Starting a<scp>DNA</scp>barcode reference library for shallow water polychaetes from the southern European Atlantic coast

<jats:title>Abstract</jats:title><jats:p>Annelid polychaetes have been seldom the focus of dedicated<jats:styled-content style="fixed-case">DNA</jats:styled-content>barcoding studies, despite their ecological relevance and often dominance, particularly in soft‐bottom estuarine and coastal marine ecosystems. Here, we report the first assessment of the performance of<jats:styled-content style="fixed-case">DNA</jats:styled-content>barcodes in the discrimination of shallow water polychaete species from the southern European Atlantic coast, focusing on specimens collected in estuaries and coastal ecosystems of Portugal. We analysed cytochrome oxidase I<jats:styled-content style="fixed-case">DNA</jats:styled-content>barcodes (<jats:styled-content style="fixed-case">COI</jats:styled-content>‐5P) from 164 specimens, which were assigned to 51 morphospecies. To our data set from Portugal, we added available published sequences selected from the same species, genus or family, to inspect for taxonomic congruence among studies and collection location. The final data set comprised 290 specimens and 79 morphospecies, which generated 99 Barcode Index Numbers (<jats:styled-content style="fixed-case">BIN</jats:styled-content>s) within Barcode of Life Data Systems (<jats:styled-content style="fixed-case">BOLD</jats:styled-content>). Among these, 22<jats:styled-content style="fixed-case">BIN</jats:styled-content>s were singletons, 47 other<jats:styled-content style="fixed-case">BIN</jats:styled-content>s were concordant, confirming the initial identification based on morphological characters, and 30 were discordant, most of which consisted on multiple<jats:styled-content style="fixed-case">BIN</jats:styled-content>s found for the same morphospecies. Some of the most prominent cases in the latter category include<jats:italic>Hediste diversicolor</jats:italic>(O.F. Müller, 1776) (7),<jats:italic>Eulalia viridis</jats:italic>(Linnaeus, 1767) (2) and<jats:italic>Owenia fusiformi</jats:italic>s (delle Chiaje, 1844) (5), all of them reported from Portugal and frequently used in ecological studies as environmental quality indicators. Our results for these species showed discordance between molecular lineages and morphospecies, or added additional relatively divergent lineages. The potential inaccuracies in environmental assessments, where underpinning polychaete species diversity is poorly resolved or clarified, demand additional and extensive investigation of the<jats:styled-content style="fixed-case">DNA</jats:styled-content>barcode diversity in this group, in parallel with alpha taxonomy efforts.</jats:p>