Population genomic and morphological datasets from: An evolutionary mosaic challenges traditional monitoring of a foundation species in a coastal environment - the Baltic Fucus vesiculosus
Creators: name: Pereyra, Ricardo
name: Kinnby, Alexandra
name: Le Moan, Alan
name: Ortega-Martinez, Olga
name: Jonsson, Per
name: Piarulli, Stefania
name: Pinder, Matthew
name: Töpel, Mats
name: De Wit, Pierre
name: André, Carl
name: Knutsen, Halvor
name: Johannesson, Kerstin
Publisher: name: Zenodo
Year: 2025
Subjects: genetic monitoring
partial clonality
habitat-forming species
marginal habitat
postglacial sea
Fucus radicans
demographic inference
SNP panel

description: 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 female clone of F. vesiculosus in its northern Baltic distribution. In two Estonian sites, however, individuals are sexual but reproductively isolated from Baltic F. vesiculosus, revealing a separate diverged lineage that predates the formation of the Baltic Sea. Monitoring Baltic Fucus without considering this genetic complexity will fail to prioritise populations with adaptive potential to new climate conditions. From our genomic data, we can extract informative and diagnostic genetic markers that differentiate major genetic entities. Such an SNP panel will provide a straightforward tool for spatial and temporal monitoring and informing management decisions and actions.
description: Funding provided by: Swedish Research CouncilROR ID: https://ror.org/03zttf063Award Number: 217-2008-1719
Funding provided by: Swedish Research Council for Environment Agricultural Sciences and Spatial PlanningROR ID: https://ror.org/03pjs1y45Award Number: 2012-76, 2019/00882, 2022/02838
Funding provided by: BiodivERsAROR ID: https://ror.org/05cvqmv08Award Number: 2016-01930
Funding provided by: Swedish Agency for Marine and Water ManagementROR ID: https://ror.org/00ht4dp10Award Number: 2212-20, 2213-20
Funding provided by: The Research Council of NorwayROR ID: https://ror.org/00epmv149Award Number: 280453
description: 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: Frond width (FW), the distance between dichotomies (DBD), and the undulation index (UX). The first two characters have been used as a diagnostic to differentiate F. radicans from F. vesiculosus (Bergström et al., 2005; Pereyra et al., 2013). Each individual was characterized using the average of three measurements taken from different branches with the image analysis software ImageJ64 (Schneider et al., 2012).

The data includes a list of Sample ID codes and corresponding localities and geographic coordinates.