Population genetic software
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.
Schunter C, Garza JC, Macpherson E, Pascual M (In press) SNP development from RNA-seq data in a non-model fish: how many individuals are needed for accurate allele frequency prediction? Molecular Ecology Resources.
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.
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
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
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.
California Hatchery Review Statewide Report (2012). Garza JC, Hamelberg S, Hankin D, Lacy M, Lee D, May B, Mohr M, Nandor G, Niemela K, Reisenbichler R, True K. (Authors alphabetical) 110 p.
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 12:918-93.
Hayes S, Hanson C, Pearse DE, Bond M, 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.
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.
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, Garza JC, 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.