Data from: Evaluating DNA degradation rates in faecal pellets of the endangered pygmy rabbit
| Main Authors: | DeMay, Stephanie M., Becker, Penny A., Eidson, Chad A., Rachlow, Janet L., Johnson, Timothy R., Waits, Lisette P. |
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| Format: | info dataset Journal |
| Terbitan: |
, 2013
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| Subjects: | |
| Online Access: |
https://zenodo.org/record/5002076 |
Daftar Isi:
- Noninvasive genetic sampling of faecal pellets can be a valuable method for monitoring rare and cryptic wildlife populations, like the pygmy rabbit (Brachylagus idahoensis). To investigate this method's efficiency for pygmy rabbit monitoring, we evaluated the effect of sample age on DNA degradation in faecal pellets under summer field conditions. We placed 275 samples from known individuals in natural field conditions for 1 to 60 days and assessed DNA quality by amplifying a 294 base pair (bp) mitochondrial DNA (mtDNA) locus and 5 nuclear DNA (nDNA) microsatellite loci (111 – 221 bp). DNA degradation was influenced by sample age, DNA type, locus length, and rabbit sex. Both mtDNA and nDNA exhibited high PCR success rates (94.4%) in samples <1 day old. Success rates for microsatellite loci declined rapidly from 80.0% to 42.7% between days 5 and 7, likely due to increased environmental temperature. Success rates for mtDNA amplification remained higher than nDNA over time, with moderate success (66.7%) at 21 days. Allelic dropout rates were relatively high (17.6% at < 1 day) and increased to 100% at 60 days. False allele rates ranged from 0 to 30.0% and increased gradually over time. We recommend collecting samples as fresh as possible for individual identification during summer field conditions. Our study suggests that this method can be useful for future monitoring efforts, including occupancy surveys, individual identification, population estimation, parentage analysis, and monitoring of genetic diversity both of a reintroduced population in central Washington and across their range.
- Supp Info Table 1 datasetData file for PCR success, allelic dropout, and false allele rates for pygmy rabbit (Brachylagus idahoensis) faecal pellet DNA. Pellets were collected in the field in central Washington, USA and analyzed at the Laboratory for Ecological, Evolutionary and Conservation Genetics, University of Idaho, Moscow, ID, USA. Column headings are included in the first sheet of the workbook.Supp info SAS code PCR ADO FAText file containing SAS code for mixed models to estimate PCR success, allelic dropout, and false allele rates of DNA from pygmy rabbit (Brachylagus idahoensis) faecal pellets. Fixed effects include DNA type, locus length, sex, sample age, and sample quality. Random effects include individual rabbit and pellet pile.