Modelling species presence–absence in the ecological niche theory framework using shape-constrained generalized additive models

According to ecological niche theory, species response curves are unimodal with respect to environmental gradients. A variety of statistical methods have been developed for species distribution modelling. A general problem with most of these habitat modelling approaches is that the estimated response curves can display biologically implausible shapes which do not respect ecological niche theory. This work proposes using shapeconstrained generalized additive models (SC-GAMs) to build species distribution models under the ecological niche theory framework, imposing concavity constraints in the linear predictor scale. Based on a simulation study and a real data application, we compared performance with respect to other regression models without shape-constraints (such as standard GLMs and GAMs with varying degrees of freedom) and also to models based on so-called “Plateau” climate-envelopes. The imposition of concavity for response curves resulted in a good balance between the goodness of fit (GOF) and agreement with ecological niche theory. The approach has been applied to fit distribution models for three fish species given several environmental variables

Effect of trampling and digging from shell shing on Zostera noltei (Zosteraceae) intertidal seagrass beds

Seagrass beds are among the most valuable ecosystems in the world but they are also among the ones most affected by human activities, and they have decreased significantly in recent decades. In many areas, such as in the Basque Country (northern Spain), seagrass beds occupy areas that are also of interest for human activities such as recreation and shellfishing. They may therefore face a number of pressures that cause damage or irreversible states. Taking into account the limited distribution of seagrass beds in the Basque Country and the interest in their conservation, an eight-month field experiment focusing on the Zostera noltei growing season was carried out to evaluate the effect of shellfish gathering. We used generalized linear models to assess different intensities of trampling and digging, as the most important pressures of shellfishing applied to Zostera noltei beds. The results indicated that shoot density of Z. noltei was negatively altered by trampling treatments and positively affected (as a recovery) by digging treatments. This finding suggests that shellfishing adversely affects seagrass abundance and is potentially responsible for its low density in the Oka estuary. Our findings are important for management and should be taken into account in seagrass conservation and restoration programmes

Connectivity, neutral theories and the assessment of species vulnerability to global change in temperate estuaries

One of the main adaptation strategies to global change scenarios, aiming to preserve ecosystem functioning and biodiversity, is to maximise ecosystem resilience. The resilience of a species metapopulation can be improved by facilitating connectivity between local populations, which will prevent demographic stochasticity and inbreeding. The objective of this investigation is to estimate the degree of connectivity among estuarine species along the north-eastern Iberian coast, in order to assess community vulnerability to global change scenarios. To address this objective, two connectivity proxy types have been used based upon genetic and ecological drift processes: 1) DNA markers for the bivalve cockle (Cerastoderma edule) and seagrass Zostera noltei, and 2) the decrease in the number of species shared between two sites with geographic distance; neutral biodiversity theory predicts that dispersal limitation modulates this decrease, and this has been explored in estuarine plants and macroinvertebrates. Results indicate dispersal limitation for both saltmarsh plants and seagrass beds community and Z. noltei populations; this suggests they are especially vulnerable to expected climate changes on their habitats. In contrast, unstructured spatial pattern found in macroinvertebrate communities and in C. edule genetic populations in the area suggests that estuarine soft-bottom macroinvertebrates with planktonic larval dispersal strategies may have a high resilience capacity to moderate changes within their habitats. Our findings can help environmental managers to prioritise the most vulnerable species and habitats to be restored

Global mesozooplankton communities show lower connectivity in deep oceanic layers

Mesozooplankton is a key component of the ocean, regulating global processes such as the carbon pump, and ensuring energy transfer from lower to higher trophic levels. Yet, knowledge on mesozooplankton diversity, distribution and connectivity at global scale is still fragmented. To fill this gap, we applied DNA metabarcoding to mesozooplankton samples collected during the Malaspina-2010 circumnavigation expedition across the Atlantic, Indian and Pacific oceans from the surface to bathypelagic depths. We highlight the still scarce knowledge on global mesozooplankton diversity and identify the Indian Ocean and the deep sea as the oceanic regions with the highest proportion of hidden diversity. We report no consistent alpha-diversity patterns for mesozooplankton at a global scale, neither across vertical nor horizontal gradients. However, beta-diversity analysis suggests horizontal and vertical structuring of mesozooplankton communities mostly attributed to turnover and reveals an increase in mesozooplankton beta-diversity with depth, indicating reduced connectivity at deeper layers. Additionally, we identify a water mass type-mediated structuring of mesozooplankton bathypelagic communities instead of an oceanic basin-mediated as observed at upper layers. This suggests limited dispersal at deep ocean layers, most likely due to weaker currents and lower mixing of water mass types, thus reinforcing the importance of oceanic currents and barriers to dispersal in shaping global plankton communities

Changing fish distributions challenge the effective management of European fisheries.

Changes in fish distribution are being observed across the globe. In Europe's Common Fisheries Policy, the share of the catch of each fish stock is split among management areas using a fixed allocation key known as ‘Relative Stability’: in each management area, member states get the same proportion of the total catch each year. That proportion is largely based on catches made by those member states in the 1970s. Changes in distribution can, therefore, result in a mismatch between quota shares and regional abundances within management areas, with potential repercussions for the status of fish stocks and the fisheries that depend on them. Assessing distribution changes is crucial to ensure adequate management and sustainable exploitation of our fish resources. We analysed scientific survey data using a three‐tiered analytical approach to provide, for the first time, an overview of changes in distribution for 19 northeast Atlantic fish species encompassing 73 commercial stocks over 30 yr. All species have experienced changes in distribution, five of which did so across management areas. A cross‐species analysis suggested that shifts in areas of suitable thermal habitat, and density‐dependent use of these areas, are at least partly responsible for the observed changes. These findings challenge the current use of relative stability to allocate quotas.acceptedVersio

Whistler instability driven by the sunward electron deficit in the solar wind

Context. Solar wind electrons play an important role in the energy balance of the solar wind acceleration by carrying energy into interplanetary space in the form of electron heat flux. The heat flux is stored in the complex electron velocity distribution functions (VDFs) shaped by expansion, Coulomb collisions, and field-particle interactions. Aims. We investigate how the suprathermal electron deficit in the anti-strahl direction, which was recently discovered in the near-Sun solar wind, drives a kinetic instability and creates whistler waves with wave vectors that are quasi-parallel to the direction of the background magnetic field. Methods. We combined high-cadence measurements of electron pitch-angle distribution functions and electromagnetic waves pro- vided by Solar Orbiter during its first orbit. Our case study is based on a burst-mode data interval from the Electrostatic Analyser System (SWA-EAS) at a distance of 112 RS (0.52 au) from the Sun, during which several whistler wave packets were detected by Solar Orbiter’s Radio and Plasma Waves (RPW) instrument. Results. The sunward deficit creates kinetic conditions under which the quasi-parallel whistler wave becomes unstable. We directly test our predictions for the existence of these waves through solar wind observations. We find whistler waves that are quasi-parallel and almost circularly polarised, propagating away from the Sun, coinciding with a pronounced sunward deficit in the electron VDF. The cyclotron-resonance condition is fulfilled for electrons moving in the direction opposite to the direction of wave propagation, with energies corresponding to those associated with the sunward deficit. Conclusions. We conclude that the sunward deficit acts as a source of quasi-parallel whistler waves in the solar wind. The quasilinear diffusion of the resonant electrons tends to fill the deficit, leading to a reduction in the total electron heat flux

Large-scale ocean connectivity and planktonic body size

Villarino, Ernesto ... et al.-- 13 pages, 5 figures, 5 tables, supplementary material https://dx.doi.org/10.1038/s41467-017-02535-8Global patterns of planktonic diversity are mainly determined by the dispersal of propagules with ocean currents. However, the role that abundance and body size play in determining spatial patterns of diversity remains unclear. Here we analyse spatial community structure - β-diversity - for several planktonic and nektonic organisms from prokaryotes to small mesopelagic fishes collected during the Malaspina 2010 Expedition. β-diversity was compared to surface ocean transit times derived from a global circulation model, revealing a significant negative relationship that is stronger than environmental differences. Estimated dispersal scales for different groups show a negative correlation with body size, where less abundant large-bodied communities have significantly shorter dispersal scales and larger species spatial turnover rates than more abundant small-bodied plankton. Our results confirm that the dispersal scale of planktonic and micro-nektonic organisms is determined by local abundance, which scales with body size, ultimately setting global spatial patterns of diversityThis research was funded by the project Malaspina 2010 Circumnavigation Expedition (Consolider-Ingenio 2010, CSD2008-00077) and cofounded by the Basque Government (Department Deputy of Agriculture, Fishing and Food Policy). [...] E.V. was supported by a PhD Scholarship granted by the Iñaki Goenaga−Technology Centres FoundationPeer Reviewe

Solar wind current sheets and deHoffmann-Teller analysis. First results from Solar Orbiter's DC electric field measurements

Context: Solar Orbiter was launched on 10 February 2020 with the purpose of investigating solar and heliospheric physics using a payload of instruments designed for both remote and in situ studies. Similar to the recently launched Parker Solar Probe, and unlike earlier missions, Solar Orbiter carries instruments designed to measure low-frequency DC electric fields. Aims: In this paper, we assess the quality of the low-frequency DC electric field measured by the Radio and Plasma Waves instrument (RPW) on Solar Orbiter. In particular, we investigate the possibility of using Solar Orbiter’s DC electric and magnetic field data to estimate the solar wind speed. Methods: We used a deHoffmann-Teller (HT) analysis, based on measurements of the electric and magnetic fields, to find the velocity of solar wind current sheets, which minimises a single component of the electric field. By comparing the HT velocity to the proton velocity measured by the Proton and Alpha particle Sensor (PAS), we have developed a simple model for the effective antenna length, Leff of the E-field probes. We then used the HT method to estimate the speed of the solar wind. Results: Using the HT method, we find that the observed variations in Ey are often in excellent agreement with the variations in the magnetic field. The magnitude of Ey , however, is uncertain due to the fact that the Leff depends on the plasma environment. Here, we derive an empirical model relating Leff to the Debye length, which we can use to improve the estimate of Ey and, consequently, the estimated solar wind speed. Conclusions: The low-frequency electric field provided by RPW is of high quality. Using the deHoffmann-Teller analysis, Solar Orbiter’s magnetic and electric field measurements can be used to estimate the solar wind speed when plasma data are unavailable