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Dataset: Evolution of copper tolerance in the coastal diatom Skeletonema marinoi

Björn Andersson — Tue, 04 Jul 2023 09:26:51 GMT

This project explores if, and how, contemporary populations the costal diatom Skeletonema marinoi have evolved in response to mining pollution. The study systems are two semi-enclosed inlets in the Baltic Sea, where one, Gåsfjärden (VG: 57°34.35'N, 16°34.98'E), has been affected by mining pollution for ca. 400 years, while the other, Gropviken (GP: 58°19.92N 16°42.35'E), has not. Strains were isolated, and the genome sequenced for 55 individual strains, and they were phenotyped in terms of specific growth rate and dose-responses to toxic copper concentrations (6-12 uM Cu). An artificial evolution experiment was conducted by assembling 28 and 30 strains from the two locations separately, and let them evolve with, and without, toxic Cu stress of 8.65 uM, corresponding to the concentration that inhibits the reference S. marinoi strain RO5AC’s specific growth rate with 50% in acute toxic tests (Andersson et al. 2020: DOI: 10.1016/j.aquatox.2020.105551). A recently developed 523 bp long strain-specific metabarcoding loci (*Sm_C12W1*: https://github.com/topel-research-group/Live2Tell) was used to track the selection process. This locus is located on contig 12 of S. marinoi, inside a pentatricopeptide (PPR) repeat region of gene Sm_t00009768-RA, encoding an RNA-binding protein. The locus has 38 SNP positions amongst the 58 strains used in this study, and 110 unique alleles with 100% heterozygosity, including two triploid/aneuploid strains. The outcome was contrasted against strain selection models computed according to Andersson et al. 2022 (DOI: 10.1038/s41396-021-01092-9). The data and analyses included here are raw data and R-scripts that analyses the data, together with essential data created from the analysis. However, sequencing data is not processed or included, but has been deposited and available at NCBI under BioProject PRJNA939970. The amplicon sequencing data has been analyzed as outlined in https://github.com/topel-research-group/Bamboozle/wiki/Bamboozle-Part-2:-Barcode-Quantification. For more detailed information, see README.md files associated with each step of the analysis briefly outlined below. Each of the four sections includes necessary input data and can be run separately. Barcodes This is an analysis pipeline of the amplicon sequences of the selection experiment using the hypervariable locus in S. marinoi. The locus was bioinformatically identified based on analysis of whole genome sequences of 55 strains of S. marinoi from two Baltic Sea locations. It was predicted to have at least one unique allele enabling tracking of evolution through selection on standing genetic diversity in a artificial evolution experiment (See Fig above). Two barcode loci (Sm_C2W24 and Sm_C12W1) were sequenced in the experiment, but Sm_C12W1 had much more allelic diversity so the majority of the analysis focus on this data (see Barcodes/Barcoding_C12W1/README.md for more information). This Git repository does not contain the bioinformatic sequence analyses, but starts after raw reads have been trimmed, merged, and mapped back to the known allele sequences. Data from two pre-processing approaches are included, one based on Dada2 error-correction (Barcodes/Barcoding_C12W1/C12W1_BBmergeDada2_input), and one that uses exact matches of merged amplicon sequences (Barcodes/Barcoding_C12W1/ C12W1_abundances). The latter is the one we use for the publication: Andersson et al. Strain-specific metabarcoding reveals rapid evolution of copper tolerance in populations of the coastal diatom Skeletonema marinoi, in prep. for Molecular Ecology. The zipfile Cu_evolution.zip contains all raw data, indexing information, R-scripts, and README.md files to reproduce the analysis and plot data. The documentation file README.md summarizes the contents of CU_evolution.zip. Key data from the analysis is provided as individual files, which are summarized in the documentation file Datafile_descriptions.md

Dataset: Cross-contamination risks in sediment-based resurrection studies of phytoplankton

Björn Andersson — Tue, 25 Oct 2022 08:58:02 GMT

The data contains sediment core measurements from two locations in the Baltic Sea. The aim of the study was to determine if the age of phytoplankton resting stages could be determined based on their vertical position or if contamination from surface population was a major confounding factor. To this end, the concentration of seven abundant species of diatoms and cyanobacteria were enumerated using the Most Probable Number (MPN) approach. Sediment sections were dated using standard radiometric methods, and surface sediment contamination was quantified using 4.5 μm microsphere tracers. Furthermore, ex-situ longevity was monitored over four years and decreased substantially withing this timeframe. In the cores, microspheres (>2×10^-6 fractions) were translocated from the sediment surface and could well explain the vertical distributions and abundances of viable cells (between ~106 to <0.8 g sediment^-1). Our conclusion was therefore that there are substantial contamination risks, and that age determination of resting stages using only radiometric age determination of bulk sediment is flawed without additional contamination controls. The study design consisted of two field expeditions (2017 and 2020) where six to ten, 50 cm cores were collected. Cores were inspected for signs of damage and preservation of laminated patterns, and the best cores were selected for further analysis. Selected cores were section onboard for bulk radiometric dating (210Pb and 137Cs) and Total Organic Carbon (TOC) and Nitrogen (TN) profiles. MPN enumeration of diatom and cyanobacterial resting stages was performed on cores transported intact to Gothenburg, which were processed within two to six months (reported as initial concentration). Survival ex-situ was monitored from 2017 to 2021 in surface samples stored under dark, cold (4C), and anoxic conditions, in 20-40 mL of sediment in 50 mL non-transparent Falcon tubes. To assess the validity of the radiometric age determination of diatoms from 2017, we quantified contamination during the 2020 sampling. Non-toxic, yellow-green fluorescing polystyrene microspheres (Thermo Scientific™ Fluoro-Max) were used to track surface sediment contamination in three VG20 cores. Microspheres were injected into the water headspace of three replicate cores (in Gothenburg) and allowed to settle onto the surface before sectioning. The translocation of microsphere from the sediment surface could then be traced in tandem with enumeration of resting stages. See file Metadata_Andersson2022.docx for a detailed description of files and data.

Data from: Connectivity and population structure in a marginal sea - a review

Simon Henriksson — Mon, 10 Nov 2025 12:52:33 GMT

Supplementary tables for the Review article "Connectivity and Population Structure in a Marginal Sea - a Review" (https://doi.org/10.1111/ddi.70056). Contains information on connectivity and population structure within marine species inhabiting the Skagerrak sea, summarised from scientific studies published between the years 1990 and 2023. Table S1: List of all 484 scientific studies that were screened, as well as information regarding whether they were included in the literature review. Table S2: Contains extracted data from the 172 scientific studies, published between 1990 and 2023, that were reviewed with regard to connectivity and population structure in the Skagerrak. The data includes information about both the studies' methodology (such as scientific discipline, spatial and temporal scale, and sample size) and results (such as which populations were identified and estimated connectivity between different regions). Table S3: Detailed summary of the scientific studies that studied contemporary connectivity on a "large" scale (between the Skagerrak sea and adjacent seas). For species with information from several studies, a concensus result for the species was created. Table S4: Detailed summary of the scientific studies that studied contemporary connectivity on a "small" scale (within the Skagerrak sea). For species with information from several studies, a concensus result for the species was created. Table S5: Detailed summary of the scientific studies that studied population structure, both within the Skagerrak Sea and between the Skagerrak and adjacent seas. For species with information from several studies, a concensus result for the species was created. Tables S6-S7: Settings for the BARRIER analysis conducted in the study. For more detailed descriptions of the content we refer to the text in the original study. This dataset is listed as "Deliverable 2.2" of the MARHAB project (Horizon Europe, grant number 101135307).