Data from: Reliable genotyping of the koala (Phascolarctos cinereus) using DNA isolated from a single faecal pellet

The koala, an Australian icon, has been added to the threatened species list. Rationale for the listing includes proposed declines in population size, threats to populations (e.g. disease) and loss and fragmentation of habitat. There is now an urgent need to obtain accurate data to assess the status of koala populations in Australia, to ensure the long-term viability of this species. Advances in genetic techniques have enabled DNA analysis to study and inform the management of wild populations; however, sampling of individual koalas is difficult in tall, often remote, eucalypt forest. The collection of faecal pellets (scats) from the forest floor presents an opportunistic sampling strategy, where DNA can be collected without capturing or even sighting an individual. Obtaining DNA via noninvasive sampling can be used to rapidly sample a large proportion of a population; however, DNA from noninvasively collected samples is often degraded. Factors influencing DNA quality and quantity include environmental exposure, diet and methods of sample collection, storage and DNA isolation. Reduced DNA quality and quantity can introduce genotyping errors and provide inaccurate DNA profiles, reducing confidence in the ability of such data to inform management/conservation strategies. Here, we present a protocol that produces a reliable individual koala genotype from a single faecal pellet and highlight the importance of optimizing DNA isolation and analysis for the species of interest. This method could readily be adapted for genetic studies of mammals other than koalas, particularly those whose diet contains high proportions of volatile materials that are likely to induce DNA damage.

考拉作为澳大利亚标志性物种，已被列入受威胁物种名录。本次列入名录的依据包括种群规模拟议下降、种群面临的各类威胁（如疾病）以及栖息地的丧失与破碎化。当前亟需获取精准数据以评估澳大利亚考拉种群的现状，保障该物种的长期存续性。遗传技术的进步使得DNA分析能够用于野生种群研究，并为其管理提供决策支持；但在高大且通常较为偏远的桉树林中，对单个考拉进行采样难度极大。从林地地表收集粪便颗粒（scats）是一种机会性采样策略，无需捕获甚至无需目击个体即可获取考拉的DNA。通过非侵入式采样获取DNA，可快速覆盖种群的大部分个体，但非侵入式采样获得的DNA通常会发生降解。影响DNA质量与含量的因素包括环境暴露、饮食以及样本采集、保存和DNA分离的操作方法。DNA质量与含量的下降会引入基因分型误差，产生不准确的DNA图谱，进而降低此类数据用于指导管理与保护策略的可信度。本研究提出了一套可从单份粪便颗粒中获取可靠考拉个体基因型的实验方案，并强调针对目标物种优化DNA分离与分析方法的重要性。该方案可轻松适配除考拉外的其他哺乳动物的遗传研究，尤其是那些饮食中含有高比例易引发DNA损伤的挥发性物质的哺乳动物。