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Subterranean ecosystems harbor globally important yet highly threatened biodiversity. Unfortunately, subterranean biodiversity is often neglected in regional and global conservation initiatives, including conservation assessments. We reviewed the conservation status and threats to subterranean species based on the two most popular conservation assessment protocols in North America, NatureServe and International Union for Conservation of Nature (IUCN) Red List, as well as federal and state/provincial protection status of the 1,460 described cave-obligate species occurring in the United States and Canada. Only 9.3% of species have been assessed under IUCN Red List criteria compared to 77.9% of species assessed under NatureServe criteria; notably, 1,065 and 116 of species are assessed at an elevated risk of extinction by NatureServe and IUCN Red List, respectively. Just 41 species are listed or proposed to be listed under the U.S. Endangered Species Act and none of the 10 species that occur in Canada are federally listed. Vertebrates (fishes and salamanders), decapods (crayfishes and shrimps), and U.S. federally listed species are overrepresented on the list of species with IUCN Red List assessments compared to other taxonomic groups, particularly arachnids, millipedes, and insects. Most species assessed under IUCN Red List criteria as well as federally listed species occur in the Edwards Plateau and Balcones Escarpment karst region of Texas. Major threats frequently reported in conservation assessments include habitat degradation, pollution/contamination, recreational activities, climate change, and groundwater exploitation; however, information on threats was lacking for most species for nearly all major taxonomic groups, except decapods, fishes, and salamanders. The intrinsic vulnerability of subterranean biodiversity coupled with the many potential threats facing species and extensive biodiversity knowledge gaps makes assessing their conservation status and ultimately their protection a challenging endeavor. We highlight several limitations of implementing current conservation assessment approaches while offering recommendations to improve our ability to assess the conservation status of subterranean biodiversity to better inform sound local to global conservation policies and actions. 

We present complete genome sequences of 12 species of Percopsiformes. 

Extreme environments serve as natural laboratories for studying evolutionary processes, with caves offering replicated instances of independent colonizations. The timing, mode and genetic underpinnings underlying cave-obligate organismal evolution remain enigmatic. We integrate phylogenomics, fossils, palaeoclimatic modelling and newly sequenced genomes to elucidate the evolutionary history and adaptive processes of cave colonization in the study group, the North American Amblyopsidae fishes. Amblyopsid fishes present a unique system for investigating cave evolution, encompassing surface, facultative cave-dwelling and cave-obligate (troglomorphic) species. Using 1105 exon markers and total-evidence dating, we reconstructed a robust phylogeny that supports the nested position of eyed, facultative cave-dwelling species within blind cavefishes. We identified three independent cave colonizations, dated to the Early Miocene (18.5 Ma), Late Miocene (10.0 Ma) and Pliocene (3.0 Ma). Evolutionary model testing supported a climate-relict hypothesis, suggesting that global cooling trends since the Early–Middle Eocene may have influenced cave colonization. Comparative genomic analyses of 487 candidate genes revealed both relaxed and intensified selection on troglomorphy-related loci. We found more loci under relaxed selection, supporting neutral mutation as a significant mechanism in cave-obligate evolution. Our findings provide empirical support for climate-driven cave colonization and offer insights into the complex interplay of selective pressures in extreme environments. 

Abstract Mitochondrial genomes play important roles in studying genome evolution, phylogenetic analyses, and species identification. Amphipods (Class Malacostraca, Order Amphipoda) are one of the most ecologically diverse crustacean groups occurring in a diverse array of aquatic and terrestrial environments globally, from freshwater streams and lakes to groundwater aquifers and the deep sea, but we have a limited understanding of how habitat influences the molecular evolution of mitochondrial energy metabolism. Subterranean amphipods likely experience different evolutionary pressures on energy management compared to surface-dwelling taxa that generally encounter higher levels of predation and energy resources and live in more variable environments. In this study, we compared the mitogenomes, including the 13 protein-coding genes involved in the oxidative phosphorylation (OXPHOS) pathway, of surface and subterranean amphipods to uncover potentially different molecular signals of energy metabolism between surface and subterranean environments in this diverse crustacean group. We compared base composition, codon usage, gene order rearrangement, conducted comparative mitogenomic and phylogenomic analyses, and examined evolutionary signals of 35 amphipod mitogenomes representing 13 families, with an emphasis on Crangonyctidae. Mitogenome size, AT content, GC-skew, gene order, uncommon start codons, location of putative control region (CR), length ofrrnLand intergenic spacers differed between surface and subterranean amphipods. Among crangonyctid amphipods, the spring-dwellingCrangonyx forbesiexhibited a unique gene order, a longnad5locus, longerrrnLandrrnSloci, and unconventional start codons. Evidence of directional selection was detected in several protein-encoding genes of the OXPHOS pathway in the mitogenomes of surface amphipods, while a signal of purifying selection was more prominent in subterranean species, which is consistent with the hypothesis that the mitogenome of surface-adapted species has evolved in response to a more energy demanding environment compared to subterranean amphipods. Overall, gene order, locations of non-coding regions, and base-substitution rates points to habitat as an important factor influencing the evolution of amphipod mitogenomes. 

Most cave-obligate species (troglobionts) have small ranges due to limited dispersal ability and the isolated nature of cave habitats. The troglobiontic linyphiid spiderPhanetta subterranea(Emerton, 1875), the only member of its genus, is a notable exception to this pattern; it has been reported from more counties and caves than any other troglobiont in North America. As many troglobionts exhibit significant genetic differentiation between populations over even small geographic distances, it has been hypothesized thatPhanettamay comprise multiple, genetically distinct lineages. To test this hypothesis, we examined genetic diversity inPhanettaacross its range at the mitochondrial cytochrome c oxidase subunit I gene for 47 individuals from 40 caves, distributed across seven states and 37 counties. We found limited genetic differentiation across the species’ range with haplotypes shared by individuals collected up to 600 km apart. Intraspecific nucleotide diversity was 0.006 +/- 0.005 (mean +/- SD), and the maximum genetic p-distance observed between any two individuals was 0.022. These values are within the typical range observed for other spider species. Thus, we found no evidence of cryptic genetic diversity inPhanetta. Our observation of low genetic diversity across such a broad distribution raises the question of how these troglobiontic spiders have managed to disperse so widely. 

A new genus and species of troglobiotic nicoletiid (Insecta, Zygentoma, Nicoletiidae) is described from northern Alabama, USA. The type species was collected from three caves in the Highland Rim section of the Interior Low Plateau physiographic province on the northern side of the Tennessee River Valley. Morphological and genetic analysis using the mitochondrial 16S rRNA locus show thatSpinanycta alabamensissp. nov.is quite distinct from related nicoletiids in North America. The species differs from members of other genera by its urosternum I, which in males is modified with a central pointy extension. The new species significantly extends the distribution of cave-dwelling members of the family into the southeastern United States and suggests that additional nicoletiid diversity remains to be discovered from karst regions of the eastern United States. 

We describe a new species of subterranean amphipod (Amphipoda: Crangonyctidae) in the genusStygobromusfrom a hypotelminorheic seepage spring at Shepherd Parkway, part of National Capital East Parks, Washington, D.C., USA, part of the National Park System, using both morphological and genetic approaches. The Anacostia Groundwater Amphipod,S. anacostensissp. nov.is a member of theS. tenuisspecies group but differs from related congeners based on body size, serrate blade-like edge of both palms of gnathopods 1 and 2, presence of rastellate setae on the posterodistal margin of the carpus of gnathopod 2, and aspects of the second antennae, mandibular palp, pereopods 5–7, uropods 1 and 2, and telson. Moreover,S. anacostensissp. nov.is genetically distinct fromS. tenuisin the Washington D.C. metropolitan area. The description ofS. anacostensissp. nov.increases the number of describedStygobromusspecies to eight in the Washington D.C. area and highlights the need for continued biodiversity studies, even in regions that have received considerable attention. 

Cave-obligate aquatic organisms are difficult to monitor for conservation due to cryptic diversity, unknown subterranean hydrological connectivity, and accessibility to habitats. Conservation management practices have benefitted from evolutionary data; however, the evolutionary and biogeographic histories of most cave-obligate organisms are unknown. The modes and patterns leading to most cave-obligate organism distributions are also uncertain. The Southern Cavefish (Typhlichthys subterraneus, Amblyopsidae) is the largest ranging cavefish in the world but represents a species complex of which the distribution and relatedness within remains unclear. To explore modes of cave-adaptive evolution, we performed population genomic analyses on a dataset of single nucleotide polymorphisms harvested from ultraconserved elements. We found five to eight strongly delineated genetic clusters. Little to no genetic exchange occurred between clusters, indicating high genetic distinctiveness and low connectivity, a concerning result for the fitness and conservation of these fishes. Genetic clusters did not correspond to caves nor to other geographic boundaries examined. Unfortunately, one of the geographic units most easily communicated for conservation– caves– do not match the biological units of interest. Our results support multiple independent colonization events from a widespread surface ancestor with a small degree of cave connectivity among, but not between, clusters. We suggest whole cave system conservation. 

Abstract National parks and other protected areas are important for preserving landscapes and biodiversity worldwide. An essential component of the mission of the United States (U.S.) National Park Service (NPS) requires understanding and maintaining accurate inventories of species on protected lands. We describe a new, national-scale synthesis of amphibian species occurrence in the NPS system. Many park units have a list of amphibian species observed within their borders compiled from various sources and available publicly through the NPSpecies platform. However, many of the observations in NPSpecies remain unverified and the lists are often outdated. We updated the amphibian dataset for each park unit by collating old and new park-level records and had them verified by regional experts. The new dataset contains occurrence records for 292 of the 424 NPS units and includes updated taxonomy, international and state conservation rankings, hyperlinks to a supporting reference for each record, specific notes, and related fields which can be used to better understand and manage amphibian biodiversity within a single park or group of parks.