Preserving biodiversity is a global challenge requiring data on species' distribution and abundance over large geographic and temporal scales. However, traditional methods to survey mobile species' distribution and abundance in marine environments are often inefficient, environmentally destructive, or resource-intensive. Metabarcoding of environmental DNA (eDNA) offers a new means to assess biodiversity and on much larger scales, but adoption of this approach for surveying whole animal communities in large, dynamic aquatic systems has been slowed by significant unknowns surrounding error rates of detection and relevant spatial resolution of eDNA surveys. Here, we report the results of a 2.5 km eDNA transect surveying the vertebrate fauna present along a gradation of diverse marine habitats associated with a kelp forest ecosystem. Using PCR primers that target the mitochondrial 12S rRNA gene of marine fishes and mammals, we generated eDNA sequence data and compared it to simultaneous visual dive surveys. We find spatial concordance between individual species' eDNA and visual survey trends, and that eDNA is able to distinguish vertebrate community assemblages from habitats separated by as little as ~60 m. eDNA reliably detected vertebrates with low false-negative error rates (1/12 taxa) when compared to the surveys, and revealed cryptic species known to occupy the habitats but overlooked by visual methods. This study also presents an explicit accounting of false negatives and positives in metabarcoding data, which illustrate the influence of gene marker selection, replication, contamination, biases impacting eDNA count data and ecology of target species on eDNA detection rates in an open ecosystem.

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Assessing vertebrate biodiversity in a kelp forest ecosystem using environmental DNA.

Age determination and validation studies of marine fishes: do deep-dwellers live longer?

Spiny lobsters and sea urchins: Analysis of a predator-prey interaction

A monograph on the Isopoda Cymothoidae (Crustacea) of the eastern Pacific

Substantial changes have occurred in assemblages of nearshore reef fishes in the Southern California Bight during the past two decades At two sites off Los Angeles, California, species richness of reef fishes fell 15-25%, and composition shifted from dom- inance by northern to southern species Additionally, by 1993, 95% of the fish species had declined in abundance by an average of 69% Concurrent declines of similar magnitude were observed for several trophic levels of the benthic ecosystem farther north at Santa Cruz Island where populations of surfperches (Pisces: Embiotocidae), the standing stock of their crustacean prey, and the biomass of understory macroalgae all declined by -80% Abundances of fishes fell because declining recruitment of age-0 fish was insufficient to compensate for losses of older age classes Annual levels of recruitment of age-0 fishes at all reefs examined fell more than one order of magnitude over two decades and was correlated among years with a broad indicator of Bight-wide productivity, the biomass of macrozooplankton in the California Current Lower productivity of the coastal marine ecosystem, associated with a climate regime shift in 1976-1977, likely caused large, but unforeseen, impacts on population abundances and trophic structure in nearshore benthic communities

Daniel J. Miller

Papers

Guide to the coastal marine fishes of California