4440 Mountain Laurel Circle Phone: (916) 425-4569

M. Baerwald CV 1 4440 Mountain Laurel Circle Phone: (916) 425- 4569 Collegeville, PA 19426 [email protected]

EDUCATION Ph.D. Genetics. University of California, Davis. 2007 B.S. Biology. Indiana University, Bloomington. 1997

PROFESSIONAL EXPERIENCE Assistant Project Scientist, University of California, Davis 2010 – present  Design, conduct, and analyze studies pertaining to fish ecology, disease, diet analysis, and population structure  Authored/co-authored 22 peer-reviewed scientific publications in past six years  Served as primary research mentor for two graduate students and supervised activities of laboratory technician Postdoctoral Fellow, University of California, Davis 2007 – 2010  Studied whirling disease resistance in rainbow trout  Mentored three graduate and two undergraduate students in research activities  USDA Animal Genome postdoctoral fellowship Graduate Researcher, University of California, Davis 2002 – 2007  Dissertation research to assess the Sacramento Splittail population genetics  Completed graduate coursework, maintaining 4.0 GPA  Safety officer for laboratory with 15-20 researchers Molecular Biologist, Dow AgroSciences, Indianapolis, IN 1999 – 2002  Constructed over 200 recombinant vectors and codon-biased four antibody genes for biopharmaceutical development  Supervised daily laboratory activities of three contract employees Research Technician, Walther Oncology Center, Indianapolis, IN 1997 – 1999  Identified proteins in signal transduction pathways implicated in cancer progression  Laboratory equipment maintenance and supply ordering M. Baerwald CV 2 RESEARCH FUNDING US Fish and Wildlife Service, Co-PI, $200,000 2015 – 2017 Using fecal DNA survey protocols to optimize traditional exit hole surveys and increase detection rates for Valley Elderberry Longhorn Beetle

Interagency Ecological Program, Co-PI, $127,550 2015 – 2016 Methods development for environmental DNA surveying of the wild Delta Smelt population Colorado State University, PI, $81,000 2014 – 2016 Genetic monitoring of rainbow trout lineages in Colorado rivers CALFED Ecosystem Restoration Program, Co-PI, $730,307 2012 – 2016 Linking habitat and spatial variability to native fish predation CA Department of Water Resources, PI, $92,320 2013 – 2015 Characterizing the predation threat of Mississippi silversides to larval native fishes Delta Science Program, PI, $600,000 2011 – 2015 Understanding the scale and mechanisms of connectivity between splittail populations and the implications for management State and Federal Contractors Water Agency, PI, $112,000 2011 – 2014 Patterns of distribution, habitat use, and predation on delta smelt in the north Delta Colorado State University, PI, $42,000 2012 – 2013 Genetic identification of specific rainbow trout lineages in Colorado rivers Colorado Division of Wildlife, PI, $38,839 2012 – 2013 Genetic discrimination of Hofer and Harrison Lake rainbow trout lineages in Colorado California Department of Fish & Game, Co-PI, $2,039,692 2008 – 2013 Salmonid genetics research and management planning - San Joaquin River Colorado Parks and Wildlife, PI, $5,000 2012 Using RAD-seq to identify rainbow trout strain-specific SNP markers Colorado State University, PI, $35,002 2011 – 2012 Genetic identification of Hofer lineage rainbow trout in Colorado Interagency Ecological Program, Co-PI, $139,891 2010 – 2012 Using genetic techniques to detect Mississippi silverside predation on larval delta smelt Colorado Division of Wildlife, PI, $37,708 2010 – 2011 M. Baerwald CV 3 Genetic identification of Hofer lineage rainbow trout in Colorado

PEER-REVIEWED PUBLICATIONS (*mentored undergraduate or graduate student) 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. 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. M. Baerwald CV 4 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. M. Baerwald CV 5 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. LIMITED DISTRIBUTION PUBLICATIONS Stephens M, Erickson B, Schreier A, Tomalty K, Baerwald M, May B, Meek M. 2013. Genetic management plan for California Golden Trout. 73 pgs. Scientific genetic management plan for the US Fish and Wildlife Service. Meek M, Stephens M, Baerwald M, Tomalty K, May B. 2012. San Joaquin River steelhead genetic considerations, 33 pgs. Genetic advisory document for the CA Dept. of Fish and Wildlife. Tomalty K*, Stephens M, Baerwald M, Bork K, Meek M, May B. 2012. Genetic considerations for fall-run Chinook salmon during the San Joaquin River Restoration. 27 pgs. Genetic advisory document for the CA Dept. of Fish and Wildlife. Baerwald MR, Stephens MR, Bork KS, Meek MH, Tomalty K, May B. 2011. Spring-run Chinook salmon genetic management plan – San Joaquin River Restoration Program. 118 pgs. Scientific genetic management plan for the CA Dept. of Fish and Wildlife. http://dx.doi.org/10.6084/m9.figshare.801104 Sommer T, Reece K, Feyrer F, Brown R, Baerwald M. 2010. Splittail persistence in the Petaluma River. Interagency Ecological Program Newsletter 23: 7-8.

FELLOWSHIPS AND AWARDS Postdoctoral Fellowship: USDA NRICGP (Animal Genome), $125,000 2008 – 2010 Travel Awards: Plant and Animal Genomics Aquaculture Group, UC Davis 2006 – 2009 Postdoctoral Scholars Association, UC Davis Graduate Student Association, James E. Wright Graduate Award, $3,800 Graduate Scholarships: Marin Rod and Gun Club, Golden West Women 2005 – 2007 Flyfishers Foundation, Matthew Clow Fund, $4,500 Graduate Fellowships: UC Davis Wildlife Health Center, UC Davis Animal 2003 – M. Baerwald CV 6 2006 Science Dept. Hart, Cole and Goss, UC Davis Animal Science Dept. McOmie, UC Davis Graduate Research Mentorship, $35,000 and tuition waivers Research Awards: UC Davis Jastro Shields, Dow AgroSciences Increasing 1997 – 2005 the Slope Award, Indiana Univ. Undergraduate Research Award, $10,500

SELECT CONFERENCE PRESENTATIONS (from 53 total; *mentored student) Meek M, Baerwald M, Stephens M, Goodbla A, Miller M, Tomalty K*, May B. 2015. Protecting life history diversity: Using genomics to aid conservation of imperiled salmon. 100th Annual Ecological Society of America Meeting. Baltimore, MD. Oral presentation. Baerwald M, Meek M, Goodbla A, Nagarajan R, Tomalty K*, May B, Nichols K, Stephens M. 2014. Epigenetic modifications are associated with propensity to migrate in rainbow trout. American Genetics Association Annual Symposium. Seattle, WA. Oral presentation. Baerwald M, Fangue N, Foin T, Mahardja B*, Feyrer F. 2014. Integrating genetics, physiology, and modeling to understand the scale and mechanisms of minnow population connectivity in a stochastic environment. 144th Annual American Fisheries Society Meeting. Quebec City, Canada. Poster presentation. Baerwald M, Meek M, Nagarajan R, Stephens M, Goodbla A, Tomalty K*, Nichols K, May B. 2013. The role of epigenetic regulation in rainbow trout migration using large-scale DNA methylation profiling. Evolution Conference, Snowbird, UT. Oral presentation. Tomalty K*, Meek M, Stephens M, Fangue N, May B, Baerwald M. 2013. Transcriptional profiling to assess Chinook salmon adaptation to thermal stress in the southern edge of the species range. Evolution Conference, Snowbird, UT. Oral presentation. Meek M, Baerwald M, Stephens M, Goodbla A, Miller M, Tomalty K, May B. 2013. Conservation genomics of Central Valley Chinook salmon. Ecological Society of America 98th Annual Meeting, Minneapolis, MT. Oral presentation Baerwald MR, Meek MH, Tomalty KM, Stephens MR, Goodbla A, May BP. 2012. New genetic tools and their research applications for Central Valley Chinook salmon. Bay-Delta Science Conference, Sacramento, CA. Poster presentation. Mahardja B*, May B, Feyrer F, Baerwald M. 2012. Comparison of effective population sizes for the two splittail populations in the San Francisco Estuary. Bay-Delta Science Conference, Sacramento, CA. Oral presentation. Brandl S*, Schreier B, Conrad JL, Baerwald M. 2012. Persistence of delta smelt DNA in the gut of Mississippi silversides and other preliminary experiments for detecting prey in non- native fish stomachs using real-time PCR. Bay-Delta Science Conference, Sacramento, CA. Oral presentation. Tomalty KM*, Stephens MR, Fangue NA, Rincon G, Meek MH, May BP, Baerwald MR. 2012. Transcriptome response to acute thermal stress in juvenile Chinook salmon. Coastwide Salmonid Genetics Meeting, Davis, CA. Oral presentation. Baerwald M, Petersen J, Hedrick R, Schisler G, May B. 2011. Are we stocking resistance? Genetic detection of a resistant rainbow trout strain lineage in whirling disease infected waters. Plant and Animal Genome XIX, San Diego, CA. Oral presentation. M. Baerwald CV 7 TEACHING EXPERIENCE Instructor, Ursinus College, Issues in Ecology and Evolution Laboratory 2015  Instructed 31 undergraduate students in field and laboratory methods focused on applying the scientific method and quantitative analyses to topics in Ecology and Evolution  Mentoring of Teaching Assistant Instructor, UC Davis, Molecular Methods in Conservation Genetics Course 2008  Co-developed and co-instructed course for 15 undergraduate students to provide working knowledge of common molecular techniques used to answer ecological questions  Format: lecture and student discussions to understand the conceptual basis of techniques, along with hands-on laboratory exercises Guest Lecturer 2006 – 2015  Invited guest lecturer for two courses at UC Davis (Ecological Genetics, Population Genetic Software) and two courses at SUNY Oswego (Conservation Biology, Evolution) Teaching Workshop Series Certification, UC Davis 2006  Topics: Theories of Teaching, Teaching and Learning Styles, Alternative Assessment Techniques, Hot Topics Facing Teachers, Teaching Philosophy Teaching Assistant, UC Davis Genes and Gene Expression Course 2004  Led discussion sections and held office hours, created concept-based exam questions, held review sessions, and graded exams. Class size: 300 students

MENTORING EXPERIENCE  Research mentor of a Masters student (B. Mahardja) in UC Davis Graduate 2011 – 2013 Group in Ecology  Research mentor of two Ph.D. students (S. Brandl and K. Tomalty) in UC 2009 – 2016 Davis Integrative Genetics and Genomics Graduate Group

 Trained three undergraduate students, eight graduate students, and three post- 2003 – 2014 doctoral fellows at UC Davis in a variety of molecular techniques and analyses  Supervised daily activities of two full-time and three contact employees at 1999 – 2002 Dow AgroSciences

SERVICE Professional Contributions Reviewer 2007 – present Manuscripts: PNAS USA, Journal of Molecular Evolution, Heredity, BMC Genomics, G3: Genes | Genomes | Genetics, Conservation Genetics, BMC Genetics, Molecular Ecology, Molecular Ecology Resources, Science for the Total Environment, Fisheries, Transactions of the American Fisheries Society, Journal of Fish M. Baerwald CV 8 Biology, Journal of Parasitology Proposals: National Geographic Society, National Science Foundation (DEB ad-hoc, IOS panel member), Great Lakes Fishery Commission, Austrian Science Fund, Washington Sea Grant Awards: James Wright Genetic Travel Award

Advisory group member 2008 – present Interagency Ecological Program Work Teams: Salmonid and Resident Fishes

Meeting co-organizer 2012 Coastwide Salmonid Genetics Meeting, UC Davis Conference session moderator 2014 American Fisheries Society Conference, trout session, Quebec, Canada

University Contributions Thesis committee member for MS student in Graduate Group in Ecology 2011 – 2013 Academic advising committee member for MS student in Graduate Group 2011 – 2013 in Ecology Session chair for Undergraduate Research, Scholarship, and Creative Activities 2010 Conference at UC Davis Genetics Graduate Group Admissions Committee member 2007 Genetics Graduate Group Seminar Series organizer 2005 – 2006 UC Davis Dept. of Animal Science Advancement Committee member 2005 – 2006

Community Contributions Organizer of Genomic Variation Laboratory Picnic Day Exhibit at UC Davis 2011 – 2012 High school outreach: Presented research findings and interacted with students 2007, 2010 enrolled in Davis High School's Biotechnology Program and Casa Grande High School's Salmon Hatchery Program