NOAA National Marine Fisheries Service Southwest Fisheries Science Center

Our growing awareness of the microbial world's importance and diversity contrasts starkly with our limited understanding of its fundamental structure. Despite recent advances in DNA sequencing, a lack of standardized protocols and common analytical frameworks impedes comparisons among studies, hindering the development of global inferences about microbial life on Earth. Here we present a meta-analysis of microbial community samples collected by hundreds of researchers for the Earth Microbiome Project. Coordinated protocols and new analytical methods, particularly the use of exact sequences instead of clustered operational taxonomic units, enable bacterial and archaeal ribosomal RNA gene sequences to be followed across multiple studies and allow us to explore patterns of diversity at an unprecedented scale. The result is both a reference database giving global context to DNA sequence data and a framework for incorporating data from future studies, fostering increasingly complete characterization of Earth's microbial diversity.

Identifying causal networks is important for effective policy and management recommendations on climate, epidemiology, financial regulation, and much else. We introduce a method, based on nonlinear state space reconstruction, that can distinguish causality from correlation. It extends to nonseparable weakly connected dynamic systems (cases not covered by the current Granger causality paradigm). The approach is illustrated both by simple models (where, in contrast to the real world, we know the underlying equations/relations and so can check the validity of our method) and by application to real ecological systems, including the controversial sardine-anchovy-temperature problem.

We demonstrate that the mean ratio of the number of alleles to the range in allele size, which we term M, calculated from a population sample of microsatellite loci, can be used to detect reductions in population size. Using simulations, we show that, for a general class of mutation models, the value of M decreases when a population is reduced in size. The magnitude of the decrease is positively correlated with the severity and duration of the reduction in size. We also find that the rate of recovery of M following a reduction in size is positively correlated with post-reduction population size, but that recovery occurs in both small and large populations. This indicates that M can distinguish between populations that have been recently reduced in size and those which have been small for a long time. We employ M to develop a statistical test for recent reductions in population size that can detect such changes for more than 100 generations with the post-reduction demographic scenarios we examine. We also compute M for a variety of populations and species using microsatellite data collected from the literature. We find that the value of M consistently predicts the reported demographic history for these populations. This method, and others like it, promises to be an important tool for the conservation and management of populations that are in need of intervention or recovery.

Assessing Biodiversity Declines Understanding human impact on biodiversity depends on sound quantitative projection. Pereira et al. (p. 1496 , published online 26 October) review quantitative scenarios that have been developed for four main areas of concern: species extinctions, species abundances and community structure, habitat loss and degradation, and shifts in the distribution of species and biomes. Declines in biodiversity are projected for the whole of the 21st century in all scenarios, but with a wide range of variation. Hoffmann et al. (p. 1503 , published online 26 October) draw on the results of five decades' worth of data collection, managed by the International Union for Conservation of Nature Species Survival Commission. A comprehensive synthesis of the conservation status of the world's vertebrates, based on an analysis of 25,780 species (approximately half of total vertebrate diversity), is presented: Approximately 20% of all vertebrate species are at risk of extinction in the wild, and 11% of threatened birds and 17% of threatened mammals have moved closer to extinction over time. Despite these trends, overall declines would have been significantly worse in the absence of conservation actions.

Knowledge of mammalian diversity is still surprisingly disparate, both regionally and taxonomically. Here, we present a comprehensive assessment of the conservation status and distribution of the world's mammals. Data, compiled by 1700+ experts, cover all 5487 species, including marine mammals. Global macroecological patterns are very different for land and marine species but suggest common mechanisms driving diversity and endemism across systems. Compared with land species, threat levels are higher among marine mammals, driven by different processes (accidental mortality and pollution, rather than habitat loss), and are spatially distinct (peaking in northern oceans, rather than in Southeast Asia). Marine mammals are also disproportionately poorly known. These data are made freely available to support further scientific developments and conservation action.

Climate change challenges organisms to adapt or move to track changes in environments in space and time. We used two measures of thermal shifts from analyses of global temperatures over the past 50 years to describe the pace of climate change that species should track: the velocity of climate change (geographic shifts of isotherms over time) and the shift in seasonal timing of temperatures. Both measures are higher in the ocean than on land at some latitudes, despite slower ocean warming. These indices give a complex mosaic of predicted range shifts and phenology changes that deviate from simple poleward migration and earlier springs or later falls. They also emphasize potential conservation concerns, because areas of high marine biodiversity often have greater velocities of climate change and seasonal shifts.

Abstract The Pacific decadal oscillation (PDO), the dominant year-round pattern of monthly North Pacific sea surface temperature (SST) variability, is an important target of ongoing research within the meteorological and climate dynamics communities and is central to the work of many geologists, ecologists, natural resource managers, and social scientists. Research over the last 15 years has led to an emerging consensus: the PDO is not a single phenomenon, but is instead the result of a combination of different physical processes, including both remote tropical forcing and local North Pacific atmosphere–ocean interactions, which operate on different time scales to drive similar PDO-like SST anomaly patterns. How these processes combine to generate the observed PDO evolution, including apparent regime shifts, is shown using simple autoregressive models of increasing spatial complexity. Simulations of recent climate in coupled GCMs are able to capture many aspects of the PDO, but do so based on a balance of processes often more independent of the tropics than is observed. Finally, it is suggested that the assessment of PDO-related regional climate impacts, reconstruction of PDO-related variability into the past with proxy records, and diagnosis of Pacific variability within coupled GCMs should all account for the effects of these different processes, which only partly represent the direct forcing of the atmosphere by North Pacific Ocean SSTs.

Abstract Strongly positive temperature anomalies developed in the NE Pacific Ocean during the boreal winter of 2013–2014. Based on a mixed layer temperature budget, these anomalies were caused by lower than normal rates of the loss of heat from the ocean to the atmosphere and of relatively weak cold advection in the upper ocean. Both of these mechanisms can be attributed to an unusually strong and persistent weather pattern featuring much higher than normal sea level pressure over the waters of interest. This anomaly was the greatest observed in this region since at least the 1980s. The region of warm sea surface temperature anomalies subsequently expanded and reached coastal waters in spring and summer 2014. Impacts on fisheries and regional weather are discussed. It is found that sea surface temperature anomalies in this region affect air temperatures downwind in Washington state.

Decadal fluctuations in salinity, nutrients, chlorophyll, a variety of zooplankton taxa, and fish stocks in the Northeast Pacific are often poorly correlated with the most widely‐used index of large‐scale climate variability in the region ‐ the Pacific Decadal Oscillation (PDO). We define a new pattern of climate change, the North Pacific Gyre Oscillation (NPGO) and show that its variability is significantly correlated with previously unexplained fluctuations of salinity, nutrients and chlorophyll. Fluctuations in the NPGO are driven by regional and basin‐scale variations in wind‐driven upwelling and horizontal advection – the fundamental processes controlling salinity and nutrient concentrations. Nutrient fluctuations drive concomitant changes in phytoplankton concentrations, and may force similar variability in higher trophic levels. The NPGO thus provides a strong indicator of fluctuations in the mechanisms driving planktonic ecosystem dynamics. The NPGO pattern extends beyond the North Pacific and is part of a global‐scale mode of climate variability that is evident in global sea level trends and sea surface temperature. Therefore the amplification of the NPGO variance found in observations and in global warming simulations implies that the NPGO may play an increasingly important role in forcing global‐scale decadal changes in marine ecosystems.

Abstract As the number of fish reproduction studies has proliferated, so has the number of gonadal classification schemes and terms. This has made it difficult for both scientists and resource managers to communicate and for comparisons to be made among studies. We propose the adoption of a simple, universal terminology for the phases in the reproductive cycle, which can be applied to all male and female elasmobranch and teleost fishes. These phases were chosen because they define key milestones in the reproductive cycle; the phases include immature, developing, spawning capable, regressing, and regenerating. Although the temporal sequence of events during gamete development in each phase may vary among species, each phase has specific histological and physiological markers and is conceptually universal. The immature phase can occur only once. The developing phase signals entry into the gonadotropin-dependent stage of oogenesis and spermatogenesis and ultimately results in gonadal growth. The spawning capable phase includes (1) those fish with gamete development that is sufficiently advanced to allow for spawning within the current reproductive cycle and (2) batch-spawning females that show signs of previous spawns (i.e., postovulatory follicle complex) and that are also capable of additional spawns during the current cycle. Within the spawning capable phase, an actively spawning subphase is defined that corresponds to hydration and ovulation in females and spermiation in males. The regressing phase indicates completion of the reproductive cycle and, for many fish, completion of the spawning season. Fish in the regenerating phase are sexually mature but reproductively inactive. Species-specific histological criteria or classes can be incorporated within each of the universal phases, allowing for more specific divisions (subphases) while preserving the overall reproductive terminology for comparative purposes. This terminology can easily be modified for fishes with alternate reproductive strategies, such as hermaphrodites (addition of a transition phase) and livebearers (addition of a gestation phase).

We show that a citizen science, self-selected cohort shipping samples through the mail at room temperature recaptures many known microbiome results from clinically collected cohorts and reveals new ones. Of particular interest is integrating n = 1 study data with the population data, showing that the extent of microbiome change after events such as surgery can exceed differences between distinct environmental biomes, and the effect of diverse plants in the diet, which we confirm with untargeted metabolomics on hundreds of samples.

BACKGROUND: Resolving threats to widely distributed marine megafauna requires definition of the geographic distributions of both the threats as well as the population unit(s) of interest. In turn, because individual threats can operate on varying spatial scales, their impacts can affect different segments of a population of the same species. Therefore, integration of multiple tools and techniques--including site-based monitoring, genetic analyses, mark-recapture studies and telemetry--can facilitate robust definitions of population segments at multiple biological and spatial scales to address different management and research challenges. METHODOLOGY/PRINCIPAL FINDINGS: To address these issues for marine turtles, we collated all available studies on marine turtle biogeography, including nesting sites, population abundances and trends, population genetics, and satellite telemetry. We georeferenced this information to generate separate layers for nesting sites, genetic stocks, and core distributions of population segments of all marine turtle species. We then spatially integrated this information from fine- to coarse-spatial scales to develop nested envelope models, or Regional Management Units (RMUs), for marine turtles globally. CONCLUSIONS/SIGNIFICANCE: The RMU framework is a solution to the challenge of how to organize marine turtles into units of protection above the level of nesting populations, but below the level of species, within regional entities that might be on independent evolutionary trajectories. Among many potential applications, RMUs provide a framework for identifying data gaps, assessing high diversity areas for multiple species and genetic stocks, and evaluating conservation status of marine turtles. Furthermore, RMUs allow for identification of geographic barriers to gene flow, and can provide valuable guidance to marine spatial planning initiatives that integrate spatial distributions of protected species and human activities. In addition, the RMU framework--including maps and supporting metadata--will be an iterative, user-driven tool made publicly available in an online application for comments, improvements, download and analysis.

Abstract The value of big old fat fecund female fish (BOFFFFs) in fostering stock productivity and stability has long been underappreciated by conventional fisheries science and management, although Hjort (1914) indirectly alluded to the importance of maternal effects. Compared with smaller mature females, BOFFFFs in a broad variety of marine and freshwater teleosts produce far more and often larger eggs that may develop into larvae that grow faster and withstand starvation better. As (if not more) importantly, BOFFFFs in batch-spawning species tend to have earlier and longer spawning seasons and may spawn in different locations than smaller females. Such features indicate that BOFFFFs are major agents of bet-hedging strategies that help to ensure individual reproductive success in environments that vary tremendously in time and space. Even if all else were equal, BOFFFFs can outlive periods that are unfavourable for successful reproduction and be ready to spawn profusely and enhance recruitment when favourable conditions return (the storage effect). Fishing differentially removes BOFFFFs, typically resulting in severe truncation of the size and age structure of the population. In the worst cases, fishing mortality acts as a powerful selective agent that inhibits reversal of size and age truncation, even if fishing intensity is later reduced. Age truncation is now known to destabilize fished populations, increasing their susceptibility to collapse. Although some fisheries models are beginning to incorporate maternal and other old-growth effects, most continue to treat all spawning-stock biomass as identical: many small young females are assumed to contribute the same to stock productivity as an equivalent mass of BOFFFFs. A growing body of knowledge dictates that fisheries productivity and stability would be enhanced if management conserved old-growth age structure in fished stocks, be it by limiting exploitation rates, by implementing slot limits, or by establishing marine reserves, which are now known to seed surrounding fished areas via larval dispersal. Networks of marine reserves are likely to be the most effective means of ensuring that pockets of old-growth age structure survive throughout the geographic range of demersal species.

Over the past 3 decades, the status of sea turtles and the need for their protection to aid population recovery have increasingly captured the interest of government agencies, non-governmental organisations (NGOs) and the general public worldwide. This interest has been matched by increased research attention, focusing on a wide variety of topics relating to sea turtle biology and ecology, together with the interrelations of sea turtles with the physical and natural environments. Although sea turtles have been better studied than most other marine fauna, management actions and their evaluation are often hindered by the lack of data on turtle biology, human-turtle interactions, turtle population status and threats. In an effort to inform effective sea turtle conservation a list of priority research questions was assembled based on the opinions of 35 sea turtle researchers from 13 nations working in fields related to turtle biology and/or conservation. The combined experience of the contributing researchers spanned the globe as well as many relevant disciplines involved in conservation research. An initial list of more than 200 questions gathered from respondents was condensed into 20 metaquestions and classified under 5 categories: reproductive biology, biogeography, population ecology, threats and conservation strategies. © Inter-Research 2010.

A comparison between the northwestern Hawaiian islands (NWHI), a large, remote, and lightly fished area, and the main Hawaiian islands (MHI), an urbanized, heavily fished area, revealed dramatic differences in the numerical density, size, and biomass of the shallow reef fish assemblages. Grand mean fish standing stock in the NWHI was more than 260% greater than in the MHI. The most striking difference was the abundance and size of large apex predators (primarily sharks and jacks) in the NWHI compared to the MHI. More than 54% of the total fish biomass in the NWHI consisted of apex predators, whereas this trophic level accounted for less than 3% of the fish biomass in the MHI. In contrast, fish biomass in the MHI was dominated by herbivores (55%) and small-bodied lower-level carnivores (42%). Most of the dominant species by weight in the NWHI were either rare or absent in the MHI and the target species that were present, regardless of trophic level, were nearly always larger in the NWHI. These differences represent both near-extirpation of apex predators and heavy exploitation of lower trophic levels in the MHI compared to the largely unfished NWHI. The reefs in the NWHI are among the few remaining large-scale, intact, predator-dominated reef ecosystems left in the world and offer an opportunity to understand how unaltered ecosystems are structured, how they function, and how they can most effectively be preserved. The differences in fish assemblage structure in this study are evidence of the high level of exploitation in the MHI and the pressing need for ecosystem-level management of reef systems in the MHI as well as the NWHI.

In 1990, Andrew Bakun proposed that increasing greenhouse gas concentrations would force intensification of upwelling-favorable winds in eastern boundary current systems that contribute substantial services to society. Because there is considerable disagreement about whether contemporary wind trends support Bakun's hypothesis, we performed a meta-analysis of the literature on upwelling-favorable wind intensification. The preponderance of published analyses suggests that winds have intensified in the California, Benguela, and Humboldt upwelling systems and weakened in the Iberian system over time scales ranging up to 60 years; wind change is equivocal in the Canary system. Stronger intensification signals are observed at higher latitudes, consistent with the warming pattern associated with climate change. Overall, reported changes in coastal winds, although subtle and spatially variable, support Bakun's hypothesis of upwelling intensification in eastern boundary current systems.

Where conservation resources are limited and conservation targets are diverse, robust yet flexible priority-setting frameworks are vital. Priority-setting is especially important for geographically widespread species with distinct populations subject to multiple threats that operate on different spatial and temporal scales. Marine turtles are widely distributed and exhibit intra-specific variations in population sizes and trends, as well as reproduction and morphology. However, current global extinction risk assessment frameworks do not assess conservation status of spatially and biologically distinct marine turtle Regional Management Units (RMUs), and thus do not capture variations in population trends, impacts of threats, or necessary conservation actions across individual populations. To address this issue, we developed a new assessment framework that allowed us to evaluate, compare and organize marine turtle RMUs according to status and threats criteria. Because conservation priorities can vary widely (i.e. from avoiding imminent extinction to maintaining long-term monitoring efforts) we developed a "conservation priorities portfolio" system using categories of paired risk and threats scores for all RMUs (n = 58). We performed these assessments and rankings globally, by species, by ocean basin, and by recognized geopolitical bodies to identify patterns in risk, threats, and data gaps at different scales. This process resulted in characterization of risk and threats to all marine turtle RMUs, including identification of the world's 11 most endangered marine turtle RMUs based on highest risk and threats scores. This system also highlighted important gaps in available information that is crucial for accurate conservation assessments. Overall, this priority-setting framework can provide guidance for research and conservation priorities at multiple relevant scales, and should serve as a model for conservation status assessments and priority-setting for widespread, long-lived taxa.

By accounting for the sparse compositional nature of microbiome data sets, robust Aitchison PCA can yield high discriminatory power and salient feature ranking between microbial niches. The software to perform this analysis is available under an open-source license and can be obtained at https://github.com/biocore/DEICODE; additionally, a QIIME 2 plugin is provided to perform this analysis at https://library.qiime2.org/plugins/deicode/.

The Yangtze River dolphin or baiji (Lipotes vexillifer), an obligate freshwater odontocete known only from the middle-lower Yangtze River system and neighbouring Qiantang River in eastern China, has long been recognized as one of the world's rarest and most threatened mammal species. The status of the baiji has not been investigated since the late 1990s, when the surviving population was estimated to be as low as 13 individuals. An intensive six-week multi-vessel visual and acoustic survey carried out in November-December 2006, covering the entire historical range of the baiji in the main Yangtze channel, failed to find any evidence that the species survives. We are forced to conclude that the baiji is now likely to be extinct, probably due to unsustainable by-catch in local fisheries. This represents the first global extinction of a large vertebrate for over 50 years, only the fourth disappearance of an entire mammal family since AD 1500, and the first cetacean species to be driven to extinction by human activity. Immediate and extreme measures may be necessary to prevent the extinction of other endangered cetaceans, including the sympatric Yangtze finless porpoise (Neophocaena phocaenoides asiaeorientalis).

Tight coupling to ecosystems and dependence on common-pool resources threaten fisheries and aquaculture.