Osborne Megan J, Caeiro-Dias Guilherme, Turner Thomas F
Department of Biology and Museum of Southwestern Biology, University of New Mexico, Albuquerque, New Mexico, USA.
Mol Ecol. 2023 Jan;32(2):316-334. doi: 10.1111/mec.16760. Epub 2022 Nov 16.
Many long-term genetic monitoring programmes began before next-generation sequencing became widely available. Older programmes can now transition to new marker systems usually consisting of 1000s of SNP loci, but there are still important questions about comparability, precision, and accuracy of key metrics estimated using SNPs. Ideally, transitioned programmes should capitalize on new information without sacrificing continuity of inference across the time series. We combined existing microsatellite-based genetic monitoring information with SNP-based microhaplotypes obtained from archived samples of Rio Grande silvery minnow (Hybognathus amarus) across a 20-year time series to evaluate point estimates and trajectories of key genetic metrics. Demographic and genetic monitoring bracketed multiple collapses of the wild population and included cases where captive-born repatriates comprised the majority of spawners in the wild. Even with smaller sample sizes, microhaplotypes yielded comparable and in some cases more precise estimates of variance genetic effective population size, multilocus heterozygosity and inbreeding compared to microsatellites because many more microhaplotype loci were available. Microhaplotypes also recorded shifts in allele frequencies associated with population bottlenecks. Trends in microhaplotype-based inbreeding metrics were associated with the fraction of hatchery-reared repatriates to the wild and should be incorporated into future genomic monitoring. Although differences in accuracy and precision of some metrics were observed between marker types, biological inferences and management recommendations were consistent.
许多长期遗传监测项目在新一代测序技术广泛应用之前就已启动。早期项目如今可转向通常由数千个单核苷酸多态性（SNP）位点组成的新标记系统，但对于使用SNP估计的关键指标的可比性、精度和准确性，仍存在重要问题。理想情况下，转型后的项目应利用新信息，同时不牺牲时间序列推断的连续性。我们将基于微卫星的现有遗传监测信息与从格兰德河银汉鱼（Hybognathus amarus）存档样本中获取的基于SNP的微单倍型信息相结合，跨越20年时间序列，以评估关键遗传指标的点估计和轨迹。人口统计和遗传监测涵盖了野生种群的多次崩溃情况，包括圈养繁殖放流个体在野生种群中占多数产卵者的案例。即便样本量较小，与微卫星相比，微单倍型仍能得出可比的方差遗传有效种群大小、多位点杂合度和近亲繁殖估计值，在某些情况下估计更为精确，因为可用的微单倍型位点更多。微单倍型还记录了与种群瓶颈相关的等位基因频率变化。基于微单倍型的近亲繁殖指标趋势与放流到野外的圈养繁殖个体比例相关，应纳入未来的基因组监测。尽管在标记类型之间观察到某些指标在准确性和精度上存在差异，但生物学推断和管理建议是一致的。
