Dr. Amanda Finger - Associate Director
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 microsatellites. Please see below for more details on some of my projects.
B.S., Ecology and Evolutionary Biology, UC Santa Cruz, 2003
Ph.D., Graduate Group in Ecology, UC Davis, 2012
Research
Development of a hatchery genetic management plan for the conservation of longfin smelt
Conservation genetics and development of management actions for Lahontan cutthroat trout
Developing tools and methods for assessing grandparentage in wild-caught delta smelt
Conservation genetics of lamprey in California
Using genomic data and 10 years of pedigree analysis to understand domestication selection in an intensively managed conservation hatchery for Delta Smelt
Population genetic structure of longfin smelt (Spirinchus thaleichthys) from California to Alaska using RADsequencing
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)
Using RAD-seq to inform the reintroduction of the threatened Paiute cutthroat trout (Oncorhynchus clarkii seleniris)
Vernal Pool fairy shrimp conservation and biodiversity using eDNA
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)
Habibi, Ensieh, Michael R. Miller, Andrea Schreier, Matthew A. Campbell, Tien‐Chieh Hung, Daphne Gille, Melinda Baerwald, and Amanda J. Finger. "Single generation epigenetic change in captivity and reinforcement in subsequent generations in a delta smelt (Hypomesus transpacificus) conservation hatchery." Molecular Ecology (2024): e17449. DOI: 10.1111/mec.17449
Chase, S.N., Davis, B.E., Carson, E.W., Ellison, L., Finger, A.J., Baerwald, M.R. and Hung, T.C., 2024. Evaluating the impact of captive ancestry on the growth and survival of Delta Smelt in a captive environment. Aquaculture Reports, 36, p.102169.
DOI: 10.1016/j.aqrep.2024.102169
LaCava, Melanie EF, Donohue I. M.*, Badger, M. E.*, Hung, T-C., Ellison, L., Rahman, M. M., Kelvas, K., Finger A. J., Carson, E. W. (2024): Assessing captive spawning strategies for supplementation production of Delta Smelt. Transactions of the American Fisheries Society 153, no. 1 129-138. DOI: 10.1002/tafs.10450
Auringer, G.*, Campbell, M. A., Goertler, P. A., & Finger, A. J. (2023). Lampreys in California (Lampetra spp. and Entosphenus spp.): Mitochondrial phylogenetic analysis reveals previously unrecognized lamprey diversity. North American Journal of Fisheries Management, 43(6), 1511-1530. DOI: 10.1002/nafm.10959
LaCava, M. E., Griffiths, J. S., Ellison, L., Carson, E. W., Hung, T. C., Finger, A. J. (2023). Loss of plasticity in maturation timing after ten years of captive spawning in a delta smelt conservation hatchery. Evolutionary Applications, 16(11), 1845-1857. DOI: 10.1111/eva.13611
Ellison, L., Rahman, M. M., Finger, A. J., Sandford, M., Hsueh, C. H., Schultz, A. A., & Hung, T. C. (2023). Size, fecundity and condition factor changes in endangered delta smelt Hypomesus transpacificus over 10 generations in captivity. Aquaculture, Fish and Fisheries, 3(4), 353-365. DOI: 10.1371/journal.pone.0286027
Holmes, A. E.*, Baerwald, M. R., Rodzen, J., Schreier, B. M., Mahardja, B., Finger, A. J. (2024). Evaluating environmental DNA detection of a rare fish in turbid water using field and experimental approaches. PeerJ, 12, e16453.
Kieran Blair SR, Schreier A, Escalona M, Finger AJ, Joslin SEK, Sahasrabudhe R, Marimuthu MPA, Nguyen O, Chumchim N, Morris ER, Mangelson H, Hull J. A chromosome-level reference genome for the Versatile Fairy Shrimp, Branchinecta lindahli. J Hered. 2023 Mar 16;114(1):74-80. doi: 10.1093/jhered/esac057. PMID: 36223244; PMCID: PMC10019023.
Shannon Rose Kieran Blair, Andrea Schreier, Merly Escalona, Amanda J Finger, Shannon E K Joslin, Ruta Sahasrabudhe, Mohan P A Marimuthu, Oanh Nguyen, Noravit Chumchim, Emily Reister Morris, Hayley Mangelson, Joshua Hull, A draft reference genome of the Vernal Pool Fairy Shrimp, Branchinecta lynchi, Journal of Heredity, Volume 114, Issue 1, January 2023, Pages 81–87, https://doi.org/10.1093/jhered/esac056
Baerwald MR, Kwan N, Pien C, Auringer G*, Carson EW, Cocherell DE, Ellison L, Fangue NA, Finger AJ, Gille DA, Hudson H. Captive-reared Delta Smelt (Hypomesus transpacificus) exhibit high survival in natural conditions using in situ enclosures. Plos one. 2023 May 26;18(5):e0286027.
Campbell, M. A., Badger, M. E.*, Buckmaster, N., Starostka, A. B., Hawks, T., & Finger, A. J. (2023) Molecular Phylogenetic and Population Genetic Relationships of a Putative Species of Sucker (Catostomus sp.) from Surprise Valley in the Great Basin, USA. Transactions of the American Fisheries Society. https://doi.org/10.1002/tafs.10407
Campbell, M. A., Habibi, E. H.*, Auringer, G. M.*, Stephens, M., Rodzen, J., Conway, K. W., Finger, A. J. (2023) “Description of a new subspecies of Rainbow Trout (Salmonidae: Oncorhynchus mykiss) from the McCloud River” (In proofing Zootaxa).
Shannon Rose Kieran Blair, Joshua Hull and Merly Escalona et al. The reference genome of the Vernal Pool Tadpole Shrimp, Lepidurus packardi. J. Hered. 2022. Vol. 113(6):706-711. DOI: 10.1093/jhered/esac051
Su, Y.*, Moyle, P. B., Campbell, M. A., Finger, A. J., O’Rourke, S. M., Baumsteiger, J., Miller, M. R. (2022) Population genomic analysis of the speckled dace species complex (Rhinichthys osculus) identifies three evolutionary lineages in California. Transactions of the American Fisheries Society 151(6):695-710. https://doi.org/10.1002/tafs.10388
Habibi, E.*, Miller, M. R., Gille, D., Sanders, L., Rodzen, J., Stephens, M., Finger, A. J. (2022). Genomics Facilitates Evaluation and Monitoring of McCloud River Redband Trout (Oncorhynchus mykiss stonei). Conservation Genetics 23:773–789 https://doi.org/10.1007/s10592-022-01453-7.
Campbell, M. A., Joslin, S. E. K.*, Goodbla, A., Hobbs, J. A., Wilmes, M., Lewis, L. S., & Finger, A. J. (2022). Polygenic Discrimination of Migratory Phenotypes in an Estuarine Forage Fish. G3 Genes|Genomes|Genetics, 12(8), August 2022, jkac133. https://doi.org/10.1093/g3journal/jkac133.
Finger, A. J., Benjamin, A.*, Crookshanks, C., Campbell, M. A., & Sağlam, İ. K. (2022). Broad‐and fine‐scale structure across the distribution of the relict dace (Relictus solitarius) in the Great Basin desert, USA. Conservation Science and Practice, e12672. DOI:10.1111/csp2.12672
Finger, A. J., Gille, D. A., Kwan, N. M. Baerwald, M. R. (2021) Diary of a Wimpy Fish: how to grow up in a conservation hatchery and survive in the real world. Frontiers for Young Minds, Biodiversity, 9(Article 612102). doi: 10.3389/frym.2021.612102
Sağlam, İ. K., Hobbs, J., Baxter, R., Lewis, L. S., Benjamin, A.*, & Finger, A. J. (2021). Genome-wide analysis reveals regional patterns of drift, structure, and gene flow in longfin smelt (Spirinchus thaleichthys) in the northeastern Pacific. Canadian Journal of Fisheries and Aquatic Sciences, 78(12), 1793-1804. https://doi.org/10.1139/cjfas-2021-0005
Kieran, S. R. C.*, Hull, J. M., & Finger, A. J. (2021). Environmental DNA sampling provides new management strategies for vernal pool branchiopods in California. Plos one, 16(4), e0243338. doi.org/10.1371/journal.pone.0243338
Kieran S. R.*, Hull, J. & Finger, A. J. (2019) Using environmental DNA to monitor the spatial distribution of the California Tiger Salamander Ambystoma californiense. Journal of Wildlife Management https://doi.org/10.3996/052019-JFWM-041
Kieran, S. R.*, Joshua Hull, J., & Amanda Finger. (2019) Using Environmental DNA to Monitor Vernal Pool Organisms in California. In: Vernal Pool Landscapes: Past, Present and Future, editors Robert Schlising, Matt Guillams, and Erin Gottschalk Fischer. California State University, Chico.
Mahardja, B., Hobbs, J.A., Ikemiyagi, N., Healey, B., Benjamin, A.*, & Finger, A.J. (2019) Role of freshwater floodplain-tidal slough complex in the persistence of the endangered delta smelt. PLoS ONE 14(1):e0208084. https://doi.org/10.1371/journal.pone.0208084
Lessard, J., Cavallo, B., Anders, P., Sommer, T., Schreier, B., Gille, D., Schreier, A., Finger, A. J., Hung, T-C., Hobbs, J., May, B., Schultz, A., Burgess, O., & Clarke, R. (2018) Considerations for the Use of Captive-Reared Delta Smelt for Species Recovery and Research. San Francisco Estuary and Watershed Science, 16(3):Article 3 https://doi.org/10.15447/sfews.2018v16iss3art3
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. https://doi.org/10.1093/jhered/esy035
Peacock, Mary M, Neville Helen M, & 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. https://doi.org/10.47886/9781934874509.ch10
Benjamin, A., Saglam, I.K., Mahardja, B., Hobbs, J., Hung, T-C., & Finger A.J. (2018) Use of single nucleotide polymorphisms identified backcrossing and species misidentifications among three San Francisco Estuary Osmerids. Conservation Genetics, online. https://link.springer.com/article/10.1007%2Fs10592-018-1048-9
Saglam, I., Prince, D. J., Miller, M. R., Meek, M.H., Neville, H., Peacock, M., Goodbla, A., Mellison, C., Somer, W., May, B. P., & Finger, A. J. (2017) Genomic Analysis reveals genetic distinctiveness of the Paiute cutthroat trout. Transactions of the American Fisheries Society, 146(6). http://dx.doi.org/10.1080/00028487.2017.1356373
Finger, A. J., Schumer G., Benjamin, A., & 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., May, B. P., O’Brian, J., & Finger, A. J. (2016) Conservation genetics of an urban desert fish: the Arroyo Chub (Gila orcuttii) 145(2):277-286. https://doi.org/10.1080/00028487.2015.1121925
Lew, R. M., Finger, A. J., Baerwald, M. R., Goodbla, A., May, B., & Meek, M. H. (2015) Using next-generation sequencing to assist a conservation hatchery: A single-nucleotide polymorphism panel for the genetic management of endangered Delta Smelt. Transactions of the American Fisheries Society, 144(4):767-779. https://doi.org/10.1080/00028487.2015.1037016
LaCava M., Lindberg, J.L., Fisch, K. M., May, B. P. & Finger, A. J. (2015) Spawning behavior of cultured delta smelt (Hypomesus transpacificus) in a Conservation Hatchery. North American Journal of Aquaculture, 77(3): 255-266. http://dx.doi.org/10.1080/15222055.2015.1007192
Finger, A. J. & May, B. P. (2015) Conservation genetics of a desert fish species: The Lahontan tui chub (Siphateles bicolor ssp.). Conservation Genetics, 16:743-758. https://doi.org/10.1007/s10592-015-0697-1
Finger, A. J., Parmenter, S., & May B. P. (2013) Conservation of the Owens Pupfish: Genetic Effects of Multiple Translocations and Extirpations, Transactions of the American Fisheries Society, 142(5):1430-1443. https://doi.org/10.1080/00028487.2013.811097
Finger, A. J., Anderson, E. A., Stephens, M. R., & 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. https://doi.org/10.1139/f2011-075
Finger, A. J. (2010) 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). https://www.whollyh2o.org/wp-content/uploads/2014/08/ConfluenceTuolumneV1.pdf.
Finger, A. J., Stephens, M. R., Clipperton, N. C. & May, B. P. (2009) Characterization of Six Single Nucleotide Polymorphisms Distinguishing Lahontan and Paiute cutthroat trouts. Molecular Ecology Resources, 9:759-763. https://doi.org/10.1111/j.1755-0998.2009.02532.x