Declining wintering shorebird populations at a temperate estuary in California: A 30-year perspective

Worldwide, shorebird populations are declining. Our objectives were to examine abundance trends of shorebirds regularly wintering at Tomales Bay, Marin County, California, accounting for the local effects of rainfall, raptors, and the restoration of part of the bay to tidal wetlands. From November 1989 to February 2019, we conducted 177 comprehensive winter shorebird surveys of Tomales Bay; we averaged 5.7 ± 0.9 (mean ± SD) winter surveys per year. In 30 yr, we counted 1,215,821 shorebirds of 31 species. We used generalized linear models and multi-model inference to evaluate trends in shorebird abundance while accounting for local sources of variation. We conducted separate analyses for 14 species seen in at least 20 of the 30 yr of monitoring and for all shorebird species combined. During the study, the abundance of all species combined declined 66% (52% in the North Bay and 81% in the South Bay) with the most rapid decline in the first 10 yr of monitoring. Of 13 species for which year was in the top model, 10 species decreased in abundance and 3 species increased. Dunlin and Western Sandpiper accounted for the greatest losses in total numbers. The best-supported models to estimate trends in shorebirds included predictors for year and North Bay vs. South Bay. Of the local variables we considered, rainfall was included in 10 of the 15 best-supported models (including all species combined), negatively affecting the numbers of all species except Willets. The wetland restoration project was included in 5 top models, with a short-term positive impact. Raptor abundance was included in 3 top models with mixed results. Our results show that effective conservation and management of local shorebird populations must be linked with regional/global efforts if we are to reverse negative shorebird trends.

Differential Mortality and High Viral Load in Naive Pacific Oyster Families Exposed to OsHV-1 Suggests Tolerance Rather than Resistance to Infection

Pacific oysters, Crassostrea gigas, are one of the most productive aquaculture species in the world. However, they are threatened by the spread of Ostreid herpesvirus-1 (OsHV-1) and its microvariants (collectively “µvars”), which cause mass mortalities in all life stages of Pacific oysters globally. Breeding programs have been successful in reducing mortality due to OsHV-1 variants following viral outbreaks; however, an OsHV-1-resistant oyster line does not yet exist in the United States (US), and it is unknown how OsHV-1 µvars will affect US oyster populations compared to the current variant, which is similar to the OsHV-1 reference, found in Tomales Bay, CA. The goals of this study were to investigate the resistance of C. gigas juveniles produced by the Molluscan Broodstock Program (MBP) to three variants of OsHV-1: a California reference OsHV-1, an Australian µvar, and a French µvar. This is the first study to directly compare OsHV-1 µvars to a non-µvar. The survival probability of oysters exposed to the French (FRA) or Australian (AUS) µvar was significantly lower (43% and 71%, respectively) than to the reference variant and controls (96%). No oyster family demonstrated resistance to all three OsHV-1 variants, and many surviving oysters contained high copy numbers of viral DNA (mean ~3.53 × 108). These results indicate that the introduction of OsHV-1 µvars could have substantial effects on US Pacific oyster aquaculture if truly resistant lines are not achieved, and highlight the need to consider resistance to infection in addition to survival as traits in breeding programs to reduce the risk of the spread of OsHV-1 variants.

First evaluation of resistance to both a California OsHV-1 variant and a French OsHV-1 microvariant in Pacific oysters

Background Variants of the Ostreid herpesvirus 1 (OsHV-1) cause high losses of Pacific oysters globally, including in Tomales Bay, California, USA. A suite of new variants, the OsHV-1 microvariants (μvars), cause very high mortalities of Pacific oysters in major oyster-growing regions outside of the United States. There are currently no known Pacific oysters in the United States that are resistant to OsHV-1 as resistance has yet to be evaluated in these oysters. As part of an effort to begin genetic selection for resistance to OsHV-1, 71 families from the Molluscan Broodstock Program, a US West Coast Pacific oyster breeding program, were screened for survival after exposure to OsHV-1 in Tomales Bay. They were also tested in a quarantine laboratory in France where they were exposed to a French OsHV-1 microvariant using a plate assay, with survival recorded from three to seven days post-infection. Results Significant heritability for survival were found for all time points in the plate assay and in the survival phenotype from a single mortality count in Tomales Bay. Genetic correlations between survival against the French OsHV-1 μvar in the plate assay and the Tomales Bay variant in the field trait were weak or non-significant. Conclusions Future breeding efforts will seek to validate the potential of genetic improvement for survival to OsHV-1 through selection using the Molluscan Broodstock Program oysters. The lack of a strong correlation in survival between OsHV-1 variants under this study’s exposure conditions may require independent selection pressure for survival to each variant in order to make simultaneous genetic gains in resistance.

A reappraisal of the California Roach/Hitch (Cypriniformes, Cyprinidae, Hesperoleucus/Lavinia) species complex

The California Roach (Hesperoleucus symmetricus) and Hitch (Lavinia exilicauda) form a species complex largely endemic to California (CA), USA. Using previous studies of this complex along with a recent comprehensive genomic analysis, we developed a highly supported taxonomic hierarchy of two genera, five species, four subspecies and multiple distinct population segments within two presently recognized species. The genera Lavinia and Hesperoleucus are supported as representing distinct lineages, despite occasional hybridization between them. While hybridization is one pathway to some speciation in this complex, hierarchical levels correlate nicely between genomic results and earlier morphological work. Hesperoleucus symmetricus is newly divided into four species (H. parvipinnis—Gualala Roach, H. mitrulus—Northern Roach, H. venustus—Coastal Roach, and H. symmetricus—California Roach) and two subspecies (H. s. serpentinus—Red Hills Roach, H. s. symmetricus—California Roach). Within H. venustus, two subspecies are identified (H. v. navarroensis—Northern Coastal Roach, and H. v. subditus—Southern Coastal Roach), which are supported by previous morphological studies but resolve discrepancies between those studies. Finally, six distinct population segments are identified within different species/subspecies: Kaweah, Russian River, Navarro River, Monterey, and Tomales Bay. Clear Lake Roach are introgressed between California and Coastal Roach, making them distinct but difficult to formally name. Results should greatly improve management and conservation of each taxonomic entity and help resolve past ambiguities. Additional studies are needed to improve range-wide boundaries and to investigate population structure within all species and subspecies identified in both Lavinia and Hesperoleucus lineages.

Wild Things

A group of sea otters laze at the edge of Elkhorn Slough. They float on their backs in the steel- gray water, paws folded against their chests, gazing at the small boat steered by ecologist Brent Hughes of the University of California– Santa Cruz. Hughes has documented a profound shift in the slough’s ecology, triggered by the otters. Sea otters were nearly driven to extinction by fur hunters in the 1800s, and were gone from Elkhorn Slough for a century. In 1984, when the first sea otters recolonized, Elkhorn Slough’s once bountiful eelgrass beds had dwindled to a few small, scattered patches. Now, more than thirty years after the sea otters’ return, expanding eelgrass beds grow lush beneath the water’s surface, the dense leaves sheltering juvenile fish and feeding an array of invertebrate grazers. The slough, on the central California coast, is one of the most severely polluted estuaries on the planet. Artificial fertilizer applied to 2.69 million acres of farmland in the neighboring Salinas Valley runs into its waters. The excess nutrient load causes eutrophication. It also fuels the growth of epiphytic algae that thrive on the surface of eelgrass leaves, blocking the sunlight the grass needs and smothering whole beds. The problem is common in estuaries around the globe, which receive heavy loads of nutrients from rivers draining polluted watersheds. Seagrass meadows filter contaminants from water and prevent coastal erosion in addition to acting as nurseries for fish and invertebrates. These crucial habitats are disappearing. The global distribution of seagrasses has decreased by 29 percent over the last 140 years, and 58 percent of the surviving seagrass meadows are in decline. Nutrient pollution of coastal waters had long been thought to be the main driver of this trend. But in Elkhorn Slough, the eelgrass has made a remarkable comeback even as pollution loads continued to climb. The mechanism of this welcome ecological shift was unknown until Hughes demonstrated that sea otters are the key. He began to put the pieces of the puzzle together when he went diving in Tomales Bay, an unpolluted estuary to the north. The eelgrass in Elkhorn Slough was lush and green despite intense pollution; in Tomales Bay, where there are no sea otters, the eelgrass was a dull brown, smothering under epiphytic algae.