Identifying source populations and genetic structure for savannah elephants in human-dominated landscapes and protected areas in the Kenya-Tanzania borderlands.

Marissa A Ahlering,David Western,Jesus E Maldonado,Linus Munishi,Robert Fleischer,Anna Estes,Melissa Roberts,Lori S Eggert

doi:10.1371/journal.pone.0052288

Abstract

We investigated the genetic metapopulation structure of elephants across the trans Rift Valley region of Kenya and Tanzania, one of the remaining strongholds for savannah elephants (Loxodonata africana) in East Africa, using microsatellite and mitochondrial DNA (mtDNA) markers. We then examined this population structure to determine the source population for a recent colonization event of savannah elephants on community-owned land within the trans rift valley region. Four of the five sampled populations showed significant genetic differentiation (p<0.05) as measured with both mtDNA haplotypes and microsatellites. Only the samples from the adjacent Maasai Mara and Serengeti ecosystems showed no significant differentiation. A phylogenetic neighbour-joining tree constructed from mtDNA haplotypes detected four clades. Clade four corresponds to the F clade of previous mtDNA studies that reported to have originated in forest elephants (Loxodonta cyclotis) but to also be present in some savannah elephant populations. The split between clade four and the other three clades corresponded strongly to the geographic distribution of mtDNA haplotypes across the rift valley in the study area. Clade four was the dominant clade detected on the west side of the rift valley with rare occurrences on the east side. Finally, the strong patterns of population differentiation clearly indicated that the recent colonists to the community-owned land in Kenya came from the west side of the rift valley. Our results indicate strong female philopatry within the isolated populations of the trans rift valley region, with gene flow primarily mediated via male movements. The recent colonization event from Maasai Mara or Serengeti suggests there is hope for maintaining connectivity and population viability outside formal protected areas in the region.

Highlights

African savannah elephants (Loxodonta africana) once ranged across much of the African continent [1,2], but the increase in human population, and resulting habitat loss, fragmentation and continuous poaching for ivory, have resulted in dramatic population declines and isolation
Five of our microsatellite loci can be compared with previously published allele size values for elephants, and the allele sizes for these loci all fall within the size ranges reported for savannah elephants (Table S2)
We found a clear segregation of mitochondrial DNA (mtDNA) haplotypes between the east and west sides of the rift valley in southern Kenya and northern Tanzania, and the signal is not as strong, this separation was detected with the nuclear DNA using both FST values and STRUCTURE

Summary

Introduction

African savannah elephants (Loxodonta africana) once ranged across much of the African continent [1,2], but the increase in human population, and resulting habitat loss, fragmentation and continuous poaching for ivory, have resulted in dramatic population declines and isolation. Populations in Kenya were hard hit by illegal killing in the 1970s and 1980s prior to the ivory ban [3,4], causing extreme fragmentation and isolation of elephant populations as they retreated into protected areas This anthropogenic isolation has created a metapopulation structure for elephants in Kenya and Tanzania. On a more local scale for many species, population structure is often apparent using mitochondrial DNA (mtDNA) with more subtle structure detected using nuclear DNA [4], a pattern which is often explained by isolated populations showing female philopatry and male-biased dispersal [9] In species, such as elephants, where female philopatry is so strong that females rarely disperse, mtDNA and biparentally inherited markers often show incongruent patterns [10,11,12,13,14,15,16,17,18]. In this case, a large number of female savannah elephants have dispersed across the landscape, and the strong female philopatry isolating mtDNA should be useful in helping to determine the population origin for these elephants

Methods

Results

Conclusion