Energy and speleogenesis: Key determinants of terrestrial species richness in caves

Novel genome sequence of Chinese cavefish (Triplophysa rosa) reveals pervasive relaxation of natural selection in cavefish genomes

All cavefishes, living exclusively in caves across the globe, exhibit similar phenotypic traits, including the characteristic loss of eyes. To understand whether such phenotypic convergence shares similar genomic bases, here we investigated genome-wide evolutionary signatures of cavefish phenotypes by comparing whole-genome sequences of three pairs of cavefishes and their surface fish relatives. Notably, we newly sequenced and generated a whole-genome assembly of the Chinese cavefish Triplophysa rosa. Our comparative analyses revealed several shared features of cavefish genome evolution. Cavefishes had lower mutation rates than their surface fish relatives. In contrast, the ratio of nonsynonymous to synonymous substitutions (ω) was significantly elevated in cavefishes compared to in surface fishes, consistent with the relaxation of purifying selection. In addition, cavefish genomes had an increased mutational load, including mutations that alter protein hydrophobicity profiles, which were considered harmful. Interestingly, however, we found no overlap in positively selected genes among different cavefish lineages, indicating that the phenotypic convergence in cavefishes was not caused by positive selection of the same sets of genes. Analyses of previously identified candidate genes associated with cave phenotypes supported this conclusion. Genes belonging to the lipid metabolism functional ontology were under relaxed purifying selection in all cavefish genomes, which may be associated with the nutrient-poor habitat of cavefishes. Our work reveals previously uncharacterized patterns of cavefish genome evolution and provides comparative insights into the evolution of cave-associated phenotypic traits.

Diplura in caves: diversity, ecology, evolution and biogeography

Diplurans (Hexapoda) are considered the ‘ideal cavernicolous animal’ having one of the highest ratios of cave-adapted vs. non-cave-adapted species. They are successful colonizers of subterranean habitats, thriving in all cryptic, dark, terrestrial environments. Diplurans play an important role in the decomposition of organic matter below the ground and are sensitive to anthropogenic pressures. We present the first comprehensive review about cave Diplura diversity, ecology, evolution, distribution and biogeography. We provide a roadmap for research questions regarding the ecology, aimed at stimulating the pursuit of new studies on this fascinating group. Filling these current knowledge gaps will contribute to conservation efforts for cave ecosystems.

Switching from mesopredator to apex predator: how do responses vary in amphibians adapted to cave living?

Abstract

The effective detection of both prey and predators is pivotal for the survival of mesopredators. However, the condition of being a mesopredator is strongly context dependent. Here we focus on two aquatic caudate species that have colonised caves: the Pyrenean newt (Calotriton asper) and the olm (Proteus anguinus). The former maintains both surface and subterranean populations, while only cave-adapted populations of the latter exist. Both species are apex predators in underground waterbodies, while the Pyrenean newt is a mesopredator in surface waterbodies. Shifting to a higher level of the trophic web through colonising caves may promote the loss of anti-predator response against surface apex predators, and an increase in the ability to detect prey. To test these two non-exclusive hypotheses, we integrated classical behavioural characterisations with a novel approach: the assessment of lateralisation (i.e. preference for one body side exposure). Behavioural experiments were performed using laboratory-reared individuals. We performed 684 trials on 39 Pyrenean newts and eight olms. Under darkness and light conditions, we tested how exposure to different chemical cues (predatory fish, prey and unknown scent) affected individuals’ activity and lateralisation. Both cave and surface Pyrenean newts responded to predator cues, while olms did not. In Pyrenean newts, predator cues reduced the time spent in movement and time spent in lateralisation associated with hunting. Our results show that predator recognition is maintained in a species where recently separated populations inhabit environments lacking of higher predators, while such behaviour tends to be lost in populations with longer history of adaptation.

Significance statement

Predator recognition can be maintained in animals adapted to predator free habitats, but varies with their history of adaptation. Species that are not at the apex of the food web can become top predators if they colonise subterranean environments. We compared the behavioural responses of the olm, a strictly cave species with a long underground evolutionary history, and of the Pyrenean newt, a facultative cave species that also has stream-dwelling populations. Moreover, we integrated a classical behavioural characterisation, such as movement detection, with a novel approach: the assessment of lateralisation. While olms do not respond to external predators scent, cave-dwelling newts still recognise it. This clearly indicates that predator recognition is still maintained in species that have colonised predator-free environments more recently.

Same Diet, Different Strategies: Variability of Individual Feeding Habits across Three Populations of Ambrosi’s Cave Salamander (Hydromantes ambrosii)

European cave salamanders of the genus Hydromantes are a group of eight species endemic to Italy and south-eastern France. Knowledge on the trophic niche of European Hydromantes is poor, and the few available studies only partially investigate their feeding habits. We performed an in-depth study on the trophic niche of the Ambrosi’s cave salamander (H. ambrosii), assessing the potential divergences among three different populations. All the populations had a similar diet composition, showing a wider trophic niche in fall compared to spring. In only one population, “true specialists” were present; however, in all three populations, generalist individuals always represented the larger proportion. Interspecific and intraspecific competition did not play an important role in determining individual dietary specialisation in H. ambrosii; contrarily, the characteristics of the surrounding environment seemed to be an important factor. The best body conditions were observed in the population located in the site where the non-arboreal vegetation cover was the highest. Besides providing new information on the trophic niche of H. ambrosii, we here showed that studies encompassing both intrinsic and extrinsic factors at the population level are needed to fully understand the trophic dynamics occurring among European cave salamanders.

Ecotoxicological effects of anthropogenic stressors in subterranean organisms: A review

How anthropogenic stressors affect biodiversity is a central question in a changing world. Subterranean ecosystems and their biodiversity are particularly vulnerable to change, yet, these species are frequently neglected in analyses of global biodiversity and assessments of ecological status and risk. Are these hidden species affected by anthropogenic stressors? Do they survive outside of the current thermal limits of their ecosystems? These and other important questions can be addressed with ecotoxicological testing, relating contaminants and temperature resistance of species with measured environmental concentrations and climatic data. Ecotoxicological knowledge specific to subterranean ecosystems is crucial for establishing thresholds for their protection, but such data are both scarce and scattered. Here, we review the existing ecotoxicological studies of these impacts to subterranean-adapted species. An effort that includes 167 measured endpoints and presents a database containing experimentally derived species' tolerance data for 28 contaminants and temperature, for 46 terrestrial and groundwater species, including fungi and animals. The lack of standard data among the studies is currently the major impediment to evaluate how stressors affect subterranean-adapted species and how differently they respond from their relatives at surface. Improving understanding of ecotoxicological effects on subterranean-adapted species will require extensive analysis of physiological responses to a wide range of untested stressors, standardization of testing protocols and evaluation of exposures under realistic scenarios.

Local- versus broad-scale environmental drivers of continental β-diversity patterns in subterranean spider communities across Europe

Macroecologists seek to identify drivers of community turnover (β-diversity) through broad spatial scales. However, the influence of local habitat features in driving broad-scale β-diversity patterns remains largely untested, owing to the objective challenges of associating local-scale variables to continental-framed datasets. We examined the relative contribution of local- versus broad-scale drivers of continental β-diversity patterns, using a uniquely suited dataset of cave-dwelling spider communities across Europe (35-70° latitude). Generalized dissimilarity modelling showed that geographical distance, mean annual temperature and size of the karst area in which caves occurred drove most of β-diversity, with differential contributions of each factor according to the level of subterranean specialization. Highly specialized communities were mostly influenced by geographical distance, while less specialized communities were mostly driven by mean annual temperature. Conversely, local-scale habitat features turned out to be meaningless predictors of community change, which emphasizes the idea of caves as the human accessible fraction of the extended network of fissures that more properly represents the elective habitat of the subterranean fauna. To the extent that the effect of local features turned to be inconspicuous, caves emerge as experimental model systems in which to study broad biological patterns without the confounding effect of local habitat features.

Exploring the Interplay Between Local and Regional Drivers of Distribution of a Subterranean Organism

Caves are excellent model systems to study the effects of abiotic factors on species distributions due to their selective conditions. Different ecological factors have been shown to affect species distribution depending on the scale of analysis, whether regional or local. The interplay between local and regional factors in explaining the spatial distribution of cave-dwelling organisms is poorly understood. Using the troglophilic subterranean spider Artema nephilit (Araneae: Pholcidae) as a model organism, we investigated whether similar environmental predictors drive the species distribution at these two spatial scales. At the local scale, we monitored the abundance of the spiders and measured relevant environmental features in 33 caves along the Jordan Rift Valley. We then extended the analysis to a regional scale, investigating the drivers of the distribution using species distribution models. We found that similar ecological factors determined the distribution at both local and regional scales for A. nephilit. At a local scale, the species was found to preferentially occupy the outermost, illuminated, and warmer sectors of caves. Similarly, mean annual temperature, annual temperature range, and solar radiation were the most important drivers of its regional distribution. By investigating these two spatial scales simultaneously, we showed that it was possible to achieve an in-depth understanding of the environmental conditions that governs subterranean species distribution.

Energy and speleogenesis: Key determinants of terrestrial species richness in caves

The aim of this study was to unravel the relative role played by speleogenesis (i.e., the process in which a cave is formed), landscape‐scale variables, and geophysical factors in the determination of species richness in caves. Biological inventories from 21 caves located in the southeastern Iberian Peninsula along with partial least square (PLS) regression analysis were used to assess the relative importance of the different explanatory variables. The caves were grouped according to the similarity in their species composition; the effect that spatial distance could have on similarity was also studied using correlation between matrices. The energy and speleogenesis of caves accounted for 44.3% of the variation in species richness. The trophic level of each cave was the most significant factor in PLS regression analysis, and epigenic caves (i.e., those formed by the action of percolating water) had significantly more species than hypogenic ones (i.e., those formed by the action of upward flows in confined aquifers). Dissimilarity among the caves was very high (multiple‐site β_sim = 0.92). Two main groups of caves were revealed through the cluster analysis, one formed by the western caves and the other by the eastern ones. The significant—but low—correlation found between faunistic dissimilarity and geographical distance (r = .16) disappeared once the caves were split into the two groups. The extreme beta‐diversity suggests a very low connection among the caves and/or a very low dispersal capacity of the species. In the region under study, two main factors are intimately related to the richness of terrestrial subterranean species in caves: the amount of organic material (trophic level) and the formation process (genesis). This is the first time that the history of a cave genesis has been quantitatively considered to assess its importance in explaining richness patterns in comparison with other factors more widely recognized.