Molly Stephens

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Assistant Project Scientist

530.754.4155 (office) 530.752.6351 (lab)

UC Davis, Dept. of Animal Science
One Shields Avenue, Davis, CA 95616

Curriculum Vitae


PhD, Ecology 2007 UC Davis

MA, Biology 2001 Sonoma State University

BS, Biology, 1997 Westmont College

Research Interests

Introgressive hybridization between native trout species and introduced hatchery rainbow trout; hybridization dynamics of secondary contact zones; species restoration and reintroduction genetics, threatened and endangered species management.

Research Projects

Hybridization and Conservation genetics of native trout:

Several of my research projects examine native trout species of California using SNP and microsatellite markers to detect and quantify patterns of hatchery rainbow trout introgression. Our studies on California golden trout and Little Kern golden trout evaluate the genetic “purity” of within-basin and out-of-basin transplanted populations, describe introgression patterns on geographic and temporal scales, and examine the genetic consequences of previous intensive watershed-level species restoration efforts for these species. Genetic management plans are also being created to aid the translation of scientific research to adaptive management of these native species. I collaborate with Bjorn Erickson on Kern River rainbow trout projects, examining extant KRRT populations both for conservation and for potential native broodstock development. I also work on Paiute cutthroat trout with Mandi Finger and am continuing some of Rachel Simmons’ work on native redband trout.

San Joaquin River Restoration Project:

This project, funded by California Department of Fish and Game San Joaquin River Restoration Program, supports the creation of management documents related to the planned reintroduction of spring run Chinook salmon to the San Joaquin River; this includes a Hatchery and Genetic Management Plan (an effort led by former graduate student, Karrigan Bork) covering the planned production of fish at the proposed Conservation Hatchery facility, and a Genetic Management Plan (Baerwald et al. 2010), which outlines broader genetic considerations for stock selection and monitoring of reintroduced populations. This project also supports genetic research on San Joaquin salmonid species, including genetic stock identification and genetic monitoring of Chinook salmon using SNP markers, additional SNP marker discovery efforts for run-timing identification in Chinook salmon, RNAseq gene expression analysis of thermal tolerance in Chinook salmon led by graduate student Kat Tomalty, and other developing projects.

Molly stephens grassy field image of a woman working in a field


Teglas, M.B., B.P. May, P.R. Crosbie, M.R. Stephens, and W.M. Boyce. 2005. Genetic structure of the tick Ornithodoros coriaceus (Acari: Argasidae) in California, Nevada and Oregon. Journal of Medical Entomology 42(3):247-253.

Amanda J. Finger, Eric C. Anderson, Molly R. Stephens, Bernard P. May. 2011. Application of a method for estimating effective population size and admixture using diagnostic single nucleotide polymorphisms (SNPs): implications for conservation of threatened Paiute cutthroat trout (Oncorhynchus clarkii seleniris) in Silver King Creek, California. Canadian Journal of Fisheries and Aquatic Sciences. 68(8): 1369-1386.

Finger, A.J., M.R. Stephens, N.W. Clipperton and B. May. 2009. Six diagnostic SNP markers for detecting introgression between cutthroat and rainbow trout. Molecular Ecology Resources. 9:759-763.

Stephens, M.R., N.W. Clipperton, and B.P. May. 2009. Subspecies-informative TaqMan probes for evaluating introgression between native golden trout and introduced rainbow trout. Molecular Ecology Resources. 9:339-343.

Sprowles, A.E., M.R. Stephens, N.W. Clipperton, and B.P. May. 2006. Fishing for SNPs: a targeted locus approach for Single Nucleotide Polymorphism discovery in rainbow trout. Transactions of the American Fisheries Society. 135:1698-1721.

Cordes, J.F., M.R. Stephens, M.A. Blumberg, and B.P. May. 2006. Identifying introgressive hybridization in native populations of California golden trout based on molecular markers. Transactions of the American Fisheries Society. 134:110-128.