DOI: 10.5061/dryad.44j0zpcpz
title: Data from: Whole-genome resequencing reveals polygenic signatures of directional and balancing selection on alternative migratory life histories

description: Migration in animals and associated adaptations to contrasting
 environments are underpinned by complex genetic
 architecture. Here, we explore the genomic basis of facultative
 anadromy in brown trout (Salmo trutta), wherein some individuals migrate
 to sea while others remain resident in natal rivers, to better
 understand how alternative migratory tactics (AMTs) are
 maintained evolutionarily. To identify genomic variants
 associated with AMTs, we sequenced whole genomes for 194 individual trout
 from five anadromous–resident population pairs, situated above
 and below waterfalls, in five different Irish rivers. These waterfalls
 act as natural barriers to upstream migration and hence we
 predicted that loci underpinning AMTs should be under similar
 divergent selection across these replicate pairs. A sliding
 windows based analysis revealed a highly polygenic adaptive divergence
 between anadromous and resident populations, encompassing 329
 differentiated genomic regions. These regions were associated with
 292 genes involved in various processes crucial for AMTs,
 including energy homeostasis, reproduction, osmoregulation,
 immunity, circadian rhythm and neural function. Furthermore,
 examining patterns of diversity we were able to link specific genes and
 biological processes to putative AMT trait classes:
 migratory-propensity, migratory-lifestyle and residency.
 Importantly, AMT outlier regions possessed higher genetic
 diversity than the background genome, particularly in the anadromous
 group, suggesting balancing selection may play a role in
 maintaining genetic variation. Overall, the results from this study
 provide important insights into the genetic architecture of
 migration and the evolutionary mechanisms shaping genomic diversity within
 and across populations.
description: We have submitted our supplementary tables and main code (bash and R
 scripts) used for analyses. ## Description of the data and file structure
 The Supplementary tables are provided in a spreadsheet
 (00_*Moran_2024_Suppl_Tables*_v2.xlsx) and captions for the tabs are
 below: **Table S1.** Per sample summary of raw read quality and predicted
 coverage based on genome length. **Table S2.** Global summary of read
 mapping (clean and filtered reads from fastp) based on Qualimap and
 multiQC reports. **Table S3.** Genes (n=292) within 10kb up or downstream
 of AMT outliers (regions of overlap for *FST* windows and C2 SNPs).
 Chromosome name (chr), gene name, ensemble gene id,  gene start and end
 positions, distance from outlier windows to gene (bp, 0=range overlap),
 and gene description. **Table S4.** GO term enrichment results for 292 AMT
 genes. Go terms with p&lt;0.01 (weight Fihser i.e. not padjusted) shown.
 **Table S5.** Genes that overlapped between putative AMT genes (n=292)
 with differentially expressed (DE) genes in smolts vs. non-smolts (Wynne
 et al., 2021). **Table S6.** The number of AMT outlier windows (n=329) and
 associated genes (n=292) assigned to one of four groups based on TD. Note
 nine genes were assigned to more than one *ZTD* group. **Table S7.** Genes
 associated with (within 10kb up or downstream) AMT outliers assigned to
 the four *ZTD* groups. Columns indicate chromosome name (chr), gene name,
 ensemble gene id,  gene start and end positions, distance from outlier
 windows to gene (bp, 0=range overlap), and gene description. **Table
 S7.A)** Genes (n=4) associated with (within 10kb up or downstream) AMT
 outliers assigned to the *ZTD* *LA_LR* group (lower tertile for both
 anadromous and resident pools). **Table S7.B)** Genes (n=39) associated
 with (within 10kb up or downstream) AMT outliers assigned to the *ZTD*
 *LA_MHR* group (lower tertile for anadromous pool versus middle and upper
 tertiles for resident pool). **Table S7.C)** Genes (n=102) associated with
 (within 10kb up or downstream) AMT outliers assigned to the *ZTD* *MHA_LR*
 group (middle and upper tertiles for anadromous pool versus lower tertile
 for resident pool). **Table S7.D)** Genes (n=176) associated with (within
 10kb up or downstream) AMT outliers assigned to the *ZTD* *MHA_MHR* group
 (middle and upper tertiles for anadromous and resident pools). **Table
 S8.A-B)** Genes associated with (within 10kb up or downstream) AMT
 outliers assigned to the top 1% of *ZTD* in the (A) anadromous and (B)
 resident pools. Columns indicate chromosome name (chr), gene name,
 ensemble gene id,  gene start and end positions and gene description.
 **Table S9.A-B)** Genes associated with (within 10kb up or downstream) AMT
 outliers assigned to the top 1% of Betascores in the (A) anadromous and
 (B) resident pools. Columns indicate chromosome name (chr), gene name,
 ensemble gene id,  gene start and end positions and gene description.
 **Table S10.A-B)** Genes associated with (within 10kb up or downstream)
 AMT outliers assigned to the top 1% of intersex *FST* in the (A)
 anadromous and (B) resident pools. Columns indicate chromosome name (chr),
 gene name, ensemble gene id,  gene start and end positions and gene
 description. Note gene IDs were retrieved from Ensembl using the biomaRt
 package (v.2.57.1; Durinck et al., 2009) as of May 2024. In some cases,
 the 'Gene' column may have empty cells despite the presence of
 an Ensembl ID. This occurs when genes have not yet been functionally
 annotated or assigned a name. ## Code/software Main bash scripts for
 running software and R code used for analyses. Additional custom scripts
 are available from the corresponding authors upon request. ## Access
 information Other publicly accessible locations of the data: * Related
 data: Whole genome resequencing data used in this study is available from
 the European Nucleotide Archive (ENA) (PRJEB72781). ## Version changes
 **04/11/2024**: We identified a minor issue in the initial BayPass
 analysis where two chromosomes (chr 33 and chr 39) were unintentionally
 excluded due to a data merging error. After resolving this and rerunning
 the analysis, the results remained highly consistent with our original
 findings, with no effect on the main results or conclusions. However, this
 reanalysis led to small adjustments in the outlier data: **ATM Outlier
 Windows**: Increased from 310 to 329. **Number of Genes**: Increased from
 273 to 292. These changes are now reflected in the updated supplementary
 data tables.