Carson Jeffres

Ephemeral floodplain habitats provide best growth conditions for juvenile Chinook salmon in a California river

We reared juvenile Chinook salmon for two consecutive flood seasons within various habitats of the Cosumnes River and its floodplain to compare fish growth in river and floodplain habitats. Fish were placed in enclosures during times when wild salmon would naturally be rearing in floodplain habitats. We found significant differences in growth rates between salmon reared in floodplain and river enclosures. Salmon reared in seasonally inundated habitats with annual terrestrial vegetation experienced higher growth rates than those reared in a perennial pond on the floodplain. Growth of fish in the non-tidal river upstream of the floodplain varied with flow in the river. When flows were high, there was little growth and high mortality, but when the flows were low and clear, the fish grew rapidly. Fish displayed very poor growth in tidally influenced river habitat below the floodplain, a habitat type to which juveniles are commonly displaced during high flow events due to a lack of channel complexity in the main-stem river. Overall, ephemeral floodplain habitats supported higher growth rates for juvenile Chinook salmon than more permanent habitats in either the floodplain or river. Variable responses in both growth and mortality, however, indicate the importance of providing habitat complexity for juvenile salmon in floodplain reaches of streams, so fish can find optimal places for rearing under different flow conditions.

RAD Capture (Rapture): Flexible and Efficient Sequence-Based Genotyping

Massively parallel sequencing has revolutionized many areas of biology, but sequencing large amounts of DNA in many individuals is cost-prohibitive and unnecessary for many studies. Genomic complexity reduction techniques such as sequence capture and restriction enzyme-based methods enable the analysis of many more individuals per unit cost. Despite their utility, current complexity reduction methods have limitations, especially when large numbers of individuals are analyzed. Here we develop a much improved restriction site-associated DNA (RAD) sequencing protocol and a new method called Rapture (RAD capture). The new RAD protocol improves versatility by separating RAD tag isolation and sequencing library preparation into two distinct steps. This protocol also recovers more unique (nonclonal) RAD fragments, which improves both standard RAD and Rapture analysis. Rapture then uses an in-solution capture of chosen RAD tags to target sequencing reads to desired loci. Rapture combines the benefits of both RAD and sequence capture, i.e., very inexpensive and rapid library preparation for many individuals as well as high specificity in the number and location of genomic loci analyzed. Our results demonstrate that Rapture is a rapid and flexible technology capable of analyzing a very large number of individuals with minimal sequencing and library preparation cost. The methods presented here should improve the efficiency of genetic analysis for many aspects of agricultural, environmental, and biomedical science.

When Good Fish Make Bad Decisions: Coho Salmon in an Ecological Trap

Abstract Coho salmon Oncorhynchus kisutch are a threatened species in California. In the Shasta River, they may be caught in an ecological trap that is exacerbating their decline. Adults appear to have equal preferences for spawning habitat that reduces the survival of their young and that of apparently similar quality where survival would be more likely. The primary cause of juvenile mortality is water withdrawals, which degrade summer water quality and create barriers to movement to habitats with more suitable rearing conditions. The situation has been exacerbated by the addition of gravel to support spawning fall-run Chinook salmon O. tshawytscha, creating habitat that is also attractive to spawning coho salmon in locations where juvenile coho salmon survival will be extremely low. The Shasta River acts as a conceptual model of how habitat degradation and ecologically naive restoration actions may combine to create severe ecological traps for nontarget species. Received March 10, 2011; accepted October...

Floodplain farm fields provide novel rearing habitat for Chinook salmon

When inundated by floodwaters, river floodplains provide critical habitat for many species of fish and wildlife, but many river valleys have been extensively leveed and floodplain wetlands drained for flood control and agriculture. In the Central Valley of California, USA, where less than 5% of floodplain wetland habitats remain, a critical conservation question is how can farmland occupying the historical floodplains be better managed to improve benefits for native fish and wildlife. In this study fields on the Sacramento River floodplain were intentionally flooded after the autumn rice harvest to determine if they could provide shallow-water rearing habitat for Sacramento River fall-run Chinook salmon (Oncorhynchus tshawytscha). Approximately 10,000 juvenile fish (ca. 48 mm, 1.1 g) were reared on two hectares for six weeks (Feb-March) between the fall harvest and spring planting. A subsample of the fish were uniquely tagged to allow tracking of individual growth rates (average 0.76 mm/day) which were among the highest recorded in fresh water in California. Zooplankton sampled from the water column of the fields were compared to fish stomach contents. The primary prey was zooplankton in the order Cladocera, commonly called water fleas. The compatibility, on the same farm fields, of summer crop production and native fish habitat during winter demonstrates that land management combining agriculture with conservation ecology may benefit recovery of native fish species, such as endangered Chinook salmon.

Application of Passive Integrated Transponder Technology to Juvenile Salmon Habitat Use on an Experimental Agricultural Floodplain

AbstractPassive integrated transponder (PIT) technology allows passive, individual identification of small fish, making it a potentially useful tool to address an information gap of juvenile salmon habitat use in off-channel environments. We investigated the combined use of field enclosures and PIT technology as a method for studying the habitat preference of juvenile Chinook Salmon Oncorhynchus tshawytscha on a flooded rice field, a potential surrogate for lost floodplain habitat. We stocked two field enclosures (182 m2) with 42 juvenile salmon. One enclosure had equal portions of rice stubble, disced, and fallow habitat treatments, and the second contained only the disced treatment. Fish were tagged with 8- or 12-mm-sized PIT tags, and generated approximately 1 million detections in each enclosure over 14 d. We used a condensing procedure to reduce the data volume while preserving habitat use patterns. The smaller 8-mm tags were only detected along antenna edges, and the 12-mm tags had broader but more ...

Seasonal aquatic macrophytes reduce water temperatures via a riverine canopy in a spring-fed stream

Maximum water temperatures in streams throughout the western USA typically occur in late summer and early autumn, coinciding with low stream flow. However, in the spring-fed Big Springs Creek in northern California, where constant-temperature groundwater springs provide relatively stable stream flow throughout the year, peak water temperatures and maximum diurnal variability occur in spring. We attribute this anomaly to the riverine canopy provided by emergent aquatic macrophytes (e.g., Polygonum hydropiperoides and Nasturtium officinale), which mimics the shade function of a riparian canopy. Macrophyte biomass increased 264% between January and August 2011. This increase coincided with a 111% reduction in flow velocity and a 53% increase in stream depth. Solar radiation was reduced by an average of 88% in patches of macrophytes that covered ~50% of the water surface during the summer. Decreased solar radiation reduced rates of stream heating, maximum temperatures, and temperature variability. We tested the riverine canopy hypothesis analytically based on a 2-dimensional hydrodynamic and water-temperature model. The model predicted that emergent aquatic macrophytes reduce maximum water temperatures by an average of 5.1°C (p < 0.001) during late summer, when water temperatures in northern California streams typically increase. Our study shows the influence of a riverine canopy on naturally occurring temporal patterns of water temperature in a spring-fed stream. Our results could inform basin-scale management or regulatory strategies to address water-temperature conditions.