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It is a critical time to reflect on the National Ecological Observatory Network (NEON) science to date as well as envision what research can be done right now with NEON (and other) data and what training is needed to enable a diverse user community. NEON became fully operational in May 2019 and has pivoted from planning and construction to operation and maintenance. In this overview, the history of and foundational thinking around NEON are discussed. A framework of open science is described with a discussion of how NEON can be situated as part of a larger data constellation—across existing networks and different suites of ecological measurements and sensors. Next, a synthesis of early NEON science, based on >100 existing publications, funded proposal efforts, and emergent science at the very first NEON Science Summit (hosted by Earth Lab at the University of Colorado Boulder in October 2019) is provided. Key questions that the ecology community will address with NEON data in the next 10 yr are outlined, from understanding drivers of biodiversity across spatial and temporal scales to defining complex feedback mechanisms in human–environmental systems. Last, the essential elements needed to engage and support a diverse and inclusive NEON user community are highlighted: training resources and tools that are openly available, funding for broad community engagement initiatives, and a mechanism to share and advertise those opportunities. NEON users require both the skills to work with NEON data and the ecological or environmental science domain knowledge to understand and interpret them. This paper synthesizes early directions in the community’s use of NEON data, and opportunities for the next 10 yr of NEON operations in emergent science themes, open science best practices, education and training, and community building.

The opposing forces of gene flow and isolation are two major processes shaping genetic diversity. Understanding how these vary across space and time is necessary to identify the environmental features that promote diversification. The detection of considerable geographic structure in taxa from the arid Nearctic has prompted research into the drivers of isolation in the region. Several geographic features have been proposed as barriers to gene flow, including the Colorado River, Western Continental Divide (WCD), and a hypothetical Mid-Peninsular Seaway in Baja California. However, recent studies suggest that the role of barriers in genetic differentiation may have been overestimated when compared to other mechanisms of divergence. In this study, we infer historical and spatial patterns of connectivity and isolation in Desert Spiny Lizards (Sceloporus magister) and Baja Spiny Lizards (Sceloporus zosteromus), which together form a species complex composed of parapatric lineages with wide distributions in arid western North America. Our analyses incorporate mitochondrial sequences, genomic-scale data, and past and present climatic data to evaluate the nature and strength of barriers to gene flow in the region. Our approach relies on estimates of migration under the multispecies coalescent to understand the history of lineage divergence in the face of gene flow. Results show that the S. magister complex is geographically structured, but we also detect instances of gene flow. The WCD is a strong barrier to gene flow, while the Colorado River is more permeable. Analyses yield conflicting results for the catalyst of differentiation of peninsular lineages in S. zosteromus. Our study shows how large-scale genomic data for thoroughly sampled species can shed new light on biogeography. Furthermore, our approach highlights the need for the combined analysis of multiple sources of evidence to adequately characterize the drivers of divergence. [ABSTRACT FROM AUTHOR]

The validity of the Baldwin effect and genetic assimilation in conveying concepts of evolutionary biology through phenotypic plasticity is assessed. They are explained in terms of genetic accommodation, suggesting that each could play an important role in evolutionary diversification.

In Rees et al. (2014b), we reviewed the current status of environmental DNA ( eDNA) to monitor aquatic populations. Our aim was to focus on discussion of methodologies used, application of eDNA analysis as a survey tool in ecology, and to include some innovative ideas for using eDNA in conservation and management., Roussel et al. (2015) claim that analysis of Rees et al. (2014b) and other publications highlights the downsides of the method, and they suggest that some conclusions should be toned down. Many of their arguments were covered in our original paper (Rees et al., 2014b); however, they make the point that modelling approaches should be encouraged, and we fully agree with this suggestion., Roussel et al. (2015) also claim that we neglected to recognize that there are two sources of imperfect detection (at the field level and at the laboratory level). We feel that our review paper implies this point., Synthesis and applications. Roussel et al. (2015) reiterate many of the points made in the original paper but do cover some additional areas that improve the debate on the use of environmental DNA ( eDNA). Both the comment (Roussel et al., 2015) and our rebuttal clearly highlight that detailed laboratory protocols and rigorous field sampling design are crucial factors which require sufficient reporting in the literature to allow for experimental comparison and replication. Any development of a new method for eDNA detection should be compared directly with established 'gold standard' methods for the detection of the species or habitat under investigation. None of the issues raised in Roussel et al. (2015) would alter our main conclusions. [ABSTRACT FROM AUTHOR]

To prevent the invasion of exotic species causing a decline in an endangered endemic species, it is important to determine the distribution of both species at an early stage, when the density of the exotic species is still low, and to manage the invasion immediately. However, distinguishing between closely related species is difficult because they share similar characteristics., The identification of DNA fragments sampled from a body of water (environmental DNA) has become a popular technique for rapidly determining the distribution of a target species. In this study, we analysed environmental DNA in water samples from 37 sites across the Katsura River basin in Japan. We used TaqMan real-time PCR to distinguish the Japanese giant salamander Andrias japonicus from the closely related Chinese giant salamander Andrias davidianus, which is known to invade Japanese rivers and hybridize with the Japanese species., In environmental samples, we detected mt DNA of the endemic species at 25 sites and mt DNA of the exotic species at nine sites. The DNA detection sites were concentrated in the upstream region. The exotic species DNA was found beyond the limits of an earlier capturing survey., Synthesis and applications. Using environmental DNA to monitor the two salamander species requires less time and effort than traditional surveys, so a wide-ranging survey can be conducted rapidly. Our results showed that performing three environmental DNA surveys for each site between autumn and winter is desirable for giant salamanders. Further collection of environmental DNA, in combination with conventional population surveys, will provide valuable information that can help protect rare endemic species in a variety of aquatic ecosystems and can help monitor the invasion of exotic species. [ABSTRACT FROM AUTHOR]

One of the greatest threats to lotic ecosystems is flow regulation. The impacts of flow regulation on native fish are often mitigated using periodic water allocations, termed environmental flows. The effectiveness of environmental flows has been studied in some systems, but the role of flow conditions prior to water allocation (i.e. antecedent conditions) has rarely been quantified., We evaluated the effects of floodplain inundation due to variable river flows on fish abundance in wetlands of the mid-Murray River, Australia, using a hierarchical multi-species model parameterized to estimate fish abundance while accounting for variable detection. We evaluated the effects of antecedent conditions on three time-scales, including patterns in long-term (5 years prior), medium-term (1 year prior) and short-term (3 months prior) wetland inundations., While species-specific responses to antecedent conditions varied, we found a general divergence in the responses of native and non-native species. Native fish tended to respond positively to consistent frequent inundation of wetlands, while non-native fish tended to respond positively to long- or medium-term dry periods and short-term wet periods., Fish detection probability varied among species, sampling gears, wetland areas and wetlands, indicating that accounting for variable detection can be critical when evaluating patterns in fish abundance., Synthesis and applications. We found that antecedent conditions can be important for determining environmental water allocation policies. Our results indicated that native fish generally responded positively to frequent inundation of wetlands, while non-native species generally responded positively to long dry periods followed by short-term inundation events. For some non-native species, long dry periods not only generated a positive response in abundance, but enhanced the positive response to short-term inundation events. The divergence between native and non-native fishes' responses to antecedent conditions provides opportunities for managers to allocate water to favour native fish assemblages. Future research of environmental flows for managing fish assemblages should consider antecedent conditions and apply models that account for incomplete detection, such as the one developed here, to better inform the management process. [ABSTRACT FROM AUTHOR]

China is Asia's most important upstream riparian country, sharing 110 rivers and lakes with 18 downstream countries. Consequently, China's management of transboundary water resources must consider both environmental and geopolitical risks., The major threats to and conflicts over international rivers in China revolve around biotic homogenisation due to the installation of transport links, water allocation, water pollution, alteration of natural flow patterns and disruption of fisheries due to the installation of hydropower dams, and droughts and floods exacerbated by climate change. Because these problems have an international component, they fall under China's Peaceful Rise strategy, mandating that transboundary conflicts be resolved amicably as part of the overarching goal of increasing regional economic growth with as little conflict as possible., Science-backed policy is more likely to result in long term, mutually agreeable solutions; the results of applied ecological research have already resulted in a number of mitigation measures, including setting operational thresholds to reduce the downstream impact of dams, designating protected areas along key river stretches where dams cannot be installed (one dam in a critical location has been cancelled), and the installation of terrestrial protected-area networks., Synthesis and applications. Applied ecology will continue to play an important role in the diagnosis and resolution of environmental threats to China's transboundary waters. More importantly, applied ecology can inform the development of a transboundary environmental compensation mechanism and regional consultative mechanisms that support informed, cooperative decision-making for China and its riparian neighbours. [ABSTRACT FROM AUTHOR]

Knowledge of species distribution is critical to ecological management and conservation biology. Effective management requires the detection of populations, which can sometimes be at low densities and is usually based on visual detection and counting., Recently, there has been considerable interest in the detection of short species-specific environmental DNA (e DNA) fragments to allow aquatic species monitoring within different environments due to the potential of greater sensitivity over traditional survey methods which can be time-consuming and costly., Environmental DNA analysis is increasingly being used in the detection of rare or invasive species and has also been applied to e DNA persistence studies and estimations of species biomass and distribution. When combined with next-generation sequencing methods, it has been demonstrated that entire faunas can be identified., Different environments require different sampling methodologies, but there remain areas where laboratory methodologies could be standardized to allow results to be compared across studies., Synthesis and applications. We review recently published studies that use e DNA to monitor aquatic populations, discuss the methodologies used and the application of e DNA analysis as a survey tool in ecology. We include innovative ideas for how e DNA can be used for conservation and management citing test cases, for instance, the potential for on-site analyses, including the application of e DNA analysis to carbon nanotube platforms or laser transmission spectroscopy to facilitate rapid on-site detections. The use of e DNA monitoring is already being adopted in the UK for ecological surveys. [ABSTRACT FROM AUTHOR]

The introduction of non-native species is a major threat to biodiversity. While eradication programs of well-established invaders are costly and hazardous for non-target species, the early detection of a non-native species at low density is critical for preventing biological invasions in recipient ecosystems. Recent studies reveal that environmental DNA (e DNA) is a powerful tool for detecting target species in aquatic ecosystems, but these studies focus mostly on fish and amphibians., We examine the reliability of using e DNA to detect the presence of an invasive freshwater crustacean species, the red swamp crayfish Procambarus clarkii. Species-specific primers and probes were designed; their specificity was tested using in silico PCR simulations and against tissues of other crayfish species. Limits of detection and quantification were specified for the target DNA sequence by means of quantitative PCR amplifications on dilution series of known amount of P. clarkii DNA., The method was applied to water samples collected in 158 ponds in a French Nature Park, and results were compared to a traditional method using food-baited funnel traps. Environmental DNA had a better detection efficiency but predominantly led to divergent results compared with the trapping method. While habitat features partly explained the failure of crayfish detection by trapping, detection by e DNA was problematic at low crayfish abundances. When P. clarkii was detected, the estimated concentrations of crayfish DNA in water samples were always below the limit of quantification for the target DNA sequence., Synthesis and applications. The combination of environmental DNA (e DNA) and conventional trapping methods is recommended to monitor the invasion by P. clarkii in small waterbodies such as ponds. However, the risk of mortality for non-target species, notably amphibians, has to be carefully evaluated before large-scale deployment of traps. Contrary to fish and amphibians, a low amount of extracellular DNA in water is suspected to be the major limitation for crayfish detection by molecular approaches. Current advancements in PCR technology, together with optimization of the water sampling method, promise upcoming developments of e DNA detection for aquatic invertebrate species. [ABSTRACT FROM AUTHOR]

Pervasive and accelerating changes to ecosystems due to human activities remain major sources of uncertainty in predicting the structure and dynamics of ecological communities. Understanding which biotic interactions within natural multitrophic communities are weakened or augmented by invasions of non-native species in the context of other environmental pressures is needed for effective management., We used multivariate autoregressive models with detailed time-series data from largely freshwater and brackish regions of the upper San Francisco Estuary to assess the topology, direction and strength of trophic interactions following major invasions and establishment of non-native zooplankton in the early 1990s. We simultaneously compared the effects of fish and clam predation, environmental temperature and salinity intrusion using time-series data from >60 monitoring locations spanning more than three decades., We found changes in the networks of biotic interactions in both regions after the major zooplankton invasions. Our results imply an increased pressure on native herbivores; intensified negative interactions between herbivores and omnivores; and stronger bottom-up influence of juvenile copepods but weaker influence of phytoplankton as a resource for higher trophic levels following the invasions. We identified salinity intrusion as a primary pressure but showed relatively stronger importance of biotic interactions for understanding the dynamics of entire communities., Synthesis and applications. Our findings highlight the dynamic nature of biotic interactions and provide evidence of how simultaneous invasions of exotic species may alter interaction networks in diverse natural ecosystems over large spatial and temporal scales. Efforts to restore declining fish stocks may be in vain without fully considering the trophic dynamics that limit the flow of energy to target populations. Focusing on multitrophic interactions that may be threatened by invasions rather than a limited focus on responses of individual species or diversity is likely to yield more effective management strategies. [ABSTRACT FROM AUTHOR]

Gene flow among populations in different selective environments should favor the evolution of phenotypic plasticity over local adaptation. Plasticity in development is a common response to long-term hypoxia in some widespread African fishes, including Pseudocrenilabrus multicolor, a cichlid that exploits both normoxic (high oxygen) rivers/lakes and hypoxic (low oxygen) swamps. Previous studies have shown that fish from normoxic and hypoxic sites differ in many traits, including gill size, brain size and body shape, and that much of this variation reflects developmental plasticity. However, these earlier studies focused on areas in Uganda where gene flow between swamp and river or lake populations is high. In this study we tested the hypothesis that P. multicolor from a relatively isolated lake population (Lake Saka, Uganda) exhibit low levels of plasticity in traits related to oxygen uptake. Multiple broods of P. multicolor from Lake Saka were reared under low and high dissolved oxygen, and traits related to gill size, brain mass and body shape were quantified. Surprisingly, both gill size and brain mass showed high levels of developmental plasticity. We suggest that high levels of plasticity, particularly in the gill size of P. multicolor, reflects low costs of maintaining the plastic response, even in relatively isolated populations. [ABSTRACT FROM AUTHOR]

Culvert pipes are regularly used around the world for conveying stream flows underground, through embankments or under road crossings. Installation of these features can have significant negative effects on the passage of freshwater biota and potentially exclude many species from large areas of river networks., We investigated the installation of mussel spat ropes as a potentially rapid and cost-effective tool for improving passage of freshwater biota through culvert pipes where internal barrel conditions impede passage. We assessed passage success for two fish species, juvenile rainbow trout Oncorhynchus mykiss ( Walbaum 1972) and adult inanga Galaxias maculatus ( Jenyns 1842), and one migratory shrimp, Paratya curvirostris ( Heller 1862), through culverts of differing length (3 and 6 m), slope (1·5 and 3°) and flow (0·24 and 0·75 L s−1). We hypothesized that ropes would enhance the passage success of these three species, but success rates would differ between species and trial combinations., Ropes resulted in a reduced water velocity within culvert barrels and significantly improved passage success for all three species. Shrimp benefited most by the presence of ropes, being unable to negotiate any of the pipe combinations in their absence, but exhibiting varying rates of success across all combinations with their presence. Both G. maculatus and O. mykiss were able to negotiate some of the non-roped pipe combinations, but as the level of difficulty increased, successful passage was only achieved with the ropes present., Synthesis and applications. We conclude that this relatively inexpensive and easy-to-install tool has the potential to substantially improve passage for a range of aquatic biota through various culvert scenarios. We consider that ropes would be particularly useful in situations where internal culvert access is difficult and where various culvert parameters (slope, flow, length) result in internal barrel hydraulics that would normally limit or exclude passage of aquatic biota. [ABSTRACT FROM AUTHOR]

The success of ecological restoration is often judged by the number and abundance of species, especially rare ones that have established since restoration. However, the effects of habitat improvement upon connectivity are rarely assessed, although this can readily be performed using modern molecular genetic methods., We evaluated the functional connectivity of populations of a wet grassland plant Lychnis flos-cuculi in an intensively managed agricultural landscape in Switzerland. One third of the study populations had been recently restored by sowing wildflower seed mixtures, while all other populations were of natural origin. We used assignment tests to identify first-generation migrants and to estimate recent patterns of gene flow among the populations of L. flos-cuculi., Assignment tests revealed higher levels of recent gene flow among natural populations of L. flos-cuculi than between sown and natural populations. Most probably, this result simply reflected the formerly good connectivity of natural populations in the study landscape., We detected a few first-generation migrants between sown and natural populations and among natural populations, suggesting that functional connectivity was now rather restricted. Migration among sown and natural populations was more likely to occur when natural and sown populations were nearby and when source populations were large., Synthesis and applications. We demonstrated that genetic methods offer a valuable tool for examining the effects of restoration measures on functional connectivity of plant populations. The connectivity of wet grasslands is likely to be best enhanced by establishing a relatively dense network of large habitat patches. [ABSTRACT FROM AUTHOR]

Urbanization has been identified as a global threat to biodiversity. Human population growth in coastal areas, including estuaries, is expected to increase considerably in coming decades, which will result in a proliferation of infrastructure such as jetties, wharfs and marinas. This infrastructure is often associated with artificial night lighting, yet the implications of these unnatural lighting regimes for the fish fauna in coastal ecosystems are unknown., We conducted novel, night-time surveys of the fish community directly adjacent to an artificial structure using an acoustic camera ( didson). By manipulating the artificial lighting conditions (lighting either 'on' or 'off'), we tested the effects of artificial light on fish abundance and behaviour., Clear differences in the abundance of fish were observed between the two light treatments. The occurrence of large-bodied predators (>500 mm TL) increased when the artificial lights were on. The behaviour of these fish also differed as they attempted to maintain their position within the illuminated area adjacent to the associated anthropogenic structure. The abundance of small shoaling fish also increased when the lights were on., It is possible that the conditions created by artificial lighting benefit piscivores through the concentration of prey and enhanced foraging capabilities in the case of visual predators. This has the potential to create unnatural top-down regulation of fish populations within urban estuarine and coastal waters., Synthesis and applications. As a consequence of a positive phototaxic response, the findings of this study suggest that artificial light often associated with man-made structures has the potential to alter fish communities within urban estuarine ecosystems by creating optimal conditions for predators. Future coastal developments should consider the ecological implications of lighting on aquatic communities. We recommend that lighting be minimized around coastal infrastructure and the use of red lights, which have limited penetration though water, be considered. [ABSTRACT FROM AUTHOR]

Two general processes may influence gene flow among populations. One involves divergent selection, wherein the maladaptation of immigrants and hybrids impedes gene flow between ecological environments (i.e. ecological speciation). The other involves geographic features that limit dispersal. We determined the relative influence of these two processes in natural populations of Trinidadian guppies ( Poecilia reticulata). If selection is important, gene flow should be reduced between different selective environments. If geography is important, gene flow should be impeded by geographic distance and physical barriers. We examined how genetic divergence, long-term gene flow, and contemporary dispersal within a watershed were influenced by waterfalls, geographic distance, predation, and habitat features. We found that waterfalls and geographic distance increased genetic divergence and reduced dispersal and long-term gene flow. Differences in predation or habitat features did not influence genetic divergence or gene flow. In contrast, differences in predation did appear to reduce contemporary dispersal. We suggest that the standard predictions of ecological speciation may be heavily nuanced by the mating behaviour and life history strategies of guppies. [ABSTRACT FROM AUTHOR]

The vaccine strain of Cryptobia salmositica multiplies in Atlantic salmon Salmo salar and it can modulate the severity of the disease in Cryptobia-infected individuals. Fish injected with the vaccine 3 d post-infection with C. salmositica had lower peak parasitaemias and higher antibody titres than infected fish given the vaccine 7 d post-infection or those infected fish that were not given the vaccine.