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bioRxiv2019

The challenges of estimating the distribution of flight heights from telemetry or altimetry data

BackgroundGlobal positioning systems (GPS) and altimeters are increasingly used to monitor vertical space use by aerial species, a key aspect of their niche that we need to know to understand their ecology and conservation needs, and to manage our own use of the airspace. However, there are various sources of error in flight height data (\"height\" above ground, as opposed to \"altitude\" above a reference like the sea level): vertical error from the devices themselves, error in the ground elevation below the tracked animals, and error in the horizontal position of the animals and thus the predicted ground elevation below them.\n\nMethodsWe used controlled field trials, simulations, and the reanalysis of raptor case studies with state-space models to illustrate the effect of improper error management.\n\nResultsErrors of a magnitude of 20 meters appear in benign conditions (expected to be larger in more challenging context). These errors distort the shape of the distribution of flight heights, inflate the variance in flight height, bias behavioural state assignments, correlations with environmental covariates, and airspace management recommendations. Improper data filters such as removing all negative recorded flight height records introduce several biases in the remaining dataset, and preclude the opportunity to leverage unambiguous errors to help with model fitting. Analyses that ignore the variance around the mean flight height, e.g., those based on linear models of flight height, and those that ignore the variance inflation caused by telemetry errors, lead to incorrect inferences.\n\nConclusionThe state-space modelling framework, now in widespread use by ecologists and increasingly often automatically implemented within on-board GPS data processing algorithms, makes it possible to fit flight models directly to raw flight height records, with minimal data pre-selection, and to analyse the full distribution of flight heights, not just the mean. In addition to basic research about aerial niches, behaviour quantification, and environmental interactions, we highlight the applied relevance of our recommendations for airspace management and the conservation of aerial wildlife.

ecology↗

bioRxiv2019

Assessing the potential of plains zebra to maintain African horse sickness in the Western Cape Province, South Africa

African horse sickness (AHS) is a disease of equids that results in a non-tariff barrier to the trade of live equids from affected countries. AHS is endemic in South Africa except for a controlled area in the Western Cape Province (WCP) where sporadic outbreaks have occurred in the past 2 decades. There is potential that the presence of zebra populations, thought to be the natural reservoir hosts for AHS, in the WCP could maintain AHS virus circulation in the area and act as a year-round source of infection for horses. However, it remains unclear whether the epidemiology or the ecological conditions present in the WCP would enable persistent circulation of AHS in the local zebra populations.\n\nHere we developed a hybrid deterministic-stochastic vector-host compartmental model of AHS transmission in plains zebra (Equus quagga), where host populations are age- and sex-structured and for which population and AHS transmission dynamics are modulated by rainfall and temperature conditions. Using this model, we showed that populations of plains zebra present in the WCP are not sufficiently large for AHS introduction events to become endemic and that coastal populations of zebra need to be >2500 individuals for AHS to persist >2 years, even if zebras are infectious for more than 50 days. AHS cannot become endemic in the coastal population of the WCP unless the zebra population involves at least 50,000 individuals. Finally, inland populations of plains zebra in the WCP may represent a risk for AHS to persist but would require populations of at least 500 zebras or show unrealistic duration of infectiousness for AHS introduction events to become endemic.\n\nOur results provide evidence that the risk of AHS persistence from a single introduction event in a given plains zebra population in the WCP is extremely low and it is unlikely to represent a long-term source of infection for local horses.

ecology↗

bioRxiv2019

Population-level sensitivity to landscape variables reflects individual-based habitat selection in a woodland bat species

Understanding the relationship between habitat quality and population dynamics is fundamental for long-term management and range predictions in ecology. However, habitat quality is generally only investigated at the individual scale, as it is the case for the lesser horseshoe bat (Rhinolophus hipposideros), a species of conservation concern. Using a statistical modelling approach and census data of 94 lesser horseshoe bat colonies located in Brittany (France), we analysed the effect of landscape composition and configuration on the demographic components of surveyed maternity colonies (i.e. colony size, fecundity and growth rate), and compared our result to those provided by individual-based studies. Our results validated that the landscape in a 500-meter buffer around colonies (core foraging area) is crucial for population size and dynamics, and confirmed the positive influence of broadleaved woodland proportion on bat colony size. We revealed a positive effect of lakeshores and riverbanks on colony size and growth rate, underlying the importance of these habitats for the long-term conservation of this non-migratory forest species. Importantly, our results refine previous knowledge concerning the threat posed by the intensification of human activities (e.g. urbanization, agriculture, habitat fragmentation), and highlight the negative effect of large and regular patches of artificial and crop lands and of open land patches shape complexity on all demographic variables investigated. While our results support the dependence of population dynamics and associated conservation management to individual behaviour and sensitivity, environmental responses differed between the population metrics investigated, showing that efficient range prediction will require to fully grasp the complexity of the interaction between landscape and the different population dynamic parameters.

ecology↗

bioRxiv2019

A test of the socioecological model in female Asian elephants: the effects of food abundance, food distribution, and competitor density on within-clan and between-clan contests

O_LISocioecological theory attributes variation in social organization of female-bonded species to differences in within- and between-group competition, shaped by food distribution. Strong between-group contests are expected over large, monopolisable resources, and are not generally expected in species that feed on low quality resources distributed across large, undefended home ranges. Within groups, frequent contests are expected over discrete feeding sites but not over low-quality, dispersed resources. C_LIO_LIWe report on the first tests of socioecological theory, largely unexplored in non-primate species, in female Asian elephants. Asian elephants show graminivory, overlapping home ranges, and high fission-fusion dynamics, traits that are thought to be associated with infrequent contests. C_LIO_LIWe studied agonistic interactions within and between female elephant clans with respect to food distribution, food abundance, and competitor density effects of group size and clan density, in a grassland habitat around the Kabini backwaters, southern India. C_LIO_LIWe found that the Kabini grassland had three times the grass biomass as adjacent forests, and between-clan encounters were considerably higher than that known from a neighbouring forest. Individual-level agonism was also more frequent between clans than within clans. Thus, the food-rich habitat patch probably enabled strong between-clan contest competition under graminivory. Moreover, the rate of between-clan encounters increased when more clans were present, and the duration of encounters was positively related to grass biomass at the contested sites. Despite fission-fusion dynamics, within-clan agonism was also somewhat frequent, but not influenced by food distribution, in contradiction to classic socioecological predictions, possibly because of intensified competition due to high density. Interestingly, within-clan agonism increased with female group size until intermediate group sizes, suggesting that the tension between within-group and between-group competition might govern group size, since larger groups are advantageous in this strong between-clan contest regime. C_LIO_LIOur findings refine the current understanding of female elephant socioecology. Despite predominant graminivory and fission-fusion dynamics, within-group agonism can be frequent, especially when large groups face ecological constraints at high density. Further, frequent between-group contests may arise despite graminivory and non-territoriality when food becomes patchy and density is high. These changes may be effected by anthropogenic alteration of habitats. C_LI

ecology↗

bioRxiv2019

A framework for quantifying deviations from dynamic equilibrium theory

Community assembly is governed by colonization and extinction processes, and the simplest model describing it is Dynamic Equilibrium (DE) theory, which assumes that communities are shaped solely by stochastic colonization and extinction events. Despite its potential to serve as a null model for community dynamics, there is currently no accepted methodology for measuring deviations from the theory and testing it. Here we propose a novel and easily applicable methodology for quantifying deviations from the predictions and assumptions of DE by comparing observed community time-series to a randomization-based null model. We show that this methodology has good statistical properties on simulated data, and it can detect deviations from both the assumptions and predictions of DE in the classical Florida Keys experiment. We discuss alternative methods and present guidelines for practical use of the methodology, hoping it will enhance the applicability of DE as a reference for studying changes in ecological communities.

ecology↗

bioRxiv2019

Using a residency index to estimate the economic value of saltmarsh provisioning services for commercially important fish species

Every year, 100 hectares of saltmarsh in the United Kingdom are lost due to sea level rise. The remaining areas are threatened by land conversion, agricultural activities, and climate change. There are important economic consequences to saltmarsh loss, as saltmarsh provides valuable ecosystem services including flood protection, carbon sequestration, and nursery habitat for commercially fished species. Quantifying the economic value of these ecosystem services can help target policies for saltmarsh restoration, or managed realignment, of new saltmarsh areas. In this study, we quantify the economic value of saltmarsh as a habitat for commercially fished species by developing a residency index. The residency index weights the relative importance of saltmarsh along a species lifecycle by explicitly incorporating the target species life histories and the estimated proportion of time it spends in saltmarsh at juvenile and adult life stages. Using this index, we estimate the value of saltmarsh to UK commercial fisheries landings. We find that UK saltmarsh contributes annually between 16.7% and 18.2% of total UK commercial landings for European seabass (Dicentrarchus labrax), European plaice (Pleuronectes platessa), and Common sole (Solea solea). Our findings highlight the importance of saltmarsh protection and restoration. Furthermore, our approach provides a general framework that integrates population ecology methods and economic analyses to assess the value of saltmarsh and other coastal habitats for fisheries worldwide.

ecology↗

bioRxiv2019

Movement and space-use responses of a large herbivore to experimental alteration of resource availability

The link between spatio-temporal resource patterns and movement behaviour is a key ecological process, however, limited experimental support has been produced at the home range scale. In this study, we analysed the spatial responses of a resident large herbivore (roe deer Capreolus capreolus) during an in situ manipulation of a concentrated food resource. Specifically, we experimentally altered feeding site accessibility to roe deer and recorded (for 25 animal-years) individual responses by GPS tracking. We found that, following the loss of their preferred resource, roe deer actively tracked resource dynamics leading to more exploratory movements, and larger, spatially-shifted home ranges. Then, we showed, for the first time experimentally, the importance of site fidelity in the maintenance of large mammal home ranges by demonstrating the return of individuals to their familiar, preferred resource despite the presence of alternate, equally-valuable food resources. This behaviour was modulated at the individual level, where roe deer characterised by a high preference for feeding sites exhibited more pronounced behavioural adjustments during the manipulation. Together, our results establish the connections between movement, space-use, individual preference, and the spatio-temporal pattern of resources in home ranging behaviour.

ecology↗

bioRxiv2019

Novel Universal Primers For Metabarcoding eDNA Surveys Of Marine Mammals And Other Marine Vertebrates

Metabarcoding studies using environmental DNA (eDNA) and high throughput sequencing (HTS) are rapidly becoming an important tool for assessing and monitoring marine biodiversity, detecting invasive species, and supporting basic ecological research. Several barcode loci targeting teleost fish and elasmobranchs have previously been developed, but to date primer sets focusing on other marine megafauna, such as marine mammals have received less attention. Similarly, there have been few attempts to identify potentially universal barcode loci which may be informative across multiple marine vertebrate Orders. Here we describe the design and validation of four new sets of primers targeting hypervariable regions of the vertebrate mitochondrial 12S and 16S rRNA genes, which have conserved priming sites across virtually all cetaceans, pinnipeds, elasmobranchs, boney fish, sea turtles and birds, and amplify fragments with consistently high levels of taxonomically diagnostic sequence variation. In silico validation using the OBITOOLS software showed our new barcode loci outperformed most existing vertebrate barcode loci for taxon detection and resolution. We also evaluated sequence diversity and taxonomic resolution of the new barcode loci in 680 complete marine mammal mitochondrial genomes demonstrating that they are effective at resolving amplicons for most taxa to the species level. Finally, we evaluated the performance of the primer sets with eDNA samples from aquarium communities with known species composition. These new primers will potentially allow surveys of complete marine vertebrate communities in single HTS metabarcoding assessments, simplifying workflows, reducing costs, and increasing accessibility to a wider range of investigators.

ecology↗

bioRxiv2019

Mean growth rate when rare is not a reliable metric for persistence of species

The coexistence of many species within ecological communities poses a long-standing theoretical puzzle. Modern coexistence theory (MCT) and related techniques explore this phenomenon by examining the chance of a species population growing from rarity in the presence of all other species. The mean growth rate when rare, [E][r], is used in MCT as a metric that measures persistence properties (like invasibility or time to extinction) of a population. Here we critique this reliance on [E][r] and show that it fails to capture the effect of random abundance variations on persistence properties. The problem becomes particularly severe when an increase in the amplitude of stochastic temporal environmental variations leads to an increase in [E][r], since at the same time it enhances random abundance fluctuations and the two effects are inherently intertwined. In this case, the chance of invasion and the mean extinction time of a population may even go down as [E][r] increases.

ecology↗

bioRxiv2019

A simple pyrocosm for studying soil microbial response to fire reveals a rapid, massive response by Pyronema species

We have designed a simple, inexpensive system for the studying the response of soil microbes to fire. This system allows one to create post-fire environments in soil in reproducible and realistic ways. Using it we show that the peak soil temperature achieved at a given depth occurs hours after the fire is out, lingers near peak temperature for a significant time, and is accurately predicted by the log of soil depth and the mass charcoal burned. Flash fuels that left no large coals were found to have a negligible soil heating effect. Coupling this system with Illumina MiSeq sequencing of the control and post-fire soil we show that we can stimulate a rapid, massive response by Pyronema, a well-known genus of postfire fungus, from uninoculated forest soil within two weeks of a test fire. This specific stimulation occurs in a background of many other fungal taxa that do not change significantly with the fire, although there is an overall reduction in richness and evenness. Extrapolating from the physical relationships we predict soil heating effects in wild fires are likely to be very patchy across the forest floor but the width of a survivable \"goldilocks zone\" will stay relatively constant across a range of fuel loads. We further predict that a necromass zone above it, which represents an open niche for pyrophilous microbes, increases in size rapidly with addition of fuel, and then remains nearly constant over a broad range of fuel loads. The simplicity of this experimental system, coupled with the availability of a set of sequenced, assembled and annotated genomes of pyrophilous fungi, offers a powerful tool for dissecting the ecology of post-fire microbial communities.

ecology↗

bioRxiv2019

Is the distribution of the Acorn Woodpecker (Melanerpes formicivorus flavigula) associated with oaks and granaries? A local study in an urban area in northern South America

Abiotic and biotic factors are known to be key in limiting the geographical distribution of species. However, our understanding on the influence of habitat heterogeneity on ecological interactions and behavior in tropical animals is limited. We studied groups of Acorn Woodpeckers (Melanerpes formicivorus flavigula) in urban and rural areas in northern South America to understand how habitat and resource requirements (food storage structures) influences patterns of distribution across the Aburra Valley, in the northern area of the Central Andes of Colombia. Using focal observations of 10 different groups over nearly a two-year period, we estimated territory size, habitat use, and described the use and presence of granaries. We found that territory size, tree diversity, and the use of granaries varied among groups. Accordingly, Acorn Woodpeckers use a wide variety of tree species to make cavities, to feed and to build granaries for social interactions. Our study supports the hypothesis that Acorn Woodpeckers do not rely on the Colombian Oak (Quercus humboldtii Bonpl.) for feeding, nesting or foraging in the Aburra Valley, and that the construction of granaries to store food is present in urban populations, despite the lack of strong seasonal changes in tropical areas. We suggest that the distribution of the Acorn Woodpecker in our study area is strongly associated with one particular species of tree, Albizia carbonaria Britton, and the behavior of granaries construction might be hardwired in this species for the maintenance and cohesion of family groups.

ecology↗

bioRxiv2019

Intra-Specific variability in fluctuating environments - mechanisms of impact on species diversity

Recent studies have found considerable trait variations within species. The effect of such intra-specific trait variability (ITV) on the stability, coexistence and diversity of ecological communities received considerable attention and in many models it was shown to impede coexistence and decrease species diversity. Here we present a numerical study of the effect of genetically inherited ITV on species persistence and diversity in a temporally fluctuating environment. Two mechanisms are identified. First, ITV buffers populations against varying environmental conditions (portfolio effect) and reduces abundance variations. Second, the interplay between ITV and environmental variations tends to increase the mean fitness of diverse populations. The first mechanism promotes persistence and tends to increase species richness, while the second reduces the chance of a rare species population (which is usually homogenous) to invade and decreases species richness. We show that for large communities the portfolio effect is dominant, leading to ITV promoting species persistence and richness.

ecology↗

bioRxiv2019

Timing and duration of phenological subsidies: toward a mechanistic understanding of impacts on community structure and ecosystem processes in stream food chains

Phenological resources are common across many ecological communities, and can strongly affect community dynamics. Recent field manipulation experiments in stream food chains found that seasonal timing and duration of terrestrial prey inputs affected the feeding behavior, growth, and maturation of fish predators, caused predator-mediated indirect effects on aquatic prey, and modified trophic-cascading effects on litter processing. These experiments described impacts of resource phenological changes over a few month period, and long-term impacts of continued changes in resource phenology are unknown. Here we develop a mathematical model to extrapolate long-term predictions about the effects of changes in resource phenology from the results of field manipulation experiments. The model predicts that advanced timing generally decreases aquatic prey and litter processing and prolonged duration will either increase or decrease aquatic prey and litter processing depending on the total amount and pre-disturbed timing and duration of terrestrial prey inputs. Importantly, our modeling approach clarifies the mechanisms by which stage-specific responses of life history processes in fish, such as growth, maturation, and reproduction, respond to phenological changes in terrestrial prey inputs and mediate indirect effects on aquatic prey and litter processing. Stage-specific responses of life history processes are an integral part of the mechanisms with which to predict the consequences of phenological species interactions at the community and ecosystem levels.

ecology↗

bioRxiv2019

Intraspecific trait variability and community assembly in hawkmoths (Lepidoptera: Sphingidae) across an elevational gradient in the eastern Himalayas, India

O_LIRecent progress in functional ecology has advanced our understanding of the role of intraspecific (ITV) and interspecific (STV) trait variation in community assembly across environmental gradients. Studies on plant communities have generally found STV as the main driver of community trait variation, whereas ITV plays an important role in determining species co-existence and community assembly. However, similar studies of faunal taxa, especially invertebrates, are very few in number.\nC_LIO_LIWe investigated variation of hawkmoth (Lepidoptera: Sphingidae) traits along an environmental gradient spanning 2600 m in the eastern Himalayas and its role in community assembly, using the morpho-functional traits of body mass (BM), wing loading (WL) and wing aspect ratio (AR).\nC_LIO_LIWe employ the recently proposed T-statistics to test for non-random assembly of hawkmoth communities and the relative importance of the two opposing forces for trait divergence (internal filters) and convergence (external filters).\nC_LIO_LICommunity-wide trait-overlap decreased for all three traits with increasing environmental distance, suggesting the presence of elevation specific optimum morphology (i.e. functional response traits). Community weighted mean of BM and AR increased with elevation. Overall, the variation was dominated by species turnover but ITV accounted for 25%, 23% and <1% variability of BM, WL and AR, respectively. T-statistics, which incorporates ITV, revealed that elevational communities had a non-random trait distribution, and that community assembly was dominated by internal filtering throughout the gradient.\nC_LIO_LIThis study was carried out using easily measurable morpho-traits obtained from calibrated field images of a large number (3301) of individuals. That these also happened to be important environmental response traits resulted in a significant signal in the metrics that we investigated. Such studies of abundant and hyperdiverse invertebrate groups across large environmental gradients should considerably improve our understanding of community assembly processes.\nC_LI

ecology↗

bioRxiv2019

Patterns of smallpox mortality in London, England, over three centuries

Smallpox is unique among infectious diseases in the degree to which it devasted human populations, its long history of control interventions, and the fact that it has been successfully eradicated. Mortality from smallpox in London, England, was carefully documented, weekly, for nearly 300 years, providing a rare and valuable source for the study of ecology and evolution of infectious disease. We describe and analyze smallpox mortality in London from 1664 to 1930. We digitized the weekly records published in the London Bills of Mortality and the Registrar Generals Weekly Returns. We annotated the resulting time series with a sequence of historical events that appear to have influenced smallpox dynamics in London. We present a spectral analysis that reveals how periodicities in smallpox dynamics changed over decades and centuries, and how these changes were related to control interventions and public health policy changes. We also examine how the seasonality of smallpox epidemics changed from the 17th to 20th centuries in London.

ecology↗

bioRxiv2019

Small terrestrial mammal distributions in Simien Mountains National Park, Ethiopia: A reassessment after 88 years

Little is known about the distribution and ecology of small mammals inhabiting Simien Mountains National Park despite the presence of mostly endemic species. Prior to this study, the most comprehensive dataset was collected in 1927. This provides a unique opportunity to assess the possible role of climate change over the last 88 years on the elevational distribution of mammals in the Ethiopian highlands. Between September and November 2015, three of us (EWC, WTS, YM) collected non-volant small mammals at four sites (2900, 3250, 3600, and 4000 m a.s.l.) along the western slope of the Simien Mountains using standardized sampling. Over a four-week period we recorded 13 species, comprising 11 rodents and two shrews, all endemic to the Ethiopian Plateau. We found greatest species richness at mid-elevations (3250 m), consistent with a general pattern found on many other mountains worldwide but less so in Africa. We discovered one potentially new species of shrew. No previously unrecorded rodent species were observed. Finally, we compared our species distribution results to the 1927 dataset and found upward elevational shifts in species ranges, suggesting the role and influence of climate change on the small mammal community. Simien Mountains National Park represents an exceptionally valuable core area of endemism and the best protected natural habitat in northern Ethiopia.

ecology↗

bioRxiv2019

Environmental decomposition of cuticular hydrocarbons generates a volatile pheromone that guides insect social behavior

Once emitted, semiochemicals are exposed to reactive environmental factors that may alter them, thus disrupting chemical communication. Some species, however, might have adapted to detect environmentally mediated breakdown products of their natural chemicals as semiochemicals. We demonstrate that air, water vapor, and ultraviolet (UV) radiation break down unsaturated cuticular hydrocarbons (CHCs) of Periplaneta americana (American cockroach), resulting in the emission of volatile organic compounds (VOCs). In behavioral assays, nymphs strongly avoided aggregating in shelters exposed to the breakdown VOCs from cuticular alkenes. The three treatments (air, water vapor, UV) produced the same VOCs, but at different time-courses and ratios. Fourteen VOCs from UV-exposed CHCs elicited electrophysiological responses in nymph antennae; 10 were identified as 1-pentanol, 1-octanol, 1-nonanol, tetradecanal, acetic acid, propanoic acid, butanoic acid, pentanoic acid and hexanoic acid. When short-chain fatty acids were tested as a mix and a blend of the alcohols and aldehyde was tested as a second mix, nymphs exhibited no preference for control or treated shelters. However, nymphs avoided shelters that were exposed to VOCs from the complete 10-compound mix. Conditioned shelters (occupied by cockroaches with feces and CHCs deposited on the shelters), which are normally highly attractive to nymphs, were also avoided after UV-exposure, confirming that breakdown products from deposited metabolites, including CHCs, mediate this behavior. Our results demonstrate that common environmental and anthropogenic agents degrade CHCs into volatile semiochemicals that may serve as necromones or epideictic pheromones, mediating group formation and dissolution.\n\nSignificance StatementCuticular hydrocarbons (CHCs) cover the outer surface of insects, where they prevent water loss and serve as sex pheromones and in nest-mate recognition in social insects. Although CHCs are not volatile, they can be broken into volatile fragments by reacting with environmental agents. We demonstrate that volatile breakdown products of CHCs affect the social behavior of the American cockroach. A synthetic mix of volatiles dispersed cockroaches away from shelters, signaling an unsuitable shelter. These results highlight that some insect species have evolved communication strategies that exploit environmental and anthropogenic agents to produce bioactive compounds that mediate ecological interactions.

ecology↗

bioRxiv2019

The power of mixed survey methodologies for detecting decline of the Bornean orangutan

For many threatened species, it is difficult to assess precisely for large areas the change in their abundances over time and the relative impacts of climate and anthropogenic land use. This is because surveys of such species are typically restricted to small geographic areas, are conducted during short time periods, and use different survey protocols. We assessed the change in the abundance of Bornean orangutan Pongo pygmaeus morio in Sabah, Malaysia, and to identify environmental drivers affecting the change by integrating different types of survey data. We used nest count data obtained from aerial and ground transect surveys and occurrence data obtained from reconnaissance walks and interview survey over the past decade. We built a spatially-explicit dynamic population model within the Bayesian framework allowing these varying survey data to be analyzed jointly by explicitly accounting for each surveys sampling rate. We found that sampling rates vary across survey types, reflecting each surveys associated effort. Orangutan survival rates were strongly determined by natural forest extent and moderately by temperature. Orangutan migration rates across more than 1 km distance between forest patches were low, which underlines the importance of maintaining ecological connectivity. The paucity of species abundance data collected in a consistent manner over many years across broad extents often hinders the assessment of species population trend and their persistence across regional scales. We demonstrate that this can be addressed by integrating multiple survey data across different localities, provided that sampling rate inherent to each survey is accounted for.

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