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Partnerships for enhanced engagement in research (PEER)
Cycle 4 (2015 Deadline)

Enhancing elephant conservation and protection in East Africa with molecular genetic tools   

PI: Moses Otiende (, Kenya Wildlife Service
U.S. Partner: Samuel and David Wasser and Schindel, Smithsonian Institution
Project Dates: October 2015-March 2020

Project Overview

DNA tools are becoming increasingly useful for investigating and prosecuting wildlife crimes, including matching carcasses to biological products being smuggled and determining the location of poaching hotspots from which large quantities of biological material were derived. Elephant-specific microsatellites have been developed and accurately used to map elephant populations over the entire African continent using DNA derived from their feces (Wasser et al., 2004). The map is currently being used to trace illegal ivory shipments back to their origin using DNA extracted from seized ivory (Wasser et al., 2004). Elephant poaching within East Africa has progressively increased since 2006 (Underwood et al., 2013) with the greatest concentration of large ivory seizures coming from East Africa and especially southern Tanzania. Since 2013, the number of large ivory seizures made in Kenya, Uganda, and Tanzania has grown to levels beyond those made in Asia. Timely identification of the origins of these seizures is vital, both for timely prosecutions but also to provide time-sensitive intelligence on major shifts in poaching activities across East Africa. This project aims to build a collaborative forensic network between Kenya, Tanzania, and Uganda by enhancing the forensic capabilities of newly formed wildlife DNA labs in both Kenya and Tanzania, where the largest elephant populations reside in East Africa and considerable cross-border movement of elephants occur.

A major part of this effort also involves enhancing coverage of the existing continent-wide elephant DNA database (Wasser et al., 2004) by sampling and genotyping elephant dung in all important elephant areas within the region where samples are still lacking. Enhancing this comprehensive elephant DNA database for East Africa will greatly increase the capacities of authorities to monitor changes in areas of concentrated poaching as well as bring cases to successful prosecution in a timely basis. The U.S. Government-supported partner will contribute all existing genotypes from these areas to this effort and use these collections to enhance this continent-wide microsatellite DNA map used to assign origin to large ivory seizures made throughout the world.

Planned capacity building activities under the project include proficiency testing and validation using the laboratory of the Smithsonian-based partner. Other components of this training will include proper sampling protocols for large seizures, as well as training of rangers and lab technicians across East Africa on how to maintain chain of custody throughout sample collection and analyses, including use of tamper proof containers, pre-printed barcode labels, and proper documentation of a full audit trail of the sampling process. The most important product of this initiative will be to increase effectiveness of tools to monitor and police the illegal killing of elephants within East Africa and enhance local capacity to produce credible evidence for prosecution of illegal ivory traffickers. The genetic database established for East African elephants will be used to enhance the detection and validation of poaching hot spots within the region and link seized products to their original crime scene to enhance prosecution of ivory traffickers in a court of law. 

Summary of Recent Activities

During this quarter, Kenya Wildlife Service Genetics and Forensic lab, conducted elephant fecal sample collection in the field and laboratory analyses including DNA extraction, DNA amplification of both micro-satellite loci and the D-loop locus of mtDNA. In addition, PCR products were submitted for sequence analyses and genotyping. Fifteen tissue samples were opportunistically collected from Solio ranch during the translocation of elephants from Solio ranch to Tsavo West. DNA extraction was carried out on twenty seven samples; 22 from Tsavo Conservation Area and 5 from Amboseli National Park. In addition PCR amplification of the Dloop was conducted on 48 samples; 16 from Arbedares and Mt Kenya and 32 s from Tsavo Conservation Area. These samples are currently being sequenced.

Seventy D-loop mtDNA products have been successfully sequenced from previous submissions and 29 samples have been genotyped at 6 microsatellite loci. The genotyping success rate for 60% with failures locus specific suggesting a need to optimize microsatellite PCR condition for these loci. Samples have been sent for Sequencing of the mtDNA D-loop.

Several online meetings to plan and organize the evidence to action training of rangers on chain of custody procedure for evidence collection and presentation.

In the next few months, the team plans to fill up sampling gaps in Kenya, particularly, Chyulu Hills NP, mt. Kenya NP, Aberdares NP, Arabuko Sokoke NR and Shimba Hills NP. In addition, we plan to continue with the laboratory analysis of micro-satellite loci and mtDNA from already collected samples in Kenya and Tanzania

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