The role of TRPA1 channels in thermosensation

Transient receptor potential ankyrin 1 (TRPA1) is a polymodal nonselective cation channel sensitive to different physical and chemical stimuli. TRPA1 is associated with many important physiological functions in different species and thus is involved in different degrees of evolution. TRPA1 acts as a polymodal receptor for the perceiving of irritating chemicals, cold, heat, and mechanical sensations in various animal species. Numerous studies have supported many functions of TRPA1, but its temperature-sensing function remains controversial. Although TRPA1 is widely distributed in both invertebrates and vertebrates, and plays a crucial role in tempreture sensing, the role of TRPA1 thermosensation and molecular temperature sensitivity are species-specific. In this review, we summarize the temperature-sensing role of TRPA1 orthologues in terms of molecular, cellular, and behavioural levels.

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.

Seasonal modifications of longitudinal distribution patterns within a stream: Interspecific interactions in the niche overlap zones of two Ephemera mayflies

Niche differentiation between closely related species leads to differentiation of their habitats. Segregation based on slight differences in environmental factors, that is niche differentiation on the microhabitat scale, allows more species to inhabit a certain geographic space. Therefore, such fine scale niche differentiation is an important factor in the support of species diversity. In addition, niche differentiation on the microhabitat scale and/or the differentiation of breeding seasons can be considered typical mechanisms that facilitate multispecies' co-existence. In this study, sister species (Commonly, Ephemera japonica inhabit at upstream region and Ephemera strigata inhabit at middle stream region), which often coexist in the upper to middle reaches of river systems of the Japanese Islands, were targeted and the following aspects were investigated. First, differences in habitat preference and interspecific differences in flow distribution patterns on a geographically fine scale were tracked in detail. Subsequently, the temporal transitions of their distribution patterns were investigated in detail and seasonal changes were investigated. Finally, we thoroughly investigated the disappearance of nymphs of each species from the river due to emergence affected the distribution of each species (by conducting daily emergence surveys). Combining results of these multiple studies also suggested that there may be spatiotemporal interspecial interaction between these two species within/around their overlapping regions. Traditionally, the longitudinal distribution pattern of these two Ephemera mayflies has been thought to be established based on a difference in habitat preferences, but this study revealed that the interspecific interaction between the two species also plays an important role. This study provides new insights into species diversity and distribution pattern formation in river-dwelling species.

Molecular assessment of dietary niche partitioning in an endemic island radiation of tropical mammals

Island radiations represent unique evolutionary histories in unique ecological contexts. These radiations provide opportunities to investigate ecological diversification in groups that typically exhibit niche partitioning among their constituents, including partitioning of food resources. DNA metabarcoding produces finer levels of diet identification than traditional methods, allowing us to examine dietary niche partitioning in communities or clades in which species share superficially similar diets. Here, we use DNA metabarcoding to investigate dietary niche partitioning in an endemic radiation of mammals in the Philippines. Our data reveal niche partitioning as well as phylogenetically-uncorrelated adaptive evolution in this small mammal community. Because 70% of the focal species belong to the tribe Chrotomyini, an endemic Philippine radiation of murid rodents that feed extensively on earthworms, this study sheds light on dietary adaptation and its role in the co-occurrence of closely related species. Our results reveal fine-scale resource partitioning within this community; our data provide compelling evidence for niche partitioning of diet that was masked by previous diet categories and will help in further dissecting the model adaptive radiation of endemic small mammals on Luzon. This study reinforces the notion that DNA metabarcoding can be a valuable tool for investigating both ecological relationships and evolutionary ecology at the community and phylogenetic level, respectively.

Detection of genes positively selected in Cuban Anolis lizards that naturally inhabit hot and open areas and currently thrive in urban areas

Species of Anolis lizards of the West Indies that naturally inhabit hot and open areas also tend to thrive in urban areas. In this study, transcriptome was sequenced for nine species of Cuban Anolis lizards that are closely related to each other, but inhabit different thermal microhabitats. Using PAML and HyPhy software, we attempted to identify genes and amino acid sites under positive selection in the common ancestral branch of A. porcatus and A. allisoni, and the branch of A. sagrei, which inhabit hot and open areas, and thrive in urban areas. Although there were no genes where positive selection was commonly detected on both of the tested branches, positive selection was detected in genes involved in the stress response (e.g., DNA damage and oxidative stress) and cardiac function, which could be related to adaptive evolution of tolerance to heat or ultraviolet radiation, on both branches. These findings suggest that adaptive evolution of the response to stress caused by heat or ultraviolet radiation might have occurred in ancestors of Anolis species inhabiting hot and open areas and might be related to the current thriving in urban areas of them.

Phylogeographic and phenotypic outcomes of brown anole colonization across the Caribbean provide insight into the beginning stages of an adaptive radiation

Some of the most important insights into the ecological and evolutionary processes of diversification and speciation have come from studies of island adaptive radiations, yet relatively little research has examined how these radiations initiate. We suggest that Anolis sagrei is a candidate for understanding the origins of the Caribbean Anolis adaptive radiation and how a colonizing anole species begins to undergo allopatric diversification, phenotypic divergence and, potentially, speciation. We undertook a genomic and morphological analysis of representative populations across the entire native range of A. sagrei, finding that the species originated in the early Pliocene, with the deepest divergence occurring between western and eastern Cuba. Lineages from these two regions subsequently colonized the northern Caribbean. We find that at the broadest scale, populations colonizing areas with fewer closely related competitors tend to evolve larger body size and more lamellae on their toepads. This trend follows expectations for post-colonization divergence from progenitors and convergence in allopatry, whereby populations freed from competition with close relatives evolve towards common morphological and ecological optima. Taken together, our results show a complex history of ancient and recent Cuban diaspora with populations on competitor-poor islands evolving away from their ancestral Cuban populations regardless of their phylogenetic relationships, thus providing insight into the original diversification of colonist anoles at the beginning of the radiation. Our research also supplies an evolutionary framework for the many studies of this increasingly important species in ecological and evolutionary research.

Factors affecting interspecific differences in genetic divergence among populations of Anolis lizards in Cuba

BACKGROUND

Geographical patterns and degrees of genetic divergence among populations differ between species, reflecting relative potentials for speciation or cladogenesis and differing capacities for environmental adaptation. Identification of factors that contribute to genetic divergence among populations is important to the understanding of why some species exhibit greater interpopulation genetic divergence. In this study, we calculated the mean pairwise genetic distances among populations as species' average genetic divergence by a phylogeny using nuclear and mitochondrial genes of 303 individuals from 33 Cuban Anolis species and estimated species ages by another phylogeny using nuclear and mitochondrial genes of 51 Cuban and 47 non-Cuban Anolis species. We identified factors that influence species' differences in genetic divergence among 26 species of Anolis lizards from Cuba. Species ages, environmental heterogeneity within species ranges, and ecomorph types were considered as factors affecting average genetic divergences among populations.

RESULTS

The phylogenies presented in this study provide the most comprehensive sampling of Cuban Anolis species to date. The phylogeny showed more conservative evolution of Anolis ecomorphs within Cuba and identified twig anoles as a monophyletic group. Subsequent Phylogenetic Generalized Least Squares (PGLS) analyses showed that species age was positively correlated with species' average genetic divergence among populations.

CONCLUSION

Although previous studies have focused on factors affecting genetic divergence within species, the present study showed for the first time that species differences in genetic divergence could be largely affected by species age.

Co-occurrence of ecologically similar species of Hawaiian spiders reveals critical early phase of adaptive radiation

Background

The processes through which populations originate and diversify ecologically in the initial stages of adaptive radiation are little understood because we lack information on critical steps of early divergence. A key question is, at what point do closely related species interact, setting the stage for competition and ecological specialization? The Hawaiian Islands provide an ideal system to explore the early stages of adaptive radiation because the islands span ages from 0.5–5 Mya. Hawaiian spiders in the genus Tetragnatha have undergone adaptive radiation, with one lineage (“spiny legs”) showing four different ecomorphs (green, maroon, large brown, small brown); one representative of each ecomorph is generally found at any site on the older islands. Given that the early stages of adaptive radiation are characterized by allopatric divergence between populations of the same ecomorph, the question is, what are the steps towards subsequent co-occurrence of different ecomorphs? Using a transcriptome-based exon capture approach, we focus on early divergence among close relatives of the green ecomorph to understand processes associated with co-occurrence within the same ecomorph at the early stages of adaptive radiation.

Results

The major outcomes from the current study are first that closely related species within the same green ecomorph of spiny leg Tetragnatha co-occur on the same single volcano on East Maui, and second that there is no evidence of genetic admixture between these ecologically equivalent species. Further, that multiple genetic lineages exist on a single volcano on Maui suggests that there are no inherent dispersal barriers and that the observed limited distribution of taxa reflects competitive exclusion.

Conclusions

The observation of co-occurrence of ecologically equivalent species on the young volcano of Maui provides a missing link in the process of adaptive radiation between the point when recently divergent species of the same ecomorph occur in allopatry, to the point where different ecomorphs co-occur at a site, as found throughout the older islands. More importantly, the ability of close relatives of the same ecomorph to interact, without admixture, may provide the conditions necessary for ecological divergence and independent evolution of ecomorphs associated with adaptive radiation.

Electronic supplementary material

The online version of this article (10.1186/s12862-018-1209-y) contains supplementary material, which is available to authorized users.

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.