Campus Directory

Division Physical & Biological Sciences Division

Department/College/Unit IMS-Fisheries Collaborative Program

Title Project Scientist

Affiliation Staff

Staff Type Researcher

Web Site

Primary Office Location Remote work location
Southwest Fisheries Science Center, Santa Cruz, Room 254-F

Office Hours for Students/ Office Hours contact via email

Mail Stop NMFS

Research Interests

• Applying genetic methods to conserve and manage at-risk species

• Use of next-gen sequencing for understanding expressed phenotypes

• Identification of the genes responsible for life-history variation in salmonids

• Exploring eco-evolutionary processes with whole-genome data

Selected Publications

Anderson, EC, NF Thompson, AJ Clemento, C Columbus, E Campbell, AK Beulke & JC Garza. The genetic architecture of ecotypic differentiation in Chinook salmon of the California Central Valley. bioRxiv:2025.07. 26.666848. 

Hernandez, KM, AJ Clemento, JE Linossier, DE Crocker, DP Costa, C Reichmuth & JC Garza. 2025. Microhaplotype methods enable relationship inference in a bottlenecked mammalian species. Animal Conservation. 29(2):136-145.

Anderson, EC, AJ Clemento, MA Campbell, DE Pearse, A Beulke, C Columbus, E Cambell, NF Thompson & JC Garza. 2025. A multipurpose microhaplotype baseline for genetic analysis of California Chinook salmon. Evolutionary Applications. 18(5):e70110.

Pregler, KC, AJ Clemento, M Grill, P Adelizi, SM Carlson, JC Garza. 2024. Reintroduction of spring-run Chinook salmon in the San Joaquin River: Evaluating genetic and phenotypic effects of captive breeding. Conservation Science and Practice. 6(9):e13176.

Waters, CD, AJ Clemento, T Aykanat, JC Garza, KA Naish, S Narum and CR Primmer. 2021. Heterogeneous genetic basis of age at maturity in salmonid fishes. Molecular Ecology. 30(6):1435- 1456.

Thompson, NF, EC Anderson, AJ Clemento, MA Campbell, DE Pearse, JW Hearsey, AP Kinziger and JC Garza. 2020. A complex phenotype in salmon controlled by a simple change in migratory timing. Science. 370(6516):609-613.

Baetscher, DS, AJ Clemento, TC Ng, EC Anderson and JC Garza. 2017. Microhaplotypes provide increased power from short-read DNA sequences for relationship inference in fish and wildlife. Molecular Ecology Resources. 18(2):296-305.

Arciniega, M, AJ Clemento, MR Miller, M Peterson, JC Garza and DE Pearse. 2015. Parallel evolution of the summer steelhead ecotype in multiple populations from Oregon and Northern California. Conservation Genetics. 17(1):165-175.

Clemento, AJ, ED Crandall, JC Garza and EC Anderson. 2014. Evaluation of a single nucleotide polymorphism baseline for genetic stock identification of Chinook salmon (Oncorhynchus tshawytscha) in the California Current large marine ecosystem. Fishery Bulletin. 112(2-3):112-130.

Clemento, AJ, EC Anderson, D Boughton, D Girman and JC Garza. 2009. Population genetic structure and ancestry of Oncorhynchus mykiss populations above and below dams in south-central California. Conservation Genetics. 10(5):1321-1336.