Riverscape genetics of the Murrumbidgee Macquarie perch population

This repository contains data and scripts used in the manuscript

Pavlova A, Pearce L, Sturgiss F, Lake E, Sunnucks P, & Lintermans M. (2024). Immediate genetic augmentation and enhanced habitat connectivity are required to secure the future of an iconic endangered freshwater fish population. Evolutionary Applications. doi: 10.1111/eva.70019.

The content of this data repository:

I. Analysis of field data- age and length (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 category, cohorts, and calculate growth residuals for Macquarie perch captured from 2016 onwards with length data.
• Murrumbidgee_CataractRes_covariate.csv –Field data for sampling date, fish length (in mm), sites (numbered 1-12 from the most upstream to the most downstream), to be used with script 1.Analyses_of_field_data_age_length_Gompertz_growth_residuals.R.

II. Analyses of SNP genotypes

• 2.Analyses_of_DArT_genotypes.R –R script for SNP data filtering and analyses.
• Report_DMacq23-8576_6_moreOrders_SNP_mapping_2.csv - original DArT genotype data file for Macquarie perch, includes only Murrumbidgee River and Cataract Dam populations (the only ones used during genotyping), to be used with R script 2.Analyses_of_DArT_genotypes.R.
• Murrumbidgee_CataractDam_covariate.age.cohort.growth.csv– covariate file with additional information for each genotyped individual, to be used with 2.Analyses_of_DArT_genotypes.R.
• Dgen.csv- A matrix of FST-values for isolation-by-distance analysis, to be used with 2.Analyses_of_DArT_genotypes.R
• Dgeo.csv- A matrix of river distances (in km) for isolation-by-distance analysis, to be used with 2.Analyses_of_DArT_genotypes.R

III. Inbreeding depression model

• 3.Analyses_of_genetics_and_length.residuals_incl_ID.R- R script for analysing heterozygosity and inbreeding depression
• MurrCat_data_results.csv - field data, inferences from field data, genetic results and inferences from genetic analyses per individual, used as an input for R script 3.Analyses_of_genetics_and_length.residuals_incl_ID.R, the latter includes column definitions for MurrCat_data_results.csv.

We acknowledge the First Nations throughout Australia, 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 Ngarigo Country.