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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. 

Abstract Groundwater is a vital ecosystem of the global water cycle, hosting unique biodiversity and providing essential services to societies. Despite being the largest unfrozen freshwater resource, in a period of depletion by extraction and pollution, groundwater environments have been repeatedly overlooked in global biodiversity conservation agendas. Disregarding the importance of groundwater as an ecosystem ignores its critical role in preserving surface biomes. To foster timely global conservation of groundwater, we propose elevating the concept of keystone species into the realm of ecosystems, claiming groundwater as a keystone ecosystem that influences the integrity of many dependent ecosystems. Our global analysis shows that over half of land surface areas (52.6%) has a medium‐to‐high interaction with groundwater, reaching up to 74.9% when deserts and high mountains are excluded. We postulate that the intrinsic transboundary features of groundwater are critical for shifting perspectives towards more holistic approaches in aquatic ecology and beyond. Furthermore, we propose eight key themes to develop a science‐policy integrated groundwater conservation agenda. Given ecosystems above and below the ground intersect at many levels, considering groundwater as an essential component of planetary health is pivotal to reduce biodiversity loss and buffer against climate change. 

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. 

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. 

We present complete genome sequences of 12 species of Percopsiformes. 

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.