The 15th UN Convention on Biological Diversity (CBD) (COP15) will be held in Kunming, China in October 2021. Historically, CBDs and other multilateral treaties have either alluded to or entirely overlooked the subterranean biome. A multilateral effort to robustly examine, monitor, and incorporate the subterranean biome into future conservation targets will enable the CBD to further improve the ecological effectiveness of protected areas by including groundwater resources, subterranean ecosystem services, and the profoundly endemic subsurface biodiversity. To this end, we proffer a conservation roadmap that embodies five conceptual areas: (1) science gaps and data management needs; (2) anthropogenic stressors; (3) socioeconomic analysis and conflict resolution; (4) environmental education; and (5) national policies and multilateral agreements.

Variation in both inter‐ and intraspecific traits affects community dynamics, yet we know little regarding the relative importance of external environmental filters versus internal biotic interactions that shape the functional space of communities along broad‐scale environmental gradients, such as latitude, elevation, or depth. We examined changes in several key aspects of functional alpha diversity for marine fishes along depth and latitude gradients by quantifying intra‐ and interspecific richness, dispersion, and regularity in functional trait space. We derived eight functional traits related to food acquisition and locomotion and calculated seven complementary indices of functional diversity for 144 species of marine ray‐finned fishes along large‐scale depth (50–1200 m) and latitudinal gradients (29°–51° S) in New Zealand waters. Traits were derived from morphological measurements taken directly from footage obtained using Baited Remote Underwater Stereo‐Video systems and museum specimens. We partitioned functional variation into intra‐ and interspecific components for the first time using a PERMANOVA approach. We also implemented two tree‐based diversity metrics in a functional distance‐based context for the first time: namely, the variance in pairwise functional distance and the variance in nearest neighbor distance. Functional alpha diversity increased with increasing depth and decreased with increasing latitude. More specifically, the dispersion and mean nearest neighbor distances among species in trait space and intraspecific trait variability all increased with depth, whereas functional hypervolume (richness) was stable across depth. In contrast, functional hypervolume, dispersion, and regularity indices all decreased with increasing latitude; however, intraspecific trait variation increased with latitude, suggesting that intraspecific trait variability becomes increasingly important at higher latitudes. These results suggest that competition within and among species are key processes shaping functional multidimensional space for fishes in the deep sea. Increasing morphological dissimilarity with increasing depth may facilitate niche partitioning to promote coexistence, whereas abiotic filtering may be the dominant process structuring communities with increasing latitude.

Energy and environmental stability are positively correlated with species richness along broad‐scale spatial gradients in terrestrial ecosystems, so their relative importance in generating and preserving diversity cannot be readily disentangled. This study seeks to exploit the negative correlation between energy and stability along the oceanic depth gradient to better understand their relative contribution in shaping broadscale biodiversity patterns. We develop a conceptual framework by simulating speciation and extinction along energy and stability gradients to generate expected patterns of biodiversity for a suite of complementary phylogenetic diversity metrics. Using a time‐calibrated molecular phylogeny for New Zealand marine ray‐finned fishes and a replicated community ecological sampling design, we then modelled these metrics along large‐scale depth and latitude gradients. Our results indicate that energy‐rich shallow waters may be an engine of diversity for percomorphs, but also suggest that recent speciation occurs in ancient fish lineages in the deep sea, hence questioning the role of energy as a key driver of speciation. Despite potentially facing high extinction early in their evolution, ancient phylogenetic lineages specialized for the deep‐sea were likely preserved by environmental stability during the Cenozoic. Furthermore, intermediate depths might be a ‘museum’ (or zone of overlap) for distinct lineages that occur predominantly in either shallow or deep‐sea waters. These intermediate depths (500–900 m) may form a ‘phylogenetic diversity bank’, perhaps providing a refuge during ancient (Mesozoic) extreme anoxic events affecting the deep sea and more recent (Pliocene–Pleistocene) climatic events occurring in shallow ecosystems. Finally, the phylogenetic structures observed in fish communities at intermediate depths suggest other processes might restrict the co‐occurrence of closely related species. Overall, by combining a conceptual framework with models of empirical phylogenetic diversity patterns, our study paves the way for understanding the determinants of biodiversity across the largest habitat on earth.

1.Understanding patterns and processes governing biodiversity along broad‐scale environmental gradients, such as depth or latitude, requires an assessment of not just taxonomic richness, but also morphological and functional traits of organisms. Studies of traits can help to identify major selective forces acting on morphology. Currently, little is known regarding patterns of variation in the traits of fishes at broad spatial scales. 2.The aims of this study were: (i) to identify a suite of key traits in marine fishes that would allow assessment of morphological variability across broad‐scale depth (50 – 1200 m) and latitudinal (29.15 – 50.91°S) gradients; and (ii) to characterise patterns in these traits across depth and latitude for 144 species of ray‐finned fishes in New Zealand waters. 3.Here, we describe three new morphological traits: namely, fin‐base‐to‐perimeter ratio, jaw‐length‐to‐mouth‐width ratio, and pectoral‐fin‐base‐to‐body‐depth ratio. Four other morphological traits essential for locomotion and food acquisition that are commonly measured in fishes were also included in the study. Spatial ecological distributions of individual fish species were characterised in response to a standardised replicated sampling design and morphological measurements were obtained for each species from preserved museum specimens. 4.With increasing depth, fishes, on average, became larger and more elongate, with higher fin‐base‐to‐perimeter ratio and larger jaw‐length‐to‐mouth‐width ratio, all of which translates into a more eel‐like anguilliform morphology. Variation in mean trait values along the depth gradient was stronger at lower latitudes for fin‐base‐to‐perimeter ratio, elongation and total body length. Average eye size peaked at intermediate depths (500‐700 m) and increased with increasing latitude at 700 m. 5.These findings suggest that, in increasingly extreme environments, fish morphology shifts towards a body shape that favours an energy‐efficient undulatory swimming style and an increase in jaw‐length versus mouth width for opportunistic feeding. Furthermore, increases in eye size with both depth and latitude indicate that changes in both the average ambient light conditions as well as seasonal variations in day‐length can act to select ecomorphological adaptations in fishes.

The global biodiversity crisis from anthropogenic activities significantly weakens the functioning of marine ecosystems and jeopardizes their ecosystem services. Increasing monitoring of marine ecosystems is crucial to understand the breadth of the changes in biodiversity, ecosystem functioning and propose more effective conservation strategies. Such strategies should not only focus on maximizing the number of species (i.e., taxonomic diversity) but also the diversity of phylogenetic histories and ecological functions within communities. To support future conservation decisions, multicomponent biodiversity monitoring can be combined with high‐throughput species assemblage detection methods such as environmental DNA (eDNA) metabarcoding. Here, we used eDNA to assess fish biodiversity along the coast of southern Brittany (France, Iroise Sea). We filtered surface marine water from 17 sampling stations and applied an eDNA metabarcoding approach targeting Actinopterygii and Elasmobranchii taxa. We documented three complementary biodiversity components—taxonomic, phylogenetic, and functional diversity—and three diversity facets—richness, divergence and regularity. We identified a north/south contrast with higher diversity for the three facets of the biodiversity components in the northern part of the study area. The northern communities showed higher species richness, stronger phylogenetic overdispersion and lower functional clustering compared to the ones in the southern part, due to the higher diversity of habitats (reefs, rocky shores) and restricted access for fishing. Moreover, we also detected a higher level of taxonomic, phylogenetic, and functional uniqueness in many offshore stations compared to more coastal ones, with the presence of species typically living at greater depths (> 300 m), which suggests an influence of hydrodynamic structures and currents on eDNA dispersion and hence sample composition. eDNA metabarcoding can, therefore, be used as an efficient sampling method to reveal fine‐scale community compositions and in combination with functional and phylogenetic information to document multicomponent biodiversity gradients in coastal marine systems.