Palumbi Lab

Red AbaloneAbalones are the one of the most important mollusks fished in many coastal regions of the world, such as Australia, New Zealand, South Africa, Chile and California. In recent years, the different countries have implemented a variety of regulations on the fishery to avoid overfishing. However, an unresolved question is whether regulations such as these need to be implemented over large scales over thousands of miles of coast, or whether small scale regulations at the level of individual fishing towns can be successful? It has recently been shown that the populations of the various Abalone species can be genetically quite different from one another over small spatial scales, implying that these populations do not exchange dispersing larvae and that small scale fishery regulation is reasonable.  On the Northern California coastline, state regulators are poised to set up a new series of abalone fishery regions with little guidance about how populations disperse. This project is a transcriptome-wide survey of the genetic variation in California from around Cape Mendocino to Monterey Bay. The aim is to identify regions in the genome that are differentiatied at a local population level. Differences in these regions could then be correlated with environmental variables to identify the factors affecting the genetic structure of Abalones within this region. This knowledge will shed light on the structuring processes, which will be invaluable information for management efforts of Abalone fisheries not only in California, but worldwide.


Pierre divingThe Abalone fishery is one of the world’s most economically important gastropod fisheries (Leiva and Castilla, 2001). Unfortunately, due to increasing fishing effort, the stocks of gastropods have steadily decreased in the last 40 years (Leiva and Castilla, 2001). Most notably, the Californian Abalone fishery, which was peaking in landing size at around 1970 ended in the crash of stocks of all four commercially fished species, to the point where it had to be closed down completely in 1997 (Leiva and Castilla, 2001); the white Abalone, Haliotis sorenseni being the first marine invertebrate protected under the Endangered Species Act of 2001 (Micheli et al., 2008). Disappointingly, despite efforts to the contrary, the stocks of Abalone have not increased since the closure of the fishery, and all species along the California coast except the Red Abalone are currently under concern (Gruenthal and Burton, 2005; Kashiwada and Taniguchi, 2007; Micheli et al., 2008).

Recent genetic studies on various species of Abalone in California indicate that the populations differ genetically from each other, even along the same coastline (Chambers et al., 2006; Gruenthal et al., 2007; Gruenthal and Burton, 2008; Gutierrez-Gonzalez et al., 2007). This indicates that there are barriers to dispersal along the coastline, dividing the Abalones into separated populations. This is a very important realization for the management of the fishery, as one cannot expect the recovery of isolated populations without larval influx, the lack of which often is the result in a collapsed population (Miller et al., 2009). In other parts of the world such as Australia, Tasmania, China and Japan, genetic structure of Abalone populations have also been reported (Li and Kijima, 2006; Li et al., 2006; Maynard et al., 2004; Tang et al., 2004; Temby et al., 2007; Zhang et al., 2006).

In particular, a recent study on Red Abalone (Haliotis rufescens) showed that the population along the California coastline is structured geographically (Gruenthal et al., 2007). In this case, there seems to be a shift in population structure around the Cape Mendocino region. This region has also been shown to be a breakpoint in the distributions of many other species, such as mussels (Braby and Somero, 2006) and a variety of fishes (Hyde and Vetter, 2009; Tolimieri and Levin, 2006). Recently, Kelly and Palumbi (2010) showed strong population genetic structure in six species of invertebrates across the Mendocino region. This is attributed to several physical factors, especially a strong jet of upwelling water at the Cape as well as temperature gradients.


Coast lineCurrently, this project investigates the genetic population structure of Red Abalone (Haliotis rufescens) along the coastline of California. Abalone populations from northern California (Crescent City) down to Monterey Bay are being sampled. To study genetic differences on this scale, microsatellite DNA data (“DNA finger-printing”), or sequences from the control region of mitochondrial DNA are regularly used, both rather simple and cost-effective methods. Unfortunately, this kind of data has not always given good results in the past (e.g. Gruenthal et al., 2007). Therefore, the genome of the Abalone is now being studied in further detail, by extracting total RNA from select individuals and using the Illumina Hi-Seq platform to assemble a reference transcriptome. 

The reference transcriptome can then be used for multiple tasks. Candidate genes can be identified which could elucidate the population structure of H. rufescens as well as other Abalone species along the coast, which in turn could be correlated with dispersal patterns as well as local environmental conditions. Outlier tests could also identify genes under selection and perhaps help us understand how upwelling conditions with cold, low-pH water could locally affect the genetic makeup of populations along the coast.


Knowledge of how Abalones are structured geographically and what processes regulate their recruitment is crucial for management and for the task of rebuilding the stocks of these seriously overfished species. This study will help us gain an understanding of the small-scale variability which could then be extrapolated to study large scale variation, not only in California, but all over the world. As many other benthic invertebrates and fish show similar patterns, these results will hopefully also be applicable to the management of a wide variety of organisms.


Braby CE, Somero GN. 2006. Ecological gradients and relative abundance of native (Mytilus trossulus) and invasive (Mytilus galloprovincialis) blue mussels in the California hybrid zone. Marine Biology 148(6):1249-1262.

Chambers MD, VanBlaricom GR, Hauser L, Utter F, Friedman CS. 2006. Genetic structure of black abalone (Haliotis cracherodii) populations in the California islands and central California coast: Impacts of larval dispersal and decimation from withering syndrome. Journal of Experimental Marine Biology and Ecology 331(2):173-185.

Gruenthal KM, Acheson LK, Burton RS. 2007. Genetic structure of natural populations of California red abalone (Haliotis rufescens) using multiple genetic markers. Marine Biology 152(6):1237-1248.

Gruenthal KM, Burton RS. 2005. Genetic diversity and species identification in the endangered white abalone (Haliotis sorenseni). Conservation Genetics 6(6):929-939.

Gruenthal KM, Burton RS. 2008. Genetic structure of natural populations of the California black abalone (Haliotis cracherodii Leach, 1814), a candidate for endangered species status. Journal of Experimental Marine Biology and Ecology 355(1):47-58.

Gutierrez-Gonzalez JL, Cruz P, del Rio-Portilla MA, Perez-Enriquez R. 2007. Genetic structure of green abalone Haliotis fulgens population off Baja California, Mexico. Journal of Shellfish Research 26(3):839-846.

Hyde JR, Vetter RD. 2009. Population genetic structure in the redefined vermilion rockfish (Sebastes miniatus) indicates limited larval dispersal and reveals natural management units. Canadian Journal of Fisheries and Aquatic Sciences 66(9):1569-1581.

Kashiwada JV, Taniguchi IK. 2007. Application of recent red abalone Haliotis rufescens surveys to management decisions outlined in the California Abalone Recovery and Management Plan. Journal of Shellfish Research 26(3):713-717.

Kelly, RP, Palumbi, SR. 2010. Genetic Structure Among 50 Species of the Northeastern Pacific Rocky Intertidal Community. PLos One 5(1):e8594.

Leiva GE, Castilla JC. 2001. A review of the world marine gastropod fishery: evolution of catches, management and the Chilean experience. Rev Fish Biol Fish 11(4):283-300.

Li Q, Kijima A. 2006. Genetic variation of Chinese and Japanese wild Pacific abalone (Haliotis discus hannai) measured by microsatellite DNA markers. Acta Oceanologica Sinica 25(4):146-155.

Li ZB, Appleyard SA, Elliott NG. 2006. Population structure of Haliods rubra from South Australia inferred from nuclear and mtDNA analyses. Acta Oceanologica Sinica 25(4):99-112.

Maynard BT, Hanna PJ, Benzie JAH. 2004. Microsatellite DNA analysis of southeast Australian Haliotis laevigata (Donovan) populations - Implications for Ranching in Port Phillip Bay. Journal of Shellfish Research 23(4):1195-1200.

Micheli F, Shelton AO, Bushinsky SM, Chiu AL, Haupt AJ, Heiman KW, Kappel CV, Lynch MC, Martone RG, Dunbar RB, Watanabe J. 2008. Persistence of depleted abalones in marine reserves of central California. Biological Conservation 141(4):1078-1090.

Miller KJ, Maynard BT, Mundy CN. 2009. Genetic diversity and gene flow in collapsed and healthy abalone fisheries. Molecular Ecology 18(2):200-211.

Pespeni MH, Oliver TA, Manier MK, Palumbi SR. in prep. Resriction Site Tiling Analysis (RSTA): An accurate and cost-effective method for simultaneous discovery and genotyping of genome-wide polymorphisms.

Tang S, Tassanakajon A, Klinbunga S, Jarayabhand P, Menasveta P. 2004. Population structure of tropical abalone (Haliotis asinina) in coastal waters of Thailand determined using microsatellite markers. Marine Biotechnology 6(6):604-611.

Temby N, Miller K, Mundy C. 2007. Evidence of genetic subdivision among populations of blacklip abalone (Haliotis rubra Leach) in Tasmania. Marine and Freshwater Research 58(8):733-742.

Tolimieri N, Levin PS. 2006. Assemblage structure of eastern pacific groundfishes on the US continental slope in relation to physical and environmental variables. Trans Am Fish Soc 135(2):317-332.

Zhang G, Zhang X, Liu X. 2006. The genetic structure and variation of wild populations of Pacific abalone, Haliotis discus hannai Ino in China seas. Studia Marina Sinica 47:194-205.
Hopkins Marine Station, Stanford University, 120 Ocean View Blvd., Pacific Grove, CA 93950