Advancing Marine Conservation: Metabarcoding and Metaphylogeography for a Multi‐Year Biomonitoring of Benthic Communities of National Parks Across Two Seas

ABSTRACT Aim We have applied a combined metabarcoding and metaphylogeography approach to temporal monitoring of marine protected areas. Biomonitoring is central to conservation, and new molecular methods, in particular metabarcoding‐based techniques, are changing our ability to track diversity in space and time. Protected areas are a cornerstone of conservation policies whose correct management requires sound time series data. Location Two Spanish National Parks with maritime domain, situated in two biogeographic regions, one in the Mediterranean and the other in the Atlantic. We compiled a multi‐year dataset spanning 9 years based on direct sampling of representative benthic communities in these parks. Methods We used as a marker a fragment of the cytochrome oxidase I (COI) gene, amplified with generalist primers. We developed a bioinformatic pipeline based on establishing sample‐wise exact sequence variants (ESVs) using stringent denoising and filtering methods. ESVs were clustered into molecular operational taxonomic units (OTUs) at the end of the study period, and we combined α‐ and β‐diversity estimates with metaphylogeographic analyses. Results We uncovered a rich biodiversity, with ca. 27,000 ESVs and 5500 eukaryotic OTUs, with significant β‐diversity variation across the studied factors, in the order parks > communities > years. The patterns of genetic differentiation within OTUs matched those of β‐diversity. A temporal pattern emerged, as the communities' structure changed when comparing the initial and final periods of our monitoring, with a marked decline in richness and diversity. Main Conclusions Biodiversity varied strongly with geography, community type and year, shaping both species turnover and genetic connectivity. Differentiation was evident even at short spatial scales, such as between communities. A concerning loss of diversity was detected over the study period, likely related to global change. We showcased the feasibility and effectiveness of combining metabarcoding with metaphylogeography for monitoring and conservation efforts in marine protected areas and elsewhere.