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Data from: Evaluating genotyping-in-thousands by sequencing as a genetic monitoring tool for a climate sentinel mammal using non-invasive and archival samples (Dataset)
| Content Provider | Dryad |
|---|---|
| Author | Arpin, Kate Schmidt, Danielle Sjodin, Bryson Einfeldt, Anthony Galbreath, Kurt Russello, Michael |
| Abstract | Genetic tools for wildlife monitoring can provide valuable information on spatiotemporal population trends and connectivity, particularly in systems experiencing rapid environmental change. Though many DNA sequencing approaches still require high quality and quantity of DNA obtained from traditional sources (e.g. blood and tissue), rapid genotyping tools such as Genotyping-in-Thousands by sequencing (GT-seq) have improved our ability to make use of degraded and less concentrated DNA commonly obtained from non-invasive and archival samples. Here, we developed a multi-purpose GT-seq panel (307 single nucleotide polymorphisms) for a climate sentinel mammal (the American pika, Ochotona princeps) for use as a genetic tool for monitoring populations in the Canadian Rocky Mountains. We optimized the panel using contemporary tissue samples (n = 77) and subsequently applied it to archival tissue (n = 17) and contemporary fecal pellet samples (n = 129) to evaluate its effectiveness at identifying individuals and sex, estimating relatedness, and inferring population structure. The panel demonstrated high efficacy with contemporary and archival tissue samples (94.7% and 90.5% genotyping success, respectively) and negligible genotyping error (0.001% and 0.0%, respectively). Despite relatively high genotyping success for fecal pellet samples (79.7%), high genotyping error (28.4%) limited its power as a monitoring tool to assess genetic variation using non-invasive samples and highlighted the need for further optimization around sample and data collection. |
| File Size | 404057 |
| File Format | HTM / HTML |
| ISSN | 20457758 |
| DOI | 10.5061/dryad.s1rn8pkdv |
| Alternate Webpage(s) | https://datadryad.org/stash/downloads/file_stream/2967593 |
| Alternate Webpage(s) | https://datadryad.org/stash/downloads/file_stream/2967594 |
| Alternate Webpage(s) | https://datadryad.org/stash/downloads/file_stream/2967601 |
| Alternate Webpage(s) | https://datadryad.org/stash/downloads/file_stream/2967596 |
| Alternate Webpage(s) | https://datadryad.org/stash/downloads/file_stream/2967595 |
| Language | English |
| Publisher Date | 2024-03-01 |
| Access Restriction | Open |
| Subject Keyword | Molecular Ecology Gt-seq Non-invasive Genetic Sampling Archival Genetic Sampling Sentinel Species Wildlife Monitoring Nature and Landscape Conservation Ecology Behavior and Systematics |
| Content Type | Text |
| Resource Type | Data Set |
| Subject | Ecology Ecology, Evolution, Behavior and Systematics Nature and Landscape Conservation |
