High power line collision mortality of threatened bustards at a regional scale in the Karoo,South Africa

Quantifying avian collisions with power lines at large spatial scales is difficult, but such mortality is of serious conservation concern for many bird species worldwide. To investigate effects on the Endangered Ludwig's Bustard Neotis ludwigii and two other bustard species, mortality surveys were conducted quarterly along high‐voltage transmission lines at five sites (total length 252 km) across the Karoo for 2 years and one low‐voltage distribution line site (95 km) for 1 year. Thirty bird species were found, with Ludwig's Bustards constituting 69% and other bustards a further 18% of carcasses (n = 679 birds). Significant explanatory variables of Ludwig's Bustard collisions were season (collisions more likely in winter), rainfall (less likely in drier areas) and year on transmission lines (highlighting variability between years). Season and proximity to roads were significant variables on distribution lines, with collisions more likely during winter and away from roads. Ludwig's Bustard collision rates (corrected for survey biases) were higher on transmission (1.12; 95% confidence interval (CI) 0.40–2.58 bustards/km/year) than on distribution lines (0.86; 95% CI 0.30–1.96), but these smaller lines are four times as extensive in South Africa and so probably kill more birds. Despite being much less abundant, Kori Bustards Ardeotis kori were the second most commonly recovered species, with collision rates of 0.10 (95% CI 0.05–0.19) on transmission lines in the Nama Karoo alone. Collision rates are highly variable but suggest mortality suffered by these two species is worryingly high. This adds to growing concern about the impacts of power lines on bustards globally, so given ongoing expansion to the power grid, collision mitigation measures should be implemented at all new power lines.     

Survival of Greater Sage‐Grouse broods: survey method affects disturbance and age‐specific detection probability

Investigators rely on brood surveys to estimate annual fecundity of game birds. However, investigators often do not account for factors that influence brood detection probability nor rarely document how much females and their broods are disturbed (flush rates) during surveys, which could lead to biased survival estimates. We used 45 radio‐tagged female Greater Sage‐Grouse (Centrocercus urophasianus) with broods to compare detection probabilities and document disturbance among four survey methods to allow future investigators to select the method that best meets their objectives. These methods included daytime flush, daytime visual, nocturnal spotlight, and fecal surveys at nocturnal roost sites, with the latter being a novel method. We used Cormack–Jolly–Seber (CJS) models to compare detection probability and daily survival estimates for visual and fecal surveys of broods 0–47 d post‐hatch and a double‐survey approach to compare detection probabilities among flush, fecal, and spotlight surveys ~42 d post‐hatch when investigators often determine brood fate. From CJS models, detection probability for visual surveys increased with brood age (0.618–0.881), whereas detection probability for fecal surveys did not (0.748). Daily survival probability estimates increased with brood age and differed annually based on fecal surveys (2016: 0.978–1.000 and 2017: 0.839–0.998). We detected age‐specific daily survival probability with visual surveys (0.956–0.997), but not annual differences. Based on the double‐survey approach, detection probability was high (0.857–1.000) for all methods. We flushed ~310–750% fewer females and broods during fecal and spotlight surveys than during both types of daytime surveys. Our results highlight the need to account for detection probabilities among methods and document disturbance to hens and broods that can help investigators design surveys to minimize impacts to birds. Furthermore, our result suggest that actions to improve brood survival during the first week post‐hatch may improve local recruitment.     

Environmental DNA analysis for estimating the abundance and biomass of stream fish

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Computer‐automated bird detection and counts in high‐resolution aerial images: a review

Bird surveys conducted using aerial images can be more accurate than those using airborne observers, but can also be more time‐consuming if images must be analyzed manually. Recent advances in digital cameras and image‐analysis software offer unprecedented potential for computer‐automated bird detection and counts in high‐resolution aerial images. We review the literature on this subject and provide an overview of the main image‐analysis techniques. Birds that contrast sharply with image backgrounds (e.g., bright birds on dark ground) are generally the most amenable to automated detection, in some cases requiring only basic image‐analysis software. However, the sophisticated analysis capabilities of modern object‐based image analysis software provide ways to detect birds in more challenging situations based on a variety of attributes including color, size, shape, texture, and spatial context. Some techniques developed to detect mammals may also be applicable to birds, although the prevalent use of aerial thermal‐infrared images for detecting large mammals is of limited applicability to birds because of the low pixel resolution of thermal cameras and the smaller size of birds. However, the increasingly high resolution of true‐color cameras and availability of small unmanned aircraft systems (drones) that can fly at very low altitude now make it feasible to detect even small shorebirds in aerial images. Continued advances in camera and drone technology, in combination with increasingly sophisticated image analysis software, now make it possible for investigators involved in monitoring bird populations to save time and resources by increasing their use of automated bird detection and counts in aerial images. We recommend close collaboration between wildlife‐monitoring practitioners and experts in the fields of remote sensing and computer science to help generate relevant, accessible, and readily applicable computer‐automated aerial photographic census techniques.     

A genome‐wide survey reveals abundant rice blast R genes in resistant cultivars

Plant resistance genes (R genes) harbor tremendous allelic diversity, constituting a robust immune system effective against microbial pathogens. Nevertheless, few functional R genes have been identified for even the best‐studied pathosystems. Does this limited repertoire reflect specificity, with most R genes having been defeated by former pests, or do plants harbor a rich diversity of functional R genes, the composite behavior of which is yet to be characterized? Here, we survey 332 NBS‐LRR genes cloned from five resistant Oryza sativa (rice) cultivars for their ability to confer recognition of 12 rice blast isolates when transformed into susceptible cultivars. Our survey reveals that 48.5% of the 132 NBS‐LRR loci tested contain functional rice blast R genes, with most R genes deriving from multi‐copy clades containing especially diversified loci. Each R gene recognized, on average, 2.42 of the 12 isolates screened. The abundant R genes identified in resistant genomes provide extraordinary redundancy in the ability of host genotypes to recognize particular isolates. If the same is true for other pathogens, many extant NBS‐LRR genes retain functionality. Our success at identifying rice blast R genes also validates a highly efficient cloning and screening strategy.     

New insights into the northward migration route of gray whales between Vancouver Island,British Columbia,and southeastern Alaska

The route taken by northward migrating gray whales during spring between Vancouver Island and southeastern Alaska, a distance of about 575 km, has long been uncertain. It is generally believed that the whales closely follow the western, outer coastline of Haida Gwaii (formerly the Queen Charlotte Islands), an archipelago lying between Vancouver Island and southeastern Alaska, consistent with their pattern of migrating close to shore over the majority of their northward migratory corridor. By tracking satellite‐tagged individuals and surveying whales from shore bases, we provide evidence that this is not the primary migratory corridor, but instead that most whales migrate through Hecate Strait and Dixon Entrance, broad waterways that lie to the east and north of Haida Gwaii. By using this route, northbound gray whales potentially face a wider range of industrial activities and developments than they would by migrating along the outer coast.     

Long‐term endemism of two highly divergent lineages of the amphibian‐killing fungus in the Atlantic Forest of Brazil

The recent global spread of the amphibian‐killing fungus [Batrachochytrium dendrobatidis (Bd)] has been closely tied to anthropogenic activities; however, regional patterns of spread are not completely understood. Using historical samples, we can test whether Bd was a spreading or endemic pathogen in a region within a particular time frame, because those two disease states provide different predictions for the regional demographic dynamics and population genetics of Bd. Testing historical patterns of pathogen prevalence and population genetics under these predictions is key to understanding the evolution and origin of Bd. Focusing on the Atlantic Forest (AF) of Brazil, we used qPCR assays to determine the presence or absence of Bd on 2799 preserved postmetamorphic anurans collected between 1894 and 2010 and used semi‐nested PCRs to determine the frequency of rRNA ITS1 haplotypes from 52 samples. Our earliest date of detection was 1894. A mean prevalence of 23.9% over time and spatiotemporal patterns of Bd clusters indicate that Bd has been enzootic in the Brazilian AF with no evidence of regional spread within the last 116 years. ITS1 haplotypes confirm the long‐term presence of two divergent strains of Bd (BdGPL and Bd‐Brazil) and three spatiotemporally broad genetic demes within BdGPL, indicating that Bd was not introduced into southeast Brazil by the bullfrog trade. Our data show that the evolutionary history and pathogen dynamics of Bd in Brazil is better explained by the endemic pathogen hypothesis.     

Evaluating performance of aerial survey data in elephant habitat modelling

Aerial survey data are widely used to model distribution of wildlife. However, their performance in habitat modelling remains largely untested. We used aerial survey and satellite‐linked Global Positioning System (GPS) collar data for elephants, to test (i) whether there is an optimal spatial resolution of predictor variables at which habitat models based on aerial survey data that are uncorrected for locational error can accurately predict elephant habitat and (ii) whether habitat models based on these data sets can accurately predict the presence of elephants in closed woodland habitats. We applied maximum entropy modelling (Maxent) to these data sets and used the Normalised Difference Vegetation Index (NDVI) as well as distance from water points as the habitat predictors to answer these questions. Our results demonstrate better ability of aerial survey data to predict elephant presence at the coarser spatial resolution of 1000 m of both predictor variables. Habitat models derived from aerial survey data underpredicted elephant presence in more closed woodland habitats than those derived from GPS collar data. This result implies that elephants located under dense tree canopies are likely missed during an aerial survey. Our study is one of the first to empirically test and report results on the poor performance of aerial survey data in habitat modelling especially in dense woodlands.     

Impact of prey occupancy and other ecological and anthropogenic factors on tiger distribution in Thailand's western forest complex

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Integrating sign surveys and telemetry data for estimating brown bear (Ursus arctos) density in the Romanian Carpathians

Accurate population size estimates are important information for sustainable wildlife management. The Romanian Carpathians harbor the largest brown bear (Ursus arctos) population in Europe, yet current management relies on estimates of density that lack statistical oversight and ignore uncertainty deriving from track surveys. In this study, we investigate an alternative approach to estimate brown bear density using sign surveys along transects within a novel integration of occupancy models and home range methods. We performed repeated surveys along 2‐km segments of forest roads during three distinct seasons: spring 2011, fall‐winter 2011, and spring 2012, within three game management units and a Natura 2000 site. We estimated bears abundances along transects using the number of unique tracks observed per survey occasion via N‐mixture hierarchical models, which account for imperfect detection. To obtain brown bear densities, we combined these abundances with the effective sampling area of the transects, that is, estimated as a function of the median (± bootstrapped SE) of the core home range (5.58 ± 1.08 km²) based on telemetry data from 17 bears tracked for 1‐month periods overlapping our surveys windows. Our analyses yielded average brown bear densities (and 95% confidence intervals) for the three seasons of: 11.5 (7.8–15.3), 11.3 (7.4–15.2), and 12.4 (8.6–16.3) individuals/100 km². Across game management units, mean densities ranged between 7.5 and 14.8 individuals/100 km². Our method incorporates multiple sources of uncertainty (e.g., effective sampling area, imperfect detection) to estimate brown bear density, but the inference fundamentally relies on unmarked individuals only. While useful as a temporary approach to monitor brown bears, we urge implementing DNA capture–recapture methods regionally to inform brown bear management and recommend increasing resources for GPS collars to improve estimates of effective sampling area.     

Fin whale (Balaenoptera physalus) target strength measurements

Active acoustic techniques can be used to detect whales. The ability to detect whales from a moving vessel or stationary buoy could reduce conflicts between hazardous human activities and whales, enabling implementation of mitigation procedures. In order to identify acoustic targets correctly as whales, knowledge of whale target strength (TS) is required. Active acoustic detections of fin whales (Balaenoptera physalus) were made in the Norwegian Sea; acoustic data were collected using calibrated omnidirectional sonar, operating at a discrete frequency of 110 kHz. Three fin whales of similar size (estimated between 16 and 18 m total length) had an overall average TS for all insonified body aspects of ?11.4 dB [95% CI ?12.05, ?10.8] at 110 kHz, with a total spread of nearly 14 dB. As expected, the received signals were stronger when the fin whales were insonified at broadside (?5.6 dB). Individual fin whale TS varied by approximately 12 dB, probably due to variation in lung volume with breathing, and to dynamic swimming kinematics. Our TS values are consistent with values reported previously for other large whales. All data together pave the way for development of automated acoustic whale detection protocols that could aid whale conservation.