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A comparison of density estimation methods for monitoring marked and unmarked animal populations

Citation

Twining, Joshua et al. (2022), A comparison of density estimation methods for monitoring marked and unmarked animal populations, Dryad, Dataset, https://doi.org/10.5061/dryad.xwdbrv1g2

Abstract

These data were generated to compare different methods of estimating population density from marked and unmarked animal populations. We compare conventional live trapping with two more modern, non-invasive field methods of population estimation: genetic fingerprinting from hair-tube sampling and camera trapping for the European pine marten (Martes martes). We used arrays of camera traps, live traps, and hair tubes to collect the relevant data in the Ring of Gullion in Northern Ireland. We apply marked spatial capture-recapture models to the genetic and live trapping data where individuals were identifiable, and unmarked spatial capture-recapture (uSCR), distance sampling (CT-DS), and random encounter models (REM) to the camera trap data where individual ID was not possible. All five approaches produced plausible and relatively consistent point estimates (0.41 – 0.99 animals per km2), despite differences in precision, cost, and effort being apparent.

In addition to the data, we provide novel code for running unmarked spatial capture-recapture (uSCR) and random encounter models (REM) to the camera trap data where individual ID was not possible. 

Methods

All fieldwork was carried out in the Ring of Gullion, Northern Ireland, UK. 

Cameras

Thirty Bushnell HD Trophy Cam 8MP camera traps (model number: 119577) with 8GB SD cards were deployed during June and July 2019. Thirty Bushnell HD Trophy Cam 8MP camera traps (model number: 119577) with 8GB SD cards were deployed during June and July 2019. At the end of the survey period, camera traps were checked and for each detection (the first image in a trigger sequence of an individual pine marten) distance to animal (m) and angle of detection (°) were measured in situ.

Noninvasive genetic sampling

Twenty hair tubes based on those developed by Mullins et al. (2010), were deployed across the study site between June and July 2019. Hair-tubes were checked weekly and sticky patches and bait were replaced on each visit. Hair samples were frozen at -20oC prior to DNA extraction. Microsatellite analysis to identify individual pine marten was carried out using up to 11 microsatellite markers. Each sample was analysed in duplicate and only samples giving identical results in the replicates were scored.

Live traps

Twelve Tomahawk 205 live cage traps were deployed along two perpendicular transects spaced approximately 400m apart. Trapping was conducted from August - October 2019 with daily trap checks. Trapped animals were anaesthetised with an intramuscular injection of ketamine (25mg per kg) and midazolam (0.2mg per kg) and scanned for a microchip. 

Statistical analyses

Spatially explicit capture-recapture (SECR) models were used to estimate density for both live trapping and gNIS (Efford & Boulanger, 2019). Occasion lengths for live trapping were one day, whilst for gNIS were one week. For live trapping, we specified a single-use detector type, whilst for gNIS we specified a proximity-based detector type. Density was calculated from camera traps using REM (Rowcliffe et al. 2008), CT-DS (Howe et al. 2017) and uSCR (Chandler & Royle, 2013).

Usage Notes

Please refer to the README file.

Funding