DOI: 10.5061/dryad.j3tx95xqr
title: Temporal changes in Tasmanian devil genetic diversity at sites with and without supplementation

description: Management interventions for threatened species are well documented with
 genetic data now playing a pivotal role in informing their outcomes.
 However, in situ actions, such as supplementations (the release of
 individuals into an existing population of conspecifics) are often
 restricted to a single site to advise species-level management decisions.
 A considerable amount of research and management effort has been dedicated
 to conserving the endangered Tasmanian devil (Sarcophilus harrisii),
 offering a unique opportunity to investigate the temporal genetic
 consequences of supplementation at multiple sites, in comparison to
 outcomes observed in the absence management interventions. Using 1,778
 genome-wide SNPs across 1,546 individuals, we compared four wild
 supplemented sites to four monitoring-only sites (not supplemented;
 control sites) over nine years (2014-2022). By the end of the study,
 genetic differentiation among supplemented sites had significantly
 decreased compared to among not-supplemented sites. We found statistically
 significant variation in patterns of genetic change over time between
 sites using linear mixed-effects modelling with random slopes.
 Investigating this among-site variation showed that three of the
 supplemented sites conformed to predictions that supplementations would
 have a positive impact on the genetic diversity of devils. We predicted
 there would be no change over time at our fourth site due to relatively
 high gene flow previously observed there, however, that site did not align
 with predictions, instead showing a decrease in genetic diversity and
 increase in relatedness. Amongst not supplemented sites, there was no
 consistent pattern of temporal genetic change, suggesting that devil sites
 across Tasmania are highly heterogeneous, likely reflecting variation in
 connectivity among sites, genetic drift, and non-genetic factors. Our
 study demonstrates that long term concurrent monitoring of multiple sites,
 including controls, is necessary to contextualize the influence of
 management interventions against natural fluctuations within a species
 system.
description: There is once dataset included in the Excel workbook:
 A set of SNPs generated using DArTSeq, a form of reduced
 representation sequencing. Genotype SNP data were quality filtered using
 the dartR package (v 2.9.7) in Rstudio (v 4.3.1). We filtered out
 monomorphic loci and SNPs with low (lower threshold = 5) and high (upper
 threshold) mean read counts. Further filtered on a reproducibility of
 ≥95%, loci with a call rate of ≥70%, 0.001 minor allele frequency,
 individual call rate of ≥70%. Loci were filtered out if the SNP position
 was outside the trimmed sequence tag, secondary SNPs in the same sequence,
 or predicted to be sex linked. Data was subset to include individuals for
 the current study, monomorphic loci were removed here and refiltered with
 a call rate of ≥70%.
description: # Temporal changes in Tasmanian devil genetic diversity at sites with and
 without supplementation
 [https://doi.org/10.5061/dryad.j3tx95xqr](https://doi.org/10.5061/dryad.j3tx95xqr) ## Description of the data and file structure ##### General Information * Title of dataset  * Data to: Temporal changes in Tasmanian devil genetic diversity at sites with and without supplementation. * Author information (principal investigator) * Name: Prof. Carolyn Hogg * Institution: The University of Sydney * Email: [carolyn.hogg@sydney.edu.au](mailto:carolyn.hogg@sydney.edu.au) * Dates of data collection * 2014 to 2022  * Geographic location of data collection * Tasmanian devil wild sites, Tasmania Australia. * Information about funding sources. * The Australian Research Council (LP180100244), The University of Sydney, Save the Tasmanian Devil Program and the San Diego Zoo Wildlife Alliance. ##### Sharing/Access Information * Links to publications that cite or use data * Andrea L. Schraven, Elspeth A. McLennan, Katherine A. Farquharson, Andrea V. Lee, Katherine Belov, Samantha Fox, Catherine E. Grueber and Carolyn J. Hogg (in press). Temporal changes in Tasmanian devil genetic diversity at sites with and without supplementation. Molecular Ecology. ### Files and variables #### File: Schraven\_et\_al.\_Molecular\_Ecology\_data.xlsx **Description:** The excel workbook contains two sheets. For details of SNP calling and filtering, see the Methods section of the paper. ##### Variables * Metadata (sheet 1) - contains the list of devil sample IDs and associated site metadata. Metadata includes the sample site and year the individual was trapped (see methods of the paper for details). Sample IDs are named with F (female), M (male), H (hermaphrodite), U (sex unknown) as the prefix, followed by their location (site), and an individual identifier per location. * Data (sheet 2) - contains the SNP genotypes in a two-row format for the 1,546 devil samples generated using the DArT proprietary pipeline. Columns A to S includes the locus metadata and rows 1 to 6 include the plate information for each sequenced sample. Genotypes are encoded in a 2-row format (1st row is the reference allele and the 2nd row is the alternate allele) where a "1" in the 1st row and a "0" in the 2nd row is homozygous for REF, a "1" in the 1st and the 2nd row is heterozygous, and a "0" in the 1st row, a "1" in the 2nd row is homozygous for ALT, and a "-" represents missing data ## Code/software All filtering was performed using the dartR package (v 2.9.7) in R (v 4.3.1). ## Access information Other publicly accessible locations of the data: * N/A Data was derived from the following sources: * Genetic data was derived from Tasmanian devil tissue sample (ear biopsies) collected from 2014 to 2022 during annual monitoring trips run by the Save the Tasmanian Devil Program (STDP)