Genetic consequences of improved river connectivity in brown trout (Salmo trutta)

Fragmentation of watercourses poses a significant threat to biodiversity, particularly for migratory fish species. Mitigation measures such as fishways, have been increasingly implemented to restore river connectivity and support fish migration. The effects of such restoration efforts are typically tested using telemetry and fisheries methods, which do not fully capture the broader population movements that may have important consequences for population viability. We performed a before-and-after control-impact (BACI) study using genetic tools (SNPs) to investigate the effect of a newly implemented fishway, aiming to enhance upstream spawning migration of brown trout (Salmo trutta Linnaeus) in a reservoir with two headwater tributaries fragmented by man-made weirs. Another reservoir with two barrier-free tributaries was also analysed as a control. Our results showed that the isolated brown trout population was spawning in the reservoir before the installation of the fishway, and we found..., , , # Files and code for: Moccetti et al. 2024 - Genetic consequences of improved river connectivity in brown trout (Salmo trutta) - Evolutionary Applications

## Description of the data

The folder 'input_files' contains SNP data, map file, and other necessary files to run the analyses. Specifically:

* 'allChr_orderedped_trout.txt': this is the 'ped' file containing the SNP calls for each individual
* 'trout_all_chr.map.txt': this is the 'map' file containing information for each SNP marker. The four columns represent (from left to right): Chromosome ID (e.g. '1'), SNP ID (e.g. '470946'), Genetic distance (in this case unknown for all SNPs, labelled as'0') and physical position in centimorgans (e.g. '42.452').
* 'AMP7_Lang_and_Grim_before_only_29.06.23': this is a list of individuals used to subset the dataset in the example provided in the code.
* 'Samples_INFO.csv': this is the file with all the information for each sample included in the study. It includes the following columns:

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