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Diagnostic SNPs to Detect Hybridization Between Delta Smelt, Longfin Smelt, and Wakasagi Smelt

Diagnostic SNPs to Detect Hybridization Between Delta Smelt, Longfin Smelt, and Wakasagi Smelt

A map of Spring Kodiak Trawl sample sites in the San Francisco Bay Delta

Background and Significance of Study

The Delta Smelt (Hypomesus transpacificus) and Longfin Smelt (Spirinchus thaleichthys) are two threatened osmerid species native to the San Francisco Estuary (SFE). They have experienced steep declines since the 1980s, most notably attributed to habitat modifications, entrainment in water divisions, and changes in the estuary’s biota. Both species are subject to intensive monitoring efforts that rely on morphological identifications. However, these identifications can be challenging due to damage and decomposition of fish caught in traps as well as the co-occurrence of a closely related introduced fish, the Wakasagi (Hypomesus nipponensis). Field differentiation of Delta Smelt and Wakasagi is particularly difficult because of their morphological similarity during early life stages and their capacity for hybridization.

We are seeking to improve current species identification methods by using restriction site-associated DNA sequencing (RAD-seq) to develop a SNP marker panel for identifying Delta Smelt, Longfin Smelt, Wakasagi, and their hybrid progeny. We will use this SNP panel on a group of osmerids collected in the Yolo Bypass (where Wakasagi have been detected with increasing frequency) to detect hybrids and quantify the accuracy of morphological species identifications. Our goal is that this SNP panel will constitute an accurate, efficient, and cost-effective resource to complement traditional survey methods in the SFE.


Department of Water Resources

Ismail Saglam, Koc University

Fish Conservation and Culture Laboratory

When every fish counts - UC Davis press release from February 21, 2018

Resulting Paper

Finger, A.J., Mahardja, B.M., Benjamin, A., Lindberg, J., Ellison, L., Fisch, K., Hung, T-C., May, B.P. (2018) Evidence of domestication selection in a conservation hatchery for Delta Smelt. Journal of Heredity109(6):689-699). (pdf)

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