Characterization of eight polymorphic loci for Maasai giraffe ( Giraffa camelopardalis tippelskirchi ) using non-invasiv
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TECHNICAL NOTE
Characterization of eight polymorphic loci for Maasai giraffe (Giraffa camelopardalis tippelskirchi) using non-invasive genetic samples Rachel S. Crowhurst • Tom D. Mullins • Benezeth M. Mutayoba • Clinton W. Epps
Received: 27 July 2012 / Accepted: 6 August 2012 / Published online: 11 August 2012 Ó Springer Science+Business Media B.V. 2012
Abstract We used Illumina sequencing to develop eight novel microsatellite loci for Maasai giraffe (Giraffa camelopardalis tippelskirchi), and screened them using fecal DNA. Genetic diversity was assessed for 40 individuals from the Katavi National Park/Rukwa Game Reserve ecosystem in Tanzania. The number of alleles per locus ranged from 2 to 14 (mean = 6.2) and mean expected heterozygosity was moderate (range 0.025–0.838, mean = 0.527). These markers were successfully tested using degraded DNA and may be useful for future studies of giraffe, especially those that use non-invasive sampling techniques. Keywords Giraffa camelopardalis Microsatellite Illumina sequencing Non-invasive sampling
The IUCN classifies giraffe as a species of least concern due to their wide geographic range and estimate of 80–100,000 individuals worldwide (IUCN 2011). However, multiple subspecies have been characterized based on pelage characteristics and genetic analyses (Dagg and Foster 1976; Kingdon 1997; Brown et al. 2007), and the IUCN does not assess all of these subspecies individually. Although some R. S. Crowhurst (&) C. W. Epps Department of Fisheries and Wildlife, Oregon State University, 104 Nash Hall, Corvallis, OR 97331, USA e-mail: [email protected] T. D. Mullins Forest and Rangeland Ecosystem Science Center, US Geological Survey, 3200 SW Jefferson Way, Corvallis, OR 97331, USA B. M. Mutayoba Department of Veterinary Physiology, Biochemistry, Pharmacology and Toxicology, Sokoine University of Agriculture, PO Box 3017, Morogoro, Tanzania
subspecies appear to be stable, others are declining due to habitat loss or poaching (Fennessy and Brown 2010). The Maasai subspecies (Giraffa camelopardalis tippelskirchi) is found throughout Tanzania and southern Kenya, and while assumed to be widely distributed within protected areas, no recent population estimates have been gathered. Conservation of this subspecies would be aided by knowledge of the genetic diversity and structure within populations. We used Illumina sequencing to design 8 novel microsatellite loci for Maasai giraffe and characterized them using noninvasive samples. Previous studies have presented microsatellite primers for Maasai giraffe (Huebinger et al. 2002; Brown et al. 2007), but several of those loci did not amplify in Maasai giraffe from southern Tanzania, while others were monomorphic. Carter et al. (2012) developed markers for Angolan giraffe (G. c. angolensis) and screened them using DNA extracted from tissue. This study presents the first suite of giraffe primers verified to amplify from relatively degraded DNA. Genomic DNA was extracted from a tissue sample collected from a Maasai giraffe car
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