The problem of precision and trend detection posed by small elephant populations in West Africa

The precision of elephant estimates from aerial sample surveys and dung counts is inversely proportional to abundance. West African elephant populations are already small, and the power of a monitoring programme to detect changes in abundance diminishes as the population shrinks in size. Thus it will be difficult to evaluate the effects on elephant numbers of new management policies in West Africa. The same will be true of monitoring schemes for antelope and primate populations that are hunted for bushmeat. Elephant estimates from dung counts are more precise than those from aerial sample surveys, and changes in elephant numbers are more likely to be detected in the subregion by dung counts than by aerial sample surveys.     

Intrasite variation in the ability to detect tropical forest mammals

Monitoring programs are essential for an adequate management of large mammal populations. Within Central Africa data on abundance of important bushmeat species, such as duikers and primates are often lacking. Relative densities [(encounter rates (ERs)] are often the only available data, but there is little knowledge on the factors affecting ERs and detection of these animals. Here we investigate how different environmental factors and observers influence large mammal ERs in a pristine rainforest in the Nouabalé‐Ndoki National Park, Republic of Congo. Our results show large daily and monthly variation in ERs of duikers and primates. ERs varied between habitat types, seasons and observers′ ability to detect animals. Season and rainfall had a strong effect on understory visibility and duiker detection, respectively. Detection of duikers often happened by sound instead of visual observations. Our study shows that the use of ER is a poor monitoring approach and more robust methods need to be used to evaluate rates of population change reliably.     

Amphibian declines: future directions

Abstract. The amphibian decline problem is complex, and there is no easy solution. I highlight four major areas of future research that should increase our ability to detect declines, elucidate their underlying mechanisms, and advance our capacity to manage and conserve amphibian populations. First, a statistically sensitive monitoring approach is necessary to determine the distribution and abundance of amphibian populations, to assess whether they are declining, and to quantify the extent of declines. Most amphibian populations characteristically fluctuate, detection probabilities may be low for many species and populations tend to decline in numbers between years more often than they increase. These traits make establishing monitoring programmes difficult and distinguishing declines from natural fluctuations challenging. It is thus necessary to determine the best monitoring techniques based on their statistical power and to use appropriate statistical methods for detecting population trends. Secondly, although amphibian population studies occur most commonly at single or few breeding sites, research should occur often at the landscape level, and conservation efforts should focus on suitable habitat (whether or not it is occupied) and dispersal capabilities of species. Metapopulation dynamics are probably important for many species, but we must be cautious how we define metapopulations. That is, the term ‘metapopulation’ is currently used to define a wide range of demographic situations in amphibian populations, each with different management implications. Thirdly, recent advances in molecular genetic techniques make it possible to infer demographic events such as effects of recent fragmentation, bottlenecks or hybridization. Molecular techniques can be used in conjunction with census surveys to bolster knowledge about demographic processes such as declines. Alternatively, in the absence of long‐term census data, molecular data can be used to infer population trends. New genomic approaches may make estimating adaptive genetic variation more feasible. Fourthly, multi‐factorial studies are needed to disentangle the complexity of the several putative causes that probably interact to cause amphibian declines. Recent studies demonstrate the value of a multi‐factorial approach, and more work is needed to elucidate the synergistic effects of multiple environmental factors affecting amphibian populations simultaneously worldwide.     

Oscillations in large mammal populations: are they related to predation or rainfall?

Cyclic population dynamics is relatively common among populations of small mammals in high latitudes but is not yet established among African savanna ungulates. However, oscillations may be expected in large mammal populations subject to quasi‐periodic oscillations in regional rainfall. We evaluated evidence for environmentally entrained oscillations in a large‐mammal predator–prey system in Kruger National Park (KNP), South Africa, where rainfall exhibits quasi‐periodic oscillations. The evaluation is based on analysis of comparative changes in the abundance of twelve ungulate species throughout South Africa's KNP using population counts over the period 1965–1996. We present evidence suggesting that (i) twelve ungulate populations display cyclic variability with half‐periods ranging between 10 and 18 years, (ii) this variability was associated with lagged rainfall between 3 and 10 years back in the past for different ungulate species, and (iii) the ungulate species respond in contrasting ways to rainfall, with some reaching highest abundance during periods of low rainfall and others under conditions of high rainfall. These findings are not consistent with the response pattern we would expect if the population oscillations were driven directly by the rainfall influence on food availability. Instead they seem to be an outcome of predator–prey interactions, which are entrained by the effect of rainfall on habitat conditions affecting the relative susceptibility of the different ungulate species to predation.     

Future hotspots of terrestrial mammal loss

Current levels of endangerment and historical trends of species and habitats are the main criteria used to direct conservation efforts globally. Estimates of future declines, which might indicate different priorities than past declines, have been limited by the lack of appropriate data and models. Given that much of conservation is about anticipating and responding to future threats, our inability to look forward at a global scale has been a major constraint on effective action. Here, we assess the geography and extent of projected future changes in suitable habitat for terrestrial mammals within their present ranges. We used a global earth-system model, IMAGE, coupled with fine-scale habitat suitability models and parametrized according to four global scenarios of human development. We identified the most affected countries by 2050 for each scenario, assuming that no additional conservation actions other than those described in the scenarios take place. We found that, with some exceptions, most of the countries with the largest predicted losses of suitable habitat for mammals are in Africa and the Americas. African and North American countries were also predicted to host the most species with large proportional global declines. Most of the countries we identified as future hotspots of terrestrial mammal loss have little or no overlap with the present global conservation priorities, thus confirming the need for forward-looking analyses in conservation priority setting. The expected growth in human populations and consumption in hotspots of future mammal loss mean that local conservation actions such as protected areas might not be sufficient to mitigate losses. Other policies, directed towards the root causes of biodiversity loss, are required, both in Africa and other parts of the world.     

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.     

Statistical power of replicated helicopter surveys in southern African conservation areas

Understanding the ecology of large ungulates in southern Africa requires accurate and precise measures of population size. Recovery or exploitation of ungulates in reserves is currently instigated when population size changes exceed 15% per annum, but monitoring is usually undertaken with single counts from helicopters, for which precision and the power to detect change are untested. In essence, power being the strength of a monitoring result in showing change over time. Retrospective power analysis is a useful technique to investigate the variability of single‐count aerial surveys. Using replicated helicopter‐based counts of southern African ungulates and post hoc analysis, we investigated the power of currently used single‐count surveys across five common ungulate species and 11 wildlife reserves. We expected high variability in count data and set α = 0.1 and 0.2 (α being the type I error rate), and asked two questions: ‘How much does power vary in replicated aerial counts of southern African wildlife across reserves and species?’ and ‘Can current single‐count aerial surveys detect population changes in response to management actions or are the statistical errors intractable?’ Single counts were mostly unreliable; only one of 42 had sufficient power to detect meaningful changes in population size or their trends at α = 0.1, and only three had sufficient power at α = 0.2. Power varied widely according to species (e.g. warthog, median power at α = 0.1; 0.12–0.37: blue wildebeest, median power at α = 0.1; 0.23–0.74), and, within species, between replicates and reserves. Our retrospective calculations demonstrated insensitivity and ineffectiveness in most currently applied single counts from helicopters. Consequently, it is impossible to interpret the effects of ungulate conservation actions on many southern African reserves. Retrospective power analyses enables determination of which previous aerial surveys were useful for population assessment and adaptive management, and which should be discarded. We recommend that prospective power analyses are undertaken to determine future helicopter survey sample size and replication requirements, especially in small reserves.     

Bayesian estimation of group sizes for a coastal cetacean using aerial survey data

Many small cetacean, sirenian, and pinniped species aggregate in groups of large or variable size. Accurate estimation of group sizes is essential for estimating the abundance and distribution of these species, but is challenging as individuals are highly mobile and only partially visible. We developed a Bayesian approach for estimating group sizes using wide‐angle aerial photographic or video imagery. Our approach accounts for both availability and perception bias, including a new method (analogous to distance sampling) for estimating perception bias due to small image size in wide‐angle images. We demonstrate our approach through an application to aerial survey data for an endangered population of beluga whales (Delphinapterus leucas) in Cook Inlet, Alaska. Our results strengthen understanding of variation in group size estimates and allow for probabilistic statements about the size of detected groups. Aerial surveys are a standard tool for estimating the abundance and distribution of various marine mammal species. The role of aerial photographic and video data in wildlife assessment is expected to increase substantially with the widespread uptake of unmanned aerial vehicle technology. Key aspects of our approach are relevant to group size estimation for a broad range of marine mammal, seabird, other waterfowl, and terrestrial ungulate species.     

Co‐declining mammal–dung beetle faunas throughout the Atlantic Forest biome of South America

The millennial–scale evolutionary relationships between mammals and dung beetles have been eroded due to several drivers of contemporary biodiversity loss. Although some evidence of co‐decline has been shown for mammals and dung beetles at some Neotropical sites, a biome‐scale analysis for the entire Atlantic Forest of South America would strengthen our understanding of how relictual sets of mammal species can affect dung beetle co‐occurrences and co‐declines. We therefore collated hundreds of assemblages of both dung beetles and medium‐ to large‐bodied mammals throughout the world's longest tropical forest latitudinal gradient to examine to what extent mammal assemblages may exert a positive influence on dung beetle species composition and functional assembly, and whether this relationship is scale dependent. We also collated several climatic and other environmental variables to examine the degree to which they shape mammal–dung beetle relationships. The relationships between local mammal and dung beetle faunas were examined using regression models, variation partitioning, dissimilarity indices and ecological networks. We found a clear positive relationship between mammal and dung beetle species richness across this forest biome, indicating an ongoing process of mammal–dung beetle niche‐mediated co‐decline. We found a strong relationship between the species composition of both taxa, in which dung beetle species dissimilarity apparently track changes in mammalian dissimilarity, typically in 80% of all cases. Co‐variables such as phytomass and climatic variables also influenced mammal–dung beetle patterns of co‐decline along the Atlantic Forest. We conclude that dung beetle diversity and community assembly are shaped by the remaining co‐occurring mammal assemblages and their functional traits, and both groups were governed by environmental features. We emphasize that ecosystem‐wide effects of mammal population declines remain poorly understood both quantitatively and qualitatively, and curbing large vertebrate defaunation will ensure the persistence of co‐dependent species.     

Carrion fly‐derived DNA metabarcoding is an effective tool for mammal surveys: Evidence from a known tropical mammal community

Metabarcoding of vertebrate DNA derived from carrion flies has been proposed as a promising tool for biodiversity monitoring. To evaluate its efficacy, we conducted metabarcoding surveys of carrion flies on Barro Colorado Island (BCI), Panama, which has a well‐known mammal community, and compared our results against diurnal transect counts and camera trapping. We collected 1,084 flies in 29 sampling days, conducted metabarcoding with mammal‐specific (16S) and vertebrate‐specific (12S) primers, and sequenced amplicons on Illumina MiSeq. For taxonomic assignment, we compared blast with the new program protax , and we found that protax improved species identifications. We detected 20 mammal, four bird, and one lizard species from carrion fly metabarcoding, all but one of which are known from BCI. Fly metabarcoding detected more mammal species than concurrent transect counts (29 sampling days, 13 species) and concurrent camera trapping (84 sampling days, 17 species), and detected 67% of the number of mammal species documented by 8 years of transect counts and camera trapping combined, although fly metabarcoding missed several abundant species. This study demonstrates that carrion fly metabarcoding is a powerful tool for mammal biodiversity surveys and has the potential to detect a broader range of species than more commonly used methods.     

Genetic quality of domesticated African tilapia populations

Anecdotal and empirical evidence exists for substantial (up to 40%) declines in growth among Oreochromis populations domesticated in both large and small‐scale fish farms in Africa. These declines are at least partly attributable to poor genetic management, including inadvertent selection, inbreeding, bottle‐necks and founder effects. Due to restricted cash flow and investment capital, genetic management and selective breeding for the improvement of domesticate populations are difficult for small‐scale farmers, but feasible on larger‐scale farms. In managing domesticated gene pools, feral populations can serve as a broodstock reservoir, making the use of indigenous species advantageous. A development model of large‐scale hatcheries producing selected lines of sex‐reversed, indigenous tilapia for sale to smaller‐scale farmers is proposed as a solution to the problems of poor genetic management in African aquaculture.     

Status of mammals on Groote Eylandt: Safe haven or slow burn?

Native mammals across northern Australia have suffered severe decline, with feral cats (Felis catus), introduced herbivores and changed fire regimes being implicated as drivers. However, uncertainty surrounding the relative contribution of each of these threats, and the interactions between them, is limiting the development of effective management strategies. The absence of introduced herbivores and cane toads (Rhinella marina) on Groote Eylandt, Northern Territory, provides an opportunity to evaluate some hypothesised threats in isolation of others. We used camera traps to investigate the correlates of native mammal distribution and abundance at 112 lowland savanna sites across Groote Eylandt. Two large grids of camera traps were also deployed to obtain estimates of feral cat density. We hypothesised that native mammal populations would be negatively associated with feral cat occupancy as well as frequent, large fires. Native mammal site‐occupancy on Groote Eylandt was generally higher compared to mainland Northern Territory. Feral cats were infrequently detected, precluding both an estimate of feral cat density and an evaluation of the relationship between feral cats and native mammals. We found no evidence that native mammal site‐occupancy or relative abundance is negatively associated with frequent, large fires. The relatively healthy state of native mammal populations on Groote Eylandt is likely due to the low density of feral cats, the benign fire regime and the absence of large introduced herbivores and cane toads. However, due to a lack of historical data, the current state of mammals should not be taken as evidence that these populations are safe from decline. This study highlights that the apparent resilience of mammal populations is a result of complex interactions between factors that vary substantially across the landscape. Caution is therefore required when making broad inferences about the drivers of mammal decline from studies that are spatially and temporally limited.     

Large Mammal Distribution in a Transfrontier Landscape: Trade‐offs Between Resource Availability and Human Disturbance

Understanding factors that affect the persistence of charismatic megafauna in human‐dominated landscapes is crucial to inform conservation decision‐making and reduce human‐wildlife conflict. We assessed the effect of environmental and anthropogenic factors at different landscape and management scales in predicting the distribution of African elephant (Loxodonta africana) within the Greater Mapungubwe Transfrontier Conservation Area in Southern Africa. We combined aerial distribution counts over a 12‐yr period with 14 variables, representing food availability, landscape, and anthropogenic effects, into generalized linear models. Generalized linear models were run for the broader landscape, as well as three separate management units within the broader landscape, namely ecotourism, trophy hunting, and a combination of hunting and ecotourism. Human activities within different management units forced elephant to trade‐off between disturbance avoidance, and good food and water availability. In addition, the important predictors of elephant distribution within each of the management units differed from the predictors at the broader landscape. Overall, our results suggest that at the fine scale, elephant are constraint by factors that may be masked at the broader landscape scale. We suggest that accounting for anthropogenic disturbance is important in determining the distribution of large, wide‐ranging, mammal species in increasingly human‐dominated landscapes, and that modeling needs to be done at the spatial scales at which conservation decisions are made.     

Historical surveys reveal a long‐term decline in muskrat populations

The muskrat (Ondatra zibethicus) is an iconic species in Canada, valued for both its fur and its integral role in wetland ecosystems, and widely regarded for its perseverance. However, the resilience of this semiaquatic mammal seems to be in question now as increasing evidence points to widespread population declines. Recent analyses of harvest data across North America suggest a reduction in their numbers, but this has not been widely corroborated by population surveys. In this study we replicated historic muskrat house count surveys at two large Great Lakes coastal wetlands and present confirmation that declines in muskrat harvest correspond to actual declines in muskrat abundance. At the Point Pelee National Park marsh and the Matchedash Bay‐Gray Marsh wetland we found that mean muskrat house counts declined by 93% and 91% respectively between historic surveys 40–50 yrs ago and contemporary surveys over the past 7 yrs. The factors responsible for these dramatic declines remain unclear but there may be a relationship with changes in the habitat quality of these wetlands that have occurred over the same time frame. Not only is the loss of muskrats an issue for the resulting loss of the wetland ecosystem services they provide, but it may be an indication of broader marsh ecosystem degradation. As such, a scarcity of muskrats should be considered a red flag for the state of biodiversity in our wetlands. Continued surveys and ongoing research are needed to shed more light on the current status of muskrat populations and their marsh habitats across their native range.     

Densities of mammals in partially protected areas: the Katavi ecosystem of western Tanzania

1. In Africa the majority of conservation areas sanction some sort of human activities within their borders but few of them are part of community-based conservation schemes. The effectiveness of these state-owned, partially protected areas in conserving mammalian fauna is largely unknown.
2. Large and medium-sized mammal densities in three different sorts of partially protected area were compared to mammal densities in an adjacent national park in western Tanzania by driving 2953 km of strip transects over a 14-month period.
3. In a Game Controlled Area that permitted temporary settlement, cattle grazing and tourist big game hunting, mammal diversity and mammal densities were relatively high. In a Forest Reserve that permitted limited hardwood extraction and resident hunting, most large species were absent. In a third, Open Area that allowed settlement, cattle grazing, firewood collection and beekeeping activities, mammal diversity and densities were again low but some large ungulates still used the area seasonally.
4. The chief factors responsible for lowered mammal densities outside the Park were illegal hunting, especially in close proximity to town, and to a lesser extent, resident hunting quotas that were too high.
5. These data suggest that state-owned conservation areas permitting human activities within their borders cannot be relied upon as a means of conserving large and middle-sized mammals in Africa.
6. Two methods are being employed to ameliorate this problem in Africa: excluding people from conservation areas while upgrading ground protection effort, and initiation of community-based conservation schemes. As yet, however, very few quantitative data are available to evaluate the efficacy of these methods in enhancing mammal populations.     

Marine mammal culling programs: review of effects on predator and prey populations

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Will Elephants Soon Disappear from West African Savannahs?

Precipitous declines in Africa's native fauna and flora are recognized, but few comprehensive records of these changes have been compiled. Here, we present population trends for African elephants in the 6,213,000 km2 Sudano-Sahelian range of West and Central Africa assessed through the analysis of aerial and ground surveys conducted over the past 4 decades. These surveys are focused on the best protected areas in the region, and therefore represent the best case scenario for the northern savanna elephants. A minimum of 7,745 elephants currently inhabit the entire region, representing a minimum decline of 50% from estimates four decades ago for these protected areas. Most of the historic range is now devoid of elephants and, therefore, was not surveyed. Of the 23 surveyed elephant populations, half are estimated to number less than 200 individuals. Historically, most populations numbering less than 200 individuals in the region were extirpated within a few decades. Declines differed by region, with Central African populations experiencing much higher declines (-76%) than those in West Africa (-33%). As a result, elephants in West Africa now account for 86% of the total surveyed. Range wide, two refuge zones retain elephants, one in West and the other in Central Africa. These zones are separated by a large distance (～900 km) of high density human land use, suggesting connectivity between the regions is permanently cut. Within each zone, however, sporadic contacts between populations remain. Retaining such connectivity should be a high priority for conservation of elephants in this region. Specific corridors designed to reduce the isolation of the surveyed populations are proposed. The strong commitment of governments, effective law enforcement to control the illegal ivory trade and the involvement of local communities and private partners are all critical to securing the future of elephants inhabiting Africa's northern savannas.     

Threatened mammals become more predatory after small‐scale prescribed fires in a high‐rainfall rocky savanna

Understanding mechanisms underlying fire regime effects on savanna fauna is difficult because of a wide range of possible trophic interactions and feedbacks. Yet, understanding mechanisms underlying fauna dynamics is crucial for conservation management of threatened species. Small savanna mammals in northern Australia are currently undergoing widespread declines and regional extinctions partly attributable to fire regimes. This study investigates mammal trophic and ecosystem responses to fire in order to identify possible mechanisms underlying these declines. Mammal trophic responses to fire were investigated by surveying mammal abundance, mammal diet, vegetation structure and non‐mammal fauna dynamics in savannas six times at eight sites over a period of 3 years. Known site‐specific fire history was used to test for trophic responses to post‐fire interval and fire frequency. Mammal and non‐mammal fauna showed only minor responses of post‐fire interval and no effect of fire frequency. Lack of fauna responses differed from large post‐fire vegetation responses. Dietary analysis showed that two mammal species, Dasyurus hallucatus and Isoodon auratus, increased their intake of large prey groups in recently burnt, compared to longer unburnt vegetation. This suggests a fire‐related change in trophic interactions among predators and their prey, after removal of ground‐layer vegetation. No evidence was found for other changes in food resource uptake by mammals after fire. These data provide support for a fire‐related top‐down ecosystem response among savanna mammals, rather than a bottom‐up resource limitation response. Future studies need to investigate fire responses among other predators, including introduced cats and dingoes, to determine their roles in fire‐related mammal declines in savannas of northern Australia.