Arpin Kate E, Schmidt Danielle A, Sjodin Bryson M F, Einfeldt Anthony L, Galbreath Kurt, Russello Michael A
Department of Biology The University of British Columbia Kelowna British Columbia Canada.
Parks Canada East Kootenay G British Columbia Canada.
Ecol Evol. 2024 Feb 7;14(2):e10934. doi: 10.1002/ece3.10934. eCollection 2024 Feb.
Genetic tools for wildlife monitoring can provide valuable information on spatiotemporal population trends and connectivity, particularly in systems experiencing rapid environmental change. Multiplexed targeted amplicon sequencing techniques, such as genotyping-in-thousands by sequencing (GT-seq), can provide cost-effective approaches for collecting genetic data from low-quality and quantity DNA samples, making them potentially useful for long-term wildlife monitoring using non-invasive and archival samples. Here, we developed a GT-seq panel as a potential monitoring tool for the American pika () and evaluated its performance when applied to traditional, non-invasive, and archival samples, respectively. Specifically, we optimized a GT-seq panel (307 single nucleotide polymorphisms (SNPs)) that included neutral, sex-associated, and putatively adaptive SNPs using contemporary tissue samples ( = 77) from the Northern Rocky Mountains lineage of American pikas. The panel demonstrated high genotyping success (94.7%), low genotyping error (0.001%), and excellent performance identifying individuals, sex, relatedness, and population structure. We subsequently applied the GT-seq panel to archival tissue ( = 17) and contemporary fecal pellet samples ( = 129) collected within the Canadian Rocky Mountains to evaluate its effectiveness. Although the panel demonstrated high efficacy with archival tissue samples (90.5% genotyping success, 0.0% genotyping error), this was not the case for the fecal pellet samples (79.7% genotyping success, 28.4% genotyping error) likely due to the exceptionally low quality/quantity of recovered DNA using the approaches implemented. Overall, our study reinforced GT-seq as an effective tool using contemporary and archival tissue samples, providing future opportunities for temporal applications using historical specimens. Our results further highlight the need for additional optimization of sample and genetic data collection techniques prior to broader-scale implementation of a non-invasive genetic monitoring tool for American pikas.
用于野生动物监测的遗传工具可以提供有关时空种群趋势和连通性的宝贵信息，特别是在经历快速环境变化的系统中。多重靶向扩增子测序技术，如测序数千分型法（GT-seq），可以提供经济高效的方法，从低质量和低数量的DNA样本中收集遗传数据，使其有可能用于使用非侵入性和存档样本的长期野生动物监测。在这里，我们开发了一个GT-seq面板作为美国鼠兔潜在的监测工具，并分别评估了其应用于传统、非侵入性和存档样本时的性能。具体而言，我们使用来自美国鼠兔北落基山脉谱系的当代组织样本（n = 77），优化了一个GT-seq面板（307个单核苷酸多态性（SNP）），其中包括中性、性别相关和假定适应性SNP。该面板显示出高基因分型成功率（94.7%）、低基因分型错误率（0.001%），以及在识别个体、性别、亲缘关系和种群结构方面的出色性能。随后，我们将GT-seq面板应用于在加拿大落基山脉收集的存档组织样本（n = 17）和当代粪便样本（n = 129），以评估其有效性。尽管该面板在存档组织样本中显示出高效能（基因分型成功率90.5%，基因分型错误率0.0%），但粪便样本并非如此（基因分型成功率79.7%，基因分型错误率28.4%），这可能是由于使用所实施的方法回收的DNA质量/数量极低。总体而言，我们的研究强化了GT-seq作为使用当代和存档组织样本的有效工具，为使用历史标本的时间应用提供了未来机会。我们的结果进一步强调，在更广泛地实施美国鼠兔非侵入性遗传监测工具之前，需要对样本和遗传数据收集技术进行额外优化。
