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Modern Applied Statistics With S

Beginning with Emlen (1966) and MacArthur and Pianka (1966) and extending through the last ten years, several authors have sought to predict the foraging behavior of animals by means of mathematical models. These models are very similar,in that they all assume that the fitness of a foraging animal is a function of the efficiency of foraging measured in terms of some "currency" (Schoener, 1971) -usually energy- and that natural selection has resulted in animals that forage so as to maximize this fitness. As a result of these similarities, the models have become known as "optimal foraging models"; and the theory that embodies them, "optimal foraging theory." The situations to which optimal foraging theory has been applied, with the exception of a few recent studies, can be divided into the following four categories: (1) choice by an animal of which food types to eat (i.e., optimal diet); (2) choice of which patch type to feed in (i.e., optimal patch choice); (3) optimal allocation of time to different patches; and (4) optimal patterns and speed of movements. In this review we discuss each of these categories separately, dealing with both the theoretical developments and the data that permit tests of the predictions. The review is selective in the sense that we emphasize studies that either develop testable predictions or that attempt to test predictions in a precise quantitative manner. We also discuss what we see to be some of the future developments in the area of optimal foraging theory and how this theory can be related to other areas of biology. Our general conclusion is that the simple models so far formulated are supported are supported reasonably well by available data and that we are optimistic about the value both now and in the future of optimal foraging theory. We argue, however, that these simple models will requre much modification, espicially to deal with situations that either cannot easily be put into one or another of the above four categories or entail currencies more complicated that just energy.

Citation classic - optimal foraging - a selective review of theory and tests

A DNA test to sex most birds.

Human activities, especially conversion and degradation of habitats, are causing global biodiversity declines. How local ecological assemblages are responding is less clear--a concern given their importance for many ecosystem functions and services. We analysed a terrestrial assemblage database of unprecedented geographic and taxonomic coverage to quantify local biodiversity responses to land use and related changes. Here we show that in the worst-affected habitats, these pressures reduce within-sample species richness by an average of 76.5%, total abundance by 39.5% and rarefaction-based richness by 40.3%. We estimate that, globally, these pressures have already slightly reduced average within-sample richness (by 13.6%), total abundance (10.7%) and rarefaction-based richness (8.1%), with changes showing marked spatial variation. Rapid further losses are predicted under a business-as-usual land-use scenario; within-sample richness is projected to fall by a further 3.4% globally by 2100, with losses concentrated in biodiverse but economically poor countries. Strong mitigation can deliver much more positive biodiversity changes (up to a 1.9% average increase) that are less strongly related to countries' socioeconomic status.

/pdf/global-effects-of-land-use-on-local-terrestrial-biodiversity-31yzxze5ly.pdf

Global effects of land use on local terrestrial biodiversity

Summary

1
Humans have traded and transported alien species for millennia with two notable step-changes: the end of the Middle Ages and beginning of the Industrial Revolution. However, in recent decades the world has entered a new phase in the magnitude and diversity of biological invasions: the Era of Globalization. This Special Profile reviews the links between the main drivers of globalization and biological invasions and examines state-of-the-art approaches to pathway risk assessment to illustrate new opportunities for managing invasive species.

2
Income growth is a primary driver of globalization and a clear association exists between Gross Domestic Product and the richness of alien floras and faunas for many regions of the world. In many cases, the exposure of these economies to trade is highlighted by the significant role of merchandise imports in biological invasions, especially for island ecosystems.

3
Post-1950, technical and logistic improvements have accelerated the ease with which commodities are transported across the globe and hindered the traceability of goods and the ease of intercepting pests. New sea, land and air links in international trade and human transport have established novel pathways for the spread of alien species. Increasingly, the science advances underpinning invasive species management must move at the speed of commerce.

4
Increasing transport networks and demand for commodities have led to pathway risk assessments becoming the frontline in the prevention of biological invasions. The diverse routes of introduction arising from contaminant, stowaway, corridor and unaided pathways, in both aquatic and terrestrial biomes are complex. Nevertheless, common features enable comparable approaches to risk assessment. By bringing together spatial data on climate suitability, habitat availability and points of entry, as well a demographic models that include species dispersal (both natural and human-mediated) and measures of propagule pressure, it is possible to generate risk maps highlighting potential invasion hotspots that can inform prevention strategies.

5
Synthesis and applications. To date, most attempts to model pathways have focused on describing the likelihood of invader establishment. Few have modelled explicit management strategies such as optimal detection and inspection strategies and assessments of the effectiveness of different management measures. A future focus in these areas will ensure research informs response.

https://besjournals.onlinelibrary.wiley.com/doi/epdf/10.1111/j.1365-2664.2008.01600.x

Trade, transport and trouble: managing invasive species pathways in an era of globalization

Summary
Reliable assessment of animal populations is a long-standing challenge in wildlife ecology. Technological advances have led to widespread adoption of camera traps (CTs) to survey wildlife distribution, abundance and behaviour. As for any wildlife survey method, camera trapping must contend with sources of sampling error such as imperfect detection. Early applications focused on density estimation of naturally marked species, but there is growing interest in broad-scale CT surveys of unmarked populations and communities. Nevertheless, inferences based on detection indices are controversial, and the suitability of alternatives such as occupancy estimation is debatable.
We reviewed 266 CT studies published between 2008 and 2013. We recorded study objectives and methodologies, evaluating the consistency of CT protocols and sampling designs, the extent to which CT surveys considered sampling error, and the linkages between analytical assumptions and species ecology.
Nearly two-thirds of studies surveyed more than one species, and a majority used response variables that ignored imperfect detection (e.g. presence–absence, relative abundance). Many studies used opportunistic sampling and did not explicitly report details of sampling design and camera deployment that could affect conclusions.
Most studies estimating density used capture–recapture methods on marked species, with spatially explicit methods becoming more prominent. Few studies estimated density for unmarked species, focusing instead on occupancy modelling or measures of relative abundance. While occupancy studies estimated detectability, most did not explicitly define key components of the modelling framework (e.g. a site) or discuss potential violations of model assumptions (e.g. site closure). Studies using relative abundance relied on assumptions of equal detectability, and most did not explicitly define expected relationships between measured responses and underlying ecological processes (e.g. animal abundance and movement).
Synthesis and applications. The rapid adoption of camera traps represents an exciting transition in wildlife survey methodology. We remain optimistic about the technology's promise, but call for more explicit consideration of underlying processes of animal abundance, movement and detection by cameras, including more thorough reporting of methodological details and assumptions. Such transparency will facilitate efforts to evaluate and improve the reliability of camera trap surveys, ultimately leading to stronger inferences and helping to meet modern needs for effective ecological inquiry and biodiversity monitoring.

https://besjournals.onlinelibrary.wiley.com/doi/epdf/10.1111/1365-2664.12432

REVIEW: Wildlife camera trapping: a review and recommendations for linking surveys to ecological processes

Summary
1Anthropogenic noise is rapidly increasing in wilderness areas as a result of industrial expansion. While many road studies have attempted to assess the effects of industrial noise on birds, conflicting factors such as edge effects often inhibit the ability to draw strong conclusions.
2We assessed pairing success and age distribution of male ovenbirds Seiurus aurocapilla in the boreal forest of Alberta, Canada, in areas around noise-generating compressor stations compared with areas around habitat-disturbed, but noiseless, wellpads. This allowed us to control for edge effects, human visitation and other factors that are not controlled for in studies of noise generated by roads. Generalized estimating equations (GEE) were used to assess the impacts of noise on ovenbird pairing success, age structure and body morphology.
3We found a significant reduction in ovenbird pairing success at compressor sites (77%) compared with noiseless wellpads (92%). These differences were apparent regardless of territory quality or individual male quality. Significantly more inexperienced birds breeding for the first time were found near noise-generating compressor stations than noiseless wellpads (48% vs. 30%).
4While there are multiple proximate explanations for these results, the ultimate cause of the changes seems to be noise pollution. We hypothesize that noise interferes with a male's song, such that females may not hear the male's song at greater distances and/or females may perceive males to be of lower quality because of distortion of song characteristics.
5Synthesis and applications. This work demonstrates that chronic background noise could be an important factor affecting bird populations. It can impact upon pairing success and age structure of passerines; in boreal Alberta this could pose a problem for certain species as energy development expands rapidly.

/pdf/chronic-industrial-noise-affects-pairing-success-and-age-1s3gweo6qx.pdf

Chronic industrial noise affects pairing success and age structure of ovenbirds Seiurus aurocapilla

The effects of human activities in forests are often examined in the context of habitat conversion. Changes in habitat structure and composition are also associated with increases in the activity of people with vehicles and equipment, which results in increases in anthropogenic noise. Anthropogenic noise may reduce habitat quality for many species, particularly those that rely on acoustic signals for communication. We compared the density and occupancy rate of forest passerines close to versus far from noise-generating compressor stations and noiseless well pads in the boreal forest of Alberta, Canada. Using distance-based sampling, we found that areas near noiseless energy facilities had a total passerine density 1.5 times higher than areas near noise-producing energy sites. The White-throated Sparrow (Zonotrichia albicollis), Yellow-rumped Warbler (Dendroica coronata), and Red-eyed Vireo (Vireo olivaceus) were less dense in noisy areas. We used repeat sampling to estimate occupancy rate for 23 additional species. Seven had lower conditional or unconditional occupancy rates near noise-generating facilities. One-third of the species examined showed patterns that supported the hypothesis that abundance is influenced by anthropogenic noise. An additional 4 species responded negatively to edge effects. To mitigate existing noise impacts on birds would require approximately $175 million. The merits of such an effort relative to other reclamation actions are discussed. Nevertheless, given the $100 billion energy-sector investment planned for the boreal forest in the next 10 years, including noise suppression technology at the outset of construction, makes noise mitigation a cost-effective best-management practice that might help conserve high-quality habitat for boreal birds.

/pdf/impacts-of-chronic-anthropogenic-noise-from-energy-sector-1fl4uw72lr.pdf

Impacts of Chronic Anthropogenic Noise from Energy-Sector Activity on Abundance of Songbirds in the Boreal Forest

Fragmentation of forested landscapes can reduce the reproductive success of birds occupying residual forest patches. Previous studies, however, have focused primarily on how nest predation can change when landscapes become fragmented by agriculture rather than by logging. To determine if predation on artificial nests in forest patches was influenced by the surrounding landscape, we placed ground and shrub nests along the edge and interior of forest patches located in agricultural, logged, and contiguous forest landscapes within a single region of the southern boreal mixedwood forest of central Canada. Nest predators were identified using remotely triggered cameras and by marks left in plasticine eggs, whereas the relative abundance of nest predators such as corvids and small mammals was estimated by surveys and live-trapping. The percentage of ground nests destroyed at the edge and interior of patches in the logged and contiguous forest landscapes was significantly lower than at the edge or interior of patches in the agricultural landscape. No differences in predation rate were observed for shrub nests among landscapes. We attributed higher rates of predation in the agricultural landscape to higher densities of red squirrels (  Tamiasciurus hudsonicus) in the interior and a greater diversity of predators along edges. The similarity in predation rate between logged and contiguous forest landscapes suggests that fragmentation caused by logging may result in little change in predator communities and in this respect, might be similar to fragmentation caused by natural disturbance regimes such as fire. In contrast, fragmentation by agriculture seems to have more serious consequences for nesting birds. Policy changes that limit the growth of agriculture in the southern boreal mixedwood forest are required to conserve the diverse avifauna of this region.



Comparacion de los Efectos de la Fragmentacion del Paisaje Causada por la Accion Forestal y Agrico sobre la Depredacion de Nidos Artificiales



La fragmentacion de paisajes forestales puede reducir el exito reproductivo de aves que ocupan los parches residuales del bosque. Sin embargo, estudios previos se han enfocado principalmente al modo en que puede cambiar la depredacion de nidos cuando los paisajes son fragmentados para agricultura en lugar de para foresteria. Para determinar si el paisaje circundante influyel sobre la depredacion de nidos artificiales, en parches de bosque colocamos nidos sobre el suelo y en arbustos a lo largo del borde y en el interior de parches de bosque, localizados en paisajes agricolas, talados, de bosque continuo, en una sola region del bosque boreal mixto de Canada central. Los depredadores de nidos fueron identificados mediante camaras disparadas remotamente y por marcas dejades en huevos de plastilina, mientras que la abundancia relativa de depredadores de nidos como corvidos y mamiferos pequenos se estimo mediante reconocimientos y trampeos. El porcentaje de nidos sobre el suelo destruidos en el borde e interior de parches en los paisajes talados y continuos fue significativamente menor que en el borde o interior de parches en el paisaje agricola. No se observo diferencia en las tasas de depredacion de nidos en arbustos en los paisajes estudiados. Atribuimos las mayores tasas de depredacion en el paisaje agricola a la mayor densidad de ardillas rojas (  Tamiascuirus hudsonicus) en el interior y a una mayor diversidad de depredadores en los bordes. La similitud de tasas de depredacion en paisajes talados y continuos sugiere que la fragmentacion causada por la foresteria puede producir cambios pequenos en las comunidades de depredadores y en este sentido puede ser similar a la fragmentacion causada por regimenes de perturbacion natural tales como fuego. En contraste, la fragmentacion por agricultura parece tener consecuencias mas serias para aves anidantes. Se requieren cambios politicos para limitar la expansion de la agricultura en el bosque boreal mixto para conservar la diversidad de la avifauna de esta region.

Comparing the effects of landscape fragmentation by forestry and agriculture on predation of artificial nests.

Acoustic surveys are a widely used sampling tool in ecological research and monitoring. They are used to monitor populations and ecosystems and to study various aspects of animal behavior. Autonomous recording units (ARUs) can record sound in most environments and are increasingly used by researchers to conduct acoustic surveys for birds. In this review, we summarize the use of ARUs in avian ecological research and synthesize current knowledge of the benefits and drawbacks of this technology. ARUs enable researchers to do more repeat visits with less time spent in the field, with the added benefits of a permanent record of the data collected and reduced observer bias. They are useful in remote locations and for targeting rare species. ARUs are mostly comparable to human observers in terms of species richness, but in some cases, they detect fewer species and at shorter distances. Drawbacks of ARUs include the cost of equipment, storage of recordings, loss of data if units fail, and potential sampling trade-offs in spatial vs. temporal coverage. ARUs generate large data sets of audio recordings, but advances in automated species recognition and acoustic processing techniques are contributing to make the processing time manageable. Future applications of ARUs include biodiversity monitoring and studying habitat use, animal movement, and various behavioral ecology questions based on vocalization activity. ARUs have the potential to make significant advances in avian ecological research and to be used in more innovative ways than simply as a substitute for a human observer in the field. Unités d'enregistrement autonomes en écologie aviaire : utilisations actuelles et futures RÉSUMÉ. Les relevés acoustiques sont largement employés comme outil d'échantillonnage pour la recherche et les suivis écologiques. Ils sont utilisés pour suivre les populations et les écosystèmes et étudier le comportement animal sous divers angles. Les unités d'enregistrement autonomes (ARU, pour autonomus recording units) peuvent enregistrer les sons dans la plupart des environnements et sont utilisés de plus en plus souvent par les chercheurs pour effectuer des relevés acoustiques d'oiseaux. Dans la présente revue, nous résumons l'utilisation d'ARU en écologie aviaire et synthétisons les avantages et désavantages connus de cette technologie. Les ARU permettent aux chercheurs de faire plus de visites répétées tout en passant moins de temps sur le terrain, avec l'avantage d'avoir un enregistrement permanent des données récoltées et de réduire le biais associé à l'observateur. Ils sont utiles en milieu éloigné et dans les cas où on cible des espèces rares. Les ARU sont comparables aux observateurs humains pour ce qui est de la richesse spécifique, mais dans certains cas, ils détectent moins d'espèces et à des distances plus courtes. Les désavantages des ARU comprennent le coût de l'équipement, la sauvegarde des enregistrements, la perte de données en cas de défaillance des unités, et le compromis possible à devoir faire sur le plan de la couverture d'échantillonnage (spatiale ou temporelle). Les ARU génèrent une grande quantité d'enregistrements sonores, mais les avancées quant à la reconnaissance automatisée des espèces et aux techniques de traitement acoustique contribuent à réduire le temps de traitement. Les utilisations éventuelles d'ARU comprennent le suivi de la biodiversité, l'étude de l'utilisation de l'habitat, les déplacements animaux et diverses questions en écologie comportementale fondées sur l'activité vocale. Les ARU ont le potentiel de permettre des avancées importantes en écologie aviaire et pourraient être utilisées de façon plus novatrice qu'en tant que simples substituts d'observateurs sur le terrain.

/pdf/autonomous-recording-units-in-avian-ecological-research-vtnshybh8f.pdf

Erin M. Bayne

Papers

REVIEW: Wildlife camera trapping: a review and recommendations for linking surveys to ecological processes

Chronic industrial noise affects pairing success and age structure of ovenbirds Seiurus aurocapilla

Impacts of Chronic Anthropogenic Noise from Energy-Sector Activity on Abundance of Songbirds in the Boreal Forest

Comparing the effects of landscape fragmentation by forestry and agriculture on predation of artificial nests.

Autonomous recording units in avian ecological research: current use and future applications