Surface to subsurface freshwater connections: phylogeographic and habitat analyses of Cambarus tenebrosus, a facultative cave-dwelling crayfish

Aliens in caves: the global dimension of biological invasions in subterranean ecosystems

Alien species are a significant threat to natural ecosystems and human economies. Despite global efforts to address this challenge, the documented number of alien species is rapidly increasing worldwide. However, the magnitude of the impact of alien species may vary significantly across habitats. For example, some habitats are naturally less prone to biological invasions due to stringent abiotic and biotic characteristics, selecting for a limited number of introduced species possessing traits closely related to the native organisms. Subterranean ecosystems are quintessential examples of habitats with strong environmental filters (e.g. lack of light and scarcity of food), driving convergent adaptations in species that have successfully adapted to life in darkness. Despite these stringent environmental constraints, the number of records of alien species in subterranean ecosystems has increased in recent decades, but the relevant literature remains largely fragmented and mostly anecdotal. Therefore, even though caves are generally considered very fragile ecosystems, their susceptibility to impacts by alien species remains untested other than for some very specific cases. We provide the first systematic literature survey to synthesise available knowledge on alien species in subterranean ecosystems globally. This review is supported by a database summarising the available literature, aiming to identify gaps in the distribution and spread of alien invertebrate species in subterranean habitats, and laying the foundations for future management practices and interventions. First, we quantitatively assessed the current knowledge of alien species in subterranean ecosystems to shed light on broader questions about taxonomic biases, geographical patterns, modes of dispersal, pathways for introductions and potential impacts. Secondly, we collected species-specific traits for each recorded alien species and tested whether subterranean habitats act as ecological filters for their establishment, favouring organisms with pre-adaptive traits suitable for subterranean life. We found information on the presence of 246 subterranean alien species belonging to 18 different classes. The dominant alien species were invertebrates, especially insects and arachnids. Most species were reported in terrestrial subterranean habitats from all continents except Antarctica. Palaearctic and Nearctic biogeographic regions represented the main source of alien species. The main routes of introductions into the recipient country are linked to commercial activities (84.3% of cases for which there was information available). Negative impacts have been documented for a small number of case studies (22.7%), mostly related to increased competition with native species. For a limited number of case studies (6.1%), management strategies were reported but the effectiveness of these interventions has rarely been quantified. Accordingly, information on costs is very limited. Approximately half of the species in our database can be considered established in subterranean habitats. According to our results, the presence of suitable traits grants access to the stringent environmental filter posed by subterranean environments, facilitating establishment in the new habitat. We recommend that future studies deepen the understanding of invasiveness into subterranean habitats, raising public and scientific community awareness of preserving these fragile ecosystems.

Evidence for speciation underground in diving beetles (Dytiscidae) from a subterranean archipelago

Most subterranean animals are assumed to have evolved from surface ancestors following colonization of a cave system; however, very few studies have raised the possibility of "subterranean speciation" in underground habitats (i.e., obligate cave-dwelling organisms [troglobionts] descended from troglobiotic ancestors). Numerous endemic subterranean diving beetle species from spatially discrete calcrete aquifers in Western Australia (stygobionts) have evolved independently from surface ancestors; however, several cases of sympatric sister species raise the possibility of subterranean speciation. We tested this hypothesis using vision (phototransduction) genes that are evolving under neutral processes in subterranean species and purifying selection in surface species. Using sequence data from 32 subterranean and five surface species in the genus Paroster (Dytiscidae), we identified deleterious mutations in long wavelength opsin (lwop), arrestin 1 (arr1), and arrestin 2 (arr2) shared by a sympatric sister-species triplet, arr1 shared by a sympatric sister-species pair, and lwop and arr2 shared among closely related species in adjacent calcrete aquifers. In all cases, a common ancestor possessed the function-altering mutations, implying they were already adapted to aphotic environments. Our study represents one of the first confirmed cases of subterranean speciation in cave insects. The assessment of genes undergoing pseudogenization provides a novel way of testing modes of speciation and the history of diversification in blind cave animals.

The Evolution of Gene Expression Underlying Vision Loss in Cave Animals

Dissecting the evolutionary genetic processes underlying eye reduction and vision loss in obligate cave-dwelling organisms has been a long-standing challenge in evolutionary biology. Independent vision loss events in related subterranean organisms can provide critical insight into these processes as well as into the nature of convergent loss of complex traits. Advances in evolutionary developmental biology have illuminated the significant role of heritable gene expression variation in the evolution of new forms. Here, we analyze gene expression variation in adult eye tissue across the freshwater crayfish, representing four independent vision-loss events in caves. Species and individual expression patterns cluster by eye function rather than phylogeny, suggesting convergence in transcriptome evolution in independently blind animals. However, this clustering is not greater than what is observed in surface species with conserved eye function after accounting for phylogenetic expectations. Modeling expression evolution suggests that there is a common increase in evolutionary rates in the blind lineages, consistent with a relaxation of selective constraint maintaining optimal expression levels. This is evidence for a repeated loss of expression constraint in the transcriptomes of blind animals and that convergence occurs via a similar trajectory through genetic drift.

Phylogenetic evidence from freshwater crayfishes that cave adaptation is not an evolutionary dead-end

Caves are perceived as isolated, extreme habitats with a uniquely specialized biota, which long ago led to the idea that caves are "evolutionary dead-ends." This implies that cave-adapted taxa may be doomed for extinction before they can diversify or transition to a more stable state. However, this hypothesis has not been explicitly tested in a phylogenetic framework with multiple independently evolved cave-dwelling groups. Here, we use the freshwater crayfish, a group with dozens of cave-dwelling species in multiple lineages, as a system to test this hypothesis. We consider historical patterns of lineage diversification and habitat transition as well as current patterns of geographic range size. We find that while cave-dwelling lineages have small relative range sizes and rarely transition back to the surface, they exhibit remarkably similar diversification patterns to those of other habitat types and appear to be able to maintain a diversity of lineages through time. This suggests that cave adaptation is not a "dead-end" for freshwater crayfish, which has positive implications for our understanding of biodiversity and conservation in cave habitats.

Microsatellite development and first population size estimates for the groundwater isopod Proasellus walteri

Effective population size (N e) is one of the most important parameters in, ecology, evolutionary and conservation biology; however, few studies of N e in surface freshwater organisms have been published to date. Even fewer studies have been carried out in groundwater organisms, although their evolution has long been considered to be particularly constrained by small N e. In this study, we estimated the contemporary effective population size of the obligate groundwater isopod: Proaselluswalteri (Chappuis, 1948). To this end, a genomic library was enriched for microsatellite motifs and sequenced using 454 GS-FLX technology. A total of 54,593 reads were assembled in 10,346 contigs or singlets, of which 245 contained candidate microsatellite sequences with suitable priming sites. Ninety-six loci were tested for amplification, polymorphism and multiplexing properties, of which seven were finally selected for N e estimation. Linkage disequilibrium and approximate Bayesian computation methods revealed that N e in this small interstitial groundwater isopod could reach large sizes (> 585 individuals). Our results suggest that environmental conditions in groundwater, while often referred to as extreme, are not necessarily associated with small N e.

"Population dynamics of crustaceans": introduction to the symposium

Crustaceans are a globally-distributed faunal group, found across all habitats from the equator to the poles. They are an ideal focal assemblage for assessment of the impacts of climatic change and anthropogenic disturbance on nonmodel systems, such as how sea currents influence the movements of zooplankton communities in the open ocean, or how ecosystem processes affect phytoplanktonic species with restricted geographic distributions across a cluster of island lakes that could be a new model system for studies of speciation. This symposium introduced early-career researchers working in the fields of phylogeography, ecogenomics, fisheries management, and ecosystem processes with the aim of highlighting the different genetic and ecological approaches to the study of population dynamics of freshwater, estuarine, and marine crustacean species.

Under the volcano: phylogeography and evolution of the cave-dwelling Palmorchestia hypogaea (Amphipoda, Crustacea) at La Palma (Canary Islands)

BACKGROUND

The amphipod crustacean Palmorchestia hypogaea occurs only in La Palma (Canary Islands) and is one of the few terrestrial amphipods in the world that have adapted to a strictly troglobitic life in volcanic cave habitats. A surface-dwelling closely related species (Palmorchestia epigaea) lives in the humid laurel forest on the same island. Previous studies have suggested that an ancestral littoral Orchestia species colonized the humid forests of La Palma and that subsequent drought episodes in the Canaries reduced the distribution of P. epigaea favouring the colonization of lava tubes through an adaptive shift. This was followed by dispersal via the hypogean crevicular system.

RESULTS

P. hypogaea and P. epigaea did not form reciprocally monophyletic mitochondrial DNA clades. They showed geographically highly structured and genetically divergent populations with current gene flow limited to geographically close surface locations. Coalescence times using Bayesian estimations assuming a non-correlated relaxed clock with a normal prior distribution of the age of La Palma, together with the lack of association of habitat type with ancestral and recent haplotypes, suggest that their adaptation to cave life is relatively ancient.

CONCLUSION

The data gathered here provide evidence for multiple invasions of the volcanic cave systems that have acted as refuges. A re-evaluation of the taxonomic status of the extant species of Palmorchestia is needed, as the division of the two species by habitat and ecology is unnatural. The information obtained here, and that from previous studies on hypogean fauna, shows the importance of factors such as the uncoupling of morphological and genetic evolution, the role of climatic change and regressive evolution as key processes in leading to subterranean biodiversity.