PreprintArticleVersion 2Preserved in Portico This version is not peer-reviewed
Evaluating Metabarcoding Markers for Identifying Zooplankton and Ichthyoplankton Communities to Species in the Salish Sea: Morphological Comparisons and Rare, Threatened or Invasive Species
Version 1
: Received: 4 October 2023 / Approved: 5 October 2023 / Online: 5 October 2023 (07:49:54 CEST)
Version 2
: Received: 14 November 2023 / Approved: 15 November 2023 / Online: 15 November 2023 (10:01:49 CET)
Stepien, C.A.; Schultz, H.K.; McAllister, S.M.; Norton, E.L.; Keister, J.E. Evaluating Metabarcoding Markers for Identifying Zooplankton and Ichthyoplankton Communities to Species in the Salish Sea: Morphological Comparisons and Rare, Threatened or Invasive Species. DNA2024, 4, 1-33.
Stepien, C.A.; Schultz, H.K.; McAllister, S.M.; Norton, E.L.; Keister, J.E. Evaluating Metabarcoding Markers for Identifying Zooplankton and Ichthyoplankton Communities to Species in the Salish Sea: Morphological Comparisons and Rare, Threatened or Invasive Species. DNA 2024, 4, 1-33.
Stepien, C.A.; Schultz, H.K.; McAllister, S.M.; Norton, E.L.; Keister, J.E. Evaluating Metabarcoding Markers for Identifying Zooplankton and Ichthyoplankton Communities to Species in the Salish Sea: Morphological Comparisons and Rare, Threatened or Invasive Species. DNA2024, 4, 1-33.
Stepien, C.A.; Schultz, H.K.; McAllister, S.M.; Norton, E.L.; Keister, J.E. Evaluating Metabarcoding Markers for Identifying Zooplankton and Ichthyoplankton Communities to Species in the Salish Sea: Morphological Comparisons and Rare, Threatened or Invasive Species. DNA 2024, 4, 1-33.
Abstract
Zooplankton and ichthyoplankton community assessments depend on species diagnostics, yet morphological identifications are time consuming, require taxonomic expertise, and are hampered by lack of diagnostic characters –particularly for larval stages. Metabarcoding can identify multiple species in communities from short DNA sequences in comparison to reference databases. To evaluate species resolution across phylogenetic groups and food webs of zooplankton and ichthyoplankton, we compare five metabarcode mitochondrial (mt)DNA markers from gene regions of (a)cytochrome c oxidase subunit I, (b) cytochrome b, (c) 16S ribosomal RNA, and (d) 12S ribosomal RNA for DNA extracted from net tows in the Northeastern Pacific Ocean’s Salish Sea across seven sites and two seasons. Species resolved by metabarcoding are compared to invertebrate morphological identifications and biomass estimates. Results indicate that species resolution for different zooplankton and ichthyoplankton taxa can markedly vary among gene regions and markers, and in comparison to morphological identifications. Thus, researchers seeking “universal” metabarcoding should take caution that several markers and gene regions likely will be needed; all will miss some taxa and yield incomplete overlap. Species resolution requires careful attention to taxon marker selection and coverage in reference sequence repositories. In summary, combined multi-marker metabarcode and morphological approaches improve broadscale zooplankton diagnostics.
Biology and Life Sciences, Ecology, Evolution, Behavior and Systematics
Copyright:
This is an open access article distributed under the Creative Commons Attribution License which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
Commenter: Carol Stepien
Commenter's Conflict of Interests: Author