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Capturing arthropod diversity in complex cave systems
Diversity and Distributions
Abstract
Aim: Identify the optimal combination of sampling techniques to maximize the detection of diversity of cave-dwelling arthropods.
Location: Central-western New Mexico; northwestern Arizona; Rapa Nui, Chile.
Methods: From 26 caves across three geographically distinct areas in the Western Hemisphere, arthropods were sampled using opportunistic collecting, timed searches, and baited pitfall trapping in all caves, and direct intuitive searches and bait sampling at select caves. To elucidate the techniques or combination of techniques for maximizing sampling completeness and efficiency, we examined our sampling results using nonmetric multidimensional scaling (NMDS), analysis of similarity (ANOSIM), Wilcoxon signed-rank tests, species richness estimators and species accumulation curves.
Results: To maximize the detection of cave-dwelling arthropod species, one must apply multiple sampling techniques and specifically sample unique microhabitats. For example, by sampling cave deep zones and nutrient resource sites, we identified several undescribed cave-adapted and/or cave-restricted taxa in the southwestern United States and eight new species of presumed cave-restricted arthropods on Rapa Nui that would otherwise have been missed. Sampling techniques differed in their detection of both management concern species (e.g., newly discovered cave-adapted/restricted species, range expansions of cave-restricted species and newly confirmed alien species) and specific taxonomic groups. Spiders were detected primarily with visual search techniques (direct intuitive searches, opportunistic collecting and timed searches), while most beetles were detected using pitfall traps. Each sampling technique uniquely identified species of management concern further strengthening the importance of a multi-technique sampling approach.
Main conclusions: Multiple sampling techniques were required to best characterize cave arthropod diversity. For techniques applied uniformly across all caves, each technique uniquely detected between ~40% and 67% of the total species observed. Also, sampling cave deep zones and nutrient resource sites was critical for both increasing the number of species detected and maximizing the likelihood of detecting management concern species.
Supplementary resource (1)
Data
July 2018
... Biotic inventories of cave faunas often focus on obligate cave species (e.g., Culver and Pipan 2009)-as these species are typically endemic and often of management concern. A few studies have examined faunal changes from the entrance to the deep zone (e.g., Prous et al. 2004;Tobin et al. 2013;Wynne et al. 2018;Mazebedi and Hesselberg 2020). However, the definitions of the entrance and twilight zones are either not given or inconsistently applied, making comparisons on ecol ogy and diversity within these zones among caves and across regions difficult. ...
... Additionally, autochthonous nutrients are produced locally by chemoautotrophic microorganisms (e.g., Sarbu et al. 1996;Flot et al. 2010;Naaman 2011). Recognition of the importance of nutrients as a determinant of subterranean diversity has led to the strategy of concentrating efforts during biological surveys to areas where abundant nutrients occur (Culver 2008;Wynne et al. 2018). In a comprehensive study of microinvertebrates in a cave in southern Mexico, Palacios-Vargas et al. (2011) found that species abundance was greatest in the most nutrient-rich resource (guano), whereas the highest species diversity occurred in leaf-litter habitats (i.e., the most variable habitat due to the varied input of diff er ent litter types). ...
... High priority should be given to inventory subterranean habitats in poorly known regions to address knowledge gaps (Wynne et al. 2021). All taxa and microhabitats should be sampled (Wynne et al. 2018;); however, for efficiency, initial inventories may need to focus on the most promising substrates and microhabitats-in par tic u lar, the selection of sites chosen based on the influential factors described in this chapter. Biological surveys are critical for understanding cave diversity, developing effective protective management programs, and answering fundamental research questions in biospeleology (Wynne et al. 2018;Mammola et al. 2020;. ...
This chapter within the book, "Diversity and Speciation of Subterranean Fauna", is now available: https://www.press.jhu.edu/books/title/12872/cave-biodiversity
Caves are extraordinary landforms that commonly harbor communities of bizarre animals adapted to live and reproduce only underground. Although biological diversity is relatively low in comparison to overlying surface habitats, caves can support many locally endemic species. With its unique environment and specialized fauna, caves are well-suited for evolutionary ecology studies. Caves form in most geologic substrates, although the two best studied systems are solution caves in limestone, dolomite, and gypsum and in basaltic lava flows. Besides caves, animals live in the system of interconnected voids scattered through the substratum. Specialized cave animals inhabit caves and cave-like voids from huge caverns hundreds of meters in diameter and kilometers in length to tiny spaces barely one millimeter in diameter. We discuss how the number of species and their abundances are determined by biotic (living organisms, their interactions, and organic matter) and abiotic (inorganic nutrients, types of substrates, geologic history, and climate) parameters, and how these factors often interact in complex ways. For example, greater surface productivity increases subterranean biodiversity whereas pedogenesis and major disturbances can decrease diversity. Despite our increased understanding in the drivers of subterranean diversity, most caves and cave regions have yet to be inventoried, and the true biological diversity remains unknown. In addition, many cave taxa remain poorly studied or unknown because of the difficulty of collecting adequate specimens, the assumption that individuals detected are in caves accidentally, and the lack of taxonomic authorities. There is an urgency to fill this knowledge gap since the next few decades may be our last chance to conduct all taxa biological inventories of subterranean communities to determine the pre-Anthropocene biological diversity. As cave passages are not the main habitat supporting subterranean diversity, conservation programs and protected areas need to shift their priority from individual caves to protecting subterranean habitats by including sufficient surface areas around cave footprints to serve as buffer areas. This chapter reviews the main factors that affect biological diversity in terrestrial subterranean communities, which we hope will aid in planning more efficient biological studies in caves, as well as facilitate the development of data-driven conservation management programs.
... The passive collecting comprises pitfall traps, Winkler extractor, and Berlese-Tullgren funnel extractor. The active collecting includes handcollecting, timed searches, quadrat sampling, and baiting (Hunt and Millar 2001;Sabu et al. 2011;Pellegrini and Ferreira 2012a;Oliveira 2014;Bichuette et al. 2015;Wynne et al. 2018;Bichuette et al. 2019). It is recommended that the combination of multiple methods and the sampling of unique microhabitats (e.g., bat guano deposits and water bodies) seem to be efficient (Pellegrini and Ferreira 2012a;Wynne et al. 2018;Borges-Filho et al. 2019). ...
... The active collecting includes handcollecting, timed searches, quadrat sampling, and baiting (Hunt and Millar 2001;Sabu et al. 2011;Pellegrini and Ferreira 2012a;Oliveira 2014;Bichuette et al. 2015;Wynne et al. 2018;Bichuette et al. 2019). It is recommended that the combination of multiple methods and the sampling of unique microhabitats (e.g., bat guano deposits and water bodies) seem to be efficient (Pellegrini and Ferreira 2012a;Wynne et al. 2018;Borges-Filho et al. 2019). However, choosing one better-suited technique might be necessary due to time and cost limitations (Oliveira et al. 2019). ...
... Their restricted distribution in the subterranean makes them highly vulnerable to human activities. Accessing reliable diversity data is necessary for addressing ecological issues and providing information to better guide programs and strategies for the conservation of the cave community (Zagmajster et al. 2010;Jaffé et al. 2018;Wynne et al. 2018). ...
Beetles are a very diverse group of insects, both in terms of food habits and distribution across different habitats. Most of them live in the terrestrial environment, but many species are aquatic or semiaquatic. Although they are responsible for agricultural and public health damage, beetles are essential in several ecological processes and ecosystem services. The survey is one tool widely used to answer ecological and taxonomic questions involving beetles, and the choice of proper collecting methods is usually a difficult task. In this chapter, our objective is to provide information regarding the appropriate collecting methods for beetles relating to their habits and habitats. We structured the chapter grouping the methods according to beetle habitats (terrestrial, aquatic and semiaquatic, and subterranean), a specific topic for immatures, and mentioned collection methods for molecular studies. For each habitat, in which beetles live, we included active and passive collecting methods. We present 30 types of collecting methods that the collector can employ in beetle surveys. Furthermore, we provided information about the habit and habitat of 79 Coleoptera families. Therefore, we emphasize the importance of selecting the aims before sampling because each collecting method has advantages and disadvantages.
... Esto se debe a la baja intensidad de muestreo y que sólo se aplicó una única técnica de recolección (búsquedas directas intuitivas dentro de la estimada como zona profunda), en una sola visita de cada cueva. Wynne et al. (2018b) han mostrado que si se incrementa el número de técnicas de muestro empleadas y el número de visitas, se incrementa igualmente el número de especies detectadas. Por consiguiente, se deberían llevar a cabo muestreos adicionales en estas cavidades. ...
... Como nuestro muestreo estaba restringido temporalmente (habitualmente una persona empleando, aproximadamente, cuatro horas por cueva, durante una sola visita y empleando una única técnica), es muy probable que otras especies adicionales no hayan sido ni descubiertas ni descritas. Aplicando varias técnicas de muestreo en múltiples visitas, llevadas a cabo en el tiempo apropiado del año, esto permitirá caracterizar de un modo mucho más exhaustivo la diversidad de artrópodos, así como identificar especies que puedan requerir una gestión especial para su conservación (Sket 1981;Culver et al. 2004;Krejca y Weckerly 2007;Wynne et al. 2018b). Para llegar a conseguir este objetivo se recomienda aplicar la estrategia de muestreo desarrollada por Wynne et al. (2018b). ...
... Aplicando varias técnicas de muestreo en múltiples visitas, llevadas a cabo en el tiempo apropiado del año, esto permitirá caracterizar de un modo mucho más exhaustivo la diversidad de artrópodos, así como identificar especies que puedan requerir una gestión especial para su conservación (Sket 1981;Culver et al. 2004;Krejca y Weckerly 2007;Wynne et al. 2018b). Para llegar a conseguir este objetivo se recomienda aplicar la estrategia de muestreo desarrollada por Wynne et al. (2018b). Si esto no fuera posible, sugerimos que, al menos, se realice un muestreo sistemático en estas cuevas utilizando cebos (Wynne et al. 2018b), trampas de "pitfall", y búsquedas intuitivas directas (Howarth et al. 2007;Wynne 2013;Wynne et al. 2018b), dentro de las zonas profundas de las cuevas. ...
Este trabajo representa el primer inventario, a gran escala, de la biología de las cuevas del Parque Natural de la Sierra de las Nieves, Andalucía, España. Se han muestreado siete cavidades, de las cuales tres se localizan a cota relativamente baja, a una altura media de unos 1000 m.s.n.m., mientras las otras cuatro se localizan a una cota relativamente alta, con una altura media de 1600 m.s.n.m. Se han identificado, de modo preliminar, al menos 40 morfoespecies y 13 grupos taxonómicos a escala general (esto es, categorías taxonómicas de nivel orden o superior) de artrópodos que viven en cuevas, incluyendo la especie relicta de colémbolo Onychiurus gevorum Arbea 2012. Los murciélagos se detectaron en dos de las tres cuevas de cota baja; una colonia de murciélagos, posiblemente Rhinolophus ferrumequinum (Schreber, 1774), consistente en aproximadamente 100 individuos que se vio en una de las cuevas; y un murciélago (Myotis sp.) que se encontró aletargado en otra cavidad. El sapo común
(Bufo bufo (Linnaeus, 1758)) se ha encontrado en dos de las cuevas de cota baja. Se proponen recomendaciones para desarrollar una investigación complementaria que ayude a la gestión futura de estos recursos biológicos.
... Given the baseline nature of this study, we only applied one sampling technique (direct intuitive searches within estimated deep zones) during one site visit. Wynne et al. (2018) has shown that increasing the number of techniques and number of site visits results in a larger number of species detected. Therefore, additional sampling should be conducted in these caves. ...
... As our sampling was temporally constrained (typically one person at ~ four hours per cave) during one site visit and employing a single technique, additional species of potential management concern (i.e., cave-adapted taxa) likely remain to be discovered and described. Multiple sampling techniques applied through multiple site visits conducted during the appropriate time of year will be required to more fully characterize cave arthropod diversity , as well as identify species of potential management concern (Sket 1981;Culver et al. 2004;Krejca & Weckerly 2007;Wynne et al. 2018). To accomplish this, we recommend applying a sampling strategy similar to the approach developed by Wynne et al. (2018). ...
... Multiple sampling techniques applied through multiple site visits conducted during the appropriate time of year will be required to more fully characterize cave arthropod diversity , as well as identify species of potential management concern (Sket 1981;Culver et al. 2004;Krejca & Weckerly 2007;Wynne et al. 2018). To accomplish this, we recommend applying a sampling strategy similar to the approach developed by Wynne et al. (2018). If this is not possible, we minimally suggest systematically sampling these caves using baits (Howarth et al. 2007;Wynne et al. 2018), pitfall traps (Wynne 2013;Wynne et al. 2018), and direct intuitive searches (Wynne 2013;Wynne et al. 2018) within cave deep zones. ...
This work represents the first large scale cave biological inventory of caves in Sierra de las Nieves Natural Park, Andalucía, Spain. We sampled seven caves (three low and four high elevation caves) from 22 June through 01 July 2017. We have preliminarily identified at least 42 morphospecies and 13 coarse-level taxonomic groups (i.e., Order or higher) of cave-dwelling arthropods including the relict springtail species, Onychiurus gevorum Arbea 2012. Bats were detected in two of three low elevation caves; a bat roost of unknown type consisting of approximately 100 bats was observed in one cave, and one bat (Myotis sp.) was found torporing in another cave. The common toad (Bufo bufo (Linnaeus, 1758)) was identified in two low elevation caves. We also provide recommendations for additional research to aid in the future management of these resources.
... Nearly cosmopolitan Ripa et al. (1995) (as Iridomyrmex humilis Mayr.); Morrison (1997); SAG, 2008SAG, , 2010SAG, , 2011SAG, , 2012SAG, , 2013SAG, , 2014Wynne et al. (2018) Not detected, nor mentioned, by Morrison (1997) Plagiolepis alluaudi Emery, 1894 ...
... Cosmopolitan Wynne et al. (2018) Mound et al., 2017) Thrips tabaci Lindeman, 1889 ...
The terrestrial arthropod fauna of Rapa Nui has been negatively impacted by human activities, including accidental and purposeful species introductions, which have led to high levels of extinction and extirpation of the native fauna. Unfortunately, the absence of a single, standardized resource documenting all Rapa Nui's native and non-native species hinders protecting surviving native species, as well as recognizing new invasions. Here, we present a comprehensive list of terrestrial arthropod species recorded up to 2024. We compiled this list from the literature, unpublished museum records, and field sampling. We also consulted 29 taxonomic specialists, who assisted in verifying species in this checklist. A total of 539 arthropod species were cataloged including 25 endemic, 27 indigenous, 345 accidentally introduced, and 66 purposefully introduced species, and 76 species of unknown origin. Most, if not all, of the unknown records represent non-native species. Eleven endemic and 14 indigenous species have not been recorded since their original description, which suggests their extinction or extirpation. However, the lack of targeted surveys prevents verification of their persistence on the island. For non-native species, one-third (33 %) have cosmopolitan or nearly cosmopolitan distributions, while 31 % originated from the tropics. Overall, this checklist will serve as a comprehensive resource for the identification of established species and facilitate the detection of new arrivals. It will also contribute to the protection of the island's surviving native species.
... In addition, most had no or little prior experience in caves (Moseley, 2014). Exploring and collecting in caves often requires unique skills and equipment (Wynne et al., 2018), some of which were not available at the time, e.g., adequate lights, safer single rope equipment and techniques, and protective clothing (White, 2019). The equipment available to cave biologists in Europe and North America at the time was often difficult or impossible to procure in remote colonial outposts. ...
... A related issue is that past biological surveys of caves have been incomplete (Moseley, 2009;Wynne et al., 2018). All too often, taxa are omitted from surveys because of the difficulty in collecting and assumptions that the taxon is accidentally in caves, and therefore unimportant. ...
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.
... Fatores como o tempo e limitação nos recursos financeiros restringem cada vez mais a capacidade de acessar a biodiversidade e, assim, poder conservá-la (Gibney, 2015;Andrade, 2019;Thomaz et al., 2020). Tais fatores, somados às difi culdades encontradas na realização de amostragens precisas de invertebrados cavernícolas (Howarth et al., 2007;2018;Wynne et al., 2019), acabam impactando diversos aspectos na pesquisa da biodiversidade e restringindo sua aplicação na conservação e manejo das espécies. Dentre essas difi culdades, destaca-se o emprego efi caz dos métodos de coleta, a capacidade do pesquisador em acessar microhabitats e a detecção de espécies, em especial, crípticas e restritas ao meio subterrâneo. ...
... Este resultado indica que o método empregado durante um único evento amostral é capaz de acessar boa parte da fauna. Entretanto, afi m de melhorar a sufi ciência amostral, é recomendado o emprego de múltiplos eventos e técnicas de amostragem (Wynne et al., 2018). A importância de múltiplos eventos amostrais pode ser exemplifi cada com o relato de Culver e colaboradores (2004), que após mais de 100 incursões à região Cárstica Dinárica, encontraram um gênero de Amphipoda estigobionte até então, desconhecido pela ciência. ...
Avaliamos as diferenças na riqueza e suficiência amostral de espécies troglóbias e não-troglóbias em resposta às variações da extensão de 29 cavernas, localizadas no estado de Minas Gerais, Brasil. A amostragem de invertebrados se deu por meio de coleta ativa ao longo de toda a extensão acessível da caverna. A localização dos espécimes coletados e observados era registrada em um croqui da caverna, posteriormente dividida em 10 setores, sendo cada setor uma unidade amostral. Os resultados corroboram com estudos prévios, que demonstram a relação positiva entre a riqueza de invertebrados e a extensão da caverna. Foi evidenciado que, em média, é possível acessar cerca de 80% da fauna com a amostragem de 60% da extensão da caverna. Porém, considerando separadamente as espécies troglóbias e não troglóbias, fica claro que a amostragem de 60% da caverna é insuficiente para acessar a fauna troglóbia, que se concentra nas regiões mais profundas. Por fim, utilizando-se de estimadores de diversidade para medir a suficiência amostral, em média, 66% da riqueza esperada foi acessada. Os resultados indicam que o método empregado em um único evento amostral é capaz de acessar boa parte da fauna. Todavia, visando melhores estimativas da biodiversidade subterrânea, recomendamos a aplicação de múltiplos métodos de coleta, além da amostragem de toda a extensão acessível da caverna, buscando contemplar a fauna troglóbia e não-troglóbia.
... These studies have employed many sampling techniques for troglofauna and stygofauna, which differ in efficacy, affordability, accuracy and representation (Hahn, 2002) (Fig. 2). Of note, Camacho (1992) reviewed the different sampling methods for subterranean fauna and, more recently Wynne et al. (2018), in comparing different methods, focused on the difficulties when sampling for troglofauna. Whilst different countries and jurisdictions deal with surveying and monitoring of subterranean fauna in different ways, the manual for the assessment of regional groundwater biodiversity, as developed for the PASCALIS (Protocols for the Assessment and Conservation of Aquatic Life In the Subsurface) project (Malard et al., 2002), is among the most comprehensive. ...
... These may be also baited with sweet potato, peanut butter, chicken liver or fish entrails to attract certain species (Howarth et al., 2007). In some cases, pitfall traps cannot be buried deep enough in cave sediments to be flush with the floor and 'ramps' built from local materials have been used to allow arthropods to access the traps and fall in (Wynne et al., 2018). Finally, direct collection ( Fig. 2a.4) in caves can include visual searching and hand collection with a paintbrush or aspirator (Paquin and Provost, 2010 and references therein). ...
Monitoring of biota is pivotal for the assessment and conservation of ecosystems. Environments worldwide are being continuously and increasingly exposed to multiple adverse impacts, and the accuracy and reliability of the biomonitoring tools that can be employed shape not only the present, but more importantly, the future of entire habitats. The analysis of environmental DNA (eDNA) metabarcoding data provides a quick, affordable, and reliable molecular approach for biodiversity assessments. However, while extensively employed in aquatic and terrestrial surface environments, eDNA-based studies targeting subterranean ecosystems are still uncommon due to the lack of accessibility and the cryptic nature of these environments and their species. Recent advances in genetic and genomic analyses have established a promising framework for shedding new light on subterranean biodiversity and ecology. To address current knowledge and the future use of eDNA methods in groundwaters and caves, this review explores conceptual and technical aspects of the application and its potential in subterranean systems. We briefly introduce subterranean biota and describe the most used traditional sampling techniques. Next, eDNA characteristics, application, and limitations in the subsurface environment are outlined. Last, we provide suggestions on how to overcome caveats and delineate some of the research avenues that will likely shape this field in the near future. We advocate that eDNA analyses, when carefully conducted and ideally combined with conventional sampling techniques, will substantially increase understanding and enable crucial expansion of subterranean community characterisation. Given the importance of groundwater and cave ecosystems for nature and humans, eDNA can bring to the surface essential insights, such as study of ecosystem assemblages and rare species detection, which are critical for the preservation of life below, as well as above, the ground.
... It is worth emphasizing that these sampling requirements targeted a more accurate estimation of species richness, but not the continuous monitoring of focus species in time. Two sampling events are likely insufficient to obtain reliable species richness estimates for highly diverse caves (Auler & Piló, 2015;Wynne et al., 2018), so some authors have argued for the estimation of optimal sample sizes based on species accumulation curves (Trajano & Bichuette, 2010;Trajano, 2013). Our results provide the first evidence-based recommendations to optimize sampling efforts of monitoring programs seeking to assess target species abundance through time. ...
... These results suggest higher detection probabilities in the dry season for the subset of species where RMSE curves show a steeper decrease during the dry season (Fig. 3). Interestingly, this was the case for the troglobitic amblypygid Charinus ferreus, a species that is difficult to detect like other troglobionts (Wynne et al., 2018;Lunghi, 2018). Our results thus suggest that monitoring programs focusing on terrestrial subterranean fauna from our study region could concentrate sampling activity in the dry season, where most species seem to be easier to detect. ...
Understanding the factors underpinning species abundance patterns in space and time is essential to implement effective cave conservation actions. Yet, the methods employed to monitor cave biodiversity still lack standardization, and no quantitative assessment has yet tried to optimize the amount and type of information required to efficiently identify disturbances in cave ecosystems. Using a comprehensive monitoring dataset for tropical iron caves, comprising abundance measurements for 33 target taxa surveyed across 95 caves along four years, here we provide the first evidence-based recommendations to optimize monitoring programs seeking to follow target species abundance through time. We found that seasonality did not influence the ability to detect temporal abundance trends. However, in most species, abundance estimates assessed during the dry season resulted in a more accurate detection of temporal abundance trends, and at least three surveys were required to identify global temporal abundance trends. Finally, we identified a subset of species that could potentially serve as short-term disturbance indicators. Results suggest that iron cave monitoring programs implemented in our study region could focus sampling efforts in the dry season, where detectability of target species is higher, while assuring data collection for at least three years. More generally, our study reveals the importance of long-term cave monitoring programs for detecting possible disturbances in subterranean ecosystems, and for using the generated information to optimize future monitoring efforts.
... This issue is particularly germane to difficulties in sampling subterranean habitats. For example, sampling protocols were typically standardized among sites and completeness of species inventories were assessed using accumulation and rarefaction curves (Zagmajster et al., 2008;Dole-Olivier et al., 2009;Wynne et al., 2018). Also, observed species richness patterns were tested for robustness using species richness estimators (Zagmajster et al., 2014), or complemented with species richness predictions modelled from environmental data (Mokany et al., 2019). ...
... Furthermore, it is crucial to adopt innovative approaches to safeguard subterranean biodiversity (Q37), as well as to Scanning the horizon of subterranean biology determine the size and location of effective protected areas (Q38). Standardized systematic sampling techniques have been applied to terrestrial (Wynne et al., 2018(Wynne et al., , 2019 and aquatic subterranean invertebrate species (Dole-Olivier et al., 2009); to be optimally beneficial to conservation and monitoring, these techniques will need to be further scrutinized across a large breadth of taxa and systems. Recently, a cave vulnerability assessment protocol has been developed for bat cave roosts (Tanalgo, Tabora, & Hughes, 2018) and, if refined, would hold promise for use with other subterranean animals. ...
Five decades ago, a landmark paper in Science titled The Cave Environment heralded caves as ideal natural experimental laboratories in which to develop and address general questions in geology, ecology, biogeography, and evolutionary biology. Although the 'caves as laboratory' paradigm has since been advocated by subterranean biologists, there are few examples of studies that successfully translated their results into general principles. The contemporary era of big data, modelling tools, and revolutionary advances in genetics and (meta)genomics provides an opportunity to revisit unresolved questions and challenges, as well as examine promising new avenues of research in subterranean biology. Accordingly, we have developed a roadmap to guide future research endeavours in subterranean biology by adapting a well-established methodology of 'horizon scanning' to identify the highest priority research questions across six subject areas. Based on the expert opinion of 30 scientists from around the globe with complementary expertise and of different academic ages, we assembled an initial list of 258 fundamental questions concentrating on macroecology and microbial ecology, adaptation , evolution, and conservation. Subsequently, through online surveys, 130 subterranean biologists with various backgrounds assisted us in reducing our list to 50 top-priority questions. These research questions are broad in scope and ready to be addressed in the next decade. We believe this exercise will stimulate research towards a deeper understanding of subterranean biology and foster hypothesis-driven studies likely to resonate broadly from the traditional boundaries of this field.
... In recent years, researchers have undertaken considerable efforts to improve and standardize sampling techniques for terrestrial cave fauna [39][40][41] . In addition to recommendations from these studies, we had to consider special circumstances resulting from the depth, physiognomy and objective dangers of alpine vertical caves, where large-scale systematic biological surveys have not yet been performed. ...
... Interpretation and null model testing of abundance-based BD patterns are a matter of ongoing debate and yet to be fully developed and tested 47,48 . We opted for a proven, qualitative approach also because of the extreme nature of subterranean habitats, where animals are often rare and hard to sample with constant effort over space 41 . ...
Terrestrial life typically does not occur at depths greater than a few meters. Notable exceptions are massifs of fissured rock with caves and hollow spaces reaching depths of two kilometres and more. Recent biological discoveries from extremely deep caves have been reported as sensations analogous to wondrous deep sea creatures. However, the existence of unique deep terrestrial communities is questionable when caves are understood as integral parts of a bedrock fissure network (BFN) interconnecting all parts of a massif horizontally and vertically. We tested these two opposing hypotheses – unique deep cave fauna vs. BFN – by sampling subterranean communities within the 3D matrix of a typical karst massif. There was no distinction between deep core and shallow upper zone communities. Beta diversity patterns analysed against null models of random distribution were generally congruent with the BFN hypothesis, but suggested gravity-assisted concentration of fauna in deep caves and temperature-dependent horizontal distribution. We propose that the idea of a unique deep terrestrial fauna akin to deep oceanic life is unsupported by data and unwarranted by ecological considerations. Instead, the BFN hypothesis and local ecological and structural factors sufficiently explain the distribution of subterranean terrestrial life even in the deepest karst massifs.
... Knowledge gap Specific problems in subterranean biology Linnean Species taxonomy A lack of reliable estimation of subterranean diversity (Zagmajster et al. 2018) A high prevalence of cryptic species (Delić et al. 2017) A bias favoring studies on large versus subterranean microscopic animals (e.g., meiofauna), or certain taxonomic groups against others (Zagmajster et al. 2010) Wallacean Species distribution A high prevalence of endemic species (Gibert and Deharveng 2002) A high prevalence of cryptic species A lack of global data set of subterranean species distribution (Zagmajster et al. 2018 Subterranean habitats accessible to humans (e.g., caves) are often challenging to explore, requiring knowledge on caving techniques and specific equipment (Zagmajster et al. 2010, Wynne et al. 2018 (Trejo-Salazar et al. 2016). Therefore, bats' role in maintaining the quality of recreational outdoor areas; limiting disease transmission to humans, domestic animals, and agricultural crops; and, ultimately, enhancing human well-being is immense. ...
... Efforts will be also needed to document and monitor subterranean diversity through the use and evaluation of standardized sampling techniques (e.g., Dole-Olivier et al. 2009, Wynne et al. 2018, as well as vulnerability assessments (with adaptive management protocols) to determine threat levels to subterranean ecosystems and sensitive species populations (e.g., Di Lorenzo et al. 2018, Tanalgo et al. 2018. ...
... Knowledge gap Specific problems in subterranean biology Linnean Species taxonomy A lack of reliable estimation of subterranean diversity (Zagmajster et al. 2018) A high prevalence of cryptic species (Delić et al. 2017) A bias favoring studies on large versus subterranean microscopic animals (e.g., meiofauna), or certain taxonomic groups against others (Zagmajster et al. 2010) Wallacean Species distribution A high prevalence of endemic species (Gibert and Deharveng 2002) A high prevalence of cryptic species A lack of global data set of subterranean species distribution (Zagmajster et al. 2018 Subterranean habitats accessible to humans (e.g., caves) are often challenging to explore, requiring knowledge on caving techniques and specific equipment (Zagmajster et al. 2010, Wynne et al. 2018 (Trejo-Salazar et al. 2016). Therefore, bats' role in maintaining the quality of recreational outdoor areas; limiting disease transmission to humans, domestic animals, and agricultural crops; and, ultimately, enhancing human well-being is immense. ...
... Efforts will be also needed to document and monitor subterranean diversity through the use and evaluation of standardized sampling techniques (e.g., Dole-Olivier et al. 2009, Wynne et al. 2018, as well as vulnerability assessments (with adaptive management protocols) to determine threat levels to subterranean ecosystems and sensitive species populations (e.g., Di Lorenzo et al. 2018, Tanalgo et al. 2018. ...
In light of recent alarming trends in human population growth, climate change, and other environmental modifications, a "Warning to humanity" manifesto was published in BioScience in 2017. This call reiterated most of the ideas originally expressed by the Union of Concerned Scientists in 1992, including the fear that we are "pushing Earth's ecosystems beyond their capacities to support the web of life. " As subterranean biologists, we take this opportunity to emphasize the global importance and the conservation challenges associated with subterranean ecosystems. They likely represent the most widespread nonmarine environments on Earth, but specialized subterranean organisms remain among the least documented and studied. Largely overlooked in conservation policies, subterranean habitats play a critical role in the function of the web of life and provide important ecosystem services. We highlight the main threats to subterranean ecosystems and propose a set of effective actions to protect this globally important natural heritage.
... Through better characterizing this community, researchers and managers may elucidate the pseudoscorpions' role in the community, as well as better define the distribution of these two species within Maomaotou Cave based upon the distributions of suitable habitat and potential prey species. As our sampling was temporally constrained (2 people at~4 hours) during one site visit and employed a single technique, we suggest applying multiple techniques with multiple site visits conducted during the appropriate time of year to garner a more comprehensive picture of the cave arthropod community (Wynne & Voyles 2014;Wynne et al. 2018). If this is not possible, we minimally suggest the deep zone of Maomaotou Cave be intensively and systematically sampled using baits (Howarth et al. 2007), leaf-litter traps (Slaney & Weinstein 1996), and direct intuitive searches using a similar sampling protocol proposed by and Wynne et al. (2018). ...
... As our sampling was temporally constrained (2 people at~4 hours) during one site visit and employed a single technique, we suggest applying multiple techniques with multiple site visits conducted during the appropriate time of year to garner a more comprehensive picture of the cave arthropod community (Wynne & Voyles 2014;Wynne et al. 2018). If this is not possible, we minimally suggest the deep zone of Maomaotou Cave be intensively and systematically sampled using baits (Howarth et al. 2007), leaf-litter traps (Slaney & Weinstein 1996), and direct intuitive searches using a similar sampling protocol proposed by and Wynne et al. (2018). ...
Two new troglomorphic pseudoscorpion species, Bisetocreagris maomaotou sp. nov. (Family Neobisiidae) and Tyrannochthonius chixingi sp. nov. (Family Chthoniidae) are described from one cave in the tower karst of northern Guangxi Province, China. This cave is located at close proximity to a village and an adjacent urban area. As with many caves in the South China Karst, this feature occurs at an elevation slightly above agriculture and rural activities; thus, we suggest it may be partially buffered from human activities in the lowland areas. We discuss the likelihood of narrow range endemism and provide research and conservation recommendations to guide future management of these two species.
... Species accumulation curves ( Figure S1) were generated to assess if the sample depth was sufficient to cover expected diversity (Wynne et al., 2018), using the vegan package (Oksanen et al., 2022). (Team, 2022). ...
Gut bacterial communities provide flexibility to hosts during dietary changes. Despite the increasing number of studies exploring the associations between broader dietary guilds of mammalian hosts and their gut bacteria, it is generally unclear how diversity and variability in consumed diets link to gut bacterial taxa in wild non‐primate mammals, particularly in omnivores. Here, we contribute to filling this gap by exploring consumed diets and gut bacterial community compositions with metabarcoding of faecal samples for two African mammals, Civettictis civetta and Genetta spp., from the family Viverridae. For each individual sample, we characterised bacterial communities and identified dietary taxa by sequencing vertebrate, invertebrate and plant markers. This led us to establish diet compositions that diverged from what has previously been found from visual identification methods. Specifically, while the two genera have been categorised into the same dietary guild, we detected more animal dietary items than plant items in C. civetta, while in Genetta spp., we observed the opposite. We further found that individuals with similar diets have similar gut bacterial communities within both genera. This association tended to be driven by specific links between dietary items and gut bacterial genera, rather than communities as a whole, implying diet‐driven selection for specific gut microbes in individual wild hosts. Our findings underline the importance of molecular tools for improving characterisations of omnivorous mammalian diets and highlight the opportunities for simultaneously disentangling links between diets and gut symbionts. Such insights can inform robustness and flexibility in host‐microbe symbioses to dietary change associated with seasonal and habitat changes.
... The collection of invertebrates within each sampling unit was deemed complete only when all the invertebrates present had been captured and/or accounted for. Moreover, to ensure comprehensive coverage of invertebrate diversity, particularly species exclusive to cave environments, all potential habitats were thoroughly examined throughout the accessible cave length, extending beyond the designated sampling units (Ferreira, 2004;Wynne et al., 2018Wynne et al., , 2019. All collected specimens were preserved in vials containing 70% ethanol. ...
In 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.
... We combined these three sampling methods to maximize the sampling effort considering the different behaviors and habitats of arthropods (Wynne et al., 2018). We used a 1.5-m long sweep net with a 30 cm net diameter for 5 min to collect arthropods from various strata and habitats and thus cover up to nearly 90% of the arthropod species in a given site (Viana-Junior et al., 2021). ...
Understanding how primary productivity and diversity affect secondary productivity is an important debate in ecology with implications for biodiversity conservation. Particularly, how plant diversity influences arthropod diversity contributes to our understanding of trophic cascades and species coexistence. Previous studies show a positive correlation between plant and arthropod diversity. The theory of associational resistance suggests that plant herbivory rate will decrease with increasing plant diversity indicating feedbacks between primary diversity, productivity, and secondary productivity rates. However, our understanding of how these relations are mediated by anthropogenic disturbance is still limited. We surveyed 10 forest sites, half of which are disturbed by fire, logging, and tree pruning, distributed in two climatic zones in Benin, West Africa. We established 100 transects to record plant species and sampled arthropods using pitfall traps, ceramic plates with bait, and sweeping nets. We developed a structural equation model to test the mediating effect of chronic anthropogenic disturbance on plant diversity and how it influences arthropod diversity and abundance. Arthropod diversity increased but arthropod abundance decreased with increasing intensity of disturbance. We found no significant bottom‐up influence of the plant diversity on arthropod diversity but a significant plant diversity–arthropod abundance relationship. Some arthropod guilds were significantly affected by plant diversity. Finally, herbivory rates were positively associated with arthropod diversity. Synthesis. Our results highlight how chronic anthropogenic disturbance can mediate the functional links between trophic levels in terms of diversity and productivity. Our study demonstrated a decoupled response of arthropod diversity and abundance to disturbance. The direct positive influence of plant diversity on herbivory rates we found in our study provides counter‐support for the theory of associational resistance.
... Species accumulation curves ( Figure S1) were generated to assess if the sample depth was sufficient to cover expected diversity (Wynne, Sommer, & Howarth, 2018), using the vegan package (Oksanen et al., 2022). Frequency of occurrence were calculated in order to investigate the frequency of different dietary items among the individuals. ...
Gut bacterial communities provide flexibility to hosts during dietary changes. Despite the increasing number of studies exploring the associations between broader dietary guilds of mammalian hosts and their gut bacteria, it is generally unclear how diversity and variability in consumed diets link to gut bacteria in wild non-primate mammals. Here we contribute to filling this gap by exploring consumed diets and gut bacterial community compositions with metabarcoding of faecal samples for two African mammals, Civettictis civetta and Genetta spp., from the family Viverridae. For each individual sample, we characterised bacterial communities and identified dietary taxa by sequencing vertebrate, invertebrate, and plant markers. This led us to establish diet compositions that diverged from what has previously been found from visual identification methods. Specifically, while the two genera have been categorised into the same dietary guild, we detected more animal dietary items than plant items in C. Civetta, while in Genetta spp. we observed an opposite pattern. We further found that individuals with similar diets have similar gut bacterial communities in both species. This association tended to be driven by specific associations of dietary items to specific gut bacterial taxa, rather than entire communities, implying diet-driven selection for specific gut microbes in individual wild hosts. Our findings underline the importance of molecular tools for improving characterisations of wild mammalian diets and highlight the opportunities for simultaneously disentangling links between diets and gut symbionts. Such insights can inform robustness and flexibility in host-microbe symbioses to dietary change associated with seasonal and habitat change.
... Species accumulation curves ( Figure S1) were generated to assess if the sample depth was sufficient to cover expected diversity (Wynne et al., 2018), using the vegan package (Oksanen et al., 2022). (Team, 2022). ...
Microbial communities in guts flexibly adjust to changes in host dietary intakes, but the relationship between diet and gut microbiome is still poorly studied in wild animals. DNA metabarcoding approaches are frequently used to characterise diets or gut microbiomes of diverse species. However, to date, no study has combined these approaches to investigate diet-gut microbiome associations in wild mammals with diverse and fluctuating dietary intakes, such as omnivores. Here, we do this for two African mammals, Civettictis civetta and Genetta spp., from the family Viverridae. We characterised bacterial communities and identified taxonomic groups within diet by sequencing vertebrate, invertebrate and plant markers on faecal samples. This led us to establish diet compositions that diverged from what has previously been found using visual identification methods for these species. Specifically, while the two genera have been categorised into the same dietary guild, we detected more animal-based diets in C. Civetta, and higher proportions of plants consumed by Genetta spp. Diet similarity correlated with gut microbiome similarity in Genetta spp., indicating that plant consumption may be an important driver of gut microbiome structure. The novel insights we provide into the omnivorous diet of C. civetta and Genetta spp. highlight the importance of detailed identification of the dietary guild of species, not only for ecology and conservation, but also when researching how diet shapes the gut microbiome.
... Conversely, while advancing our knowledge of regional troglomorphic millipede diversity stands to contribute significantly to the conservation value of the SCK, a more comprehensive understanding (i.e., for all cave-dwelling taxa) of regional diversity, as well as advancing procedures to assessing the vulnerability of cave systems to anthropogenic impact should be considered. Wynne et al. (2018Wynne et al. ( , 2019 provides a systematic framework and guidance for sampling cave-dwelling arthropods using a repeatable framework, which can be modified for application in the SCK. Using such an approach, these data may be then be examined by applying principles similar to the cave vulnerability assessment developed by Tanalgo et al. (2018). ...
We synthesized the current knowledge of cave-dwelling millipede diversity from Guangxi Zhuang Autonomous Region (Guangxi), South China Karst, China and described six new millipede species from four caves from the Guilin area, northeastern Guangxi. Fifty-two cave-dwelling millipedes are known for the region consisting of 38 troglobionts and 14 troglophiles. Of the troglobionts, 24 are presently considered single-cave endemics. New species described here include Hyleoglomerisrukouqu sp. nov. and Hyleoglomerisxuxiakei sp. nov. (Family Glomeridae), Hylomusyuani sp. nov. (Family Paradoxosomatidae), Eutrichodesmusjianjia sp. nov. (Family Haplodesmidae), Trichopeltisliangfengdong sp. nov. (Family Cryptodesmidae), and Glyphiulusmaocun sp. nov. (Family Cambalopsidae). Our work also resulted in range expansions of Pacidesmustrifidus Golovatch & Geoffroy, 2014, Blingulussinicus Zhang & Li, 1981 and Glyphiulusmelanoporus Mauriès & Nguyen Duy-Jacquemin, 1997. As with many hypogean animals in Southeast Asia, intensive human activities threaten the persistence of both cave habitats and species. We provide both assessments on the newly described species’ distributions and recommendations for future research and conservation efforts.
... Second, to accurately address species' thermal tolerance, experimental measurements of physiological thermal limits are needed. However, obtaining such data for subterranean species is not trivial, given the logistic difficulties for sampling in caves and conducting experiments with subterranean animals (Castaño-S anchez et al., 2020;Culver et al., 2006;Mammola et al., 2021;Schneider & Culver, 2004;Wynne et al., 2018). Moreover, the rarity of subterranean species limits the number of specimens available for robust quantitative analyses . ...
The climatic variability hypothesis predicts the evolution of species with wide thermal tolerance ranges in environments with variable temperatures, and the evolution of thermal specialists in thermally stable environments. In caves, the extent of spatial and temporal thermal variability experienced by taxa decreases with their degree of specialization to deep subterranean habitats. We use phylogenetic generalized least squares to model the relationship among thermal tolerance (upper lethal limits), subterranean specialization (estimated using ecomorphological traits), and habitat temperature in 16 beetle species of the tribe Leptodirini (Leiodidae). We found a significant, negative relationship between thermal tolerance and the degree of subterranean specialization. Conversely, habitat temperature had only a marginal effect on lethal limits. In agreement with the climatic variability hypothesis and under a climate change context, we show that the specialization process to live in deep subterranean habitats involves a reduction of upper lethal limits, but not an adjustment to habitat temperature. Thermal variability seems to exert a higher evolutionary pressure than mean habitat temperature to configure the thermal niche of subterranean species. Our results provide novel insights on thermal physiology of species with poor dispersal capabilities and on the evolutionary process of adaptation to subterranean environments. We further emphasize that the pathways determining vulnerability of subterranean species to climate change greatly depend on the degree of specialization to deep subterranean environments.
... Increasing sampling sites considering different habitats and a combined use of different methods allowed us to increment the range of detected taxa, as suggested in different research (Bichuette et al. 2015;Kozel et al. 2017;Kozel 2018;Wynne et al. 2018). Being the cave size limited (ca. ...
Biological studies on factors shaping underground communities are poor, especially those considering simultaneously organisms with different degrees of adaptation to cave life. In this study, we assessed the annual dynamics and use of both horizontal and vertical microhabitats of a whole community with the aim of understanding whether cave-dwelling organisms have a similar distribution among vertical and ground-level microhabitats and to find out which microhabitat features influence such distribution. We monthly assessed from 2017 to 2018, by direct observation combined with quadrat sampling method on the ground and transects on the walls, richness and abundance of 62 cave-dwelling species in a cave of Northern Italy. Environmental factors such as light intensity, temperature, relative humidity and min-eralogical composition of the substrates were measured during each monitoring session, influencing the dynamics of the whole community and revealing significant differences between ground and wall micro-habitats. A gradient of variation of the species assemblages occurred from the entrance toward inner areas, however, evidence that the dynamics of the walls are very different from those occurring at the ground independent from the distance from the surface are shown. Biodiversity indices highlighted sampling area diversity and a discrete total cave fauna biodiversity with the highest values found near the entrance and the lowest in the inner part of the cave.
... The sampled extensions and the cave entrances widths (in its highest extensions) were determined with laser measuring tapes and from cave maps when available. Direct intuitive search and manual collection of invertebrates were carried out along the accessible extension of each cave, with special attention given to organic deposits and micro habitats (Wynne et al., 2018Souza-Silva et al., 2020). In order to standardize the sampling effort, the same team of five biologists carried out the collections in the fifteen caves, and each collector spent on average 1 minute per square meter of cave floor searching for invertebrates. ...
In the last decade, the scientific community brought to the debate gaps that slow down the advance of knowledge regarding global biodiversity. More recently, this discussion has reached subterranean environments, where these gaps are even more dramatic due to the relict and vulnerable nature of their species. In this context, we tested ecological metrics related to some of these gaps, checking if the biological relevance of the caves would change depending on ecological attributes related to each metric. The study was carried out in caves from southeastern Brazil, located in a region presenting a high richness of troglobitic species restricted to a narrow geographical extent. Thus, we verified: (a) the cave invertebrate communities' vulnerability with the Vulnerability Index and the Importance Value for Cave Conservation; (b) the distribution and endemicity of the troglobitic species with the Endemicity Index; (c) the phylogenetic diversity of the troglobitic species considering the average taxonomic distinction (∆+), their richness and evenness. We observed a considerable change in the ordering of the caves' biological relevance according to each tested attribute (index). We discussed how each of these metrics and their attributes indirectly relate to: (a) the preservation and maintenance of the phylogenetic diversity of subterranean communities; (b) the spatial restrictions of different groups, where the greater their restrictions, the greater their vulnerability; (c) the preservation of caves with high biological relevance considering these different attributes together. Thus, we recommend the use of different metrics so that different ecological attributes can be considered, supporting actions that aim to preserve caves in highly altered regions. Finally, we find that the most biologically important cave in the region is not protected (Gruta da Morena Cave). We warn that this cave needs to be contemplated by a conservation unit in the region urgently.
... Therefore, we decided to focus on the main challenges related to subterranean research and the philosophy underlying the different experimental designs suited to overcome these: Two aspects only marginally discussed in the recent literature. Readers interested in other aspects of research in subterranean biology are referred to the classic review on biomonitoring (Culver & Sket, 2002) and published syntheses on sampling approaches (Dole-Olivier et al., 2009;Oliveira et al., 2019;Weinstein & Slaney, 1995;Wynne et al., 2018Wynne et al., , 2019, species distribution modeling (Mammola & Leroy, 2018), and best practices in experimental trials with subterranean organisms (Di Lorenzo et al., 2019). Sampling techniques in non cave subterranean habitats (Box 1) have also been reviewed elsewherefor example, boreholes (Hancock & Boulton, 2009), epikarst (Brancelj, 2004), subaquatic caves (Humphreys et al., 1999;Iliffe, 2018;Iliffe & Bowen, 2001), Milieu Souterrain Superficiel (Mammola et al., 2016), hyporheic (Fraser & Williams, 1997), and interstitial habitats in coastal marine and lotic environments (Schmidt-Rhaesa, 2020). ...
• Caves and other subterranean habitats fulfill the requirements of experimental model systems to address general questions in ecology and evolution. Yet, the harsh working conditions of these environments and the uniqueness of the subterranean organisms have challenged most attempts to pursuit standardized research.
• Two main obstacles have synergistically hampered previous attempts. First, there is a habitat impediment related to the objective difficulties of exploring subterranean habitats and our inability to access the network of fissures that represents the elective habitat for the so-called “cave species.” Second, there is a biological impediment illustrated by the rarity of most subterranean species and their low physiological tolerance, often limiting sample size and complicating laboratory experiments.
• We explore the advantages and disadvantages of four general experimental setups (in situ, quasi in situ, ex situ, and in silico) in the light of habitat and biological impediments. We also discuss the potential of indirect approaches to research. Furthermore, using bibliometric data, we provide a quantitative overview of the model organisms that scientists have exploited in the study of subterranean life.
• Our over-arching goal is to promote caves as model systems where one can perform standardized scientific research. This is important not only to achieve an in-depth understanding of the functioning of subterranean ecosystems but also to fully exploit their long-discussed potential in addressing general scientific questions with implications beyond the boundaries of this discipline.
... Since the sites are almost inaccessible to humans, we used climbing gear to explore the steep rock faces. We employed the single rope access technique, which has already been applied to investigate arthropods communities of the forest canopy (Perry 1978;Vieira and Marinho-Filho 1998;Haefke et al. 2013;Anderson et al. 2015), or to explore other near-inaccessible habitats such as caves (Wynne et al. 2018) and rock cliffs (Priddel et al. 2003). To our knowledge, this is the first time this method was applied for butterfly monitoring. ...
In this study we apply a new monitoring1890 technique for butterflies in order to get more insights into the habitat use patterns of Erebia christi Rätzer (Nymphalidae: Satyrinae). This European endemic is a rare and very localized butterfly species, found alongside steep slopes in a restricted area in the Alps, at the border between Italy and Switzerland. Even though it was discovered almost 140 years ago, captivating the interest of many lepidopterists, there are still several aspects about the biology of E. christi that are not fully known. We selected two monitoring sites in Veglia–Devero Natural Park, Italy and tested whether E. christi was more likely to use rocky, almost vertical slopes than other types of habitat. Since this habitat was almost inaccessible to humans, we used the single rope access technique, in which field operators rappelled down the slopes to explore the rock faces. We demonstrate that the main characteristics of the typical habitat of E. christi are indeed very steep rock faces with grassy ledges where Festuca sp. plants are present. We also show that, E. christi is more abundant than it was previously thought, with populations that could probably be structured in a metapopulation system. Long-term monitoring with the rope access technique could represent an optimal method to provide key insights into the biology and ecology not only of E. christi but of other butterflies that use similar habitats. Finally, we propose the upgrading of its IUCN category from Vulnerable to Endangered at European level.
Implications for insect conservation
Our findings demonstrate how appropriate, long-term monitoring can contribute to improve the scarce knowledge of the ecology of an elusive species, and to devise informed proposals regarding the management and protection of populations, especially for species of conservation concern.
... These microhabitats include flood detritus, penetrating tree roots hanging from ceilings or walls, guano deposits, edges of drip pools and ponds, muddy banks, and animal or insect carcasses. These microhabitats are likely to support a high diversity or present specific functional groups (e.g., guanophiles) (Wynne et al. 2019). This methodology involves searching for the greatest possible diversity of environments found inside the cavities, giving priority to sites where the specimens can be captured manually, with the aid of tweezers and brush. ...
Orthoptera is the most diverse order in Polyneoptera, with more than 28,000 species described. They are cosmopolitan, inhabitants of tropical and subtropical regions, and are also found at high altitudes and latitudes. Their populations are generally large, and the abundance of individuals makes them an important component of the Arthropoda fauna. Orthopterans are mostly terrestrial, with some groups inhabiting semiaquatic habit, and they use a wide range of environments, from underground to canopy. In this chapter, we present the diversity of habitats and behaviors of Orthoptera and the manner in which this diversity affects their sampling, presenting specific methods for Orthoptera sampling according to habitat, taxon, and study aims. We discuss sampling methodologies for orthopterans dwelling on the ground, on shrubs, in caves and semiaquatic environments. We also consider sampling according to study group, comprehending katydids, crickets, and grasshoppers. We dedicate a special section to studies on orthopteran behavior and breeding, bioacoustics, chromosomes, and DNA. We present recommendations for specimen preservation for scientific collections. We also discuss sampling design and cautions for data analysis in ecological studies, indicating appropriate statistical distributions, analytic techniques for nested data, spatial autocorrelation, and biodiversity metrics at broad geographic scales.
... (a potentially undescribed species) arrived to Salas y Gómez island via this method. Currently, no pseudoscorpions have been identified on Rapa Nui [22][23][24]. We suggest conducting arthropod surveys (to search for pseudoscorpions) on Motu Nui (a small islet off the southwestern coast) and Rano Raraku crater, the two primary pelagic bird rookeries of Rapa Nui. ...
Background: Salas y Gómez is a small, volcanic island largely untouched by humans due to its diminutive size and remoteness. Since the waters surrounding Salas y Gómez were established as Motu Motiro Hiva Marine Park in 2010, marine investigations have been the primary research focus. Secondarily, nesting seabird communities have been censused since 2011.
Methods and findings: In 2016, terrestrial arthropods were sampled on the island. Two observers sampled two locations for 30 min per site. Fifteen morphospecies were identified including at least one likely undescribed species.
Conclusions: Our work represents the most comprehensive terrestrial arthropod inventory of Salas y Gómez island to date. We are hopeful the recommendations provided will spur additional research to both characterize the island's arthropod community, as well as identify species of management concern.
... Even when sampling caves in close proximity that theoretically should harbour the same fauna, slight or even conspicuous species turnover is observed. This may be the result of daily and seasonal changes in community composition (Lunghi et al., 2017;Mammola et al., 2017), of local habitat unsuitability due to a combination of specific environmental conditions (Jiménez-Valverde et al., 2017), of competition dynamics that may lead to the exclusion of certain species from a given community (Mammola & Isaia, 2014), or even simply the consequence of imperfect detection (Ficetola et al., 2018) when sampling such structurally complex environments (Wynne et al., 2018(Wynne et al., , 2019. ...
1. Although caves are generally perceived as isolated habitats, at the local scale, they are often interconnected via a network of fissures in the bedrock. Accordingly, caves in close proximity are expected to host the same, or very similar, animal communities.
2. We explored the extent to which subterranean arthropod communities are homogenous at a local spatial scale of less than 1 km², along with which cave‐specific environmental features result in a departure from the expected homogeneous pattern. We approached this question by studying richness and turnover in terrestrial invertebrate communities of 27 caves in a small karst massif in the Western Italian Alps.
3. Specialised subterranean species were homogeneously distributed among caves and were not influenced by seasonality. The only factor driving their distribution was the distance from the cave entrance, with deeper caves yielding a greater diversity of species.
4. Significant spatio‐temporal turnover in species not specialised to subterranean life was observed. In summer, there was a significant homogenisation of the community and a more even distribution of species among sites; in winter, these species were missing or found exclusively at greater depths, where environmental conditions were more stable. Furthermore, caves at lower elevations yielded, on average, a greater diversity and abundance of these species.
5. This study demonstrated that the theoretical expectation of no turnover in community composition in caves in close proximity is not always met. Turnover can be mostly attributed to seasonal patterns and sampling depth; thus, our findings have implications for planning sampling and monitoring activities in caves.
... The fauna was recorded by visual inspection and by pitfall trapping. We applied simultaneously two sampling methods, since it is documented that complementary sampling approaches maximize the detection and completeness of diversity assessments of cave-dwelling arthropods (Kozel et al., 2017;Wynne et al., 2018;Wynne et al., 2019). ...
Troglobionts are organisms that are specialized for living in a subterranean environment. These organisms reside prevalently in the deepest zones of caves and in shallow subterranean habitats, and complete their entire life cycles therein. Because troglobionts in most caves depend on organic matter resources from the surface, we hypothesized that they would also select the sections of caves nearest the surface, as long as environmental conditions were favorable. Over 1 year, we analyzed, in monthly intervals, the annual distributional dynamics of a subterranean community consisting of 17 troglobiont species, in relation to multiple environmental factors. Cumulative standardized annual species richness and diversity clearly indicated the existence of two ecotones within the cave: between soil and shallow subterranean habitats, inhabited by soil and shallow troglobionts; and between the transition and inner cave zones, where the spatial niches of shallow and deep troglobionts overlap. The mean standardized annual species richness and diversity showed inverse relationships, but both contributed to a better insight into the dynamics of subterranean fauna. Regression analyses revealed that temperatures in the range 7–10°C, high moisture content of substrate, large cross section of the cave, and high pH of substrate were the most important ecological drivers governing the spatiotemporal dynamics of troglobionts. Overall, this study shows general trends in the annual distributional dynamics of troglobionts in shallow caves and reveals that the distribution patterns of troglobionts within subterranean habitats may be more complex than commonly assumed.
... Conversely, while advancing our knowledge of regional troglomorphic millipede diversity stands to contribute significantly to the conservation value of the SCK, a more comprehensive understanding (i.e., for all cave-dwelling taxa) of regional diversity, as well as advancing procedures to assessing the vulnerability of cave systems to anthropogenic impact should be considered. Wynne et al. (2018Wynne et al. ( , 2019 provides a systematic framework and guidance for sampling cave-dwelling arthropods using a repeatable framework, which can be modified for application in the SCK. Using such an approach, these data may be then be examined by applying principles similar to the cave vulnerability assessment developed by Tanalgo et al. (2018). ...
We synthesized the current knowledge of cave-dwelling millipede diversity from Guangxi Zhuang Autonomous Region (Guangxi), South China Karst, China and described six new millipede species from four caves from the Guilin area, northeastern Guangxi. Fifty-two cave-dwelling millipedes are known for the region consisting of 38 troglobionts and 14 troglophiles. Of the troglobionts, 24 are presently considered single-cave endemics. New species described here include Hyleoglomeris rukouqu sp. nov. and Hyleoglomeris xuxiakei sp. nov. (Family Glomeridae), Hylomus yuani sp. nov. (Family Paradoxosomatidae), Eutrichodesmus jianjia sp. nov. (Family Haplodesmidae), Trichopeltis liangfengdong sp. nov. (Family Cryptodesmidae), and Glyphiulus maocun sp. nov. (Family Cambalopsidae). Our work also resulted in range expansions of Pacidesmus trifidus Golovatch & Geoffroy, 2014, Blingulus sinicus Zhang & Li, 1981 and Glyphiulus melanoporus Mauriès & Nguyen Duy-Jacquemin, 1997. As with many hypogean animals in Southeast Asia, intensive human activities threaten the persistence of both cave habitats and species. We provide both assessments on the newly described species’ distributions and recommendations for future research and conservation efforts.
... For instance, different arthropods may actively move from larger cave chambers to the stable network of fissures and vice versa (Chapman 1985), or rearrange their spatial distribution along the cave length in different seasons (Crouau-Roy et al. 1992, Mammola et al. 2015a, 2017a, Lunghi et al. 2017. As a direct consequence, there can be conspicuous temporal turnovers in the species composition in a typical subterranean community (Nitzu et al. 2011, Bento et al. 2016, Yun et al. 2016, Bichuette et al. 2017, especially in the vicinity of the surface (Rendoš et al. 2012) which should be taken into account when designing ecological studies and sampling protocols (Culver and Sket 2002, Meleg et al. 2015, Wynne et al. 2018). ...
The use of semi‐isolated habitats such as oceanic islands, lakes and mountain summits as model systems has played a crucial role in the development of evolutionary and ecological theory. Soon after the discovery of life in caves, different pioneering authors similarly recognized the great potential of these peculiar habitats as biological model systems. In their 1969 paper in Science, ‘The cave environment’, Poulson and White discussed how caves can be used as natural laboratories in which to study the underlying principles governing the dynamics of more complex environments. Together with other seminal syntheses published at the time, this work contributed to establishing the conceptual foundation for expanding the scope and relevance of cave‐based studies. Fifty years after, the aim of this review is to show why and how caves and other subterranean habitats can be used as eco‐evolutionary laboratories. Recent advances and directions in different areas are provided, encompassing community ecology, trophic‐webs and ecological networks, conservation biology, macroecology, and climate change biology. Special emphasis is given to discuss how caves are only part of the extended network of fissures and cracks that permeate most substrates, and thus their ecological role as habitat islands is critically discussed. Numerous studies have quantified the relative contribution of abiotic, biotic and historical factors in driving species distributions and community turnovers in space and time, from local to regional scales. Conversely, knowledge of macroecological patterns of subterranean organisms at a global scale remains largely elusive, due to major geographical and taxonomical biases. Also, knowledge regarding subterranean trophic webs and the effect of anthropogenic climate change on deep subterranean ecosystems is still limited. In these research fields, the extensive use of novel molecular and statistical tools may hold promise for quickly producing relevant information not accessible hitherto.
1. Biodiversity conservation is a central imperative of the 21st century. Subterranean ecosystems deliver critical nature's contributions to people and harbour a broad diversity of poorly understood specialised organisms. However, the subterranean biome is still largely overlooked in global biodiversity targets.
2. We assessed how well subterranean biodiversity is represented in protected areas (Natura 2000 and Emerald networks) in two global hotspots of subterranean biodiversity (the Pyrenees and the Alps). For this, we used two comprehensive databases of terrestrial subterranean taxa, that is, leiodids (beetles) from the Pyrenees and spiders from the Alps, and identified priority areas in each region using both species richness and geographic rarity patterns.
3. Our results show the incapacity of surface-protected area networks to represent subterranean biodiversity, as more than 70% and 90% of the identified priority areas (and 40% and 22% of the species) are not effectively covered by protected areas in the Pyrenees and the Alps, respectively.
4. These findings call for developing an urgent plan for subterranean biodiversity conservation within the European Biodiversity Strategy for 2030.
Alien species are a significant threat to natural ecosystems and human economies. Despite global efforts to address this challenge, the documented number of alien species is rapidly increasing worldwide. However, the magnitude of the impact of alien species may vary significantly across habitats. For example, some habitats are naturally less prone to biological invasions due to stringent abiotic and biotic characteristics, selecting for a limited number of introduced species possessing traits closely related to the native organisms. Subterranean ecosystems are quintessential examples of habitats with strong environmental filters (e.g. lack of light and scarcity of food), driving convergent adaptations in species that have successfully adapted to life in darkness. Despite these stringent environmental constraints, the number of records of alien species in subterranean ecosystems has increased in recent decades, but the relevant literature remains largely fragmented and mostly anecdotal. Therefore, even though caves are generally considered very fragile ecosystems, their susceptibility to impacts by alien species remains untested other than for some very specific cases. We provide the first systematic literature survey to synthesise available knowledge on alien species in subterranean ecosystems globally. This review is supported by a database summarising the available literature, aiming to identify gaps in the distribution and spread of alien invertebrate species in subterranean habitats, and laying the foundations for future management practices and interventions. First, we quantitatively assessed the current knowledge of alien species in subterranean ecosystems to shed light on broader questions about taxonomic biases, geographical patterns, modes of dispersal, pathways for introductions and potential impacts. Secondly, we collected species-specific traits for each recorded alien species and tested whether subterranean habitats act as ecological filters for their establishment, favouring organisms with pre-adaptive traits suitable for subterranean life. We found information on the presence of 246 subterranean alien species belonging to 18 different classes. The dominant alien species were invertebrates, especially insects and arachnids. Most species were reported in terrestrial subterranean habitats from all continents except Antarctica. Palaearctic and Nearctic biogeographic regions represented the main source of alien species. The main routes of introductions into the recipient country are linked to commercial activities (84.3% of cases for which there was information available). Negative impacts have been documented for a small number of case studies (22.7%), mostly related to increased competition with native species. For a limited number of case studies (6.1%), management strategies were reported but the effectiveness of these interventions has rarely been quantified. Accordingly, information on costs is very limited. Approximately half of the species in our database can be considered established in subterranean habitats. According to our results, the presence of suitable traits grants access to the stringent environmental filter posed by subterranean environments, facilitating establishment in the new habitat. We recommend that future studies deepen the understanding of invasiveness into subterranean habitats, raising public and scientific community awareness of preserving these fragile ecosystems.
Community assembly, how it changes in space and time, and how it will be affected by global threats, is one of the most pressing issues in ecology, evolution, and conservation biology. To fully understand assembly rules and future community change, one has to delve into multiple interrelated factors, such as the history of environmental and habitat changes in the past, current biotic and abiotic factors, spatial constraints, and future scenarios for all these. Yet, two factors have prevented us from obtaining a complete picture for any organism or system. First, communities are utterly complex, typically encompassing thousands of species and millions of interspecific interactions. Second, future scenarios are overwhelming to model without the challenge of dealing with chaotic systems, where even small changes can lead to large, unpredictable, consequences. We propose to use cave communities as the simplest and easiest setting to model assembly rules and future change across space and time. Caves offer unique opportunities for eco evolutionary studies because they are characterized by a low abundance and diversity of organisms and interactions, they receive limited external inputs, and are easily modelled. The potential of subterranean systems as "natural laboratories" for exploring general, non cave specific agendas has emerged in recent years, with many cave based studies starting to resonate outside caves.
the lepidopteran fauna of caves remains poorly known largely because of the difficulty in collecting specimens suitable for identification in the physically demanding environment. Here we provide the results of biological surveys spanning more than 40 years in Hawai'i. Lava tube caves are an important landform throughout the islands and especially on the younger islands of Maui and Hawai'i. these caves support communities of a diverse array of organisms including Lepidoptera. we list 25 morphospecies of moths now known occur in Hawaiian caves. of these, six are nonnative and mostly are found only in the entrance and twilight zones. three native species are typical surface species, that probably entered caves accidentally. three species of endemic Mestolobes seek shelter in caves and other dark habitats, and some may be associated with caves. Schrankia altivolans are occasionally found living in caves. the remaining species display behav-ioral or morphological adaptations to utilize cave habitats. the speciose endemic genus Hyposmocoma is represented in caves by at least six species. Four species of large native moths were known historically to use caves for communal daytime roosts including Hypocala velans and three species of Peridroma; these emerge at dusk and fly long distances to forage and reproduce, and then return to the same caves at dawn. Most interesting are three species (Schrankia howarthi, Pseudoschrankia nohoana, and Orthomecyna species) that live and reproduce deep in caves and show some morphological features characteristic of obligate cave animals. these results indicate that Lepidoptera are an important component of cave ecosystems and should be included in faunal surveys of caves. we also provide a brief biography of our co-author and dear friend, dr. Fred d. Stone 1938-2018.
The conservation of biodiversity is a central imperative of the 21st century. Subterranean ecosystems deliver critical nature's contributions to people and harbour a broad diversity of poorly-understood specialized organisms that are of interest from both a conservation and evolutionary perspective. However, the subterranean biome is still systematically overlooked in global biodiversity targets and conservation agendas. The main objective of this study was to assess how far subterranean biodiversity is represented in protected areas (Natura 2000 and Emerald networks) in two global hotspots of subterranean biodiversity (the Pyrenees and the Alps). For this, we used the most complete databases of terrestrial subterranean biodiversity known to us, i.e., leiodids (beetles) from the Pyrenees and spiders from the Alps, and identi ed priority areas in each region using both species richness and geographic rarity patterns. Our results show the incapacity of surface protected area networks to represent subterranean fauna, as more than 70 and 90% of the identi ed priority areas (and the 40 and 22% of the species) are not effectively covered by protected areas in the Pyrenees and the Alps, respectively. These ndings call for urgent policies and would be key to developing a coherent plan for subterranean biodiversity conservation within the European Biodiversity Strategy for 2030.
Subterranean ecosystems are among the most widespread environments on Earth, yet we still have poor knowledge of their biodiversity. To raise awareness of subterranean ecosystems, the essential services they provide, and their unique conservation challenges, 2021 and 2022 were designated International Years of Caves and Karst. As these ecosystems have traditionally been overlooked in global conservation agendas and multilateral agreements, a quantitative assessment of solution-based approaches to safeguard subterranean biota and associated habitats is timely. This assessment allows researchers and practitioners to understand the progress made and research needs in subterranean ecology and management. We conducted a systematic review of peer-reviewed and grey literature focused on subterranean ecosystems globally (terrestrial, freshwater, and saltwater systems), to quantify the available evidence-base for the effectiveness of conservation interventions. We selected 708 publications from the years 1964 to 2021 that discussed, recommended, or implemented 1,954 conservation interventions in subterranean ecosystems. We noted a steep increase in the number of studies from the 2000s while, surprisingly, the proportion of studies quantifying the impact of conservation interventions has steadily and significantly decreased in recent years. The effectiveness of 31% of conservation interventions has been tested statistically. We further highlight that 64% of the reported research occurred in the Palearctic and Nearctic biogeographic regions. Assessments of the effectiveness of conservation interventions were heavily biased towards indirect measures (monitoring and risk assessment), a limited sample of organisms (mostly arthropods and bats), and more accessible systems (terrestrial caves). Our results indicate that most conservation science in the field of subterranean biology does not apply a rigorous quantitative approach, resulting in sparse evidence for the effectiveness of interventions. This raises the important question of how to make conservation efforts more feasible to implement, cost-effective, and long-lasting. Although there is no single remedy, we propose a suite of potential solutions to focus our efforts better towards increasing statistical testing and stress the importance of standardising study reporting to facilitate meta-analytical exercises. We also provide a database summarising the available literature, which will help to build quantitative knowledge about interventions likely to yield the greatest impacts depending upon the subterranean species and habitats of interest. We view this as a starting point to shift away from the widespread tendency of recommending conservation interventions based on anecdotal and expert-based information rather than scientific evidence, without quantitatively testing their effectiveness.
(1) Caves and other subterranean habitats fulfill the requirements of experimental model systems to address general questions in ecology and evolution. Yet, the harsh working conditions of these environments and the uniqueness of the subterranean organisms have challenged most attempts to pursuit standardized research
(2) Two main obstacles have synergistically hampered previous attempts. First, there is a habitat impediment related to the objective difficulties of exploring subterranean habitats and our inability to access the network of fissures that represent the elective habitat for the so-called “cave species.” Second, there is a biological impediment illustrated by the rarity of most subterranean species and their low physiological tolerance, often limiting sample size and complicating lab experiments.
(3) We explore the advantages and disadvantages of four general experimental setups (in-situ, quasi in-situ, ex-situ, and in-silico) in the light of habitat and biological impediments. We also discuss the potential of indirect approaches to research. Furthermore, using bibliometric data, we provide a quantitative overview of the model organisms that scientists have exploited in the study of subterranean life.
(4) Our over-arching goal is to promote caves as model systems where one can perform standardised scientific research. This is important not only to achieve an in-depth understanding of the functioning of subterranean ecosystems but also to fully exploit their long-discussed potential in addressing general scientific questions with implications beyond the boundaries of this discipline.
We review the diversity of moths, Lepidoptera, known from caves in Hawai'i. Twenty-five spp are listed, of which 6 are alien, 3 are natives accidentally in caves; and 16 natives show morphological or behavioral traits to live in caves.
Two new troglomorphic pseudoscorpion species, Parobisium magangensis sp. n. and P. yuantongi sp. n., belonging to the family Neobisiidae, are described based on specimens collected in karst caves from Beijing, China. These are the first troglomorphic pseudoscorpions discovered from caves in northern China. Detailed diagnosis, descriptions, and illustrations are provided. We also offer future research and management recommendations for these two new pseudoscorpion species.
Ever-increasing human pressures on cave biodiversity have amplified the need for systematic, repeatable, and intensive surveys of cave-dwelling arthropods to formulate evidence-based management decisions. We examined 110 papers (from 1967 to 2018) to: (i) understand how cave-dwelling invertebrates have been sampled; (ii) provide a summary of techniques most commonly applied and appropriateness of these techniques, and; (iii) make recommendations for sampling design improvement. Of the studies reviewed, over half (56) were biological inventories, 43 ecologically focused, seven were techniques papers, and four were conservation studies. Nearly one-half (48) of the papers applied systematic techniques. Few papers (24) provided enough information to repeat the study; of these, only 11 studies included cave maps. Most studies (56) used two or more techniques for sampling cave-dwelling invertebrates. Ten studies conducted ≥10 site visits per cave. The use of quantitative techniques was applied in 43 of the studies assessed. More than one-third (42) included some level of discussion on management. Future studies should employ a systematic study design, describe their methods in sufficient detail as to be repeatable, and apply multiple techniques and site visits. This level of effort and detail is required to obtain the most complete inventories, facilitate monitoring of sensitive cave arthropod populations, and make informed decisions regarding the management of cave habitats. We also identified naming inconsistencies of sampling techniques and provide recommendations towards standardization.
The vegan package provides tools for descriptive community ecology. It has most basic functions of diversity analysis, community ordination and dissimilarity analysis. Most of its multivariate tools can be used for other data types as well.
The functions in the vegan package contain tools for diversity analysis, ordination methods and tools for the analysis of dissimilarities. Together with the labdsv package, the vegan package provides most standard tools of descriptive community analysis. Package ade4 provides an alternative comprehensive package, and several other packages complement vegan and provide tools for deeper analysis in specific fields. Package https://CRAN.R-project.org/package=BiodiversityR provides a Graphical User Interface (GUI) for a large subset of vegan functionality.
The vegan package is developed at GitHub (https://github.com/vegandevs/vegan/). GitHub provides up-to-date information and forums for bug reports. Most important changes in vegan documents can be read with news(package="vegan") and vignettes can be browsed with browseVignettes("vegan"). The vignettes include a vegan FAQ, discussion on design decisions, short introduction to ordination and discussion on diversity methods. A tutorial of the package at http://cc.oulu.fi/~jarioksa/opetus/metodi/vegantutor.pdf provides a more thorough introduction to the package. To see the preferable citation of the package, type citation("vegan").
This is the first study to specifically sample for cave-adapted arthropods in one of the most promising caves to yield cave-adapted insects on Grand Canyon-Parashant National Monument. For this study, we: (a) deployed baits within four areas of the cave to further inventory troglomorphic arthropods, (b) searched for and collect additional samples of the presumed facultative troglobitic Polydesmid millipede, and (c) collected data to gain further insights regarding the distributions of cave-dwelling arthropods. Additionally, we collected arthropod specimens from the surface near the cave entrance to identify species that may one day colonize caves due to global climate change.
The vegan package provides tools for descriptive community ecology. It has most basic functions of diversity analysis, community ordination and dissimilarity analysis. Most of its multivariate tools can be used for other data types as well.
The functions in the vegan package contain tools for diversity analysis, ordination methods and tools for the analysis of dissimilarities. Together with the labdsv package, the vegan package provides most standard tools of descriptive community analysis. Package ade4 provides an alternative comprehensive package, and several other packages complement vegan and provide tools for deeper analysis in specific fields. Package https://CRAN.R-project.org/package=BiodiversityR provides a Graphical User Interface (GUI) for a large subset of vegan functionality.
The vegan package is developed at GitHub (https://github.com/vegandevs/vegan/). GitHub provides up-to-date information and forums for bug reports. Most important changes in vegan documents can be read with news(package="vegan") and vignettes can be browsed with browseVignettes("vegan"). The vignettes include a vegan FAQ, discussion on design decisions, short introduction to ordination and discussion on diversity methods. A tutorial of the package at http://cc.oulu.fi/~jarioksa/opetus/metodi/vegantutor.pdf provides a more thorough introduction to the package. To see the preferable citation of the package, type citation("vegan").
Austrotyla awishoshola n. sp. is described from the moss gardens of one lava tube cave in El Malpais National Monument, Cibola Co., New Mexico. Most chordeumatidans require mesic conditions, and these environments are limited to moss gardens in several cave entrances and beneath cave skylights in El Malpais. Presently, this species is known from the moss gardens of a single of cave in the monument. We suggest A. awishoshola may be a climatic relict, having become restricted to the cave environment following the end of the Pleistocene. We discuss the importance of cave moss gardens as refugial and relictual habitats. Recommendations are provided to aid in the conservation and management of A. awishoshola and these habitats.
Populations of cave invertebrates are generally considered to be food-limited. The cave entrance is a major source of food input into the community in the form of decaying organic matter. Thus, the densities of scavenging terrestrial cave invertebrates should be related to the distance from the cave entrance because this represents a measure of food abundance. A test showed this expectation to be true in Crossings Cave, Alabama. A population density peak occurred 10 m inside the cave where the dark zone and detritus infall regions meet. The greatest population peak occurred at 100 m where densities of crickets and their guano are highest. The pattern should hold for most caves, but the actual distances will vary in each site depending on its circumstances. When the fauna was removed from the cave, the remnant had not regained community equilibrium a year later. Removal of the dominant scavenger, a milliped, allowed other species populations to expand because of decreased competitions.
Nine species of terrestrial isopods are reported for the Polynesian island of Rapa Nui (Easter Island) based upon museum materials and recent collections from field sampling. Most of these animals are non-native species, but two are new to science: Styloniscus
manuvaka
sp. n. and Hawaiioscia
rapui
sp. n. Of these, the former is believed to be a Polynesian endemic as it has been recorded from Rapa Iti, Austral Islands, while the latter is identified as a Rapa Nui island endemic. Both of these new species are considered ‘disturbance relicts’ and appear restricted to the cave environment on Rapa Nui. A short key to all the oniscidean species presently recorded from Rapa Nui is provided. We also offered conservation and management recommendations for the two new isopod species.
Caves are considered buffered environments in terms of their ability to sustain near-constant microclimatic conditions. However,
cave entrance environments are expected to respond rapidly to changing conditions on the surface. Our study documents an assemblage
of endemic arthropods that have persisted in Rapa Nui caves, despite a catastrophic ecological shift, overgrazing, and surface
ecosystems dominated by invasive species. We discovered eight previously unknown endemic species now restricted to caves—a
large contribution to the island's natural history, given its severely depauperate native fauna. Two additional species, identified
from a small number of South Pacific islands, probably arrived with early Polynesian colonizers. All of these animals are
considered disturbance relicts—species whose distributions are now limited to areas that experienced minimal historical human
disturbance. Extinction debts and the interaction of global climate change and invasive species are likely to present an uncertain
future for these endemic cavernicoles.
Eight species of Collembola are reported from recent collections made in caves on the Polynesian island of Rapa Nui (Eas-ter Island). Five of these species are new to science and apparently endemic to the island: Coecobrya aitorererere n. sp., Cyphoderus manuneru n. sp., Entomobrya manuhoko n. sp., Pseudosinella hahoteana n. sp. and Seira manukio n. sp. The Hawaiian species Lepidocyrtus olena Christiansen & Bellinger and the cosmopolitan species Folsomia candida Wil-lem also were collected from one or more caves. Coecobrya kennethi Jordana & Baquero, recently described from Rapa Nui and identified as endemic, was collected in sympatric association with C. aitorererere n.sp. With the exception of F. candida, all species are endemic to Rapa Nui or greater Polynesia and appear to be restricted to the cave environment on Rapa Nui. A key is provided to separate Collembola species reported from Rapa Nui. We provide recommendations to aid in the conservation and management of these new Collembola, as well as the other presumed cave-restricted arthropods.
Local species diversity of terrestrial arthropods was determined from a combination of trapping and census in an area of variable passage type in Flint Ridge Cave System in Mammoth Cave National Park, Kentucky. We measured evaporative rate, substrate moisture, substrate organic content, predictability and stability of food and microclimate, substrate diversity, and intensity of flooding. We found significant correlations of species diversity with substrate diversity, substrate organic content, and intensity of flooding.
Subterranean environments, even though they do not possess a primary production (photosynthesis), may present high biodiversity, faunistic originality, endemism, phylogenetic isolations and unique ecological and/or evolution events, in addition to rare taxa. Studies investigating the biological diversity in Neotropical caves are relatively rare and recent, and most of them have been conducted in Brazil. We sampled caves from the state of Bahia, northeastern Brazil, and through sampling sufficiency tests and richness estimators, we demonstrate that the normatization for the Brazilian cave laws is not adequate for its conservation and that only α diversity index is not enough to verify faunistic patterns. We suggest that a phylogenetic diversity index be more robust and accurate for conservation purposes, particularly the Taxonomic Distinctness index. Moreover, we propose that the sandstone complex caves from Chapada Diamantina National Park need to be classified as being of high subterranean biodiversity in a global scope.
This study reports on the pseudoscorpion fauna of the subterranean ecosystems of northern Arizona, U.S.A. Our work resulted in the descriptions of two new species, Hesperochernes bradybaughi sp. nov. and Tuberochernes cohni sp. nov. (Chernetidae) and the range expansion of one species, Larca cavicola (Muchmore 1981) (Larcidae). All of these species were cave-adapted and found within caves on Grand Canyon-Parashant National Monument in northwestern Arizona. Based upon this work, the genus Archeolarca Hoff and Clawson is newly synonymized with Larca Chamberlin, and the following species are transferred from Archeolarca to Larca, forming the new combinations L. aalbui (Muchmore 1984), L. cavicola (Muchmore 1981), L. guadalupensis (Muchmore 1981) and L. welbourni (Muchmore 1981). Despite intensive sampling on the monument, the two new species were detected in only one cave. This cave supports the greatest diversity of troglomorphic arthropod species on the monument—all of which are short-range endemics occurring in only one cave. Maintaining the management recommendations provided by Peck and Wynne (2013) for this cave should aid in the long-term persistence of these new pseudoscorpion species, as well as the other troglomorphic arthropods.
In the present paper, a new subgenus and two new species of the cave-dwelling genus Dongodytes Deuve, 1993 are described and illustrated: Dongodytes (Dongodytodes) deharvengi, subgen. and sp. nov. and Dongodytes baxian, sp. nov. from Du'an Xian, North Guangxi, China.
Cave ecosystems are considered one of the most poorly studied and fragile systems on Earth. Belize
caves are no exception. This paper represents the first effort to synthesize information on both invertebrate
and vertebrate observations from a Belize cave. Based on limited field research and a review of literature,
we identified two ecologically sensitive areas, and developed a species inventory list containing
41 vertebrate and invertebrate morphospecies in Actun Chapat, Vaca Plateau, west-central Belize. Actun
Chapat contains two ecologically sensitive areas: (1) a large multiple species bat roost, and (2) a subterranean
pool containing troglobites and stygobites. The inventory list is a product of sporadic research
conducted between 1973 and 2001. Ecological research in this cave system remains incomplete. An
intensive systematic ecological survey of Actun Chapat with data collection over multiple seasons using
a suite of survey techniques will provide a more complete inventory list. To minimize human disturbance
to the ecologically sensitive areas, associated with ecotourism, we recommend limited to no access in the
areas identified as “sensitive.”
A major challenge confronting many contemporary systematists is how to integrate standard taxonomic research with conservation outcomes. With a biodiversity crisis looming and ongoing impediments to taxonomy, how can systematic research continue to document species and infer the ‘Tree of Life’, and still maintain its significance to conservation science and to protecting the very species it strives to understand? Here we advocate a systematic research program dedicated to documenting short-range endemic taxa, which are species with naturally small distributions and, by their very nature, most likely to be threatened by habitat loss, habitat degradation and climate change. This research can dovetail with the needs of industry and government to obtain high-quality data to inform the assessment of impacts of major development projects that affect landscapes and their biological heritage. We highlight how these projects are assessed using criteria mandated by Western Australian legislation and informed by guidance statements issued by the Environmental Protection Authority (Western Australia). To illustrate slightly different biological scenarios, we also provide three case studies from the Pilbara region of Western Australia, which include examples demonstrating a rapid rise in the collection and documentation of diverse and previously unknown subterranean and surface faunas, as well as how biological surveys can clarify the status of species thought to be rare or potentially threatened. We argue that ‘whole of biota’ surveys (that include all invertebrates) are rarely fundable and are logistically impossible, and that concentrated research on some of the most vulnerable elements in the landscape – short-range endemics, including troglofauna and stygofauna – can help to enhance conservation and research outcomes.
We used molecular and morphological techniques to study troglobitic schizomids inhabiting a variety of subterranean landforms in semiarid Western Australia. The study was designed to explore the taxonomic and phylogenetic status of newly discovered populations of subterranean schizomids. Molecular sequences of the mitochondrial DNA (mtDNA) cytochrome oxidase subunit 1 (COI) and small subunit rRNA (12S) were obtained from a total of 73 schizomid specimens. Populations sampled from boreholes within mesa landforms in the Robe Valley were highly genetically distinct from species of Draculoides Harvey, 1992 found elsewhere in the Pilbara (Cape Range and Barrow Island). Pronounced genetic structuring was also evident at a fine spatial scale within the Robe Valley, with populations from each of the mesas examined exhibiting unique and highly divergent mtDNA lineages. These molecular data were generally supported by small but significant morphological features, usually in the secondary male structures, but some species were represented only by female specimens that possessed more conservative morphologies. The molecular data defined two major in-group clades, which were supported by morphological differences. One clade was widespread and included the type species of Draculoides, D. vinei (Harvey), along with D. bramstokeri Harvey & Humphreys, D. brooksi Harvey, D. julianneae Harvey, D. mesozeirus, sp. nov. and D. neoanthropus, sp. nov. The second clade was restricted to the Robe Valley and deemed to represent a new genus, Paradraculoides, which included four new species P. anachoretus, sp. nov., P. bythius, sp. nov., P. gnophicola, sp. nov. and P. kryptus, sp. nov. (type species).
Arthropods are critical ecosystem components due to their high diversity and sensitivity to perturbation. Furthermore, due to their ease of capture they are often the focus of environmental health surveys. There is much debate regarding the best sampling method to use in these surveys. Sweep netting and pan trapping are two sampling methods commonly used in agricultural arthropod surveys, but have not been contrasted in natural grassland systems at the community level. The purpose of this study was to determine whether sweep netting was effective at estimating arthropod diversity at the community level in grasslands or if supplemental pan trapping was needed. Arthropods were collected from grassland sites in Montana, USA, in the summer of 2011. The following three standardized evaluation criteria (consistency, reliability, and precision) were developed to assess the efficacy of sweep netting and pan trapping, based on analyses of variations in arthropod abundances, species richness, evenness, capture frequency, and community composition. Neither sampling method was sufficient in any criteria to be used alone for community-level arthropod surveys. On a taxa-specific basis, however, sweep netting was consistent, reliable, and precise for Thysanoptera, infrequently collected (i.e., rare) insects, and Arachnida, whereas pan trapping was consistent, reliable, and precise for Collembola and bees, which is especially significant given current threats to the latter's populations worldwide. Species-level identifications increase the detected dissimilarity between sweep netting and pan trapping. We recommend that community-level arthropod surveys use both sampling methods concurrently, at least in grasslands, but likely in most nonagricultural systems. Target surveys, such as monitoring bee communities in fragmented grassland habitat or where detailed information on behavior of the target arthropod groups is available can in some instances employ singular methods. As a general ecological principle, consistency, reliability, and precision are appropriate criteria to evaluate the applicability of a given sampling method for both community-level and taxa-specific arthropod surveys in any ecosystem.
Ptomaphagus parashant Peck and Wynne, new species, is described from a cave in northwestern Arizona. This is the most cave-modified (troglomorphic) cholevine species known in western North America. Presently, the type locality is the only known location for this new species. We offer management recommendations including annual monitoring to document unauthorized human visitation to this cave and other suggestions to help protect the species from future human disturbance.
Lava tube caves at El Malpais National Monument have received little scientifi c attention with regard to their bat and arthropod populations. From an all taxa biological inventory of 11 caves, I identified seven new species of cave-dwelling arthropods (including two potential troglobites) and range expansions of two parasitoidal wasps. The presence of unique microhabitats, tree root “curtains” hanging from the ceilings, and moss gardens in cave entrances resulted in higher species richness of arthropods at four caves. For bats, I confi rmed continued use of one large bat hibernaculum cave and one signifi cant bat maternity roost. While several recommendations have been made to better conserve and manage sensitive cave resources, additional research and monitoring will be required for the long-term management and protection of several caves. Finally, I introduce three new terms to cave biology: two for entrance-dwelling animals (eisodophiles and eisodoxenes) and one for animals that hunt deep within or near the entrances of caves (xenosylles).
We define the genus Cyptophania with characters that clearly separate it from other genera of the Family Lepidopsocidae in which wing reduction has occurred. We redescribe the generotype, C. hirsuta Banks (Hawaii, presumably introduced), and describe three new species, C. australica n.sp. (Queensland, Australia), C. costalis n.sp. (Gulf of Mexico and Caribbean), and C. pakaratii n.sp. (Rapa Nui = Easter Island, probably endemic). The latter species is described from both sexes and presents the first males known for the genus. One female of this species presents a large spermatophore protruding from the genital chamber, thus indicating the mode of sperm transfer in sexual members of this genus. A key to the known species is included. All of the species of Cyptophania are highly neotenic, but differences in the level of neoteny are noted among the species studied. We question the synonymy of the genus Ptenocorium Enderlein with Cyptophania on the basis of several characters illustrated in the original description of Ptenocorium. We note similarities of Cyptophania to the entirely macropterous genus Lepidopsocus Enderlein and suggest a possible close relationship between the two genera.
Records for 173 cavernicolous invertebrate species of Platyhelminthes, Nematoda, Nemertea, Annelida, Mollusca, and Arthropoda from 47 caves in Georgia are presented. The checklist includes eight species of cave-dwelling cellular slime molds and endosymbiotic trichomycete fungi associated with cave millipedes and isopods.
Several aspects of the ecology of Cueva de los Roques were studied: the survey initiated by other speleologists was completed; the flora at the entrance to the cave was studied; and the fauna of the whole cave was analysed by sampling on two occasions three months apart, using a combination of visual searching and baited trapping. The most striking result was the difference in both physical conditions and biology between the two branches of the cave. Branch A has several entrances and thus appreciable air movements, with the result that it is inhabited only by trogloxenes and a few troglophiles. In contrast, branch B is a blind tube with constant high humidity and stable temperature, here there is a community of troglobites. We have found a total of 27 species of invertebrates; these include nine troglobites, of which seven are already known from other lava tubes on Tenerife. This suggests the occurrence of dispersal through a network of cracks in the subsoil, as in other volcanic and karst regions.
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Four new species of presumed troglobitic polydesmidan millipeds in two new genera are described from caves in the states of Arizona, Nevada and California. Pratherodesmus, n. gen., is comprised of the type species, P. voylesi, n. sp., P. ecclesia, n. sp., and P. despaini, n. sp. The genus is found in Arizona and California. Nevadesmus ophimontis, n. gen., n. sp., is from White Pine Co., Nevada; the new genus also includes N. hubbsi (Chamberlin) 1943, new combination. All four species were collected in or near United States National Parks, Bureau of Land Management lands, and in a private preserve. All new taxa are authored by W. A. Shear only.
The Hawaiian Islands provide the venue of one of nature's grand experiments in evolution. Here, we present morphological, behavioral, genetic, and geologic data from a young subterranean insect lineage in lava tube caves on Hawai'i Island. The Oliarus polyphemus species complex has the potential to become a model for studying rapid speciation by stochastic events. All species in this lineage live in extremely similar environments but show strong differentiation in behavioral and morphometric characters, which are random with respect to cave age and geographic distribution. Our observation that phenotypic variability within populations decreases with increasing cave age challenges traditional views on founder effects. Furthermore, these cave populations are natural replicates that can be used to test the contradictory hypotheses. Moreover, Hawaiian cave planthoppers exhibit one of the highest speciation rates among animals and, thus, radically shift our perception on the evolutionary potential of obligate cavernicoles.
Key words: density-dependent selection | dynamic adaptive landscape | nonadaptive speciation | sexual behavior | vibrational communication
In agriculture, sustainability can be linked to ecological resilience. In view of present or imminent environmental changes in agricultural landscapes, the diversity of species and genotypes, particularly of potential beneficials and alternative prey, may become of increasing importance. However, the available methods and empirical data concerning species diversity of above-ground insects in agricultural landscapes do not yet allow comprehensive evaluation. Standardized inventory methods must be used more rigorously and over longer time periods to detect significant differences in space and in time. Indicator groups for biodiversity estimates must be defined.
Methods for optimizing the reliability and comparability of faunistic inventories are proposed, including rarefaction for reference functions and estimation of species numbers per unit area. Recommendations for optimum sampling periods and average empirical numbers for species diversity and abundance of major arthropod groups are given and compared to published data.
In general, organismal biodiversity is higher in less intensely cultivated habitats. Apart from the impact of biocides, variation in species diversity often depends on the biodiversity of the surroundings (mosaic landscape) rather than on differing management regimes. The focus in preserving or enhancing, but also in evaluating biodiversity in cultivated areas thus should clearly be on the landscape level. Structural biodiversity in agricultural areas appears to be correlated with functional and organismal biodiversity of the above-ground insect fauna.
FIGURE 36. Map of parts of the states of Arizona, California, Nevada and Utah, showing localities for milliped collections (Map by S. Taylor).
One troglobite, 13 troglophiles, 6 habitual trogloxenes, 7 occasional trogloxenes and 4 accidentals were pitfall trapped in the caverns. Four factors influence the cavernicolous fauna trapped: 1) the distance traps were placed from an outside entrance, 2) substrate composition in the area of the trap, 3) humidity and 4) the subdued climatic seasonal influences bringing into the caverns its associated trogloxene and accidental fauna. -from Author
Plant roots are an important component of underground food webs in mesocaverns, lava tubes, and solution caves. Trees such as Metrosideros , Eucalyptus , Ficus , and Brachychiton are adapted to send their roots through porous rock to get water and nutrients. These trees are primary producers, photosynthesizing and sending energy in the form of carbohydrates into their roots. Surface species that live on and around roots may venture deep underground along roots, but most are not able to survive deep in caves and become food for predators and scavengers. In some groups, including the planthopper family Cixiidae and the moth family Noctuidae, new species have evolved traits that allow them to spend their entire life cycle underground. Besides these primary consumers (herbivores), tree root communities in caves include carnivores, detritivores, decomposers, and fungivores. Many of these animals are obligate cave species (troglobites) and are generally restricted to habitats with high humidity and low air motion found in mesocaverns and the deep cave zone. Protection of troglobites in tree root communities requires more than simply protecting the caves in which they occur, it requires determining the plant species that provide the roots, and protecting these species on the surface over the cave and associated mesocaverns.
Obligatory cavernicoles, or troglobites, have traditionally been of special interest to evolutionary biologists for several reasons. The existence of animal life in caves and other subterranean spaces at first attracted attention because of its novelty; intensive biological exploration of caves began little more than a century ago. Although the discovery and description of the cave faunas of the world is far from complete, especially in the Western Hemisphere, so much descriptive information has been compiled that we can safely assert that, at least in unglaciated, temperate parts of the world, the occurrence of numerous species of troglobites in any major limestone region is a common and highly probable phenomenon.
Some 178 species of free-living terrestrial non-insect invertebrates are reported; 29 of these species are troglobites, 62 troglophiles. The troglobites include 3 snails, 1 terrestrial isopod, 7 pseudoscorpions, 7 spiders, 2 harvestmen, and 9 millipedes. -from Author
(1) I examined the factors influencing the habitation of caves by troglobites in semi-arid tropical Western Australia. Such low energy caves receive water and energy in unpredictable pulses sometimes separated by many years. (2) An experiment was established, involving the addition of water and energy (organic matter), in a cave which had become largely defaunate as a result of drying and energy depletion. (3) The water added to the experimental plots increased the overall relative humidity of the cave, but this alone was insufficient to reestablish the populations. (4) Both the water and organic carbon content of the mud-banks were homogeneous between treatments at the start of the experiment. (5) The soil water content increased in those treatments to which water was added and no cross-watering occurred. (6) The addition of water alone to the cave soil resulted in a loss of organic carbon in the absence of macrofauna. (7) No species were recorded within the control plots but seven taxa were recorded in the other treatments. The three numerically dominant taxa are millipedes, isopods and schizomids. (8) There was a progressive increase in numbers during the 61 days of the experiment resulting from colonization followed by reproduction. (9) The combination of added water and organic matter (130 X numbers in control) was by far the most populous treatment, followed by litter alone (X25) and water alone (X3). (10) The fauna did not incorporate organic matter into the soil of the cave.
The Kentucky cave shrimp Palaemonias ganteri is known only from base level cave passages in the Mammoth Cave System, Kentucky. Since the shrimp was not seen between 1967 and 1979, it was assumed to be extinct. Between May 1979 and February 1981, I looked for shrimp in base level pools by searching visually or by seining and dip netting once a month. SCUBA divers on four occasions searched deep pools and submerged cave passages. No live shrimp were found in residual pools, where they were readily observed before 1967. A few shrimp were found in deep pools of streams and in submerged passages. Foraging at the water surface was observed.
This study assesses the effect of temporal and spatial heterogeneity of preferred prey on the foraging strategies of two carabid cave beetles, Neaphaenops tellkampfii and Pseudanophthalmus menetriesii. Neaphaenops tellkampfii prefers the eggs and nymphs of the common cave cricket (Hadenoecus subterraneus) which are patchy in time but not in space. Cave cricket eggs are laid in sandy habitats which support few alternate prey. As a result N. tellkampfii is forced to switch diet, habitat, and foraging mode in the fall when cricket eggs and nymphs become rare. Pseudanophthalmus menetriesii preys on collembola that are confined to habitats with organic matter. These items are patchily distributed but continuously available. In sand or mud habitats collembola are rare and P. menetriesii appears to incur higher foraging costs in these habitats than in litter areas. As a result P. menetriesii shows restricted habitat preference and tracks its prey between various organic patches.
"Measuring Biological Diversity assumes no specialist mathematical knowledge and includes worked examples and links to web-based software. It will be essential reading for all students, researchers, and managers who need to measure biological diversity."--BOOK JACKET.
ABSTRACT We studied species richness patterns of obligate subterranean (troglobiotic) beetles in the Dinaric karst of the western Balkans, using five grid sizes with cells of 80 × 80, 40 × 40, 20 × 20, 10 × 10, and 5 × 5 km. The same two hotspots could be recognized at all scales, although details differed. Differences in sampling intensity were not sufficient to explain these patterns. Correlations between number of species and number of sampled localities increased with increasing cell size. Additional species are expected to be found in the region, as indicated by jackknife 1, jackknife 2, Chao2, bootstrap, and incidence-based coverage (ICE) species richness estimators. All estimates increased with increasing cell size, except Chao2, with the lowest prediction at the intermediate 20 × 20 km cell size. Jackknife 2 and ICE gave highest estimates and jackknife 1 and bootstrap the lowest. Jackknife 1 and bootstrap estimates changed least with cell size, while the number of single cell species increased. In the highly endemic subterranean fauna with many rare species, bootstrap may be most appropriate to consider. Positive autocorrelation of species numbers was highest at 20 × 20 km scale, so we used this cell size for further analyses. At this scale we added 137 localities with less positional accuracy to 1572 previously considered, and increased 254 troglobiotic species considered to 276. Previously discovered hotspots and their positions did not change, except for a new species-rich cell which appeared in the south-eastern region. There are two centres of troglobiotic species richness in the Dinaric karst. The one in the north-west exhibited high species richness of Trechinae (Carabidae), while in the south-east, the Leptodirinae (Cholevidae) were much more diverse. These centres of species richness should serve as the starting point for establishing a conservation network of important subterranean areas in Dinaric karst.
We assembled a list of obligate cave-dwelling species and subspecies, their county distribution, and their provisional global conservation rank. A total of 927 species and 46 additional subspecies in 96 families exclusively from cave and associated subterranean habitats have been described in the 48 contiguous states of the United States. The terrestrial (troglobitic) species are concentrated in northeast Alabama (especially Jackson County), with other concentrations in Kentucky, Texas, Virginia, and West Virginia. Only 23 counties, comprising less than 1% of the land area of the 48 contiguous states, account for over 50% of the terrestrial species and subspecies. The aquatic (stygobitic) species are concentrated in Hays County, Texas, with other concentrations in Florida, Oklahoma, Texas, Virginia, and West Virginia. Only 18 counties, comprising less than 1% of the land area, account for over 50% of the aquatic species and subspecies. Endemism is high, with 54% of the species known from a single county. Approximately 95% of the species are listed by The Nature Conservancy as vulnerable or imperiled in the United States. These cave species comprise 50% of all vulnerable or imperiled species listed in databases of the Natural Heritage Program. Less than 4% of these subterranean species have federal status. Conservation can best be accomplished through habitat protection, which must include protection of the associated surface habitat.
Two procedures, the jackknife and the bootstrap, are discussed as methods for estimating the number of species by the sampling of quadrats. Explicit formulas for both procedures are presented and evaluated under a model with a random distribution of individuals. The jackknife and bootstrap are shown to reduce the bias although they underestimate the actual number of species if there is a large number of rare species and the number of quadrats sampled is small. When a small number of quadrats is sampled, the jackknife is shown to give better estimates. When the number of quadrats is large, the jackknife tends to overestimate the number of species and the bootstrap performs better.