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By analyzing sedimentary ancient DNA from two sediment cores in the Yellow Sea, we reconstructed mid-late Holocene phytoplankton dynamics during the intensification of the Yellow Sea Warm Current (YSWC). We found that phytoplankton communities differed significantly between sites, with stronger spatial differentiation in eukaryotes than in cyanobacteria. Dinoflagellates and chlorophytes dominated overall, while Dictyochophyceae (silicoflagellates) were unexpectedly abundant relative to diatoms. Phylogenetic reconstruction recovered diverse Dictyochophyceae lineages (two orders, six genera) dominated by Pseudopedinella, indicating greater regional diversity than previously recognized. The cyanobacterial assemblages comprised SIO2C1, UCYN-A, and PCC-6307 lineages. Following the intensification of the YSWC since ~3\u00a0ka BP, eukaryotic community structure shifted in the central basin. 18S rRNA gene abundance increased, whereas diversity and silicifier-to-dinoflagellate ratios declined. Although the absolute age of core B07 remains tentative, a pronounced stratigraphic turnover occurred in the frontal zone around 100 cmbsf, with a shift from chlorophyte to dinoflagellate dominance, consistent with reduced freshwater influence and an enhanced YSWC impact. Numerous indicator species exhibited contrasting abundance patterns before and after these transitions. These findings demonstrate the sensitivity of coastal phytoplankton to circulation-driven regime shifts.<\/jats:p>","DOI":"10.1093\/ismeco\/ycag172","type":"journal-article","created":{"date-parts":[[2026,6,16]],"date-time":"2026-06-16T12:29:27Z","timestamp":1781612967000},"source":"Crossref","is-referenced-by-count":0,"title":["Warm current intensification altered phytoplankton communities in the Yellow Sea: insights from sedimentary ancient DNA metabarcoding"],"prefix":"10.1093","volume":"6","author":[{"ORCID":"https:\/\/orcid.org\/0009-0004-7021-9486","authenticated-orcid":false,"given":"Haoyuan","family":"Zhang","sequence":"first","affiliation":[{"name":"School of Marine Sciences, Sun Yat-sen University, and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai) , Zhuhai 519082 ,","place":["China"]},{"name":"Guangdong Provincial Key Laboratory of Marine Resources and Coastal Engineering , Zhuhai 519082 ,","place":["China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yaping","family":"Wang","sequence":"additional","affiliation":[{"name":"School of Marine Sciences, Sun Yat-sen University, and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai) , Zhuhai 519082 ,","place":["China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Huiwen","family":"Deng","sequence":"additional","affiliation":[{"name":"School of Marine Sciences, Sun Yat-sen University, and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai) , Zhuhai 519082 ,","place":["China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Linxuan","family":"Li","sequence":"additional","affiliation":[{"name":"School of Marine Sciences, Sun Yat-sen University, and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai) , Zhuhai 519082 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