Mapping migration in a songbird using high‐resolution genetic markers

Neotropic migratory birds are declining across the Western Hemisphere, but conservation efforts have been hampered by the inability to assess where migrants are most limited—the breeding grounds, migratory stopover sites or wintering areas. A major challenge has been the lack of an efficient, reliable and broadly applicable method for measuring the strength of migratory connections between populations across the annual cycle. Here, we show how high‐resolution genetic markers can be used to identify genetically distinct groups of a migratory bird, the Wilson's warbler (Cardellina pusilla), at fine enough spatial scales to facilitate assessing regional drivers of demographic trends. By screening 1626 samples using 96 highly divergent single nucleotide polymorphisms selected from a large pool of candidates (~450 000), we identify novel region‐specific migratory routes and timetables of migration along the Pacific Flyway. Our results illustrate that high‐resolution genetic markers are more reliable, precise and amenable to high throughput screening than previously described intrinsic marking techniques, making them broadly applicable to large‐scale monitoring and conservation of migratory organisms.     

Validation of a landscape‐scale planning tool for cavity‐dependent wildlife

Tree cavities provide important habitat for wildlife. Effective landscape‐scale management of cavity‐dependent wildlife requires an understanding of where cavities occur, but tree cavities can be cryptic and difficult to survey. We assessed whether a landscape‐scale map of mature forest habitat availability, derived from aerial photographs, reflected the relative availability of mature trees and tree cavities. We assessed cavities for their suitability for use by wildlife, and whether the map reflected the availability of such cavities. There were significant differences between map categories in several characteristics of mature trees that can be used to predict cavity abundance (i.e. tree form and diameter at breast height). There were significant differences between map categories in the number of potential cavity bearing trees and potential cavities per tree. However, the index of cavity abundance based on observations made from the ground provided an overestimate of true cavity availability. By climbing a sample of mature trees we showed that only 5.1% of potential tree cavities detected from the ground were suitable for wildlife, and these were found in only 12.5% of the trees sampled. We conclude that management tools developed from remotely sensed data can be useful to guide decision‐making in the conservation management of tree cavities but stress that the errors inherent in these data limit the scale at which such tools can be applied. The rarity of tree cavities suitable for wildlife in our study highlights the need to conserve the tree cavity resource across the landscape, but also the importance of increasing the accuracy of management tools for decision‐making at different scales. Mapping mature forest habitat availability at the landscape scale is a useful first step in managing habitat for cavity‐dependent wildlife, but the potential for overestimating actual cavity abundance in a particular area highlights the need for complementary on‐ground surveys.     

Identifying threshold densities for wild deer in the UK above which negative impacts may occur

• 1 At high densities, deer populations may have adverse effects upon and within their environment. In this review we explore published and unpublished information to derive density thresholds for deer species in relation to impacts upon agriculture, forestry, conservation habitats, road traffic, and human and livestock health in the UK. Impact levels are affected by many factors other than absolute density. We therefore seek to establish the range of densities within which negative impacts might start to occur and which should trigger objective monitoring of actual impacts.
• 2 In commercial forestry, a threshold of 4 deer per 100ha has been suggested. Unfenced native woodlands seem to regenerate naturally if there are fewer than 4–5 large deer or fewer than 25 roe deer Capreolus capreolus per 100ha; open habitats may suffer only light or moderate impacts from red deer Cervus elaphus at landscape densities of 7–8 per 100ha.
• 3 Woodland bird species may have declined where deer densities are high but absolute thresholds seem impossible to establish. One study suggests maximum diversity at about 8 white‐tailed deer Odocoileus virginianus per 100ha.
• 4 Deer–vehicle collisions are affected by various factors in addition to deer density, but British and American studies suggest that accident frequencies decline at densities below 7–8 per 100ha.
• 5 Fallow deer Dama dama populations may maintain bovine TB (bTB) infection at much lower densities (25/100ha) than red or roe deer (91/100ha and 200/100ha, respectively) assuming 100% prevalence. Even at 30% prevalence a density of 75 fallow deer per 100ha could maintain bTB within the population.
• 6 We conclude that deer density alone is unlikely to be a good predictor of impact, and suggest that long‐term management should be based on assessment both of actual impacts and apparent density of deer.

     

A single‐nucleotide polymorphism‐based approach for rapid and cost‐effective genetic wolf monitoring in Europe based on noninvasively collected samples

Noninvasive genetics based on microsatellite markers has become an indispensable tool for wildlife monitoring and conservation research over the past decades. However, microsatellites have several drawbacks, such as the lack of standardisation between laboratories and high error rates. Here, we propose an alternative single‐nucleotide polymorphism (SNP)‐based marker system for noninvasively collected samples, which promises to solve these problems. Using nanofluidic SNP genotyping technology (Fluidigm), we genotyped 158 wolf samples (tissue, scats, hairs, urine) for 192 SNP loci selected from the Affymetrix v2 Canine SNP Array. We carefully selected an optimised final set of 96 SNPs (and discarded the worse half), based on assay performance and reliability. We found rates of missing data in this SNP set of <10% and genotyping error of ~1%, which improves genotyping accuracy by nearly an order of magnitude when compared to published data for other marker types. Our approach provides a tool for rapid and cost‐effective genotyping of noninvasively collected wildlife samples. The ability to standardise genotype scoring combined with low error rates promises to constitute a major technological advancement and could establish SNPs as a standard marker for future wildlife monitoring.     

Ecological impacts of human‐induced animal behaviour change

A growing body of literature has documented myriad effects of human activities on animal behaviour, yet the ultimate ecological consequences of these behavioural shifts remain largely uninvestigated. While it is understood that, in the absence of humans, variation in animal behaviour can have cascading effects on species interactions, community structure and ecosystem function, we know little about whether the type or magnitude of human‐induced behavioural shifts translate into detectable ecological change. Here we synthesise empirical literature and theory to create a novel framework for examining the range of behaviourally mediated pathways through which human activities may affect different ecosystem functions. We highlight the few empirical studies that show the potential realisation of some of these pathways, but also identify numerous factors that can dampen or prevent ultimate ecosystem consequences. Without a deeper understanding of these pathways, we risk wasting valuable resources on mitigating behavioural effects with little ecological relevance, or conversely mismanaging situations in which behavioural effects do drive ecosystem change. The framework presented here can be used to anticipate the nature and likelihood of ecological outcomes and prioritise management among widespread human‐induced behavioural shifts, while also suggesting key priorities for future research linking humans, animal behaviour and ecology.     

Uncover the conserved property underlying sequence‐distant and structure‐similar proteins

It is widely accepted that a protein's sequence determines its structure. The surprising finding that proteins of distant sequence can adopt similar 3D structures has raised interesting questions regarding underlying conserved properties that are essential for protein folding and stability. Uncovering the conserved properties may shed light on the folding mechanism of proteins and help with the development of computational tools for protein structure prediction. We compiled and analyzed a structure pair dataset of 66 high‐resolution and low sequence identity (16–38%) soluble proteins. Structure deviation for each pair was confirmed by calculating its C_α SiMax value and comparing its potential energy per residue. Analysis of favorable inter‐residue interactions for each structure pair indicated that the average number of inter‐residue interactions within each structure represents a conserved feature of homologous structures of distant sequence. Detailed comparison of individual types of interactions showed that the average number of either hydrophobic or hydrogen bonding interactions remains unchanged for each structure pair. These findings should be of help to improving the quality of homology models based on templates of low sequence identity, thus broadening the application of homology modeling techniques for protein studies. © 2009 Wiley Periodicals, Inc. Biopolymers 93: 340–347, 2010. This article was originally published online as an accepted preprint. The “Published Online” date corresponds to the preprint version. You can request a copy of the preprint by emailing the Biopolymers editorial office at biopolymers@wiley.com     

Biodiversity in cities needs space: a meta‐analysis of factors determining intra‐urban biodiversity variation

Understanding varying levels of biodiversity within cities is pivotal to protect it in the face of global urbanisation. In the early stages of urban ecology studies on intra‐urban biodiversity focused on the urban–rural gradient, representing a broad generalisation of features of the urban landscape. Increasingly, studies classify the urban landscape in more detail, quantifying separately the effects of individual urban features on biodiversity levels. However, while separate factors influencing biodiversity variation among cities worldwide have recently been analysed, a global analysis on the factors influencing biodiversity levels within cities is still lacking. We here present the first meta‐analysis on intra‐urban biodiversity variation across a large variety of taxonomic groups of 75 cities worldwide. Our results show that patch area and corridors have the strongest positive effects on biodiversity, complemented by vegetation structure. Local, biotic and management habitat variables were significantly more important than landscape, abiotic or design variables. Large sites greater than 50 ha are necessary to prevent a rapid loss of area‐sensitive species. This indicates that, despite positive impacts of biodiversity‐friendly management, increasing the area of habitat patches and creating a network of corridors is the most important strategy to maintain high levels of urban biodiversity.     

Understanding Yurok traditional ecological knowledge and wildlife management

Indigenous communities have often been marginalized in the sciences through research approaches that are not inclusive of their cultures and histories. The term traditional ecological knowledge (TEK) has entered the discourse in wildlife management and conservation; however, there can be challenges in cross-cultural communication and conceptualizations of TEK when working between Western and Indigenous paradigms. Indigenous research methodologies (IRM) is an area of scholarship intended to build ethically and culturally appropriate ways to conduct research with Indigenous communities. I implemented 7 tenets of IRM in research to explore the conceptualization of TEK and wildlife management with the Yurok Tribe of California, USA. After conducting semi-structured interviews with 20 Yurok community members from 2011 to 2013, I conducted emergent analysis and present 5 themes from the interviews related to phases of time, the conceptualization of Yurok TEK, and views on wildlife management through the Yurok cultural lens. This research may be helpful to wildlife biologists, students, academics, and others who are interested in IRM and culturally sensitive wildlife research with Indigenous communities. By bridging concepts from Indigenous studies, wildlife management, and human dimensions of wildlife, this work may serve as a nascent trajectory that creates more inclusive space for Indigenous peoples and worldviews in The Wildlife Society and other scientific disciplines.     

A meta‐analysis of human disturbance impacts on Antarctic wildlife

Evidence‐based assessments are increasingly recognized as the best‐practice approach to determine appropriate conservation interventions, but such assessments of the impact of human disturbance on wildlife are rare. Human disturbance comprises anthropogenic activities that are typically non‐lethal, but may cause short‐ and/or longer‐term stress and fitness responses in wildlife. Expanding human activity in the Antarctic region is of particular concern because it increases the scope and potential for increased human disturbance to wildlife in a region that is often thought of as relatively untouched by anthropogenic influences. Here, we use a meta‐analytical approach to synthesise research on human disturbance to wildlife over the last three decades in the Antarctic and sub‐Antarctic region. We combine data from 62 studies across 21 species on the behavioural, physiological and population responses of wildlife to pedestrian, vehicle and research disturbances. The overall effect size indicated a small, albeit statistically significant negative effect of disturbance (?0.39; 95% CI: ?0.60 to ?0.18). Negative effects were found for both physiological and population responses, but no evidence was found for a significant impact on wildlife behavioural responses. Negative effects were found across pedestrian, vehicle and research disturbances. Significant and high among‐study heterogeneity was found in both disturbance and response sub‐groups. Among species, it remains unclear to what extent different forms of disturbance translate into negative population responses. Most current guidelines to limit wildlife disturbance impacts in Antarctica recommend that approaches be tailored to animal behavioural cues, but our work demonstrates that behavioural changes do not necessarily reflect more cryptic, and more deleterious impacts, such as changes in physiology. In consequence, we recommend that pedestrian approach guidelines in the Antarctic region be revisited. Due to the high heterogeneity in effects, management guidelines for different sites and species will need to be developed on a case‐by‐case basis, ideally in conjunction with carefully designed experiments. Guidelines to reduce the impact of research activities per se require development to reduce the potential impacts of conducting research. We identify research questions that, if answered, will further improve the evidence base for guidelines to manage human disturbance in Antarctica.     

Extinction debt of cities and ways to minimise their realisation: a focus on Melbourne

The formation and growth of cities sets in train a slow process of local species extinction, although it can take a long time for that extinction to be realised. Using Melbourne as an example, the authors ask ‘What plant species are potentially at risk and what strategies and actions could minimise the predicted negative outcomes?’     

The virtuous circle: predator‐friendly farming and ecological restoration in Australia

In Australia, dingoes are widely regarded as enemies of livestock, and accordingly livestock producers commonly attempt to reduce or eradicate them by lethal control. This can have two forms of perverse outcomes: lethal control often does not succeed in reducing dingo populations and can even result in increased attacks on livestock; and the environmental benefits provided by dingoes, some of which are valuable to livestock production, are lost. We describe these outcomes and suggest mechanisms by which tolerance of dingoes could provide benefits to livestock enterprises, at the same time widening the scope of ecological restoration, and humane treatment of wildlife in Australia.     

Using genetic tools to estimate the prevalence of non‐native red deer (Cervus elaphus) in a Western European population

Game species like the red deer have been subjected to anthropogenic impacts for centuries. Translocations are often carried out—sometimes illegally—not only for sporting purposes, but also to increase trophy quality, reduce inbreeding, or mitigate bottlenecks after excessive persecution. Apart from the blurring of large‐scale genetic structure, translocations without adequate quarantine measure risk introducing pathogens into potentially immunologically naïve populations. It is therefore important to understand the frequency of clandestine translocations. Identification of non‐autochthonous animals and their potential origin is often difficult and, in red deer, has been hampered by the lack of large‐scale genotypic datasets for comparison. In the present study, we make use of a recently published European‐wide microsatellite dataset to detect and quantify the presence of non‐autochthonous red deer in a large population sample (n = 1,780) from Central Europe (Belgium). Using factorial correspondence analysis, assignment tests and Bayesian clustering algorithms we arrive at an estimate of 3.7% non‐autochthonous animals (or their descendants). Some of these animals were assigned to a nearby French population and may have immigrated into Belgium naturally, but the large majority must have been introduced by humans. Our analysis pointed to the British Isles and Germany/Poland as the potential origin of many introduced deer, regions known to have been source populations for translocations in Europe and beyond. We found evidence for recreational hunters using carcasses from farmed deer to fulfill mandatory hunting quotas. Our study is the first to quantify the extent of human‐mediated introductions in a European game species at such a large scale with large and representative sample sizes.     

Do not feed the wildlife: associations between garbage use,aggression, and disease in banded mongooses (Mungos mungo)

Urbanization and other human modifications of the landscape may indirectly affect disease dynamics by altering host behavior in ways that influence pathogen transmission. Few opportunities arise to investigate behaviorally mediated effects of human habitat modification in natural host–pathogen systems, but we provide a potential example of this phenomenon in banded mongooses (Mungos mungo), a social mammal. Our banded mongoose study population in Botswana is endemically infected with a novel Mycobacterium tuberculosis complex pathogen, M. mungi, that primarily invades the mongoose host through the nasal planum and breaks in the skin. In this system, several study troops have access to human garbage sites and other modified landscapes for foraging. Banded mongooses in our study site (N = 4 troops, ~130 individuals) had significantly higher within‐troop aggression levels when foraging in garbage compared to other foraging habitats. Second, monthly rates of aggression were a significant predictor of monthly number of injuries in troops. Finally, injured individuals had a 75% incidence of clinical tuberculosis (TB) compared to a 0% incidence in visibly uninjured mongooses during the study period. Our data suggest that mongoose troops that forage in garbage may be at greater risk of acquiring TB by incurring injuries that may allow for pathogen invasion. Our study suggests the need to consider the indirect effects of garbage on behavior and wildlife health when developing waste management approaches in human‐modified areas.     

Using species distribution models to define nesting habitat of the eastern metapopulation of double‐crested cormorants

When organisms with similar phenotypes have conflicting management and conservation initiatives, approaches are needed to differentiate among subpopulations or discrete groups. For example, the eastern metapopulation of the double‐crested cormorant (Phalacrocorax auritus) has a migratory phenotype that is culled because they are viewed as a threat to commercial and natural resources, whereas resident birds are targeted for conservation. Understanding the distinct breeding habitats of resident versus migratory cormorants would aid in identification and management decisions. Here, we use species distribution models (SDM: Maxent) of cormorant nesting habitat to examine the eastern P. auritus metapopulation and the predicted breeding sites of its phenotypes. We then estimate the phenotypic identity of breeding colonies of cormorants where management plans are being developed. We transferred SDMs trained on data from resident bird colonies in Florida and migratory bird colonies in Minnesota to South Carolina in an effort to identify the phenotype of breeding cormorants there based on the local landscape characteristics. Nesting habitat characteristics of cormorant colonies in South Carolina more closely resembled those of the Florida phenotype than those of birds of the Minnesota phenotype. The presence of the resident phenotype in summer suggests that migratory and resident cormorants will co‐occur in South Carolina in winter. Thus, there is an opportunity for separate management strategies for the two phenotypes in that state. We found differences in nesting habitat characteristics that could be used to refine management strategies and reduce human conflicts with abundant winter migrants and, at the same time, conserve less common colonies of resident cormorants. The models we use here show potential for advancing the study of geographically overlapping phenotypes with differing conservation and management priorities.     

A Land System representation for global assessments and land‐use modeling

Current global scale land‐change models used for integrated assessments and climate modeling are based on classifications of land cover. However, land‐use management intensity and livestock keeping are also important aspects of land use, and are an integrated part of land systems. This article aims to classify, map, and to characterize Land Systems (LS) at a global scale and analyze the spatial determinants of these systems. Besides proposing such a classification, the article tests if global assessments can be based on globally uniform allocation rules. Land cover, livestock, and agricultural intensity data are used to map LS using a hierarchical classification method. Logistic regressions are used to analyze variation in spatial determinants of LS. The analysis of the spatial determinants of LS indicates strong associations between LS and a range of socioeconomic and biophysical indicators of human‐environment interactions. The set of identified spatial determinants of a LS differs among regions and scales, especially for (mosaic) cropland systems, grassland systems with livestock, and settlements. (Semi‐)Natural LS have more similar spatial determinants across regions and scales. Using LS in global models is expected to result in a more accurate representation of land use capturing important aspects of land systems and land architecture: the variation in land cover and the link between land‐use intensity and landscape composition. Because the set of most important spatial determinants of LS varies among regions and scales, land‐change models that include the human drivers of land change are best parameterized at sub‐global level, where similar biophysical, socioeconomic and cultural conditions prevail in the specific regions.     

Characteristics of hollows and hollow‐bearing trees in semi‐arid river red gum woodland and potential limitations for hollow‐dependent wildlife

Up to 37 species of the birds and microbats inhabiting inland Australia are dependent on tree cavities for breeding or roosting. The river red gum (Eucalyptus camaldulensis), a well‐known hollow‐bearing tree species, occurs in linear semi‐arid woodland along thousands of kilometres of ephemeral river channels and is the only tree species that provides widespread, aggregated hollow resources across a landscape otherwise dominated by shrublands. Here we assess the type and quantity of hollows available along ephemeral rivers of the MacDonnell Ranges bioregion in central Australia and determine which characteristics of river red gums best predict the abundance and characteristics of different tree hollows, as first steps towards assessing the current availability of hollows in the region. Approximately a third of all river red gums sampled were hollow‐bearing, but individual trees with abundant hollows were rare. Further, 36% of hollows had an entrance ≤ 5 cm, and 37% had entrances which were 6–10 cm in diameter, whereas only 13% of hollows had an entrance diameter > 20 cm suitable for larger hollow‐using species. Large and high hollows only occurred on trees that did not display post‐disturbance resprouting. Trees with multiple and diverse hollows were rare and tended to be in advanced stages of senescence and had larger stems (82.3 ± 3.33 cm) and were taller (14.4 ± 0.53 m) compared to non‐hollow‐bearing trees (23.44 ± 1.68 cm, 8.0 ± 0.34 m). Further research is required to establish whether the current abundance of hollows and diversity of hollow types are limiting to cavity‐dependent wildlife, and to identify any threats to availability of hollows.