jaccard index to quantify parallel evolution, we found a negligible proportion of statistically significant parallel evolution of J_corr = 0.0032 at the level of SNPs, divergent genome regions (J_corr = 0.0061) and genes therein (J_corr = 0.0091). At the level of metabolic pathways, the overlap was J_corr = 0.2545, indicating increasing parallelism with increasing level of biological integration. The majority of pathways contained positively selected genes in both sulphide populations. Hence, adaptation to sulphidic habitats necessitated adjustments throughout the genome. The largely unique evolutionary trajectories may be explained by a high proportion of de novo mutations driving the divergence. Our findings favour Gould's view that evolution is often the unrepeatable result of stochastic events with highly contingent effects.     

Control of the pars intermedia of the lizard,Anolis carolinensis

Summary The capacity of colour change in intact lizards and in animals with a transected hypophysial stalk was studied during extended periods. It was concluded that, with certain exceptions, the skin colour of the lizards gives information on the circulating levels of MSH, and thereby on the function of the pars intermedia.After transection of the hypophysial stalk, three phases of chromatic behaviour were recognised. During Phase I, which lasted for about 6 days (average), dark skin was retained irrespective of the colour of the background (= high MSH levels), whereas Phase II (19 days) was characterised by the inability of the animals to become brown (= low MSH levels). A gradual recovery toward normal adaptive capacity was seen during Phase III.In the disconnected neuro-intermediate lobe, aldehyde fuchsin (AF)-positive material in the rostral region rapidly clumped and disappeared within a few days. In the caudal portion, the stainability and the varicose arrangement of fibres were retained longer, but disappeared within approximately 14 days after the operation. Proximal to the lesion, the preoptic system exhibited a marked increase in stainability with AF, starting in the median eminence and progressing in a retrograde direction toward the peptidergic nuclei.Revascularisation of the disconnected neuro-intermediate lobe occurred during the first few days. A reinnervation of AF-fibres across the transected area into the neural lobe was observed during Phase III in most animals, but AF-fibres did not reoccupy the entire lobe. In association with an outgrowth of capillaries, the regenerating fibres formed new neural lobules. This regenerative process was accompanied by an increase in blood supply from the primary plexus of the median eminence to the neuro-intermediate lobe.Supported by grants from the Swedish Natural Science Research Council and the Royal Physiographic Society of LundThe authors are indebted to Mrs. Ingrid Hallberg and Mrs. Kirsten Thörneby for valuable technical assistance and skillful attention to the animals and to Miss Inger Norling for photographic aid     

The fine structure of early tooth formation in an lguanid lizard,Anolis carolinensis

Cytodifferentiation and hard tissue formation were studied in Anolis to collect information regarding the phylogenetic history of enamel and the functional significance of the events seen in the mammalian tooth during differentiation. The differentiation of the ameloblasts of Anolis, like that of mammals, shows two phases: In the early phase, the cells are short and rich in free ribosomes, in the late phase the cells elongate, develop an extensive rough endoplasmic reticulum, and the Golgi apparatus moves into that part of the cell next to the basal lamina (the cell apex). The early epithelial-mesenchymal interface resembles that of mammals, suggesting that early mechanisms of induction and epithelial-mesenchymal interaction are similar in Anolis and in mammals. Preameloblast processes and preameloblast-preodontoblast contacts in Anolis are rudimentary compared to those of mammals. While in mammals the preameloblast processes shape the future DEJ (dentin-enamel junction), their involvement in establishing the shape of the DEJ of Anolis is questionable. We suggest that the great development of preameloblast-preodontoblast contacts in mammals may simply increase the efficiency of inductive interactions between these cell types.     

Control of the pars intermedia of the lizard,Anolis carolinensis

Summary Morphological changes in the disconnected neuro-intermediate lobe were studied in the lizard, Anolis carolinensis from the 2nd to the 14th post-operative day using a threefold aldehyde fixative (Rodríguez, 1969). Two phases of colour change capacity were exhibited: Phase I started immediately after the transection, lasted for 6 days (mean) and was characterised by an excessive MSH release (brown skin). This phase proceeded gradually into Phase II, designated by an interruption of the MSH release (green skin).The degenerative processes and final elimination of neurons in the disconnected neural lobe propagate in a rostro-caudal direction from the transected area. The aminergic fibres (Type II) disappear within 2 days postoperatively, whereas the degeneration continues for more than 10 days in the peptidergic fibres (Type III, IV and V). The glia cells (ependyma and pituicytes) serve as very active macrophages, engulfing fragments of axons already affected by autolysis and transferring them into glial lysosomes. No apparent morphological changes occur in the shift from Phase I to II.The great majority of the secretory cells of the intermediate lobe are not affected by degenerative processes and appear to be markedly activated by the stalk transection. They exhibit numerous mitochondria, well-developed Golgi complexes forming numerous Golgi vesicles and extensive parallel cisternae of the rough endoplasmic reticulum, sometimes forming large intracisternal droplets (7 m in diameter). Numerous pale vacuoles are seen, especially toward the intact capillaries, suggesting their coupling to the MSH release by extension of the active membrane area toward the perivascular septum. The number of these vacuoles is very markedly reduced in Phase II (no release), whereas the formation of new granules seems to proceed in early stages. The interruption of the MSH release implies a successive refilling of gradually growing secretory granules and a concomitant reduction in the development of the synthetic apparatus. Mechanisms probably involved in the control of the synthesis and release of MSH are discussed.Supported by grants from the Swedish Natural Science Research Council (to P. Meurling) and the Royal Physiographic Society of LundThe authors are indebted to Mrs. Lena Sandell, Mrs. Ingrid Hallberg and Mrs. Kirsten Thörneby for technical assistance and skillful attention of the animals and to Miss Inger Norling for photographic aid.     

Control of the pars intermedia of the lizard,Anolis carolinensis

Summary The ultrastructure of the intermediate lobe of the hypophysis was studied in Anolis carolinensis with the use of a threefold aldehyde fixative. Lizards with a brown skin were selected. The possibility of two types of secretory cells is discussed; neither cell type is innervated. Type I cells are rarely found and contain dense granules approximately 0.3 m in diameter; Type II cells vary widely in secretory activity. Most of the Type II cells contain a large number of dense secretory granules (up to about 1.3 m in diameter) almost filling the cytoplasm. Rough endoplasmic reticulum (RER), Golgi apparatus and mitochondria are poorly developed. Only some of these cells show signs suggesting a high secretory activity, namely a well developed RER, Golgi apparatus and numerous mitochondria. In these cells the RER sometimes forms large intracisternal droplets (up to 7 m in diameter). Two of the animals exhibited a more uniform, high secretory activity. Large (about 2 m in diameter), pale vacuoles, probably of extracellular character, were found mostly in the vicinity of the perivascular septum. Their role in the release of MSH is discussed. The present data, which are discussed with reference to earlier findings (Forbes, 1972), form the morphological basis for an experimental study on regulation of MSH release (Larsson et al., 1979).Supported by grants from the Swedish Natural Science Research Council (to P. Meurling) and the Royal Physiographic Society of LundThe authors are indebted to Mrs. Ingrid Hallberg, Mrs. Kirsten Thörneby and Mrs. Lena Sandell for valuable technical assistance and to Miss Inger Norling for photographic aid     

Control of the pars intermedia of the lizard,Anolis carolinensis

Summary The distribution of the tracer substance horseradish peroxidase (HRP, Mw 40,000) in the neuro-intermediate lobe of the lizard, Anolis carolinensis, was studied at various time intervals (13 min to 24 h) after vascular injection. HRP rapidly entered the extracellular lumen of the neural lobe, but did not penetrate into the third ventricle. The tracer was found in micropinocytotic vesicles (MPVs) of ependymal cells within 13 min after injection. The number of cellular inclusions containing HRP increased during the period of observation (24 h). The tracer was sparsely taken up by aminergic and peptidergic nerve terminals of the external layer. After transection of the hypophysial stalk, numerous dense, labelled droplets were found in the peptidergic terminals, and the number of labelled inclusions in ependymal cells increased.MPVs were frequently found in extensions of stellate cells of the intermediate lobe, and endocytotic vacuoles (EVs) developed especially in the perikaryon. HRP was also found in large cisternae of the secretory cells, appearing predominantly towards the perivascular septum (PVS). These cisternae were found to communicate with the extracellular lumen, probably representing a system of the extracellular space extending into the secretory cell. After transection of the hypophysial stalk, there was an increase in the number of small EVs in secretory cells of the intermediate lobe.The results are discussed in terms of MSH-release regulation and possible participation of the extracellular lumen, glial and stellate cells in the transport of regulating factors and secretory material.Supported by grants from the Swedish Natural Science Research Council (to Dr. Patrick Meurling) and the Royal Physiographic Society of LundThe author is indebted to Mrs. Lena Sandell and Miss Inger Norling for excellent technical assistance and photographic aid; and to Dr. Rolf Libelius and Dr. Ingmar Lundquist for generous advice and stimulating discussions concerning the tracer technique     

Control of the pars intermedia of the lizard,Anolis carolinensis

Summary The ultrastructure of the neural lobe of the lizard, Anolis carolinensis, was studied after fixation in a threefold aldehyde solution. The neural lobe appeared as narrow vertical diverticula separated from one another and from the pars intermedia by a continuous vascular septum. No nerves passed through this septum. The ependymal, fibrous and external layers were readily recognized. Peptidergic fibres were the main component of the fibrous layer. The peptidergic endings were in intimate contact with the ependymal cells, suggesting that the ependyma mediates the release of neural lobe peptides. The external layer contained ependymal end-feet and numerous aminergic terminals, ending directly on the perivascular basal lamina and/or on the ependymal end-feet. The functional aspects are discussed in terms of intermediate lobe control. The findings suggest that aminergic substances take part in the control of the intermedia, but do not exclude the involvement of peptide hormones.Supported by grants from the Swedish Natural Science Research Council and the Royal Physiographic Society of LundThe authors are indebted to Mrs. Lena Sandell for valuable technical assistance and to Miss Inger Norling and the late Mr. Lajos Erdös for photographic aid     

Notes from a snail island: Littorinid evolution and adaptation

The most successful study systems are built on a foundation of decades of research on the basic biology, ecology and life history of the organisms in question. Combined with new technologies, this can provide a formidable means to address important issues in evolutionary biology and molecular ecology. Littorinid marine snails are a good example of this, with a rich literature on their taxonomy, speciation, thermal tolerance and behavioural adaptations. In August 2017, an international meeting on Littorinid evolution was held at the Tjärnö Marine Research Laboratory in Western Sweden. In this meeting review, I provide a summary of some of the exciting work on parallel evolution, sexual selection and adaptation to environmental stress presented there. I argue that newly available genomic resources present an opportunity for integrating the traditionally divergent fields of speciation and environmental adaptation in Littorinid research.     

The genetic basis of evolution, adaptation and speciation

A primary question in biology concerns the genetic basis of the evolution of novel traits, often in response to environmental changes, and how this can subsequently cause species isolation. This topic was the focus of the symposium on the Genetics of Speciation and Evolution at the annual meeting of the Canadian Society for Ecology and Evolution, held in Banff in May 2011. The presentations revealed some of the rapid advances being made in understanding the genetic basis of adaptation and speciation, as well as the elegant interplay between an organism's genetic complement and the environment that organism experiences.     

Genome‐wide epigenetic isolation by environment in a widespread Anolis lizard

Epigenetic changes can provide a pathway for organisms to respond to local environmental conditions by influencing gene expression. However, we still know little about the spatial distribution of epigenetic variation in natural systems, how it relates to the distribution of genetic variation and the environmental structure of the landscape, and the processes that generate and maintain it. Studies examining spatial patterns of genetic and epigenetic variation can provide valuable insights into how ecological and population processes contribute to epigenetic divergence across heterogeneous landscapes. Here, we perform a comparative analysis of spatial genetic and epigenetic variation based on 8,459 single nucleotide polymorphisms (SNPs) and 8,580 single methylation variants (SMVs) from eight populations of the Puerto Rican crested anole, Anolis cristatellus, an abundant lizard in the adaptive radiations of anoles on the Greater Antilles that occupies a diverse range of habitats. Using generalized dissimilarity modelling and multiple matrix regression, we found that genome‐wide epigenetic differentiation is strongly correlated with environmental divergence, even after controlling for the underlying genetic structure. We also detected significant associations between key environmental variables and 96 SMVs, including 42 located in promoter regions or gene bodies. Our results suggest an environmental basis for population‐level epigenetic differentiation in this system and contribute to better understanding how environmental gradients structure epigenetic variation in nature.     

Evolutionary assembly of island faunas reverses the classic island–mainland richness difference in Anolis lizards

Aim Islands are widely considered to be species depauperate relative to mainlands but, somewhat paradoxically, are also host to many striking adaptive radiations. Here, focusing on Anolis lizards, we investigate if cladogenetic processes can reconcile these observations by determining if in situ speciation can reduce, or even reverse, the classical island–mainland richness discrepancy. Location Caribbean islands and the Neotropical mainland. Methods We constructed range maps for 203 mainland anoles from museum records and evaluated whether geographical area could account for differences in species richness between island and mainland anole faunas. We compared the island species–area relationship with total mainland anole diversity and with the richness of island‐sized mainland areas. We evaluated the role of climate in the observed differences by using Bayesian model averaging to predict island richness based on the mainland climate–richness relationship. Lastly, we used a published phylogeny and stochastic mapping of ancestral states to determine if speciation rate was greater on islands, after accounting for differences in geographical area. Results Islands dominated by in situ speciation had, on average, significantly more species than similarly sized mainland regions, but islands where in situ speciation has not occurred were species depauperate relative to mainland areas. Results were similar at the scale of the entire mainland, although marginally non‐significant. These findings held even after accounting for climate. Speciation has not been faster on islands; instead, when extinction was assumed to be low, speciation rate varied consistently with geographical area. When extinction was high, there was some evidence that mainland speciation was faster than expected based on area. Main conclusions Our results indicate that evolutionary assembly of island faunas can reverse the general pattern of reduced species richness on islands relative to mainlands.     

STRONG SELECTION GENOME‐WIDE ENHANCES FITNESS TRADE‐OFFS ACROSS ENVIRONMENTS AND EPISODES OF SELECTION

Fitness trade‐offs across episodes of selection and environments influence life‐history evolution and adaptive population divergence. Documenting these trade‐offs remains challenging as selection can vary in magnitude and direction through time and space. Here, we evaluate fitness trade‐offs at the levels of the whole organism and the quantitative trait locus (QTL) in a multiyear field study of Boechera stricta (Brassicaceae), a genetically tractable mustard native to the Rocky Mountains. Reciprocal local adaptation was pronounced for viability, but not for reproductive components of fitness. Instead, local genomes had a fecundity advantage only in the high latitude garden. By estimating realized selection coefficients from individual‐level data on viability and reproductive success and permuting the data to infer significance, we examined the genetic basis of fitness trade‐offs. This analytical approach (Conditional Neutrality‐Antagonistic Pleiotropy, CNAP) identified genetic trade‐offs at a flowering phenology QTL (costs of adaptation) and revealed genetic trade‐offs across fitness components (costs of reproduction). These patterns would not have emerged from traditional ANOVA‐based QTL mapping. Our analytical framework can be applied to other systems to investigate fitness trade‐offs. This task is becoming increasingly important as climate change may alter fitness landscapes, potentially disrupting fitness trade‐offs that took many generations to evolve.     

Fine‐scale temporal adaptation within a salmonid population: mechanism and consequences

We demonstrate a clear example of local adaptation of seasonal timing of spawning and embryo development. The consequence is a population of pink salmon that is segmented into spawning groups that use the same limited habitat. We synthesize published observations with results of new analyses to demonstrate that genetic variation of these traits results in survival differentials related to that variation, and that density‐dependent embryo mortality and seasonally variable juvenile mortality are a mechanism of selection. Most examples of local adaptation in natural systems depend on observed correlations between environments and fitness traits, but do not fully demonstrate local adaptation: that the trait is genetically determined, exhibits different fitness in common environments or across different environments, and its variation is mechanistically connected to fitness differences. The geographic or temporal scales of local adaptation often remain obscure. Here, we show that heritable, fine‐scale differences of timing of reproductive migration in a pink salmon (Oncorhynchus gorbuscha) resulted in temporal structure that persisted several generations; the differences enable a density‐dependent population to pack more spawners into limited spawning habitat, that is, enhance its fitness. A balanced trade‐off of survivals results because embryos from early‐migrating fish have a lower freshwater survival (harsh early physical conditions and disturbance by late spawners), but emigrant fry from late‐migrating fish have lower marine survivals (timing of their vernal emergence into the estuarine environment). Such fine‐scale local adaptations increase the genetic portfolio of the populations and may provide a buffer against the impacts of climate change.     

Immunocytochemical localization of cysteine‐rich beta‐proteins in the extensible epidermis of the dewlap in the lizard Anolis carolinensis

The dewlap in the lizard Anolis carolinensis is made of scales separated by large interscale regions capable of broad stretching during fan extension. This indicates that the skin contains proteins that allow extension of interscale regions. The immunocytochemical analysis of the epidermis indicates that HgG5, a glycine‐rich hydrophobic beta‐protein poor in cysteine is localized only in the stiff beta‐layer of the outer scale surface, but is completely absent in mesos and alpha‐layers and in hinge regions. HgGC10, a cysteine‐medium‐rich beta‐protein is present in beta‐layers but especially in alpha‐layers of interscale epidermis that presents folds and lacks a beta‐layer. HgGC3 is weakly localized in the alpha‐layer, but is mainly found in hinge regions. HgGC8 and HgG13 are low to absent in the alpha‐ and beta‐layer. The immunolocalization of cysteine‐rich beta‐proteins such as HgGC10/3 in alpha‐layers and interscale epidermis suggests that these small proteins are involved in the formation of a corneous material compatible with dewlap extension. The basement membrane underneath scales is joined to bundles of collagen fibrils in the dermis through anchoring fibrils that likely determine flattening of the epidermis during the extension of the throat fan.     

The Park Grass Experiment and next‐generation approaches: local adaptation of sweet vernal grass revisited

Long‐term ecological experiments provide unique opportunities to observe the effects of natural selection. The Park Grass Experiment at Rothamsted Experiment Station in Hertfordshire, UK, is the longest running ecological experiment that incorporates fertilization treatments and has been ongoing since 1856. In the 1970s, local adaptation was observed in the grass Anthoxanthum odoratum to the elevated soil aluminium levels of the fertilized plots. Gould et al. ( 2014 ) have utilized this system to reevaluate the extent of local adaptation, first documented nearly 45 years ago (Snaydon 1970 ), and to use emerging molecular approaches to identify candidate genes for the adaptation. From their work, they identify several plausible candidate loci for aluminium tolerance. This work shows the power of long‐term field‐based trials in a scientific age concentrated on rapidly emerging molecular techniques often utilized in short, narrowly focused laboratory or controlled environment experiments. The current study clearly illustrates the benefits gained by combining these molecular approaches within long‐term monitoring experiments that can be regularly revisited in a changing world and used to address questions on evolutionary scales.     

Evaluation of genetic isolation within an island flora reveals unusually widespread local adaptation and supports sympatric speciation

It is now recognized that speciation can proceed even when divergent natural selection is opposed by gene flow. Understanding the extent to which environmental gradients and geographical distance can limit gene flow within species can shed light on the relative roles of selection and dispersal limitation during the early stages of population divergence and speciation. On the remote Lord Howe Island (Australia), ecological speciation with gene flow is thought to have taken place in several plant genera. The aim of this study was to establish the contributions of isolation by environment (IBE) and isolation by community (IBC) to the genetic structure of 19 plant species, from a number of distantly related families, which have been subjected to similar environmental pressures over comparable time scales. We applied an individual-based, multivariate, model averaging approach to quantify IBE and IBC, while controlling for isolation by distance (IBD). Our analyses demonstrated that all species experienced some degree of ecologically driven isolation, whereas only 12 of 19 species were subjected to IBD. The prevalence of IBE within these plant species indicates that divergent selection in plants frequently produces local adaptation and supports hypotheses that ecological divergence can drive speciation in sympatry.     

The role of genetic structure in the adaptive divergence of populations experiencing saltwater intrusion due to relative sea‐level rise

Saltwater intrusion into estuaries creates stressful conditions for nektonic species. Previous studies have shown that Gambusia affinis populations with exposure to saline environments develop genetic adaptations for increased survival during salinity stress. Here, we evaluate the genetic structure of G. affinis populations, previously shown to have adaptations for increased salinity tolerance, and determine the impact of selection and gene flow on structure of these populations. We found that gene flow was higher between populations experiencing different salinity regimes within an estuary than between similar marsh types in different estuaries, suggesting the development of saline‐tolerant phenotypes due to local adaptation. There was limited evidence of genetic structure along a salinity gradient, and only some of the genetic variation among sites was correlated with salinity. Our results suggest limited structure, combined with selection to saltwater intrusion, results in phenotypic divergence in spite of a lack of physical barriers to gene flow.     

Climatic stability and genetic divergence in the tropical insular lizard Anolis krugi,the Puerto Rican ‘Lagartijo Jardinero de la Montaña’

Two factors that can lead to geographic structuring in conspecific populations are barriers to dispersal and climatic stability. Populations that occur in different physiographic regions may be restricted to those areas by physical and/or ecological barriers, which may facilitate the formation of phylogeographic clades. Long‐term climatic stability can also promote genetic diversification, because new clades are more likely to evolve in areas that experience lesser climatic shifts. We conducted a phylogeographic study of the Puerto Rican lizard Anolis krugi to assess whether populations of this anole show genetic discontinuities across the species’ range, and if they do, whether these breaks coincide with the boundaries of the five physiographic regions of Puerto Rico. We also assessed whether interpopulation genetic distances in A. krugi are positively correlated with relative climatic stability in the island. Anolis krugi exhibits genetic structuring, but the phylogroups do not correspond to the physiographic regions of Puerto Rico. We used climatic reconstructions of two environmental extremes of the Quaternary period, the present conditions and those during the last glacial maximum (LGM), to quantify the degree of climatic stability between sampling locations. We documented positive correlations between genetic distances and relative climatic stability, although these associations were not significant when corrected for autocorrelation. Principal component analyses indicated the existence of climatic niche differences between some phylogeographic clades of A. krugi. The approach that we employed to assess the relationship between climatic stability and the genetic architecture of A. krugi can also be used to investigate the impact of factors such as the spatial distribution of food sources, parasites, predators or competitors on the genetic landscape of a species.