Archived DNA reveals marine heatwave‐associated shifts in fish assemblages

Abstract

Marine heatwaves can drive large‐scale shifts in marine ecosystems, but studying their impacts on whole species assemblages is difficult. Analysis combining microscopic observations with environmental DNA (eDNA) metabarcoding of the ethanol preservative of an ichthyoplankton biorepository spanning a 23 years time series captures major and sometimes unexpected changes to fish assemblages in the California Current Large Marine Ecosystem during and after the 2014–2016 Pacific Marine Heatwave. Joint modeling efforts reveal patterns of tropicalization with increases in southern, mesopelagic species and associated declines in commercially important temperate fish species (e.g., North Pacific Hake [Merluccius productus] and Pacific Sardine [Sardinops sagax]). Data show shifts in fisheries assemblages (e.g., Northern Anchovy, Engraulis mordax) even after the return to average water temperatures, corroborating ecosystem impacts found through multiple traditional surveys of this study area. Our innovative approach of metabarcoding preservative eDNA coupled with quantitative modeling leverages the taxonomic breadth and resolution of DNA sequences combined with microscopy‐derived ichthyoplankton identification to yield higher‐resolution, species‐specific quantitative abundance estimates. This work opens the door to economically reconstruct the historical dynamics of assemblages from modern and archived samples worldwide.

Evaluating Metabarcoding Markers for Identifying Zooplankton and Ichthyoplankton Communities to Species in the Salish Sea: Morphological Comparisons and Rare, Threatened or Invasive Species

“…Those approaches require additional/modified sequencing protocols, which further studies should consider adopting. Our findings highlight the need to adopt protocol adaptations [110,[114][115][116][117] that facilitate quantitative comparisons of sequence proportions with biomass.…”

“…Multiple factors can lead to differences between true biomass estimates and read count data, including those prior to amplification (e.g., mt copy number, DNA extraction efficiency, sampling stochasticity, sample preservation) and others that influence the PCR reaction itself (e.g., PCR biases resulting from primer mismatch, inhibition, and other non-primer-mismatch sources leading to differences in amplification efficiency) [109][110][111][112][113][114][115][116]. For example, a meta-analysis by Piñol et al (2015) [113] found that primer mismatches accounted for 75% of amplification variation in studies.…”

“…For example, a meta-analysis by Piñol et al (2015) [113] found that primer mismatches accounted for 75% of amplification variation in studies. Strategies have been proposed to address amplification biases, aiming to employ a mechanistic framework for quantitative metabarcoding data [110,[114][115][116]. Those approaches require additional/modified sequencing protocols, which further studies should consider adopting.…”