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The species concept is the cornerstone of biodiversity science, and any paradigm shift in the delimitation of species affects many research fields. Many biologists now are embracing a new "species" paradigm as separately evolving populations using different delimitation criteria. Individual criteria can emerge during different periods of speciation; some may never evolve. As such, a paradigm shift in the species concept relates to this inherent heterogeneity in the speciation process and species category-which is fundamentally overlooked in biodiversity research. Cryptic species fall within this paradigm shift: they are continuously being reported from diverse animal phyla but are poorly considered in current tests of ecological and evolutionary theory. The aim of this review is to integrate cryptic species in biodiversity science. In the first section, we address that the absence of morphological diversification is an evolutionary phenomenon, a "process" counterpart to the long-studied mechanisms of morphological diversification. In the next section regarding taxonomy, we show that molecular delimitation of cryptic species is heavily biased towards distance-based methods. We also stress the importance of formally naming of cryptic species for better integration into research fields that use species as units of analysis. Finally, we show that incorporating cryptic species leads to novel insights regarding biodiversity patterns and processes, including large-scale biodiversity assessments, geographic variation in species distribution and species coexistence. It is time for incorporating multicriteria species approaches aiming to understand speciation across space and taxa, thus allowing integration into biodiversity conservation while accommodating for species uncertainty.

1.  River corridors can be visualised as a three‐dimensional mosaic of surface–subsurface exchange patches over multiple spatial scales. Along major flow paths, surface water downwells into the sediment, travels for some distance beneath or along the stream, eventually mixes with ground water, and then returns to the stream. 2.  Spatial variations in bed topography and sediment permeability result in a mosaic of patch types (e.g. gravel versus sandy patches) that differ in their hydrological exchange rate with the surface stream. Biogeochemical processes and invertebrate assemblages vary among patch types as a function of the flux of advected channel water that determines the supply of organic matter and terminal electron acceptors. 3.  The overall effect of surface–subsurface hydrological exchanges on nutrient cycling and biodiversity in streams not only depends on the proportion of the different patch types, but also on the frequency distribution of patch size and shape. 4.  Because nutrients are essentially produced or depleted at the downwelling end of hyporheic flow paths, reach‐scale processing rates of nutrients should be greater in stretches with many small patches (e.g. short compact gravel bars) than in stretches with only a few large patches (e.g. large gravel bars). 5.  Based on data from the Rhône River, we predict that a reach with many small bars should offer more hyporheic refugia for epigean fauna than a reach containing only a few large gravel bars because benthic organisms accumulate preferentially in sediments located at the upstream and downwelling edge of bars during floods. However, large bars are more stable and may provide the only refugia during severe flood events. 6.  In river floodplain systems exhibiting pronounced expansion/contraction cycles, hyporheic assemblages within newly created patches not only depend on the intrinsic characteristics of these patches but also on their life span, hydrological connection with neighbouring patches, and movement patterns of organisms. 7.  Empirical and theoretical evidence illustrate how the spatial arrangement of surface–subsurface exchange patches affects heterogeneity in stream nutrient concentration, surface water temperature, and colonisation of dry reaches by invertebrates. 8.  Interactions between fluvial action and geomorphic features, resulting from seasonal and episodic flow pulses, alter surface–subsurface exchange pathways and repeatedly modify the configuration of the mosaic, thereby altering the contribution of the hyporheic zone to nutrient transformation and biodiversity in river corridors.

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.

1. The first part of this review focuses on the oxygen status of natural groundwater systems (mainly porous aquifers) and hyporheic zones of streams. The second part examines the sensitivity of groundwater organisms, especially crustaceans, to low oxygen concentrations (< 3.0 mg L−1 O2). 2. Dissolved oxygen (DO) in groundwater is spatially heterogeneous at macro‐ (km), meso‐ (m) and micro‐ (cm) scales. This heterogeneity, an essential feature of the groundwater environment, reflects changes in sediment composition and structure, groundwater flow velocity, organic matter content, and the abundance and activity of micro‐organisms. Dissolved oxygen also exhibits strong temporal changes in the hyporheic zone of streams as well as in the recharge area of aquifers, but these fluctuations should be strongly attenuated with increasing distance from the stream and the recharge zone. 3. Dissolved oxygen gradients along flow paths in groundwater systems and hyporheic zones vary over several orders of magnitude (e.g. declines of 9 × 10−5 to 1.5 ×10−2 mg L−1 O2 m−1 in confined aquifers and 2 × 10−2 to 1 mg L−1 O2 m−1 in parafluvial water). Several factors explain this strong variation. Where the water table is close to the surface, oxygen is likely to be consumed rapidly in the first few metres below the water table because of incomplete degradation of soil‐generated labile dissolved organic carbon (DOC) in the vadose zone. Where the water table is far from the surface, strong oxygen depletion in the vicinity of the water table does not occur, DO being then gradually consumed as groundwater flows down the hydraulic gradient. In unconfined groundwater systems, oxygen consumption along flow paths may be compensated by down‐gradient replenishment of DO, resulting either from the ingress of atmospheric oxygen or water recharge through the vadose zone. In confined groundwater systems, where replenishment of oxygen is impossible, the removal time of DO varies from a few years to more than 10 000 years, depending mainly on the organic carbon content of the sediment. Comparison of the hyporheic zones between systems also revealed strong differences in the removal time and length of underground pathways for DO. This strong variability among systems seems related to differences in contact time of water with sediment. 4. Although groundwater macro‐crustaceans are much more resistant to hypoxia than epigean species, they cannot survive severe hypoxia (DO < 0.01 mg L−1 O2) for very long (lethal time for 50% of the population ranged from 46.7 to 61.7 h). In severe hypoxia, none of the hypogean crustaceans examined utilized a high‐ATP yielding metabolic pathway. High survival times are mainly a result of the combination of three mechanisms: a high storage of fermentable fuels (glycogen and phosphagen), a low metabolic rate in normoxia, and a further reduction in metabolic rate by reducing locomotion and ventilation. It is suggested here that the low metabolic rate of many hypogean species may be an adaptation to low oxygen and not necessari...

With 10 figures and 5 tables in the text Abstract: Val Roseg in the Swiss Alps is a complex alluvial valley formed in glacial outwash. The braided flood plain, 2.6 km long and 130-510 m wide, begins 1.2 km downstream of the glacier terminus and extends to a "knickpoint" at 1990 m a.s.!. where water upwells before entering a constrained reach. A long-term study has been initiated to investigate habitat heterogeneity and how such heterogeneity (I) contribu tes to the biodiversity of benthos, groundwater fauna, and periphyton in a harsh envi ronment and (2) influences ecosystem processes such as productivity and decomposi tion dynamics. As a first step we have distinguished different channel types based on the correspondence between hydrological connectivity and physico-chemical attrib utes. This functional characterization will serve as a habitat template to structure future ecological research in the Val Roseg flood plain. Six distinct channel types have been identified within the fl oodplain ecosystem: (i) Main channel. (ii) Side channels, (iii) Intermittently-connected channels. (iv) Mixed channels, (v) Ground water channels, and (vi) Tributaries. Distinct seasonal and daily runoff patterns, caused by ice melt, change the hydrological connectivity between individual channel types. Results clearly demonstrate that the whole flood plain shifts from dominance by surface water at high summer discharge to a groundwater-controlled system in winter. Temporal variability, rather than the means of environmental values, has been used to differentiate between individual floodplain channel types. Groundwater chan nels exhibit the highest spatial but the lowest temporal variability. In contrast, inter mittently-connected channels are characterized by a low spatial but an extraordinary temporal variability. High spatio-temporal heterogeneity resulting from a diversity of channel types is believed to play a major role in maintaining what appears to be re markably high biodiversity in this glacial flood plain.

Running water ecology is a young science, the conceptual foundations of which were derived largely from research conducted in Europe and North America. However, virtually all European river corridors were substantially regulated well before the science of river ecology developed. While regulation of North American river systems occurred later than in European systems, river ecology also developed later. Therefore, there is a general impression of rivers as being much less heterogeneous and much more stable than they actually are in the natural state. The thesis of this paper is that established research and management concepts may fail to fully recognize the crucial roles of habitat heterogeneity and fluvial dynamics owing to a lack of fundamental knowledge of the structural and functional features of morphologically intact river corridors. Until quite recently, most concepts in river ecology were based on the implicit assumption that rivers are stable, single-thread channels isolated from adjacent floodplains. Unfortunately, many rivers are in just such a state, but it should be recognized that this is not the natural condition. This incomplete understanding constrains scientific advances in river ecology and renders management and restoration initiatives less effective. Examples are given of the high level of spatio-temporal heterogeneity that may be attained in rivers where natural processes still operate on a large scale. The objective of this paper is to promulgate a broader and more integrative understanding of natural processes in river corridors as a necessary prelude to effective river conservation and management.

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