John Carlos Garza

Research Interests:

I use population and molecular genetic methods to provide biological inference regarding a broad range of questions in ecology, evolution, conservation and management of marine and aquatic species. Much of this work is with salmonid fishes in the genus Oncorhynchus and rockfishes in the genus Sebastes, but we also have collaborative projects on other fishes, pinnipeds, otters and cephalopods.

I am involved in a large number of research projects that span topics as diverse as 1) the eludication of patterns of distribution and abundance of Chinook salmon in the coastal ocean of North America, 2) the evaluation of patterns of population structure and multiple paternity in the rockfishes, 3) the estimation of genomic parameters from DNA sequences and sequence polymorphism in salmon and trout, 4) the evaluation of novel release strategies for reintroduction of endangered salmon, 5) development of genetic markers in salmon and trout and their application to map genes involved in life history variation, and 6) development and implementation of intergenerational genetic tagging methods in salmonids and rockfishes with applications to harvest management, evaluation of hatcheries and estimation of dispersal rates.

I supervise the Molecular Ecology and Genetic Analysis Team, a joint federal/state research group, and have appointments as both a Supervisory Research Geneticist at the National Oceanic and Atmospheric Administration’s Southwest Fisheries Science Center, and as adjunct faculty at the University of California, Santa Cruz in the Department of Ocean Sciences. My group plays a significant role in advising federal and state management of both protected and exploited species. We also provide training to the next generation of population biologists, through graduate and advanced undergraduate education, both at the University of California and through internships and committee work with students from both US and international universities.

Education:

• Ph.D. in Integrative Biology: University of California, Berkeley 1998
• M.S. in Biology: University of California, San Diego 1991
• B.A. in Biology (Magna Cum Laude): University of California, San Diego 1990

Additional Information:

Software:

Population genetic software

Publications:

Pearse DE, Martinez E, Garza JC (2011) Disruption of historical patterns of isolation by distance in coastal steelhead. Conservation Genetics 12:691–700.

Martínez 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.

Abadía-Cardoso A, Clemento AJ, Garza JC (2011) Discovery and characterization of single-nucleotide polymorphisms in steelhead/rainbow trout, Oncorhynchus mykiss. Molecular Ecology Resources 11(1):31-49.

Clemento AJ, Abadía-Cardoso A, Starks HA, Garza JC (2011) Discovery and characterization of single nucleotide polymorphisms in Chinook salmon, Oncorhynchus tshawytscha. Molecular Ecology Resources 11(1):50-66.

Spence BC, Duffy WG, Garza JC, Harvey BC, Sogard SM, Weitkamp LA, Williams TH, Boughton DA (2011) Historical occurrence of coho salmon (Oncorhynchus kisutch) in streams of the Santa Cruz Mountain region of California: response to an Endangered Species Act petition to delist coho salmon south of San Francisco Bay. NOAA Technical Memorandum NOAA-TM-NMFS-SWFSC-472. 131 p.

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

Pearse DE, Hayes SA, Bond MH, Hanson CV, Anderson EC, MacFarlane RB, Garza JC (2009) Over the falls? rapid evolution of ecotypic differentiation in steelhead/rainbow trout (Oncorhynchus mykiss) Journal of Heredity 100:515-525.

Anderson EC, Garza JC (2009) Estimation of Population Size with Molecular Genetic Data. NOAA Technical Memorandum NOAA-TM-NMFS-SWFSC-448. 57 p.

Lindley ST, Grimes CB, Mohr MS, Peterson W, Stein J, Anderson JT, Botsford LW, Bottom DL, Busack CA, Collier TK, Ferguson J, Garza JC, Grover AM, Hankin DG, Kope RG, Lawson PW, Low A, MacFarlane RB, Moore K, Palmer-Zwahlen M, Schwing FB, Smith J, Tracy C, Webb R, Wells BK, Williams TH (2009) What caused the Sacramento River fall Chinook stock collapse? NOAA Technical Memorandum NOAA-TM-NMFS-SWFSC-447. 61 p.

Sturm EA, Gilbert-Horvath EA, Garza JC, MacFarlane RB (2009) Creation of a Captive Broodstock Program for Southern Coho Salmon (Oncorhynchus kisutch): Results from the Initial Rearing and Spawning of the First Brood Year. NOAA Technical Memorandum NOAA-TM-NMFS-SWFSC-436. 66 p.

Kinziger AP, Loudenslager EJ, Hankin DG, Anderson EC, Garza JC (2008) Hybridization between spring- and fall-run Chinook salmon returning to the Trinity River, California. North American Journal of Fisheries Management 28:1426–1438.

Aguilar A, Garza JC (2008) Isolation of 15 single nucleotide polymorphisms from coastal steelhead, Oncorhynchus mykiss (Salmonidae). Molecular Ecology Resources 8: 659-662.

Narum SR, Banks M, Beacham TD, Bellinger MR, Campbell MR, DeKoning J, Elz A, Guthrie CM, Kozfkay C, Miller KM, Moran P, Phillips R, Seeb LW, Smith CT, Warheit K, Young SF, Garza JC (2008) Differentiating salmon populations at broad and fine geographic scales with microsatellites and SNPs. Molecular Ecology 17:3464-3477.

Aguilar A, Jessup DA, Estes J, Garza JC (2008) The distribution of nuclear genetic variation and historical demography of sea otters. Animal Conservation 11:35–45.

Sogard SM, Gilbert-Horvath E, Anderson EC, Fisher R, Berkeley SA, Garza JC (2008) Multiple paternity in viviparous kelp rockfish, Sebastes atrovirens. Environmental Biology of Fishes 81:7-13.

Spence BC, Bjorkstedt EP, JC Garza, Smith JJ, Hankin DG, Fuller D, Jones WE, Macedo R, Williams TH, Mora E (2008) A framework for assessing the viability of threatened and endangered salmon and steelhead in the North-Central California Coast Recovery Domain. NOAA Technical Memorandum NMFS-SWFSC-423. 173 p.

Aguilar A, Garza JC (2007) Patterns of historical balancing selection on the salmonid major histocompatibility complex class II beta gene. Journal of Molecular Evolution 65:34-43.

Pearse DE, Donohoe CJ, Garza JC (2007) Population genetics of steelhead (Oncorhynchus mykiss) in the Klamath River. Environmental Biology of Fishes 80:377-387.

Seeb LW, Antonovich A, Banks MA, Beacham TD, Bellinger MR, Campbell MR, Decovich NA, Garza JC, Guthrie CM, Moran P, Narum SR, Stephenson JJ, Supernault KJ, Teel DJ, Templin WD, Wenburg JK, Young SF, Smith CT (2007) Development of a standardized DNA database for Chinook salmon. Fisheries 32:540-552.

Deiner K, Garza JC, Coey R, Girman DJ (2007) Population structure and genetic diversity of trout (Oncorhynchus mykiss) above and below natural and manmade-barriers in the Russian River, California. Conservation Genetics 8:437-454. Citations: 22

Pearse DP, Wooninck L, Dean CA, Garza JC (2007) Identification of northeastern Pacific rockfish using multilocus nuclear DNA genotypes. Transactions of the American Fisheries Society 136:272-280.

Pastor T, Garza JC, Aguilar A, Tounta E, Androukaki E (2007) Genetic diversity and differentiation between the two remaining populations of the critically endangered Mediterranean monk seal. Animal Conservation 10:461-469.

Gilbert-Horvath EA, Larson RJ, Garza JC (2006) Temporal recruitment patterns and gene flow in kelp rockfish (Sebastes atrovirens). Molecular Ecology 15:3801-3815.

Desmarais E, Belkhir K, Garza JC, Bonhomme F (2006) Local mutagenic impact of insertions of LTR retrotransposons on the mouse genome. Journal of Molecular Evolution 63:662-675.

Hayes SA, Pearse DE, Costa DP, Harvey JT, Le Boeuf BJ, Garza JC (2006) Mating system and reproductive success in eastern Pacific harbour seals. Molecular Ecology 15:3023-3034.

Anderson EC, Garza JC (2006) The power of single-nucleotide polymorphisms for large-scale parentage inference. Genetics 172:2567-2582.

Aguilar A, Garza JC (2006) A comparison of variability and population structure for major histocompatibility complex and microsatellite loci in California coastal steelhead (Oncorhynchus mykiss Walbaum). Molecular Ecology 15:923-937.

Hankin DG, Clark JH, Deriso RB, Garza JC, Morishima GS, Riddell BE, Schwarz C, Scott JB (2005) Report of the expert panel on the future of the coded wire tag recovery program for Pacific salmon. Final Report to the Pacific Salmon Commission. 243pp. Available from: www.psc.org/info_codedwiretagreview.htm

Aguilar A, Garza JC (2005) Analysis of major histocompatibility complex class II Beta genes from rockfishes (genus Sebastes) Journal of Fish Biology 67:1021–1028.

Lessa EP, Wlasiuk G, Garza JC (2005) Dynamics of Genetic Differentiation in the Río Negro Tuco-tuco (Ctenomys rionegrensis) at the Local and Geographical Scales. In Mammalian Diversification: from Chromosomes to Phylogeography, eds. Lacey E.A., Myers P. UC Publications in Zoology 133:155-173.

Bjorkstedt EP, Spence BC, Garza JC, Hankin DG, Fuller D, Jones WE, Smith JJ, Macedo R (2005) An analysis of historical population structure for Evolutionarily Significant Units of Chinook salmon, coho salmon, and steelhead in the North-Central California Coast Recovery Domain. NOAA Technical Memorandum NMFS-SWFSC-382. 210 p.

Pastor T, Garza JC, Allen P, Amos W, Aguilar A (2004) Low genetic variability in the highly endangered Mediterranean monk seal. Journal of Heredity 95:291-300.

Wlasiuk G, Garza JC, Lessa EP (2003) Genetic and geographic differentiation in the Río Negro tuco-tuco (Ctenomys rionegrensis): inferring the roles of migration and drift from multiple genetic markers. Evolution 57:913-926.

Garza JC, Williamson EG (2001) Detection of reduction in population size using data from microsatellite DNA. Molecular Ecology 10:305-318.

Garza JC, Desmarais E (2000) Derivation of a simple microsatellite locus from a compound ancestor in the genus Mus. Mammalian Genome 11:1117-1122.

Weber DS, Stewart BS, Garza JC, Lehman N (2000) An empirical genetic assessment of the severity of the northern elephant seal population bottleneck. Current Biology 10:1287-1290.

Garza JC, Dallas J, Duryadi D, Gerasimov S, Croset H, Boursot P (1997) Social structure of the mound-building mouse Mus spicilegus revealed by genetic analysis with microsatellites. Molecular Ecology 6:1009-1017.

Garza JC, Freimer NB (1996) Homoplasy for size at microsatellite loci in humans and chimpanzees. Genome Research 6:211-217.

Garza JC, Slatkin M, Freimer NB (1995). Microsatellite allele frequencies in humans and chimpanzees, with implications for constraints on allele size. Molecular Biology and Evolution 12:594-603.

Di Rienzo A, Peterson AC, Garza JC, Valdes AM, Slatkin M, Freimer NB (1994). Mutational processes of simple-sequence repeat loci in human populations. Proceedings of the National Academy of Sciences, USA 91:3166-3170.

Garza JC, Woodruff DS (1994) Crested gibbon (Hylobates [Nomascus]) identification using noninvasively obtained DNA. Zoo Biology 13:383-387.

Garza JC, Woodruff DS (1992) A phylogenetic study of the gibbons (Hylobates) using DNA obtained noninvasively from hair. Molecular Phylogenetics and Evolution 1:202-210.