DOI: 10.5061/dryad.80gb5mkxk
title: Data from: Genetic consequences of improved river connectivity in brown trout (Salmo trutta)

description: 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 genetic
 structuring and differentiation between fragmented headwater tributaries
 before the fishway construction, but not in the control reservoir.
 Unexpectedly, after the fishway construction we observed signals
 consistent with increased genetic differentiation between populations of
 newly recruited juvenile fish in the reservoir tributary and fish in the
 reservoir. We propose this was caused by newly enabled philopatric
 behaviour of brown trout to their natal spawning tributary. In contrast,
 we did not find any genetic changes in the tributary without a fishway or
 in the barrier-free reservoir system. Given the scarcity of similar
 studies, we advocate for an increased use of genetic analyses in BACI
 studies to monitor and evaluate the effect of efforts to restore habitat
 connectivity and inform future management strategies.
description: # 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: * sampling.date: exact date of sampling when available
 (format: DD/MM/YYYY) * Year: year of sampling. * Period:
 "Before" or "After" the construction of the fish pass
 on the RLD. * Group: information about the location (i.e.,
 'BGB'= Blea Gill beck, 'Grimwith'=Grimwith Reservoir,
 'GUG'=Gate Up Gill, 'RLD'=River Little Don,
 'Langsett'= Langsett Reservoir, 'TWB'= Thickwoods
 Brook) combined with period of sampling ('Before' or
 'After'). * Location: sampling location (i.e., 'BGB',
 'Grimwith res', 'GUG', 'RLD', 'Langsett
 res', 'TWB'). * Tributary: the tributary of origin of the
 samples (if not the main reservoir). * Site: sampling site name. *
 Site.notes: when available notes about sampling locations. * Length..mm.:
 fork length of samples in mm. * ref.genetics: ID used for genetic analyses
 * System: reservoir system of origin ('Langsett' or
 'Grimwith') ** IMPORTANT NOTE:** the extensions of the following
 files must be changed manually in the following way to be able to run the
 provided code. 'allChr_orderedped_trout.txt' --&gt; change
 into'allChr_orderedped_trout.ped'
 'trout_all_chr.map.txt' --&gt; change
 into'trout_all_chr.map.map' ## Code An example code to run the
 analyses of the study using the provided files is included in the folder
 called: 'CODE_Moccetti_et_Al_2024_EvoAppl'. Here, the script is
 contained in the file called
 'CODE_Moccetti_et_Al_2024_EvoAppl.md', while some supporting
 figures mentioned in or produced through the code can be found in the
 "Figures" subfolder.