Last updated June 2012
Published or in press
Campbell NR, Amish SJ, Pritchard V, Mckelvey K, Young M, Schwartz M, Garza JC, Luikart G, Narum S (In press) Development and evaluation of 200 novel SNP assays for population genetic studies of westslope cutthroat trout and genetic identification of related taxa. Molecular Ecology Resources.
Hayes SA, Hanson CV, Pearse DE, Bond MH, Garza JC, MacFarlane RB Should I stay or should I go? (In press) The influence of genetic origin on emigration behavior and physiology of resident and anadromous juvenile Oncorhynchus mykiss. North American Journal of Fisheries Management.
Ruegg, KC, Anderson EC, Slabbekorn, HW (in press) Differences in timing of migration and response to sexual signaling drive asymmetric hybridization across a migratory divide. Journal of Evolutionary Biology.
Pritchard VL, Abadia-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. doi: 10.1111/j.1755-0998.2012.03149.x
Almudevar A, Anderson EC (2012) A new version of PRT software for sibling groups reconstruction with comments regarding several issues in the sibling reconstruction problem. Molecular Ecology Resources 12:164-178.
Garza JC, Hamelberg S, Hankin D, Lacy M, Lee D, May B, Mohr M, Nandor G, Niemela K, Reisenbichler R, True K (2012) California Hatchery Review Statewide Report. 110 p.
Rundio DE, Williams TH, Pearse DE, Lindley ST (2012) Male-biased sex ratio of nonanadromous Oncorhynchus mykiss in a partially migratory population in California. Ecology of Freshwater Fish 21:293-299.
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.
Abadia-Cardoso A, Clemento AJ, Garza JC (2011) Discovery and characterization of single-nucleotide polymorphisms in steelhead/rainbow trout, Oncorhynchus mykiss. Molecular Ecology Resources 11(Suppl. 1):31-49.
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.
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.
Pearse DE, Gunckel SL, Jacobs SE (2011) Population structure and genetic divergence of coastal rainbow and redband trout in the upper Klamath basin. Transactions of the American Fisheries Society 140:587-597.
Finger, AJ, Anderson, EC, Stephens, MR and May, BP (2011) Application of a method for estimating effective population size and admixture using diagnostic single nucleotide polymorphisms (SNPs): implications for conservation of threatened Paiute cutthroat trout (Oncorhynchus clarkii seleniris) in Silver King Creek, California. Canadian Journal of Fisheries and Aquatic Sciences 68:1368-1386.
Kinziger, AP, Nakamoto, RJ, Anderson, EC, and Harvey, BC (2011) Small founding number and low genetic diversity in an introduced species exhibiting limited invasion success (speckled dace, Rhinichthys osculus). Ecology and Evolution 1:73-84.
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.
Ruegg K, Anderson EC, Baker CS, Vant M, Jackson JA, Palumbi SR (2010) Are Antarctic minke whales unusually abundant because of 20th century whaling? Molecular Ecology 19:281-291.
Pearse DE, Anderson EC (2009) Multiple paternity increases effective population size. Molecular Ecology 18:3124-3127.
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.
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.
Anderson EC (2009) Statistical methods for identifying hybrids and groups. In "Population genetics and animal conservation", p. 25-41, ed. G. Bertorelle, et al., Cambridge University Press.
Israel JA, Bando KJ, Anderson EC, May B (2009) Stock complexity in North American green sturgeon: the utility of polysomic markers in mixed stock fishery analysis. Canadian Journal of Fisheries and Aquatic Sciences 66:1491-1504.
Kinziger, A.P., E.J. Loudenslager, D.G. Hankin, E.C. Anderson and J.C. Garza (2008) Hybridization between spring-run and fall-run Chinook salmon returning to Trinity River, California North American Journal of Fishery Management. 28: 1426-1438.
Anderson, E. C. and K.K. Dunham (2008) The influence of family groups on inferences made with the program structure. Molecular Ecology Resources. 8: 1219-1229
Narum, S.R., M. Banks, T.D. Beacham, R. Bellinger, M. Campbell, J. DeKoning, A. Elz, C. Guthrie, C. Kozfkay, K.M. Miller, P. Moran, R. Phillips, L. Seeb, C. T. Smith, K. Warheit, S. Young, and J.C. Garza (2008) Differentiating populations at broad and fine geographic scales with microsatellites and SNPs. Molecular Ecology 17: 3464-3477.
Spence, B.C., E.P. Bjorkstedt, J. C. Garza, D. Hankin, D. Fuller, W. Jones, J. Smith, and R. Macedo. (2008) Preliminary biological viability criteria for salmonid ESUs in the North-Central California Coast Recovery Domain. NOAA Technical Memorandum NMFS-SWFSC-423. 173 p.
Aguilar, A., D. Jessup, J.A. Estes, and J.C. Garza (2008) The distribution of nuclear genetic variation and historical demography of sea otters. Animal Conservation 11: 35-45.
Anderson, E.C. (2008) Bayesian inference of species hybrids using multilocus dominant genetic data. Philosophical Transactions of the Royal Society, B. 363:2841-50
Anderson, E. C., R. S. Waples and S. T. Kalinowski. (2008) An improved method for predicting the accuracy of genetic stock identification. Canadian Journal of Fisheries and Aquatic Sciences 65:1475-1486.
Hayes, S. A., M. H. Bond, C. V. Hanson, E. V. Freund, J. J. Smith, E. C. Anderson, A. J. Ammann and R. B. MacFarlane (2008) Steelhead growth in a small central California watershed: upstream and estuarine rearing patterns Transactions of the American Fisheries Society 137:114-128.
Sogard, S. M., E. A. Gilbert-Horvath, E. C. Anderson, R. Fisher, S. A. Berkeley and J. C. Garza (2008) Multiple paternity in viviparous kelp rockfish, Sebastes atrovirens. Environmental Biology of Fishes 81: 7-13.
Aguilar A., and J.C. Garza (2007) Isolation of 15 single nucleotide polymorphisms from coastal steelhead (Oncorhynchus mykiss). Molecular Ecology Notes 8: 659-662.
Rice AM, Pearse DE, Becker T, Newman RA, Lebonville C, Harper GR, Pfennig KS (2008) Development and characterization of nine polymorphic microsatellite markers for Mexican spadefoot toads (Spea multiplicata) with cross-amplification in Plains spadefoot toads (S. bobmifrons). Molecular Ecology Resources 8:1386-1389.
Seeb, L. W., A. Antonovich, M. A. Banks, T. D. Beacham, M. R. Bellinger, M. Campbell, N. A. Decovich, J. C. Garza, C. M. Guthrie III, P. Moran, S. R. Narum, J. J. Stephenson, K. J. Supernault, D. J. Teel, W. D. Templin, J. K. Wenburg, S. F. Young, and C. T. Smith. (2007) Development of a standardized DNA database for Chinook salmon. Fisheries. 32: 540-552.
Pastor, T., J. C. Garza, A. Aguilar, E. Tounta, and E. Androukaki (2007) Genetic diversity and differentiation between the two remaining populations of the critically endangered Mediterranean monk seal. Animal Conservation 10: 461-469.
Pearse, D. E., C. J. Donohoe, and J. C. Garza. (2007) Population genetics of steelhead (Oncorhynchus mykiss) in the Klamath River. Environmental Biology of Fishes 80: 377-387.
Anderson, E.C., and M. Slatkin. (2007) Estimation of the number of individuals founding colonized populations. Evolution 61: 972-983
Aguilar, A., and J. C. Garza. (2007) Patterns of historical balancing selection on the salmonid major histocompatibility complex class II beta gene. Journal of Molecular Evolution 65: 34-43
Deiner, K., J. C. Garza, R. Coey, and D. J. Girman. (2007) Population structure and genetic diversity of trout (Oncorhynchus mykiss) above and below natural and man-made barriers in the Russian River, California. Conservation Genetics 8:437-454.
Spies, I. B, E. C. Anderson, K. Naish, and P. Bentzen. (2007) Evidence for the existence of a native population of sockeye salmon (Oncorhynchus nerka) and subsequent introgression with introduced populations in a Pacific Northwest watershed. Can. J. Fish. Aquat. Sciences 64: 1209-1221
Pearse, D. E., L. Wooninck, C. A. Dean, and J. C. Garza. (2007) Identification of northeastern Pacific rockfish using multilocus nuclear DNA genotypes. Transactions of the American Fisheries Society 136:272-280.
Boughton DA, Adams PB, Anderson E, Fusaro C, Keller E, Kelley E, Lentsch L, Nielsen J, Perry K, Regan H, Smith J, Swift C, Thompson L, Watson F (2007) Viability criteria for steelhead of the south-central and southern California coast. NOAA Technical Memorandum NMFS-SWFSC-407. 33 p.
Aguilar, A., and J. C. Garza. (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.
Anderson, E. C., & J.C. Garza. (2006) The power of single-nucleotide polymorphisms for large-scale parentage inference. Genetics 172:2567-2582.
Boughton, D. A., P. B. Adams, E. Anderson, C. Fusaro, E. Keller, E. Kelley, L. Lentsch, J. Nielsen, K. Perry, H. Regan, J. Smith, C. Swift, L. Thompson, and F. Watson. (2006) Steelhead of the south-central / southern California coast: population characterization for recovery planning. NOAA Technical Memorandum NMFS-SWFSC-394. 116 p.
Desmarais, E., K. Belkhir, J. C. Garza, and F. Bonhomme. (2006) Local mutagenic impact of insertions of LTR retrotransposons on the mouse genome. Journal of Molecular Evolution 63:662-675.
Gilbert-Horvath, E. A., R. J. Larson, and J. C. Garza. (2006) Temporal recruitment patterns and gene flow in kelp rockfish (Sebastes atrovirens). Molecular Ecology 15:3801-3815.
Hayes, S. A., D. E. Pearse, D. P. Costa, J. T. Harvey, B. J. Le Boeuf, and J. C. Garza. (2006) Mating system and reproductive success in eastern Pacific harbour seals. Molecular Ecology 15:3023-3034.
Anderson, E. C., and K. K. Dunham. (2005) SPIP 1.0: program for simulating pedigrees and genetic data in age-structured populations. Molecular Ecology Notes 5:459-461.
Anderson, E. C. (2005) An efficient Monte Carlo method for estimating Ne from temporally spaced samples using a coalescent-based likelihood. Genetics 170:955-967.
Palsboll, P. J., M. Berube, E. C. Anderson, and K. K. Dunham. (2005) High levels of statistical uncertainty in 'gametic' recapture estimates of male abundance in humpback whales. Marine Ecology Progress Series 295:305-307.
Bjorkstedt, E. B., B. Spence B, J. C. Garza, D. G. Hankin, D. Fuller D, W. Jones, J. Smith J, R. Macedo. (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.
Shurtliff, Q. R., D. E. Pearse, and D. S. Rogers. (2005) Parentage analysis of the canyon mouse (Peromyscus crinitus): evidence for multiple paternity. Journal of Mammalogy 86(3):531-540.
Lessa, E. P, G. Wlasiuk G, and J. C. Garza. (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.
Aguilar, A., and J. C. Garza (2005) Isolation of major histocompatibility complex class II Beta genes from rockfishes (genus Sebastes) Journal of Fish Biology 67: 1-8.
Pastor, T., J. C. Garza, P. Allen, W. Amos, and A. Aguilar (2004). Low genetic variability in the highly endangered Mediterranean monk seal. Journal of Heredity 5: 291-300.
Pearse, D. E., and K. A. Crandall. (2004) Beyond FST: analysis of population genetic data for conservation. Conservation Genetics 5:585-602.
Wlasiuk, G., J. C. Garza, and E. P. Lessa. (2003) Genetic and geographic differentiation in the Rio Negro tuco-tuco (Ctenomys rionegrensis): inferring the roles of migration and drift from multiple genetic markers. Evolution 57: 913-926.
Garza, J. C., and E. Williamson. (2001) Detection of reduction in population size using data from microsatellite DNA. Molecular Ecology 10: 305-318
Garza, J. C., and E. Desmarais (2000) Derivation of a simple microsatellite locus from a compound ancestor in the genus Mus. Mammalian Genome 11: 1117-1122.
Weber, D. S., B. S. Stewart, J. C. Garza, N. Lehman (2000) An empirical genetic assessment of the severity of the northern elephant seal population bottleneck Current Biology 10: 1287-1290.
In review or in revision
Aguilar A, Abadia-Cardoso A, Charrier G, Garza JC (In revision) SNP and microsatellite markers reveal concordant patterns of population structure but not genetic variation in coastal California steelhead (Oncorhynchus mykiss). Heredity.
Pritchard VL, Peacock MM, Campbell NR, Narum SR, Garza JC (In review) Discovery and characterization of novel genetic markers for use in the management of Lahontan cutthroat trout (Oncorhynchus clarkii henshawi). Molecular Ecology Resources.
Field J. C., Elliger, C., Baltz, K., Gillespie, G. E., Gilly, W. F., Ruiz-Cooley, I., Pearse D.E., S. Stewart, J. S., Matsubu, W. & Walker, W. (In review) Foraging ecology and movement patterns of jumbo squid (Dosidicus gigas) in the California Current System. Deep Sea Research II.
Millan-Marquez AM, Salinas-Zavala CA, Cruz P, Bernardi G, Pearse D (In review). Isolation and characterization of microsatellites markers in the jumbo squid Dosidicus gigas (D'Orbigny, 1835) (Ommastrephidae)./Aislamiento y caracterizacion de marcadores moleculares microsatelites en Dosidicus gigas (D'Orbigny, 1835) (Ommastrephidae). Hidrobiologica.
Heeg RH, Rioux-Paquette S, Dedual M, Abadia-Cardoso, Garza JC, Ritchie PA (In review) Tracing aquatic introductions and assessing the genetic changes from the source: a case study investigating the origins of New Zealand rainbow trout (Oncorhynchus mykiss). Canadian Journal of Fisheries and Aquatic Sciences.
Crandall ED, Treml EA, Barber PH (In Review) Coalescent and biophysical models of stepping-stone gene flow in Neritid snails. Molecular Ecology.
Reports
Smith C, Hawkins D, Garza JC (2011) Summary of genetic data collected for rapid response Chinook salmon assignment, and evaluation of new markers and assignment tools. Report to Coleman National Fish Hatchery. 29 p.
Pearse D.E. 2011. Population genetics of Jumbo squid, Dosidicus gigas. Final report for UC MEXUS Faculty Research Grant. 4p.
Anderson EC (2010) Computational algorithms and user-friendly software for parentage-based tagging of Pacific salmonids. Final report submitted to the Pacific Salmon Commission's Chinook Technical Committee (US Section). 46 p.
Stillwater Sciences, Rosi Dagit, and John Carlos Garza. 2010. Lifecycle monitoring of O. mykiss in Topanga Creek, California: Final report. Prepared for California Department of Fish and Game, Contract No. P0750021. 198 p.
Garza, J. C., and D. E. Pearse. (2008) Population genetic structure of Oncorhynchus mykiss in the California Central Valley. 54p.
Pearse, D. E., and J. C. Garza. (2008) Historical baseline for genetic monitoring of coastal California steelhead, Oncorhynchus mykiss. 31p.
Garza, J. C., and D. E. Pearse. (2008) Population genetics of Oncorhynchus mykiss in the Santa Clara Valley Region. 53p.
Garza, J. C., and A. C. Clemento. (2008) Population genetic structure of Oncorhynchus mykiss in the Santa Ynez River, California. 55p.
Manoukis, N.C. and E.C. Anderson. (2008) GuiLiner: a configurable and extensible graphical user interface for scientific analysis and simulation software. http://arxiv.org/abs/0806.0314v1}{arXiv:0806.0314v1
Garza, J .C., S. M. Blankenship, C. Lemaire, and G. Charrier. (2008) Genetic population structure of Chinook salmon (Oncorhynchus tshawytscha) in California's Central Valley. 82p.
Garza, J. C. and E. C. Anderson. (2007) Large Scale Parentage Inference as an Alternative to Coded-wire Tags for Salmon Fishery Management in Pacific Salmon Commission GSI Workshops: Logistics Workgroup Final Report and Recommendations. 55p.
Aguilar, A., and J. C. Garza. (2007) MHC evolution in rockfishes. In: E. A. Berntson, P. S. Levin, and P. Moran (eds.), Conservation of north Pacific rockfishes: ecological genetics and stock structure: Proceedings of the workshop, p. 44-46. NOAA Technical Memorandum NMFS-NWFSC-80.
Girman, D., and J. C. Garza. (2006) Population structure and ancestry of O. mykiss populations in South-Central California based on genetic analysis of microsatellite data. 48p.
Hankin, D. G., J. H. Clark, R. B. Deriso, J. C. Garza, G. S. Morishima, B. E. Riddell, C. Schwarz, and J. B. Scott. (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. 243p. Available from: www.psc.org/info_codedwiretagreview.htm
Anderson, E. C., and J. C. Garza. (2005) A description of full parental genotyping. Report submitted to the Pacific Salmon Commission, Vancouver, British Columbia. 11p. Incorporated into Hankin et al. 2005.
Garza, J. C., L. Gilbert-Horvath, J. Anderson, T. Williams, B. Spence, and H. Fish. (2004) Population structure and history of steelhead trout in California. In: J. Irvine, et al. (eds.), Workshop on Application of Stock Identification in Defining Marine Distribution and Migration of Salmon (Honolulu, Hawaii, USA, November 1-2, 2003). North Pacific Anadromous Fish Commission, Technical Report 5:129-131.
Garza, J. C., and E. Gilbert-Horvath. (2003) Report on the genetics of coho salmon (Oncorhynchus kisutch) held at Warm Springs (Don Clausen) Hatchery for recovery efforts in the Russian River. 17p.