Molecular Ecology (2006) 15, 3801–3815 doi: 10.1111/j.1365-294X.2006.03033.x © 2006 The Authors Journal compilation © 2006 Blackwell Publishing Ltd Blackwell Publishing Ltd Temporal recruitment patterns and gene flow in kelp rockfish (Sebastes atrovirens) ELIZABETH A. GILBERT-HORVATH,*† RALPH J. LARSON † and JOHN CARLOS GARZA * *NOAA Southwest Fisheries Science Center, 110 Shaffer Road, Santa Cruz, CA 95060, USA, †Department of Biology, San Francisco State University, 1600 Holloway Avenue, San Francisco, CA 94132, USA Abstract Pelagic dispersal of marine organisms provides abundant opportunity for gene flow and presumably inhibits population genetic divergence. However, ephemeral, fine-scale, temporal and spatial genetic heterogeneity is frequently observed in settled propagules of marine species that otherwise exhibit broad-scale genetic homogeneity. A large variance in reproductive success is one explanation for this phenomenon. Here, genetic analyses of 16 microsatellite loci are used to examine temporal patterns of variation in young-of-year kelp rockfish (Sebastes atrovirens) recruiting to nearshore habitat in Monterey Bay, California, USA. Population structure of adults from central California is also evaluated to determine if spatial structure exists and might potentially contribute to recruitment patterns. Genetic homogeneity was found among 414 young-of-year sampled throughout the entire 1998 recruitment season. No substantial adult population structure was found among seven populations spanning 800 km of coastline that includes the Point Conception marine biogeographic boundary. Comparison of young-of-year and adult samples revealed no genetic differentiation and no measurable reduction in genetic variation of offspring, indicating little variance in reproductive success and no reduction in effective population size for this year class. Simulation analyses determined that the data set was sufficiently powerful to detect both slight population structure among adults and a small reduction in effective number of breeders contributing to this year class. The findings of high gene flow and low genetic drift have important implications for fisheries management and conservation efforts. Keywords: dispersal, gene flow, panmixia, population genetics, recruitment, Sebastes atrovirens Received 11 March 2006; revision accepted 22 May 2006 Introduction Pelagic larvae of marine organisms can disperse long dis- tances before settlement in habitat suitable for maturation (Scheltema 1971, 1986). Larval transport and dispersion may perpetuate population genetic homogeneity over large geographical areas (Crisp 1978; Slatkin 1985), as has been observed in many marine species (Winans 1980; Palumbi & Wilson 1990; Gold & Richardson 1998; Bagley et al . 1999; Knutsen et al . 2003). However, some marine organisms display small-scale, fluctuating genetic hetero- geneity, a phenomenon termed as chaotic genetic patchiness ( Johnson & Black 1982, 1984), within large regions of genetic homogeneity, indicating that local-scale processes are important in the ecology of these populations. Genetic patchiness is characterized by significant instability of allele frequencies over short temporal and/or spatial scales and has been observed in pelagically dispersing invertebrates, fishes, and kelp (Hedgecock 1986; Doherty et al . 1995; Johnson & Wernham 1999; Kusumo & Druehl 2000; Moberg & Burton 2000). The causal mechanisms of this transient heterogeneity are not well understood. One explanation for the observation of chaotic genetic patchiness is the ‘sweepstakes-chance matching’ hypo- thesis (Hedgecock 1994a, b). This idea proposes that a large variance in reproductive success, brought about by limited spatial and temporal windows of opportunity for survival during the larval stage (Cushing 1975; Bakun 1996), causes surviving offspring to exhibit some characteristics of a Correspondence: Elizabeth A. Gilbert-Horvath, Fax: 1-831-420- 3977; E-mail: libby.gilbert@noaa.gov