It's all in the poo

(A version of this article originally appeared in The Horn, autumn 2009. Authors: Antony Wandera, Rhino Programme, Kenya Wildlife Service; Bradley Cain, School of Biology, Chemistry and Health Sciences, Manchester Metropolitan University and Kenya Wildlife Service)

Or, more accurately, “Molecular tracking of black rhinoceros in the Chyulu Hills National Park: using microsatellite, mtDNA and sex gene analysis.” We proposed this project back in 2006 and, finally, we’re now on the verge of publishing the report, which will inform the future rhino management plans of the Kenya Wildlife Service and the Maasailand Preservation Trust.

The use of dung DNA analysis for determining the genetic make-up of black rhinos is a new, cutting-edge technique in Kenya, and is being introduced to improve the country’s wildlife management. This pioneering method has proven to be invaluable for surveying rhino demographics and their genetic status, enhancing the conservation efforts for this endangered species. Kenya is home to 12% of Africa’s endangered black rhino, and 85% of the Eastern black subspecies. Sound biological and genetic decision making and management of these animals is therefore vital for ensuring the sustainability the country’s natural resources.

The aims of the project were two-fold: to build the KWS’s capacity in rhino conservation genetic studies and management through training in molecular genetic analysis; and to assess the genetic make-up of a rare, indigenous rhino population in the Chyulu Hills, Southern Kenya.

The secondary aims of the project, in relation to the work at the Chyulu Hills were to:

  • Establish the minimum number of individuals in the population through probability of identification based on microsatellite genotypes
  • Determine the sex of all identified individuals by analysis of Y- specific restriction digests of the ZFX/Y gene
  • Reconstruct pedigrees and determine levels of inbreeding
  • Determine the effective population size
  • Examine rank-order relatedness between breeding males in the population
  • Determine levels of genetic diversity present in the two study populations through microsatellite and mtDNA analysis
  • Compare levels of diversity found in study population with those found in other extant Kenyan populations and with museum samples
  • Calculate the genetic distance between the study population and other extant populations in Kenya

What actually happened?

Bradley Cain with a dung DNA sample on the left, and Richard Bonham, Chairman of the Maasailand Preservation Trust on the rightCredit: Save the Rhino International

Collection of samples

  • 6 weeks sample collection started in Oct 2007
  • Fresh faecal samples collected in collaboration with KWS rangers and Mbirikani scouts
  • For each sample GPS location, possible sex and approximate age of sample was recorded
  • Faecal samples preserved by dessication with silica gel
  • A total of 43 samples collected from across Chyulu range

Molecular analysis

  • DNA extracted at ILRI labs in Nairobi
  • DNA extracted from faeces
  • Genotyped for 11 polymorphic microsatellite loci
  • 507 bp region of mitochondrial control region sequenced
  • 5’exonuclease assay performed (TaqMan SNP) to determine sex
  • DNA from Chyulu samples was extremely degraded
  • Subsequently 3 microsatellite loci were excluded from the final analysis
  • Multiple repeats of all molecular analysis performed to ensure reliability of genotyping in light of allelic dropout
  • Genotypes only recorded as unique if they couldn’t be due to allelic dropout


  • Minimum population of 14 animals: 6 male; 6 female; 1 male calf; and 1 unknown
  • Population admixed with 2 animals from Ngulia
  • One female originating from Ngulia has a calf
  • Population shows significantly higher levels of inbreeding and lower levels of genetic diversity compared to other genotyped populations in Kenya


The results were discussed at a site-specific workshop, held in July 2009 in Tsavo West National Park, and attended by representatives from the Kenya Wildlife Service and from the Maasailand Preservation Trust. The workshop presented the findings of the study to management and stakeholders on molecular tracking project; and proposed a site-specific black rhino management plan that will become part of the overall national black rhino strategy. Ambitious plans for an IPZ and increased security were put forward, and we are waiting eagerly to see what the final approved plan will include. The workshop proceedings and recommendations arising will be circulated as soon as they become available to all funders.


The total cost of the project was £25,923, which was supported by the following: KWS US $20,000; Chester Zoo £4,080; EAZA Rhino Campaign 7,860 euros; Amnéville Zoo 5,000 euros; Save the Rhino £750; Manchester Metropolitan University, 3,145 euros. In addition, Chester Zoo and Save the Rhino each contributed £200 towards the cost of the workshop. Our thanks to everyone who made this project possible.