# Microsatellite Variation of African Elephants Loxodonta africana Blumenbach 1797 in a Savannah Protected Area of South Sudan

## TL;DR

This study examines the genetic diversity and population health of African elephants in South Sudan after a significant population decline.

## Contribution

The study provides new insights into the genetic status of a savannah elephant population that experienced an 80% decline.

## Key findings

- The population showed moderate genetic diversity with no recent genetic bottleneck.
- Low inbreeding and high proportion of unrelated individuals were observed.
- A historical bottleneck was detected, indicating past population decline.

## Abstract

Anthropogenic activities such as poaching and habitat loss lead to a drop in population size, range overlap and hybridisation. The decline in population size results in reduced genetic diversity, an increase in homozygosity and inbreeding. Here, we genotyped 16 polymorphic microsatellite loci on 80 elephant dung samples to determine genetic diversity, genetic bottleneck, genetic relatedness and inbreeding in the savannah elephant in Nimule National Park, which experienced an 80% fall in population size. Results revealed that the elephant population in the park comprised 26 savannah elephants. The study also found genetic variation, average number of observed alleles Ao, observed heterozygosity Ho and expected heterozygosity He to be 5.31 ± 2.62, 0.61 ± 0.22 and 0.56 ± 0.21, respectively, but with no difference between observed Ho and expected He heterozygosity. There was no evidence that the elephant population in the park went through a recent genetic bottleneck (p = 0.94167; and normal L‐shaped distribution); however, evidence for a historical bottleneck was detected (M ratio = 0.44 ± 0.22). Mean pairwise relatedness was generally low (ML‐r = 0.09 ± 0.22) with a high proportion of unrelated individuals (U = 85.8%), and there was no indication of inbreeding (FIS = −0.08, p > 0.05). We conclude that the observed decline in the population size is not an artefact of using different methods, as shown by the historical bottleneck. Despite the observed reduction in census size, there is an exchange of individuals with the neighbouring savannah elephant population.

Poaching and habitat loss reduce population size, genetic diversity, genetic bottleneck, genetic relatedness and inbreeding in the savannah elephant population.