Eastern bettong (Bettongia gaimardi) reintroduced to Mulligan's Flat Woodland Sanctuary and Tidbinbilla Nature Reserve: DArT SNPs + individual information

Incorporating genetic data into conservation programmes improves management outcomes, but the impact of different sample-grouping methods on genetic diversity analyses is poorly understood. To this end, the multi-source reintroduction of the eastern bettong (Bettongia gaimardi) was used as a long-term case study to investigate how sampling regimes may affect common genetic metrics, and hence management decisions. The dataset comprised 5307 SNPs sequenced across 263 individuals. Samples included 45 founders from five genetically distinct Tasmanian source regions, and 218 of their descendants captured during annual monitoring at Mulligan’s Flat Woodland Sanctuary (MFWS; 121 samples across eight generations), and Tidbinbilla Nature Reserve (TNR; 97 samples across nine generations). The most management-informative sampling regime was found to be generational cohorts, providing detailed long-term trends in genetic diversity. When these generation-specific trends were not investigated, recent..., Genotyping 

Following the reintroduction monitoring protocol, adults were marked by PIT microchip at first capture and an ear biopsy was taken (Manning et al. 2019). DNA was extracted from these ear clips using a modified proteinase-K digestion and salting-out method (Miller et al., 1988) with ethanol precipitation. Plates were prepared according to DArT specifications (https://www.diversityarrays.com/orderinstructions/). SNP data was obtained by DArT’s Bettong DArTseq 1.0, an optimised complexity reduction technique using restriction enzymes PstI and SphI in a digestion/ligation modified from Kilian et al. (2012). The sequences produced were processed using DArT’s proprietary analytical pipelines. 

Data Filtration 

The initial 11,097 candidate SNPs returned by DArT were filtered in R v3.6.2 (R Core Team 2019), using the dartR package (Grueber and Georges, 2019). Firstly, a frequency plot was constructed, showing that missingness in the data was loci-based. Therefore, filtratio...,