Molecular Support for Marine Sculpin (Cottidae; Oligocottinae)
Total Page：16
File Type：pdf, Size：1020Kb
Available online at www.sciencedirect.com Molecular Phylogenetics and Evolution 46 (2008) 475–483 www.elsevier.com/locate/ympev Molecular support for marine sculpin (Cottidae; Oligocottinae) diversification during the transition from the subtidal to intertidal habitat in the Northeastern Pacific Ocean Marina L. Ramon a,*, Matthew L. Knope b,1 a University of California Santa Cruz, Department of Ecology and Evolutionary Biology, Long Marine Laboratory, 100 Shaffer Road COH 247, Santa Cruz, CA 95064, USA b San Francisco State University, Department of Biology, 1600 Holloway Avenue, San Francisco, CA 94132, USA Received 27 March 2007; revised 3 November 2007; accepted 9 November 2007 Available online 22 November 2007 Abstract Sculpins in the genera Ruscarius, Artedius, Clinocottus, and Oligocottus are common intertidal and subtidal benthic fishes of the Northeastern Pacific Ocean. While there has been a long history of attempts to reconstruct the evolutionary relationships within this clade, studies have largely resulted in conflicting conclusions. Current ideas regarding the limits of species and genera in this subfamily (Oligocottinae) and their branching order are based primarily on morphology [Bolin, R.L., 1944. A Review of the Marine Cottid Fishes of California. Natural History Museum of Stanford University, Stanford University, California; Bolin, R.L., 1947. The Evolution of the Marine Cottidae of California with a Discussion of the Genus as a Systematic Category. Stanford University, California]. The primary objectives of this study are: (a) to determine if the phylogenetic relationships inferred from DNA characters are concordant with those inferred from morphological characters and (b) to determine if a habitat shift from the subtidal to the intertidal environment resulted in the diversification of the group. Cytochrome b and Nicotinamide Adenine Dinucleotide Dehydrogenase subunit one mitochondrial gene fragments and one nuclear intron (S7 ribosomal protein) were sequenced in order to infer the phylogenetic relationships within this sub- family. Maximum likelihood and Bayesian algorithms were employed to reconstruct phylogenetic trees. We found that several genera in this clade are not monophyletic and that there is a clear phylogenetic signal indicating that a habitat shift from the subtidal to the inter- tidal habitat has resulted in the diversification of the Oligocottinae. Ó 2007 Elsevier Inc. All rights reserved. Keywords: Cottidae; Phylogeny; mtDNA; Nuclear DNA; Sculpins; Intertidal 1. Introduction radiations (Appelbaum et al., 2002; Burton et al., 2006; Marko, 2005). In a review of the systematics of intertidal The origin of marine intertidal communities has long fishes, Chotkowski et al. (1999) concluded that the ichthy- been a perplexing question to natural historians. Approxi- ofaunal assemblage is a result of repeated invasions by sub- mately 150 years ago, Charles Darwin asked what causes tidal species and subsequent speciation events. While it is some lineages to diversify more than others. More recently, clear that intertidal fish assemblages have evolved from evolutionary ecologists have begun to explore the particu- multiple independent lineages, how these radiations have lar mechanisms that may have facilitated marine intertidal evolved remains an unanswered question. Intertidal fish are found in several superorders through- * out the world (including Euteleostei, Paracanthopterygii, Corresponding author. Fax: +1 831 459 3383. and Acanthopterygii). Within the Acanthopterygii, the per- E-mail address: [email protected] (M.L. Ramon). 1 Present address: University of Hawaii, Manoa, Department of comorph orders Scorpaeniformes, and Perciformes contain Zoology, Edmondson 256, Honolulu, HI 96822, USA. the greatest number of intertidal species. However, neither 1055-7903/$ - see front matter Ó 2007 Elsevier Inc. All rights reserved. doi:10.1016/j.ympev.2007.11.005 476 M.L. Ramon, M.L. Knope / Molecular Phylogenetics and Evolution 46 (2008) 475–483 of these orders are comprised exclusively of intertidal spe- phological characters and (b) to determine if a habitat shift cies (Chotkowski et al., 1999; Nelson, 2006). Within the from the subtidal to the intertidal environment caused the order Scorpaeniformes, sculpins in the family Cottidae pro- diversification of the group. To evaluate these questions, vide an excellent opportunity to examine whether a habitat we generated a molecular phylogeny based on two mito- shift into the intertidal has lead to speciation. In particular, chondrial genes (cytochrome b and Nicotinamide Adenine we chose to examine the subfamily Oligocottinae, which is Dinucleotide Dehydrogenase subunit one) and a nuclear considered to be a monophyletic group comprised of 16 intron (ribosomal protein S7) for 27 recognized taxa. species. Within this subfamily some species are found only in the intertidal, others only in the subtidal, and some in 2. Materials and methods both habitats. Hence, this is an ideal system for a case study exploring whether a habitat shift can lead to 2.1. Collection, amplification, and sequencing diversification. Samples of sculpins were collected from several loca- 1.1. Background on Northeast Pacific sculpins tions in Baja California, California, Oregon, Washington, and Alaska (Table 1). Whenever possible, several individu- Worldwide, sculpins in the family Cottidae include als were collected from different locations to assess geo- approximately 275 species found primarily in boreal and graphical intraspecific genetic variation. Intertidal cold-temperate regions (Nelson, 2006). Cottids (sensu specimens were collected in the field by dipnet at low tides. stricto) are generally small, intertidal and subtidal benthic Nearshore subtidal specimens were collected by dipnet or fishes that exhibit extensive diversity in their reproductive pole speared by divers using SCUBA. Deepwater speci- biology, feeding ecology, and habitat choice (Bolin, 1944; mens were collected by trawl on the R/V David Starr Jor- Normark et al., 1991; Petersen et al., 2005; Yaakub et al., dan. Whole genomic DNA was extracted from muscle 2006; Yoshiyama et al., 1986). The family Cottidae is gen- tissue or fin clippings that had been stored in 95% ethanol. erally considered to be of recent (Oligocene or Miocene) Tissues were digested overnight at 55 °C in 500 ll salt North Pacific origin (Berg, 1947; Macfarlane, 1923) but extraction buffer (400 mM NaCl, 10 mM Tris, 2 mM is not well represented in the fossil record. Although scul- EDTA, 1% SDS, and 20 lg/ml proteinase K). DNA was pins are found in all oceans of the world except the purified by standard chloroform extractions and isopropa- Indian Ocean, the Northern Pacific has been identified nol precipitation (Sambrook et al., 1989). Samples were as the center of origin and diversity for the family (Esch- processed using a standard PCR method to amplify mito- meyer, 1983; Watanabe, 1969; Yabe, 1985). With over 40 chondrial cytochrome b (GluDG-L and CB3H from currently recognized genera and 90 species distributed Palumbi, 1991), Nicotinamide Adenine Dinucleotide Dehy- between Baja California and the Aleutian Islands, the drogenase subunit one (L3827, L4500, H5191 modified Cottidae represent one of the most species-rich taxa with from Sorenson et al., 1999) and the first nuclear intron approximately 10% of the known species in the ichthyofa- S7 ribosomal protein (S7RPEX1F and S7RPEX2R, Chow una of this region (Bolin, 1944; Howe and Richardson, and Hazama, 1998). PCR amplifications were performed in 1978). a 25 ll volume with 1 U AmpliTaq DNA Polymerase (Per- While there has been a long history of attempts to recon- kin-Elmer), the manufacturer’s buffer, 2.5 mM MgCl2, struct the phylogenetic relationships of the Northeastern 0.25 mM each dNTP, and 1 lM each primer. PCR prod- Pacific cottids (Bolin, 1947; Gill, 1889), many relationships ucts were gel purified in 1% agarose, excised from the gel, remain largely unresolved. Current ideas about the evolu- and then recovered using a QIAquick Gel Extraction Kit tionary history and definitions of genera in this group of (QIAGEN). Double-stranded PCR products were cottids are based primarily on Bolin (1944, 1947). Using sequenced directly with the same primers used for the a phenetic approach, Bolin (1947) was the first to offer a PCR amplifications using BigDye Chemistry (Applied Bio- branching diagram for the Northeastern Pacific cottids. systems). The sequencing reaction products were cleaned of There has since been little formal re-investigation of Bolin’s unincorporated dyes and salts by isoproponal precipitation proposed phylogeny. Yabe (1985) used 60 osteologic and and then run on an ABI3100 DNA Sequencer (Applied myologic characters to construct a hand-rendered cladistic Biosystems). Sequences of the two DNA strands were phylogeny of 61 genera of the superfamily Cottoidea. In aligned and reconciled in Sequence Navigator (Applied addition, Jackson (2003) used 100 plus morphological Biosystems). All sequences have been deposited in Gen- characters to address the phylogenetic relationships within Bank (Accession Nos. EF521313–EF521387). the Cottoidea. Although these phylogenies helped to resolve cottoid/cottid arguments, most generic and specific 2.2. Phylogenetic analysis of mtDNA and nuclear data relationships within the Cottidae remain largely unresolved. Alignments of mitochondrial gene regions were unam- The primary objectives of this study are: (a) to deter- biguous and were aligned by eye using the program Se– mine if the phylogenetic