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Sponge aggregations and reefs are recognized as vulnerable marine ecosystems (or VMEs) due to their susceptibility to damage from bottom-contact fishing gears. Ensuring their long-term sustainability, preservation, and ecosystem functions requires the implementation of sound scientific conservation tools. Here, the genetic diversity, structure, and connectivity of the deep-sea glass sponge, <jats:italic>Vazella pourtalesii<\/jats:italic> (Schmidt, 1870), was investigated using 1,102 neutral SNPs obtained in RADseq.\u00a0This species is distributed across the northwest Atlantic from Florida, USA to Nova Scotia, Canada and we sequenced samples covering this full distribution and provided evidence of strong genetic structure with two distinct clusters: Florida together with the Carolina Shelves and the Scotian Shelf. We estimated moderate levels of diversity with low migration across large distances (&gt;\u20091000 kms) and high connectivity at smaller scales (&lt;\u2009300 kms). Further, fishing pressure on genetic diversity was evaluated, within two Sponge Conservation Areas (SCAs) on the Scotian Shelf. Those areas have different disturbance histories, and cumulative fishing pressure. Slightly lower levels of genetic diversity were found inside the SCAs, and yet they encompassed a high proportion of the diversity observed within the Scotian Shelf. We provide baseline data for future monitoring of the SCAs, discussing our findings in the light of existing area-based management tools.<\/jats:p>","DOI":"10.1038\/s41598-024-82462-z","type":"journal-article","created":{"date-parts":[[2025,1,9]],"date-time":"2025-01-09T18:08:54Z","timestamp":1736446134000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":4,"title":["Population genomics and connectivity of Vazella pourtalesii sponge grounds of the northwest Atlantic with conservation implications of deep sea vulnerable marine ecosystems"],"prefix":"10.1038","volume":"15","author":[{"given":"Anna","family":"Patova","sequence":"first","affiliation":[]},{"given":"Pedro A.","family":"Ribeiro","sequence":"additional","affiliation":[]},{"given":"Francisco J.","family":"Murillo","sequence":"additional","affiliation":[]},{"given":"Ana","family":"Riesgo","sequence":"additional","affiliation":[]},{"given":"Sergi","family":"Taboada","sequence":"additional","affiliation":[]},{"given":"Shirley A.","family":"Pomponi","sequence":"additional","affiliation":[]},{"given":"Hans Tore","family":"Rapp","sequence":"additional","affiliation":[]},{"given":"Ellen","family":"Kenchington","sequence":"additional","affiliation":[]},{"given":"Joana R.","family":"Xavier","sequence":"additional","affiliation":[]}],"member":"297","published-online":{"date-parts":[[2025,1,9]]},"reference":[{"key":"82462_CR1","doi-asserted-by":"crossref","unstructured":"Bell, J. 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