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Description

Abstract

Invasive species management practices often include genetic analyses to better inform decision-making and resource allocation. Yet, past management actions may artificially bias recovered patterns of genetic variation; for example, a population bottleneck caused by contemporary culling may mirror some patterns associated with historical isolation. Here, we aimed to disentangle the impacts of past management activities from natural processes for Sitka black-tailed deer (Odocoileus hemionus sitkensis), an invasive species that has been repeatedly culled on two islands, SGang Gwaay and Reef, within the Haida Gwaii archipelago (Canada). We applied a recently developed Genotyping-in-Thousands by sequencing panel to contemporary (e.g., blood, serum, tissue, muscle, feces) and archived deer samples, the latter collected prior to management activity within the system (c. 1997–1998), which allowed us to contextualize conflicting patterns of isolation and connectivity previously observed on SGang Gwaay and Reef. Successful genotyping (92.6%) and population genetic analysis of 292 individuals at 236 SNPs revealed signals of historical isolation on SGang Gwaay and Reef, provided evidence of a founder effect during initial colonization, and indicated an absence of ongoing gene flow. Furthermore, our spatiotemporal analyses consistently supported a priori predictions associated with bottlenecks within post-cull populations, such as within-island loss of genetic variation, elevated within-island kinship, and increased levels of among-island genetic differentiation. These findings are promising for future management of deer on SGang Gwaay and Reef, suggesting that eradications on these islands may be durable. More broadly, our work highlights the importance of understanding management history before interpreting contemporary population genetic data.

Samples were genotyped using a Genotyping-in-Thousands by sequencing (GTseq; Campbell et al. 2015) panel developed in Burgess et al. (2022; https://doi.org/10.1002/ece3.8993) following the modified protocol therein. Raw data were processed using the GTseq workflow (https://github.com/GTseq).</p>
Usage notes

236loci_292deer.ped: ped file of genotypic data at 236 SNPs collected via GTseq for 292 deer samples.

metadata.csv: text file containing individual metadata for all samples used including sample identifiers, location, year, sex and sample type.