Macquarie perch: inbreeding depression and genetic rescue in the Cotter River

These are R scripts, data files for the analyses and Supplementary Material for the manuscript

Planning and implementing genetic rescue of an isolated population of an endangered freshwater fish in a regulated river, where low flow triggers inbreeding depression and reduces breeding opportunities

by Alexandra Pavlova, Nadja Schneller, Mark Lintermans, Matt Beitzel, Diana A. Robledo-Ruiz, Paul Sunnucks

submitted to Evolutionary Applications.

We acknowledge the Traditional Owners of Country throughout Australia and recognise their continuing connection to land, waters and culture, and pay our respects to their Elders past, present and emerging. This research was conducted on Ngunnawal Country.

The content of this data repository:

1. Analysis of field data- age and fitness proxy

• 1.Analyses_of_field_data_age_length_Gompertz_growth_residuals.R–R Script for using fish length and sampling dates to estimate age, cohorts, and calculate growth residuals for Macquarie perch captured from 2016 onwards with length data
• Cotter2016onwards_length.csv–Individual lengths data for Gompertz_growth_model.R

2. Analyses of SNP genotypes

• 2.Analyses_of_DArT_genotypes.R –R script for SNP data filtering and analyses.
• Report_DMacq21-6666_12_moreOrders_SNP_mapping_2.csv- original DArT genotype data file for Macquarie perch; includes populations other than Cotter River and Cataract Dam.
• DMacq21-6666_covariate_CotterR_CatD.csv – covariate file to be used with Analyses_of_DArT_genotypes.R.
• filter.excess.het.R –R function used in Analyses_of_DArT_genotypes.R
• gl2colony.R –R function used in Analyses_of_DArT_genotypes.R

3. Inbreeding depression model

• 3.Analyses_of_genetics_and_length.residuals_incl_ID.R- R script for analysing heterozygosity and inbreeding depression
• Cotter_Cataract.genetics.finess.csv- data for R script Analyses_of_genetics_and_lenth.residuals_incl_ID.R, comprising field data, inferences from field data, results of individual genetic analyses and inferences from genetic analyses

4. Analyses of flow and its influence on Ne and dispersal distances

• 4.Analyses_of_flow_Ne_disp.dist.R --R script to plot flow data and analyze relationships between flow and max dispersal distances between full-siblings in each families and per birth-cohort
• ACT_flow_data_Vanitys.csv –Data on flow collected at Vanitys
• Flow_vs_NE.csv –Estimates of Ne and average flow per cohort 2016-2020
• Families_dispersal_flow.csv –Data for dispersal distances analysis

Supplementary Material S1

• Inbreeding depression models with interaction.docx -Supplementary Material S1
• ID_models_with_interaction.R- R code for models with heterozygosity*cohort interactions