Molecular Ecology and Genetic Analysis (MEGA) Team

SteelheadWe are biologists that use population genetic data and analytical techniques to address a broad array of questions in ecology, evolution, behavior, conservation, and management of marine and anadromous organisms. Our work is based on the collection and analysis of statistically robust molecular population genetic datasets. We actively implement novel methods for the acquisition and analysis of molecular data, providing inference for both specific and general problems in biology. Most of our current research involves salmon, trout and groundfish, but we also work on marine mammals and other fishes, and much of our methodology development is more broadly applicable. Our work supports federal, state and local efforts to conserve and manage marine, anadromous and coastal species and populations, particularly in California.

The MEGA Team operates as a cooperative research unit of NOAA and University of California staff, postdoctoral researchers, graduate, and undergraduate students. It was formed as a result of the move to the UC Santa Cruz Marine Sciences Campus of the now defunct Tiburon lab of the Southwest Fisheries Science Center in 2000 and the concurrent expansion of the division to include both state of the art laboratory facilities and new staff and programs. We operate a modern molecular biology laboratory, equipped with instrumentation and automation for high throughput DNA extraction, thermal cycling, DNA sequencing, microsatellite and SNP genotyping capacity. We also maintain a collection of over 100,000 tissue samples and DNA extracts of fishes and mammals, primarily salmonids and rockfishes from California. We also provide expertise in the analysis and interpretation of genetic data for a variety of applications and provide educational opportunities to graduate and advanced undergraduate students through faculty appointments at the University of California.

Much of our work is collaborative with other agencies, research groups, and individuals. We invite you to contact us to discuss such collaboration.

Our research is diverse, with over 50 active projects that include the following:

Steelhead tree-Extensive investigation of population genetic structure of California salmon and trout in space and time. Recent or ongoing projects include range-wide evaluation of Chinook salmon, fine-scale analysis of intra basin structure for Chinook salmon and steelhead/rainbow trout in the Sacramento/San Joaquin, Klamath/Trinity systems and in coastal streams and rivers, and a comprehensive assessment of coho salmon population structure in California.

-Genetic stock identification to estimate composition of Chinook salmon in ocean fisheries and evaluate distribution and abundance of fish during ocean migration and residence. This work involves evaluation of port-sampled fish and a collaboration with other state agencies and fishermen to collect exact GPS coordinates of catch locations for individual fish.

-The development of novel methodology and software for genetic stock identification, reconstruction of pedigrees, and estimation of population size.

-Evaluation of behavioral ecology and life history variation in steelhead in Scott Creek, CA, in collaboration with the Salmon Ecology Team. This long-term project includes the construction of pedigrees for wild fish through large-scale parentage inference, the evaluation of variation in reproductive success, investigation of the determinants of mate choice, identification of the signals and targets of natural selection on fish of different phenotypes, and the eventual mapping of genes involved in ecologically important trait variation.

-Discovery and characterization of polymorphic molecular markers and annotation of gene structure through large scale re-sequencing of expressed sequence tags in various salmonid species.

Chinook gel-Genetic management of coho salmon in California to avoid extirpation and assist recovery. This includes intensive broodstock management for two captive broodstock programs in the critically endangered Central California Coast ESU, the collection and evaluation of data on population structure and size, and the investigation of reintroduction, recolonization and recovery.

-Evaluation of the spatial and temporal variation of population structure in multiple rockfish species, including black, widow, blue, kelp and shortbelly rockfish.

Team members


Recent publications

  • Garza JC, Gilbert-Horvath EA, Spence B, Williams TH, Fish H, Gough S, Anderson JH, Hamm D, Anderson EC (In press) Population structure of steelhead in coastal California. Transactions of the American Fisheries Society.
  • Abadía-Cardoso A, Anderson EC, Pearse DE, Garza JC (2013) Large-scale parentage analysis reveals reproductive patterns and heritability of spawn timing in a hatchery population of steelhead Oncorhynchus mykiss. Molecular Ecology 22:4733–4746.
  • Conrad JL, Gilbert-Horvath EA, Garza JC (2013) Genetic and phenotypic effects on reproductive outcomes for captively-reared coho salmon, Oncorhynchus kisutch. Aquaculture 404-405:95-104.
  • Anderson EC (2012) Large-scale parentage inference with SNPs: an efficient algorithm for statistical confidence of parent pair allocations. Statistical Applications in Genetics and Molecular Biology 11:5. doi:10.1515/1544-6115.1833.
  • Pritchard VL, Abadía-Cardoso A, Garza JC (2012) Discovery and characterization of a large number of diagnostic markers to discriminate Oncorhynchus mykiss and O. clarkii. Molecular Ecology Resources 12:918-931.
  • Pearse DE, Martinez E, Garza JC (2011) Disruption of historical patterns of isolation by distance in coastal steelhead. Conservation Genetics 12:691-700.
  • Martinez A, Garza JC, Pearse DE (2011) A microsatellite genome screen identifies chromosomal regions under differential selection in steelhead and rainbow trout. Transactions of the American Fisheries Society 140:829–842.
  • Clemento AJ, Abadia-Cardoso A, Starks HA, Garza JC (2011) Discovery and characterization of single nucleotide polymorphisms in Chinook salmon, Oncorhynchus tshawytscha. Molecular Ecology Resources 11(Suppl. 1):50-66.
  • Anderson EC (2010) Assessing the power of informative subsets of loci for population assignment: standard methods are upwardly biased. Molecular Ecology Resources 10:701-710.
  • Clemento, A. J., E.C. Anderson, D. Boughton, D. Girman, and J. C. Garza (2009) Population genetic structure and ancestry of Oncorhynchus mykiss populations above and below dams in South-Central California. Conservation Genetics 10:1321–1336.

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Last modified: 1/29/2015