Parallels between two geographically and ecologically disparate cave invasions by the same species, Asellus aquaticus (Isopoda, Crustacea)

Genetic bias in repeated evolution of pigment loss in cave populations of the Asellus aquaticus species complex

Similar phenotypes can evolve repeatedly under the same evolutionary pressures. A compelling example is the evolution of pigment loss and eye loss in cave-dwelling animals. While specific genomic regions or genes associated with these phenotypes have been identified in model species, it remains uncertain whether a bias towards particular genetic mechanisms exists. An isopod crustacean, Asellus aquaticus, is an ideal model organism to investigate this phenomenon. It inhabits surface freshwaters throughout Europe but has colonized groundwater on multiple independent occasions and evolved several cave populations with distinct ecomorphology. Previous studies have demonstrated that three different cave populations utilized common genetic regions, potentially the same genes, in the evolution of pigment and eye loss. Expanding on this, we conducted analysis on two additional cave populations, distinct either phylogenetically or biogeographically from those previously examined. We generated F2 hybrids from cave × surface crosses and tested phenotype-genotype associations, as well as conducted complementation tests by crossing individuals from different cave populations. Our findings revealed that pigment loss and orange eye pigment in additional cave populations were associated with the same genomic regions as observed in the three previously tested cave populations. Moreover, the lack of complementation across all cross combinations suggests that the same gene likely drives pigment loss. These results substantiate a genetic bias in the recurrent evolution of pigment loss in this model system. Future investigations should focus on the cause behind this bias, possibly arising from allele recruitment from ancestral surface populations' genetic variation or advantageous allele effects via pleiotropy.

Multiple transitions between realms shape relict lineages of Proteus cave salamanders

In comparison to biodiversity on Earth's surface, subterranean biodiversity has largely remained concealed. The olm (Proteus anguinus) is one of the most enigmatic extant cave inhabitants, and until now little was known regarding its genetic structure and evolutionary history. Olms inhabit subterranean waters throughout the Dinaric Karst of the western Balkans, with a seemingly uniform phenotypic appearance of cave-specialized traits: an elongate body, snout and limbs, degenerated eyes and loss of pigmentation ("white olm"). Only a single small region in southeastern Slovenia harbours olms with a phenotype typical of surface animals: pigmented skin, eyes, a blunt snout and short limbs ("black olm"). We used a combination of mitochondrial DNA and genome-wide single nucleotide polymorphism data to investigate the molecular diversity, evolutionary history and biogeography of olms along the Dinaric Karst. We found nine deeply divergent species-level lineages that separated between 17 and 4 million years ago, while molecular diversity within lineages was low. We detected no signal of recent admixture between lineages and only limited historical gene flow. Biogeographically, the contemporaneous distribution of lineages mostly mirrors hydrologically separated subterranean environments, while the historical separation of olm lineages follows microtectonic and climatic changes in the area. The reconstructed phylogeny suggests at least four independent transitions to the cave phenotype. Two of the species-level lineages have miniscule ranges and may represent Europe's rarest amphibians. Their rarity and the decline in other lineages call for protection of their subterranean habitats.

A collaborative backbone resource for comparative studies of subterranean evolution: The World Asellidae database

Transition to novel environments, such as groundwater colonization by surface organisms, provides an excellent research ground to study phenotypic evolution. However, interspecific comparative studies on evolution to groundwater life are few because of the challenge in assembling large ecological and molecular resources for species-rich taxa comprised of surface and subterranean species. Here, we make available to the scientific community an operational set of working tools and resources for the Asellidae, a family of freshwater isopods containing hundreds of surface and subterranean species. First, we release the World Asellidae database (WAD) and its web application, a sustainable and FAIR solution to producing and sharing data and biological material. WAD provides access to thousands of species occurrences, specimens, DNA extracts and DNA sequences with rich metadata ensuring full scientific traceability. Second, we perform a large-scale dated phylogenetic reconstruction of Asellidae to support phylogenetic comparative analyses. Of 424 terminal branches, we identify 34 pairs of surface and subterranean species representing independent replicates of the transition from surface water to groundwater. Third, we exemplify the usefulness of WAD for documenting phenotypic shifts associated with colonization of subterranean habitats. We provide the first phylogenetically controlled evidence that body size of males decreases relative to that of females upon groundwater colonization, suggesting competition for rare receptive females selects for smaller, more agile males in groundwater. By making these tools and resources widely accessible, we open up new opportunities for exploring how phenotypic traits evolve in response to changes in selective pressures and trade-offs during groundwater colonization.

Standing genetic variation as a potential mechanism of novel cave phenotype evolution in the freshwater isopod, Asellus aquaticus

Novel phenotypes can come about through a variety of mechanisms including standing genetic variation from a founding population. Cave animals are an excellent system in which to study the evolution of novel phenotypes such as loss of pigmentation and eyes. Asellus aquaticus is a freshwater isopod crustacean found in Europe and has both a surface and a cave ecomorph which vary in multiple phenotypic traits. An orange eye phenotype was previously revealed by F₂ crosses and backcrosses to the cave parent within two examined Slovenian cave populations. Complete loss of pigmentation, both in eye and body, is epistatic to the orange eye phenotype and therefore the orange eye phenotype is hidden within the cave populations. Our goal was to investigate the origin of the orange eye alleles within the Slovenian cave populations by examining A. aquaticus individuals from Slovenian and Romanian surface populations and Asellus aquaticus infernus individuals from a Romanian cave population. We found orange eye individuals present in lab raised surface populations of A. aquaticus from both Slovenia and Romania. Using a mapping approach with crosses between individuals of two surface populations, we found that the region known to be responsible for the orange eye phenotype within the two previously examined Slovenian cave populations was also responsible within both the Slovenian and the Romanian surface populations. Complementation crosses between orange eye Slovenian and orange eye Romanian surface individuals suggest that the same gene is responsible for the orange eye phenotype in both surface populations. Additionally, we observed a low frequency phenotype of eye loss in crosses generated between the two surface populations and also in the Romanian surface population. Finally, in a cave population from Romania, A. aquaticus infernus, we found that the same region is also responsible for the orange eye phenotype as the Slovenian cave populations and the Slovenian and Romanian surface populations. Therefore, we present evidence that variation present in the cave populations could originate from standing variation present in the surface populations and/or transgressive hybridization of different surface phylogenetic lineages rather than de novo mutations.

Both Light Stimuli and Predation Risk Affect the Adult Behavior of a Stygobiont Crustacean

Stygobiont species show common, typical traits derived from their adaptation to subterranean life. Due to the general absence of light in cave environments, the majority of them are eyeless. Although the absence of eyes generally does not allow them to perceive luminous stimuli, some stygobionts still present phototaxis. Previous studies determined that different species of the eyeless amphipod crustaceans of the genus Niphargus are able to react to light; this has been interpreted as an adaptation to avoid dangerous surface habitats, even if recent studies suggest that this could also be an adaptation to exploit them when a situation is less dangerous (i.e., during the night). Niphargus thuringius is a stygobiont amphipod that can also be observed in spring environments despite possessing all the main morphological features of subterranean organisms, such as depigmentation and a lack of eyes. In the present study, we test how the species respond to light stimuli according to the light cycle and predation risk experienced during a conditioning period. We assessed the reactions to light stimuli of adult individuals of N. thuringius after 30 days of rearing in microcosms with different conditions of light occurrence (total darkness or a light/darkness daily cycle) and predation risk (without predators, with one predator, and with two predators). Both light stimuli during the test and rearing conditions affected the behavior of Niphargus thuringius. With light stimuli, individuals presented a strong photophobic response. Moreover, individuals reared in conditions of high predation risk preferred a more sheltered environment during behavioral tests than individuals reared in safe conditions. Our results add a new species to those of stygobiont amphipods known to display negative phototaxis, confirming that this pattern is widespread and conserved in the field. N. thuringius could be a good candidate model to perform further studies aiming to assess if differences occur between spring populations and populations present in deeper groundwater.

Natural selection versus neutral mutation in the evolution of subterranean life: A false dichotomy?

Throughout the evolutionary tree, there are gains and losses of morphological features, physiological processes, and behavioral patterns. Losses are perhaps nowhere so prominent as for subterranean organisms, which typically show reductions or losses of eyes and pigment. These losses seem easy to explain without recourse to natural selection. Its most modern form is the accumulation of selectively neutral, structurally reducing mutations. Selectionist explanations include direct selection, often involving metabolic efficiency in resource poor subterranean environments, and pleiotropy, where genes affecting eyes and pigment have other effects, such as increasing extra-optic sensory structures. This dichotomy echoes the debate in evolutionary biology in general about the sufficiency of natural selection as an explanation of evolution, e.g., Kimura’s neutral mutation theory. Tests of the two hypotheses have largely been one-sided, with data supporting that one or the other processes is occurring. While these tests have utilized a variety of subterranean organisms, the Mexican cavefish, Astyanax mexicanus, which has eyed extant ancestral-like surface fish conspecifics, is easily bred in the lab, and whose whole genome has been sequenced, is the favored experimental organism. However, with few exceptions, tests for selection versus neutral mutations contain limitations or flaws. Notably, these tests are often one sided, testing for the presence of one or the other process. In fact, it is most likely that both processes occur and make a significant contribution to the two most studied traits in cave evolution: eye and pigment reduction. Furthermore, narrow focus on neutral mutation hypothesis versus selection to explain cave-evolved traits often fails, at least in the simplest forms of these hypotheses, to account for aspects that are likely essential for understanding cave evolution: migration or epigenetic effects. Further, epigenetic effects and phenotypic plasticity have been demonstrated to play an important role in cave evolution in recent studies. Phenotypic plasticity does not by itself result in genetic change of course, but plasticity can reveal cryptic genetic variation which then selection can act on. These processes may result in a radical change in our thinking about evolution of subterranean life, especially the speed with which it may occur. Thus, perhaps it is better to ask what role the interaction of genes and environment plays, in addition to natural selection and neutral mutation.

Living on the edge – An overview of invertebrates from groundwater habitats prone to extreme environmental conditions

Groundwater ecosystems from cold polar and circumpolar regions, hot springs, as well as those developed in salt, gypsum or in volcanic rocks are one of the environments considered to exhibit extreme environmental conditions such as low (below 0°C) or high (over 45°C) temperatures, hypersaline waters, or with elevated content of toxic gases like hydrogen sulfide or methane. They represent the “unseen ecosystem beneath our feet” and are inhabited by a large diversity of organisms, persisting and flourishing under severe environmental conditions that are usually hostile to the majority of organisms. These types of groundwater ecosystems are remarkable “evolutionary hotspots” that witnessed the adaptive radiation of morphologically and ecologically diverse species, whereas the organisms living here are good models to understand the evolutionary processes and historical factors involved in speciation and adaptation to severe environmental conditions. Here, we provide an overview of the groundwater invertebrates living in continental groundwater habitats prone to extreme environmental conditions in one or more physico-chemical parameters. Invertebrates are represented by a wide variety of taxonomic groups, however dominated by crustaceans that show specific adaptations mostly metabolic, physiologic, and behavioral. Symbiotic associations among bacteria and invertebrates are also discussed enlightening this biological interaction as a potential adaptation of different groundwater invertebrates to cope with severe environmental conditions. Given the high pressures that anthropogenic activities pose on groundwater habitats worldwide, we predict that several of these highly specialized organisms will be prone to extinction in the near future. Finally, we highlight the knowledge gaps and future research approaches in these particular groundwater ecosystems by using integrative-omic studies besides the molecular approach to shed light on genetic variation and phenotypic plasticity at species and populational levels.

GRAPHICAL ABSTRACT

Exploratory behaviour divergence between surface populations, cave colonists and a cave population in the water louse, Asellus aquaticus

Abstract

Behaviour is considered among the most important factors in colonising new habitats. While population divergence in behaviour is well-documented, intraspecific variation in exploratory behaviour in species with populations successfully colonising and adapting to extreme (compared to the ‘typical’) habitats is less understood. Here, by studying surface- vs. cave-adapted populations of water louse (Asellus aquaticus), we tested whether (i) adaptation to the special, ecologically isolated cave habitat includes a decrease in explorativeness and (ii) recent, surface-type cave colonists are more explorative than their surface conspecifics from the source population. We repeatedly tested dispersal related novel area exploration and dispersal speed in both the presence and absence of light. We found that surface populations showed higher behavioural activity in dark than in light, and they were more explorative and dispersed faster than their cave conspecifics. Recent colonists showed a trend of higher dispersal speed compared to their source surface population. We suggest that extreme and isolated habitats like caves might work as ‘dispersal traps’ following successful colonisation, because adaptation to these habitats includes the reduction of explorativeness. Furthermore, we suggest that individuals with higher explorativeness are likely to colonise markedly new environments. Finally, we provide experimental evidence about surface A. aquaticus moving more in dark than in light.

Significance statement

Environmental conditions in caves are differing drastically from those of the surface. Consequently, animals colonising subterranean habitats are subject to different selective forces than those experienced by the ancestral surface-living population. Behaviour is believed to be a key factor in successful colonisation to novel habitats; however, intraspecific behavioural variation in species with both surface- and cave-adapted populations is less known. Here, we compared dispersal related novel area exploration and dispersal speed across surface and cave-adapted populations of the freshwater crustacean Asellus aquaticus. Our results show that cave-adapted A. aquaticus are significantly less explorative and disperse slower than surface-type populations, indicating that caves may act as ‘dispersal traps’, where adaptation includes the loss of explorativeness. Also, recent cave colonists show a trend to be faster dispersers than peers from the surface source population, suggesting that individuals with higher explorativeness are likely to colonise markedly different new environments.

Phylogenetic relationships and species delimitation in Haemopis (Annelida: Hirudinea: Haemopidae)

The Holarctic leech genus Haemopis currently includes 11 species, all of which are macrophagous, as opposed to their more infamous bloodfeeding counterparts among hirudiniform leeches. In spite of their ecological importance as fish food and predators of freshwater invertebrates, there is a paucity of data regarding morphology and genetic variation that might guide future identification efforts for members of the genus. The lack of detailed descriptions of distinguishing morphological features, coupled with the absence of a robust phylogenetic hypothesis for the genus, have conspired to prevent meaningful inferences on the natural history of the group. In an attempt to remedy this, we present new genetic (using COI, 12S rDNA, 28S rDNA and 18S rDNA) data for the majority of the known species diversity within the genus in order to both infer a phylogenetic hypothesis and to introduce authoritative DNA barcodes for the newly collected species. The potential of these barcodes is increased through rigorous morphological investigations of the specimens, with comparisons to the original literature. Our resulting phylogenetic hypothesis is agnostic as to the geographic origin of the genus, with equal probability afforded to both a Nearctic and Palearctic origin. Beyond this, we show that there is a strong tendency towards a barcoding gap within the genus, but that a distinct gap is lacking due to the relatively high genetic variation found within H. marmorata. Taken together, our results shed light on species delimitation within, and evolutionary history of, this often-neglected group of leeches.

A reassessment of the origin and distribution of the subterranean genus Pseudolimnocythere Klie, 1938 (Ostracoda, Loxoconchidae), with description of two new species from Italy

Groundwater ecosystems host a rich and unique, but still largely unexplored and undescribed, biodiversity. Several lineages of ostracod crustaceans have subterranean representatives or are exclusively living in groundwaters. The stygobitic genus Pseudolimnocythere Klie, 1938 has a West Palearctic distribution, and includes few living and fossil species of marine origin. Through a comprehensive literature review and the description of the two new living species, Pseudolimnocythere abditasp. nov. and Pseudolimnocythere sofiaesp. nov., from springs in the Northern Apennines, Italy, a morphological analysis was carried out with the aim of comparing the valve morphology of living and fossil species, and to discuss previous hypotheses about time and mode of colonization of inland waters. Pseudolimnocythere species show a low variability in valve morphology, with a remarkable stasis over geological times. The distribution of extant and fossil species is consistent with a scenario of multiple and independent events of colonization of continental habitats linked to sea level variations starting from Middle Miocene in the Paratethys and, later, in the Mediterranean. The most common colonization routes of inland waters have taken place through karst formations along ancient coastlines, although we cannot exclude some minor active migration through the hyporheic zone of streams. Available distribution data suggest a poor dispersal ability of Pseudolimnocythere species after they had colonized continental waters.

Diversity and dispersal of aquatic invertebrate species from surface and groundwater: Development and application of microsatellite markers for the detection of hydrological exchange processes

Groundwater is one of our most important resources, however groundwater ecosystems are among the most understudied habitats of the planet earth. Studies on groundwater organisms are hampered by the difficult accessibility of species, the lack of morphological differentiation and the limitation for laboratory cultures. One important approach to overcome these shortcomings is to provide sensitive genetic methods to unravel patterns of biodiversity, population structure and gene flow in natural populations. In this study we present five sets of microsatellite markers developed for the isopods Asellus aquaticus and Proasellus slavus, the cyclopoides Paracyclops fimbriatus and Acanthocyclops sensitivus and the harpacticoide Bryocamptus echinatus (Crustacea). Two of these species were subjected to detailed population genetic analyses: We studied 501 specimens of Asellus aquaticus from four different regions in Northern Germany using nine microsatellite markers and 70 specimens of Bryocamptus echinatus using nine microsatellite markers from three different sampling sites in South-Western Germany. Our results show that genetic diversity is high (A. aquaticus: 10 to 20 and B. echinatus: 4 to 18 alleles per locus) among populations of aquatic invertebrates, populations are highly differentiated (F_ST > 0.2) and genetic differentiation was associated with geographic patterns. Applications of molecular genetic methods and their use for the detection of hydrological exchange processes relevant for drinking water suppliers are demonstrated and discussed.

Building on 150 Years of Knowledge: The Freshwater Isopod Asellus aquaticus as an Integrative Eco-Evolutionary Model System

Interactions between organisms and their environments are central to how biological diversity arises and how natural populations and ecosystems respond to environmental change. These interactions involve processes by which phenotypes are affected by or respond to external conditions (e.g., via phenotypic plasticity or natural selection) as well as processes by which organisms reciprocally interact with the environment (e.g., via eco-evolutionary feedbacks). Organism-environment interactions can be highly dynamic and operate on different hierarchical levels, from genes and phenotypes to populations, communities, and ecosystems. Therefore, the study of organism-environment interactions requires integrative approaches and model systems that are suitable for studies across different hierarchical levels. Here, we introduce the freshwater isopod Asellus aquaticus, a keystone species and an emerging invertebrate model system, as a prime candidate to address fundamental questions in ecology and evolution, and the interfaces therein. We review relevant fields of research that have used A. aquaticus and draft a set of specific scientific questions that can be answered using this species. Specifically, we propose that studies on A. aquaticus can help understanding (i) the influence of host-microbiome interactions on organismal and ecosystem function, (ii) the relevance of biotic interactions in ecosystem processes, and (iii) how ecological conditions and evolutionary forces facilitate phenotypic diversification.

Parallel morphological evolution and habitat-dependent sexual dimorphism in cave- vs. surface populations of the Asellus aquaticus (Crustacea: Isopoda: Asellidae) species complex

Studying parallel evolution (repeated, independent evolution of similar phenotypes in similar environments) is a powerful tool to understand environment-dependent selective forces. Surface-dwelling species that repeatedly and independently colonized caves provide unique models for such studies. The primarily surface-dwelling Asellus aquaticus species complex is a good candidate to carry out such research, because it colonized several caves in Europe. By comparing 17 functional morphological traits between six cave and nine surface populations of the A. aquaticus species complex, we investigated population divergence in morphology and sexual dimorphism. We found habitat-dependent population divergence in 10 out of 17 traits, likely reflecting habitat-driven changes in selection acting on sensory systems, feeding, grooming, and antipredator mechanisms. Sexual dimorphism was present in 15 traits, explained by sexual selection acting on male traits important in male-male agonistic behavior or mate guarding and fecundity selection acting on female traits affecting offspring number and nursing. In eight traits, the degree of sexual dimorphism was habitat dependent. We conclude that cave-related morphological changes are highly trait- and function-specific and that the strength of sexual/fecundity selection strongly differs between cave and surface habitats. The considerable population variation within habitat type warrants further studies to reveal cave-specific adaptations besides the parallel patterns.

No room for males in caves: Female-biased sex ratio in subterranean amphipods of the genus Niphargus

Sex allocation theory predicts that the proportion of daughters to sons will evolve in response to ecological conditions that determine the costs and benefits of producing each sex. All else being equal, the adult sex ratio (ASR) should also vary with ecological conditions. Many studies of subterranean species reported female-biased ASR, but no systematic study has yet been conducted. We test the hypothesis that the ASR becomes more female-biased with increased isolation from the surface. We compiled a data set of ASRs of 35 species in the subterranean amphipod Niphargus, each living in one of three distinct habitats (surface-subterranean boundary, cave streams, phreatic lakes) representing an environmental gradient of increased isolation underground. The ASR was female-biased in 27 of 35 species; the bias was statistically significant in 12 species. We found a significant difference in the ASR among habitats after correction for phylogeny. It is most weakly female-biased at the surface-subterranean boundary and most strongly female-biased in phreatic lakes. Additional modelling suggests that the ASR has evolved towards a single value for both surface-subterranean boundary and cave stream-dwelling species, and another value for 9 of 11 phreatic lake dwellers. We suggest that a history of inbreeding in subterranean populations might lower inbreeding depression such that kin selection favours mating with siblings. This could select for a female-biased offspring sex ratio due to local mate competition among brothers. The observed patterns in sex ratios in subterranean species make them a group worthy of more attention from those interested in sex allocation theory.

Postojna-Planina Cave System in Slovenia, a Hotspot of Subterranean Biodiversity and a Cradle of Speleobiology

The Postojna-Planina Cave System (PPCS) in central Slovenia is a globally exceptional site of subterranean biodiversity, comprised of many interconnected caves with cumulative passage length exceeding 34 km. Two rivers sink into the caves of the PPCS, called the Pivka and Rak, and join underground into Unica River, which emerges to the surface. The studies of fauna of PPCS began in the 19th century with the first scientific descriptions of specialized cave animals in the world, making it “the cradle of speleobiology”. Currently, the species list of PPCS contains 116 troglobiotic animal species belonging to eight phyla, confirming its status as the richest in the world. Of these, 47 species have been scientifically described from the PPCS, and more than 10 await formal taxonomic descriptions. We expect that further sampling, detailed analyses of less studied taxa, and the use of molecular methods may reveal more species. To keep the cave animals’ checklist in PPCS up-to-date, we have supplemented the printed checklist with an online interface. As the revised checklist is a necessary first step for further activities, we discuss the importance of PPCS in terms of future research and conservation.

The genomics of phenotypically differentiated Asellus aquaticus cave, surface stream and lake ecotypes

Organisms well suited for the study of ecotype formation have wide distribution ranges, where they adapt to multiple drastically different habitats repeatedly over space and time. Here we study such ecotypes in a Crustacean model, Asellus aquaticus, a commonly occurring isopod found in freshwater habitats as diverse as streams, caves and lakes. Previous studies focusing on cave vs. surface ecotypes have attributed depigmentation, eye loss and prolonged antennae to several south European cave systems. Likewise, surveys across multiple Swedish lakes have identified the presence of dark-pigmented "reed" and light-pigmented "stonewort" ecotypes, which can be found within the same lake. In this study, we sequenced the first draft genome of A. aquaticus, and subsequently use this to map reads and call variants in surface stream, cave and two lake ecotypes. In addition, the draft genome was combined with a RADseq approach to perform a quantitative trait locus (QTL) mapping study using a laboratory bred F₂ and F₄ cave × surface intercross. We identified genomic regions associated with body pigmentation, antennae length and body size. Furthermore, we compared genome-wide differentiation between natural populations and found several genes potentially associated with these habitats. The assessment of the cave QTL regions in the light-dark comparison of lake populations suggests that the regions associated with cave adaptation are also involved with genomic differentiation in the lake ecotypes. These demonstrate how troglomorphic adaptations can be used as a model for related ecotype formation.

Ecophysiological and life-history adaptations of Gammarus balcanicus (Schäferna, 1922) in a sinking-cave stream from Western Carpathians (Romania)

Freshwater gammarids are known to colonise occasionally sinking-cave streams, providing contrasting morphological, life-history and ecophysiological adaptations compared to their surface conspecifics. In this study, a subterranean and a surface population of the species Gammarus balcanicus was surveyed for one year in a sinking-cave stream from the Western Carpathians (Romania). The results showed that the cave-dwelling population comprised individuals that were significantly larger compared to their surface conspecifics, had larger body-size at sexual maturity and that the females produced fewer, but larger eggs, compared to the population situated outside the cave. The trophic position and the omnivory were significantly higher for the cave-dwelling compared to surface population and the elemental imbalance for C:P molar ratios lower, but similar for C:N. However, the subterranean population did not present troglomorphic characters or longer lifespan as known for other cave-surface paired crustaceans. This, together with the rather extensive hydrological connection of the habitats, suggests active gene-flow between populations and similar response to seasonality for body-size distributions, indicating that the observed ecophysiological and life-history differences are rather the consequence of phenotypic plasticity than the result of genetic adaptation.

The interplay between habitat use, morphology and locomotion in subterranean crustaceans of the genus Niphargus

Locomotion is an important, fitness-related functional trait. Environment selects for type of locomotion and shapes the morphology of locomotion-related traits such as body size and appendages. In subterranean aquatic arthropods, these traits are subjected to multiple, at times opposing selection pressures. Darkness selects for enhanced mechano- and chemosensory systems and hence elongation of appendages. Conversely, water currents have been shown to favor short appendages. However, no study has addressed the variation in locomotion of invertebrates inhabiting cave streams and cave lakes, or questioned the relationship between species' morphology and locomotion. To fill this knowledge gap, we studied the interplay between habitat use, morphology and locomotion in amphipods of the subterranean genus Niphargus. Previous studies showed that lake and stream species differ in morphology. Namely, lake species are large, stout and long-legged, whereas stream species are small, slender and short-legged. We here compared locomotion mode and speed between three lake and five stream species. In addition, we tested whether morphology predicts locomotion. We found that the stream species lie on their body sides and move using slow crawling or tail-flipping. The species inhabiting lakes move comparably faster, and use a variety of locomotion modes. Noteworthy, one of the lake species almost exclusively moves in an upright or semi-upright position that resembles walking. Body size and relative length of appendages predict locomotion mode and speed in all species. We propose that integrating locomotion in the studies of subterranean species might improve our understanding of their morphological evolution.

Developmental Transcriptomic Analysis of the Cave-Dwelling Crustacean, Asellus aquaticus

Cave animals are a fascinating group of species often demonstrating characteristics including reduced eyes and pigmentation, metabolic efficiency, and enhanced sensory systems. Asellus aquaticus, an isopod crustacean, is an emerging model for cave biology. Cave and surface forms of this species differ in many characteristics, including eye size, pigmentation, and antennal length. Existing resources for this species include a linkage map, mapped regions responsible for eye and pigmentation traits, sequenced adult transcriptomes, and comparative embryological descriptions of the surface and cave forms. Our ultimate goal is to identify genes and mutations responsible for the differences between the cave and surface forms. To advance this goal, we decided to use a transcriptomic approach. Because many of these changes first appear during embryonic development, we sequenced embryonic transcriptomes of cave, surface, and hybrid individuals at the stage when eyes and pigment become evident in the surface form. We generated a cave, a surface, a hybrid, and an integrated transcriptome to identify differentially expressed genes in the cave and surface forms. Additionally, we identified genes with allele-specific expression in hybrid individuals. These embryonic transcriptomes are an important resource to assist in our ultimate goal of determining the genetic underpinnings of the divergence between the cave and surface forms.

Description of Acanthocephalus anguillae balkanicus subsp. n. (Acanthocephala: Echinorhynchidae) from Proteus anguinus Laurenti (Amphibia: Proteidae) and the cave ecomorph of Asellus aquaticus (Crustacea: Asellidae) in Slovenia

Acanthocephalus balkanicus Batchvarov et Combes, 1974 was incompletely described from the northern crested newt, Triturus cristatus (Laurenti) (Amphibia: Salamandridae), a possible synonym of the Balkan crested newt, Triturus ivanbureschi Arntzen et Wielstra, from a pond in village of Pesnopoy, southern Bulgaria. We provide a full description of adult males and females of the same taxon from the olm, Proteus anguinus Laurenti (Amphibia: Proteidae), the only exclusively aquatic cave-dwelling vertebrate in Europe, captured in Postojna-Planina Cave System in Slovenia. Cystacanths were also collected from the cave ecomorph of Asellus aquaticus (Linnaeus) (Crustacea: Asellidae) in the same location. Molecular analysis of specimens from Slovenia revealed that they are genetically almost identical to those of Acanthocephalus anguillae (Müller, 1780), a common parasite of European freshwater fishes. We propose to recognise the morphological and host differences by describing A. balkanicus as a new subspecies of A. anguillae. Acanthocephalus anguillae balkanicus is rather small and cylindrical with cylindrical proboscis having 10 rows of 6 hooks with simple roots each, long neck, large balloon-shaped lemnisci, small spherical anterior testis, and 6 club-shaped cement glands in 3 pairs. SEM images reveal more morphological details and the X-ray scans of gallium cut hooks shows considerably higher levels of phosphorus and calcium in adult hooks than in cystacanth hooks, especially in basal areas. Sulfur levels were higher in the arch and basal area of cystacanth hooks than adult hooks. Considering that both definitive and intermediate hosts of the Slovenian population of this acanthocephalan are bound to cave life, it is possible that its entire life cycle is uniquely completed underground.

Chronic radiation exposure at Chernobyl shows no effect on genetic diversity in the freshwater crustacean, Asellus aquaticus thirty years on

Analysis of genetic diversity represents a fundamental component of ecological risk assessments in contaminated environments. Many studies have assessed the genetic implications of chronic radiation exposure at Chernobyl, generally recording an elevated genetic diversity and mutation rate in rodents, plants, and birds inhabiting contaminated areas. Only limited studies have considered genetic diversity in aquatic biota at Chernobyl, despite the large number of freshwater systems where elevated dose rates will persist for many years. Consequently, the present study aimed to assess the effects of chronic radiation exposure on genetic diversity in the freshwater crustacean, Asellus aquaticus, using a genome-wide SNP approach (Genotyping-by-sequencing). It was hypothesized that genetic diversity in A. aquaticus would be positively correlated with dose rate. A. aquaticus was collected from six lakes in Belarus and the Ukraine ranging in dose rate from 0.064 to 27.1 µGy/hr. Genotyping-by-sequencing analysis was performed on 74 individuals. A significant relationship between geographical distance and genetic differentiation confirmed the Isolation-by-Distance model. Conversely, no significant relationship between dose rate and genetic differentiation suggested no effect of the contamination gradient on genetic differentiation between populations. No significant relationship between five measures of genetic diversity and dose rate was recorded, suggesting that radiation exposure has not significantly influenced genetic diversity in A. aquaticus at Chernobyl. This is the first study to adopt a genome-wide SNP approach to assess the impacts of environmental radiation exposure on biota. These findings are fundamental to understanding the long-term success of aquatic populations in contaminated environments at Chernobyl and Fukushima.

Embryonic origin and genetic basis of cave associated phenotypes in the isopod crustacean Asellus aquaticus

Characteristics common to animals living in subterranean environments include the reduction or absence of eyes, lessened pigmentation and enhanced sensory systems. How these characteristics have evolved is poorly understood for the majority of cave dwelling species. In order to understand the evolution of these changes, this study uses an invertebrate model system, the freshwater isopod crustacean, Asellus aquaticus, to examine whether adult differences between cave and surface dwelling individuals first appear during embryonic development. We hypothesized that antennal elaboration, as well as eye reduction and pigment loss, would be apparent during embryonic development. We found that differences in pigmentation, eye formation, and number of segments of antenna II were all present by the end of embryonic development. In addition, we found that cave and surface hatchlings do not significantly differ in the relative size of antenna II and the duration of embryonic development. To investigate whether the regions responsible for eye and pigment differences could be genetically linked to differences in article number, we genotyped F2 hybrids for the four previously mapped genomic regions associated with eye and pigment differences and phenotyped these F2 hybrids for antenna II article number. We found that the region previously known to be responsible for both presence versus absence of pigment and eye size also was significantly associated with article number. Future experiments will address whether pleiotropy and/or genetic linkage play a role in the evolution of cave characteristics in Asellus aquaticus.

Day–night and seasonal variations of a subterranean invertebrate community in the twilight zone

Being characterized by the absence of light and a reduced environmental cyclicity, the subterranean domain is generally regarded as temporally stable. Yet, in the proximity of cave entrances (twilight zones), patterns of sunlight and darkness can be detected within the 24-hour day–night cycle. In parallel, changes in the abiotic and biotic conditions are expected; however, these patterns have been rarely explored in animal communities dwelling in the twilight zone. We performed a biological investigation in a small abandoned mine in the Western Alps, monitoring it once per season, both during the day and at night. At each survey, we collected data on the spatial distribution of the resident species, their activity patterns, and the main microclimatic parameters. We observed significant daily variations in the environmental conditions during winter and spring, namely higher temperature, relative humidity and availability of trophic resources at night. In conjunction with these disparate nocturnal conditions, the abundance of troglophile species was also higher, as well as the activity patterns of one of the most frequent species inhabiting the entrance area – the orb-weaver spiderMetamenardi. We further documented temporal changes in the composition of the parietal community, due to species using the mine as a diurnal, nocturnal or overwintering shelter. Overall, our results suggest that the communities of the twilight zone are not temporally stable and we highlight the importance of taking into account not only their seasonal, but also their daily variations.

The role of isolation on contrasting phylogeographic patterns in two cave crustaceans

BACKGROUND

The underlying mechanisms and processes that prompt the colonisation of extreme environments, such as caves, constitute major research themes of evolutionary biology and biospeleology. The special adaptations required to survive in subterranean environments (low food availability, hypoxic waters, permanent darkness), and the geographical isolation of caves, nominate cave biodiversity as ideal subjects to answer long-standing questions concerning the interplay amongst adaptation, biogeography, and evolution. The present project aims to examine the phylogeographic patterns exhibited by two sympatric species of surface and cave-dwelling peracarid crustaceans (Asellus aquaticus and Niphargus hrabei), and in doing so elucidate the possible roles of isolation and exaptation in the colonisation and successful adaptation to the cave environment.

RESULTS

Specimens of both species were sampled from freshwater hypogean (cave) and epigean (surface) habitats in Hungary, and additional data from neighbouring countries were sourced from Genbank. Sequencing of mitochondrial and nuclear loci revealed, through haplotype network reconstruction (TCS) and phylogenetic inference, the genetic structure, phylogeographic patterns, and divergence-time estimates of A. aquaticus and N. hrabei surface and cave populations. Contrasting phylogeographic patterns were found between species, with A. aquaticus showing strong genetic differentiation between cave and surface populations and N. hrabei lacking any evidence of genetic structure mediated by the cave environment. Furthermore, N. hrabei populations show very low levels of genetic differentiation throughout their range, which suggests the possibility of recent expansion events over the last few thousand years.

CONCLUSIONS

Isolation by cave environment, rather than distance, is likely to drive the genetic structuring observed between immediately adjacent cave and surface populations of A. aquaticus, a predominantly surface species with only moderate exaptations to subterranean life. For N. hrabei, in which populations exhibit a fully 'cave-adapted' (troglomorphic) phenotype, the lack of genetic structure suggests that subterranean environments do not pose a dispersal barrier for this surface-cave species.

Comparative study of acetylcholinesterase and glutathione S-transferase activities of closely related cave and surface Asellus aquaticus (Isopoda: Crustacea)

The freshwater isopod crustacean Asellus aquaticus has recently been developed as an emerging invertebrate cave model for studying evolutionary and developmental biology. Mostly morphological and genetic differences between cave and surface A. aquaticus populations have been described up to now, while scarce data are available on other aspects, including physiology. The purpose of this study was to advance our understanding of the physiological differences between cave A. aquaticus and its surface-dwelling counterparts. We sampled two surface populations from the surface section of the sinking Pivka River (central Slovenia, Europe), i.e. locality Pivka Polje, and locality Planina Polje, and one cave population from the subterranean section of the sinking Pivka River, i.e. locality Planina Cave. Animals were sampled in spring, summer and autumn. We measured the activities of acetylcholinesterase (AChE) and glutathione S-transferase (GST) in individuals snap-frozen in the field immediately after collection. Acetylcholinesterase is likely related to animals’ locomotor activity, while GST activity is related to the metabolic activity of an organism. Our study shows significantly lower AChE and GST activities in the cave population in comparison to both surface A. aquaticus populations. This confirms the assumption that cave A. aquaticus have lower locomotor and metabolic activity than surface A. aquaticus in their respective natural environments. In surface A. aquaticus populations, seasonal fluctuations in GST activity were observed, while these were less pronounced in individuals from the more stable cave environment. On the other hand, AChE activity was generally season-independent in all populations. To our knowledge, this is the first study of its kind conducted in A. aquaticus. Our results show that among closely related cave and surface A. aquaticus populations also physiological differences are present besides the morphological and genetic. These findings contribute to a better understanding of the biology of A. aquaticus and cave crustaceans in general.

Exoskeletal cuticle of cavernicolous and epigean terrestrial isopods: A review and perspectives

Comparative ultrastructural studies of the integument in terrestrial isopod crustaceans show that specific environmental adaptations of different eco-morphotypes are reflected in cuticle structure. The biphasic molting in isopods is a valuable experimental model for studies of cuticular matrix secretion and degradation in the same animal. The aim of this review is to show structural and functional adaptations of the tergal cuticle in terrestrial isopods inhabiting cave habitats. Exoskeletal cuticle thickness, the number of cuticular layers, epicuticle structure, mineralization, pigmentation and complexity of sensory structures are compared, with greater focus on the well-studied cave trichoniscid Titanethes albus. A large number of thinner cuticular layers in cave isopods compared to fewer thicker cuticular layers in related epigean species of similar body-sizes is explained as a specific adaptation to the cavernicolous life style. The epicuticle structure and composition are compared in relation to their potential waterproofing capacity in different environments. Cuticle mineralization is described from the functional point of view as well as from the aspect of different calcium storage sites and calcium dynamics during the molt cycle. We also discuss the nature and reduction of pigmentation in the cave environment and outline perspectives for future research.

Light triggers habitat choice of eyeless subterranean but not of eyed surface amphipods

Boundaries of species distributions are the result of colonization-extinction processes. Survival on the boundary depends on how well individuals discriminate optimal from suboptimal habitat patches. Such behaviour is called habitat choice and was only rarely applied to macroecology, although it links species ecological niche and species distribution. Surface and subterranean aquatic species are spatially strongly segregated, even in the absence of physical barriers. We explored whether a behavioural response to light functions as a habitat choice mechanism that could explain species turnover between surface and subterranean aquatic ecosystems. In a controlled laboratory experiment, we studied the behavioural response to light of ten pairs of surface and subterranean amphipods that permanently co-occur in springs. Surface species showed a weak photophobic, photoneutral, and in one case, photophilic response, whereas all subterranean species showed a strong photophobic response. Eyeless subterranean but not eyed surface amphipods appear to orient themselves with light cues. On a local scale, this difference possibly diminishes harmful interactions between the co-occurring amphipods, whereas on a regional scale, photophobia could explain limited dispersal and a high degree of endemism observed among subterranean species.