Molecular Ecology and Genetic Analysis Team Publications

Last updated September 2013

Published or in press

Hess JE, Chittaro P, Elz A, Gilbert-Horvath EA, Simon V, Garza JC (In press) Cryptic population structure in the severely depleted cowcod, Sebastes levis. Canadian Journal of Fisheries and Aquatic Sciences.

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.

Satterthwaite WH, Mohr MS, O’Farrell MR, Anderson EC, Banks MA, Bates SJ, Bellinger MR, Borgerson LA, Crandall ED, Garza JC, Kormos BJ, Lawson PW, Palmer-Zwahlen ML (In press) Use of genetic stock identification data for comparison of the ocean spatial distribution, size-at-age, and fishery exposure of an untagged stock and its indicator: California Coastal versus Klamath River Chinook. Transactions of the American Fisheries Society.

Field JC, Elliger C, Baltz K, Gillespie GE, Gilly WF, Ruiz-Cooley RI, Pearse D, Stewart JS, Matsubu W, Walker WA (In press) Foraging ecology and movement patterns of jumbo squid (Dosidicus gigas) in the California Current System. Deep Sea Research II doi: 10.1016/j.dsr2.2012.09.006.

Schunter C, Garza JC, Macpherson E, Pascual M (2013) SNP development from RNA-seq data in a non-model fish: how many individuals are needed for accurate allele frequency prediction? Molecular Ecology Resources doi: 10.1111/1755-0998.12155.

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.

Ackiss AS, Pardede S, Crandall ED, Ablan-Lagman MCA, Ambariyanto, Romena N, Barber PH, Carpenter KE (2013) Pronounced genetic structure in a highly mobile coral reef fish, Caesio cuning, in the Coral Triangle. Marine Ecology Progress Series 480:185-197.

Kinziger AP, Hellmair M, Hankin DG, Garza JC (2013) Contemporary population structure in Klamath River basin Chinook salmon revealed by analysis of microsatellite genetic data. Transactions of the American Fisheries Society 142:1347-1357.

Ostberg, CO, Hauser L, Pritchard VL, Garza JC, Naish KA (2013) Chromosome rearrangements, recombination suppression, and limited segregation distortion in hybrids between Yellowstone cutthroat trout (Oncorhynchus clarkii bouvieri) and rainbow trout (O. mykiss) BMC Genomics, 14:570 doi:10.1186/1471-2164-14-570

Steele CA, Anderson EC, Ackerman MW, Hess MA, Campbell N, Narum SR, Campbell M (2013) A validation of parentage-based tagging using hatchery steelhead in the Snake River basin. Canadian Journal of Fisheries and Aquatic Sciences 70:1046-1054.

Pritchard VL, Garza JC (2013) Discovery and characterization of novel genetic markers for coastal cutthroat trout (Oncorhynchus clarkii clarkii). Conservation Genetics Resources 5:611-618.

Venerus LA, Ciancio JE, Riva-Rossi C, Gilbert-Horvath EA, Gosztonyi AE, Garza JC (2013) Genetic structure and different color morphotypes suggest the occurrence and bathymetric segregation of two incipient species of Sebastes off Argentina. Naturwissenschaften 100:645-658

Ruegg KC, Rosenbaum HC, Anderson EC, Engel M, Rothschild A, Baker CS, Palumbi SR (2013) Long-term population size of the North Atlantic humpback whale within the context of worldwide population structure. Conservation Genetics 14:103–114.

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.

Moran P, Teel DJ, Banks MA, Beacham TD, Bellinger MR, Blankenship SM, Candy JR, Garza JC, Hess JE, Narum SR, Seeb LW, Templin WD, Wallace CG, Smith CT (2013) Divergent life-history races do not represent Chinook salmon coast-wide: the importance of scale in Quaternary biogeography. Canadian Journal of Fisheries and Aquatic Sciences 70:415-435.

Pritchard VL, Peacock MM, Campbell NR, Narum SR, Garza JC (2013) Discovery and characterization of novel genetic markers for use in the management of Lahontan cutthroat trout (Oncorhynchus clarkii henshawi). Molecular Ecology Resources 13:276-288.

Williams TH, Garza JC, Hetrick NJ, Lindley ST, Mohr MS, Myers JM, O'Farrell MR, Quinones RM, Teel DJ (2013) Upper Klamath and Trinity River Chinook salmon Biological Review Team report. NOAA Technical Memorandum NMFS-SWFSC-502. 47 p.

Campbell NR, Amish SJ, Pritchard V, Mckelvey K, Young M, Schwartz M, Garza JC, Luikart G, Narum S (2012) 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 12:942-949.

Hayes SA, Hanson CV, Pearse DE, Bond MH, Garza JC, MacFarlane RB (2012) Should I stay or should I go? the influence of genetic origin on emigration behavior and physiology of resident and anadromous juvenile Oncorhynchus mykiss. North American Journal of Fisheries Management 32:772-780.

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.

Crandall ED, Treml EA, Barber PH (2012) Coalescent and biophysical models of stepping-stone gene flow in Neritid snails. Molecular Ecology 21:5579-5598

Ruegg KC, Anderson EC, Slabbekoorn HW (2012) Differences in timing of migration and response to sexual signaling drive asymmetric hybridization across a migratory divide. Journal of Evolutionary Biology 25:1741-1750.

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.

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.

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(Suppl. 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(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 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, 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, 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.

Anderson EC (2009) Statistical methods for identifying hybrids and groups. In “Population Genetics and Animal Conservation”, p. 25-41, ed. Bertorelle G, 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 AP, Loudenslager EJ, Hankin DG, Anderson EC, Garza JC (2008) Hybridization between spring-run and fall-run Chinook salmon returning to the Trinity River, California. North American Journal of Fisheries Management 28:1426–1438.

Anderson EC, Dunham KK (2008) The influence of family groups on inferences made with the program structure. Molecular Ecology Resources 8:1219-1229.

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

Spence BC, Bjorkstedt EP, Garza JC, Hankin D, Fuller D, Jones W, Smith J, Macedo R (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, Jessup D, Estes JA, Garza JC (2008) The distribution of nuclear genetic variation and historical demography of sea otters. Animal Conservation 11:35–45.

Anderson, EC (2008) Bayesian inference of species hybrids using multilocus dominant genetic data Philosophical Transactions of the Royal Society, B. 363:2841-50.

Anderson EC, Waples RS, Kalinowski ST (2008) An improved method for predicting the accuracy of genetic stock identification. Canadian Journal of Fisheries and Aquatic Sciences 65:1475-1486.

Hayes SA, Bond MH, Hanson CV, Freund EV, Smith JJ, Anderson EC, Ammann AJ, MacFarlane RB (2008) Steelhead growth in a small central California watershed: upstream and estuarine rearing patterns. Transactions of the American Fisheries Society 137:114-128.

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

Aguilar A, Garza JC (2008) Isolation of 15 single nucleotide polymorphisms from coastal steelhead (Oncorhynchus mykiss). Molecular Ecology Resources 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. bombifrons). Molecular Ecology Resources 8:1386-1389.

Seeb LW, Antonovich A, Banks MA, Beacham TD, Bellinger MR, Campbell M, 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.

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.

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

Anderson EC, Slatkin M (2007) Estimation of the number of individuals founding colonized populations. Evolution 61:972-983.

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.

Deiner K, Garza JC, Coey R, Girman DJ (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 IB, Anderson EC, Naish K, Bentzen P (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. Canadian Journal of Fisheries and Aquatic Sciences 64:1209-1221.

Pearse DE, 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.

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, 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.

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

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 (2006) Steelhead of the south-central / southern California coast: population characterization for recovery planning. NOAA Technical Memorandum NMFS-SWFSC-394. 116 p.

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.

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

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, Dunham KK (2005) SPIP 1.0: program for simulating pedigrees and genetic data in age-structured populations. Molecular Ecology Notes 5:459-461.

Anderson EC (2005) An efficient Monte Carlo method for estimating Ne from temporally spaced samples using a coalescent-based likelihood. Genetics 170:955-967.

Palsbøll PJ, Bérubé M, Anderson EC, Dunham KK (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, Spence B, Garza JC, Hankin DG, Fuller D, Jones W, Smith J, 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.

Shurtliff QR, Pearse DE, Rogers DS (2005) Parentage analysis of the canyon mouse (Peromyscus crinitus): evidence for multiple paternity. Journal of Mammalogy 86:531-540.

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 EA, Myers P, UC Publications in Zoology 133:155-173.

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.

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.

Pearse DE, Crandall KA (2004) Beyond FST: analysis of population genetic data for conservation. Conservation Genetics 5:585-602.

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 E (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.


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.

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, Dagit R, Garza JC (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 JC, Pearse DE (2008) Population genetic structure of Oncorhynchus mykiss in the California Central Valley. 54p.

Pearse DE, Garza JC (2008) Historical baseline for genetic monitoring of coastal California steelhead, Oncorhynchus mykiss. 31p.

Garza JC, Pearse DE (2008) Population genetics of Oncorhynchus mykiss in the Santa Clara Valley Region. 53p.

Garza JC, Clemento AJ (2008) Population genetic structure of Oncorhynchus mykiss in the Santa Ynez River, California. 55p.

Manoukis NC, Anderson EC (2008) GuiLiner: a configurable and extensible graphical user interface for scientific analysis and simulation software.

Garza JC, Blankenship SM, Lemaire C, Charrier G (2008) Genetic population structure of Chinook salmon (Oncorhynchus tshawytscha) in California’s Central Valley. 82p.

Garza JC, Anderson EC (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, Garza JC (2007) MHC evolution in rockfishes. In: Berntson EA, Levin PS, Moran P (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, Garza JC (2006) Population structure and ancestry of O. mykiss populations in South-Central California based on genetic analysis of microsatellite data. 48p.

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. 243p. Available from:

Anderson EC, Garza JC (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 JC, Gilbert-Horvath E, Anderson J, Williams T, Spence B, Fish H (2004) Population structure and history of steelhead trout in California. In: Irvine J, 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 JC, Gilbert-Horvath E (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.

Last modified: 12/24/2014