Biology subjects

Jeffres, C.

Publications and source records attributed to Jeffres, C..

5 recordsLinked to original sources

bioRxiv2026

Automated morphometry and weight prediction of juvenile Chinook Salmon leveraging open-source deep learning models

Minimizing handling of threatened and endangered fish has become increasingly important as populations have dwindled. To minimize handling in morphometric measurements, the HandsFreeFishing program has been developed for juvenile Chinook Salmon (Oncorhynchus tshawytscha). By segmenting a 2D image many morphometric measurements are able to be estimated; from these measurements a weight prediction model is built based on fish whose ground truthed weights were measured using a digital scale. While many segmentation methods may be used, here Metas Segment Anything model (SAM) is employed to produce segmentation masks of raw images. This model is open-source and easily used on any image (of any size) with good performance. In the proposed framework, the user supplies a bounding box around a target fish along with minimal orientation data (left or right facing, upside down or right-side up); the rest of the segmentation, feature extraction, and final weight prediction is completely automated. A main goal of the segmentation is to estimate the surface area of the side profile of the fish. Then, assuming an ellipsoidal shape, this surface area can be related to the volume of the fish, which is directly proportional to the weight. Even on a relatively small dataset of 149 images (fork length 27-90mm) our results confirm the predictive qualities of the morphometric features measured. The model achieved weight prediction with a mean absolute error of 0.16 g with a mean absolute percentage error of 12%, and an r-squared value of 0.99, on fish ranging from 0.31g - 7.74g. The raw images come from a variety of fish viewers, the design of which is relatively inexpensive and reproducible, and, in conjunction with the HandsFreeFishing program, allows for minimal handling compared to traditional length and weight measurement methods.

ecology↗

bioRxiv2024

Does method of field preparation affect survival and growth of juvenile Chinook salmon in agricultural floodplains?

There is growing interest to integrate conservation initiatives into agricultural practices using a reconciliation ecology framework. In Californias Central Valley, one approach to improving crucial nursery habitat for threatened and endangered fish species is by re-creating floodplain habitats through the inundation of agricultural fields during the non-growing season. We conducted a series of field experiments in agricultural floodplains (winter-flooded rice fields that were once natural floodplains) to explore whether different field preparation methods enhanced growth and survival of floodplain-dependent fish species. Approximately 8,000 juvenile fall-run Chinook Salmon (Oncorhynchus tshawytscha) were reared for at least 28 days on eight, 0.2 ha experimental fields. Each experimental field represented one of four treatments (two replicates per treatment): addition of large wood, addition of in-field canals, addition of both large wood and in-field canals, and control-where no additional field preparations were implemented beyond standard post-growing practices: i.e., chopping rice into stubble, baling and removing excess rice straw, and discing the field with a single pass by plowing rice straw into the ground to promote decomposition. We found no significant difference in water temperature, fish growth or fish survival among habitat treatments. Across treatments, survival ranged from 50.1%-78.3% and averaged 65.75% (/- 7.89% SE). These findings suggest agricultural floodplains require no additional modifications to promote fish growth and survival. Results illustrate the benefits of integrating working landscapes with conservation initiatives by creating more accessible and beneficial habitat for native fishes.

ecology↗

bioRxiv2023

Foodscapes for Salmon and Other Mobile Consumers in River Networks

Mobile consumers track fluctuating resources across heterogeneous landscapes to grow and survive. In river networks, the abundance and accessibility of food and the costs of foraging vary between habitats and through time, providing a shifting mosaic of growth opportunities for mobile consumers. However, a framework integrating the spatiotemporal dynamics of growth potential within riverscapes has been lacking. Here we present the concept of "foodscapes" to depict the dynamic changes in food abundance, food accessibility, and foraging costs that contribute to spatial and temporal variation of fish growth in rivers. Drawing on case studies of salmonid fishes from Alaska to California, we illustrate that "healthy" foodscapes provide a plethora of foraging opportunities--promoting diverse life history strategies that potentially enhance population stability. We identify knowledge gaps in understanding foodscapes, and approaches for management that focus on restoring trophic pathways which support diverse foraging and growth opportunities for fish in river networks.

ecology↗

bioRxiv2023

Connecting Thiamine Availability to the Microbial Community Composition in Chinook Salmon Spawning Habitats of the Sacramento River Basin

Thiamine Deficiency Complex (TDC) is a major emerging threat to global populations of culturally and economically important populations of salmonids. Salmonid eggs and embryos can assimilate exogenous thiamine, and evidence suggests that microbial communities in benthic environments can produce substantial amounts of thiamine. We therefore hypothesize that microbially produced thiamine in both riverine surface water and hyporheic zones could serve to rescue early life stages of salmonids suffering from TDC. The distributions of thiamine and its metabolically related compounds (dTRCs) have never been determined in freshwater systems. Similarly, the microbial cycling of these compounds has never been investigated. Here we determine that all dTRCs are present in femto-picomolar concentrations across diverse salmon spawning habitats in Californias Sacramento River system. We observed that thiamine concentrations in the Sacramento River are orders of magnitude lower than marine environments, indicating substantial differences in thiamine cycling between these two environments. Our data suggest that the hyporheic zone is likely the source of thiamine to the overlying surface water. Temporal variations in dTRC concentration were observed where highest concentrations were seen when Chinook salmon were actively spawning. Significant correlations were identified between the richness of differentially abundant ASVs and dTRC concentrations. The influence of these ASVs on dTRC concentrations provide evidence of dTRC cycling by microbes in the hyporheic zone, which would influence the conditions where embryonic salmon incubate. Together, these results indicate a connection between microbial communities in freshwater habitats and the availability of thiamine to spawning TDC-impacted California Central Valley Chinook salmon.

microbiology↗

bioRxiv2019

Detrital Food Web Drives Aquatic Ecosystem Productivity in a Seasonally Inundated Managed Floodplain

Differences in basal carbon sources, invertebrate density and salmon growth rate were observed in food webs across a lateral transect of aquatic habitats in the Sacramento River Valley, California. Similar to many large river valleys globally, the Sacramento River Valley has been extensively drained and leveed, hydrologically divorcing most floodplain wetlands and off-channel aquatic habitats from river channels. Today, the former floodplain is extensively managed for agriculture and wildlife habitat. Food web structure and juvenile Chinook Salmon (Oncorhynchus tshawytscha) growth were compared in three aquatic habitat types-river channel, a perennial drainage canal in the floodplain, and agricultural floodplain wetlands, which was seasonally inundated to provide bird and fish habitat during the non-agricultural growth season (late winter). Zooplankton densities on the floodplain wetland were 53 times more abundant, on average, than in the river. Juvenile Chinook Salmon raised on the floodplain wetland grew at mm/day, a rate 5x faster than fish raised in the adjacent river habitat (0.18 mm/day). Mean water residence times calculated for the floodplain agricultural wetland, perennial drainage canal and Sacramento River were 2.15 days, 23.5 seconds, and 1.7 seconds, respectively. Carbon in the floodplain wetland food web was sourced primarily through heterotrophic detrital pathways while carbon in the river was primarily autotrophic and sourced from in situ phytoplankton production. Hydrologic conditions typifying the ephemeral floodplain-shallower depths, warmer water, longer residence times and detrital carbon sources compared to deeper, colder, swifter water and an algal-based carbon source in the adjacent river channel-appear to facilitate the dramatically higher rates of food web production observed in floodplain verses river channel habitats. These results suggest that hydrologic patterns associated with winter flooding provide Mediterranean river systems access to detrital carbon sources that appear to be important energy sources for the production of fisheries and other aquatic resources.

ecology↗