Morphological Discrimination of Genetically Distinct Chinook Salmon Populations: an Example from California's Central Valley

Abstract

AbstractWe compared a length-at-date growth model to truss network (morphometric) models for classifying emigrating juvenile (age 0 through age 1) California Central Valley Chinook Salmon Oncorhynchus tshawytscha to three genetically identified races at upstream (salmon generally younger and smaller) and downstream (salmon generally older and larger) monitoring stations. Morphometric models including capture date and head to standard length ratio performed better than the growth model at distinguishing genetically assigned fall-run and late fall-run juveniles; prediction accuracy increased from 54.6% to 63.8% for upstream salmon and from 17% to 73% for downstream salmon. The growth model may over inflate downstream estimates of federally listed Chinook Salmon by misidentifying fall and late-fall runs (nonlisted) as winter and spring runs (both listed) as much as 83% of the time. Morphometric models did not improve run assignment for the listed runs; the growth model outperformed morphometric models at downstream stations. Morphometric models including head shape and sample date had similar accuracy measures to models, including multiple fish measurement ratios, suggesting head shape is the strongest predictor of the juvenile Central Valley Chinook Salmon race. Our results indicate morphometric modeling can improve identification of nonlisted juvenile Central Valley Chinook Salmon from federally listed runs, potentially benefitting monitoring, water management, and protection of sensitive species.

Received May 5, 2014; accepted August 13, 2014

ACKNOWLEDGMENTS

This project was funded by the U.S. Department of Interior, Bureau of Reclamation (BOR) contract number 09PG200118. We thank B. Beckett, N. Buckmaster, K. Martens, and C. Watry for field data collection and image analysis; V. Apkenas, C. Columbus, and E. Crandall for help with genetic sample processing and data collection; California Department of Fish and Wildlife staff for collecting physical data, genetic samples, and images from individual Chinook Salmon captured at the Knights Ferry rotary screw trap; and BOR staff for data and samples from fish captured at the Tracy Fish Collection Facility. We thank R. Johnson and three anonymous reviewers for substantial constructive reviews, which significantly improved this manuscript.