Who are the elephants living in the hybridization zone? How genetics may guide conservation to better protect endangered elephants

Trenches reduce crop foraging by elephants: Lessons from Kibale National Park, Uganda for elephant conservation in densely settled rural landscapes

Crop loss to wildlife, particularly elephants, threatens livelihoods and support for conservation around many protected areas in Africa and Asia. Low-cost elephant barriers have been successfully deployed in savannas but seldom tested around isolated forest parks where the stakes are high for local farmers and isolated elephant populations. We measured the effectiveness of a series of ≥3 m deep trenches dug by farmers neighboring Kibale National Park, Uganda. We monitored trench quality and crop loss to elephants weekly for a year across 47 transects in four park-adjacent communities, and conducted controlled, before-and-after comparisons of verified damage. Elephants damaged or destroyed >4 ha of crops during 48 independent foraging events, the majority <220m from the forest boundary. The frequency of damage varied significantly between and within communities. The majority of trenches were not breached by elephants but five suffered ≥4 breaches. Elephant-breached trenches and their neighboring trenches were lower quality than those not breached in the same week (Wilcoxon test: p<0.001). Trenches were also more likely to be breached where people had planted more crops favored by elephants (Wilcoxon test: p = 0.014). Thus, trench quality and the draw of palatable crops both appeared to influence elephant damage. Although trenches may deter elephants, challenges include heavy labor and difficulties of digging in rocky and swampy areas. Trenches alone will not prevent conflict but this strategy holds promise for hot-spots of conflict at forest edges. Given the stakes for farmers and biodiversity, we call for systematic assessment of crop losses and offer recommendations on monitoring and analysis. Such data will allow for stronger inference about effectiveness before investment of effort and resources in interventions.

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.

Phenotypical characterization of African savannah and forest elephants, with special emphasis on hybrids: the case of Kibale National Park, Uganda

The IUCN now recognizes the savannah Loxodonta africana and forest Loxodonta cyclotis elephants to be separate species. Despite ecological, behavioural and morphological differences, and different habitat ranges, genetic studies confirm that the two species and hybrids coexist in forest–savannah ecotones. However, the hybrid phenotypes have not yet been described. In this survey we examined whether the phenotypes of the two species and of hybrids can be distinguished. In the first step, we used a machine learning algorithm (K-nearest neighbours) to compare 296 reference images of African elephants from five forest areas and six savannah areas where hybrids have not been recorded, confirming that six morphological criteria can be used to distinguish the species with more than 90% confidence. In the second step, we analysed 1,408 videos of elephants from 14 camera traps in Sebitoli, in Kibale National Park, Uganda, part of the main hybridization area. We used a multiple correspondence analysis and a species assignment key, highlighting the presence of three categories of phenotypes. Compared to the savannah and forest phenotypes (36.8 and 12.1%, respectively), the intermediate phenotypes, which could include hybrids, were more frequent (51.1%). Further studies combining morphology and genetics of the same individuals will be necessary to refine this species assignment key to characterize phenotypes confidently. This non-invasive, fast and inexpensive phenotypical-based method could be a valuable tool for conservation programmes.