# Dataset title: Data and R scripts for the article "Using conservation genetics to prioritise management options for an endangered songbird." --- ## Data contributors: Fernanda Alves, Sam Banks and Max Edworthy ## License: Use of these data is covered by the following license: # Title: CC0 1.0 Universal (CC0 1.0) # Specification: https://creativecommons.org/publicdomain/zero/1.0/; the authors respectfully request to be contacted by researchers interested in the re-use of these data so that the possibility of collaboration can be discussed. ## Contact information: # Name: Fernanda Alves # Affiliation: Fenner School of Environment and Society, Australian National University # ORCID ID: https://orcid.org/0000-0001-8825-6358 # Email: fernanda.alves@anu.edu.au # Alternate email: fernandabiologia@gmail.com ## Description of the data and file structure The two csv files archived comprise the raw dataset for all the analyses conducted in this manurscript. The csv file "SNP_data.csv" contains Single nucleotide polymorphisms data (SNPs), and the "individual metadata.csv" information on each individual sampled. Given the species in this study is listed as endangered, we removed from the archived data coordinates of the exact locations of where samples were collected. The available individual metadata contain the following variables: id = individual id pop = population where the sample was collected sex = female, male age = adult or nestling bird nest_id = id of the nest the nestling came from; samples from adult birds were not collected in the nest, therefore these cells are empty. The data went through several filtering processess to conduct the analyses, see the methods section of the manuscript and comments in the R scripts for details. All data analyses was conducted in R version 4.2.1 (2022-06-23 ucrt). ## Code/Software The R scripts are in the order that analyses were undertaken, comments about the rationale behind each analysis can be found in the scripts and detailed information in the manuscript. The scripts attached are: 01_pardalote_dart_SNP_filtering.R = In this script we take the raw data and conduct several filtering steps and created a new dataset for subsequent analyses. 02_genetic_diversity_stats.R = Script to run basic genetic diversity metrics 03_DAPC.R = script to run Discriminant Analysis of Principal Components (DAPC) 04_STRUCTURE.R = script to run population structure analysis using the strataG package. Note that to run this analysis the software STRUCTURE needs to be installed (https://web.stanford.edu/group/pritchardlab/structure.html) 05_individual_assignment(Rubias).R = script to run individal assignment using package Rubias described in Moran and Anderson, 2019 (https://doi.org/10.1139/cjfas-2018-0016) 06_Allelic_richness&contribution_analysis.R = script to run allelic richness analysis described in Petit et al., 1998 (https://doi.org/10.1111/j.1523-1739.1998.96489.x) 07_Marxan_analysis.R = Script to run Systematic Conservation Prioritization using package "prioritizr" 08_estimate_Ne_with_dartRwrapper.R = Script to estimate effective population size (Ne) using the wrapper function for the software (10.1111/1755-0998.12157) in "dartR" package. The R scripts are provided "as is" with the intention of reproducibility and WITHOUTH WARRANTY OF ANY KIND. In no event shall the authors be liable of any claim, damages or other liability.