Journal of Biogeography (J. Biogeogr.) (2011) 38, 1600–1612 ORIGINAL Phylogeography of Emerita analoga ARTICLE (Crustacea, Decapoda, Hippidae), an eastern Pacific Ocean sand crab with long-lived pelagic larvae Michael N Dawson1,2, Paul H. Barber3*, Laura I. Gonza´lez-Guzma´n4, Robert J. Toonen5, Jenifer E. Dugan6 and Richard K. Grosberg1 1Center for Population Biology, College of ABSTRACT Biological Sciences, 1 Shields Avenue, Aim Phylogeographic analyses have confirmed high dispersal in many marine University of California, Davis, CA 95616, USA, 2School of Natural Sciences, 5200 North taxa but have also revealed many cryptic lineages and species, raising the question Lake Road, University of California, Merced, of how population and regional genetic diversity arise and persist in dynamic CA 95343, USA, 3Department of Ecology and oceanographic settings. Here we explore the geographic evolution of Emerita Evolutionary Biology, 621 Charles E. Young analoga, an inter-tidal sandy beach crab with an exceptionally long pelagic larval Drive South, University of California, Los phase and wide latitudinal, amphitropical, distribution. We test the hypothesis Angeles, CA 90095, USA, 4Section of that eastern Pacific E. analoga constitute a single panmictic population and Integrative Biology, University of Texas at examine the location(s), timing and cause(s) of phylogeographic differentiation. Austin, 1 University Station A6700, Austin, TX Location Principally the eastern Pacific Ocean. 78712, USA, 5The Hawai’i Institute of Marine Biology, University of Hawaii at Manoa, Methods We sequenced cytochrome c oxidase subunit I (COI) from 742 E. analoga Coconut Island, PO Box 1346, Kane’ohe, HI specimens collected between 1997 and 2000 and downloaded homologous 96744, USA, 6Marine Science Institute, sequences of congeners from GenBank. We reconstructed a phylogeny for Emerita University of California, Santa Barbara, CA species using maximum likelihood and Bayesian methods and estimated times to 93106, USA most recent common ancestors (TMRCAs), using a COI divergence rate of 1% ) Myr 1 and timing of closure of the Central American Seaway. We constructed the COI haplotype network of E. analoga using statistical parsimony, calculated population genetic and spatial structure statistics in Arlequin, and estimated the demographic history of E. analoga using Bayesian skyline analysis. Results Population subdivision and allele frequency differences were insignificant among north-eastern Pacific locations over 2000 km apart (FST = 0.00, P = 0.70), yet two distinct phylogroups were recovered from the north-eastern and south- eastern Pacific (FCT = 0.87, P < 0.001). Amphitropical differentiation of these temperate clades occurred after TMRCA 1.9 ± 0.02 (mean ± SE) Ma and E. analoga has expanded into its present-day north-eastern Pacific range since c. 250 ka. Main conclusions Emerita analoga is not panmictic but is very widely dispersed and approaching genetic homogeneity, i.e. ‘eurymixis’, in the north-eastern Pacific. North-eastern and south-eastern Pacific populations of E. analoga probably became isolated c. 1.5 Ma as the tropical eastern Pacific Ocean warmed and expanded, intensifying barriers to gene flow. The fragmentation of a widespread ancestral species previously connected by long-distance gene flow (‘soft vicariance’) coincident with changing oceanographic conditions may be a common theme in the evolution of Emerita species and in other highly dispersive taxa. Highly dispersive species may differentiate because of, not despite, the dynamic oceanographic setting. *Correspondence: Paul Barber, Department of Ecology and Evolutionary Biology, 621 Charles Keywords E. Young Drive South, University of California, Los Angeles, CA 90095, USA. Dispersal, Emerita, gene flow, habitat, marine biogeography, Pacific Ocean, E-mail: [email protected] pelagic larval duration, phylogeography, sand crab, vicariance. 1600 http://wileyonlinelibrary.com/journal/jbi ª 2011 Blackwell Publishing Ltd doi:10.1111/j.1365-2699.2011.02499.x Phylogeography of a sand crab on sandy beaches from Salavary, Peru, to False Bay, Argentina INTRODUCTION (Efford, 1970, 1976). Across this range, life-history parameters Numerous molecular genetic analyses of population structure such as size and age at maturity, growth rate, maximum in marine taxa reveal a limited phylogeographic structure (e.g. individual size and survival, all vary significantly with latitude Lessios & Robertson, 2006), consistent with planktonic (Osorio et al., 1967; Dugan et al., 1994). Recruitment, which dispersal driven by ocean currents (Hardy, 1962; Palumbi, can occur from April to November throughout California, also 1994; Hellberg, 2009) over geographic scales considerably varies both locally and regionally (Diehl et al., 2007). broader than in terrestrial systems (e.g. Kinlan & Gaines, The high abundance, long pelagic larval duration and broad 2003). However, the discovery of many cryptic lineages in what range that encompasses environmental gradients across which were once thought to be widely distributed species (Knowlton, many other taxa exhibit genetic discontinuities or range limits, 2000; Bickford et al., 2007) raises the question of how suggest that E. analoga is an ecological generalist consisting of population and regional genetic diversity arise and persist in a single, large population (Dugan et al., 2000). Alternatively, dynamic oceanographic settings expected to thoroughly mix geographic variation in recruitment in California, coupled genes among distant localities (Palumbi, 1994; Hickerson & with the occurrence of disjunct populations in the Gulf of Meyer, 2008). California and South America, imply that gene flow could be Developmental mode, especially the time that larvae spend limited across at least some parts of the range, promoting in the plankton, undoubtedly plays a critical role in governing differentiation and perhaps local adaptation in E. analoga. genetic and phylogeographic structure in the sea (e.g. Schel- Molecular analyses to date have provided little clarification, tema, 1988; Doherty et al., 1995; Bohonak, 1999; Dawson, with studies of different scale and scope variously evincing 2001; Lester et al., 2007); however, oceanography and its high gene flow (Beckwitt, 1985) or substantial regional effects on larval transport (e.g. Cowen et al., 2000; Byers & differentiation (Tam et al., 1996; Haye et al., 2002). Here, we Pringle, 2006; Galindo et al., 2006), sea-level or land-level bridge prior analyses to describe phylogeographic structure in change (e.g. Lessios, 2008) and selection (e.g. Hilbish & Koehn, E. analoga of the eastern Pacific Ocean and to infer the 1985; Gilg & Hilbish, 2003) may also influence the geographic location(s), timing and cause(s) of any phylogeographic distribution of genetic variation and spatial pattern of differentiation. evolution (e.g. Hellberg, 1998; Dawson & Hamner, 2005; Faucci et al., 2007; Hickerson & Meyer, 2008; Lessios, 2008; MATERIALS AND METHODS Rocha & Bowen, 2008). The emerging picture is that life history strongly influences gene flow, population structure and Sample collection, DNA extraction, amplification and species ranges (e.g. Bohonak, 1999), but regional phylogeo- sequencing graphic and biogeographic patterns emerge from the interac- tions, past and present, between larval life histories and shared We collected E. analoga from North American beaches environmental constraints (Lester et al., 2007; Pelc et al., throughout California in October 1997, 1998 and 1999, from 2009). sites in Chile in 1998, and from Baja California to Oregon in The vast majority of marine phylogeographic studies focus 2000 (Table 1). We haphazardly sampled crabs from targeted on rocky shore, estuarine and shallow reef macroinvertebrate sandy beaches, preserved them in ethanol, and when a large epifauna and fishes (see, for example, meta-analyses and number of crabs were collected we arbitrarily chose 15–20 reviews by Dawson, 2001; Hellberg, 2009; and Kelly & individuals from each beach for genetic analysis. Palumbi, 2009; see also Dugan et al., 2010). Given these We extracted genomic DNA using a 10% Chelex solution environmental biases, an important question is whether (Bio-Rad, Hercules, CA, USA; Walsh et al., 1991) or Gentra emerging phylogeographic generalities also apply to other Systems’ (Minneapolis, MN, USA) PureGene marine inverte- groups living in more spatially and temporally dynamic brate (no. 00690) extraction protocol. We used polymerase habitats, such as infauna of exposed sandy beaches and chain reaction (PCR) to amplify cytochrome c oxidase subunit holoplankton, or whether such under-represented biotas have I (COI) using the generic primers LCO1490 and HCO2198 a suite of quantitatively different characteristics? (Folmer et al., 1994) or with E. analoga-specific internal The mole crab Emerita analoga (Stimpson, 1857) inhabits primer pairs EA-LCO (5¢-TAT ACT TCA TTT TCG GAG CC) the inter-tidal zone of wave-exposed sandy beaches of the with EA-HCO (5¢-AGG TGT TGA TAT AGA ACT GG) or temperate eastern Pacific Ocean. It is the most abundant ECL1 (5¢-GGA ACA TTA TAC TTC ATT TTC GGA) with resident of these dynamic habitats, with up to 79,000 ECH1 (5¢-GGA TTC TTG ACT CAC AAT ATG G). Thermo- individuals per metre of shoreline (Dugan et al., 2003). cycling began with a hotstart followed by 32–40 cycles of 30– Emerita analoga also has extensive dispersal potential due to 45 s at 94 °C, 30–45 s at 48–55 °C, and 45–60 s at 72 °C, and its 3- to 4-month-long planktonic larval