Local adaptation and the evolution of genome architecture in threespine stickleback

Theory predicts that local adaptation should favour the evolution of a concentrated genetic architecture, where the alleles driving adaptive divergence are tightly clustered on chromosomes. Adaptation to marine vs. freshwater environments in threespine stickleback has resulted in an architecture that seems consistent with this prediction: divergence among populations is mainly driven by a few genomic regions harbouring multiple quantitative trait loci (QTL) for environmentally adapted traits, as well as candidate genes with well-established phenotypic effects. One theory for the evolution of these “genomic islands” is that rearrangements remodel the genome to bring causal loci into tight proximity, but this has not been studied explicitly. We tested this theory using synteny analysis to identify micro- and macro-rearrangements in the stickleback genome and assess their potential involvement in the evolution of genomic islands. To identify rearrangements, we conducted a de novo assembly ..., This archive contains materials related to the paper \"Local adaptation and the evolution of genome architecture in threespine stickleback\", by Li et al. There are 3 main directories. The directory of genomic resources is on Dryad, the directories of scripts and supplemental information are on Zenodo. - Genomic_resources: the genome assemblies, annotations, and lists of genes - Supplemental information: contains the processed intermediate data files necessary to generate the figures and tables in the paper, as well as the Hi-C config files - scripts: contains the scripts for running the main analyses and generating the figures/tables, Please contact [e-mail] with any questions., This archive contains material related to the paper \"Local adaptation and the evolution of genome architecture in threespine stickleback\", by Li et al. GENERAL INFORMATION * Data (genomic\_resources): the genome assemblies, annotations, and lists of genes * Supplemental information: contains the processed intermediate data files necessary to generate the figures and tables in the paper, as well as the Hi-C config files * scripts: contains the scripts for running the main analyses and generating the figures/tables SHARING/ACCESS INFORMATION 1. Licenses/restrictions placed on the data: CC0 1.0 Universal (CC0 1.0) Public Domain 2. Links to publications that cite or use the data: Li Q, Lindtke D, Rodríguez-Ramírez C, et al. Local adaptation and the evolution of genome architecture in threespine stickleback. Genome Biology and Evolution. 2022,14(6): evac075. https://doi.org/10.1093/gbe/evac075 3. Recommended citation for this dataset: Li Q, Lindtke D, Rodríguez-Ramírez C, et al (2022). D...