Search

Understanding the frequency, spatiotemporal dynamics and impacts of parasite coinfections is fundamental to developing control measures and predicting disease impacts. The European turtle dove (Streptopelia turtur) is one of Europe’s most threatened bird species. High prevalence of infection by the protozoan parasite Trichomonas gallinae has previously been identified, but the role of this and other coinfecting parasites in turtle dove declines remains unclear. Using a high-throughput sequencing approach, we identified seven strains of T. gallinae, including two novel strains, from ITS1/5.8S/ITS2 ribosomal sequences in turtle doves on breeding and wintering grounds, with further intra-strain variation and four novel sub-types revealed by the iron-hydrogenase gene. High spatiotemporal turnover was observed in T. gallinae strain composition, and infection was prevalent in all populations (89–100%). Coinfection by multiple Trichomonas strains was rarer than expected (1% observed compared to 38.6% expected), suggesting either within-host competition, or high mortality of coinfected individuals. In contrast, coinfection by multiple haemosporidians was common (43%), as was coinfection by haemosporidians and T. gallinae (90%), with positive associations between strains of T. gallinae and Leucocytozoon suggesting a mechanism such as parasite-induced immune modulation. We found no evidence for negative associations between coinfections and host body condition. We suggest that longitudinal studies involving the recapture and investigation of infection status of individuals over their lifespan are crucial to understand the epidemiology of coinfections in natural populations.

Logistical constraints concerning parasite sample storage can hinder progress with the discovery of genetic variation on a global scale. New storage methods are being developed to address this, but require testing in order to understand how widely applicable these methods are. Whatman FTA cards have been tested previously under laboratory conditions for storing low-concentration Trichomonas gallinae isolates with the conclusion that they are not suitable, but have not been tested under field conditions. Here, we conducted a field-test, comparing FTA cards with storage in ethanol for T. gallinae samples collected and cultured from wild Columbiformes in Africa using standard field methods, before transportation to the UK. After 6 months storage, both methods resulted in an overall prevalence of 100% following PCR amplification (n = 59), suggesting that FTA cards are suitable for estimation of T. gallinae prevalence. However, samples stored in ethanol produced more, and longer, sequences than those stored on FTA cards. These data suggest storage in ethanol is preferable for the acquisition of high quality genetic strain data, but that FTA cards can be used successfully to ascertain infection prevalence and identify parasite strains under field conditions.

Trichomonas gallinae, a protozoan parasite infecting a wide range of birds, has been a cause 3 for conservation concern since its recognition as an emerging infectious disease, having had 4 notable impacts on several avian species, including causing widespread mortality in 5 greenfinches (Chloris chloris), and chaffinches (Fringilla coelebs), and hindering the recovery 6 of the endangered pink pigeon (Nesoenas mayeri). Horizontal transmission between birds 7 congregating at feeding sites, such as those provided for conservation and species management 8 purposes, is an important driver in the spread of T. galliane. Supplementary feeding is a key 9 conservation intervention for the European turtle dove (Streptopelia turtur), which is declining 10 across its range, driven at least partially by a loss of natural food resources. Due to the link 11 between T. gallinae transmission and supplementary feeding, we consider the prevalence of 12 this parasite amongst European turtle dove in relation to diet, in the first study to analyse these 13 two factors in the decline of this species together. Using birds sampled from breeding and 14 wintering grounds, the dietary composition of individuals was compared to the presence of T. 15 gallinae, and specific T. gallinae strains. Dietary variation was summarised into two axes using 16 detrended correspondence analysis, neither were associated with the presence of T. gallinae, 17 or any specific strains. The proportion of diet accounted for by cultivated seeds did not affect 18 parasite presence, despite the spread of this parasite being associated with supplementary 19 feeding due to an increase in contact between potentially infected and uninfected birds 20 gathering at high densities at feeding sites. Significant dietary overlap was observed between 21 infected and uninfected individuals in all sites, with almost complete dietary overlap being 22 observed in one breeding site. The level of dietary overlap between individuals infected with 23 specific strains fluctuated between sampling seasons, indicating no consistent relationship 24 between diet and infection status.

Sex-specific niche differentiation is common in marine vertebrates, but how this varies long-term is poorly understood. Here we investigated interannual variation in sexual segregation among breeding northern gannets Morus bassanus, wide-ranging central-place foragers with slight sexual dimorphism. Over 11 breeding seasons, we used GPS tracking and/or stable isotopes to test for sex differences in foraging trip characteristics (range, duration and timing); spatial distribution; habitat selection; and carbon and nitrogen isotopes in blood. When combining data from all years, females foraged further and for longer than males, yet despite this, the foraging areas of the sexes almost completely overlapped. Males and females selected foraging habitats that differed in terms of oceanography but not fishing vessel density. We also detected temporal segregation: females were more likely to be at sea during the day than at night, while males were more likely to be at sea during the night. However, foraging behaviour quantified by all GPS analyses varied interannually, with sex differences detected in some years but not others. Finally, males had consistently higher red blood cell δ13C and δ15N than females across all years, which was not driven by size dimorphism, instead likely by prey choice or very fine-scale habitat selection. We conclude that environmental variation influenced short-term sex differences in movement, but sex differences in stable isotopes that integrate behaviour over longer periods reveal more consistent differences. Our results suggest that inferences drawn from single-year studies may not relate to general patterns, highlighting the importance of long-term studies and combining methods.

Tropical rainforest disturbance and conversion are critical drivers of biodiversity loss. A key knowledge gap is understanding the impacts of habitat modification on mechanisms of community assembly, which are predicted to respond differently between taxa and across spatial scales. We use a null model approach to detect trait assembly of species at local- and landscape-scales, and then subdivide communities with different habitat associations and foraging guilds to investigate whether the detection of assembly mechanisms varies between groups. We focus on two indicator taxa, dung beetles and birds, across a disturbance gradient of primary rainforest, selectively logged rainforest, and oil palm plantations in Borneo, Southeast Asia. Random community assembly was predominant for dung beetles across habitats, whereas trait convergence, indicative of environmental filtering, occurred across the disturbance gradient for birds. Assembly patterns at the two spatial scales were similar. Subdividing for habitat association and foraging guild revealed patterns hidden when focusing on the overall community. Dung beetle forest specialists and habitat generalists showed opposing assembly mechanisms in primary forest, community assembly of habitat generalists for both taxa differed with disturbance intensity, and insectivorous birds strongly influenced overall community assembly relative to other guilds. Our study reveals the sensitivity of community assembly mechanisms to anthropogenic disturbance via a shift in the relative contribution of stochastic and deterministic processes. This highlights the need for greater understanding of how habitat modification alters species interactions and the importance of incorporating species’ traits within assessments. Supplementary Information The online version contains supplementary material available at 10.1007/s00442-020-04829-z.

Ecological restoration is considered to play an important role in mitigating climate change, protecting biodiversity and preventing environmental degradation. Yet, there are often multiple perspectives on what outcomes restoration should be aiming to achieve, and how we should get to that point. In this paper we interview a range of policy makers, academics and NGO representatives to explore the range of perspectives on the restoration of Indonesia's tropical peatlands – key global ecosystems that have undergone large‐scale degradation. Thematic analysis suggests that participants agreed about the importance of restoration, but had differing opinions on how effective restoration activities to date have been and what a restored peatland landscape should look like. These results exemplify how ecological restoration can mean different things to different people, but also highlight important areas of consensus for moving forward with peatland restoration strategies.

Tropical peat swamp forests retain large carbon stocks and support unique biodiversity, but clearance and drainage for agriculture have resulted in fires, carbon emissions and biodiversity losses. Initiatives to re-wet cultivated peatlands may benefit biodiversity if this protects remaining forests from fire and agricultural encroachment, but there are concerns that re-wetting could reduce yields and damage livelihoods, as relationships between drainage, on-farm biodiversity, and crop yields have not been studied. We examined oil palm fruit yields and bird diversity on 41 smallholder farms in Jambi (Sumatra, Indonesia), which varied in drainage intensity (12-month mean water table per plot from August 2018 to August 2019: −52 to −3 cm below-ground). We also compared farm bird diversity with a neighbouring area of protected peat swamp forest (11,000 ha, 21 plots; mean water table per plot −3 to +15 cm). Bird species richness (3–18 species per plot), species composition and oil palm yields (4.5–19.2 t fresh fruit bunch ha−1 year−1) varied among farms, but were not detectably affected by water table depth, although ground-level vegetation was more complex on wetter farms. Bird richness in oil palm (mean = 10.3 species per plot) was

Understanding the frequency, spatiotemporal dynamics and impacts of parasite coinfections is fundamental to developing control measures and predicting disease impacts. The European turtle dove (Streptopelia turtur) is one of Europe’s most threatened bird species. High prevalence of infection by the protozoan parasite Trichomonas gallinae has previously been identified, but the role of this and other coinfecting parasites in turtle dove declines remains unclear. Using a high-throughput sequencing approach, we identified seven strains of T. gallinae, including two novel strains, from ITS1/5.8S/ITS2 ribosomal sequences in turtle doves on breeding and wintering grounds, with further intra-strain variation and four novel sub-types revealed by the iron-hydrogenase gene. High spatiotemporal turnover was observed in T. gallinae strain composition, and infection was prevalent in all populations (89–100%). Coinfection by multiple Trichomonas strains was rarer than expected (1% observed compared to 38.6% expected), suggesting either within-host competition, or high mortality of coinfected individuals. In contrast, coinfection by multiple haemosporidians was common (43%), as was coinfection by haemosporidians and T. gallinae (90%), with positive associations between strains of T. gallinae and Leucocytozoon suggesting a mechanism such as parasite-induced immune modulation. We found no evidence for negative associations between coinfections and host body condition. We suggest that longitudinal studies involving the recapture and investigation of infection status of individuals over their lifespan are crucial to understand the epidemiology of coinfections in natural populations.

The southern North Sea holds the world's highest concentration of offshore wind farms (OWFs). Northern gannets (Morus bassanus), a species considered at high risk from OWF impacts, show a strong seasonal peak there in November, but it is unclear which populations and age classes are most at risk of collision with wind turbines. We tagged adult and juvenile gannets at the world's largest colony (Bass Rock) and reviewed two sources of survey data for different age classes to study their movements through southern North Sea waters. Tracked birds showed peak numbers in the southern North Sea in mid-October, with much smaller numbers there during November. Adults were distributed throughout the area, including waters close to OWFs, whereas juveniles were confined to the coast. Survey data indicated high proportions of immature gannets in southern North Sea waters, suggesting higher collision risk than for adults. Gannets present in November may be predominantly from colonies further north than Bass Rock.

Studying the at-sea movements and behaviour of juvenile seabirds is logistically challenging, but new technologies now allow tracking birds on their first migration, giving a more complete picture of population-level spatial ecology. We investigated the post-fledging migration of juvenile northern gannets Morus bassanus from the world’s largest colony, at Bass Rock, Scotland. We first examined the movements and survival of 38 juveniles over their initial days at sea with GPS precision for up to 53 d post-fledging. We then compared their migration journeys with those of 35 adults tracked with geolocators. Almost one-third of juveniles died within 2 mo of leaving the colony, and this mortality was often associated with apparent uncertainties in their direction of migration, including marked, abrupt and often repeated changes in bearing within the North Sea. Both juveniles and adults then migrated as far as the Canary Current Large Marine Ecosystem (CCLME) off the Atlantic coast of West Africa, initially taking both clockwise and counter-clockwise routes around the UK. Juveniles covered a distance each day similar to that of adults, but they reached the CCLME much more quickly, mainly because they travelled more directly, staying close to the coast throughout most of their migration, whereas adults additionally spent long periods over relatively restricted areas of ocean further offshore. The CCLME is a hotspot of unregulated fishing activity, and our findings highlight the importance of this region across different age-classes of birds, echoing previous calls that the regional strengthening of marine conservation should be a high priority.

The work was funded by the Natural Environment Research Council (Standard Research Grant NE/H007466/1) and donations from Evan Fountain (In Memoriam donations for Issy Fountain) and Mike Matthewson. Marine vertebrates show a diversity of migration strategies, including sex differences. This may lead to differential demography, but the consequences of such between-sex variation are little understood. Here, we studied the migration of known-sex northern gannets Morus bassanus — a partial migrant with females ~8 % heavier than males. We used geolocators to determine wintering areas of 49 breeding adults (19 females and 30 males during 2010 to 2014) from 2 colonies in the northeast Atlantic (Bass Rock and Grassholm, UK). We also tested for sex-specific survival probabilities using capture−mark−recapture methods (n = 72 individuals Bass Rock, n = 229 individuals Grassholm; 2010−2018) and applied sex-specific population projection matrices (PPMs) to quantify population-level effects. Tracked gannets wintered in a range of large marine ecosystems (LMEs): Canary Current LME (CCLME; 69 %), Celtic-Biscay Shelf LME (16 %), Iberian Coastal LME (8 %), North Sea LME (4 %) or Mediterranean LME (2 %). Migratory destination differed between the sexes: 90 % of females vs. 57 % of males wintered in the CCLME. Survival was similar between the sexes at Bass Rock (mean ± 95 % CI = 0.951 ± 0.053 and 0.956 ± 0.047 for females and males, respectively). At Grassholm, there was evidence of slight sex differences in breeder survival: females had lower annual survival (0.882 ± 0.040) than males (0.946 ± 0.026). At Bass Rock, PPMs with no sex effect best fitted the observed population increase (1994−2014). Sex-specific PPMs fitted the population estimates for Grassholm (1995−2015). Our results reveal that female gannets are more likely to travel further than males to winter in the CCLME. This difference is unlikely due to morphological differences, unlike in other bird species. However, the reason for slightly higher over-winter female mortality at Grassholm is unclear. Publisher PDF

We present a genome assembly from an individual female Streptopelia turtur (the European turtle dove; Chordata; Aves; Columbidae). The genome sequence is 1.18 gigabases in span. The majority of the assembly is scaffolded into 35 chromosomal pseudomolecules, with the W and Z sex chromosomes assembled.

There is much debate about how best to mitigate the effects of agricultural expansion on biodiversity, especially in the tropics. Recent studies have emphasized that proximity to natural habitats can enhance farmland biodiversity, yet few studies have examined whether or not such proximity mediates local trade-offs between yields and biodiversity, and hence alters conclusions about the ecological benefits of alternative farming strategies. Here we examine yield-biodiversity trade-offs, focusing on birds in oil palm smallholdings at different distances from remaining areas of forest, including a large forest reserve, in Ghana. We found significantly fewer birds on higher-yielding than lower-yielding farms, in terms of both species richness and abundance. For forest specialist birds (likely to be highly vulnerable to conversion of land to agriculture) we also found a greater trade-off (i.e., lower richness and abundance for a given yield) at farms further from forest, to the extent that increasing distance to the nearest forest from 1 to 10 km had a similar effect as a 3- to 5-fold increase in fruit yield brought about by increased intensification. Our study highlights the importance of accounting for the effects of natural forest in the landscape when considering agricultural policies for biodiversity protection, underlining the importance of a landscape-scale approach to conservation.

Aim Palms are an iconic, diverse and often abundant component of tropical ecosystems that provide many ecosystem services. Being monocots, tree palms are evolutionarily, morphologically and physiologically distinct from other trees, and these differences have important consequences for ecosystem services (e.g., carbon sequestration and storage) and in terms of responses to climate change. We quantified global patterns of tree palm relative abundance to help improve understanding of tropical forests and reduce uncertainty about these ecosystems under climate change. Location Tropical and subtropical moist forests. Time period Current. Major taxa studied Palms (Arecaceae). Methods We assembled a pantropical dataset of 2,548 forest plots (covering 1,191ha) and quantified tree palm (i.e., ≥10cm diameter at breast height) abundance relative to co‐occurring non‐palm trees. We compared the relative abundance of tree palms across biogeographical realms and tested for associations with palaeoclimate stability, current climate, edaphic conditions and metrics of forest structure. Results On average, the relative abundance of tree palms was more than five times larger between Neotropical locations and other biogeographical realms. Tree palms were absent in most locations outside the Neotropics but present in >80% of Neotropical locations. The relative abundance of tree palms was more strongly associated with local conditions (e.g., higher mean annual precipitation, lower soil fertility, shallower water table and lower plot mean wood density) than metrics of long‐term climate stability. Life‐form diversity also influenced the patterns; palm assemblages outside the Neotropics comprise many non‐tree (e.g., climbing) palms. Finally, we show that tree palms can influence estimates of above‐ground biomass, but the magnitude and direction of the effect require additional work. Conclusions Tree palms are not only quintessentially tropical, but they are also overwhelmingly Neotropical. Future work to understand the contributions of tree palms to biomass estimates and carbon cycling will be particularly crucial in Neotropical forests.

The Indonesian government committed to restoring over 2 million ha of degraded peatland by the end of 2020, mainly to reduce peat fires and greenhouse gas emissions. Although it is unlikely the government will meet this target, restoration projects are still underway. One restoration strategy involves blocking peatland drainage canals, but the consequences of this for smallholder farmers whose livelihoods are dependent on agriculture are unclear. This paper investigates perceived impacts of canal blocks on smallholder farmers and identifies factors that affect their willingness to accept canal blocks on their land. We use data from 181 household questionnaires collected in 2018 across three villages in Jambi province, Sumatra. We found that the majority of respondents would accept canal blocks on their farms, perceiving that the blocks would have no impact on yields or farm access, and would decrease fire risk. Respondents who would not accept blocks on their farms were more likely to use canals to access their farms and perceive that canal blocks would decrease yields. The majority of farmers unwilling to accept canal blocks did not change their mind when provided with an option of a block that would allow boat travel. Our results improve understanding of why some smallholders may be unwilling to engage with peatland restoration. Further research is needed to understand the impact of canal blocks on smallholders’ yields. Engaging with stakeholders from the outset to understand farmers’ concerns, and perceptions is key if the government is to succeed in meeting its peatland restoration target and to ensure that the costs and benefits of restoration are evenly shared between local stakeholders and other actors. Supplementary Information The online version contains supplementary material available at 10.1007/s10113-020-01737-z.

There is a pressing need to quantify the risks of renewable energy developments such as offshore wind farms for protected populations. However, assessments are often based on incomplete data, or fail to consider variation in risk between sexes and at different times of year. We tracked northern gannets foraging from the world's largest colony (Bass Rock, Scotland) across five consecutive breeding seasons. We examine how seasonal and sex differences in behaviour affect the collision risk from planned and operational wind farms within their foraging range and assess the likely consequences for long-term population viability. Both sexes made shorter trips during chick-rearing than prior to chick-hatching, spent a greater proportion of time within wind farm sites and had an eight times greater potential collision risk during chick-rearing. Females made longer trips than males at both these times of year, flew higher and spent more time within wind farm sites, leading to three times greater collision risk for females. After accounting for the potential additional mortality from collisions, and assuming that the death of a parent also led to the loss of its offspring, the breeding population was projected to increase by 3.57% (95% CI: 2.16–5.15%) per year, compared with 6.56% (95% CI: 4.59–8.73%) in the absence of turbines, suggesting a negligible effect on population viability. However, additional mortality could result in greater immigration from neighbouring colonies, potentially affecting their viability and highlighting a need for research within a metapopulation framework to assess the impacts of offshore wind developments on vulnerable species across multiple connected sites.

Individual foraging site fidelity (IFSF) has been documented in a wide range of species, but few studies have examined the incidence or implications of variation among individuals in levels of fidelity, especially among short-ranging species where costs of travel place fewer constraints on exploring alternative foraging sites. Using combined GPS and dive data for 560 trips by 70 birds, we quantified the repeatability of foraging behaviour including IFSF in a short-ranging, mainly benthic predator, the European shag Phalacrocorax aristotelis, across 3 consecutive breeding seasons at a colony in NE England. There was significant repeatability in a wide range of foraging trip parameters, with highest consistency in those related to foraging location and maximum dive depth, and lowest consistency in those related to trip duration and time spent in different activities. Birds also had high IFSF overall but there was marked variation among individuals in this respect: some were highly consistent in the locations visited over multiple years whereas others frequently changed their foraging locations between successive trips. IFSF was typically higher from one year to the next than within a single year, with most birds retaining similar levels of consistency from year to year. Females with higher IFSF during chick-rearing were in better condition than birds with lower consistency and had earlier hatching dates. These data strongly suggest IFSF may be beneficial even in short-ranging species, at least in benthic feeders where prior knowledge and experience of particular habitat patches and associated prey capture techniques may be advantageous.

Rain forests on Borneo support exceptional concentrations of endemic insect biodiversity, but many of these forest‐dependent species are threatened by land‐use change. Totally protected areas (TPAs) of forest are key for conserving biodiversity, and we examined the effectiveness of the current TPA network for conserving range‐restricted butterflies in Sabah (Malaysian Borneo). We found that mean diurnal temperature range and precipitation of the wettest quarter of the year were the most important predictors of butterfly distributions (N = 77 range‐restricted species), and that species richness increased with elevation and aboveground forest carbon. On average across all species, TPAs were effective at conserving ~43% of species’ ranges, but encompassed only ~40% of areas with high species richness (i.e., containing at least 50% of our study species). The TPA network also included only 33%–40% of areas identified as high priority for conserving range‐restricted species, as determined by a systematic conservation prioritization analysis. Hence, the current TPA network is reasonably effective at conserving range‐restricted butterflies, although considerable areas of high species richness (6,565 km2) and high conservation priority (11,152–12,531 km2) are not currently protected. Sabah's remaining forests, and the range‐restricted species they support, are under continued threat from agricultural expansion and urban development, and our study highlights important areas of rain forest that require enhanced protection. Abstract in Malay is available with online material.

Individual specialisations in animals are important contributors to a wide range of ecological and evolutionary processes, and have been particularly documented in relation to multiple aspects of foraging behaviours. Central-place foragers, such as seabirds, frequently exhibit pronounced specialisations and individual differences in a variety of foraging traits. In particular, the availability of fisheries discards alongside natural prey resources provides additional potential for differentiation and specialisation for opportunistically scavenging seabird species. However, the consequences of such specialisations for at-sea distributions and intraspecific interactions are not well known. Here, we investigated the links between the degree of dietary specialisation on natural or discarded prey and the foraging movements and spatial occupancy of northern gannets Morus bassanus in relation to differing intraspecific competition at 6 colonies of differing sizes. We found that, at most colonies, individuals with different dietary strategies concentrated foraging at differing levels of intraspecific competition. In addition, individuals pursuing different strategies were frequently, but not consistently, spatially separated, distinctions that were most acutely seen in females. However, this variation in individual strategy had no significant impact on current body condition. These analyses demonstrate how foraging-associated metrics need not covary within an unconstrained system. They also reveal that specialisation can have important consequences for the competitive regimes individuals experience, highlighting the complexity of examining interacting consequences at large spatial scales.

Forest biomass is an essential indicator for monitoring the Earth’s ecosystems and climate. It is a critical input to greenhouse gas accounting, estimation of carbon losses and forest degradation, assessment of renewable energy potential, and for developing climate change mitigation policies such as REDD+, among others. Wall-to-wall mapping of aboveground biomass (AGB) is now possible with satellite remote sensing (RS). However, RS methods require extant, up-to-date, reliable, representative and comparable in situ data for calibration and validation. Here, we present the Forest Observation System (FOS) initiative, an international cooperation to establish and maintain a global in situ forest biomass database. AGB and canopy height estimates with their associated uncertainties are derived at a 0.25 ha scale from field measurements made in permanent research plots across the world’s forests. All plot estimates are geolocated and have a size that allows for direct comparison with many RS measurements. The FOS offers the potential to improve the accuracy of RS-based biomass products while developing new synergies between the RS and ground-based ecosystem research communities., Measurement(s)above-ground biomass • organic materialTechnology Type(s)tree species census • measurement methodFactor Type(s)geographic location • tree speciesSample Characteristic - Environmentforest biomeSample Characteristic - LocationEarth (planet) Machine-accessible metadata file describing the reported data: 10.6084/m9.figshare.9850571

1. As conservation increasingly recognises the importance of species’ functional roles in ecosystem processes, studies are shifting away from measuring species richness towards measures that account for the functional differences between species in a community. These functional diversity (FD) indices have received much recent attention and refinement, but their greatest limitation remains their inability to incorporate information about intraspecific trait variation (ITV). 2. We use an individual-based model to account for ITV when calculating the functional diversity of two avian communities in Borneo; one in primary (unlogged) forest and one in selectively logged forest. We deal with the scarcity of trait data for individual species by developing a simulation approach, taking data from the literature where necessary. Using a bootstrapping procedure, we produce a range of ecologically feasible FD values taking account of ITV for five commonly-used FD indices, and we quantify the confidence that can be placed in these values using a newly-developed bootstrapping method: btFD. 3. We found that incorporating ITV significantly altered the FD values of all indices used in our models. The rank order of FD for the two communities, indicating whether diversity was higher in primary or selectively logged forest, was largely unchanged by the inclusion of ITV. However, by accounting for ITV, we were able to reveal previously unrecognized impacts of selective logging on avian functional diversity through a narrower dispersion of individuals in functional trait space in logged forest. 4. Our results highlight the importance of incorporating ITV into measures of functional diversity, whilst our simulation approach addresses the frequently encountered difficulty of working with sparse trait data and quantifies the confidence that should be placed in such findings.

The sensitivity of tropical forest carbon to climate is a key uncertainty in predicting global climate change. Although short-term drying and warming are known to affect forests, it is unknown if such effects translate into long-term responses. Here, we analyze 590 permanent plots measured across the tropics to derive the equilibrium climate controls on forest carbon. Maximum temperature is the most important predictor of aboveground biomass (-9.1 megagrams of carbon per hectare per degree Celsius), primarily by reducing woody productivity, and has a greater impact per °C in the hottest forests (>32.2°C). Our results nevertheless reveal greater thermal resilience than observations of short-term variation imply. To realize the long-term climate adaptation potential of tropical forests requires both protecting them and stabilizing Earth's climate., Our plot monitoring networks havebeen supported by multiple grants from a large number of funding bodies: European Research Council; Natural Environment Research Council; European Union’s Fifth, Sixth, and Seventh Framework Programme; Royal Society, Leverhulme Trust; Gordon and Betty Moore Foundation; David and Lucile Packard Foundation; State of São Paulo Research Foundation (FAPESP); National Council for Science and Technology Development of Brazil (CNPq); Agence Nationale de la Recherche; Conservation International; Missouri Botanical Garden; Smithsonian Institution; Wildlife Conservation Society; National Geographic Society; Centre for International Forestry; and Gabon’s National Park Agency.

1. The recent availability of high spatial and temporal resolution optical and radar satellite imagery has dramatically increased opportunities for mapping land cover at fine scales. Fusion of optical and radar images has been found useful in tropical areas affected by cloud cover because of their complementarity. However, the multitemporal dimension these data now offer is often neglected because these areas are primarily characterised by relatively low levels of seasonality and because the consideration of multitemporal data requires more processing time. Hence, land cover mapping in these regions is often based on imagery acquired for a single date or on an average of multiple dates. 2. The aim of this work is to assess the added value brought by the temporal dimension of optical and radar time series when mapping land cover in tropical environments. Specifically, we compared the accuracies of classifications based on (i) optical time series, (ii) their temporal average, (iii) radar time series, (iv) their temporal average, (v) a combination of optical and radar time series and (vi) a combination of their temporal averages for mapping land cover in Jambi province, Indonesia, using Sentinel‐1 and Sentinel‐2 imagery. 3. Using the full information contained in the time series resulted in significantly higher classification accuracies than using temporal averages (+14.7% for Sentinel‐1, +2.5% for Sentinel‐2 and +2% combining Sentinel‐1 and Sentinel‐2). Overall, combining Sentinel‐2 and Sentinel‐1 time series provided the highest accuracies (Kappa = 88.5%). 4. Our study demonstrates that preserving the temporal information provided by satellite image time series can significantly improve land cover classifications in tropical biodiversity hotspots, improving our capacity to monitor ecosystems of high conservation relevance such as peatlands. The proposed method is reproducible, automated, and based on open‐source tools satellite imagery.

Abstract Identifying and understanding patterns in movement data are amongst the principal aims of movement ecology. By quantifying the similarity of movement trajectories, inferences can be made about diverse processes, ranging from individual specialisation to the ontogeny of foraging strategies. Movement analysis is not unique to ecology however, and methods for estimating the similarity of movement trajectories have been developed in other fields but are currently under-utilised by ecologists. Here, we introduce five commonly used measures of trajectory similarity: dynamic time warping (DTW), longest common subsequence (LCSS), edit distance for real sequences (EDR), Fréchet distance and nearest neighbour distance (NND), of which only NND is routinely used by ecologists. We investigate the performance of each of these measures by simulating movement trajectories using an Ornstein-Uhlenbeck (OU) model in which we varied the following parameters: (1) the point of attraction, (2) the strength of attraction to this point and (3) the noise or volatility added to the movement process in order to determine which measures were most responsive to such changes. In addition, we demonstrate how these measures can be applied using movement trajectories of breeding northern gannets (Morus bassanus) by performing trajectory clustering on a large ecological dataset. Simulations showed that DTW and Fréchet distance were most responsive to changes in movement parameters and were able to distinguish between all the different parameter combinations we trialled. In contrast, NND was the least sensitive measure trialled. When applied to our gannet dataset, the five similarity measures were highly correlated despite differences in their underlying calculation. Clustering of trajectories within and across individuals allowed us to easily visualise and compare patterns of space use over time across a large dataset. Trajectory clusters reflected the bearing on which birds departed the colony and highlighted the use of well-known bathymetric features. As both the volume of movement data and the need to quantify similarity amongst animal trajectories grow, the measures described here and the bridge they provide to other fields of research will become increasingly useful in ecology. Significance statement As the use of tracking technology increases, there is a need to develop analytical techniques to process such large volumes of data. One area in which this would be useful is the comparison of individual movement trajectories. In response, a variety of measures of trajectory similarity have been developed within the information sciences. However, such measures are rarely used by ecologists who may be unaware of them. To remedy this, we apply five common measures of trajectory similarity to both simulated data and real ecological dataset comprising of movement trajectories of breeding northern gannets. Dynamic time warping and Fréchet distance performed best on simulated data. Using trajectory similarity measures on our gannet dataset, we identified distinct foraging clusters centred on different bathymetric features, demonstrating one application of such similarity measures. As new technology and analysis techniques proliferate across ecology and the information sciences, closer ties between these fields promise further innovative analysis of movement data.

Funding: UK Natural Environment Research Council (NERC Standard Grant NE/H007466/1). SB is currently funded by an ERC consolidator’s grant (310820: STATEMIG). EW is funded by the NERC (Independent Research Fellowship NE/M017990/1). Migration is a fundamental behavioral process prevalent among a wide variety of animal taxa. As individuals are increasingly shown to present consistent responses to environmental cues for breeding or foraging, it may be expected that approaches to migration would present similar among-individual consistencies. Seabirds frequently show consistent individual differences in a range of traits related to foraging and space-use during both the breeding and non-breeding seasons, but the causes and consequences of this consistency are poorly understood. In this study, we combined analysis of geolocation and stable isotope data across multiple years to investigate individual variation in the non-breeding movements and diets of northern gannets Morus bassanus, and the consequences for changes in body condition. We found that individuals were highly repeatable in their non-breeding destination over consecutive years even though the population-level non-breeding distribution spanned >35° of latitude. Isotopic signatures were also strongly repeatable, with individuals assigned to one of two dietary clusters defined by their distinct trophic (δ15N) and spatial (δ13C) position. The only non-breeding destination in which the two dietary clusters co-occurred was off the coast of northwest Africa. The majority of individuals adopted a consistent foraging strategy, as they remained within the same dietary cluster across years, with little variation in body mass corrected for size among these consistent individuals. In contrast, the few individuals that switched clusters between years were in better condition relative to the rest of the population, suggesting there may be benefits to flexibility during the non-breeding period. Our results indicate that a consistent migratory strategy can be effective regardless of wintering region or diet, but that there may be benefits to those individuals able to display flexibility. This appears to be an important behavioral strategy that may enhance individual condition. Publisher PDF

The demand for timber products is facilitating the degradation and opening up of large areas of intact habitats rich in biodiversity. Logging creates an extensive network of access roads within the forest, yet these are commonly ignored or excluded when assessing impacts of logging on forest biodiversity. Here we determine the impact of these roads on the overall condition of selectively logged forests in Borneo, Southeast Asia. Focusing on dung beetles along > 40 km logging roads we determine: (i) the magnitude and extent of edge effects alongside logging roads; (ii) whether vegetation characteristics can explain patterns in dung beetle communities, and; (iii) how the inclusion of road edge forest impacts dung beetle assemblages within the overall logged landscape. We found that while vegetation structure was significantly affected up to 34 m from the road edge, impacts on dung beetle communities penetrated much further and were discernible up to 170 m into the forest interior. We found larger species and particularly tunnelling species responded more than other functional groups which were also influenced by micro-habitat variation. We provide important new insights into the long-term ecological impacts of tropical logging. We also support calls for improved logging road design both during and after timber extraction to conserve more effectively biodiversity in production forests, for instance, by considering the minimum volume of timber, per unit length of logging road needed to justify road construction. In particular, we suggest that governments and certification bodies need to highlight more clearly the biodiversity and environmental impacts of logging roads., Highlights • Distinct edge effects along roads penetrate > 100 m into the logged forest interior. • Vegetation changes however, differed within a maximum of 34 m of the road edge. • Large diurnal, and tunnelling dung beetles are affected more by proximity to roads. • Micro-habitat variations shown to influence large tunnelling species.

In many taxa, environmental changes that alter resource availability and energetics, such as climate change and land use change, are associated with changes in body size. We use wing length as a proxy for overall structural body size to examine a paradoxical trend of declining wing length within a Yellowhammer Emberiza citrinella population sampled over 21 years, in which it has been previously shown that longer wings are associated with higher survival rates. Higher temperatures during the previous winter (prior to the moult determining current wing length) explained 23% of wing length decrease within our population, but changes may also be correlated with non-climatic environmental variation such as changes in farming mechanisms linked to food availability. We found no evidence for within-individual wing length shrinkage with age, but our data suggested a progressive decline in the sizes of immature birds recruiting to the population. This trend was weaker, although not significantly so, among adults, suggesting that the decline in the sizes of recruits was offset by higher subsequent survival of larger birds post-recruitment. These data suggest that ecological processes can contribute more than selection to observed phenotypic trends and highlight the importance of long-term studies for providing longitudinal insights into population processes.

The loss of huge areas of peat swamp forest in Southeast Asia and the resulting negative environmental effects, both local and global, have led to an increasing interest in peat restoration in the region. Satellite remote sensing offers the potential to provide up‐to‐date information on peat swamp forest loss across large areas, and support spatial explicit conservation and restoration planning. Fusion of optical and radar remote sensing data may be particularly valuable in this context, as most peat swamp forests are in areas with high cloud cover, which limits the use of optical data. Radar data can ‘see through’ cloud, but experience so far has shown that it doesn't discriminate well between certain types of land cover. Various approaches to fusion exist, but there is little information on how they compare. To assess this untapped potential, we compare three different classification methods with Sentinel‐1 and Sentinel‐2 images to map the remnant distribution of peat swamp forest in the area surrounding Sungai Buluh Protection Forest, Sumatra, Indonesia. Results show that data fusion increases overall accuracy in one of the three methods, compared to the use of optical data only. When data fusion was used with the pixel‐based classification using the original pixel values, overall accuracy increased by a small, but statistically significant amount. Data fusion was not beneficial in the case of object‐based classification or pixel‐based classification using principal components. This indicates optical data are still the main source of information for land cover mapping in the region. Based on our findings, we provide methodological recommendations to help those involved in peatland restoration capitalize on the potential of big data.

This work was funded by the Natural Environment Research Council and the Department for Business, Energy and Industrial Strategy. The development of foraging strategies that enable juveniles to efficiently identify and exploit predictable habitat features is critical for survival and long-term fitness. In the marine environment, meso- and sub-mesoscale features such as oceanographic fronts offer a visible cue to enhanced foraging conditions, but how individuals learn to identify these features is a mystery. In this study, we investigate age-related differences in the fine-scale foraging behaviour of adult (aged ≥ 5 years) and immature (aged 2-4 years) northern gannets Morus bassanus. Using high-resolution GPS-loggers, we reveal that adults have a much narrower foraging distribution than immature birds and much higher individual foraging site fidelity. By conditioning the transition probabilities of a hidden Markov model on satellite-derived measures of frontal activity, we then demonstrate that adults show a stronger response to frontal activity than immature birds, and are more likely to commence foraging behaviour as frontal intensity increases. Together, these results indicate that adult gannets are more proficient foragers than immatures, supporting the hypothesis that foraging specialisations are learned during individual exploratory behaviour in early life. Such memory-based individual foraging strategies may also explain the extended period of immaturity observed in gannets and many other long-lived species. Publisher PDF

Many established models of animal foraging assume that individuals are ecologically equivalent. However, it is increasingly recognized that populations may comprise individuals who differ consistently in their diets and foraging behaviors. For example, recent studies have shown that individual foraging site fidelity (IFSF, when individuals consistently forage in only a small part of their population's home range) occurs in some colonial breeders. Short-term IFSF could result from animals using a win-stay, lose-shift foraging strategy. Alternatively, it may be a consequence of individual specialization. Pelagic seabirds are colonial central-place foragers, classically assumed to use flexible foraging strategies to target widely dispersed, spatiotemporally patchy prey. However, tracking has shown that IFSF occurs in many seabirds, although it is not known whether this persists across years. To test for long-term IFSF and to examine alternative hypotheses concerning its cause, we repeatedly tracked 55 Northern Gannets (Morus bassanus) from a large colony in the North Sea within and across three successive breeding seasons. Gannets foraged in neritic waters, predictably structured by tidal mixing and thermal stratification, but subject to stochastic, wind-induced overturning. Both within and across years, coarse to mesoscale (tens of kilometers) IFSF was significant but not absolute, and foraging birds departed the colony in individually consistent directions. Carbon stable isotope ratios in gannet blood tissues were repeatable within years and nitrogen ratios were also repeatable across years, suggesting long-term individual dietary specialization. Individuals were also consistent across years in habitat use with respect to relative sea surface temperature and in some dive metrics, yet none of these factors accounted for IFSF. Moreover, at the scale of weeks, IFSF did not decay over time and the magnitude of IFSF across years was similar to that within years, suggesting that IFSF is not primarily the result of win-stay, lose-shift foraging. Rather, we hypothesize that site familiarity, accrued early in-life, causes IFSF by canalizing subsequent foraging decisions. Evidence from this and other studies suggests that IFSF may be common in colonial central-place foragers, with far-reaching consequences for our attempts to understand and conserve these animals in a rapidly changing environment.

A large increase in offshore wind turbine capacity is anticipated within the next decade, raising concerns about possible adverse impacts on birds as a result of collision risk. Birds' flight heights greatly influence this risk, yet height estimates are currently available only using methods such as radar- or ship-based observations over limited areas. 2. Bird-borne data-loggers have the potential to provide improved estimates of collision risk and here, we used data from Global Position System (GPS)-loggers and barometric pressure loggers to track the three-dimensional movements of northern gannets rearing chicks at a large colony in south-east Scotland (Bass Rock), located

Habitat destruction and degradation are major drivers of biodiversity loss and attention is increasingly focused on how different traits of species affect their vulnerability. Dietary traits are critical in this respect, and are typically examined by assigning species to different feeding and foraging guilds. However, such guilds may mask large variation in species’ trophic interactions, limiting our understanding of species’ responses. Here we use stable isotopes to quantify trophic positions within a Family of insectivorous understory birds, the Timaliidae (babblers), within Bornean rainforests. We then relate changes in species’ abundances following intensive selective logging of forest to their trophic positions, body sizes and foraging heights. We found that trophic positions within this single feeding guild spanned more than an entire trophic level. Moreover, changes in abundance following logging were significantly and independently related to mean trophic position in primary forest, body size and foraging height: large ground-feeding species occupying high trophic positions were more adversely affected than small understory-feeders with lower trophic positions. These three variables together explained 81% of the variance in species’ responses to logging. The single most important predictor, however, was a species’ mean trophic position. Species recorded in both habitats also had significantly higher trophic positions in logged forest. These data provide critical new understanding of species’ responses to disturbance. They also indicate previously unrecognised functional changes to species assemblages following logging, highlighting the importance of numerical assessments of trophic position within individual feeding guilds.

Current fishing extraction methods often generate huge quantities of dead or dying biomass that is returned to the sea in the form of discards. This practice produces a readily available clumped resource for many scavengers such as seabirds, but in the face of declining stocks and via policy change, the amount of discards produced is set to decline in the future. To understand how discards have influenced seabird foraging in the past and how birds may respond to future change requires studies examining consistent individual foraging choices. There is increasing evidence that populations may be made up of generalist or specialist foragers and this is key to the population's ability to adapt to change. Here we test for consistent individual foraging behaviour of northern gannets Morus bassanus in relation to fishing vessels and examine consequences of scavenging behaviour in terms of foraging effort and body condition. Using a combination of bird-borne bio-logging devices (GPS and Time Depth Recorders) with high resolution GPS data acquired through vessel monitoring systems on fishing boats, we examined the overlap between birds and fisheries. We found that during repeat foraging trips in the same breeding season, gannets regularly foraged at fishing boats but there were also clear among individual differences in the extent of fisheries overlap. Furthermore, we show for the first time that these differences represent consistent strategies – individual differences in scavenging were highly repeatable across multiple trips within a period of several weeks. However, despite this finding, we found no differences in foraging effort or body condition between scavengers and non-scavengers. Moreover, scavenging strategy did not appear to influence diving behaviour or vary by sex. Scavenging on discards appears to be a strategy employed consistently by a subsection of the population and future work should examine whether these specialisations persist throughout and between years and what causes these individual differences, exploring possible demographic and fitness consequences in light of global changes to fish stocks and fisheries management.

Less than half of anthropogenic carbon dioxide emissions remain in the atmosphere. While carbon balance models imply large carbon uptake in tropical forests, direct on-the-ground observations are still lacking in Southeast Asia. Here, using long-term plot monitoring records of up to half a century, we find that intact forests in Borneo gained 0.43 Mg C ha−1 per year (95% CI 0.14–0.72, mean period 1988–2010) in above-ground live biomass carbon. These results closely match those from African and Amazonian plot networks, suggesting that the world’s remaining intact tropical forests are now en masse out-of-equilibrium. Although both pan-tropical and long-term, the sink in remaining intact forests appears vulnerable to climate and land use changes. Across Borneo the 1997–1998 El Niño drought temporarily halted the carbon sink by increasing tree mortality, while fragmentation persistently offset the sink and turned many edge-affected forests into a carbon source to the atmosphere., The existence of a pan-tropical forest carbon sink remains uncertain due to the lack of data from Asia. Here, using direct on-the-ground observations, the authors confirm remaining intact forests in Borneo have provided a long-term carbon sink, but carbon net gains are vulnerable to drought and edge effects.

Knowing the spatial scales at which effective management can be implemented is fundamental for conservation planning. This is especially important for mobile species, which can be exposed to threats across large areas, but the space use requirements of different species can vary to an extent that might render some management approaches inefficient. Here the space use patterns of seabirds were examined to provide guidance on whether conservation management approaches should be tailored for taxonomic groups with different movement characteristics. Seabird tracking data were synthesised from 5419 adult breeding individuals of 52 species in ten families that were collected in the Atlantic Ocean basin between 1998 and 2017. Two key aspects of spatial distribution were quantified, namely how far seabirds ranged from their colony, and to what extent individuals from the same colony used the same areas at sea. There was evidence for substantial differences in patterns of space-use among the ten studied seabird families, indicating that several alternative conservation management approaches are needed. Several species exhibited large foraging ranges and little aggregation at sea, indicating that area-based conservation solutions would have to be extremely large to adequately protect such species. The results highlight that short-ranging and aggregating species such as cormorants, auks, some penguins, and gulls would benefit from conservation approaches at relatively small spatial scales during their breeding season. However, improved regulation of fisheries, bycatch, pollution and other threats over large spatial scales will be needed for wide-ranging and dispersed species such as albatrosses, petrels, storm petrels and frigatebirds. Fil: Oppel, Steffen. Royal Society For The Protection Of Birds; Fil: Bolton, Mark. Royal Society For The Protection Of Birds; Fil: Carneiro, Ana P.B.. Birdlife International; Fil: Dias, Maria P.. Birdlife International; Fil: Green, Jonathan A.. University of Liverpool; Reino Unido Fil: Masello, Juan F.. Justus Liebig University Giessen; Fil: Phillips, Richard A.. British Antarctic Survey; Fil: Owen, Ellie. Royal Society For The Protection Of Birds; Fil: Quillfeldt, Petra. Justus Liebig University Giessen; Fil: Beard, Annalea. Environmental And Natural Resources Directorate; Fil: Bertrand, Sophie. Universidad Federal Rural Pernambuco; Brasil. Centre National de la Recherche Scientifique. Institut de Recherche pour le Développement; Francia Fil: Blackburn, Jez. British Trust For Ornithology; Fil: Boersma, P. Dee. University Of Washington, Seattle; Fil: Borges, Alder. Projecto Vitó; Fil: Broderick, Annette C.. University of Exeter; Reino Unido Fil: Catry, Paulo. Ispa - Instituto Universitário; Portugal Fil: Cleasby, Ian. Royal Society For The Protection Of Birds; Fil: Clingham, Elizabeth. Environmental And Natural Resources Directorate; Fil: Creuwels, Jeroen. Naturalis Biodiversity Center; Fil: Crofts, Sarah. Falklands Conservation; Fil: Cuthbert, Richard J.. Royal Society For The Protection Of Birds; Fil: Dallmeijer, Hanneke. Veda Consultancy; Fil: Davies, Delia. University Of Cape Town; Fil: Davies, Rachel. Marinelife; Fil: Dilley, Ben J.. University Of Cape Town; Fil: Dinis, Herculano Andrade. Parque Natural Do Fogo; Fil: Dossa, Justine. Birdlife International; Fil: Dunn, Michael J.. British Antarctic Survey; Fil: Efe, Marcio A.. Universidade Federal de Alagoas; Brasil Fil: Fayet, Annette L.. University of Oxford; Reino Unido Fil: Figueiredo, Leila. Universidade Federal de Alagoas; Brasil Fil: Frederico, Adelcides Pereira. Projecto Vitó; Fil: Gjerdrum, Carina. Environment Canada; Canadá Fil: Godley, Brendan J.. University of Exeter; Reino Unido Fil: Granadeiro, José Pedro. Faculdade de Ciências, Universidade de Lisboa; Portugal Fil: Guilford, Tim. University of Oxford; Reino Unido Fil: Hamer, Keith C.. University Of Leeds; Fil: Hazin, Carolina. Birdlife International; Fil: Hedd, April. Environment Canada; Canadá Fil: Henry, Leeann. Environmental And Natural Resources Directorate; Fil: Hernández-Montero, Marcos. Projeto Biodiversidade; Fil: Hinke, Jefferson. Noaa Fisheries Service; Fil: Kokubun, Nobuo. National Institute Of Polar Research; Fil: Leat, Eliza. Ascension Island Government; Fil: Tranquilla, Laura McFarlane. Royal Society For The Protection Of Birds; . Environmental And Natural Resources Directorate; Fil: Metzger, Benjamin. Birdlife Malta; Malta Fil: Militão, Teresa. Universidad de Barcelona; España Fil: Montrond, Gilson. Projecto Vitó; Fil: Mullié, Wim. Veda Consultancy; Fil: Padget, Oliver. University of Oxford; Reino Unido Fil: Pearmain, Elizabeth J.. Birdlife International; Fil: Pollet, Ingrid L.. Bird Studies Canada; Canadá Fil: Pütz, Klemens. Antarctic Research Trust; Fil: Quintana, Flavio Roberto. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Centro Nacional Patagónico. Instituto de Biología de Organismos Marinos; Argentina Fil: Ratcliffe, Norman. British Antarctic Survey; Fil: Ronconi, Robert A.. Environment Canada; Canadá Fil: Ryan, Peter G.. University Of Cape Town; Fil: Saldanha, Sarah. Universidad de Barcelona; España Fil: Shoji, Akiko. University of Oxford; Reino Unido Fil: Sim, Jolene. Ascension Island Government; Fil: Small, Cleo. Royal Society For The Protection Of Birds; Fil: Soanes, Louise. University of Liverpool; Reino Unido Fil: Takahashi, Akinori. National Institute Of Polar Research; Fil: Trathan, Phil. British Antarctic Survey; Fil: Trivelpiece, Wayne. Noaa Fisheries Service; Fil: Veen, Jan. Veda Consultancy; Fil: Wakefield, Ewan. University of Glasgow; Reino Unido Fil: Weber, Nicola. University of Exeter; Reino Unido. Ascension Island Government; Fil: Weber, Sam. Ascension Island Government; . University of Exeter; Reino Unido Fil: Zango, Laura. Universidad de Barcelona; España Fil: González-Solís, Jacob. Universidad de Barcelona; España Fil: Croxall, John. Birdlife International