And Then There was One: A Camera Trap Survey of the Declining Population of African Elephants in Knysna, South Africa

Combining methods for non-invasive fecal DNA enables whole genome and metagenomic analyses in wildlife biology

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.

Using camera traps to study hyenas: challenges, opportunities, and outlook

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.

Non-Invasive Assessment of Body Condition and Stress-Related Fecal Glucocorticoid Metabolite Concentrations in African Elephants (Loxodonta africana) Roaming in Fynbos Vegetation

Simple Summary

The Western Cape Province of South Africa is characterized by Fynbos vegetation. This unique endemic vegetation type belongs to the Cape Floral Kingdom, the smallest of the six floral kingdoms in the world, and only a few provincial, national and private game reserves in this area currently support populations of African elephants (Loxodonta africana). As a result, not much is known about the ability of elephants to thrive in such a unique environment. External factors such as a nutritionally poor diet can be perceived as a stressor by mammals, and establishing links between these two factors was the focus of this study. The results of monitoring individual stress-related hormone levels and body conditions suggest that elephants can obtain adequate nutrition from Fynbos vegetation.

Abstract

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.