Cave Species Research Articles

Two new hypogean species of the genus Triplophysa (Osteichthyes, Cypriniformes, Nemacheilidae) from Guizhou Province, Southwest China, with underestimated diversity.

Two new species of the genus Triplophysa from southwestern Guizhou Province, China, are described. These are Triplophysaziyunensis Wu, Luo, Xiao & Zhou, sp. nov. and Triplophysayaluwang Lan, Liu, Zhou & Zhou, sp. nov. from Maoying Town, Ziyun County, Guizhou Province, China. Triplophysaziyunensis Wu, Luo, Xiao & Zhou, sp. nov. is distinguished from other hypogean species of the genus Triplophysa by having a combination of the following characteristics: body naked, scaleless, pigmented markings on surface of body, except ventral; eyes reduced, diameter 2.4-4.9% of head length; pelvic-fin tip extending to anus; tip of pectoral fin not reaching pelvic fin origin; anterior and posterior nostrils closely set, with anterior nostril elongated to a barbel-like tip; tip of outrostral barbel extending backward, not reaching anterior margin of the eye; lateral line complete; posterior chamber of air bladder degenerated; and fin differences. Triplophysayaluwang Lan, Liu, Zhou & Zhou, sp. nov. is distinguished from other hypogean species of the genus Triplophysa by having a combination of the following characteristics: body naked, scaleless, with irregular pale and dark brownish brown markings, except ventrally; eyes reduced, diameter 4.6-6.1% of head length; pelvic-fin tip reaching anus; tip of pectoral fin not reaching to pelvic fin origin; anterior and posterior nostrils closely set, with anterior nostril elongated to a barbel-like tip; tip of outrostral barbel extending backward, not reaching to anterior margin of the eye; lateral line complete; posterior chamber of air bladder degenerated; and fin differences. Mitochondrial Cyt b revealed relatively small genetic differences, 1.4-2.0%, between the two new species and close relatives. Nuclear gene RAG1 indicated that the two new species possessed unique haplotypes with multiple linking mutations. This study emphasizes the importance of utilizing nuclear genes to identify new species in rapidly speciation cave species, with small genetic differences due to mitochondrial introgression occurring interspecies.

A phylogeographic approach to Sulawesi’s Maros karst shrimp fauna (Decapoda, Atyidae) reveals several cave invasions and challenges current taxonomic hypotheses

Abstract The unique endemic cave fauna of the Maros karst cave system (Sulawesi, Indonesia) includes atyid freshwater shrimps only known from their species descriptions. An extensive survey revealed a total of ten species in epigean and subterranean rivers: Two non-endemic, four species endemic to Sulawesi (genus Caridina) and four stygobiont species (genus Caridina, Marosina, and Parisia) only endemic to the Maros karst. A molecular phylogeny revealed (1) two independent colonizations of Sulawesi’s Maros karst caves by species of Caridina (Clade 1) derived from endemic ancestors, and (2) an exclusively stygobiont group (Clade 2, Marosina, Parisia) possibly derived from an amphidromous, anchialine cave-dweller. Our approach revealed another cryptic cave species of Caridina and challenges the taxonomic status of four Sulawesi endemics. In conclusion, the freshwater shrimps of the Maros karst are a challenging but rewarding group that can contribute to our understanding of the evolution of cave-dwelling species and atyid phylogenetics.

A New Genus of Prodidominae Cave Spider from a Paleoburrow and Ferruginous Caves in Brazil (Araneae: Prodidomidae)

A new monotypic genus of Prodidominae, Paleotoca gen. n., is proposed to include one cave species collected in a paleoburrow and ferruginous caves from Quadrilátero Ferrífero, Minas Gerais, Brazil: Paleotoca diminassp. n. (♂♀). The new genus is closely related to other Neotropical Prodidominae by sharing the classic claw tuft clasper. Paleotoca gen. n. is diagnosed by the absence of a dorsal abdominal scutum, a ventral parallel rows of strong spines on the tibia and metatarsus I–II, a lack of a conductor, a discrete median apophysis on the bulb and a bifid retrolateral tibial apophysis in the male palp, a posterior extension that is beak-shaped, and folds of a copulatory duct ventrally visible in the female epigyne. Like other Prodidominae species from caves, P. diminassp. n. is a troglobitic spider with morphological characteristics that indicate specialization to live in subterranean environments, including reduction in cuticular pigments, eye loss, heavy spination and trichobothria.

From the front door to the basement: Invertebrate communities' structure as a proxy for determining cave zonation in Neotropics

AbstractIn caves, the absence of natural light in deeper regions starkly contrasts with the entrance areas, which still exhibit a light gradient extending into the cave interior. This interplay with the structural gradient of the environment potentially exerts distinct influences on invertebrate communities residing in different cave light zones. To investigate this, we formulated a hypothesis positing that communities within distinct cave light zones respond differently to habitat structure and microclimatic conditions. Our approach involved a spatial multi‐scale sampling of invertebrates and the application of statistical analyses to contrast the responses of communities inhabiting photic and aphotic zones. Photic zone richness is influenced by factors such as air moisture, resource availability, root presence, and shelter diversity. In contrast, the richness of communities in aphotic zones is shaped by resource availability, the presence of roots, branches, and distance from the cave entrance. As expected, the richness in the photic zone surpasses that of the deeper regions, highlighting the challenges faced by invertebrates attempting to establish themselves in the aphotic zone. The species composition of faunal communities varied predictably from the entrance to the aphotic zone, and the three most important factors driving this variation were geographic distance, humidity, and distance from the entrance. The composition between these cave zones differs significantly, primarily due to the high number of obligate cave species predominantly inhabiting the aphotic region. Indeed, communities associated with different cave zones exhibit distinct responses to resource, microclimatic, and structural variables.Abstract in Portuguese is available with online material.

Sensing in the dark: Constructive evolution of the lateral line system in blind populations of Astyanax mexicanus.

Cave-adapted animals evolve a suite of regressive and constructive traits that allow survival in the dark. Most studies aiming at understanding cave animal evolution have focused on the genetics and environmental underpinnings of regressive traits, with special emphasis on vision loss. Possibly as a result of vision loss, other non-visual sensory systems have expanded and compensated in cave species. For instance, in many cave-dwelling fish species, including the blind cavefish of the Mexican tetra, Astyanax mexicanus, a major non-visual mechanosensory system called the lateral line, compensated for vision loss through morphological expansions. While substantial work has shed light on constructive adaptation of this system, there are still many open questions regarding its developmental origin, synaptic plasticity, and overall adaptive value. This review provides a snapshot of the current state of knowledge of lateral line adaption in A. mexicanus, with an emphasis on anatomy, synaptic plasticity, and behavior. Multiple open avenues for future research in this system, and how these can be leveraged as tools for both evolutionary biology and evolutionary medicine, are discussed.

Microclimatic Influences on the Abundance of Three Non-Troglobiont Species

Subterranean environments are often characterized by a natural gradient of microclimatic conditions and trophic resources, showing a higher trophic availability and a lower microclimatic stability in the shallowest area (close to the cave entrance), while the opposite occurs in the deepest sections. The shallowest areas of subterranean environments (e.g., the entrance and twilight zone, Mesovoid Shallow Substratum) act as ecotones between the surface habitats and the deep areas, creating a particular habitat which can be exploited by numerous species with different degrees of adaptation to subterranean environments. Species living in these ecotones may hold a key role in sustaining the entire ecosystem, as they are likely one of the major drivers of allochthonous organic matter. Indeed, these species are usually facultative cave-dwellers, meaning that they are able to exit and forage on the surface. Once these species are back inside the cave, they provide the local community with different typologies of organic matter (e.g., feces, eggs), which represent one of the most important sources of organic carbon. Therefore, studying which ecological features may exert significant effects on the abundance of these species may be of great help in understanding the ecosystem dynamics and the functional role of each species. In this study we analyzed the data collected through a year-round monitoring program, aiming to assess the potential effects that both abiotic and biotic features may have on the abundance of three facultative cave species. We focused on seven caves located in Monte Albo (Sardinia, Italy). The cave environments were divided into 3-meter sectors, and within each cave sector, microclimatic and biological data were seasonally recorded. We focused on the following facultative cave species: the spiders Metellina merianae and Tegenaria sp. and the snail Oxychilus oppressus. Different relationships were observed between the ecological features and the abundance of the three species. The two spiders were more abundant in warmer cave sectors closer to the cave entrance, especially the M. merianae. On the other hand, the snail tended to be more abundant farther from the cave entrance and in more illuminated cave sectors, probably because sunlight promotes the abundance of some of its trophic resources (e.g., lichens, vegetation). Furthermore, O. oppressus was the only species whose abundance and cave distribution was significantly affected by seasonality. This study provides useful and novel information to understand the population dynamics of facultative cave species and their role in subterranean ecosystems.

Description of five new species of the subgenus Tachycines (Gymnaeta) (Rhaphidophoridae: Aemodogryllinae: Aemodogryllini) from caves in Guizhou, China.

The genus Tachycines contains two subgenera: T. (Tachycines) and T. (Gymnaeta), and the species of this genus occur mainly in Southeast and East Asia, including Myanmar, Philippines, Vietnam, India, and China. Many species of the subgenus Tachycines (Gymnaeta) are cavernicolous. In this study, five new cave species of this subgenus, namely Tachycines (Gymnaeta) lingulatus sp. nov., Tachycines (Gymnaeta) multispinus sp. nov., Tachycines (Gymnaeta) microtuberculatus sp. nov., Tachycines (Gymnaeta) ovalius sp. nov., and Tachycines (Gymnaeta) conicus sp. nov., from Guizhou Province, China are identified and described. Morphological information of males and females of the five new species are provided.

Four new hypogean species of the genus Triplophysa (Osteichthyes, Cypriniformes, Nemacheilidae) from Guizhou Province, Southwest China, based on molecular and morphological data

Recently described cave species of the genus Triplophysa have been discovered in southwestern China, suggesting that the diversity of the genus is severely underestimated and that there may be many undescribed species. In this work, four new species of the genus Triplophysa are described from southwestern Guizhou Province, China, namely Triplophysa cehengensis Luo, Mao, Zhao, Xiao & Zhou, sp. nov. and Triplophysa rongduensis Mao, Zhao, Yu, Xiao & Zhou, sp. nov. from Rongdu Town, Ceheng County, Guizhou, Triplophysa panzhouensis Yu, Luo, Lan, Xiao & Zhou, sp. nov. from Hongguo Town, Panzhou City, Guizhou, and Triplophysa anlongensis Song, Luo, Lan, Zhao, Xiao & Zhou, sp. nov. from Xinglong Town, Anlong County, Guizhou. These four new species can be distinguished from all recognized congeners by a combination of morphological characteristics and significant genetic divergences. The discovery of these species increases the number of known cave species within the genus Triplophysa to 39, making the genus the second most diverse group of cave fishes in China after the golden-line fish genus Sinocyclocheilus. Based on the non-monophyletic relationships of the different watershed systems in the phylogenetic tree, this study also discusses the use of cave species of the genus Triplophysa to determine the possible historical connectivity of river systems.

The first record of a stygobiotic form of Garra rufa (Heckel, 1843), sympatric with Garra tashanensis Mousavi-Sabet, Vatandoust, Fatemi & Eagderi, 2016 (Teleostei, Cyprinidae), in Iranian subterranean waters

We report the first finding of the stygobiotic form of the cyprinid fish Garra rufa (Heckel, 1843), discovered in a single locality in southwestern Iran, while the epigean form of the species is widely distributed in western Asia (Iran, Jordan, Lebanon, Turkey, and Syria). We also report a new locality for its hypogean congener, Garra tashanensis, about 5 km east of its type locality. The two species occur in syntopy in outflows of the Tang-e-Ban, a seasonal karstic spring that only has flowing water during winter and spring, when fish individuals are washed from the cave to the surface. Identification of the investigated samples was confirmed by morphological analyses, COI distances, and a phylogenetic tree. These findings suggest the existence of a large karst aquifer in the Tashan area that harbours several cave species of fish, crustaceans, and gastropods and may have considerable conservation implications.

There and Back Again—The Igatu Hotspot Siliciclastic Caves: Expanding the Data for Subterranean Fauna in Brazil, Chapada Diamantina Region

The caves of Igatu, municipality of Andaraí, belonging to the region known as Chapada Diamantina represent a new hotspot of subterranean fauna. These caves are siliciclastic, which are sedimentary rocks where silica predominates, such as sandstones and (following metamorphism) quartzites, which makes them even more relevant from the point of view of subterranean diversity. For five caves, which we named Igatu Cave System (ICS), thirty-seven obligate cave species were found, of which thirty-five were troglobitic and two were stygobitic. The troglobitic taxa for ICS belong to three phyla, nine classes, 18 orders, and 32 families, representing a high phylogenetic diversity. Some taxa were, for the first time, reported as troglobitic in Brazil and even worldwide, such as Acari and scutigeromorphans (Chilopoda). We started the studies in 2009 and continue trough long-term monitoring projects. Some threats, severe in the past, such as “garimpo’’ (illegal small-scale artisanal mining) continue nowadays in an incipient way; however, the urban expansion due to the touristic appeal is also considered a threat. Our data ranked ICS as the Brazilian hotspot with the highest number of troglobitic/stygobitic species.

The general significance of variability in cave regressive traits for evolution

Abstract Rudimentary structures are variable, which is most impressively demonstrated by the eyes and dark body pigmentation of species evolving in caves. As these can often still be crossed with their ancestral surface sister forms, variability is usually attributed to hybridization. For two invertebrate and two vertebrate cave species, I show here that in spite of genetic separation between surface and cave forms, variability of the rudimentary structures is nonetheless present. This probably results from the loss of stabilizing selection, because neutral deleterious mutations are no longer eliminated. In contrast, compensatory traits in caves do not differ from their surface forms with respect to variability, because both are subject to selection. In the phylogenetically young Astyanax cave populations, traits compensatory to cave life have achieved different stages of adaptation compared to the phylogenetically old populations. They may show the same degree of differentiation, be intermediate or do not differ from the surface ancestor. This is attributed to different intensities of selection.

Status of vertebrate species in Danial Cave, northern Iran

AbstractCave biodiversity and ecosystems are underexplored. To guide conservation needs for visitor management, we surveyed the 2,158 m long Danial Cave in northern Iran for vertebrate fauna. We identified four mammalian and two amphibian species in the cave: the greater horseshoe bat Rhinolophus ferrumequinum, Blasius's horseshoe bat Rhinolophus blasii, the lesser mouse-eared myotis Myotis blythii, the Hyrcanian field mouse Apodemus hyrcanicus, the Hyrcanian wood frog Rana pseudodalmatina and the Eurasian marsh frog Pelophylax ridibundus. Considering the increasing tourism pressures at Danial Cave, information on cave fauna is imperative for the conservation management of unique and endemic cave species.

The Água Clara Cave System in Northeastern Brazil: The Richest Hotspot of Subterranean Biodiversity in South America

The Água Clara Cave System (ACCS) in Brazil is the richest hotspot of subterranean biodiversity in South America. In this study, we present an updated list of cave-restricted species in the ACCS and compare it with previously published hotspots in Brazil. Our list of cave-obligate fauna comprises 31 species, including 23 troglobionts and 8 stygobionts. The exceptional diversity of the ACCS can be attributed to factors related to the high dispersal potential of cave fauna within the system, high surface productivity, and the large size of the cave system size. Notably, we observed highly troglomorphic species in the ACCS, some of which are the most troglomorphic species in their respective groups in Brazil. The huge volume of galleries, high humidity, and trophic conditions prevailing in the ACCS may have played a role in shaping the strong troglomorphic traits observed in these species. However, all the obligate cave species in the ACCS require conservation attention and are at an elevated risk of extinction due to their limited ranges, few occurrences, and many potential threats. This study sheds light on the biodiversity and conservation status of cave-restricted fauna in the ACCS and highlights the importance of protecting these unique ecosystems.

Density estimation of the main structuring sessile species in underwater marine caves with a deep learning approach

Monitoring marine biodiversity is a challenge in some vulnerable and difficult-to-access habitats, such as underwater caves. Underwater caves are a great focus of biodiversity, concentrating a large number of species in their environment. However, most of the sessile species that live on the rocky walls are very vulnerable, and they are often threatened by different pressures. The use of these spaces as a destination for recreational divers can cause different impacts on the benthic habitat. In this work, we propose a methodology based on video recordings of cave walls and image analysis with deep learning algorithms to estimate the spatial density of structuring species in a study area. We propose a combination of automatic frame overlap detection, estimation of the actual extent of surface cover, and semantic segmentation of the main 10 species of corals and sponges to obtain species density maps. These maps can be the data source for monitoring biodiversity over time. In this paper, we analyzed the performance of three different semantic segmentation algorithms and backbones for this task and found that the Mask R-CNN model with the Xception101 backbone achieves the best accuracy, with an average segmentation accuracy of 82%.

Trait Loss in Evolution: What Cavefish Have Taught Us About Mechanisms Underlying Eye Regression.

Reduction or complete loss of traits is a common occurrence throughout evolutionary history. In spite of this, numerous questions remain about why and how trait loss has occurred. Cave animals are an excellent system in which these questions can be answered as multiple traits, including eyes and pigmentation, have been repeatedly reduced or lost across populations of cave species. This review focuses on how the blind Mexican cavefish, Astyanax mexicanus, has been used as a model system for examining the developmental, genetic and evolutionary mechanisms that underlie eye regression in cave animals. We focus on multiple aspects of how eye regression evolved in A. mexicanus, including the developmental and genetic pathways that contribute to eye regression, the effects of evolution of eye regression on other traits that have also evolved in A. mexicanus, and the evolutionary forces contributing to eye regression. We also discuss what is known about the repeated evolution of eye regression, both across populations of A. mexicanus cavefish, and across cave animals more generally. Finally, we offer perspectives on how cavefish can be used in the future to further elucidate mechanisms underlying trait loss using tools and resources that have recently become available.

Sponge Fauna of the Apulian Marine Caves (Southern Italy): Current State of Knowledge

Submerged and semi-submerged marine caves are considered a European habitat of Community Interest as they preserve one of the most important biodiversity heritages in the Mediterranean and serve as refugia for endemic and/or “relict” species. Among sessile benthic taxa, caves represent significant reservoirs of sponge species richness and are well representative of the entire poriferan Mediterranean fauna. In order to assess the current knowledge of sponge species in marine caves along the Apulian coast, this study gathered data from the available literature (national and international scientific publications and grey literature) with original data, surveying 26 marine caves in the area. A total of 145 Porifera species were reported in marine caves on the Apulian coast, including 117 in the Tremiti archipelago, 33 along the Adriatic coast of Bari and 73 along the Salento Peninsula. Original data includes new records for nine species in the Corvine cave, two in the Murene cave and one in the Zinzulusa cave. Our results suggest that marine cave communities along the Apulian coast are not uniformly surveyed, being the caves of the Tremiti Islands and those of the Salento Peninsula among the best studied, while large stretches of the regional coast, although particularly rich in marine caves, are poorly investigated for their sponge fauna.

Biodiversity Of Bryophyte Of Photic Zones Of Caves In The Kutuk Tract (Southern Ural, Bashkiria)

This article presents results of a study of bryophytes in seven caves of the Kutuk tract of the National Park «Bashkiria» of the Republic of Bashkortostan, including the largest cave in Bashkiria – Kutuk-Sumgan.Fifty-five bryophytes species were found in the studied caves. The dominant species in all caves was Timmia bavarica. The species composition of bryophytes of each cave is unique. Among identified bryophytes species 23, species were found only in one cave, and 11 species in 2 caves. During our survey, we found 31 species in Kutuk-Sumgan Cave, 21 species in Kutuk-2 and Kutuk-3 caves, 19 species in Kutuk-4 caves, 18 species in Vintovaya and Zigzag caves and 14 species in Kutuk-1 cave. Using the Jaccard and Phi-squared similarity indices, we revealed the stability of the bryoflora of the caves in different years and show its changes. Changes in the composition and structure of mosses in the Kutuk tract may be caused by mechanical influences. Benchmark similarity analysis allowed us to determine the influence of entrance morphology and glaciation in the photic zone of the caves on the composition of bryophytes.Using the Kutuk tract caves as an example, it is shown that in the primary analysis of the bryoflora, when selecting a characteristic cave, up to 40% of the total species composition of the caves can be identified in a single cave. The current study of Kutuk tract caves shows that identification of the primere analyses of bioflora permits identification of up to 40% of species composition of an individual cave.Three criteria for selecting a characteristic cave were identified: size of the photic zone and morphology of the entrance, diversity of habitats, and the least degree of disturbance.

Why the delay in recognizing terrestrial obligate cave species in the tropics?

“Nothing could possibly live there!” They believed. Indeed, until recently, few specialized cave- adapted animals were known from volcanic, tropical, or oceanic island caves, and plausible theories had been put forward to explain their absence. But assume nothing in science! One must illuminate, explore, and survey habitats before declaring them barren. Our understanding of cave biology changed dramatically about 50 years ago following the serendipitous discovery of cave-adapted terrestrial arthropods in Brazil and on the young oceanic islands of the Galápagos and Hawai‘i. These discoveries and subsequent studies on the evolutionary ecology of cave animals have revealed a remarkable hidden fauna and created new sub- disciplines within biospeleology. Biological surveys of caves in other regions have continued to expand our understanding of the evolution, adaptation, and ecology of the subterranean biome. We now predict that, rather than being relicts trapped in caves by changing climate, many animals actively colonized caves and adapted to exploit food resources wherever there were suitable subterranean voids. The physical environment in caves can be determined with great precision because the habitat is buffered by rock. Furthermore, the bizarre adaptations displayed by obligatory cave animals are similar across many taxonomic groups. These two characteristics make caves nearly ideal natural laboratories for studying evolution and ecology. However, to the untrained researcher, caves can appear hostile and dangerous, and in fact, fieldwork in caves requires a unique marriage of athletic ability and science. In other words, cave research is exciting! In this contribution, I describe the exploration, discovery, and research in tropical caves and describe the factors that delayed the recognition of a significant tropical cave fauna.

Introduced species in Mediterranean marine caves: an increasing but neglected threat

Marine caves are protected habitats with high biodiversity and low ecological resilience, vulnerable to multiple pressures including biological invasions. Therefore, comprehensive lists of alien species in sea caves and assessments of their impacts are urgently needed. This study aimed to provide an updated and validated list of introduced species in marine caves of the Mediterranean Sea based on the latest available checklist (2014). The number of introduced species in the updated list (December 2022 status) has doubled in the last eight years. The updated checklist includes 126 species (107 alien, 15 cryptogenic, two crypto-expanding, and two questionable) belonging to 12 phyla. The highest number of introduced species in caves was evidenced in the eastern Mediterranean (105), specifically in the Levantine (99) and the Aegean (34) ecoregions. Most introduced species originated from the Indo-Pacific. Most species entered the Mediterranean Sea through the Suez Canal, followed by species transferred via vessels. Most introduced species were found at the entrance and in the semi-dark zone of caves (60 and 52 species, respectively), with only 19 species being reported from the dark zone. Approximately 28% of the introduced species have a high impact on ecosystems, including nine of the ten worst invasive species in the Mediterranean Sea. Despite the lack of data on the impact of introduced species on marine cave biodiversity, given their high species richness and the recently reported population explosions of some alien fish in the eastern Mediterranean, our results highlight the need for continuous inventorying and monitoring.

Geology, climate, and hydrochemistry shape the spatial patterns of multiple diversity facets and functional traits of fishes

AbstractIn a large river with significant environmental variations in space (i.e., microhabitat) or over time (i.e., seasonality and/or long‐term trend), discovering the spatial changes in fish diversity, distributions, and functional traits would provide an important foundation for the understanding of ecosystem structure and function. In the Pearl River in China, three datasets as fish distribution, species functional traits, and environmental variables were constructed and sorted to (1) test the relationships between and congruence of taxonomic diversity, functional diversity, and phylogenetic diversity by a randomisation procedure, (2) map the spatial pattern of diversity and the correlation to environmental variables by maximal information coefficient, and (3) determine the fish traits tendency under environmental changes by the fourth‐corner method. The Pearl River possesses the highest fish richness among all the rivers in China, with 438 freshwater fish species including 119 cave species. At basin scale, phylogenetic diversity showed faster change than functional diversity, suggesting a little divergence of functional traits despite high phenotypic or genetic diversity across species, as parallel evolution. However, at a small scale, when only considering cave fishes, the variation rate of species traits was faster than that of species increase, as evolutionary radiation in a variety of microhabitats. For all three aspects of diversity, random permutation tests confirmed that congruence values in each grid cell were significantly different from the random expectations. Besides widely accepted variables such as altitude, precipitation, and slope concerned with fish biogeography, hydrochemical variables showed influential impacts on the morphological and growth traits of fishes in the Pearl River characterised by the dominance of the karst habitat.