Abstract
Marine phytoplankton play essential roles in global primary production and biogeochemical cycles. Yet, the evolutionary genetic underpinnings of phytoplankton adaptation to complex marine and coastal environments, where many environmental variables fluctuate and interact, remain unclear. We combined population genomics with experimental transcriptomics to investigate the genomic basis underlying a natural evolutionary experiment that has played out over the past 8000 years in one of the world's largest brackish water bodies: the colonisation of the Baltic Sea by the ancestrally marine diatom Skeletonema marinoi. To this end, we combined target capture of the entire nuclear genome with pooled shotgun sequencing, and showed that the method performs well on both cultures and single cells. Genotype-environment association analyses identified > 1000 genes with signals of selection in response to major environmental gradients in the Baltic Sea, which apart from salinity, include marked differences in temperature and nutrient supply. Locally adapted genes were related to diverse metabolic processes, including signal transduction, cell cycle, DNA methylation and maintenance of homeostasis. The locally adapted genes showed significant overlap with salinity-responsive genes identified in a laboratory common garden experiment, suggesting the Baltic salinity gradient contributes to local adaptation of S. marinoi. Taken together, our data show that local adaptation of phytoplankton to complex coastal environments, which are characterised by a multitude of environmental gradients, is driven by widespread changes in diverse metabolic pathways and functions.
| Original language | English |
|---|---|
| Article number | e17817 |
| Pages (from-to) | e17817 |
| Journal | Molecular Ecology |
| Volume | 34 |
| Issue number | 13 |
| DOIs | |
| Publication status | Published - 10 Jun 2025 |
| MoE publication type | A1 Journal article-refereed |
Funding
This work was supported by grants from the Simons Foundation (403249 to A.J.A. and 725407 to E.P.), grants from the National Science Foundation (1651087 to A.J.A. and DBI\u20102146866 to M.W.H.), and a grant from the Science Foundation Flanders, FWO (1221323N to E.P.). This research used resources available through the Arkansas High Performance Computing Center, which is funded through multiple NSF grants and the Arkansas Economic Development Commission. We thank Geoffrey House for help with the sampling design, and we are grateful to Sirje Sildever (Tallinn University of Technology, Estonia), Bj\u00F6rn Andersson (University of Gothenburg, Sweden), Andrzej Witkowski (University of Szczecin, Poland), J\u00F6rg Dutz (Leibniz Institute for Baltic Sea Research Warnemuende, Germany), Justyna Kobos (University of Gdansk, Poland) and Anu Vehmaa (University of Helsinki, Finland) for sample collection. This work was supported by grants from the Simons Foundation (403249 to A.J.A. and 725407 to E.P.), grants from the National Science Foundation (1651087 to A.J.A. and DBI\u20102146866 to M.W.H.), and a grant from the Science Foundation Flanders, FWO (1221323N to E.P.). This research used resources available through the Arkansas High Performance Computing Center, which is funded through multiple NSF grants and the Arkansas Economic Development Commission. Funding: