scholarly journals Estimating the movements of terrestrial animal populations using broad-scale occurrence data

2021 ◽  
Vol 9 (1) ◽  
Author(s):  
Sarah R. Supp ◽  
Gil Bohrer ◽  
John Fieberg ◽  
Frank A. La Sorte
Keyword(s):  
Population Level ◽  
Sampling Bias ◽  
Population Movements ◽  
Spatial And Temporal Scales ◽  
Temporal Sampling ◽  
Multiple Observations ◽  
Occurrence Data ◽  
Population Distributions ◽  
Animal Populations ◽  
Broad Scale

AbstractAs human and automated sensor networks collect increasingly massive volumes of animal observations, new opportunities have arisen to use these data to infer or track species movements. Sources of broad scale occurrence datasets include crowdsourced databases, such as eBird and iNaturalist, weather surveillance radars, and passive automated sensors including acoustic monitoring units and camera trap networks. Such data resources represent static observations, typically at the species level, at a given location. Nonetheless, by combining multiple observations across many locations and times it is possible to infer spatially continuous population-level movements. Population-level movement characterizes the aggregated movement of individuals comprising a population, such as range contractions, expansions, climate tracking, or migration, that can result from physical, behavioral, or demographic processes. A desire to model population movements from such forms of occurrence data has led to an evolving field that has created new analytical and statistical approaches that can account for spatial and temporal sampling bias in the observations. The insights generated from the growth of population-level movement research can complement the insights from focal tracking studies, and elucidate mechanisms driving changes in population distributions at potentially larger spatial and temporal scales. This review will summarize current broad-scale occurrence datasets, discuss the latest approaches for utilizing them in population-level movement analyses, and highlight studies where such analyses have provided ecological insights. We outline the conceptual approaches and common methodological steps to infer movements from spatially distributed occurrence data that currently exist for terrestrial animals, though similar approaches may be applicable to plants, freshwater, or marine organisms.

scholarly journals The role of habitat configuration in shaping animal population processes: a framework to generate quantitative predictions

Oecologia ◽  
2021 ◽  
Author(s):  
Peng He ◽  
Pierre-Olivier Montiglio ◽  
Marius Somveille ◽  
Mauricio Cantor ◽  
Damien R. Farine
Keyword(s):  
Population Level ◽  
R Package ◽  
Habitat Configuration ◽  
Modelling Framework ◽  
Alternative Habitat ◽  
Animal Populations ◽  
Research Questions ◽  
Habitat Networks ◽  
Animal Habitat

AbstractBy shaping where individuals move, habitat configuration can fundamentally structure animal populations. Yet, we currently lack a framework for generating quantitative predictions about the role of habitat configuration in modulating population outcomes. To address this gap, we propose a modelling framework inspired by studies using networks to characterize habitat connectivity. We first define animal habitat networks, explain how they can integrate information about the different configurational features of animal habitats, and highlight the need for a bottom–up generative model that can depict realistic variations in habitat potential connectivity. Second, we describe a model for simulating animal habitat networks (available in the R package AnimalHabitatNetwork), and demonstrate its ability to generate alternative habitat configurations based on empirical data, which forms the basis for exploring the consequences of alternative habitat structures. Finally, we lay out three key research questions and demonstrate how our framework can address them. By simulating the spread of a pathogen within a population, we show how transmission properties can be impacted by both local potential connectivity and landscape-level characteristics of habitats. Our study highlights the importance of considering the underlying habitat configuration in studies linking social structure with population-level outcomes.

scholarly journals Bias-Variance Trade-Off in Continuous Test Norming

Assessment ◽  
2020 ◽  
pp. 107319112093915
Author(s):  
Lieke Voncken ◽  
Casper J. Albers ◽  
Marieke E. Timmerman
Keyword(s):  
Generalized Additive Models ◽  
Population Level ◽  
Additive Models ◽  
Distributed Data ◽  
Score Distribution ◽  
Population Distributions ◽  
Continuous Test ◽  
Model Flexibility ◽  
Bias Variance ◽  
T Distribution

In continuous test norming, the test score distribution is estimated as a continuous function of predictor(s). A flexible approach for norm estimation is the use of generalized additive models for location, scale, and shape. It is unknown how sensitive their estimates are to model flexibility and sample size. Generally, a flexible model that fits at the population level has smaller bias than its restricted nonfitting version, yet it has larger sampling variability. We investigated how model flexibility relates to bias, variance, and total variability in estimates of normalized z scores under empirically relevant conditions, involving the skew Student t and normal distributions as population distributions. We considered both transversal and longitudinal assumption violations. We found that models with too strict distributional assumptions yield biased estimates, whereas too flexible models yield increased variance. The skew Student t distribution, unlike the Box–Cox Power Exponential distribution, appeared problematic to estimate for normally distributed data. Recommendations for empirical norming practice are provided.

The importance of superior-quality wildlife habitats

2004 ◽  
Vol 80 (1) ◽  
pp. 75-81 ◽  
Author(s):  
Ian D Thompson
Keyword(s):  
Habitat Selection ◽  
Habitat Quality ◽  
Population Level ◽  
Individual Fitness ◽  
Animal Populations ◽  
Cumulative Change ◽  
Few Data ◽  
Managed Landscapes ◽  
The Relationship

While animals may use many habitat types, relatively few are preferred and fewer yet are superior in quality (referring to individual fitness as the measure of quality). Historical reduction in habitat quality for some wildlife species has occurred such that we may now have limited reference to original superior-quality habitats. As time passes, managers may be unaware that superior habitats are slowly disappearing and that the slow but cumulative change is significant to a species at the population level. The perception of superior-quality habitat also changes with each successive generation of managers based on their experiences. This paper raises the concern that retrospective work may often be required to determine past forest habitats and associated animal populations to avoid the risk of falling into a trap of not recognizing ever-declining habitat quality through time and relegating animals to what is in fact much poorer quality habitat than those to which they are actually best adapted. Further, the relationship between relative abundance and habitat quality may often be uncertain owing to maladaptive habitat selection by animals, inappropriate survey timing or interannual population differences. While we have begun to appreciate aspects of habitat selection for many forest species, few data are yet available that relate selected habitats to fitness of individual animals. Hence, while we may have models to predict habitat use, considerable research remains to be done to be able to predict long-term sustainability of species in managed landscapes. Key words: habitat quality, forest management, sustainability, biodiversity

scholarly journals Abundance and genetic diversity responses of a lizard (Eulamprus heatwolei) to logging disturbance

2017 ◽  
Vol 65 (6) ◽  
pp. 362
Author(s):  
Francesca Lyndon-Gee ◽  
Joanna Sumner ◽  
Yang Hu ◽  
Claudio Ciofi ◽  
Tim S. Jessop
Keyword(s):  
Genetic Diversity ◽  
Forest Management ◽  
Management Practices ◽  
Forest Disturbance ◽  
Population Level ◽  
Landscape Scale ◽  
Population Abundance ◽  
Animal Populations ◽  
Eastern Australia ◽  
Logging Disturbance

Rotational logging practices are used with the goal of reducing forest disturbance impacts on biodiversity. However, it is poorly understood whether such forest management practices conserve the demographic and genetic composition of animal populations across logged landscapes. Here we investigated whether rotational logging practices alter patterns of landscape-scale population abundance and genetic diversity of a forest-dwelling lizard (Eulamprus heatwolei) in south-eastern Australia. We sampled lizards (n = 407) at up to 48 sites across a chronosequence of logging disturbance intervals (<10 to >60 years after logging) to assess site-specific population changes and genetic diversity parameters. Lizard abundances exhibited a significant curvilinear response to time since logging, with decreased numbers following logging (<10 years), increased abundance as the forest regenerated (10–20 years), before decreasing again in older regenerated forest sites (>30 years). Lizard genetic diversity parameters were not significantly influenced by logging disturbance. These results suggest that logging practices, whilst inducing short-term changes to population abundance, had no measurable effects on the landscape-scale genetic diversity of E. heatwolei. These results are important as they demonstrate the value of monitoring for evaluating forest management efficacy, and the use of different population-level markers to make stronger inference about the potential impacts of logging activities.

scholarly journals From daily movements to population distributions: weather affects competitive ability in a guild of soaring birds

2013 ◽  
Vol 10 (88) ◽  
pp. 20130612 ◽  
Author(s):  
Emily L. C. Shepard ◽  
Sergio A. Lambertucci
Keyword(s):  
Competitive Ability ◽  
Meteorological Factors ◽  
Interspecific Interactions ◽  
Wing Loading ◽  
Spatial And Temporal Scales ◽  
Population Distributions ◽  
Common Resource ◽  
Soaring Flight ◽  
The Cost ◽  
Ephemeral Resources

The ability of many animals to access and exploit food is dependent on the ability to move. In the case of scavenging birds, which use soaring flight to locate and exploit ephemeral resources, the cost and speed of movement vary with meteorological factors. These factors are likely to modify the nature of interspecific interactions, as well as individual movement capacity, although the former are less well understood. We used aeronautical models to examine how soaring performance varies with weather within a guild of scavenging birds and the consequences this has for access to a common resource. Birds could be divided broadly into those with low wing loading that are more competitive in conditions with weak updraughts and low winds (black vultures and caracaras), and those with high wing loading that are well adapted for soaring in strong updraughts and moderate to high winds (Andean condors). Spatial trends in meteorological factors seem to confine scavengers with high wing loading to the mountains where they out-compete other birds; a trend that is borne out in worldwide distributions of the largest species. However, model predictions and carcass observations suggest that the competitive ability of these and other birds varies with meteorological conditions in areas where distributions overlap. This challenges the view that scavenging guilds are structured by fixed patterns of dominance and suggests that competitive ability varies across spatial and temporal scales, which may ultimately be a mechanism promoting diversity among aerial scavengers.

scholarly journals Convergence of broad-scale migration strategies in terrestrial birds

2016 ◽  
Vol 283 (1823) ◽  
pp. 20152588 ◽  
Author(s):  
Frank A. La Sorte ◽  
Daniel Fink ◽  
Wesley M. Hochachka ◽  
Steve Kelling
Keyword(s):  
Optimal Solution ◽  
Population Level ◽  
Western Hemisphere ◽  
Migratory Species ◽  
Spatial Convergence ◽  
Common Strategy ◽  
Annual Population ◽  
Migration Strategies ◽  
Multiple Species ◽  
Broad Scale

Migration is a common strategy used by birds that breed in seasonal environments. Selection for greater migration efficiency is likely to be stronger for terrestrial species whose migration strategies require non-stop transoceanic crossings. If multiple species use the same transoceanic flyway, then we expect the migration strategies of these species to converge geographically towards the most optimal solution. We test this by examining population-level migration trajectories within the Western Hemisphere for 118 migratory species using occurrence information from eBird. Geographical convergence of migration strategies was evident within specific terrestrial regions where geomorphological features such as mountains or isthmuses constrained overland migration. Convergence was also evident for transoceanic migrants that crossed the Gulf of Mexico or Atlantic Ocean. Here, annual population-level movements were characterized by clockwise looped trajectories, which resulted in faster but more circuitous journeys in the spring and more direct journeys in the autumn. These findings suggest that the unique constraints and requirements associated with transoceanic migration have promoted the spatial convergence of migration strategies. The combination of seasonal atmospheric and environmental conditions that has facilitated the use of similar broad-scale migration strategies may be especially prone to disruption under climate and land-use change.

scholarly journals Genomic associations with poxvirus across divergent island populations in Berthelot's pipit

2021 ◽  
Author(s):  
Eleanor Sheppard ◽  
Claudia Martin ◽  
Claire Armstrong ◽  
Catalina González-Quevedo ◽  
Juan Carlos Illera ◽  
...  
Keyword(s):  
Viral Infection ◽  
Population Level ◽  
Genomic Variation ◽  
Nucleotide Polymorphisms ◽  
Individual Level ◽  
Island Populations ◽  
Bird Populations ◽  
Animal Populations ◽  
Infection Pressure ◽  
Avian Pox

Understanding the mechanisms and genes that enable animal populations to adapt to pathogens is important from an evolutionary, health and conservation perspective. Berthelot’s pipit (Anthus berthelotii) experiences extensive and consistent spatial heterogeneity in avian pox infection pressure across its range of island populations, thus providing an excellent system with which to examine how pathogen-mediated selection drives spatial variation in immunogenetic diversity. Here we test for evidence of genetic variation associated with avian pox at both an individual and population-level. At the individual level, we find no evidence that variation in MHC class I and TLR4 (both known to be important in recognising viral infection) was associated with pox infection within two separate populations. However, using genotype-environment association (Bayenv) in conjunction with genome-wide (ddRAD-seq) data, we detected strong associations between population-level avian pox prevalence and allele frequencies of single nucleotide polymorphisms (SNPs) at a number of sites across the genome. These sites were located within genes involved in cellular stress signalling and immune responses, many of which have previously been associated with responses to viral infection in humans and other animals. Consequently, our analyses provide evidence that pathogen-mediated selection has shaped genomic variation among relatively recently colonised island bird populations, and highlights the utility of genotype-environment associations for identifying candidate genes involved in adaption to local pathogen pressures.

scholarly journals Consistent Trait-Temperature Interactions Drive Butterfly Phenology in Both Incidental and Survey Data

2021 ◽  
Author(s):  
Elise A. Larsen ◽  
Michael W. Belitz ◽  
Robert P. Guralnick ◽  
Leslie Ries
Keyword(s):  
Survey Data ◽  
Data Availability ◽  
Flight Period ◽  
Resident Species ◽  
Occurrence Data ◽  
Advanced Stages ◽  
Data Source ◽  
Temporal And Spatial ◽  
Temperature Interactions ◽  
Broad Scale

Abstract Data availability limits phenological research at broad temporal and spatial extents. Butterflies are among the few taxa with broad-scale occurrence data, from both incidental reports and formal surveys. Incidental reports have observation biases that are challenging to address, but structured surveys are often limited seasonally and may not span full flight phenologies. Thus, which data source is more useful for phenological analyses is unclear. We use parallel analyses of incidental and survey data to determine how traits and climate drive phenological patterns for common butterflies. One workflow aggregated “Pollard” surveys, where sites are visited multiple times per year; the other aggregated incidental data from online portals: iNaturalist and eButterfly. For 40 routinely observed resident species, we estimated early (10%) and mid (50%) flight period metrics, and compared the spatiotemporal patterns and drivers of phenology across species and between datasets. Results were similar between datasets. Inter-annual variability was best explained by temperature, and seasonal emergence was earlier for resident species that overwinter at more advanced stages. Other traits had mixed or no impacts. The consistency in results suggests that data integration can improve phenological research, and leveraging traits may predict phenology in poorly studied species.

scholarly journals Estimating wildlife vaccination coverage using genetic methods

2017 ◽  
Author(s):  
Freya Smith ◽  
Andrew Robertson ◽  
Graham C. Smith ◽  
Peter Gill ◽  
Robbie A. McDonald ◽  
...  
Keyword(s):  
Bovine Tuberculosis ◽  
Vaccine Coverage ◽  
Vaccination Campaign ◽  
Total Duration ◽  
Vaccine Dose ◽  
Population Level ◽  
Tuberculosis Control ◽  
Animal Populations ◽  
Hair Samples ◽  
Wildlife Vaccination

AbstractVaccination is a potentially useful approach for the control of disease in wildlife populations. The effectiveness of vaccination is contingent in part on obtaining adequate vaccine coverage at the population level. However, measuring vaccine coverage in wild animal populations is challenging and so there is a need to develop robust approaches to estimate coverage and so contribute to understanding the likely efficacy of vaccination.We used a modified capture mark recapture technique to estimate vaccine coverage in a wild population of European badgers (Meles meles) vaccinated by live-trapping and injecting with Bacillus Calmette-Guérin as part of a bovine tuberculosis control initiative in Wales, United Kingdom. Our approach used genetic matching of vaccinated animals to a sample of the wider population to estimate the percentage of badgers that had been vaccinated. Individual-specific genetic profiles were obtained using microsatellite genotyping of hair samples which were collected both directly from trapped and vaccinated badgers and non-invasively from the wider population using hair traps deployed at badger burrows.We estimated the percentage of badgers vaccinated in a single year and applied this to a simple model to estimate cumulative vaccine coverage over a four year period, corresponding to the total duration of the vaccination campaign.In the year of study, we estimated that between 44-65% (95% confidence interval, mean 55%) of the badger population received a vaccine dose. Using the model, we estimated that 70-85% of the total population would have received at least one vaccine dose over the course of the four year vaccination campaign.This study represents the first application of this novel approach for measuring vaccine coverage in wildlife. This is also the first attempt at quantifying the level of vaccine coverage achieved by trapping and injecting badgers. The results therefore have specific application to bovine tuberculosis control policy, and the approach is of significance to the wider field of wildlife vaccination.

scholarly journals Sampling bias in reptile occurrence data for the Kruger National Park

Koedoe ◽  
2020 ◽  
Vol 62 (1) ◽  
Author(s):  
Jody M. Barends ◽  
Darren W. Pietersen ◽  
Guinevere Zambatis ◽  
Donovan R.C. Tye ◽  
Bryan Maritz
Keyword(s):  
National Park ◽  
Conservation Management ◽  
Species Distributions ◽  
Sampling Bias ◽  
Kruger National Park ◽  
Data Set ◽  
Occurrence Data ◽  
Reptile Species ◽  
Sampling Biases ◽  
Occurrence Records

o effectively conserve and manage species, it is important to (1) understand how they are spatially distributed across the globe at both broad and fine spatial resolutions and (2) elucidate the determinants of these distributions. However, information pertaining to the distributions of many species remains poor as occurrence data are often scarce or collected with varying motivations, making the resulting patterns susceptible to sampling bias. Exacerbating an already limited quantity of occurrence data with an assortment of biases hinders their effectiveness for research, thus making it important to identify and understand the biases present within species occurrence data sets. We quantitatively assessed occurrence records of 126 reptile species occurring in the Kruger National Park (KNP), South Africa, to quantify the severity of sampling bias within this data set. We collated a data set of 7118 occurrence records from museum, literature and citizen science sources and analysed these at a biologically relevant spatial resolution of 1 km × 1 km. As a result of logistical challenges associated with sampling in KNP, approximately 92% of KNP is data deficient for reptile occurrences at the 1 km × 1 km resolution. Additionally, the spatial coverage of available occurrences varied at species and family levels, and the majority of occurrence records were strongly associated with publicly accessible human infrastructure. Furthermore, we found that sampled areas within KNP were not necessarily ecologically representative of KNP as a whole, suggesting that areas of unique environmental space remain to be sampled. Our findings highlight the need for substantially greater sampling effort for reptiles across KNP and emphasise the need to carefully consider the sampling biases within existing data should these be used for conservation management decision-making. Modelling species distributions could potentially serve as a short-term solution, but a concomitant increase in surveys across the park is needed.Conservation implications: The sampling biases present within KNP reptile occurrence data inhibit the inference of fine-scale species distributions within and across the park, which limits the usage of these data towards meaningfully informing conservation management decisions as applicable to reptile species in KNP.

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