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Objective The Sumatran rhinoceros is critically endangered, with fewer than 100 individuals surviving across its current range. Accurate census estimates of the remaining populations are essential for development and implementation of conservation plans. In order to enable molecular censusing, we here develop microsatellite markers with amplicon sizes of short length, appropriate for non-invasive fecal sampling. Results Due to limited sample quantity and potential lack of genome-wide diversity, Illumina sequence reads were generated from two Sumatran rhinoceros samples. Genomic screening identified reads with short tandem repeats and loci that were polymorphic within the dataset. Twenty-nine novel polymorphic microsatellite markers were characterized (A = 2.4; HO = 0.30). These were sufficient to distinguish among individuals (PID PID(sib)

Additional file 1. Detailed methods, supplementary figures and tables.

Excessive hunting pressure, due in large part to commercialization, has reduced the populations of many tropical large mammal species. Wildlife over-exploitation is severe in Indonesia, especially on Sulawesi, where human resources and funding are inadequate to monitor the wildlife trade and enforce existing protection laws. In response, the Wildlife Crimes Unit program was established in December 2001 to: (i) monitor wildlife transportation into North Sulawesi and market sales; (ii) provide legal and technical support to law enforcement agencies; and (iii) promote public awareness of wildlife and protection laws. Over a two-year period, 6963 wild mammals en route to markets were encountered (∼8 individuals h−1) and 96,586 wild mammals were documented during market surveys. The trade of some protected mammals declined significantly over this period, but overall trade in wild mammals increased by 30%. High volume of trade in non-protected animals such as the Sulawesi pig Sus celebensis and large flying foxes (Pteropodidae), raise concerns about the sustainability of current harvesting. To combat this problem, we recommend that: (1) efforts are continued to reduce trade in protected species; (2) protected status is extended to heavily traded but non-protected taxa, such as flying foxes; (3) the effects of hunting on rat and bat populations, as well as its impact on forest dynamics, are quantified; and (4) work is carried out with local communities to strengthen awareness, set sustainable limits on wild mammal harvesting, and establish practical mechanisms for enforcing these limits.