Use of affinity analysis to guide habitat restoration and enhancement for the imperiled delta smelt

Abstract

Habitat restoration efforts in the upper San Francisco Estuary, including the Sacramento-San Joaquin Delta, California, move forward, despite a paucity of information on the environmental requirements of many targeted species. The endemic delta smelt Hypomesus transpacificus, protected under the federal Endangered Species Act, is a primary focus of those efforts despite uncertainties regarding many aspects of its relationship with the estuary’s physical and biotic resources. Here we use time-series data from 4 trawl surveys and data on environmental attributes collected from throughout the delta smelt’s distribution to identify ranges of conditions acceptable to delta smelt for each of 5 environmental attributes: water-body type, temperature, turbidity, salinity, and prey availability. Low turbidity and elevated water temperatures render a large portion of the estuary seasonally unsuitable for delta smelt. Within areas in which water quality is suitable, patterns of delta smelt occurrences indicate that habitat is found in subregions where channels of intermediate depth adjoin shallow water. In certain subregions, conditions are inadequate for at least one of the environmental attributes for periods up to several months. We suggest a habitat-restoration strategy that can achieve adequate habitat conditions for delta smelt regardless of through-Delta flow levels, and which can be carried out at a number of locations, but not necessarily the same locations, during each life stage.

Captive-reared Delta Smelt (Hypomesus transpacificus) exhibit high survival in natural conditions using in situ enclosures

“…Water quality metrics from both study locations generally reflected typical winter/spring conditions (cooler temperatures, increased turbidity, decreased salinity, etc.) in the Estuary during a wet year [61] and fell within ranges consistent with Delta Smelt catches in the field [22,62]. The DWSC site, while being a long, deep channel, is effectively a dead-end slough with higher residence time and flow that is entirely driven by the tides.…”

Identifying Environmental Factors Limiting Recovery of an Imperiled Estuarine Fish

“…To offer guidance to resource managers, we previously analyzed the co-occurrence of delta smelt with several environmental factors, developing "affinity functions" that identified adequate and inadequate environmental factorcondition ranges for delta smelt (Hamilton and Murphy, 2020). Those analyses showed that the factor conditions that are suitable for delta smelt change through its life-stages and that a large portion of the upper estuary experiences habitat conditions that are seasonally unsuitable to delta smelt, and individual delta smelt frequently occupy, actually are relegated to, landscape areas that provide inadequate habitat conditions with respect to one or more essential resources at least some of the time.…”

“…Ranges of adequate conditions for four environmental factors that impact the distribution of delta smelt, drawn from occupancy studies inHamilton and Murphy (2020).…”