Population genomic and morphological datasets from: An evolutionary mosaic challenges traditional monitoring of a foundation species in a coastal environment - the Baltic Fucus vesiculosus

Genetic diversity in foundation species is critical for ecosystem functions and resilience under environmental change but remains largely overlooked in environmental monitoring. In the Baltic Sea, a key species for monitoring is the brown seaweed Fucus vesiculosus, which forms sublittoral 3D habitats providing shelter and food for fish and invertebrates.  Ecological distribution models predict a significant loss of Baltic F. vesiculosus due to ocean warming unless populations can adapt. Genetic variation and recombination during sexual reproduction are essential for adaptation, but studies have revealed large-scale clonal reproduction within the Baltic Sea. We analyzed genome-wide SNP data from the east Atlantic, the \"Transition zone\", and the Baltic Sea, and found a mosaic of divergent lineages in the Baltic Sea contrasting an outside dominance of a few genetic groups. We determined that the previously described endemic species Fucus radicans is predominantly a large&nbs..., Population genomic data was obtained through individually barcoded 2b-RAD libraries that were constructed following the procedures in Pereyra et al. (2023). The libraries were sequenced using a Novaseq6000 Illumina platform at SciLifeLab, Uppsala. A total of 962 individuals from 55 different sites were sequenced. Removal of PCR duplicates, quality filtering, and variant calling was performed in the computer cluster Albiorix (M. Töpel, IVL, Sweden), following a reference-based pipeline modified from Mikhail Matz available at https://github.com/z0on/2bRAD_GATK. Reads were mapped to an F. vesiculosus draft genome assembly previously used for population genomic studies (Kinnby et al., 2020; Pereyra et al., 2023; NCBI Bioproject No. PRJNA629489). Variant calling calibration was carried out with technical replicates labeled with the Individual name followed by the suffix \"Rep\". These replicates are included in the dataset. 
Morphological data comprises three morphometric characters: Fron..., , # Population genomic and morphological datasets from: An evolutionary mosaic challenges traditional monitoring of a foundation species in a coastal environment - the Baltic *Fucus* *vesiculosus*

[https://doi.org/10.5061/dryad.q83bk3jsh](https://doi.org/10.5061/dryad.q83bk3jsh)

## Description of the data and file structure

We have submitted the resulting Fucus_vesiculosus_SNP_data.vcf (Variant Call Format) file from the reference-based variant calling and filtering performed using the pipeline modified from Mikhail Matz available at [https://github.com/z0on/2bRAD_GATK](https://github.com/z0on/2bRAD_GATK). Reads were mapped to a *F*. *vesiculosus* draft genome assembly previously used for population genomic studies (Kinnby et al., 2020; Pereyra et al., 2023; NCBI Bioproject No. [PRJNA629489](https://www.ncbi.nlm.nih.gov/bioproject/PRJNA629489/)). This file is the primary population genomic dataset used for all the genetic analysis described in our article, \"An evolutionary mosaic chall...