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Environmental DNA (eDNA) detection methods can complement traditional biomonitoring to yield new ecological insights in aquatic systems. However, the conceptual and methodological frameworks for aquatic eDNA detection and interpretation were developed primarily in freshwater environments and have not been well established for estuaries and marine environments that are by nature dynamic, turbid, and hydrologically complex. Environmental context and species life history are critical for successful application of eDNA methods, and the challenges associated with eDNA detection in estuaries were the subject of a symposium held at the University of California Davis on January 29, 2020 (https://marinescience.ucdavis.edu/engagement/past-events/edna). Here, we elaborate upon topics addressed in the symposium to evaluate eDNA methods in the context of monitoring and biodiversity studies in estuaries. We first provide a concise overview of eDNA science and methods, and then examine the San Francisco Estuary (SFE) as a case study to illustrate how eDNA detection can complement traditional monitoring programs and provide regional guidance on future potential eDNA applications. Additionally, we offer recommendations for enhancing communication between eDNA scientists and natural resource managers, which is essential for integrating eDNA methods into existing monitoring programs. Our intent is to create a resource that is accessible to those outside the field of eDNA, especially managers, without oversimplifying the challenges or advantages of these methods.

Delta Smelt have collapsed demographically, but little is known about their current genetic status. We used 12 microsatellite loci to evaluate two measures of the effective population size (Ne) of Delta Smelt. Ne is a measure that offers predictive power regarding the loss of genetic diversity in a population over time, as well as the short and long-term genetic risks for loss of fitness resulting from low diversity. We found that the Ne of Delta Smelt is too high to accurately estimate with the data (upper 95% confidence intervals were infinity), but the lower confidence intervals of NeLD (linkage disequilibrium Ne) were above 1,000, while some of the lower confidence intervals of NeV (variance Ne) were below 1,000. We interpret this to indicate that Delta Smelt are not declining because of genetic factors, and are not at immediate risk of losing genetic diversity from low Ne. We caution that these estimates are from a short-term data set estimated from a population that has already been declining for decades, and that it is likely that Delta Smelt have lost diversity. We suggest continuing efforts to maximize abundance to prevent further loss of genetic diversity.

The dynamic Quaternary geology of the Pacific Ring of Fire created substantial challenges for biogeography. Fish life history and population genetic variation were shaped by climate change, repeated formation and subsidence of ice sheets, sea-level change, volcanism and tectonics, isostatic rebound, and now human activities. It is widely recognized in Chinook salmon (Oncorhynchus tshawytscha) that parallel evolution and phenotypic plasticity have obscured range-wide patterns of lifehistory segregation with evolutionary lineage, yet the idea of the lineages themselves persists. We employed a large, internationally standardized, microsatellite data set to explore population structure at coast-wide scale and test for two divergent lineages, whether or not related to life history. We found at least 27 distinct lineages. However, relationships among groups were poorly resolved--essentially a star phylogeny. We found pervasive isolation by distance among groups, complicating cluster analysis. Only in the interior Columbia River (east of the Cascade Mountains) is there a deep genetic bifurcation that supports both the two-lineage hypothesis and the life-history segregation hypothesis. This broad-scale perspective helps reconcile different views of Chinook salmon phylogeography and life-history distribution. La geologie quaternaire dynamique de la ceinture de feu du Pacifique est a l'origine d'importants defis sur le plan biogeographique. Le cycle biologique des poissons et la variabilite genetique de leurs populations ont ete modeles par les changements climatiques, la formation et le retrait repetes de calottes glaciaires, les variations du niveau de la mer, le volcanisme et la tectonique, le relevement isostatique et, aujourd'hui, l'activite humaine. S'il est largement admis que, chez le saumon quinnat (Oncorhynchus tshawytscha), l'evolution parallele et la plasticite phenotypique ont masque des patrons de segregation des cycles biologiques en fonction de la lignee evolutionnaire a la grandeur de l'aire de repartition, la notion des lignees comme telles persiste toutefois. Nous avons employe un grand ensemble de donnees de microsatellites normalisees a l'echelle internationale pour explorer la structure des populations a l'echelle de la cote et verifier s'il y a presence de deux lignees divergentes, reliees ou non au cycle biologique. Nous avons trouve au moins 27 lignees distinctes. Toutefois, les relations entre groupes etaient mal resolues, definissant essentiellement une phylogenie en forme d'etoile. Nous avons observe un isolement par la distance repandu parmi les groupes qui complique l'analyse topologique. Une bifurcation genetique marquee n'a ete observee que dans la partie interieure du fleuve Columbia (a l'est des monts Cascade), ce qui appuie tant l'hypothese de la presence de deux lignees que celle d'une segregation des cycles biologiques. Cette perspective facilite le rapprochement d'opinions divergentes concernant la phylogeographie et la repartition des cycles biologiques du saumon quinnat. [Traduit par la Redaction], Introduction The Quaternary zoogeography of the west coast of North America is especially complicated by the volatile earth history of this region. In particular, euryhaline species such as salmonids, sticklebacks, [...]

Due to the challenges associated with monitoring in riverine environments, unbiased and precise spawner abundance estimates are often lacking for populations of Pacific salmonOncorhynchusspp. listed under the Federal Endangered Species Act. We investigated genetic approaches to estimate the 2009 spawner abundance for a population of Columbia River Chinook SalmonOncorhynchus tshawytschavia genetic mark–recapture and rarefaction curves. The marks were the genotyped carcasses collected from the spawning area during the first sampling event. The second sampling event consisted of a collection of juveniles from a downstream migrant trap located below the spawning area. The parents that assigned to the juveniles through parentage analysis were considered the recaptures, which was a subset of the genotypes captured in the second sample. Using the Petersen estimator, the genetic mark–recapture spawner abundance estimates based on the binomial and hypergeometric models were 910 and 945 Chinook Salmon, respectively. These results were in agreement with independently derived spawner abundance estimates based on redd counts, area-under-the-curve methods, and carcass tagging based on the Jolly–Seber model. Using a rarefaction curve approach, which required only the juvenile offspring sample, our estimate of successful breeders was 781 fish. Our genetic-based approaches provide new alternatives to estimate adult Pacific salmon abundance in challenging environmental conditions or for populations with poor or unknown estimates of precision. Received December 7, 2012; accepted July 17, 2013 [ABSTRACT FROM AUTHOR]