Fraser John Combe, Evelyn Taylor cox, Graeme fox, Tommy Sandri, Bradley Cain, Edwin Harris

High-throughput sequencing tools promise to revolutionize many aspects of genetics research, e.g. by allowing the identification of functional adaptive genetic variation. However, the expense and expertise required to apply these tools to basic conservation questions is a challenge for applications outside academia, resulting in a so-called “conservation genomics gap” (Shafer et al. 2015). The conservation genetics paradigm is that basic information about inbreeding and gene flow are often critical to inform conservation management of small populations (Ouborg et al. 2010). This information is often needed quickly and ideally should be accessible to workers without special expertise in genomics (DeSalle & Amato 2004). While the inferential power of high-throughput sequencing to interrogate the genome is profound, the cost for population analysis is higher (though decreasing) than for traditional neutral markers. Thus, the use of neutral markers is still relevant in conservation applications. However, this assumes that neutral markers have been discovered and characterized for a given species of conservation concern, which is often untrue for non-model organisms. Here, we use a fast, cost-efficient, high-throughput sequencing method (Illumina MiSeq) to rapidly identify and characterize microsatellites in the mountain bongo (Tragelaphus eurycerus isaaci, hereafter bongo), which has a clear and timely conservation imperative but lacks any described neutral markers.