Dr. Melinda Baerwald

Position Title
Affiliated Researcher

California Department of Water Resources



Ph.D., Genetics, University of California Davis

BS, Biology, Indiana University


Research Interests

I use tools from population genetics to aid in the conservation of threatened species. Specific current research interests include understanding the genetic basis of traits influenced by selection (e.g., Rainbow Trout disease resistance and migration), linking predation patterns with environmental factors, and evaluating population trends and monitoring protocols for threatened species.


Research Projects

Current Projects

1. Genetic basis of whirling disease resistance in Rainbow Trout: Collaborating with the Colorado Division of Wildlife to genetically determine if stocking efforts to establish a resistant Rainbow Trout lineage in the Colorado River basin are proving successful.

2. Improving monitoring protocols for the Valley Elderberry Longhorn Beetle: We are developing a genetic assay to distinguish the federally threatened Valley Elderberry Longhorn Beetle (VELB) from its unlisted sister taxa, the California Elderberry Longhorn Beetle (CELB). We will use this assay on frass found in elderberry exit holes to provide recommendations to the USFWS for a range-wide VELB monitoring plan.

3. SNP Marker Development and Population Genetic Analysis of the San Fernando Valley Spineflower: The San Fernando Valley Spineflower (SFVS) is a state endangered plant currently restricted to only 45 acres in southern California. We are assessing genetic diversity and investigating population structure within the species to enhance conservation efforts. Additionally, we will assign parentage from controlled greenhouse studies to assess inbreeding coefficients and their correlation with fitness.

4. Association of epigenetic variation with migratory-related phenotype in Rainbow Trout: Examining differential DNA methylation of Rainbow Trout siblings with alternative life history types relating to migration (i.e. steelhead versus resident Rainbow Trout).

Other Recent Projects

  1. San Joaquin River Restoration Project (SJRRP): Provide genetic guidance and research for the SJRRP, a state and federal multi-agency led long-term project, which is restoring water flows to the upper portion of the San Joaquin River and re-establishing salmonids in this previously dewatered region.
  2. Population genetics of the Sacramento Splittail: Project included marker development, estimation of effective population size, taxonomic classification, and individual-based genetic assignment. My role on the project was to oversee contract administration with funding agency and mentor graduate student conducting genetic analyses.
  3. Fish predation patterns in the San Francisco Estuary’s Delta: Collaborating with CA Dept. of Water Resources and Cramer Fish Sciences to detect prey DNA in the gut contents of predatory species. A project goal was to link predation patterns with specific environmental factors influencing predation rates. We initially focused on the invasive Mississippi Silverside’s predation on the threatened Delta Smelt and then extended the predator and prey combinations to over a dozen invasive and native species (e.g., Longfin Smelt, Splittail, White and Green Sturgeon, Chinook Salmon, Rainbow Trout).



Meek MH, Baerwald MR, Stephens MR, Goodbla AM, Miller MR, Tomalty KMH, May B. 2016. Sequencing improves our ability to study threatened migratory species: genetic population assignment in California’s Central Valley Chinook salmon. Ecology and Evolution. DOI: 10.1002/ece3.2493

Schreier BM, Baerwald MR, Conrad JL, Schumer GP, May B. 2016. Examination of predation on early life stage Delta Smelt in the San Francisco Estuary using DNA diet analysis. Transactions of the American Fisheries Society 145(4):723-733.

Baerwald MR, Meek MH†, Stephens MR†, Nagarajan RP, Goodbla AM, Tomalty KMH, Thorgaard GH, May B, Nichols KM. 2016. Migratory-related phenotypic divergence is associated with epigenetic modifications in rainbow trout. Molecular Ecology 25(8):1785-1800. Special issue: Epigenetic Studies in Ecology and Evolution. Photo included on cover. † Contributed equally                        

Brandl SC, Schreier BM, Conrad JL, May B, Baerwald MR. 2016. Generation of quantitative polymerase chain reaction detectability half-lives and comparison of sampling protocols for genetic diet studies of San Francisco Estuary fishes. Transactions of the American Fisheries Society 145(3):441-449.

Verhille C, Dabruzzi T, Cocherell D, Mahardja B*, Feyrer F, Foin T, Baerwald M, Fangue N. 2016. Inter-population differences in salinity tolerance and osmoregulation of juvenile wild and hatchery-born Sacramento splittail. Conservation Physiology 4(1): cov063.

Tomalty KMH, Meek MH, Stephens MR, Rincon G, Fangue NA, May BP, Baerwald MR. 2015. Transcriptional response to acute thermal stress in juvenile chinook salmon determined by RNAseq. G3: Genes | Genomes | Genetics 5: 1335-1349.

Feyrer F, Hobbs J, Acuna S, Mahardja B, Grimaldo L, Baerwald M, Johnson RC, Teh S. 2015. Metapopulation structure of a semi-anadromous fish in a dynamic environment. Canadian Journal of Fisheries and Aquatic Sciences 72(5): 709-721.

Lew RM, Finger AJ, Baerwald MR, Goodbla A, May B, Meek MH. 2015. Using next-gen sequencing to assist a conservation hatchery: A SNP panel for the genetic management of endangered Delta Smelt. Transactions of the American Fisheries Society 144(4): 767-779

Mahardja B, May B, Feyrer F, Coalter R, Fangue N, Foin T, Baerwald MR. 2015. Interannual variation in connectivity and comparison of contemporary effective population size between two splittail (Pogonichthys macrolepidotus) populations in the San Francisco Estuary. Conservation Genetics 16(2): 385-398.

Welsh AB, Baerwald MR, Friday M, May B. 2015. The effect of multiple spawning events on cohort genetic diversity of lake sturgeon (Acipenser fulvescens) in the Kaministiquia River. Environmental Biology of Fishes 98: 755-762.

Brandl S, Schumer G, Schreier BM, Conrad JL, May B, Baerwald MR. 2015. Ten real-time PCR assays for detection of fish predation at the community level in the San Francisco Estuary-Delta. Molecular Ecology Resources 15: 278-284.

Lavretsky P, Schwartz R, Baerwald M, May B. 2014. Developing major histocompatibility markers in a species of concern: the Sacramento Perch Archoplites interruptus. Journal of Fish Biology 85: 1766-1776.

Meek M, Stephens M, Wong A, Tomalty K, May B, Baerwald M. 2014. Genetic characterization of California’s Central Valley Chinook salmon. Ecology 95: 1431.

Tomalty K, Stephens M, Baerwald M, Bork K, Meek M, May B. 2014. Examining the causes and consequences of hybridization during Chinook Salmon reintroductions: using the San Joaquin River as a restoration case study of management options. San Francisco Estuary and Watershed Science 12(2).

Fetherman ER, Winkelman DL, Baerwald MR, Schisler GJ. 2014. Reduced susceptibility and infection severity of age-0 rainbow trout following Myxobolus cerebralis-resistant rainbow trout introduction to the upper Colorado River. PLOS ONE 9(5).

Meek MH, Stephens MR, Tomalty KM, May BP, Baerwald MR. 2014. Genetic considerations for sourcing steelhead reintroductions: investigating possibilities for the San Joaquin River. San Francisco Estuary and Watershed Science 12(1).

Baerwald MR. 2013. Temporal expression patterns of rainbow trout immune-related genes in response to Myxobolus cerebralis exposure. Fish and Shellfish Immunology 35: 965-971.

Baerwald MR, Schreier BM, Schumer G, May B. 2012. Genetic detection of a threatened fish species (delta smelt) in the gut contents of an invasive predator (Mississippi silverside) in the San Francisco Estuary. Transactions of the American Fisheries Society 141:1600-1607.

Mahardja B, May B, Baerwald MR. 2012. Characterization of 36 additional microsatellite loci in splittail (Pogonichthys macrolepidotus) and cross-amplification in five other native Californian cyprinid species. Conservation Genetics Resources 4: 917-921.

Petersen JL, Baerwald MR, Ibarra AM, May B. 2012. A first-generation linkage map of the Pacific lion-paw scallop: initial evidence of QTL for size traits and markers linked to orange shell color. Aquaculture 350-353: 200-209.

Baerwald MR, Schumer G, Schreier B, May B. 2011. TaqMan assays for the genetic identification of delta smelt (Hypomesus transpacificus) and wakasagi smelt (Hypomesus nipponensis). Molecular Ecology Resources 11: 784-785.

Baerwald MR, Petersen JP, Hedrick RP, Schisler GJ, May B. 2011. A major effect quantitative trait locus for whirling disease resistance identified in rainbow trout (Oncorhynchus mykiss). Heredity 106: 920-926.

Meek MH, Baerwald MR, Wintzer AP, May B. 2009. Isolation and characterization of microsatellite loci in two non-native hydromedusae in the San Francisco Estuary: Maeotias marginata and Moerisia sp. Conservation Genetics Resources 1: 205-208.

Pincheira R, Baerwald M, Dunbar JD, Donner DB. 2009. Sall2 is a novel p75NTR-interacting protein that links NGF signaling to cell cycle progression and neurite outgrowth. EMBO Journal 28: 261-273.

Fisch K, Petersen J, Baerwald MR, Pedroia J, May B. 2009. Characterization of 24 microsatellite loci in delta smelt, Hypomesus transpacificus, and their cross-species amplification in two other smelt species of the Osmeridae family. Molecular Ecology Resources 9: 405-408.

Baerwald MR, Feyrer FV, May B. 2008. Distribution of genetically differentiated splittail populations during the non-spawning season. Transactions of the American Fisheries Society 137: 1335-1345.

Baerwald MR, Welsh AB, Hedrick RP, May B. 2008. Discovery of genes implicated in whirling disease infection and resistance in rainbow trout using genome-wide expression profiling. BMC Genomics 9: 37.

Feyrer F, Hobbs J, Baerwald M, Sommer T, Yin QZ, Clark K, May B, Bennett W. 2007. Otolith microchemistry provides information complimentary to microsatellite DNA for a migratory fish. Transactions of the American Fisheries Society 136: 469-476.

Baerwald M, Bien V, Feyrer F, May B. 2007. Genetic analysis reveals two distinct splittail (Pogonichthys macrolepidotus) populations. Conservation Genetics 8: 159-167.

Baerwald MR, May B. 2004. Characterization of microsatellite loci for five members of the minnow family Cyprinidae found in the Sacramento – San Joaquin Delta and its tributaries. Molecular Ecology Notes 4: 385-390.

Gustin JA, Pincheira R, Mayo LD, Ozes ON, Kessler KM, Baerwald MR, Korgaonkar CK, Donner DB. 2004. Tumor necrosis factor activates CRE-binding protein through a p38 MAPK/MSK1 signaling pathway in endothelial cells. American Journal of Physiology – Cell Physiology 286: C547-C555.

Guo DQ, Wu LW, Dunbar JD, Ozes ON, Mayo LD, Kessler KM, Gustin JA, Baerwald MR, Jaffe EA, Warren RS, Donner DB. 2000. Tumor necrosis factor employs a protein-tyrosine phosphatase to inhibit activation of KDR and vascular endothelial cell growth factor-induced endothelial cell proliferation. Journal of Biological Chemistry 275: 11216-11221.

Wu LW, Mayo LD, Dunbar JD, Kessler KM, Baerwald MR, Jaffe EA, Wang D, Warren RS, Donner DB. 2000. Utilization of distinct signaling pathways by receptors for vascular endothelial cell growth factor and other mitogens in the induction of endothelial cell proliferation. Journal of Biological Chemistry 275: 5096-5103.