Examining patterns of genetic diversity has become an integral component of many management plans concerning endangered species, yet interpreting the processes underlying such patterns remains challenging. We demonstrate low genetic diversity in a critically endangered small mammal population. A common interpretation of this pattern would be that it is the result of a known, recent decline in this population. We test this interpretation and find it to be incorrect. Instead, by using museum voucher specimens, we show that the pattern of low genetic diversity is historical. This study demonstrates the importance of choosing appropriate reference groups by which to interpret modern levels of genetic diversity in endangered species. We conclude that analysis of archival specimens may be essential in cases where genetic diversity is driving conservation management decisions because it may allow us to distinguish the effects of low genetic diversity from the process of losing diversity. We recognize that this approach can be limited due to several sampling issues: archival material may not be available, statistical power needs to be evaluated, sample sizes and sequence lengths may be suboptimal due to intrinsic difficulties associated with amplification of degraded DNA. These issues are discussed and possible solutions identified.



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