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And Then There was One: A Camera Trap Survey of the Declining Population of African Elephants in Knysna, South Africa
Abstract
Conservation agencies rely on accurate wildlife population estimates to inform management practices. The importance of accuracy increases with smaller, threatened populations, but so too does the challenge in achieving it, especially for evasive species in low-visibility terrain. Non-invasive survey techniques have been successfully applied in such conditions; however, each technique bears a unique set of limitations and often deliver different results. The shy Knysna elephants (Loxodonta africana) occur at extremely low numbers in difficult terrain, and the past few decades have seen debates raging about their numbers, fuelled in part by differing survey outcomes, although a decline has been apparent over the last 150 years. We surveyed the known range of the Knysna elephant population for 15 months (July 2016-October 2017), using camera traps, and identified one adult female elephant. The reliability of using camera trapping for surveying animal populations in conditions such as the Knysna elephant is compared with the previous faecal DNA genotyping survey. We conclude that this population has declined to a single individual and discuss the implications for local conservation authorities. Additionally, we highlight the importance of designing rigorous survey approaches where only a few individual animals are present.
... In addition to the phylogeographic analysis, we also used the Rx method developed by de Flamingh et al. (2020) to estimate the biological sex of the re-sequenced elephant with the lowest coverage (WNP01). We chose to estimate the sex of the elephant with the lowest coverage to set a lower-bound for sequencing coverage needed to successfully estimate sex, and because the sex of this individual is known based on photographic and observational evidence (Moolman et al., 2019a) while the sex of the other resequenced free-ranging individuals is unknown. We did not estimate the sex of other individuals as we were only interested in demonstrating the applicability of our method, rather than investigating sex-associated genomic patterns across the datasets. ...
... In addition to broad-scale conservation genomic questions (e.g., phylogeography and genetic structuring), the approaches used in this study may enable the study of rare or elusive species, or of species or populations where low animal density or small population size make traditional methods of sample collection (e.g., trapping/immobilization) difficult or impossible. For example, using the approach developed by de Flamingh et al. (2020), we estimated the genomic sex of the only remaining Knysna elephant in Wilderness National Park (WNP; Moolman et al., 2019a). This elephant which lives in the Afromontane Knysna Forest of South Africa is the sole survivor of a population that once comprised thousands of elephants, and there is ongoing discussion on management actions, e.g., reintroduction of other elephants (Patterson, 2012;Moolman et al., 2019a;Moolman et al., 2019b). ...
... For example, using the approach developed by de Flamingh et al. (2020), we estimated the genomic sex of the only remaining Knysna elephant in Wilderness National Park (WNP; Moolman et al., 2019a). This elephant which lives in the Afromontane Knysna Forest of South Africa is the sole survivor of a population that once comprised thousands of elephants, and there is ongoing discussion on management actions, e.g., reintroduction of other elephants (Patterson, 2012;Moolman et al., 2019a;Moolman et al., 2019b). Consistent with photographic evidence (Moolman et al., 2019a), we confirmed genetically that this individual is a female. ...
Non-invasive biological samples benefit studies that investigate rare, elusive, endangered, or dangerous species. Integrating genomic techniques that use non-invasive biological sampling with advances in computational approaches can benefit and inform wildlife conservation and management. Here, we used non-invasive fecal DNA samples to generate low- to medium-coverage genomes (e.g., >90% of the complete nuclear genome at six X-fold coverage) and metagenomic sequences, combining widely available and accessible DNA collection cards with commonly used DNA extraction and library building approaches. DNA preservation cards are easy to transport and can be stored non-refrigerated, avoiding cumbersome or costly sample methods. The genomic library construction and shotgun sequencing approach did not require enrichment or targeted DNA amplification. The utility and potential of the data generated was demonstrated through genome scale and metagenomic analyses of zoo and free-ranging African savanna elephants (Loxodonta africana). Fecal samples collected from free-ranging individuals contained an average of 12.41% (5.54–21.65%) endogenous elephant DNA. Clustering of these elephants with others from the same geographic region was demonstrated by a principal component analysis of genetic variation using nuclear genome-wide SNPs. Metagenomic analyses identified taxa that included Loxodonta, green plants, fungi, arthropods, bacteria, viruses and archaea, showcasing the utility of this approach for addressing complementary questions based on host-associated DNA, e.g., pathogen and parasite identification. The molecular and bioinformatic analyses presented here contributes towards the expansion and application of genomic techniques to conservation science and practice.
... By combining CT and LEK data, we were able to increase the spatial coverage of our study area to describe the traits allowing mammals to persist in the multifunctional landscape of the GRBR. Sixteen mammal species above 500 g in mass, cited in the mammal list of species of the GRNP (Baard et al., 2015), were detected in the diverse habitats of this mosaic landscape, with the exception of elephants (Loxodonta africana), with only one individual remaining (Moolman et al., 2019). Our results showed that protected areas play a crucial role in preserving large-bodied species and species with a more specialist diet, although a diversity of species was detected across the landscape. ...
Understanding what influences species and trait composition is critical for predicting changes in communities driven by landscape transformation.
We explored how life‐history traits are associated with the persistence of mammal species in human‐dominated habitats within the Garden Route Biosphere Reserve, South Africa. We combined data from a camera trap study and a local ecological knowledge‐based survey in an integrated occupancy model to analyse species occurrence along a gradient of anthropogenic landscape transformation.
Results confirmed that mammal occurrence in human‐modified habitats was related to specific life‐history traits. Species with more specialist diets, as well as larger body mass species were more likely to stay in protected areas. Species with slow reproductive strategies occupied more natural areas.
Combining different monitoring methods enabled us to increase spatial coverage and mammal sighting numbers. This approach fostered research participation by various stakeholders, an important step for co‐designing wildlife‐friendly anthropogenic spaces.
Synthesis and applications. Integrating data from a standard ecological protocol and structured participatory citizen knowledge allowed us to identify the species functional traits associated with mammal species occurrence in anthropogenic landscapes at a local scale. These results advocate for wisely combining methods and will guide conservation‐orientated land‐use planning towards the protection of natural habitats in the Garden Route Biosphere Reserve. This methodological approach will enable managers and conservationists to use data obtained from diverse protocols and should catalyse the involvement of citizens in biodiversity monitoring and conservation.
... The diversity of species recorded by >10 % of respondents was consistent with previous studies and distribution maps (Endangered Wildlife Trust, 2020; Hanekom and Randall, 2015). The filtering of 10 % could be discussed as it may hide the detection of rarer species such as the lonely Knysna elephant (Moolman et al., 2019). However, rarely cited species could be the expression of species misidentification (e.g. the steenbok (Raphicerus campestris) or grey rhebok (Pelea capreolus) being confounded with the more widespread species such as the Cape grysbok or the bushbuck). ...
Humans have shaped the environment through landscape transformation, disturbance, and resource exploitation, leading to major habitat modification and fragmentation. Mammal species are massively threatened by these changes and their diversity implies various responses to human disturbance. It is essential to understand the conditions for their persistence in human-dominated landscapes, and the drivers of humans-mammals' coexistence to apply relevant conservation measures. The Garden Route Biosphere Reserve, in South Africa, a mosaic landscapes where human activities and wildlife meet, is an ideal site to examine how anthropogenic attributes influence wildlife occurrence. To maximise our area coverage through a replicable, low-cost protocol, we designed an online survey aimed at residents to investigate the effect of landscape metrics and property attributes-the availability and type of anthropogenic resources, the integrity and type of natural habitats, structural disturbances and interferences-on the persistence of mammals in such environments. We collected data from 247 respondents and modelled the drivers of occurrence for 14 mammal species (>500 g). We found species-specific responses to synthetic variables describing anthropogenic features in the studied landscape and used the anthropodependence framework to categorise species profiles. We showed that human disturbance combined with the availability of anthropogenic resources and natural habitats defined various categories of species profiles, which should require differential conservation actions. Local ecological knowledge proved promising to understand conditions for mammal persistence in human-dominated landscapes. This method also allowed researchers to engage with a wide variety of stakeholders, thus creating a hub for knowledge exchange.
... Little emphasis has been put on using by-catch data from surveys targeting humans for biodiversity monitoring purposes. The effect of camera height on detection probability of mammal species was tested by comparing a standard height for monitoring biodiversity (50 cm, used in the African Snapshot safari survey, Meek et al. 2016b;Pardo et al. 2021) with a height chosen to monitor human-related events (130 cm, used in a Human-Wildlife Interface Monitoring Project, Moolman et al. 2019). It was hypothesised that lower cameras would detect smaller mammals at higher frequencies than the higher cameras, but that no difference would occur between camera heights in detecting larger species. ...
... survivor of a population that once comprised thousands of elephants, and there is ongoing discussion on management actions (e.g., reintroduction of other elephants; (Moolman, de Morney, et al., 2019;Moolman, Ferreira, et al., 2019;Patterson, 2012)). Consistent with photographic evidence (Moolman et al., 2019a), we confirmed that this is a genetically a female. ...
Non-invasive biological samples benefit studies that investigate rare, elusive, endangered, and/or dangerous species. Integrating genomic techniques that use non-invasive biological samples with advances in computational approaches can benefit and inform wildlife conservation and management. Here we present a molecular pipeline that uses non-invasive fecal DNA samples to generate low- to medium-coverage genomes (e.g., >90% of the complete nuclear genome at 6X coverage) and metagenomic sequences, combining in a novel fashion widely available and accessible DNA collection cards with commonly used DNA extraction and library building approaches. DNA preservation cards are easy to transport and can be stored non-refrigerated, avoiding cumbersome and/or costly sample methods. The genomic library construction and shotgun sequencing approach did not require enrichment or targeted DNA amplification. The utility and potential of the data generated by this pipeline was demonstrated by the application of genome-scale analysis and metagenomics to zoo and free-ranging African savanna elephants (Loxodonta africana). Fecal samples collected from free-ranging individuals contained an average of 12.41% (5.54-21.65%) endogenous elephant DNA. Clustering of these elephants with others from the same geographic region was demonstrated by a principal component analysis of genetic variation using nuclear genome-wide SNPs. Metagenomic analyses generated compositional taxon classifications that included Loxodonta, green plants, fungi, arthropods, bacteria, viruses and archaea, showcasing the utility of our approach for addressing complementary questions based on host-associated DNA, e.g., pathogen and parasite identification. The molecular pipeline presented here extends applications beyond what has previously been shown for target-enriched datasets and contributes towards the expansion and application of genomic techniques to conservation science and practice.
... Camera traps have since been used to answer a myriad of ecological and applied conservation questions including density estimation, spatiotemporal activity patterns, and occupancy, and on organisms ranging from insects (Suckling et al. 2020) to African elephants Loxodonta africana (Moolman et al. 2019). As such, camera traps have transformed scientific understanding of mammalian distributions and assemblages (Rowcliffe and Carbone 2008). ...
The use of remote camera traps has accelerated rapidly in the field of large carnivore science since the 1990s. Members of the Hyaenidae are important components of functional ecosystems in Africa and parts of the Middle East and South Asia, and make good candidates for study using camera traps. However, camera trap studies of hyenas remain rare in the literature when compared to species like tigers Panthera tigris, leopards Panthera pardus, and snow leopards Panthera uncia. In this paper, we examine the published use of camera traps for hyenas (n = 34 studies implemented between 2007 and 2020) and examine the logistical challenges of using camera traps, such as individual identification, limited sexual dimorphism, and complex social structures, for studies of hyena population biology, behavioral ecology, and conservation. We highlight what these challenges may mean for data analyses and interpretation. We also suggest potential benefits of further camera trap studies of this taxonomic family, including new insights into social behavior, range extensions, and robust density estimates.
... Today, only one Knysna elephant remains. She is an adult female in her 40s (Moolman et al., 2019b) and inhabits an area ∼18 km from the elephant tracksite containing the purported trunk-drag marks. The Knysna elephants were the most southerly group of elephants in Africa, the only free-ranging elephants in South Africa, and one of only four relict populations in South Africa (Hall-Martin, 1992). ...
Aeolianites and cemented foreshore deposits on South Africa's Cape south coast have the capacity to record and preserve events that transpired on them when they were composed of unconsolidated sand. Thirty-five Pleistocene elephant tracksites have been identified along this coastline. This abundance of sites along what was the margin of the vast Palaeo-Agulhas Plain allows for an appreciation of the forms that elephant tracks and traces can take in the context of the global proboscidean track record. They point to a significant regional elephant presence from Marine Isotope Stage (MIS) 11 (~400 ka) through MIS 5 (~130–80 ka) to MIS 3 (~35 ka) and also indicate repeated use of certain dune areas. They buttress Holocene and historical evidence that elephants made use of open areas in the region, and that the remaining “Knysna elephants” retreated into dense afrotemperate forest for protection in recent centuries. Analogies can be drawn between Pleistocene elephant tracks and Mesozoic dinosaur tracks, and some of the Cape south coast elephant tracks are among the largest Cenozoic (and hence, Quaternary) tracks ever to be described. A newly identified tracksite in this area may provide the first reported evidence of elephant trunk-drag impressions.
... The rather elaborate process involved in its execution, its labour-intensive nature and often the lowcapture rates obtained, accompanied by the high costs involved, could limit the application of this method to relatively restricted areas and small elephant populations. Camera traps can, however, be useful in areas with extremely low animal densities and difficult terrains (Moolman et al. 2019). ...
Increasing anthropogenic pressures has led to the fragmentation of Asian
elephant habitats, affecting their numbers, demography and ranging patterns across their
range. Baseline information on the demography and population dynamics of free-ranging
Asian elephants is often unavailable. Population monitoring at the landscape level has
many constraints, including those of visibility, habitat, terrain and field logistics, among
several others. While knowing elephant numbers may be important for managing local
populations, demographic parameters and distribution patterns are perhaps more crucial
to ascertain long-term trends for conservation.
... This forced the last remaining populations to utilize less accessible areas such as the foothills of the Outeniqua and Tsitsikamma mountain ranges, around the Knysna Forest, or the dense-thicket areas known today as Addo Elephant Park [5,8]. The individuals of Knysna represent the southern-most elephant population in the world [9], but recent camera trap surveys demonstrated that the former Knysna population now comprises only one remnant female [10]. While historical records suggest some elephants were supported permanently in some fynbos habitats [2], fynbos vegetation may be of sub-optimal quality, given its low nutrient status [5,11,12]. ...
Fynbos is a unique endemic vegetation type belonging to the Cape Floral Kingdom in the Western Cape Province of South Africa, representing the smallest of the six floral kingdoms in the world. Nowadays, only a few game reserves in this region support populations of African elephants (Loxodonta africana), and thus, little information exists regarding the suitability of the nutritionally poor Fynbos vegetation for these megaherbivores. Using already established non-invasive methods, the monitoring of individual body conditions and fecal glucocorticoid metabolite (fGCM) concentrations, as a measure of physiological stress, was performed to examine a herd of 13 elephants in a Western Cape Province Private Game Reserve, during two monitoring periods (April and June 2018), following a severe drought. The results indicate that overall median body condition scores (April and June: 3.0, range 2.0–3.0) and fGCM concentrations (April: 0.46 µg/g dry weight (DW), range 0.35–0.66 µg/g DW; June: 0.61 µg/g DW, range 0.22–1.06 µg/g DW) were comparable to those of other elephant populations previously studied utilizing the same techniques. These findings indicate that the individuals obtain sufficient nutrients from the surrounding Fynbos vegetation during the months monitored. However, a frequent assessment of body conditions and stress-associated fGCM concentrations in these animals would assist conservation management authorities and animal welfare practitioners in determining ways to manage this species in environments with comparably poorer nutritional vegetation.
Understanding and identifying drivers of local population declines are important in mitigating future risks and optimising conservation efforts. The Knysna elephants have, after being afforded protection since the early 1900s, declined to near extinction today. We propose three hypotheses as to why the Knysna elephant population declined. The refugee hypothesis suggests that anthropogenic activities forced the elephants to take refuge in the forest and that the low-quality food acted as the primary driver of decline. The illegal killing hypothesis suggests that the elephants adapted to the forest and its immediate fynbos habitat, with the decline being a consequence of illegal kills. The stochastic founder population hypothesis postulates that the population size and structure left it vulnerable to demographic stochasticity. We critically reviewed available evidence for these hypotheses and found that, although the historical elephant range decline most likely resulted through the refugee hypothesis, the weak demographic and life-history information limits elimination of either of the other hypotheses. We touch on the implications for decision-makers and draw attention to information requirements.
Significance:
• We highlight the knowledge and management challenges which exist for small, threatened populations of which long-term demographic data are sparse.
• We provide the first unbiased evaluation of multiple drivers that may have caused the decline of the Knysna elephants.
Background: Faecal hormone metabolite measurement is a widely used tool for monitoring
reproductive function and response to stressors in wildlife. Despite many advantages of this
technique, the delay between defaecation, sample collection and processing may influence
steroid concentrations, as faecal bacterial enzymes can alter steroid composition post-defaecation.
Objectives: This study investigated changes in faecal glucocorticoid (fGCM), androgen (fAM)
and progestagen (fPM) metabolite concentrations in faeces of a male and female African
elephant (Loxodonta africana) post-defaecation and the influence of different faeces-drying
regimes.
Method: Subsamples of fresh faeces were frozen after being dried in direct sun or shade for 6,
20, 24, 48 and 72 h and 7 and 34 days. A subset of samples for each sex was immediately frozen
as controls. Faecal hormone metabolite concentrations were determined using enzyme
immunoassays established for fGCM, fAM and fPM monitoring in male and female African
elephants.
Results: Hormone metabolite concentrations of all three steroid classes were stable at first, but
changed distinctively after 20 h post-defaecation, with fGCM concentrations decreasing over
time and fPM and fAM concentrations steadily increasing. In freeze-dried faeces fGCM
concentrations were significantly higher than respective concentrations in sun-dried material,
which were in turn significantly higher than fGCM concentrations in shade-dried material. In
contrast, fAM concentrations were significantly higher in sun- and shade-dried faeces compared
to freeze-dried faeces. Higher fPM concentrations were also found in air-dried samples
compared to lyophilised faeces, but the effect was only significant for sun-dried material.
Conclusion: The revealed time restriction for collecting faecal material for hormone
monitoring from elephants in the wild should be taken into account to assure reliable and
comparable results. However, if logistics allow a timely collection, non-invasive hormone
measurement remains a powerful and reliable approach to provide information about an
elephant’s endocrine status.
An understanding of animal behaviour is important if conservation initiatives are to be effective. However, quantifying the behaviour of wild animals presents significant challenges. Remote-sensing camera traps are becoming increasingly popular survey instruments that have been used to non-invasively study a variety of animal behaviours, yielding key insights into behavioural repertoires. They are well suited to ethological studies and provide considerable opportunities for generating conservation-relevant behavioural data if novel and robust methodological and analytical solutions can be developed. This paper reviews the current state of camera-trap-based ethological studies, describes new and emerging directions in camera-based conservation behaviour, and highlights a number of limitations and considerations of particular relevance for camera-based studies. Three promising areas of study are discussed: (1) documenting anthropogenic impacts on behaviour; (2) incorporating behavioural responses into management planning and (3) using behavioural indicators such as giving up densities and daily activity patterns. We emphasize the importance of reporting methodological details, utilizing emerging camera trap metadata standards and central data repositories for facilitating reproducibility, comparison and synthesis across studies. Behavioural studies using camera traps are in their infancy; the full potential of the technology is as yet unrealized. Researchers are encouraged to embrace conservation-driven hypotheses in order to meet future challenges and improve the efficacy of conservation and management processes.
African elephants (Loxodonta africana) are imperiled by poaching and habitat loss. Despite global attention to the plight of elephants, their population sizes and trends are uncertain or unknown over much of Africa. To conserve this iconic species, conservationists need timely, accurate data on elephant populations. Here, we report the results of the Great Elephant Census (GEC), the first continent-wide, standardized survey of African savannah elephants. We also provide the first quantitative model of elephant population trends across Africa. We estimated a population of 352,271 savannah elephants on study sites in 18 countries, representing approximately 93% of all savannah elephants in those countries. Elephant populations in survey areas with historical data decreased by an estimated 144,000 from 2007 to 2014, and populations are currently shrinking by 8% per year continent-wide, primarily due to poaching. Though 84% of elephants occurred in protected areas, many protected areas had carcass ratios that indicated high levels of elephant mortality. Results of the GEC show the necessity of action to end the African elephants' downward trajectory by preventing poaching and protecting habitat.
Camera trapping studies have become increasingly popular to produce population estimates of individually recognisable mammals. Yet, monitoring techniques for rare species which occur at extremely low densities are lacking. Additionally, species which have unpredictable movements may make obtaining reliable population estimates challenging due to low detectability. Our study explores the effectiveness of intensive camera trapping for estimating cheetah (Acinonyx jubatus) numbers. Using both a more traditional, systematic grid approach and pre-determined, targeted sites for camera placement, the cheetah population of the Northern Tuli Game Reserve, Botswana was sampled between December 2012 and October 2013. Placement of cameras in a regular grid pattern yielded very few (n = 9) cheetah images and these were insufficient to estimate cheetah density. However, pre-selected cheetah scent-marking posts provided 53 images of seven adult cheetahs (0.61 ± 0.18 cheetahs/100km²). While increasing the length of the camera trapping survey from 90 to 130 days increased the total number of cheetah images obtained (from 53 to 200), no new individuals were recorded and the estimated population density remained stable. Thus, our study demonstrates that targeted camera placement (irrespective of survey duration) is necessary for reliably assessing cheetah densities where populations are naturally very low or dominated by transient individuals. Significantly our approach can easily be applied to other rare predator species.
Distribution data form the basis of the study of zoo-geography, which has applications in, inter alia,
ecology and conservation. Written records were used to estimate the distribution patterns of some of the
medium- to large-sized terrestrial mammals in central, southern and western South Africa, and
neighbouring Lesotho, during the early historical period (late 1400 s to the 1920s). The sources of these
records comprise mainly published or unpublished letters, journals, diaries or books written by literate
pioneers – notably various missionaries, explorers, travellers, naturalists, military personnel, big game
hunters and agro-pastoralists. The classification (according to record type) of the written records in key
publications was standardised, and records overlooked by them are taken into account. Interpretation of
the spatial patterns provided by the written records was aided by reference to supporting information,
in the form of qualifying palaeontological, zoo-archaeological and museum records. Written records of
acceptable quality are shown, together with supporting records (where applicable), on a series of
species occurrence maps, which also depict the biomes that are represented in the study area. The
information on these maps is interpreted, together with relevant information in the source texts and a
map of the bioregions that constitute the biomes in question, to estimate distribution patterns that
prevailed during the period under study. Data are presented for 27 genera, 36 species and 2 subspecies,
comprising 7 carnivores and 30 herbivores. Despite the limitations associated with the use of written
records, the information provided is considered to offer a realistic distribution pattern for most of the
taxa covered. The use of supporting records is justified, since the majority of these corroborate the
ranges derived from the written records. The present study enhances our knowledge of distribution
patterns for these larger mammal species in a large part of the southern African sub-region during the
early historical period. It also provides a first attempt to describe the sub-regional scale, historical,
distribution patterns within the context of the broad biogeographical characteristics of the area in
question. There is a need to extend the coverage achieved by this study to include the remaining
approx. 30% of “South Africa”, i.e. the region incorporating South Africa, Lesotho and Swaziland, and
also the area incorporated by the countries of Namibia, Botswana, Zimbabwe and Mozambique. This
level of coverage will permit enhanced definition of historical distribution patterns for some larger
mammals in the southern African sub-region. There is also a need to better understand the drivers, as
well as the implications, of the observed changes in the distribution of the larger mammals since the
start of the historical period.
Population numbers of Knysna elephants Loxodonta africana africana, after having remained static for more than six decades, dwindled rapidly from an estimated 10 animals in 1970 to a single surviving individual. According to an explanatory model presented, the poor reproductive performance and population decline of the Knysna elephants are attributable to low nutrient/carbon ratios of the diet available to them in the predominantly forest environment to which they were largely confined as a result of residential and agricultural development in the region. The low dietary N/C ratios are postulated to result in low metabolic turnover rates and, therefore, reproductive rates too low to offset mortalities. During 1994 three sub-adult female elephants from the Kruger National Park were translocated to the Knysna forest area (southern Cape, South Africa) in order to supplement the dwindling population. Monitoring of habitat choice and nutritional faecal parameters of both the translocatd and a Knysna cow elephant tend to support the postulates of the explanatory model. The translocated elephants did not remain with the matriarch (Knysna elephant) and progressively chose to rang in more open habitat outside of the Afromontane forest area. Analyses showed that the diet selected by the translocated elephants had higher assimilable N/C ratios than that of the Knysna elephant. The results of the study emphasise the importance of clearly differentiating between sink and source habitat in conservation management.
1. Abundance is a key quantity for conservation and management strategies but remains challenging to assess in the field. Capture-recapture (CR) methods are often used to estimate abundance while correcting for imperfect detection but these methods are costly. Occupancy, sometimes considered as a surrogate for abundance, is estimated through the collection of presence/absence data and is less costly while allowing gathering of information at a large spatial scale.
2. Building on the recent pieces of work on the combination of different data sources, we showed how abundance data can be complemented by presence/absence data and can be analysed conjointly to improve abundance estimates. Our approach relies on a hierarchical model that makes explicit the link between the abundance and occupancy state variables while formally accounting for imperfect detection.
3. We used a population of Eurasian lynx in France monitored via camera-traps and a collection of presence signs as an illustration of our approach.
4. Synthesis and applications. We combined capture/recapture and occupancy data, and demonstrated that we can efficiently improve abundance estimates. Our method can be used by managers when estimates of trends in abundance lack power due to sparse data collected during an intensive survey, by simply integrating data collected during non-systematic survey. Furthermore, combining these two sampling procedures makes full use of all available data and allows the development of conservation and management strategies based on precise abundance estimates. Overall, the combination of different data sources in an integrated statistical framework has a great potential, especially for elusive species.
Invasive alien plants (IAPs) are regarded as the leading ecological threat to the recently established Garden Route National Park (GRNP) along the Cape south coast of South Africa. The extensive and long-standing presence of commercial forestry in the region has contributed substantially to the current load of IAPs in the area. The GRNP's fragmented, linear configuration and a multitude of anthropogenic and ecological disturbances in the landscape contribute to its susceptibility to alien plant invasion. In compiling a checklist of alien flora for the park, we recorded 244 species of alien plants in 77 families, of which 58% (141 species) have not been recorded for the region by the Southern African Plant Invaders Atlas. Of the GRNP alien plant species, 9% are casual aliens, 27% naturalised, 59% invasive, and 5% transformers. Among South African National Parks, the GRNP ranks second in terms of alien plant species richness and has the largest proportion of invasives and transformers for those parks where invasion status was recorded. Transformer species in the GRNP are almost exclusively tree species introduced from Australasia > 100 years ago for forestry purposes or sand stabilisation. Natural habitat within the park that is most threatened by IAPs is fynbos shrublands and riparian habitat. Our analysis indicates that the pressure of IAPs in the GRNP is escalating. Substantial and sustained management actions will be required to mitigate impacts from alien plant invasions in the GRNP. We identified species posing emerging or escalating threats that require improved control or regulation.
Camera traps are used by scientists and natural resource managers to acquire ecological data, and the rapidly increasing camera trapping literature highlights how popular this technique has become. Nevertheless, the methodological information reported in camera trap publications can vary widely, making replication of the study difficult. Here we propose a series of guiding principles for reporting methods and results obtained using camera traps. Attributes of camera trapping we cover include: (i) specifying the model(s) of camera traps(s) used, (ii) mode of deployment, (iii) camera settings, and (iv) study design. In addition to suggestions regarding best practice data coding and analysis, we present minimum principles for standardizing information that we believe should be reported in all peer-reviewed papers. Standardised reporting enables more robust comparisons among studies, facilitates national and global reviews, enables greater ease of study replication, and leads to improved wildlife research and management outcomes.
Short-range elephant Loxodonta africana movements were examined in a heterogeneous landscape mosaic of settlements, crop fields and remnant forest in the Caprivi Strip, Namibia. We explored the penetration of the landscape through the use of permanent pathways and determined the impact of pathway use on crop-raiding location. Pathways were linear, devoid of vegetation and maintained by repeated movement. Functional connectivity of pathways was not species-specific, and pathways were used by various species. Elephants travelled in single file at night and we recorded selective pathway use: females selected pathways away from settlements to access water, whereas males used pathways among settlements to launch crop raids. Proximity of raided fields to the nearest pathway was the only significant spatial variable explaining crop-raiding location. Bulls were responsible for all crop-raiding incidents. We conclude that (1) pathways were the most significant spatial variable influencing which fields were raided, (2) crop-raiding from pathways may maximize foraging efficiency by reducing time spent and distance travelled while foraging, (3) pathways may facilitate penetration of the matrix by connecting predictable resources (crops) with preferred shelter areas, crossing points at roads and preferred drinking spots, and (4) access to the Kwandu River is restricted by settlements, predictably resulting in human-elephant conflict. By highlighting the relevance of pathways for movement of elephants we show that an understanding of the use of pathways is important for land-use planning in conservation landscapes, specifically with regard to human-elephant conflict. We also argue for the need to more fully explore pathway occurrence and use at larger spatial scales.
Spatial patterns of relatedness within animal populations are important in the evolution of mating and social systems, and have the potential to reveal information on species that are difficult to observe in the wild. This study examines the fine-scale genetic structure and connectivity of groups within African forest elephants, Loxodonta cyclotis, which are often difficult to observe due to forest habitat. We tested the hypothesis that genetic similarity will decline with increasing geographic distance, as we expect kin to be in closer proximity, using spatial autocorrelation analyses and Tau Kr tests. Associations between individuals were investigated through a non-invasive genetic capture-recapture approach using network models, and were predicted to be more extensive than the small groups found in observational studies, similar to fission-fusion sociality found in African savanna (Loxodonta africana) and Asian (Elephas maximus) species. Dung samples were collected in Lopé National Park, Gabon in 2008 and 2010 and genotyped at 10 microsatellite loci, genetically sexed, and sequenced at the mitochondrial DNA control region. We conducted analyses on samples collected at three different temporal scales: a day, within six-day sampling sessions, and within each year. Spatial autocorrelation and Tau Kr tests revealed genetic structure, but results were weak and inconsistent between sampling sessions. Positive spatial autocorrelation was found in distance classes of 0-5 km, and was strongest for the single day session. Despite weak genetic structure, individuals within groups were significantly more related to each other than to individuals between groups. Social networks revealed some components to have large, extensive groups of up to 22 individuals, and most groups were composed of individuals of the same matriline. Although fine-scale population genetic structure was weak, forest elephants are typically found in groups consisting of kin and based on matrilines, with some individuals having more associates than observed from group sizes alone.
Wildlife managers are urgently searching for improved sociodemographic population assessment methods to evaluate the effectiveness of implemented conservation activities. These need to be inexpensive, appropriate for a wide spectrum of species and straightforward to apply by local staff members with minimal training. Furthermore, conservation management would benefit from single approaches which cover many aspects of population assessment beyond only density estimates, to include for instance social and demographic structure, movement patterns, or species interactions. Remote camera traps have traditionally been used to measure species richness. Currently, there is a rapid move toward using remote camera trapping in density estimation, community ecology, and conservation management. Here, we demonstrate such comprehensive population assessment by linking remote video trapping, spatially explicit capture-recapture (SECR) techniques, and other methods. We apply it to three species: chimpanzees Pan troglodytes troglodytes, gorillas Gorilla gorilla gorilla, and forest elephants Loxodonta cyclotis in Loango National Park, Gabon. All three species exhibited considerable heterogeneity in capture probability at the sex or group level and density was estimated at 1.72, 1.2, and 1.37 individuals per km(2) and male to female sex ratios were 1:2.1, 1:3.2, and 1:2 for chimpanzees, gorillas, and elephants, respectively. Association patterns revealed four, eight, and 18 independent social groups of chimpanzees, gorillas, and elephants, respectively: key information for both conservation management and studies on the species' ecology. Additionally, there was evidence of resident and nonresident elephants within the study area and intersexual variation in home range size among elephants but not chimpanzees. Our study highlights the potential of combining camera trapping and SECR methods in conducting detailed population assessments that go far beyond documenting species diversity patterns or estimating single species population size. Our study design is widely applicable to other species and spatial scales, and moderately trained staff members can collect and process the required data. Furthermore, assessments using the same method can be extended to include several other ecological, behavioral, and demographic aspects: fission and fusion dynamics and intergroup transfers, birth and mortality rates, species interactions, and ranging patterns.
Automatically triggered cameras taking photographs or videos of passing animals (camera traps) have emerged over the last decade as one of the most powerful tool for wildlife research. In parallel, a wealth of camera trap systems and models has become commercially available, a phenomenon mainly driven by the increased use of camera traps by sport hunters. This has raised the need for developing criteria to choose the suitable camera trap model in relation to a range of factors, primarily the study aim, but also target species, habitat, trapping site, climate and any other aspect that affects camera performance. There is also fragmented information on the fundamentals of sampling
designs that deploy camera trapping, such as number of sampling sites, spatial arrangement and sampling duration. In this review, we describe the relevant technological features of camera traps and propose a set of the key ones to be evaluated when choosing camera models. These Features are camera specifications such as trigger speed, sensor sensitivity, detection zone, flash type and flash intensity, power autonomy, and related specifications. We then outline sampling design and camera features for the implementation of major camera trapping applications, specifically: (1) faunal inventories, (2) occupancy studies, (3) density estimation through Capture-Mark-Recapture and (4) density estimation through the Random Encounter Model. We also review a range of currently available models and stress the need for standardized testing of camera models that should be frequently updated and widely distributed. Finally we summarize the “ultimate camera trap”, as desired by wildlife biologists, and the current technological limitations of camera traps in relation to their potential for a number of emerging applications.
Individual identification of animals from DNA in field-collected faecal samples is becoming an increasingly important tool in wildlife population monitoring. A major issue relevant to the application of this technique is the reliability of the genotypes obtained. I investigated the effect of sample age and season of collection on amplification rates and reliability of microsatellite genotypes amplified from faecal DNA of a marsupial herbivore, the brush-tailed rock-wallaby (Petrogale penicillata) and a eutherian carnivore, the red fox (Vulpes vulpes). Comparison of DNA profiles from 1 day to 6 months for both species suggests that as the age of the faeces increases there is less good-quality DNA present on the surface of the faeces, resulting in significantly decreasing amplification rates and increasing genotyping error rates over time. No microsatellite PCR products were obtained from samples older than 3 months from any faecal DNA extract in either season. For both species, faeces collected during the summer trial yielded high-quality DNA for up to one week. Faeces collected in winter had significantly lower amplification rates and higher genotyping errors than the summer-collected samples. Computer simulations were used to estimate the probability of obtaining false genotypes when genotyping faecal samples of various ages. These revealed that three replicates is sufficient to prevent identification of false individuals for P. penicillata from faeces up to one week old in both summer and winter but more replicates may be required for older samples, particularly in winter. In contrast, up to eight replicates may be required for fox faeces collected in winter, particularly if more than one week old. These results also suggest that it is difficult to visually identify faecal age for V. vulpes, and any study using fox faeces would need to account for the likely inclusion of older faeces in a field collection. For P. penicillata, faecal age could be accurately assessed, particularly when less than one week old and targeting faeces that match the two most reliable appearance classes described here would be an efficient sampling strategy. It is recommended that the appropriate PCR replication protocol for any given study should be tailored to the error rates expected for the oldest samples likely to be collected. This study is the first to thoroughly investigate the effects of sample age and season of collection on microsatellite genotyping from faecal samples and provides guidelines for sampling and PCR repetition strategies for field-based non-invasive DNA studies.
http://www.primate-sg.org/best_practice_surveys/
Conservation planning in the Cape Floristic Region (CFR) of South Africa, a recognised world plant diversity hotspot, required information on the estimated spatial requirements of selected medium- to large-sized mammals within each of 102 Broad Habitat Units (BHUs) delineated according to key biophysical parameters. Spatial requirement estimates were derived for 19 omnivore and carnivore species, following a review and extrapolation of extant information. The estimates for 23 herbivore species were derived from a simple spreadsheet model based on forage availability estimates and the metabolic requirements of the species in question; this analysis incorporated adaptations of the agriculture-based Large Stock Unit (LSU) or Animal Unit approach. The LSU approach has various shortcomings but given the virtual absence of information on forage availability (quantity, quality and seasonality) for indigenous herbivores in the CFR, it provides the only extant measure of the influence of key biophysical factors on this parameter, especially at a regional scale. The outcomes of the exercise, viz. densities (hectares/animal), are presented here; these should be considered as testable hypotheses and a cautious 'management by hypothesis' approach should be adopted in their use. This information can be used to guide both conservation planning activities and practical conservation management decisions.
The use of non-invasive DNA-based sampling is becoming increasingly popular. However, the misidentification of individuals due to genotyping error (primarily allelic dropout) is a critical problem, especially when using individuals in the capture–mark–recapture (CMR) approach to estimate population size. We propose 2 simple and cost-effective tests, Examining Bimodality (EB) and Difference in Capture History (DCH), to determine whether a sample contains genotyping errors and the relative magnitude of the problem. These tests formalize currently used approaches for identifying genotyping errors. We evaluate the efficacy of these tests using simulated CMR data. Results show that both tests are effective at detecting genotyping errors and provide a strong indication of whether the data are error free. The EB and DCH tests apply to data in which multiple samples are associated with individuals, such as those generated by CMR sampling. Managers need to be able to identify and eliminate genotyping errors to produce population estimates that are both unbiased and scientifically defensible.
Summary • Microchiropteran bats have the potential to be important biodiversity indicator species as they are distributed globally and are important in ecosystem functioning. Survey and monitoring protocols for bats are often ineffective as sampling techniques vary in their efficacy depending on the species involved and habitats surveyed. Acoustic sampling using bat detectors may prove an alternative or complementary technique to capture methods but is largely untested in the tropics. • To compare the efficacy of bat detectors and capture methods in surveys, we used ground mist nets, sub-canopy mist nets and harp traps to sample bats while simultaneously recording the echolocation calls of insectivorous bats in a diversity of habitats in the Yucatan, Mexico. We described echolocation calls, analysed call characteristics to identify species, and compared species inventories derived from traditional capture methods with those derived from acoustic sampling. • A total of 2819 bats representing 26 species and six families were captured; 83% were captured in ground nets, 13% in sub-canopy nets and 4% in harp traps. Fourteen species and five phonic types were identified based on five echolocation call characteristics. Discriminant function analysis showed a high level of correct classification of the calls (84·1%), indicating that identification of species by their echolocation calls is feasible. • In all habitats, acoustic sampling and capture methods sampled significantly more species each night than capture methods alone. Capture methods failed to sample 30% of the bat fauna, and aerial insectivores were sampled only by bat detectors. • Synthesis and applications. Given the importance of bats in ecosystem functioning, and their potential as indicator species, developing effective methodologies to survey and monitor bats is important for sustainable forest management and biodiversity conservation. Acoustic sampling should be used with capture methods to increase inventory completeness in bat assemblage studies, and could form part of a single standardized monitoring protocol that can be used globally in tropical forests, as this method detects aerial insectivores not sampled by capture methods.
Noninvasive genotyping has not gained wide application, due to the notion that it is unreliable, and also because remedial measures are time consuming and expensive. Of the wide variety of noninvasive DNA sources, dung is the most universal and most widely used in studies. We have developed collection, extraction, and amplification protocols that are inexpensive and provide a high level of success in amplifying both mitochondrial and nuclear DNA from dung. Here we demonstrate the reliability of genotyping from elephant dung using these protocols by comparing results from dung-extracted DNA to results from blood-extracted DNA. The level of error from dung extractions was only slightly higher than from blood extractions, and conducting two extractions from each sample and a single amplification from each extraction was sufficient to eliminate error. Di-, tri-, and tetranucleotide loci were equally reliable, and low DNA quantity and quality and PCR inhibitors were not a major problem in genotyping from dung. We discuss the possible causes of error in genotyping with particular reference to noninvasive samples and suggest methods of reducing such error.
Understanding how mammals satisfy their need for space in fragmenting ecosystems is crucial for ecosystem conservation. Using state-of-the-art global positioning system (GPS) technology we tracked 11 focal African elephants (Loxodonta africana) in Kenya at 3-hourly fix intervals and collected between 34 and 406 days per individual. Our recordings gave a high spatio-temporal resolution compared to previous studies and allowed novel insights into range use. The actual ranges of the tracked elephants are smaller than usually represented. Moreover, the ranges in our sample were complex and not confined to officially designated protected areas, except where fenced. All the unfenced elephants in our sample had distinct 'home sectors' linked by 'travel' corridors. Within each home sector the elephants concentrated in favourite 'core zones'. Such core zones tended to lie in protected areas whereas corridors typically crossed unprotected range. Elephants moved significantly faster along corridors than elsewhere in their range, which suggests awareness of danger outside the protected area. We conclude that understanding the complex use of an animal's range is crucial for conservation planning aiming to balance animal interests with those of human beings that co-habit in their range.
Many social animals live in stable groups. In contrast, African savannah elephants (Loxodonta africana) live in unusually fluid, fission-fusion societies. That is, 'core' social groups are composed of predictable sets of individuals; however, over the course of hours or days, these groups may temporarily divide and reunite, or they may fuse with other social groups to form much larger social units. Here, we test the hypothesis that genetic relatedness predicts patterns of group fission and fusion among wild, female African elephants. Our study of a single Kenyan population spans 236 individuals in 45 core social groups, genotyped at 11 microsatellite and one mitochondrial DNA (mtDNA) locus. We found that genetic relatedness predicted group fission; adult females remained with their first order maternal relatives when core groups fissioned temporarily. Relatedness also predicted temporary fusion between social groups; core groups were more likely to fuse with each other when the oldest females in each group were genetic relatives. Groups that shared mtDNA haplotypes were also significantly more likely to fuse than groups that did not share mtDNA. Our results suggest that associations between core social groups persist for decades after the original maternal kin have died. We discuss these results in the context of kin selection and its possible role in the evolution of elephant sociality.
The tiger (Panthera tigris) is an endangered, large felid whose demographic status is poorly known across its distributional range in Asia. Previously applied methods for estimating tiger abundance, using total counts based on tracks, have proved unreliable. Lack of reliable data on tiger densities not only has constrained our ability to understand the ecological factors shaping communities of large, solitary felids, but also has undermined the effective conservation of these animals In this paper, we describe the use of a field method proposed by Karanth (1995), which combines camera-trap photography, to identify individual tigers, with theoretically well-founded capture-recapture models. We developed a sampling design for camera-trapping and used the approach to estimate tiger population size and density in four representative tiger habitats in different parts of India. The field method worked well and provided data suitable for analysis using closed capture-recapture models. The results suggest the potential for applying this methodology to rigorously estimate abundances, survival rates, and other population parameters for tigers and other low-density, secretive animal species in which individuals can be identified based on natural markings. Estimated probabilities of photo-capturing tigers present in the study sites ranged from 0.75 to 1.00. Estimated densities of tigers >1 yr old ranged from 4.1 ± 1.31 to 16.8 ± 2.96 tigers/100 km2 (mean ± 1 SE). Simultaneously, we used line-transect sampling to determine that mean densities of principal tiger prey at these sites ranged from 56.1 to 63.8 ungulates/km2. Tiger densities appear to be positively associated with prey densities, except at one site influenced by tiger poaching. Our results generally support the prediction that relative abundances of large felid species may be governed primarily by the abundance and structure of their prey communities.
The ability to noninvasively detect the presence of species and assess physiological health by DNA and hormone analysis makes scat a valuable tool for ecology and conservation. We assessed factors associated with DNA and hormone degradation in a four-season study that employed detection dogs to collect scats from maned wolf (Chrysocyon brachyurus) in the Brazilian Cerrado, a tropical savanna landscape mosaic. Fecal DNA sample viability was assessed by attempting polymerase chain reaction amplification of a mitochondrial DNA (mtDNA) locus (∼ 246 bp) and a nuclear DNA zinc finger protein gene (∼ 195 bp). We assessed how extraction method, environmental exposure, and amount of odor, moisture and diet items in the sample influenced DNA amplification and allelic dropout rates. Samples that amplified mtDNA were assayed for glucocorticoids and thyroid hormone. Amount of odor and moisture (indicating freshness) predicted mtDNA amplification success, as well as mean hormone levels. While factors related to sample condition were negatively correlated with lower mean hormone levels, samples comprised mainly of fruit had higher levels of glucocorticoids and lower levels of thyroid hormone, and we thus interpret this result as biologically meaningful. In summary, DNA and hormone degradation are predicted by measures of sample freshness, making the assessment of sample quality an important criterion for sample collection as well to manage measurement error in analyses of hormone concentration associated with environmental disturbance.
The Knysna Basin, a southern Cape catchment, drains into the Knysna estuary. The landscape characteristics are the product of a long geomorphic evolution resulting in high sensitivity to change. Consideration of the geomorphology is followed by examples of impacts on the estuary and adjacent areas. The need for sustainability in the context of development is argued. The paper is a southern African contribution to the landscape sensitivity issue.
The concept of refugee species provides a theoretical framework towards increasing the predictive power of the ‘declining population paradigm’ through identifying species which are expected to suffer from a declining population syndrome. Using a simple habitat model as a framework, refugee species are defined as those that can no longer access optimal habitat, but are confined to suboptimal habitats, with consequences of decreased fitness and density, and attendant conservation risks. Refugee species may be difficult to detect in the absence of information on prior habitat use and fitness and their observed ecology will be constrained by the habitat limits forced on them. Identification of refugee species, characterisation of pre-refugee ecology and the restoration of such species to optimal habitat is critical to their successful conservation. The concept is showcased by addressing the conundrum of a large grazing bovid, the European bison Bison bonasus, being managed as a forest specialist, despite its evolutionary background, dental morphology, neonatal behaviour, diet and microhabitat selection being characteristic of a grazing species inhabiting open, grass-rich habitats. It is hypothesized that a combination of increasing replacement of open steppe by forest cover after the last postglacial period and increasing human pressure forced bison into forests as a refuge habitat. This process was then reinforced through active management of bison in forests as managers committed themselves to the ‘bison as forest species’ paradigm. A research agenda to test this hypothesis using an experimental approach in the conservation management of European bison by introducing populations into diverse habitat types is suggested
Techniques for estimation of absolute abundance of wildlife populations have received a lot of attention in recent years. The statistical research has been focused on intensive small-scale studies. Recently, however, wildlife biologists have desired to study populations of animals at very large scales for monitoring purposes. Population indices are widely used in these extensive monitoring programs because they are inexpensive compared to estimates of absolute abundance. A crucial underlying assumption is that the population index (C) is directly proportional to the population density (D). The proportionality constant, β, is simply the probability of ‘detection’ for animals in the survey. As spatial and temporal comparisons of indices are crucial, it is necessary to also assume that the probability of detection is constant over space and time. Biologists intuitively recognize this when they design rigid protocols for the studies where the indices are collected. Unfortunately, however, in many field studies the assumption is clearly invalid. We believe that the estimation of detection probability should be built into the monitoring design through a double sampling approach. A large sample of points provides an abundance index, and a smaller sub-sample of the same points is used to estimate detection probability. There is an important need for statistical research on the design and analysis of these complex studies. Some basic concepts based on actual avian, amphibian, and fish monitoring studies are presented in this article. Copyright © 2002 John Wiley & Sons, Ltd.
The elephants of the Knysna region continue to survive, despite fears that there was only a single surviving female. Their range is larger than previously believed, and includes the Afromontane forest and mountain fynbos. The five individuals detected in this study were all females, and share a single mitochondrial DNA control region haplotype with individuals from Addo Elephant National Park. At least two of these elephants appear to be first-order relatives, and the others may be part of a single matrilineal group. The genetic diversity detected is lower than that found in most African savanna populations, but is higher than that found at Addo, where individuals represent the descendents of a severe population size bottleneck. Levels of genetic diversity are more similar to those detected at Kruger National Park, suggesting that the Knysna elephants represent a remnant of the once widespread populations of South Africa.
Noninvasive sampling allows genetic studies of free-ranging animals without the need to capture or even observe them, and thus allows questions to be addressed that cannot be answered using conventional methods. Initially, this sampling strategy promised to exploit fully the existing DNA-based technology for studies in ethology, conservation biology and population genetics. However, recent work now indicates the need for a more cautious approach, which includes quantifying the genotyping error rate. Despite this, many of the difficulties of noninvasive sampling will probably be overcome with improved methodology.
We evaluate the relative effectiveness of four methods for preserving faecal samples for DNA analysis. PCR assays of fresh faecal samples collected from free-ranging baboons showed that amplification success was dependent on preservation method, PCR-product size, and whether nuclear or mitochondrial DNA was assayed. Storage in a DMSO/EDTA/Tris/salt solution (DETs) was most effective for preserving nuclear DNA, but storage in 70% ethanol, freezing at -20 degrees C and drying performed approximately equally well for mitochondrial DNA and short (< 200 bp) nuclear DNA fragments. Because faecal DNA is diluted and degraded, repeated extractions from faeces may be necessary and short nuclear markers should be employed for genotyping. A review of molecular scatology studies further suggests that three to six faeces per individual should be collected.
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