Amanda (Mandi) Finger, PhD, Associate Director

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Project Scientist
Associate Director, Genomic Variation Lab

ajfinger@ucdavis.edu

(530) 752-6351 twitter @mandifinger

Department of Animal Science, Meyer Hall
One Shields Avenue, Davis, CA 95616

Curriculum Vitae

Education

B.S., Ecology and Evolutionary Biology, UC Santa Cruz, 2003

Ph.D., Graduate Group in Ecology, UC Davis, 2012

Research Interests

I am interested in how populations change over time in a conservation context. I enjoy collaborating with agency biologists and other researchers using a range of molecular tools to understand and manage threatened and endangered species. Some of these species include California native trout, desert fishes, Delta smelt, and longfin smelt. Among the technologies my students and I use are next generation sequencing, SNP assays, and environmental DNA sampling. Please see research interests below for more details on some of my projects.

Research Projects

Current Research

Genetic management of a hatchery population of the Delta smelt (Hypomesus transpacificus)

Vernal Pool fairy shrimp conservation and biodiversity using eDNA

Population genetic structure of longfin smelt (Spirinchus thaleichthys) from California to Alaska using RADsequencing

Ne estimation and monitoring of Delta smelt in the San Francisco Bay-Delta estuary

Using RAD-seq to inform the reintroduction of the threatened Paiute cutthroat trout (Oncorhynchus clarkii seleniris)

Using genomic data and 10 years of pedigree analysis to understand domestication selection in an intensively managed conservation hatchery for Delta Smelt

Genetic structure and diversity within and among Relict Dace (Relictus solitarius) populations (in collaboration with Nevada Department of Wildlife and US  Fish and Wildlife Service

Past Research

Conservation genetics of the Arroyo chub (Gila orcuttii)

Genetic analysis of Lahontan cutthroat trout (Oncorhynchus clarkii henshawi) in the Walker Basin, California and Nevada

Using genetic parentage analysis to examine mating strategies of Delta smelt in a conservation hatchery (in collaboration with the FCCL)

Conservation genetics of the Owens pupfish (Cyprinodon radiosus) (in collaboration with California Department of Fish and Wildlife)

Conservation genetics of the Lahontan tui chub (Siphateles bicolor ssp.) (in collaboration with Nevada Department of Fish and Wildlife)

Publications

In prep/internal review

Benjamin, A., Saglam, I.K., and Finger, A.J. Population genetic structure and variation in an isolated threatened desert fish: the Relict Dace (in preparation).

Mahardja, B., Hobbs, J.A., Ikemiyagi, N., Healey B., Benjamin, A., and Finger, A.J. Role of Freshwater Floodplain-Tidal Slough Complex in the Persistence of the Endangered Delta Smelt (submitted to PLoS ONE)

Finger, A.J., Saglam, I., Baxter, R., Benjamin, A., and Hobbs, J. “Conservation genetics of longfin smelt (Spirhinchus thaleichthys).” (in preparation)

Published

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 Heredity, 109(6):689-699). (pdf)

Peacock, Mary M, Neville Helen M, and Finger, Amanda J. (2018) The Lahontan Basin Evolutionary Lineage of Cutthroat Trout, Special Workshop on Cutthroat Trout Taxonomy. In: P. Trotter, P. Bisson B. Roper and L. Schultz, editors. Cutthroat Trout evolutionary biology and taxonomy. American Fisheries Society Special Publication, Bethesda Maryland.

Benjamin, A., Saglam, I.K., Mahardja, B., Hobbs, J., Hung, T-C., and Finger A.J. (2018) “Use of single nucleotide polymorphisms identified backcrossing and species misidentifications among three San Francisco Estuary Osmerids” Conservation Genetics (pdf)

Saglam, I., Prince, D. J., Ali, O., Miller, M. R., Meek, M.H., Neville, H., Peacock, M. Mellison, C., Somer, W., May, B. P., and Finger, A.J. (2017) Genomic analysis reveals evolutionary distinctiveness of Paiute Cutthroat Trout (Oncorhynchus clarkii seleniris). Transactions of the American Fisheries Society, 146:1291-1302 (pdf)

Finger, A. J., Schumer G., Benjamin, A., and Blankenship S. (2017) Evaluation and interpretation of genetic effective population size of Delta Smelt from 2011-2014. San Francisco Estuary and Watershed Science, 15(2)Article 5. (http://escholarship.org/uc/item/4109064c)

Benjamin, A., O’Brien, J., May, B., and Finger, A. J. (2016) Conservation genetics of an urban desert fish: the Arroyo chub (Gila orcuttii). Transactions of the American Fisheries Society, 145(2):277-286 (pdf)

Lew, R. M., Finger, A. J., Baerwald, M. R., Goodbla, A., May, B. and Meek, M. H. (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, 144:767–779 (pdf)

LaCava M., Lindberg, J.L., Fisch, K. M., May, B. P. and Finger, A. J. (2015) Spawning behavior of cultured delta smelt (Hypomesus transpacificus). North American Journal of Aquaculture 77(3): 255-266. (pdf)

Finger, A. J. and May, B. P. (2015) Conservation genetics of a desert fish species: The Lahontan tui chub (Siphateles bicolor ssp.). Conservation Genetics, 16:743-758. (pdf)

Finger, A. J., Parmenter, S. P. and May, B. P. (2013) Conservation of the Owens Pupfish: Genetic effects of multiple translocations and extirpations. Transactions of the American Fisheries Society 142:1330-1443. (pdf)

Finger, A. J., Anderson, E. A., Stephens, M. R., and May, B. P. (2011) Application of a method for estimating effective population size and admixture using diagnostic SNPs: Implications for conservation of threatened Paiute cutthroat trout in Silver King Creek, California. Canadian Journal of Fisheries and Aquatic Sciences, 68:1369-1386. (pdf)

Finger, A. J., Stephens, M. R., Clipperton, N. C. and May B. P. (2009) Characterization of Six Single Nucleotide Polymorphisms Distinguishing Lahontan and Paiute cutthroat trouts. Molecular Ecology Resources 9:759-763. (pdf)

Finger, A. J., Fishes of the Tuolumne River, book chapter in Confluence v1.0 eds. Jeffrey Mount, Sabra Purdy. University of California press, creative commons licensing. (V. 1.0). http://watershed.ucdavis.edu/tuolumne/resources/ConfluenceTuolumneV1.pdf.