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

Sex-dependent increase of movement activity in the freshwater isopod Asellus aquaticus following adaptation to a predator-free cave habitat

Populations experiencing negligible predation pressure are expected to evolve higher behavioral activity. However, when sexes have different expected benefits from high activity, the adaptive shift is expected to be sex-specific. Here, we compared movement activity of one cave (lack of predation) and three adjacent surface (high and diverse predation) populations of Asellus aquaticus, a freshwater isopod known for its independent colonization of several caves across Europe. We predicted 1) higher activity in cave than in surface populations, with 2) the difference being more pronounced in males as they are known for active mate searching behavior, while females are not. Activity was assessed both in the presence and absence of light. Our results supported both predictions: movement activity was higher in the cave than in the surface populations, particularly in males. Relaxed predation pressure in the cave-adapted population is most likely the main selective factor behind increased behavioral activity, but we also showed that the extent of increase is sex-specific.

New Insights into the Variation and Admixture of the Cave-Dwelling Spider Trogloneta yunnanensis in South China Karst

Subterranean karst caves can contain unexpected biodiversity, but few studies related to spider population genetics have been conducted in the karst area of Southern China. In this study, we investigated the population genetic structure of Trogloneta yunnanensis (Song & Zhu, 1994) based on 73 spider samples from six underground populations in South China Karst. Population genetic structure analysis showed a clear divergence (FST > 0.9 and Nm < 0.05) among populations according to mitochondrial genes. The phylogenetic gene tree constructed by BI and ML methods recovered six geographic clades. Divergence time estimation indicated that the divergence of these six populations can be traced back to the late Pleistocene. We supposed that the geographic isolation led to the extreme population structure. According to this study and previous studies about troglobites living in this region, the subterranean habitats of the Yunnan-Guizhou Plateau may contain many organisms with similar genetic structures. The subterranean biodiversity in the karst area of Southern China needs to be re-evaluated and protected.

Not the Last Piece of the Puzzle: Niphargus Phylogeny in Hungary

The Palaearctic genus Niphargus is a promising model system to understand subterranean fauna genesis in Europe. The Pannonian Plain (mainly covered by Hungary) in Central Europe, once being the area of the Paratethys, is a key area for Niphargus diversification. However, our knowledge on Hungarian species of Niphargus is primarily based on sporadic taxonomical works from the pre-molecular era. Here, we studied 14 localities, covering the eight valid Hungarian species of Niphargus and including nine previously unstudied populations. Based on sequences of three gene fragments, we reconstructed their phylogeny using maximum likelihood and Bayesian approaches. We found that not all Hungarian species of Niphargus are closely related, and even species sampled at the same localities can belong to different clades. Some Hungarian species form monophyletic clades, while others are nested in various non-Hungarian lineages. The new populations are all genetically distinct from the known species. Our results suggest that the Hungarian Niphargus fauna has originated from seven unrelated clades and its diversity is underestimated due to unknown populations and cryptic species. The detection of genetically distinct species of Niphargus from non-carbonate regions calls for further research efforts. The high diversity and the number of putative new species in the N. tatrensis clade warrants further, high-resolution phylogenetic studies.

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.

Surprisingly high genetic divergence of the mitochondrial DNA barcode fragment (COI) within Central European woodlice species (Crustacea, Isopoda, Oniscidea)

DNA barcoding has become the most popular approach for species identification in recent years. As part of the German Barcode of Life project, the first DNA barcode library for terrestrial and freshwater isopods from Germany is presented. The analyzed barcode library included 38 terrestrial (78% of the documented species of Germany) and five freshwater (63%) species. A total of 513 new barcodes was generated and 518 DNA barcodes were analyzed. This analysis revealed surprisingly high intraspecific genetic distances for numerous species, with a maximum of 29.4% for Platyarthrus hoffmannseggii Brandt, 1833. The number of BINs per species ranged from one (32 species, 68%) to a maximum of six for Trachelipus rathkii (Brandt, 1833). In spite of such high intraspecific variability, interspecific distances with values between 12.6% and 29.8% allowed a valid species assignment of all analyzed isopods. The observed high intraspecific distances presumably result from phylogeographic events, Wolbachia infections, atypical mitochondrial DNAs, heteroplasmy, or various combinations of these factors. Our study represents the first step in generating an extensive reference library of DNA barcodes for terrestrial and freshwater isopods for future molecular biodiversity assessment studies.

Food preference and food type innovation of surface- vs. cave-dwelling waterlouse (Asellus aquaticus) after 60 000 years of isolation

Abstract

Behavioural innovativeness is important for colonising new habitats; however, it is also costly. Along the colonisation event of a simple, stable and isolated habitat offering only new food sources, one could hypothesize that the colonising individuals are more innovative than the average in their source population, showing preference to the new resource, while after colonisation, the adapted population will lose its innovativeness and become specialised to the new resource. To test this hypothesis, we compared food preference and food type innovation of a cave-dwelling waterlouse (Asellus aquaticus) population (genetically isolated for at least 60 000 years) to three surface-dwelling populations, also sampling individuals that have recently entered the cave (‘colonists’). In the cave, the only food sources are endogenous bacterial mats, while surface populations feed on various living and dead plant material together with their fungal and bacterial overgrow. We assayed all populations with the familiar and unfamiliar food types from the natural habitats and two novel food types not occurring in the natural habitats of the species. We found that all populations preferred surface to cave food and consumed the unnatural novel food types. Surface populations avoided cave food and colonists spent the most time with feeding on surface food. We conclude that the cave population maintained its preference for surface food and did not lose its food type innovativeness. We suggest that adapting to the special cave food was a major challenge in colonising the cave.

Significance statement

Behavioural innovativeness is a key trait for adapting to environmental changes or to colonise new habitats. However, it has developmental and maintenance costs due to the high energy need of the necessary sensory and neural organs. Therefore, we asked whether behavioural innovativeness decreases after colonising an isolated, stable and highly specialised habitat. By comparing food type innovativeness of surface-dwelling populations of waterlouse (Asellus aquaticus) to a population that has colonised a cave at least 60 000 years ago, we found that the high innovativeness towards unnatural food was retained in the cave population. Further, all populations preferred surface food (decaying leaves), with surface populations almost completely avoiding cave food (endogenous bacteria mats). We suggest that (i) food type innovativeness is evolutionary rigid in our system and (ii) the cave food was rather an obstacle against than a trigger of cave colonisation.

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.

Population divergence in aggregation and sheltering behaviour in surface- versus cave-adapted Asellus aquaticus (Crustacea: Isopoda)

Aggregation (gathering together) and sheltering (hiding in cover) are basic behaviours that can reduce the risk of predation. However, both behaviours have costs, such as increased competition over resources and high prevalence of contact-spread parasites (aggregation) or lost opportunities for foraging and mating (sheltering). Therefore, variation in these behaviours is expected between populations with varying levels of predation risk. We compared aggregation and sheltering in surface- (various predators) and cave-adapted (no predator) populations of the isopod Asellus aquaticus in a common garden experiment. Given that the cave environment is constantly dark, we also tested for population variation in light-induced behavioural plasticity. Variation in sheltering was explained by habitat type: cave individuals sheltered less than surface individuals. We found high between-population variation in aggregation with or without shelters and their light-induced plasticity, which was not explained by habitat type. Cave individuals decreased (habituation) whereas surface individuals increased sheltering with time (sensitization). We suggest that population variation in sheltering is driven by predation, whereas variation in aggregation must be driven by other, unaccounted environmental factors, in a similar manner to light-induced behavioural plasticity. Based on habituation/sensitization patterns, we suggest that predation-adapted populations are more sensitive to disturbance related to routine laboratory procedures.

Living in isolation for almost 40 years: molecular divergence of the 28S rDNA and COI sequences between French and Polish populations of the cave beetle Speonomus normandi hydrophilus (Jeannel, 1907)

The paper gives the results of the first studies on the molecular divergence between native and non-native populations of Speonomus normandi hydrophilus (Jeannel, 1907). This species is endemic to Massif Arize in the Central Pyrenees (France), and represents highly specialised organisms that live underground. In 1982, one hundred specimens of S. normandi hydrophilus had been experimentally introduced into the Dzwonnica Cave (Poland). Since then, a numerous population has developed in the Towarna-Dzwonnica cave system, and the neighbouring Cabanowa Cave. After almost 40 years of isolation between native and non-native populations, the genetic variations were examined using the COI and 28S rDNA genes. Analyses of the haplotypes of 28S showed one common haplogroup, which confirms the origin of the Polish group. The differentiation of haplotypes for the COI marker was high for both the French and Polish populations. Altogether 18 haplotypes of this marker have been detected, 12 in the French population and 9 in the Polish. However, only a portion of the haplotypes is shared between the native and introduced population.

Is foraging innovation lost following colonization of a less variable environment? A case study in surface- vs. cave-dwelling Asellus aquaticus

Behavioral innovation is a key process for successful colonization of new habitat types. However, it is costly due to the necessary cognitive and neural demands and typically connected to ecological generalism. Therefore, loss of behavioral innovativeness is predicted following colonization of new, simple, and invariable environments. We tested this prediction by studying foraging innovativeness in the freshwater isopod Asellus aquaticus. We sampled its populations along the route of colonizing a thermokarstic water-filled cave (simple, stable habitat with only bacterial mats as food) from surface habitats (variable environment, wide variety of food). The studied cave population separated from the surface populations at least 60,000 years ago. Animals were tested both with familiar and novel food types (cave food: bacterial mats; surface food: decaying leaves). Irrespective of food type, cave individuals were more likely to feed than surface individuals. Further, animals from all populations fed longer on leaves than on bacteria, even though leaves were novel for the cave animals. Our results support that cave A. aquaticus did not lose the ability to use the ancestral (surface) food type after adapting to a simple, stable, and highly specialized habitat.

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.

Dark offshoot: Phylogenomic data sheds light on the evolutionary history of a new species of cave brittle star

Caves are a useful system for testing evolutionary and biogeographic hypotheses, as they are isolated, and their environmental conditions have resulted in adaptive selection across different taxa. Although in recent years many more cave species have been discovered, cave-dwelling members of the class Ophiuroidea (brittle stars) remain scarce. Out of the more than two thousand species of brittle stars described to date, only three are regarded as true cave-dwellers. These occurrences represent rare colonising events, compared to other groups that are known to have successfully diversified in these systems. A third species from an anchihaline cave system in the Yucatan Peninsula, Mexico, has been previously identified from cytochrome oxidase I (COI) barcodes. In this study, we reassess the species boundaries of this putative cave species using a phylogenomic dataset (20 specimens in 13 species, 100 exons, 18.7 kbp). We perform species delimitation analyses using robust full-coalescent methods for discovery and validation of hypotheses on species boundaries, as well as infer its phylogenetic relationships with species distributed in adjacent marine regions, in order to investigate the origin of this cave-adapted species. We assess which hypotheses on the origin of subterranean taxa can be applied to this species by taking into account its placement within the genus Ophionereis and its demographic history. We provide a detailed description of Ophionereis commutabilis n. sp., and evaluate its morphological characters in the light of its successful adaptation to life in caves.

Regressed but Not Gone: Patterns of Vision Gene Loss and Retention in Subterranean Mammals

Regressive evolution involves the degradation of formerly useful traits as organisms invade novel ecological niches. In animals, committing to a strict subterranean habit can lead to regression of the eyes, likely due to a limited exposure to light. Several lineages of subterranean mammals show evidence of such degeneration, which can include decreased organization of the retina, malformation of the lens, and subcutaneous positioning of the eye. Advances in DNA sequencing have revealed that this regression co-occurs with a degradation of genomic loci encoding visual functions, including protein-coding genes. Other dim light-adapted vertebrates with normal ocular anatomy, such as nocturnal and aquatic species, also demonstrate evidence of visual gene loss, but the absence of comparative studies has led to the untested assumption that subterranean mammals are special in the degree of this genomic regression. Additionally, previous studies have shown that not all vision genes have been lost in subterranean mammals, but it is unclear whether they are under relaxed selection and will ultimately be lost, are maintained due to pleiotropy or if natural selection is favoring the retention of the eye and certain critical underlying loci. Here I report that vision gene loss in subterranean mammals tends to be more extensive in quantity and differs in distribution from other dim light-adapted mammals, although some committed subterranean mammals demonstrate significant overlap with nocturnal microphthalmic species. In addition, blind subterranean mammals retain functional orthologs of non-pleiotropic visual genes that are evolving at rates consistent with purifying selection. Together, these results suggest that although living underground tends to lead to major losses of visual functions, natural selection is maintaining genes that support the eye, perhaps as an organ for circadian and/or circannual entrainment.

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.

At the confluence of vicariance and dispersal: Phylogeography of cavernicolous springtails (Collembola: Arrhopalitidae, Tomoceridae) codistributed across a geologically complex karst landscape in Illinois and Missouri

The processes of vicariance and dispersal are central to our understanding of diversification, yet determining the factors that influence these processes remains a significant challenge in evolutionary biology. Caves offer ideal systems for examining the mechanisms underlying isolation, divergence, and speciation. Intrinsic ecological differences among cavernicolous organisms, such as the degree of cave dependence, are thought to be major factors influencing patterns of genetic isolation in caves. Using a comparative phylogeographic approach, we employed mitochondrial and nuclear markers to assess the evolutionary history of two ecologically distinct groups of terrestrial cave-dwelling springtails (Collembola) in the genera Pygmarrhopalites (Arrhopalitidae) and Pogonognathellus (Tomoceridae) that are codistributed in caves throughout the Salem Plateau-a once continuous karst region, now bisected by the Mississippi River Valley in Illinois and Missouri. Contrasting phylogeographic patterns recovered for troglobiotic Pygmarrhopalites sp. and eutroglophilic Pogonognathellus sp. suggests that obligate associations with cave habitats can restrict dispersal across major geographic barriers such as rivers and valleys, but may also facilitate subterranean dispersal between neighboring cave systems. Pygmarrhopalites sp. populations spanning the Mississippi River Valley were estimated to have diverged 2.9-4.8 Ma, which we attribute to vicariance resulting from climatic and geological processes involved in Mississippi River Valley formation beginning during the late Pliocene/early Pleistocene. Lastly, we conclude that the detection of many deeply divergent, morphologically cryptic, and microendemic lineages highlights our poor understanding of microarthropod diversity in caves and exposes potential conservation concerns.