Data from: Comparative evaluation of potential indicators and temporal sampling protocols for monitoring genetic erosion

Genetic biodiversity contributes to individual fitness, species' evolutionary potential, and ecosystem stability. Temporal monitoring of the genetic status and trends of wild populations' genetic diversity can provide vital data to inform policy decisions and management actions. However, there is a lack of knowledge regarding which genetic metrics, temporal sampling protocols, and genetic markers are sufficiently sensitive and robust, on conservation-relevant timescales. Here, we tested six genetic metrics and various sampling protocols (number and arrangement of temporal samples) for monitoring genetic erosion following demographic decline. To do so, we utilized individual-based simulations featuring an array of different initial population sizes, types and severity of demographic decline, and DNA markers [single nucleotide polymorphisms (SNPs) and microsatellites] as well as decline followed by recovery. Number of alleles markedly outperformed other indicators across all situations. The type and severity of demographic decline strongly affected power, while the number and arrangement of temporal samples had small effect. Sampling 50 individuals at as few as two time points with 20 microsatellites performed well (good power), and could detect genetic erosion while 80–90% of diversity remained. This sampling and genotyping effort should often be affordable. Power increased substantially with more samples or markers, and we observe that power of 2500 SNPs was nearly equivalent to 250 microsatellites, a result of theoretical and practical interest. Our results suggest high potential for using historic collections in monitoring programs, and demonstrate the need to monitor genetic as well as other levels of biodiversity.

遗传生物多样性（genetic biodiversity）关乎个体适合度、物种进化潜力与生态系统稳定性。对野生种群遗传多样性的遗传状态与动态变化开展时序监测，可为政策制定与管理实践提供关键数据支撑。然而，当前学界尚未明确在与生物保护相关的时间尺度下，哪些遗传指标、时序采样方案以及遗传标记具备足够的灵敏度与稳定性。本研究针对种群衰退后的遗传侵蚀监测场景，评估了6种遗传指标与多种采样方案（时序样本的数量与布设方式）的表现。为此，我们采用基于个体的模拟实验，涵盖不同初始种群规模、种群衰退类型与严重程度，以及DNA标记[单核苷酸多态性（single nucleotide polymorphisms, SNPs）与微卫星（microsatellites）]等多种实验场景，同时也设置了种群衰退后恢复的情境。在所有实验情境中，等位基因数量的表现均显著优于其他指标。种群衰退的类型与严重程度对检验效能影响显著，而时序样本的数量与布设方式的影响则相对较小。仅需在2个时间点采集50个个体、使用20个微卫星标记的采样方案即表现优异（检验效能良好），可在仍保留80%~90%遗传多样性时检测到遗传侵蚀。该采样与基因分型方案通常具备较高的经济可行性。增加采样个体数或标记数量可大幅提升检验效能；本研究发现，2500个单核苷酸多态性标记的检验效能与250个微卫星标记几乎相当，这一结果兼具理论与实践价值。本研究结果表明，将历史馆藏标本用于生物多样性监测项目具备极高潜力，同时也证实了除其他层级的生物多样性外，遗传多样性的监测同样不可或缺。