DOI: 10.5061/dryad.zgmsbccd1
title: Data from: Responses of population structure and genomic diversity to climate change and fishing pressure in a pelagic fish

description: The responses of marine species to environmental changes and anthropogenic
 pressures (e.g. fishing) interact with ecological and evolutionary
 processes that are not well understood. Knowledge of changes in the
 distribution range and genetic diversity of species and their populations
 into the future is essential for the conservation and sustainable
 management of resources. Almaco jack (Seriola rivoliana) is a pelagic fish
 with high importance to fisheries and aquaculture in the Pacific Ocean. In
 this study, we assessed contemporary genomic diversity and structure in
 loci that are putatively under selection (outlier loci) and determined
 their potential functions.  Utilizing a combination of
 genotype-environment association, spatial distribution models, and
 demogenetic simulations, we modeled the effects of climate change (under
 three different RCP scenarios) and fishing pressure on the species’
 geographic distribution and genomic diversity and structure to 2050 and
 2100. Our results show that most of the outlier loci identified were
 related to biological and metabolic processes that may be associated with
 temperature and salinity. Contemporary genomic structure showed three
 populations—two in the Eastern Pacific (Cabo San Lucas and Eastern
 Pacific) and one in the Central Pacific (Hawaii). Future projections
 suggest a loss of suitable habitat and potential range contractions for
 most scenarios, while fishing pressure decreased population connectivity.
 Our results suggest that future climate change scenarios and fishing
 pressure will affect the genomic structure and genotypic composition of S.
 rivoliana and lead to loss of genomic diversity in populations distributed
 in the eastern-central Pacific Ocean, which could have profound effects in
 fisheries that depend on this resource.
description: # Outlier loci and input data for demogenetic simulations in CDMetaPOP
 Mendoza-Portillo, V., Garca-De Len F.j and von der Heyden, S. --- 1.
 Genotypes of 155 oulier loci (155.gen: SNPall dataset) identified by at
 least two methods: principal component analysis (PCA) in the pcadapt
 package for R (Luu et al., 2017), and genotype-environment association
 methods [BayeScEnv (De Villemereuil & Gaggiotti, 2015) and redundancy
 analysis (RDA, Forester et al., 2016, 2018)]. The dataset includes all
 loci identified by maximum (SNPmax) and minimum (SNPmin) environmental
 variables 2. CDMetaPOP input data-contains the files for running CDMetaPOP
 demogenetic simulations classvars_srivo.csv patchvars_srivo.csv
 popvars_sriv_c-all.csv Resistance data obtained from additive pressures of
 fishing and climate change scenarios (RCP 2.6, 4.5 and 8.5) for years 2050
 and 2100. The data represents eight scenarios of heterogeneous landscapes
 simulated: 1. Isolation by distance (no resistances, i.e., the null
 model): cd_ibd.csv 2. fishing pressure (FP): cd_fishing.csv 3. 2050-RCP2.6
 plus fishing pressure effect (+FP): cd_5026F.csv 4. 2050 RCP4.5+FP:
 cd_5045F.csv 5. 2050 RCP8.5+FP: cd_5085F.csv 6. 2100 RCP2.6+FP:
 cd_10026F.csv 7. 2100 RCP4.5+FP: cd_10045F.csv 8. 2100 RCP8.5+FP:
 cd_10085F.csv