Evolutionary challenges of extreme environments (Part 2)

Insights into the Gut Microbiome of the South American Leaf-Toed Gecko (Phylodactylus gerropygus) Inhabiting the Core of the Atacama Desert

Living in arid environments presents unique challenges to organisms, including limited food and water, extreme temperatures, and UV exposure. Reptiles, such as the South American leaf-toed gecko (Phyllodactylus gerrhopygus), have evolved remarkable adaptations to thrive in such harsh conditions. The gut microbiome plays a critical role in host adaptation and health, yet its composition remains poorly characterized in desert reptiles. This study aimed to characterize the composition and abundance of the gut microbiome in P. gerrhopygus inhabiting the hyperarid Atacama Desert, taking into account potential sex differences. Fecal samples from adult female and male geckos were analyzed by 16S rRNA gene amplicon sequencing. No significant differences in bacterial alpha diversity were observed between the sexes. However, the phylum Bacteroidota was more abundant in females, while males had a higher Firmicutes/Bacteroidota ratio. The core microbiome was dominated by the phyla Bacteroidota, Firmicutes, and Proteobacteria in both sexes. Analysis of bacterial composition revealed 481 amplicon sequence variants (ASVs) shared by female and male geckos. In addition, 108 unique ASVs were exclusive to females, while 244 ASVs were unique to males. Although the overall bacterial composition did not differ significantly between the sexes, certain taxa exhibited higher relative abundances in each sex group. This study provides insight into the taxonomic structure of the gut microbiome in a desert-adapted reptile and highlights potential sex-specific differences. Understanding these microbial communities is critical for elucidating the mechanisms underlying host resilience in Earth's most arid environments, and for informing conservation efforts in the face of ongoing climate change.

DNA barcodes reveal population-dependent cryptic diversity and various cases of sympatry of Korean leptonetid spiders (Araneae: Leptonetidae)

Leptonetidae are tiny, rarely encountered spiders that mainly inhabit moist environments, such as caves, leaf litter, and rock piles. Because they are microhabitat specialists, most leptonetid species have short-range endemism, and rarely occur in sympatry. Their small size, relatively simple habitus features and reproductive organ structure increase the difficulty of identification. The identification of leptonetids and other spiders may also be time-consuming due to their sexual dimorphism, polymorphism, and lack of diagnostic characteristics in juveniles. DNA barcoding has been used as an effective tool for species identification to overcome these obstacles. Herein, we conducted a test of DNA barcoding based on 424 specimens of Korean Leptonetidae representing 76 morphospecies. A threshold of 4.2% based on maximum intraspecific genetic divergence was estimated to efficiently differentiate the morphospecies. The species assignments tested by five species delimitation methods (ABGD, ASAP, GMYC, PTP, and bPTP) were consistent with the morphological identifications for only 47 morphospecies (61.8%), indicating many cases of cryptic diversity among the remaining morphospecies. Furthermore, sympatry in leptonetids, which are known to be rare, was revealed to be common in South Korea, especially in epigean species. Our results showed that sympatries within families, congeners, and intraclades potentially occur throughout the entire region of Korea.

Adhesive force and endurance of the pelvic sucker across different modes of waterfall-climbing in gobiid fishes: Contrasting climbing mechanisms share aspects of ontogenetic change

Waterfall-climbing gobiids from oceanic islands use a suction-based adhesive mechanism formed by fused pelvic fins (pelvic sucker) and exhibit rock-climbing behavior during upstream migration. Although adhesion is a common feature of locomotion in these fishes, two distinct climbing styles - powerburst climbing and inching - have evolved. We compared the performance of the pelvic sucker during climbing across a range of body sizes between two species that use these different styles, collecting new data from the powerburst climber Lentipes concolor, and comparing these to published data for the inching climber Sicyopterus japonicus. Suction force for adhesion generated during continuous climbing did not differ between the species, with similar mean safety factors of 2.5-3.0. However, L. concolor engaged its pelvic sucker for a significantly longer duration of time (approximately 34 % longer per climbing cycle) than S. japonicus during continuous climbing. During sustained adhesion, both species exhibited non-linear scaling of fatigue time, with intermediate-sized individuals (e.g., large juveniles to small adults) showing the greatest endurance. However, the two species exhibited strikingly different maxima and variability in the endurance of their pelvic suckers. Maximum time to fatigue in L. concolor was less than half that of S. japonicus, but L. concolor showed more than double the variability of S. japonicus in time to fatigue. Our comparisons of these species reveal that despite differences in several aspects of their adhesive performance, some features of sucker function remain similar across climbing styles, including several related to how performance changes through ontogeny.

Integrative taxonomy of Leptonetela spiders (Araneae, Leptonetidae), with descriptions of 46 new species

Extreme environments, such as subterranean habitats, are suspected to be responsible for morphologically inseparable cryptic or sibling species and can bias biodiversity assessment. A DNA barcode is a short, standardized DNA sequence used for taxonomic purposes and has the potential to lessen the challenges presented by a biotic inventory. Here, we investigate the diversity of the genus Leptonetela Kratochvíl, 1978 that is endemic to karst systems in Eurasia using DNA barcoding. We analyzed 624 specimens using one mitochondrial gene fragment (COI). The results show that DNA barcoding is an efficient and rapid species identification method in this genus. DNA barcoding gap and automatic barcode gap discovery (ABGD) analyses indicated the existence of 90 species, a result consistent with previous taxonomic hypotheses, and supported the existence of extreme male pedipalpal tibial spine and median apophysis polymorphism in Leptonetela species, with direct implications for the taxonomy of the group and its diversity. Based on the molecular and morphological evidence, we delimit and diagnose 90 Leptonetela species, including the type species Leptonetela kanellisi(Deeleman-Reinhold, 1971). Forty-six of them are previously undescribed. The female of Leptonetela zhaiWang & Li, 2011 is reported for the first time. Leptonetela tianxinensis (Tong & Li, 2008) comb. nov. is transferred from the genus Leptoneta Simon, 1872;the genus Guineta Lin & Li, 2010 syn. nov. is a junior synonym of Leptonetela; Leptonetela gigachela(Lin & Li, 2010) comb. nov. is transferred from Guineta. The genus Sinoneta Lin & Li, 2010 syn. nov. is a junior synonym of Leptonetela; Leptonetela notabilis(Lin & Li, 2010) comb. nov. and Leptonetela sexdigiti(Lin & Li, 2010) comb. nov. are transferred from Sinoneta; Leptonetela sanchahe Wang & Li nom. nov. is proposed as a replacement name for Sinoneta palmata(Chen et al, 2010) because Leptonetela palmata is preoccupied.

Reduction of Energetic Demands through Modification of Body Size and Routine Metabolic Rates in Extremophile Fish

Variation in energy availability or maintenance costs in extreme environments can exert selection for efficient energy use, and reductions in organismal energy demand can be achieved in two ways: reducing body mass or metabolic suppression. Whether long-term exposure to extreme environmental conditions drives adaptive shifts in body mass or metabolic rates remains an open question. We studied body size variation and variation in routine metabolic rates in locally adapted populations of extremophile fish (Poecilia mexicana) living in toxic, hydrogen sulfide-rich springs and caves. We quantified size distributions and routine metabolic rates in wild-caught individuals from four habitat types. Compared with ancestral populations in nonsulfidic surface habitats, extremophile populations were characterized by significant reductions in body size. Despite elevated metabolic rates in cave fish, the body size reduction precipitated in significantly reduced energy demands in all extremophile populations. Laboratory experiments on common garden-raised fish indicated that elevated routine metabolic rates in cave fish likely have a genetic basis. The results of this study indicate that adaptation to extreme environments directly impacts energy metabolism, with fish living in cave and sulfide spring environments expending less energy overall during routine metabolism.

Patterns of Macroinvertebrate and Fish Diversity in Freshwater Sulphide Springs

Extreme environments are characterised by the presence of physicochemical stressors and provide unique study systems to address problems in evolutionary ecology research. Sulphide springs provide an example of extreme freshwater environments; because hydrogen sulphide’s adverse physiological effects induce mortality in metazoans even at micromolar concentrations. Sulphide springs occur worldwide, but while microbial communities in sulphide springs have received broad attention, little is known about macroinvertebrates and fish inhabiting these toxic environments. We reviewed qualitative occurrence records of sulphide spring faunas on a global scale and present a quantitative case study comparing diversity patterns in sulphidic and adjacent non-sulphidic habitats across replicated river drainages in Southern Mexico. While detailed studies in most regions of the world remain scarce, available data suggests that sulphide spring faunas are characterised by low species richness. Dipterans (among macroinvertebrates) and cyprinodontiforms (among fishes) appear to dominate the communities in these habitats. At least in fish, there is evidence for the presence of highly endemic species and populations exclusively inhabiting sulphide springs. We provide a detailed discussion of traits that might predispose certain taxonomic groups to colonize sulphide springs, how colonizers subsequently adapt to cope with sulphide toxicity, and how adaptation may be linked to speciation processes.

Evolutionary novelty versus exaptation: oral kinematics in feeding versus climbing in the waterfall-climbing Hawaiian Goby Sicyopterus stimpsoni

Species exposed to extreme environments often exhibit distinctive traits that help meet the demands of such habitats. Such traits could evolve independently, but under intense selective pressures of extreme environments some existing structures or behaviors might be coopted to meet specialized demands, evolving via the process of exaptation. We evaluated the potential for exaptation to have operated in the evolution of novel behaviors of the waterfall-climbing gobiid fish genus Sicyopterus. These fish use an “inching” behavior to climb waterfalls, in which an oral sucker is cyclically protruded and attached to the climbing surface. They also exhibit a distinctive feeding behavior, in which the premaxilla is cyclically protruded to scrape diatoms from the substrate. Given the similarity of these patterns, we hypothesized that one might have been coopted from the other. To evaluate this, we filmed climbing and feeding in Sicyopterus stimpsoni from Hawai’i, and measured oral kinematics for two comparisons. First, we compared feeding kinematics of S. stimpsoni with those for two suction feeding gobiids (Awaous guamensis and Lentipes concolor), assessing what novel jaw movements were required for algal grazing. Second, we quantified the similarity of oral kinematics between feeding and climbing in S. stimpsoni, evaluating the potential for either to represent an exaptation from the other. Premaxillary movements showed the greatest differences between scraping and suction feeding taxa. Between feeding and climbing, overall profiles of oral kinematics matched closely for most variables in S. stimpsoni, with only a few showing significant differences in maximum values. Although current data cannot resolve whether oral movements for climbing were coopted from feeding, or feeding movements coopted from climbing, similarities between feeding and climbing kinematics in S. stimpsoni are consistent with evidence of exaptation, with modifications, between these behaviors. Such comparisons can provide insight into the evolutionary mechanisms facilitating exploitation of extreme habitats.

Chronobiology of deep-water decapod crustaceans on continental margins

Species have evolved biological rhythms in behaviour and physiology with a 24-h periodicity in order to increase their fitness, anticipating the onset of unfavourable habitat conditions. In marine organisms inhabiting deep-water continental margins (i.e. the submerged outer edges of continents), day-night activity rhythms are often referred to in three ways: vertical water column migrations (i.e. pelagic), horizontal displacements within benthic boundary layer of the continental margin, along bathymetric gradients (i.e. nektobenthic), and endobenthic movements (i.e. rhythmic emergence from the substrate). Many studies have been conducted on crustacean decapods that migrate vertically in the water column, but much less information is available for other endobenthic and nektobenthic species. Also, the types of displacement and major life habits of most marine species are still largely unknown, especially in deep-water continental margins, where steep clines in habitat factors (i.e. light intensity and its spectral quality, sediment characteristics, and hydrography) take place. This is the result of technical difficulties in performing temporally scheduled sampling and laboratory testing on living specimens. According to this scenario, there are several major issues that still need extensive research in deep-water crustacean decapods. First, the regulation of their behaviour and physiology by a biological clock is almost unknown compared to data for coastal species that are easily accessible to direct observation and sampling. Second, biological rhythms may change at different life stages (i.e. size-related variations) or at different moments of the reproductive cycle (e.g. at egg-bearing) based on different intra- and interspecific interactions. Third, there is still a major lack of knowledge on the links that exist among the observed bathymetric distributions of species and selected autoecological traits that are controlled by their biological clock, such as the diel rhythm of behaviour. Species evolved in a photically variable environment where intra- and inter-specific interactions change along with the community structure over 24 h. Accordingly, the regulation of their biology through a biological clock may be the major evolutionary constraint that is responsible for their reported bathymetric distributions. In this review, our aim is to propose a series of innovative guidelines for a discussion of the modulation of behavioural rhythms of adult decapod crustaceans, focusing on the deep waters of the continental margin areas of the Mediterranean as a paradigm for other marine zones of the world.

Do extreme environments provide a refuge from pathogens? A phylogenetic test using serpentine flax

Abiotically extreme environments are often associated with physiologically stressful conditions, small, low-density populations, and depauperate flora and fauna relative to more benign settings. A possible consequence of this may be that organisms that occupy these stressful habitats receive fitness benefits associated with reductions in the frequency and/or intensity of antagonistic species interactions. I investigated a particular form of this effect, formalized as the "pathogen refuge hypothesis," through a study of 13 species of wild flax that grow on stressful serpentine soils and are often infected by a pathogenic fungal rust. The host species vary in the degree of their serpentine association: some specialize on extreme serpentine soils, while others are generalists that occur on soils with a wide range of serpentine influence. Phylogenetically explicit analyses of soil chemistry and field-measured disease levels indicated that rust disease was significantly less frequent and severe in flax populations growing in more stressful, low-calcium serpentine soils. These findings may help to explain the persistence of extremophile species in habitats where stressful physical conditions often impose strong autecological fitness costs on associated organisms. Ancestral state reconstruction of serpentine soil tolerance (approximated using soil calcium concentrations) suggested that the ability to tolerate extreme serpentine soils may have evolved multiple times within the focal genus.

Phylogeography of a subterranean amphipod reveals cryptic diversity and dynamic evolution in extreme environments

Extreme conditions in subsurface are suspected to be responsible for morphological convergences, and so to bias biodiversity assessment. Subterranean organisms are also considered as having poor dispersal abilities that in turn generate a large number of endemic species when habitat is fragmented. Here we test these general hypotheses using the subterranean amphipod Niphargus virei. All our phylogenetic analyses (Bayesian, maximum likelihood and distance), based on two independent genes (28S and COI), revealed the same tripartite structure. N. virei populations from Benelux, Jura region and the rest of France appeared as independent evolutionary units. Molecular rates estimated via global or Bayesian relaxed clock suggest that this split is at least 13 million years old and accredit the cryptic diversity hypothesis. Moreover, the geographical distribution of these lineages showed some evidence of recent dispersal through apparent vicariant barrier. In consequence, we argue that future analyses of evolution and biogeography in subsurface, or more generally in extreme environments, should consider dispersal ability as an evolving trait and morphology as a potentially biased marker.