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Funding: Open access funding provided by FCT|FCCN (b-on). This work was funded by the Operational Programme Mar2020 MAR-02.01.01-FEAMP-0052 “Newcumber-Avanços para o cultivo sustentável de pepinos do mar”. This work was also supported by national funds through FCT–Fundação para a Ciência e a Tecnologia, I.P., within the strategic projects MARE (UIDB/04292/2020) Associate Laboratory ARNET (LA/P/0069/2020), CEAUL (UIDB/00006/2020), A.C. Brito with the Scientific Stimulus Programme–CEECIND/00095/2017, A. Pombo by the Scientific Employment Stimulus-Institutional Call-CEECINST/00051/2018 and F. Azevedo e Silva by the individual research grant (SFRH/BD/09563/2020). The demand for sea cucumbers from the NE-Atlantic is increasing as a consequence of the depletion of stocks that historically supplied Asian markets. Some species from the NE-Atlantic are already showing overfishing signs due to either inefficient policies or their total absence, and they do not offer any margins of sustainability to sea cucumber fisheries. The current lack of knowledge of biological and ecological traits has led to ineffective protection of those species. Holothuria arguinensis is a good example of a temperate sea cucumber species suffering from the effects of unregulated and illegal harvest. This study aims to determine the temporal and spatial distribution patterns of H. arguinensis, assessing density and size-class structure in a NE-Atlantic population, in SW Portugal, as a function of environmental conditions. Sampling was done every 1.5 months at 6 stations defined according to habitat heterogeneity, following the coastline from the mouth of the Sado estuary to marine coastal areas. At each station, there were two habitats (rocky substrate and sandy areas) sampled through SCUBA diving along 30-m random transects, each with three replicates. Individuals were counted and measured (total length) and individual behavioural parameters, such as sheltering and settlement surface, were recorded. Water column parameters, sediment composition, and substrate cover were also recorded. Generalised Linear Models were fit to the data, modelling density and size distribution of the species with respect to environmental conditions. The results indicate that the distribution of H. arguinensis was mainly determined by its ability to deal with physical environmental stressors (current), rather than the chemical properties of the water column or sediment composition. The hydrodynamic features of the region exert the greatest impact on this species’ distribution and help shape habitat usage by different size class groups. Publisher PDF

Funding: Systematics Research Fund 2019 to KV. John Templeton Foundation (Grant Number(s): #60501; Grant recipient(s): Kevin N Laland). 1. The size of a bird's nest can play a key role in ensuring reproductive success and is determined by a variety of factors. The primary function of the nest is to protect offspring from the environment and predators. Field studies in a number of passerine species have indicated that higher-latitude populations in colder habitats build larger nests with thicker walls compared to lower-latitude populations, but that these larger nests are more vulnerable to predation. Increases in nest size can also be driven by sexual selection, as nest size can act as a signal of parental quality and prompt differential investment in other aspects of care. It is unknown, however, how these microevolutionary patterns translate to a macroevolutionary scale. 2. Here, we investigate potential drivers of variation in the outer and inner volume of open cup nests using a large dataset of nest measurements from 1117 species of passerines breeding in a diverse range of environments. Our dataset is sourced primarily from the nest specimens at the Natural History Museum (UK), complemented with information from ornithological handbooks and online databases. 3. We use phylogenetic comparative methods to test long-standing hypotheses about potential macroevolutionary correlates of nest size, namely nest location, clutch size and variables relating to parental care, together with environmental and geographical factors such as temperature, rainfall, latitude and insularity. 4. After controlling for phylogeny and parental body size, we demonstrate that the outer volume of the nest is greater in colder climates, in island-dwelling species and in species that nest on cliffs or rocks. By contrast, the inner cup volume is associated solely with average clutch size, increasing with the number of chicks raised in the nest. We do not find evidence that nest size is related to the length of parental care for nestlings. 5. Our study reveals that the average temperature in the breeding range, along with several key life-history traits and proxies of predation threat, shapes the global interspecific variation in passerine cup nest size. We also showcase the utility of museum nest collections—a historically underused resource—for large-scale studies of trait evolution. Publisher PDF

Funding: Open access funding provided by Norwegian University of Science and Technology. Bioinformatics and computational analyses were supported by the University of St Andrews Bioinformatics Unit which is funded by a Wellcome Trust ISSF award [grant 105621/Z/14/Z] and ran on cluster marvin and Crop Diversity HPC. Contemporary sample DNA extractions were supported by People’s Trust for Endangered Species and the sequencing costs were supported by the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska- Curie grant agreement No. 663830 awarded to A.D.F., by the Total Foundation awarded to M.L., the University of Groningen awarded to M.C.F., and the Marine Alliance for Science and Technology for Scotland and The Russell Trust awarded to O.E.G. M.N. was funded by MASTS and the Crawford Hayes fund. A.D.F. was funded by Marie Skłodowska-Curie grant agreement No. 663830 and the European Research Council grant agreement No. ERC-COG-101045346. Parallel evolution provides strong evidence of adaptation by natural selection due to local environmental variation. Yet, the chronology, and mode of the process of parallel evolution remains debated. Here, we harness the temporal resolution of paleogenomics to address these long-standing questions, by comparing genomes originating from the mid-Holocene (8610-5626 years before present, BP) to contemporary pairs of coastal-pelagic ecotypes of bottlenose dolphin. We find that the affinity of ancient samples to coastal populations increases as the age of the samples decreases. We assess the youngest genome (5626 years BP) at sites previously inferred to be under parallel selection to coastal habitats and find it contained coastal-associated genotypes. Thus, coastal-associated variants rose to detectable frequencies close to the emergence of coastal habitat. Admixture graph analyses reveal a reticulate evolutionary history between pelagic and coastal populations, sharing standing genetic variation that facilitated rapid adaptation to newly emerged coastal habitats. Publisher PDF

Funding: SIMS analyses were supported by the Natural Environment Research Council, UK (IMF689/0519). Coral skeletal boron geochemistry offers opportunities to probe the pH of the calcification media (pHCM) of modern and fossil specimens, to estimate past changes in seawater pH and to explore the biomineralisation response to future ocean acidification. In this research we grew 2 Stylophora pistillata coral microcolonies over glass coverslips to allow analysis of the pH sensitive dye SNARF-1, in the extracellular calcification medium at the growing edge of colonies where the first aragonite crystals are formed, under both light and dark conditions. We use secondary ion mass spectrometry (SIMS) to measure the boron isotopic composition (δ11B) of the skeleton close to the growth edge after 2 to 3 days of additional calcification had enlarged the crystals until they joined, generating a continuous sheet of aragonite. Mean skeletal δ11B-pHCM estimates are higher than those of by SNARF-1 by 0.35 to 0.44 pH units. These differences either reflect real variations in the pH of the calcification media associated with each measurement technique or indicate other changes in the biomineralisation process which influence skeletal δ11B. SNARF-1 measures directly the pH of the extracellular calcification medium while skeletal δ11B analyses aragonite potentially formed via both extracellular and intracellular biomineralisation pathways. Analysis of a third coral specimen, also growing on a glass slide but with a 5 cm long branch, indicated good agreement between the δ11B value of the apex of the branch and the skeletal growth edge. The tissues overlying both these regions were transparent indicating they had low symbiont densities. This suggests that the biomineralisation process is broadly comparable between these sites and that studies growing corals over glass slides/coverslips provide representative data for the colony apex. Publisher PDF

This research was made possible by a grant from the Gulf of Mexico Research Initiative to the Consortium for Advanced Research on Marine Mammal Health Assessment (CARMMHA). T.A.M. acknowledges partial support by CEAUL (funded by FCT−Fundação para a Ciência e a Tecnologia, Portugal, through project UIDB/00006/2020). The Deepwater Horizon disaster resulted in the release of 490000 m3 of oil into the northern Gulf of Mexico. We quantified population consequences for pelagic cetaceans, including sperm whales, beaked whales and 11 species of delphinids. We used existing spatial density models to establish pre-spill population size and distribution, and overlaid an oil footprint to estimate the proportion exposed to oil. This proportion ranged from 0.058 (Atlantic spotted dolphin, 95% CI = 0.041-0.078) to 0.377 (spinner dolphin, 95% CI = 0.217-0.555). We adapted a population dynamics model, developed for an estuarine population of bottlenose dolphins, to each pelagic species by scaling demographic parameters using literature-derived estimates of gestation duration. We used expert elicitation to translate knowledge from dedicated studies of oil effects on bottlenose dolphins to pelagic species and address how density dependence may affect reproduction. We quantified impact by comparing population trajectories under baseline and oil-impacted scenarios. The number of lost cetacean years (difference between trajectories, summed over years) ranged from 964 (short-finned pilot whale, 95% CI = 385-2291) to 32584 (oceanic bottlenose dolphin, 95% = CI 13377-71967). Maximum proportional population decrease ranged from 1.3% (Atlantic spotted dolphin 95% CI = 0.5-2.3) to 8.4% (spinner dolphin 95% CI = 3.2-17.7). Estimated time to recover to 95% of baseline was >10 yr for spinner dolphin (12 yr, 95% CI = 0-21) and sperm whale (11 yr, 95% CI = 0-21), while 7 taxonomic units remained within 95% of the baseline population size (time to recover, therefore, as per its definition, was 0). We investigated the sensitivity of results to alternative plausible inputs. Our methods are widely applicable for estimating population effects of stressors in the absence of direct measurements. Publisher PDF

Three-dimensional filaments of quasi-geostrophic potential vorticity are generic features of atmospheric and oceanic flows. They are often generated during the strong interactions between three-dimensional quasi- geostrophic vortices. They contribute to a direct cascade of enstrophy in spectral space. These filaments correspond to shear zones. Therefore they may be sensitive to shear instabilities akin to the Kelvin-Helmholtz instability of the classical two-dimensional vorticity strip. They are however often subjected to a straining flow induced by the surrounding vortices. This straining flow affects their robustness. The paper focuses on a simplified model of this situation. We consider the effect of a pure strain on a three-dimensional filament of uniform quasi-geostrophic potential vorticity. We first consider a quasi-static situation where the strain, assumed small, only affects the cross-sectional shape of the filament, but not the velocity field. We address the linear stability of the filament in that context, and also show examples of the filament’s nonlinear evolution. We then consider the linearised dynamics of the filament in pure strain. In particular we focus on the maximum perturbation amplification observed in the filament. We conclude that small to moderate strain rates are efficient at preventing a large perturbation growth. Nonlinear effects can nevertheless leads to the roll-up of weakly strained filaments. Postprint Publisher PDF

The Oticon Foundation and theOcean Futures/Free Willy Keiko Foundation provided funding and platforms for data collection in Vestmannaeyjar 2002. Funding for data collection in Vestmannaeyjar from 2008 onwards and in Breiðafjörður was provided by the BBC Natural History Unit, Fundaç ̃ao para a Ciência e a Tecnologia (grant number SFRH/BD/30303/2006), the Icelandic Centre for Research through a START Postdoctoral Fellowship (grant number 120248042) and Project Grant (grant number 163060), the National Geographic Global Exploration Fund (grant number GEFNE65-12), a Marie Curie International Incoming Fellowship (project number 297116), the Office of Naval Research (grant number N00014-08-1-0984), and a Russell Trust Award from the University of St Andrews. A.S. was supported by a Doctoral Student Grant (grant number 206808) from the Icelandic Centre for Research. V.B.D. was supported by a grant from the University of Cumbria's Research and Scholarship Development Fund. E.M. was supported by the Doctoral Grants of the University of Iceland Research Fund (grant number 200913) and the Conservation Fund of Pálmi Jonasson. This project was funded in part by the generous support of Earthwatch. Killer whales (Orcinus orca) have group-specific call repertoires that can be used to track groups and populations using passive acoustic monitoring. To provide a detailed description of the Icelandic killer whale repertoire and its variation, we analyzed acoustic data collected in five locations between 1985 and 2016. Calls were classified manually, and CART and random forest analyses were employed to validate the manual classification. A total of 91 call categories (including call types and subtypes) were defined. Most call categories were recorded in more than one location, with the highest proportion shared between herring grounds in Vestmannaeyjar (South) and Breiðafjörður (West). However, both locations included call categories that were not recorded elsewhere in Iceland. Recordings from past herring wintering grounds in eastern Iceland included few call categories that matched other locations. Sample sizes from Reykjanes (Southwest) and Skjálfandi (North) were small and did not include unique call categories. The relative occurrence of call categories in Vestmannaeyjar changed little over a 14-year period (2002-2016), although shorter-term changes between years were observed that appeared to correlate to changes in individuals identified. This comparison of acoustic repertoires provides valuable information on the social structure and movement patterns of herring-eating killer whales around Iceland. Publisher PDF

Funding: PLT received support from ONR grants N00014-18-1-2062 and N00014-20-1-2709. Financial support for the whistle database project has come from the Protect Wild Dolphins fund at Harbor Branch Oceanographic Institute, Vulcan Machine Learning Center for Impact, Allen Institute for Artificial Intelligence, Adelaide M. & Charles B. Link Foundation, and Dolphin Quest, Inc. Human caregivers interacting with children typically modify their speech in ways that promote attention, bonding, and language acquisition. Although this “motherese,” or child-directed communication (CDC), occurs in a variety of human cultures, evidence among nonhuman species is very rare. We looked for its occurrence in a nonhuman mammalian species with long-term mother–offspring bonds that is capable of vocal production learning, the bottlenose dolphin (Tursiops truncatus). Dolphin signature whistles provide a unique opportunity to test for CDC in nonhuman animals, because we are able to quantify changes in the same vocalizations produced in the presence or absence of calves. We analyzed recordings made during brief catch-and-release events of wild bottlenose dolphins in waters near Sarasota Bay, Florida, United States, and found that females produced signature whistles with significantly higher maximum frequencies and wider frequency ranges when they were recorded with their own dependent calves vs. not with them. These differences align with the higher fundamental frequencies and wider pitch ranges seen in human CDC. Our results provide evidence in a nonhuman mammal for changes in the same vocalizations when produced in the presence vs. absence of offspring, and thus strongly support convergent evolution of motherese, or CDC, in bottlenose dolphins. CDC may function to enhance attention, bonding, and vocal learning in dolphin calves, as it does in human children. Our data add to the growing body of evidence that dolphins provide a powerful animal model for studying the evolution of vocal learning and language. Publisher PDF

Funding: This research received support from the UK Engineering and Physical Sciences Research Council (Impact Acceleration Account, both at the University of St Andrews and Newcastle University). This research received support from the UK Engineering and Physical Sciences Research Council (grants EP/R511778/1 and EP/R511584/1). Herein we describe a new approach to modelling inviscid two-dimensional stratified flows in a general domain. The approach makes use of a conformal map of the domain to a rectangle. In this transformed domain, the equations of motion are largely unaltered, and in particular Laplace's equation remains unchanged. This enables one to construct exact solutions to Laplace's equation and thereby enforce all boundary conditions. An example is provided for two-dimensional flow under the Boussinesq approximation, though the approach is much more general (albeit restricted to two-dimensions). This example is motivated by flow under a weir in a tidal estuary. Here, we discuss how to use a dynamically-evolving conformal map to model changes in the water height on either side of the weir, though the example presented keeps these heights fixed due to limitations in the computational speed to generate the conformal map. The numerical approach makes use of contour advection, wherein material buoyancy contours are advected conservatively by the local fluid velocity, while a dual contour-grid representation is used for the vorticity in order to account for vorticity generation from horizontal buoyancy gradients. This generation is accurately estimated by using the buoyancy contours directly, rather than a gridded version of the buoyancy field. The result is a highly-accurate, efficient numerical method with extremely low levels of numerical damping. Publisher PDF

Funding: The authors thank the Coordination of Superior Level Staff Improvement (CAPES) from Brazil for providing a doctoral scholarship and grant CAPES-PRINT (grant no. 88887.370641/2019-00) to M.A. The National Council for Technological and Scientific Development (CNPq) from Brazil provided research grants to F.G.D.-J. (grant no. 308867/2019-0), and P.C.S.-L. (grant no. 305573/2013-6). Kelp gulls (Larus dominicanus) commonly feed on the skin and blubber of surfacing southern right whales (SRW, Eubalaena australis) in the near shore waters of Península Valdés (PV), Argentina. Mothers and especially calves respond to gull attacks by changing their swimming speeds, resting postures and overall behaviour. Gull-inflicted wounds per calf have increased markedly since the mid-1990s. Unusually high mortality of young calves occurred locally after 2003, and increasing evidence points to gull harassment as a factor contributing to the excess deaths. After leaving PV, calves undertake a long migration with their mothers to summer feeding areas; their health during this strenuous exertion is likely to affect their probabilities of first-year survival. To explore the effects of gull-inflicted wounds on calf survival, we analysed 44 capture–recapture observations between 1974 and 2017, for 597 whales photo-identified in their years of birth between 1974 and 2011. We found a marked decrease in first-year survival associated with an increase in wound severity over time. Our analysis supports recent studies indicating that gull harassment at PV may impact SRW population dynamics. Postprint

Funding: This work was supported by Fisheries and Oceans Canada (DFO) Maritimes and National Geographic emerging explorer grant to L.J.F, with support by and Natural Sciences and Engineering Research Council of Canada (NSERC) and Killam Nova Scotia Doctoral Scholarships. Work was also supported by US Office of Naval Research and US Strategic Environmental Research and Development Program (SERDP), DFO, University of Windsor, Crown-Indigenous Relations and Northern Affairs Canada, Nunavut Fisheries Association, Government of Nunavut, and NSERC. Funding and resources for sequencing the northern bottlenose whale genome was supported by the CanSeq150 program of Canada’s Genomics Enterprise. Information on wildlife population structure, demographic history, and adaptations are fundamental to understanding species evolution and informing conservation strategies. To study this ecological context for a cetacean of conservation concern, we conducted the first genomic assessment of the northern bottlenose whale, Hyperoodon ampullatus, using whole-genome resequencing data (n = 37) from five regions across the North Atlantic Ocean. We found a range-wide pattern of isolation-by-distance with a genetic subdivision distinguishing three subgroups: the Scotian Shelf, western North Atlantic, and Jan Mayen regions. Signals of elevated levels of inbreeding in the Endangered Scotian Shelf population indicate this population may be more vulnerable than the other two subgroups. In addition to signatures of inbreeding, evidence of local adaptation in the Scotian Shelf was detected across the genome. We found a long-term decline in effective population size for the species, which poses risks to their genetic diversity and may be exacerbated by the isolating effects of population subdivision. Protecting important habitat and migratory corridors should be prioritized to rebuild population sizes that were diminished by commercial whaling, strengthen gene flow, and ensure animals can move across regions in response to environmental changes. Publisher PDF

Funding: This work was funded by the Office of Naval Research under award: N000141912464. 1. The assessment of behavioural disturbance in cetacean species (e.g., resulting from exposure to anthropogenic sources such as military sonar, seismic surveys, or pile driving) is important for effective conservation and management. Disturbance effects can be informed by Behavioural Response Studies (BRSs), involving either controlled exposure experiments (CEEs) where noise exposure conditions are presented deliberately to meet experimental objectives or in opportunistic contexts where ongoing activities are monitored in a strategic manner. In either context, animal-borne sensors or in-situ observations can provide information on individual exposure and disturbance responses. 2. The past 15 years of research have greatly expanded our understanding of behavioural responses to noise, including hundreds of experiments in nearly a dozen cetacean species. Many papers note limited sample sizes, required knowledge of baseline behaviour prior to exposure and the importance of contextual factors modulating behavioural responses, all of which in combination can lead to sampling biases, even for well-designed research programs. 3. It is critical to understand these biases to robustly identify responses. This ensures outcomes of BRSs help inform predictions of how anthropogenic disturbance impacts individuals and populations. Our approach leverages concepts from the animal behaviour literature focused on helping to avoid sampling bias by considering what shapes an animal's response. These factors include social, experience, genetic and natural changes in responsiveness. 4. We developed and applied a modified version of this framework to synthesize current knowledge on cetacean response in the context of effects observed across marine and terrestrial taxa. This new 'Sampling, Exposure, Receptor' framework (SERF) identifies 43 modulating factors, highlights potential biases, and assesses how these vary across selected focal species. 5. In contrast to studies that identified variation in 'Exposure' factors as a key concern, our analysis indicated that factors relating to 'Sampling' (e.g., deploying tags on less evasive individuals, which biases selection of subjects), and "Receptor" (e.g., health status or coping style) have the greatest potential for weakening the desired broad representativeness of BRSs. Our assessment also highlights how potential biases could be addressed with existing datasets or future developments. Publisher PDF

The KAOS voyage was supported by Australian Antarctic Science (AAS) grant 2205 and this data processing by AAS grants 4050 and 4636. Raw acoustic data were collected in East Antarctica from the RSV Aurora Australis during two surveys: the Krill Availability, Community Trophodynamics and AMISOR Surveys (KACTAS) and the Krill Acoustics and Oceanography Survey (KAOS) in the East Antarctic (centre coordinate 66.5° S, 63° E). The KACTAS survey was conducted between 14th to 21st January and 2001, and the KAOS survey was conducted between 16 January and 1 February 2003. We examine the Antarctic krill (Euphausia superba) component of these surveys and provide scientific echosounder (EK500 and EK60) data collected at 38, 120 and 200 kHz, cold water (−1 °C) echosounder calibration parameters and accompanying krill length frequency distributions obtained from trawl data. We processed the acoustic data to apply calibration values and remove noise. The processed data were used to isolate echoes arising from swarms of krill and to estimate metrics for each krill swarm, including internal density and individual swarm biomass. The krill swarm data provide insights to a predators’ views of krill distribution and density. Publisher PDF

IP would like to thank the European Commission for the funding (GAP-847014). IP is grateful to the MSCA fellowship that supported his research. MGP thanks the project IMPRESS (RTI2018-099868-B-I00), ERDF, Ministry of Science, Innovation, and Universities - State Research Agency. Species Distribution Models are pivotal for fisheries management. There has been an increasing number of fishery data sources available, making data integration an attractive way to improve model predictions. A wide range of methods have been applied to integrate different datasets in different disciplines. We focus on the use of Integrated Species Distribution Models (ISDMs) due to their capacity to formally accommodate different types of data and scale proportional gear efficiencies. ISDMs use joint modelling to integrate information from different data sources to improve parameter estimation by fitting shared environmental, temporal and spatial effects. We illustrate this method first using a simulated example, and then apply it to a case study that combines data coming from a fishery-independent trawl survey and a fishery-dependent trammel net observations on Solea solea. We explore the sensitivity of model outputs to several weightings for the commercial data and also compare integrated model results with ensemble modelling to combine population trends in the case study. We obtain similar results but discuss that ensemble modelling requires both response variables and link functions to be the same across models. We conclude by discussing the flexibility and requirements of ISDMs to formally combine different fishery datasets. Publisher PDF

Funding: This work was supported by Grant #0333 from the Templeton World Charity Foundation (TWCF) and a Brian Mason Technical Trust Fund grant to X. J. N. and A. H. T. The nature and evolution of positive emotion is a major question remaining unanswered in science and philosophy. The study of feelings and emotions in humans and animals is dominated by discussion of affective states that have negative valence. Given the clinical and social significance of negative affect, such as depression, it is unsurprising that these emotions have received more attention from scientists. Compared to negative emotions, such as fear that leads to fleeing or avoidance, positive emotions are less likely to result in specific, identifiable, behaviours being expressed by an animal. This makes it particularly challenging to quantify and study positive affect. However, bursts of intense positive emotion (joy) are more likely to be accompanied by externally visible markers, like vocalisations or movement patterns, which make it more amenable to scientific study and more resilient to concerns about anthropomorphism. We define joy as intense, brief, and event-driven (i.e. a response to something), which permits investigation into how animals react to a variety of situations that would provoke joy in humans. This means that behavioural correlates of joy are measurable, either through newly discovered 'laughter' vocalisations, increases in play behaviour, or reactions to cognitive bias tests that can be used across species. There are a range of potential situations that cause joy in humans that have not been studied in other animals, such as whether animals feel joy on sunny days, when they accomplish a difficult feat, or when they are reunited with a familiar companion after a prolonged absence. Observations of species-specific calls and play behaviour can be combined with biometric markers and reactions to ambiguous stimuli in order to enable comparisons of affect between phylogenetically distant taxonomic groups. Identifying positive affect is also important for animal welfare because knowledge of positive emotional states would allow us to monitor animal well-being better. Additionally, measuring if phylogenetically and ecologically distant animals play more, laugh more, or act more optimistically after certain kinds of experiences will also provide insight into the mechanisms underlying the evolution of joy and other positive emotions, and potentially even into the evolution of consciousness. Publisher PDF

Funding: This research was funded by the National Science Foundation (NSF) Arctic Social Science (Grants 2112463 and 2112314). KJA was supported by NSF AGS-1501834 and AGS-2102993. RD, KA, LAH, and BVG were supported by NSF OPP #2124885. GW and BVG were supported by NSF P2C2 #2002561. TJP was supported by NSERC Discovery Grant RGPIN-2016-06730. RW was supported by NERC project #NE/S000887/1. MPR was supported by NOAA Climate and Global Change Postdoctoral Fellowship Program, UCAR-CPAESS award #NA18NWS4620043B and EU2020 Marie Skłodowska-Curie Grant 101031748. Two large volcanic eruptions contributed to extreme cold temperatures during the early 1800s, one of the coldest phases of the Little Ice Age. While impacts from the massive 1815 Tambora eruption in Indonesia are relatively well-documented, much less is known regarding an unidentified volcanic event around 1809. Here, we describe the spatial extent, duration, and magnitude of cold conditions following this eruption in northwestern North America using a high-resolution network of tree-ring records that capture past warm-season temperature variability. Extreme and persistent cold temperatures were centered around the Gulf of Alaska, the adjacent Wrangell-St Elias Mountains, and the southern Yukon, while cold anomalies diminished with distance from this core region. This distinct spatial pattern of temperature anomalies suggests that a weak Aleutian Low and conditions similar to a negative phase of the Pacific Decadal Oscillation could have contributed to regional cold extremes after the 1809 eruption. Publisher PDF

Funding: This work was enabled by the NSF-NERC International Thwaites Glacier Collaboration: Thwaites-Amundsen Regional Survey and Network (ITGC: TARSAN; NERC Grant: NE/S006419/1, NE/S006591/1, NSF Grant: 1738992) and the NERC Ice Sheet Stability Programme (iSTAR; NERC Grant: NE/J005703/1). Antarctica’s ice shelves play a critical role in modulating ice loss to the ocean by buttressing grounded ice upstream. With the potential to impact ice-shelf stability, persistent polynyas (open-water areas surrounded by sea ice, persisting for multiple years at the same location) at the edge of many ice-shelf fronts, are maintained by winds and/or ocean heat, and are locations of strong ice-ocean-atmosphere interactions. However, in situ observations of polynyas are sparse due to the logistical constraints of collecting Antarctic field measurements. Here, we used wintertime (May–August) temperature and salinity observations derived from seal-borne tags deployed in 2014, 2019, and 2020, in conjunction with thermal imagery from the MODerate resolution Imaging Spectroradiometer (MODIS) and the Landsat 8 Thermal Infrared Sensor (TIRS) to investigate the spatial, temporal, and thermal structural variability of polynyas near Pine Island Glacier (PIG). Across the three winters considered, there were 148 anomalously warm (>3σ from background) seal dives near the PIG ice front, including 24 dives that coincided with MODIS images with minimal cloud cover that also showed a warm surface temperature anomaly. These warm surface temperatures correlated with ocean temperatures down to 150 m depth or deeper, depending on the year, suggesting that MODISderived surface thermal anomalies can be used for monitoring polynya presence and structure during polar night. The finer spatial resolution (100 m) of TIRS wintertime thermal imagery captures more detailed thermal structural variability within these polynyas, which may provide year-round insight into sub-ice-shelf processes if this dataset is collected operationally. Publisher PDF

Funding Information: We are especially thankful to Rob G. Bijlsma who generously shared with us his extensive dataset from the Sahel region. We are also thankful to Afan Ajang, Linn M. Bjørvik, Tamuka Chapata, Wouter van Dongen, Patrick Guay, Lenka Harmáčková, Lukasz Jankowiak, Jan van der Kamp, Lennox Kirao, Jakub Kosicki, Philista Malaki, Pretty Maoko, John Mchetto, Grayson Mwakalebe, Organisation for Tropical Studies (South Africa), Diogo Samia, Trine Hay Setsaas, Libor Vaicenbacher and Leo Zwarts for their help with data collection. MW is thankful to Allison Piper, and a Deakin University Faculty of Science, Engineering and the Built Environment National and International Research Collaboration Grant in Kenya and BEACH (Beach Ecology and Conservation Hub; Venus Bay) in Australia. In Kenya, field data collection was approved by National Commission for Science Technology and Innovation no. NACOSTI/P14/4653/660 to M.W. and P.M. and no. NACOSTI/P18/52438/25493 to MW, Kenya Wildlife Service no KWS/BRP/5001 to M.W. A Rocha Kenya and the National Museum of Kenya supported and helped conduct fieldwork in Kenya. In South Africa, the University of Cape Town Science Faculty Animal Ethics Committee (2015/V11/SC) to S.J.C., Northern Cape Department of Environment and Nature Conservation (FAUNA 1489/2015) to P.P. In Brazil, we worked on private lands where no permits were required. In Australia, research was approved by the Deakin University (B32/2012, B11/2015, B10/2018), the Charles Darwin University Animal Ethics (A11013), the Macquarie University Animal Research Committee (99021), the Queensland Parks and Wildlife Service (#FA/000379/00/SA), and the Northern Territory Parks and Wildlife (41035 and 55233). This study was financially supported by the DSI-NRF Centre of Excellence at the FitzPatrick Institute of African Ornithology, University of Cape Town (grant to S.J.C.), The Leventis Foundation through the A.P. Leventis Ornithological Research Institute, Jos Nigeria (grant to B.D.A.B.), by a fellowship of the Fulbright (Slovakia) programme to P.M. for a visit to the University of California, Los Angeles. Animal tolerance towards humans can be a key factor facilitating wildlife–human coexistence, yet traits predicting its direction and magnitude across tropical animals are poorly known. Using 10,249 observations for 842 bird species inhabiting open tropical ecosystems in Africa, South America, and Australia, we find that avian tolerance towards humans was lower (i.e., escape distance was longer) in rural rather than urban populations and in populations exposed to lower human disturbance (measured as human footprint index). In addition, larger species and species with larger clutches and enhanced flight ability are less tolerant to human approaches and escape distances increase when birds were approached during the wet season compared to the dry season and from longer starting distances. Identification of key factors affecting animal tolerance towards humans across large spatial and taxonomic scales may help us to better understand and predict the patterns of species distributions in the Anthropocene.

Funding: This study was supported by grants from the Office of Naval Research N00014-18-1-2822, DoD SERDP contract W912HQ20C0056, IPEV (Institut Paul Emile Victor) under the Antarctic research program 109 (C. Barbraud) and 1201 (C. Gilbert & C. Guinet), and CNES-TOSCA as part of the SNO-MEMO. The ability of marine mammals to accumulate sufficient lipid energy reserves is vital for mammals' survival and successful reproduction. However, long-term monitoring of at-sea changes in body condition, specifically lipid stores, has only been possible in elephant seals performing prolonged drift dives (low-density lipids alter the rates of depth change while drifting). This approach has limited applicability to other species. Using hydrodynamic performance analysis during transit glides, we developed and validated a novel satellite-linked data logger that calculates real-time changes in body density (∝lipid stores). As gliding is ubiquitous amongst divers, the system can assess body condition in a broad array of diving animals. The tag processes high sampling rate depth and three-axis acceleration data to identify 5 s high pitch angle glide segments at depths >100 m. Body density is estimated for each glide using gliding speed and pitch to quantify drag versus buoyancy forces acting on the gliding animal. We used tag data from 24 elephant seals (Mirounga spp.) to validate the onboard calculation of body density relative to drift rate. The new tags relayed body density estimates over 200 days and documented lipid store accumulation during migration with good correspondence between changes in body density and drift rate. Our study provided updated drag coefficient values for gliding (Cd,f = 0.03) and drifting (Cd,s = 0.12) elephant seals, both substantially lower than previous estimates. We also demonstrated post-hoc estimation of the gliding drag coefficient and body density using transmitted data, which is especially useful when drag parameters cannot be estimated with sufficient accuracy before tag deployment. Our method has the potential to advance the field of marine biology by switching the research paradigm from indirectly inferring animal body condition from foraging effort to directly measuring changes in body condition relative to foraging effort, habitat, ecological factors and anthropogenic stressors in the changing oceans. Expanding the method to account for diving air volumes will expand the system's applicability to shallower-diving (

Funding: HCA was supported by a studentship funded by Plymouth University School of Marine Science and Engineering. The breeding season field work was supported by Natural Environment Research Council (NERC) National Capability Funding to SMRU (NE/R015007/1). The field work in Blakeney and Donna Nook was supported by funding to DJFR from UK Department of Business, Energy and Industrial Strategy (formerly DECC) as part of their Offshore Energy Strategic Environmental Assessment programme (OESEA-14–47) and was conducted with permission from Natural England and facilitated by National Trust and Lincolnshire Wildlife Trust. Life-history-oxidative stress theory predicts that elevated energy costs during reproduction reduce allocation to defences and increase cellular stress, with fitness consequences, particularly when resources are limited. As capital breeders, grey seals are a natural system in which to test this theory. We investigated oxidative damage (malondialdehyde (MDA) concentration) and cellular defences (relative mRNA abundance of heat shock proteins (Hsps) and redox enzymes (REs)) in blubber of wild female grey seals during the lactation fast (n = 17) and summer foraging (n = 13). Transcript abundance of Hsc70 increased, and Nox4, a pro-oxidant enzyme, decreased throughout lactation. Foraging females had higher mRNA abundance of some Hsps and lower RE transcript abundance and MDA concentrations, suggesting they experienced lower oxidative stress than lactating mothers, which diverted resources into pup rearing at the expense of blubber tissue damage. Lactation duration and maternal mass loss rate were both positively related to pup weaning mass. Pups whose mothers had higher blubber glutathione-S-transferase (GST) expression at early lactation gained mass more slowly. Higher glutathione peroxidase (GPx) and lower catalase (CAT) were associated with longer lactation but reduced maternal transfer efficiency and lower pup weaning mass. Cellular stress, and the ability to mount effective cellular defences, could proscribe lactation strategy in grey seal mothers and thus affect pup survival probability. These data support the life-history-oxidative stress hypothesis in a capital breeding mammal and suggest lactation is a period of heightened vulnerability to environmental factors that exacerbate cellular stress. Fitness consequences of stress may thus be accentuated during periods of rapid environmental change. Publisher PDF

Funding: W.B.X., S.A.B., J.M.C., R.v.K., and D.M. were supported by the German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, funded by the German Research Foundation (DFG FZT-118, 20254881); B.J.M. was supported by NSF EPSCOR Track II 201947 and USDA Hatch grant (MAFES #1011538); N.J.G was supported by NSF EPSCOR Track II 201947; I.S.M. was supported by the European Union’s Horizon 2020 research and innovation program under Marie Sklodowska -Curie grant (no. 894644); H.S. was supported by Japan Society for the Promotion of Science (JP19K21569 and JP21H03402); A.E.M. and M.D. were supported by Leverhulme Trust (RPG-2019-402). A.F.E acknowledges the Fisheries Society of the British Isles Studentship. BioTIME used here was supported by ERC AdG 250189 and PoC 727440 (to A.E.M.), and Leverhulme Trust Research Centre–the Leverhulme Centre for Anthropocene Biodiversity (to M.D.). While human activities are known to elicit rapid turnover in species composition through time, the properties of the species that increase or decrease their spatial occupancy underlying this turnover are less clear. Here, we used an extensive dataset of 238 metacommunity time series of multiple taxa spread across the globe to evaluate whether species that are more widespread (large-ranged species) differed in how they changed their site occupancy over the 10–90 years the metacommunities were monitored relative to species that are more narrowly distributed (small-ranged species). We found that on average, large-ranged species tended to increase in occupancy through time, whereas small-ranged species tended to decrease. These relationships were stronger in marine than in terrestrial and freshwater realms. However, in terrestrial regions, the directional changes in occupancy were less extreme in protected areas. Our findings provide evidence for systematic decreases in occupancy of small-ranged species, and that habitat protection could mitigate these losses in the face of environmental change. Publisher PDF

Lipids may serve as energy reserves to support coral calcification, allow acclimation to higher temperatures, and are implicated in the control of CaCO3 precipitation. Here, we report the lipid composition of the soft tissues (including host and symbionts) of 7 massive Porites spp. coral colonies (4 × P. lutea and 3 × P. murrayensis), which were cultured under different pCO2 concentrations (180, 260, 400 and 750 µatm) and at two temperatures (25 ℃ and 28 ℃), below the thermal stress threshold. We report the fatty acid methyl esters (FAME), free fatty acid (FFA) to total fatty acid content, sterol and wax ester profiles, and identify two ketones (n-alkanone) and three long chain aldehyde (n-alkanal) derivatives. Increasing seawater temperature significantly increases the contributions of FFAs to the total lipids, of C18:2 and C20:0 to the total FFA pool, of C14:0 to total FAME, and of campesterol to total sterol. The temperature increase also reduces the contributions of unusual fatty acid derivatives to total lipids, of C14:0, C15:0, C16:0 and C17:0 saturated free fatty acids to total FFAs, and of C16:0 FA to total FAME. Fatty acids are implicated in the control of membrane structure fluidity and the observed changes may promote acclimation and thermostability as temperature varies. Seawater pCO2 has no significant effect on the composition of tissue lipids with the exception that the contribution of C14:0 FA to total lipid content is significantly lower at 180 µatm compared to 260 and 750 µatm. Decreased contribution of total sterols and unusual fatty acid derivatives and increased contribution of total FFAs to total lipids are observed in the fastest calcifying coral (a P. lutea specimen) compared to the other corals, under all pCO2 and temperature conditions. Although a rapid calcifier this genotype has been shown previously to exhibit pronounced abnormal changes in skeletal morphology in response to decreased seawater pCO2. Variations in tissue lipid composition between coral genotypes may influence their resilience to future climate change.

The Tonian–Cambrian Dalradian Supergroup in Scotland is a siliciclastic–carbonate succession that can be up to 10 km thick. The consensus view is that its lower part, the mid- to late Tonian Grampian and Appin groups, formed in rift basins: the deep marine turbidites of the Grampian Group infilled rift depocentres, whereas the shallow marine strata of the Appin Group mark basin-bounding palaeohighs. This scenario is used as a key line of evidence to infer the onset of the break-up of Rodinia between Laurentia and Baltica. However, deformation during the mid-Ordovician Caledonian Orogeny obscured the original depositional frameworks. Reconstructing these frameworks (and hypothesized rift basins) has relied on the trace and major element log-ratio geochemistry of minor carbonate rocks to assign the units to either the Grampian or Appin group – that is, to rift depocentres or basin-bounding palaeohighs, respectively. We report new carbon and oxygen isotope and geochemical data and use these to create a revised stratigraphic framework for the Grampian and Appin groups. Our findings show that the previous geochemical-based correlations are unreliable and that there is no evidence for palaeohighs or rift basins. Instead, the Grampian–Appin groups are a deeper marine flysch to a shallower marine molasse succession formed in response to the mid-Tonian Knoydartian Orogeny. From a Scottish perspective, evidence for the break-up of Rodinia is recorded higher in the Dalradian succession during the deposition of the early Cryogenian Argyll Group. Supplementary material: Geochemical analysis of samples is available at https://doi.org/10.6084/m9.figshare.c.6317830 Thematic collection: This article is part of the Caledonian Wilson cycle collection available at: https://www.lyellcollection.org/topic/collections/the-caledonian-wilson-cycle

Funding: M.L. is grateful to the Wildlife Conservation Network and the Disney Conservation Fund for funding. Conservation biology is a mission-driven discipline that must navigate a new relationship between conservation and science. Because conservation is a social and political as well as an ecological project, conservation biologists must practice interdisciplinarity and collaboration. In a comparative study of 7 cases (Jaguars in the Chaco, Grevy's zebra in Kenya, Beekeeping in Tanzania, Andean cats in Argentina, Jaguars in Mexico, Lobster fishing, and Black bears in Mexico), we examined motivations for collaboration in conservation, who can collaborate in conservation, and how conservation professionals can work well together. In 5 case studies, successful conservation outcomes were prioritized over livelihood benefits. In the other 2 cases, livelihoods were prioritized. All case studies employed participatory approaches. There were multiple external actors, including local and Indigenous communities, nongovernmental organizations, agencies, regional and national governments, and international organizations, which enhanced conservation and wider sustainability outcomes. Key collaboration aspects considered across the case studies were time (mismatch between relationship building and project schedules), trust required for meaningful partnerships, tools employed, and transformative potential for people, nature, and the discipline of conservation biology. We developed guidelines for successful collaboration, including long-term commitment, knowledge integration, multiscalar and plural approaches, cultivation of trust, appropriate engagement, evaluation, supporting students, and efforts for transformation. Publisher PDF

Funding: We thank LOPS and UBO for a M.Sc internship grant which allowed the first author to carry out this work. The merger of two surface quasi-geostrophic vortices is examined in detail. As the two vortices collapse towards each other in the merging process, they trap their external fronts between them; these fronts are inserted into the final merged vortex, where they form a central, nearly parallel, sheared velocity strip, sensitive to barotropic instability. As a result, this strip breaks up into an alley of small vortices. Subsequently, these small vortices may undergo merger and grow in size in the core of the large merged vortex. The number of small trapped vortices decreases correspondingly. Finally, a single or two small vortices remain. These processes are analysed using a numerical model of the surface quasi-geostrophic equations. The sensitivity of this process to the initial vortex characteristics is explored. A parallel is drawn between this problem and the instability of a rectilinear strip of temperature with a central gap. The application of this problem to the Ocean is discussed. Publisher PDF

Funding: This work was supported by the United Kingdom Research and Innovation (UKRI), Global Challenges Research Fund (GCRF), One Ocean Hub (Grant Ref: NE/S008950/1). The blue economy has roots in the international arena of sustainable development and sets out to unlock opportunities for economy and society whilst protecting and enhancing marine environments. To date there has been no analysis of how this overarching intention for sustainability has influenced the rapid development of blue economy policies at national and regional scales. In this article, we analyse the synergies and conflicts between blue economy policies from a diversity of national and regional policies and the UN Sustainable Development Goals. We show that to maintain critical alignment with targets for sustainability, place-based contextual development of blue economies that meet the needs of all actors is necessary. These needs relate to ensuring resilience against future environmental and political shocks, the maintenance of the ecological basis for thriving blue economies, and capacity development at all levels to support effective and equitable governance. Results indicate that co-production will be important to achieve sustainable blue economies. Publisher PDF

Funding: Department for Environment, Food and Rural Affairs, UK Government (Grant Number(s): ME6052; Grant recipient(s): Jamie Macaulay, Allen Kingston, Simon Northridge, Alexander Coram). University of St Andrews. 1. Entanglement in net fisheries (static and drift) is the largest known cause of direct anthropogenic mortality to many small cetacean species, including harbour porpoise (Phocoena phocoena), in UK waters. Despite this, little is known about the behaviour of small cetaceans in proximity to nets. 2. We have developed a passive acoustic monitoring (PAM) system for tracking the fine-scale three-dimensional (3D) movements of echolocating cetaceans around actively fishing nets by localising their acoustic clicks. The system consists of two compact four-channel acoustic recorders with sample-synchronised sensor packages that use 3D motion tracking technology to accurately calculate log orientation, depth, water temperature and ambient light level. Two recorders were used in tandem, with each one attached to and floating above the net floatline. The system can be deployed during normal fishing operations by a trained researcher or experienced fisheries observer. Recordings were analysed in PAMGuard software and the 3D positions of echolocating animals in the vicinity of the system were calculated using an acoustic particle filter-based localisation method. 3. We present findings from four deployments in UK waters (each 1–2 days in duration) in which 12 distinct harbour porpoise encounters yielded a sufficient number of detected clicks to track their movements around the net. The tracks show a variety of behaviours, including multiple instances of animals actively foraging in close proximity to the fishing net. 4. We show that a relatively inexpensive PAM system, which is practical to deploy from active fishing vessels, is capable of providing highly detailed data on harbour porpoise behaviour around nets. As harbour porpoises are the one of the most difficult species to localise, this methodology is likely to be suitable for elucidating the behaviour of many other toothed whale species in a variety of situations. Publisher PDF

Funding from the ECHO Program of the Vancouver Fraser Port Authority. Long-term passive acoustic monitoring of cetaceans is frequently limited by the data storage capacity and battery life of the recording system. Duty cycles are a mechanism for subsampling during the recording process that facilitates long-term passive acoustic studies. While duty cycles are often used, there has been little investigation on the impact that this approach has on the ability to answer questions about a species' behavior and occurrence. In this study, the effects of duty cycling on the acoustic detection of southern resident killer whales (SRKW) (Orcinus orca) were investigated. Continuous acoustic data were subsampled to create 288 subsampled datasets with cycle lengths from 5 to 180 min and listening proportions from 1% to 67%. Duty cycles had little effect on the detection of the daily presence of SRKW, especially when using cycle lengths of less than an hour. However, cycle lengths of 15–30 min and listening proportions of at least 33% were required to accurately calculate durations of acoustic bouts and identify those bouts to ecotype. These results show that the optimal duty cycle depends on the scale of the research question and provide a framework for quantitative analysis of duty cycles for other marine species. Publisher PDF

This work resulted from the ARISE project (NE/P006035/1, NE/P006000/1), part of the Changing Arctic Ocean programme, jointly funded by the UKRI Natural Environment Research Council (NERC). We thank Jim Ball for his help in the isotopic lab in Liverpool University. This work resulted from the ARISE project, part of the Changing Arctic Ocean programme. Multiple environmental forcings, such as warming and changes in ocean circulation and nutrient supply, are affecting the base of Arctic marine ecosystems, with cascading effects on the entire food web through bottom-up control. Stable nitrogen isotopes (δ15N) can be used to detect and unravel the impact of these forcings on this unique ecosystem, if the many processes that affect the δ15N values are constrained. Combining unique 60-year records from compound specific δ15N biomarkers on harp seal teeth alongside state-of-the-art ocean modelling, we observed a significant decline in the δ15N values at the base of the Barents Sea food web from 1951 to 2012. This strong and persistent decadal trend emerges due to the combination of anthropogenic atmospheric nitrogen deposition in the Atlantic, increased northward transport of Atlantic water through Arctic gateways and local feedbacks from increasing Arctic primary production. Our results suggest that the Arctic ecosystem has been responding to anthropogenically induced local and remote drivers, linked to changing ocean biology, chemistry and physics, for at least 60 years. Accounting for these trends in δ15N values at the base of the food web is essential to accurately detect ecosystem restructuring in this rapidly changing environment. Publisher PDF

This work was supported by Marine Scotland – Scottish Government through the Scottish Blue Carbon Forum. The saltmarsh carbon storage potential is a key topic in blue carbon research and climate policy. Ecosystem service valuations provide valuable information to policymakers for habitat management and climate change mitigation policies. Yet, only few saltmarsh valuation studies have included the carbon storage service in the UK context. This paper investigates how the public values saltmarsh ecosystem services, focussing on the carbon storage service. We used a choice experiment to elicit the willingness to pay (WTP) of a representative sample of the Scottish public to support interventions that would maintain or improve the provision of these services. Furthermore, we tested the effect of information on individuals' preferences and WTP with a split sample approach where one group received a treatment in the form of additional information. We found that (i) all attributes had a significant influence on individuals' choices; (ii) both groups had, on average, a positive marginal WTP for all presented ecosystem services; (iii) the treated sample had, on average, no significantly different marginal WTP for carbon storage than the control group. This paper adds to the limited literature on the saltmarsh carbon storage ecosystem service and demonstrates a developed nation's public's openness to nature-based climate change mitigation solutions. Publisher PDF

This work was supported by the Biotechnology and Biological Sciences Research Council (BBSRC), linked projects, references BB/S016856/1 and BB/S020640/1. Wnt signaling is essential during animal development and regeneration, but also plays an important role in diseases such as cancer and diabetes. The canonical Wnt signaling pathway is one of the most conserved signaling cascades in the animal kingdom, with the T-cell factor/lymphoid enhancer factor (TCF/LEF) proteins the major mediators of Wnt/β-catenin-regulated gene expression. In comparison to invertebrates, vertebrates possess a high diversity of TCF/LEF family genes, implicating this as a possible key change to Wnt signaling at the evolutionary origin of vertebrates. However, the precise nature of this diversification is only poorly understood. The aim of this study is to clarify orthology, paralogy and isoform relationships within the TCF/LEF gene family within chordates via in silico comparative study of TCF/LEF gene structure, molecular phylogeny and gene synteny. Our results support the notion that the four TCF/LEF paralog subfamilies in jawed vertebrates (gnathostomes) evolved via the two rounds of whole-genome duplication that occurred during early vertebrate evolution. Importantly, gene structure comparisons and synteny analysis of jawless vertebrate (cyclostome) TCFs suggest that a TCF7L2-like form of gene structure is a close proxy for the ancestral vertebrate structure. In conclusion, we propose a detailed evolutionary path based on a new pre-whole-genome duplication vertebrate TCF gene model. This ancestor gene model highlights the chordate and vertebrate innovations of TCF/LEF gene structure, providing the foundation for understanding the role of Wnt/β-catenin signaling in vertebrate evolution. Publisher PDF

Tiago Marques and Carolina Marques thank partial support by CEAUL (funded by FCT through the project UIDB/00006/2020). Aims The present study is the first attempt to grasp the scale and richness of marine biological invasions in Macaronesia. We pioneered a comprehensive non-native species (NNS), inventory in the region to determine their diversity patterns and native distribution origins. NNS were defined here as the result of both introductions and range expansions. We also used statistical modelling to examine relationships among NNS richness, anthropogenic activities, demographic and geographical variables across Macaronesia. Location Macaronesia. Methods A comprehensive literature search was conducted for marine NNS records in Macaronesia, registering the first record's location and year from 1884 to 2020. We used univariate and multivariate analyses to evaluate differences and similarities in community composition. By applying a Generalized Linear Model (GLM), we tested hypotheses regarding NNS richness as a function of anthropogenic activities, demographic and geographical variables. Results A total of 144 marine non-native species (NNS) were recorded for the whole of Macaronesia. The highest NNS richness was registered in the Canary Islands (76 NNS), followed by the Azores (66 NNS), Madeira (59 NNS) and finally Cabo Verde (18 NNS). Some differences amongst archipelagos were observed, such as the high number of non-native macroalgae in the Azores, fishes in the Canary Islands and tunicates in Cabo Verde. Overall, macroalgae, tunicates and bryozoans were the predominant taxonomic groups in the Macaronesian archipelagos. Madeira and Canary Islands were the archipelagos with more similarity in marine NNS, and Cabo Verde the most divergent. Finally, GLM suggested that non-native richness patterns across Macaronesia were dependent on the considered archipelago and strongly affected by (1) minimum distance to the mainland, (2) the total number of ports and marinas and (3) total marinas area (km2). Conclusions The model results and NNS listing in the present study will likely raise the awareness and response regarding marine NNS in the whole Macaronesia region, serving as a baseline for future research as well as implementing and enforcing regulations related to the introduction of marine NNS in oceanic islands. Publisher PDF

This work was supported by grants within the Biodiversity and Ecosystem Services Sustainability (BESS) programme. BESS was a 6-year programme (2011–2017) funded by the UK Natural Environment Research Council (NERC) and the Biotechnology and Biological Sciences Research Council (BBSRC) as part of the UK's Living with Environmental Change (LWEC) programme. Laurence Jones was supported by NERC grant ‘Location, Configuration, Distribution: the Role of Landscape Pattern and Diversity in Ecosystem Services' (NE/K015508/1). Other authors were supported by the following projects and grants: Fragments, Functions and Flows in Urban Ecosystem Services (F3UES) Project (NE/J015067/1), The DURESS project – Diversity of Upland Rivers for Ecosystem Service Sustainability (NE/J014818/1), Coastal Biodiversity and Ecosystem Services Sustainability – CBESS (NE/J015644/1) and Wessex BESS (NE/J014680/1). 1. Cultural ecosystem services (CES), a key aspect of nature's contributions to people, remain a challenge to incorporate into decision making. One contributing factor is the difficulty of defining and describing these, due partly to: ongoing poor understanding of what drives people to interact with nature, a lack of appropriate data to quantify these interactions, and basic difficulties in measuring and modelling the complex array of social, psychological and behavioural attributes which help explain people's actions. 2. In this study we present a framework which develops the concepts of cultural capital, social capital and human capital as specific forms of human-centred capital, in the context of their contribution to understanding CES. Each form of capital encompasses separate attributes of beneficiaries. 3. Testing the framework with data from a separate trans-disciplinary study illustrated that the framework was readily applicable to specific situations. A measure of cultural capital, EcoCentrism, explained more variation than a suite of seven demographic variables. 4. Applying the framework also showed that despite using a wide range of explanatory variables, a large proportion of observed variation remained unaccounted for. This suggests that more work is needed to understand and to develop metrics which can measure additional factors which underlie peoples? motivations to engage with nature. The framework is applicable to other types of ecosystem service, and may also be useful for exploring relational values. Publisher PDF

We thank the A.P. Leventis Conservation Foundation for supporting this work. One possible hypothesis for the function of post-fledging dispersal is to locate a suitable future breeding area. This post-fledging period may be particularly important in migratory species because they have a limited period to gather information prior to autumn migration, and in protandrous species, males must quickly acquire a territory after returning from spring migration to maximize their fitness. Here we use color-ring resightings to investigate how the post-fledging dispersal movements of the Cyprus wheatear Oenanthe cypriaca, a small migratory passerine, relate to their first breeding territory the following year when they return from migration. We found that males established first breeding territories that were significantly closer to their post-fledging location than to their natal sites or to post-fledging locations of other conspecifics, but these patterns were not apparent in females. Our findings suggest that familiarity with potential breeding sites may be important for juveniles of migratory species, particularly for the sex that acquires and advertises breeding territories. Exploratory dispersal prior to a migrant’s first autumn migration may contribute toward its breeding success the following year, further highlighting the importance of early seasonal breeding on fitness and population dynamics more generally. Publisher PDF

Pine Island Ice Shelf (PIIS) buttresses the Pine Island Glacier, the key contributor to sea-level rise. PIIS has thinned owing to ocean-driven melting, and its calving front has retreated, leading to buttressing loss. PIIS melting depends primarily on the thermocline variability in its front. Furthermore, local ocean circulation shifts adjust heat transport within Pine Island Bay (PIB), yet oceanic processes underlying the ice front retreat remain unclear. Here, we report a PIB double-gyre that moves with the PIIS calving front and hypothesise that it controls ocean heat input towards PIIS. Glacial melt generates cyclonic and anticyclonic gyres near and off PIIS, and meltwater outflows converge into the anticyclonic gyre with a deep-convex-downward thermocline. The double-gyre migrated eastward as the calving front retreated, placing the anticyclonic gyre over a shallow seafloor ridge, reducing the ocean heat input towards PIIS. Reconfigurations of meltwater-driven gyres associated with moving ice boundaries might be crucial in modulating ocean heat delivery to glacial ice., Glacial melt can modify heat transport, and therefore ocean processes, associated with ice front retreat, as revealed by direct observations from the Pine Island Bay region of Antarctica.

Funding: A.E.M. thanks the Leverhulme Trust (RPG-2019–402) for support. Recent research has uncovered rapid compositional and structural reorganization of ecological assemblages, with these changes particularly evident in marine ecosystems. However, the extent to which these ongoing changes in taxonomic diversity are a proxy for change in functional diversity is not well understood. Here we focus on trends in rarity to ask how taxonomic rarity and functional rarity covary over time. Our analysis, drawing on 30 years of scientific trawl data, reveals that the direction of temporal shifts in taxonomic rarity in two Scottish marine ecosystems is consistent with a null model of change in assemblage size (i.e. change in numbers of species and/or individuals). In both cases, however, functional rarity increases, as assemblages become larger, rather than showing the expected decrease. These results underline the importance of measuring both taxonomic and functional dimensions of diversity when assessing and interpreting biodiversity change. Publisher PDF

These files contain code and data used in this study., This work was funded by Leverhulme Trust grant RPG-2019-402, 'Darwin, Wallace, Bates and biodiversity change in the Anthropocene', awarded to Anne Magurran and Maria Dornelas, {"references":["Blowes, S. A., Supp, S. R., Antão, L. H., Bates, A., Bruelheide, H., Chase, J. M., … Dornelas, M. (2019). The geography of biodiversity change in marine and terrestrial assemblages. Science, 366(6463), 339–345. https://doi.org/10.1126/science.aaw1620","USGS Patuxent Wildlife Research Center (2014) North American Breeding Bird Survey ftp data set, version 2014.0. US Breeding Birds Survey. Available at: https://www.pwrc.usgs.gov/BBS/RawData/ (Accessed:2013).","DATRAS (2010) Fish trawl survey: ICES North Sea International Bottom Trawl Survey for commercial fish species. ICES Database of trawl surveys (DATRAS). The International Council for the Exploration of the Sea, Copenhagen. Available at: http://www.emodnet-biology.eu/data-catalog?%3Fmodule=dataset&dasid=2763, accessed 2013."]}

Funding: Office of Naval Research (Grant Number(s): N000142012697, N000142112096); Strategic Environmental Research and Development Program (Grant Number(s): RC20-1097, RC20-7188, RC21-3091). Quantifying the cumulative effects of stressors on individuals and populations can inform the development of effective management and conservation strategies. We developed a Bayesian state–space model to assess the effects of multiple stressors on individual survival and reproduction. In the model, stressor effects on vital rates are mediated by changes in underlying health, allowing for the comparison of effect sizes while accounting for intrinsic factors that might affect an individual's vulnerability and resilience. We applied the model to a 50-year dataset of sightings, calving events and stressor exposure of critically endangered North Atlantic right whales Eubalaena glacialis. The viability of this population is threatened by a complex set of stressors, including vessel strikes, entanglement in fishing gear and fluctuating prey availability. We estimated that blunt and deep vessel strike injuries and severe entanglement injuries had the largest effect on the health of exposed individuals, reinforcing the urgent need for mitigation measures. Prey abundance had a smaller but protracted effect on health across individuals, and estimated long-term trends in survival and reproduction followed the trend of the prey index, highlighting that long-term ecosystem-based management strategies are also required. Our approach can be applied to quantify the effects of multiple stressors on any long-lived species where suitable indicators of health and long-term monitoring data are available. Publisher PDF

This work was supported by the Office of Naval Research Marine Mammal Biology Program [grant number N00014-17-1-2868]. Timely detection and understanding of causes for population decline are essential for effective wildlife management and conservation. Assessing trends in population size has been the standard approach but we propose that monitoring population health could prove more effective. We collated data from seven bottlenose dolphin (Tursiops truncatus) populations in southeastern U.S. to develop the Veterinary Expert System for Outcome Prediction (VESOP), which estimates survival probability using a suite of health measures identified by experts as indices for inflammatory, metabolic, pulmonary, and neuroendocrine systems. VESOP was implemented using logistic regression within a Bayesian analysis framework, and parameters were fit using records from five of the sites that had a robust stranding network and frequent photographic identification (photo-ID) surveys to document definitive survival outcomes. We also conducted capture-mark-recapture (CMR) analyses of photo-ID data to obtain separate estimates of population survival rates for comparison with VESOP survival estimates. VESOP analyses found multiple measures of health, particularly markers of inflammation, were predictive of 1- and 2-year individual survival. The highest mortality risk one year following health assessment related to low alkaline phosphatase, with an odds ratio of 10.2 (95% CI 3.41-26.8), while 2-year mortality was most influenced by elevated globulin (9.60; 95% CI 3.88-22.4); both are markers of inflammation. The VESOP model predicted population-level survival rates that correlated with estimated survival rates from CMR analyses for the same populations (1-year Pearson's r = 0.99; p = 1.52e-05, 2-year r = 0.94; p = 0.001). While our proposed approach will not detect acute mortality threats that are largely independent of animal health, such as harmful algal blooms, it is applicable for detecting chronic health conditions that increase mortality risk. Random sampling of the population is important and advancement in remote sampling methods could facilitate more random selection of subjects, obtainment of larger sample sizes, and extension of the approach to other wildlife species. Publisher PDF

Funding: TAM’s time for this review was covered under the ACCURATE project, funded by the US Navy Living Marine Resources program (contract no. N3943019C2176), and he also thanks partial support by CEAUL (funded by FCT—Fundação para a Ciência e a Tecnologia, Portugal, through the project UIDB/00006/2020). Advances in technology are having a large effect on the priorities for innovation in statistical ecology. Collaborations between statisticians and ecologists have always been important in driving methodological development, but increasingly, expertise from computer scientists and engineers is also needed. We discuss changes that are occurring and that may occur in the future in surveys for estimating animal abundance. As technology advances, we expect classical distance sampling and capture-recapture to decrease in importance, as camera (still and video) survey, acoustic survey, spatial capture-recapture and genetic methods continue to develop and find new applications. We explore how these changes are impacting the work of the statistical ecologist. Publisher PDF

Funding: This work is from the MELT project, a component of the International Thwaites Glacier Collaboration (ITGC). Support from the National Science Foundation (NSF, grant no. 1739003) and the Natural Environment Research Council (NERC, grant no. NE/S006656/1). Logistics provided by NSF U.S. Antarctic Program and NERC British Antarctic Survey. The ship-based CTD data were supported by the ITGC TARSAN project (NERC grant nos. NE/S006419/1 and NE/S006591/1; NSF grant no. 1929991). ITGC contribution no. ITGC 047. Thwaites Glacier is one of the fastest-changing ice–ocean systems in Antarctica1,2,3. Much of the ice sheet within the catchment of Thwaites Glacier is grounded below sea level on bedrock that deepens inland4, making it susceptible to rapid and irreversible ice loss that could raise the global sea level by more than half a metre2,3,5. The rate and extent of ice loss, and whether it proceeds irreversibly, are set by the ocean conditions and basal melting within the grounding-zone region where Thwaites Glacier first goes afloat3,6, both of which are largely unknown. Here we show—using observations from a hot-water-drilled access hole—that the grounding zone of Thwaites Eastern Ice Shelf (TEIS) is characterized by a warm and highly stable water column with temperatures substantially higher than the in situ freezing point. Despite these warm conditions, low current speeds and strong density stratification in the ice–ocean boundary layer actively restrict the vertical mixing of heat towards the ice base7,8, resulting in strongly suppressed basal melting. Our results demonstrate that the canonical model of ice-shelf basal melting used to generate sea-level projections cannot reproduce observed melt rates beneath this critically important glacier, and that rapid and possibly unstable grounding-line retreat may be associated with relatively modest basal melt rates. Publisher PDF

Funding: This research is part of project NGANDU (The Importance of Shark Populations and Sustainable Ocean Use for Human Well-being in Cabo Verde and São Tomé and Príncipe, West Africa) funded by the Portuguese Foundation for Science and Technology (FCT) and the Aga Khan Development Network (AKDN) under grant agreement FCT AGA-KHAN/541746579/2019. All authors acknowledge funding from FCT under the strategic project UIDB/04292/2020 granted to MARE and project LA/P/0069/2020 granted to the Associate Laboratory ARNET. TM acknowledges funding from the strategic project UIDB/00006/2020 granted to CEAUL. CF acknowledges funding from FCT research contract 2020.03704.CEECIND and FCT grant agreement PTDC/CTA-AMB/30226/2017. VP acknowledges funding from FCT PhD grant 2020.05435.BD. CS acknowledges funding from FCT PhD grant SFRH/BD/117890/2016, FCT research grants under PTDC/CTA-AMB/30226/2017 through FCiencias.ID and AGA-KHAN/541746579/2019 through Nova School of Business and Economics. EN acknowledges funding from FCT PhD grant SFRH/BD/135438/2017. JRP acknowledges funding from FCT research contract 2021.01030.CEECIND. JV acknowledges funding from the Intergovernmental Panel on Climate Change (PhD grant, IPCC Scholarship Programme–Prince Albert II of Monaco Foundation) and the Camões–Instituto da Cooperação e da Língua, I.P. (Scholarship Programme). This study describes the first potential multi-species shark nursery area in Atlantic Africa (Sal Rei Bay – SRB, Boa Vista Island, Cabo Verde). From August 2016 to September 2019, 6162 neonates and juveniles of 5 different shark species were observed in SRB using beach gillnet-based bycatch surveys, namely milk (Rhizoprionodon acutus; n= 4908), scalloped hammerhead (Sphyrna lewini; n= 1035), blacktip (Carcharhinus limbatus; n=115), Atlantic weasel (Paragaleus pectoralis; n= 93) and nurse (Ginglymostoma cirratum; n= 12) sharks. Except for nurse sharks, significant seasonal variations in shark relative abundance were observed, with higher levels being recorded during summer and autumn. These findings, together with local knowledge (interviews to fishermen), denote the consistent use of SRB by juvenile sharks and its preference relative to other areas in the region. Ensuring the protection and conservation of SRB nursery area is especially relevant as, according to IUCN, all identified shark species are threatened with extinction over the near-future – in particular, scalloped hammerheads (critically endangered) and Atlantic weasel sharks (endangered). The effective protection of SRB will not only support the conservation of shark populations, but also of other charismatic fauna (e.g., loggerhead turtles) and broader benthic and pelagic ecosystems. Publisher PDF

Funding: This study was partly funded by a Scottish Government Rural and Environment Science and Analytical Service award (PM, JW and TSG). The Scottish Northern Cairngorms reconstruction was finalised through the project NERC project ‘SCOT2K: Reconstructing 2000 years of Scottish climate from tree rings (NE/ K003097/1)’ while the new central and northwest Scottish data were developed as part of a NERC Iapetus PhD project. For ancient types of barley at sites in the Scottish Isles, Faroes, and Iceland, we calculated minimum temperature requirements for grain production (grain production threshold, GPT) as accumulated degree days over the cropping season. Site suitability for barley from AD 1200 to 2000 was investigated by comparing these thresholds with reconstructions of annual cropping season degree days (CSDD) using temperature and tree-ring data. In Iceland, between AD 1200 and 1500, reconstructed CSDD were more favorable in the southwest (Reykjavik), with fewer years below the GPT, than in the North, East and West, but there were two periods (1340–1389 and 1426–1475) with low average CSDD and several years below the GPT which possibly influenced the abandonment of barley cultivation around this time. Reconstructed CSDD for the Faroes (Tórshavn) had only one year below the GPT, but 15 periods of four or more consecutive years with low CSDD which would have challenged barley cultivation, especially in the thirteenth century. Reconstructed CSDD were highest for the Scottish Isles, allowing a more prominent role of barley in the farming system and economy. Nevertheless, years with poor harvests or famines were common and about half were associated with low CSDD, resulting in a significant temperature link but also demonstrating the important contribution of other factors. Despite frequent unfavorable years in both the Faroes and Scottish Isles, resilient production systems, well-adapted barley strains and socio-economic factors allowed barley cultivation to continue, and some ancient types to survive to the present day. Publisher PDF

Funding: Engineering and Physical Sciences Research Council - EP/T025301/1. We present a family of exact inviscid three-dimensional Beltrami flows in a horizontally periodic domain lying between two parallel free-slip boundaries. Significantly, these flows are not stress free: the horizontal vorticity varies on each boundary. Using direct numerical simulations (employing horizontal hyperdiffusion only for numerical stability), we find that the largest-scale member of the family is unstable and breaks down into anisotropic turbulence, with relatively large horizontal vorticity at and near each boundary, and associated surface frontal features. We conjecture that all members of the family are similarly unstable. The free-slip boundaries play an important role in the late stages of the instability by constraining the deformation of vortex lines near the boundaries. This study appears to be the first to consider the role of boundary horizontal vorticity in an inviscid context. Publisher PDF

The pooling robustness property of distance sampling results in unbiased abundance estimation even when sources of variation in detection probability are not modeled. However, this property cannot be relied upon to produce unbiased subpopulation abundance estimates when using a single pooled detection function that ignores subpopulations. We investigate by simulation the effect of differences in subpopulation detectability upon bias in subpopulation abundance estimates. We contrast subpopulation abundance estimates using a pooled detection function with estimates derived using a detection function model employing a subpopulation covariate. Using point transect survey data from a multispecies songbird study, species-specific abundance estimates are compared using pooled detection functions with and without a small number of adjustment terms, and a detection function with species as a covariate. With simulation, we demonstrate the bias of subpopulation abundance estimates when a pooled detection function is employed. The magnitude of the bias is positively related to the magnitude of disparity between the subpopulation detection functions. However, the abundance estimate for the entire population remains unbiased except when there is extreme heterogeneity in detection functions. Inclusion of a detection function model with a subpopulation covariate essentially removes the bias of the subpopulation abundance estimates. The analysis of the songbird point count surveys shows some bias in species-specific abundance estimates when a pooled detection function is used. Pooling robustness is a unique property of distance sampling, producing unbiased abundance estimates at the level of the study area even in the presence of large differences in detectability between subpopulations. In situations where subpopulation abundance estimates are required for data-poor subpopulations and where the subpopulations can be identified, we recommend the use of subpopulation as a covariate to reduce bias induced in subpopulation abundance estimates. Publisher PDF

Funding: C.F., U.B. and D.J.R. acknowledge COST Action ‘European Soil-Biology Data Warehouse for Soil Protection’ (EUdaphobase), CA18237, supported by COST (European Cooperation in Science and Technology). AEM thanks the Leverhulme Trust (RPG-2019-401). D.B.B. was supported by an NSF Postdoc Research Fellowship in Biology (NSF 000733206), S.M.R. was supported by an NSERC Discovery Grant Author Contributions, A.V.S. was supported by NSF 1755336, C.S.M was supported by NSF 1398620 and N.J.G was supported by NSF 2019470. 1. Dated, geo-referenced museum specimens are a rich data source for reconstructing species' distribution and abundance patterns. However, museum records are potentially biased towards over-representation of rare species, and it is unclear whether museum records can be used to estimate relative abundance in the field. 2. We assembled 17 coupled field and museum datasets to quantitatively compare relative abundance estimates with the Dirichlet distribution. Collectively, these datasets comprise 73,039 museum records and 1,405,316 field observations of 2,240 species. 3. Although museum records of rare species overestimated relative abundance by 1-fold to over 100-fold (median study = 9.0), the relative abundance of species estimated from museum occurrence records was strongly correlated with relative abundance estimated from standardized field surveys (r2 range of 0.10-0.91, median study = 0.43). 4. These analyses provide a justification for estimating species relative abundance with carefully curated museum occurrence records, which may allow for the detection of temporal or spatial shifts in the rank ordering of common and rare species. Publisher PDF

Funding: Research was supported by the Portuguese Science & Technology Foundation (FCT), the Azorean Science & Technology Fund (FRCT), and the EU through research projects WATCH IT-Acores-01-0145-FEDER-000057, FCT-IF/00943/2013/CP1199/CT0001, META-FA_06_2017_017, and SUMMER-H2020 GA 817806, co-funded by FEDER, COMPETE, QREN, POPH, ESF, PO AZORES 2020, Portuguese Ministry for Science and Education, and individual contracts/grants to CO (WATCH IT-Acores-01-0145-FEDER-000057, 3/SRMCT/DRAM/2019 under RAGES-SUB/ENV.C.2-GA 110661, and INTERTAGUA-MAC2/1.1a/385), SPJ (SUMMER-H2020 GA 817806), IC (FCT-IP Project UIDP/05634/2020). PJW is funded by RANNÍS Icelandic Research Fund grant 207081. RP and MAS are co-financed by AZORES2020, through the EU Fund 01-0145-FEDER-000140 “MarAZ Researchers: Consolidate a body of researchers in Marine Sciences in the Azores”. Okeanos is funded by FCT (UIDB/05634/2020) and by the Regional Government of the Azores through the initiative to support the Research Centers of the University of the Azores (M1.1.A/REEQ.CIENTÍFICO UI&D/2021/010). Background High-resolution sound and movement recording tags offer unprecedented insights into the fine-scale foraging behaviour of cetaceans, especially echolocating odontocetes, enabling the estimation of a series of foraging metrics. However, these tags are expensive, making them inaccessible to most researchers. Time-Depth Recorders (TDRs), which have been widely used to study diving and foraging behaviour of marine mammals, offer a more affordable alternative. Unfortunately, data collected by TDRs are bi-dimensional (time and depth only), so quantifying foraging effort from those data is challenging. Methods A predictive model of the foraging effort of sperm whales (Physeter macrocephalus) was developed to identify prey capture attempts (PCAs) from time-depth data. Data from high-resolution acoustic and movement recording tags deployed on 12 sperm whales were downsampled to 1 Hz to match the typical TDR sampling resolution and used to predict the number of buzzes (i.e., rapid series of echolocation clicks indicative of PCAs). Generalized linear mixed models were built for dive segments of different durations (30, 60, 180 and 300 s) using multiple dive metrics as potential predictors of PCAs. Results Average depth, variance of depth and variance of vertical velocity were the best predictors of the number of buzzes. Sensitivity analysis showed that models with segments of 180 s had the best overall predictive performance, with a good area under the curve value (0.78 ± 0.05), high sensitivity (0.93 ± 0.06) and high specificity (0.64 ± 0.14). Models using 180 s segments had a small difference between observed and predicted number of buzzes per dive, with a median of 4 buzzes, representing a difference in predicted buzzes of 30%. Conclusions These results demonstrate that it is possible to obtain a fine-scale, accurate index of sperm whale PCAs from time-depth data alone. This work helps leveraging the potential of time-depth data for studying the foraging ecology of sperm whales and the possibility of applying this approach to a wide range of echolocating cetaceans. The development of accurate foraging indices from low-cost, easily accessible TDR data would contribute to democratize this type of research, promote long-term studies of various species in several locations, and enable analyses of historical datasets to investigate changes in cetacean foraging activity. Publisher PDF

Funding: Samples NJH-16-39 and NJH-16-41 were collected during fieldwork associated with the HiTech AlkCarb project, which was supported by the European Union’s Horizon 2020 research and innovation programme under grant agreement No. 689909. NJH gratefully acknowledges PhD funding from the NERC SoS RARE consortium NE/M010856/1 and the University of St Andrews. The luminescence spectroscopy facility used in the present study was funded by NERC grant NE/H002715/1. EPMA data were collected at the University of Edinburgh, UK, with the assistance of Dr Chris Hayward. For the purpose of open access, the authors have applied a CC BY public copyright licence to any Accepted Author Manuscript version arising. Fluorite is one of the most common minerals in the crust and is of widespread economic importance. It shows strong UV-excited luminescence, variously attributed to defects within the fluorite structure and lanthanide substitutions. We present here a detailed chemical characterisation of a suite of natural fluorite samples, chosen to represent the range of compositions observed in nature. We perform X-ray excited luminescence spectroscopy on the samples as a function of temperature (20–673 K) in the wavelength range 250–800 nm to provide insights into physical defects in the lattice and their interactions with lanthanide substituents in natural fluorite. Most broad bands in the UV are attributed to electronic defects in the fluorite lattice, whereas sharp emissions are attributed to intra-ion energy cascades in trivalent lanthanides. Lanthanides are accommodated in fluorite by substitution for Ca2+ coupled with interstitial F−, O2− (substituting for F−) and a variety of electronic defect structures which provide local charge balance. The chondrite-normalised lanthanide profiles show that fluorite accommodates a greater proportion of heavy lanthanides (and Y) as the total Rare Earth Element (REE) concentration increases; whereas cell parameters decrease and then increase as substitution continues. Luminescence intensity also goes through a maximum and then decreases as a function of REE concentration. All three datasets are consistent with a model whereby lanthanides initially act as isolated centres, but, beyond a critical threshold (~ 1000 ppm), cluster into lanthanide-rich domains. Clustering results in shorter REE-O bond distances (favouring smaller heavier ions), a larger unit cell but more efficient energy transfer between lanthanides, thereby promoting non-radiative energy loss and a drop in the intensity of lanthanide emission. Publisher PDF

Funding: This study was funded by Moray Offshore Wind Farm (East) Ltd. Mitigation measures to disperse marine mammals prior to pile-driving include acoustic deterrent devices and piling soft starts, but their efficacy remains uncertain. We developed a self-contained portable hydrophone cluster to detect small cetacean movements from the distributions of bearings to detections. Using an array of clusters within 10 km of foundation pile installations, we tested the hypothesis that harbour porpoises (Phocoena phocoena) respond to mitigation measures at offshore windfarm sites by moving away. During baseline periods, porpoise movements were evenly distributed in all directions. By contrast, animals showed significant directional movement away from sound sources during acoustic deterrent device use and piling soft starts. We demonstrate that porpoises respond to measures aimed to mitigate the most severe impacts of construction at offshore windfarms by swimming directly away from these sound sources. Portable directional hydrophone clusters now provide opportunities to characterize responses to disturbance sources across a broad suite of habitats and contexts. Publisher PDF

Funding: Financial support was provided by Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET, PIP 11220150100066 CO), UNMdP (Project EXA903457/18) and FONCYT (PICT 201-0427). 1. During the last decade, convolutional neural networks (CNNs) have revolutionised the application of deep learning (DL) methods to classification tasks and object recognition. These procedures can capture the key features of image data that are not easily visible to the human eye and use them to classify and predict outcomes with exceptional precision. 2. Here, we show for the first time that CNNs provide highly accurate predictions for small-scale genetic differentiation and diversity in Ctenomys australis, a subterranean rodent from central Argentina. Using microsatellite genotypes and high-resolution satellite imagery, we trained a simple CNN to predict local FST and mean allele richness. To identify landscape features with high impact on predicted values, we applied species distribution models to obtain the distribution of suitable habitat. Subsequent use of a machine learning algorithm (random forest) allowed us to identify the attributes that contribute the most to predictions of population genetic metrics. 3. Predictions obtained from the CNN accounted for more than 98% of the variation observed both in FST and mean allele richness values. Random forest regression on landscape metrics indicated that features involving connectivity and consistent prevalence of suitable habitat promoted genetic diversity and reduced genetic differentiation in C. australis. 4. Validation with synthetic data via simulations of genetic differentiation based on the landscape structure of the study area and of a nearby area showed that DL models are able to capture complex relationships between actual data and synthetic data in the same landscape and between synthetic data generated under different landscapes. 5. Our approach represents an objective and powerful approach to landscape genetics because it can extract information from patterns that are not easily identified by humans. Spatial predictions from the CNN may assist in the identification of areas of interest for biodiversity conservation and management of populations. Postprint