Utility of psbA and nSSU for phylogenetic reconstruction in the Corallinales based on New Zealand taxa Judith E.S. Broom a, * , Darren R. Hart a , Tracy J. Farr b , Wendy A. Nelson b , Kate F. Neill b , Adele S. Harvey c , William J. Woelkerling c a Department of Biochemistry, University of Otago, P.O. Box 56, Dunedin, New Zealand b National Institute of Water and Atmospheric Research Ltd. (NIWA), Private Bag 14901, Wellington, New Zealand c Department of Botany, La Trobe University, Melbourne, Australia Received 28 May 2007; revised 17 December 2007; accepted 18 December 2007 Available online 28 December 2007 Abstract A number of molecular studies of the Corallinales, a calcified order of the red algae, have used the conservative nSSU gene to inves- tigate relationships within the order. However interspecific variation at this locus is low for closely related species, limiting resolution of recently diverged groups. In this study, we obtained psbA sequence data from specimens of the order from New Zealand that had been identified according to current taxonomic criteria. We compared phylogenetic analyses based on psbA with those based on nSSU for the same dataset, and also analysed nSSU sequences of the New Zealand material with nSSU sequences of Corallinales taxa from other parts of the world. Our study shows that psbA has considerable potential as a marker for this group, being easily amplified and considerably more variable than nSSU. Combined analyses using both markers provide significant support for relationships at both distal and termi- nal nodes of the analysis. Our analysis supports the monophyly of all three families currently defined in Corallinales: the Sporolithaceae, Hapalidiaceae and Corallinaceae, and indicates cryptic speciation in Mesophyllum and Spongites. Ó 2007 Elsevier Inc. All rights reserved. Keywords: Corallinales; nSSU; psbA; Hapalidiaceae; Corallinaceae; Sporolithaceae; New Zealand; Mesophyllum; Spongites 1. Introduction Members of the order Corallinales (Rhodophyta) are macroscopic calcareous algae, showing substantial calcifi- cation of the cell walls. These algae grow from the polar regions to the tropics, and are important components of coastal ecosystems in both intertidal and subtidal environ- ments. Coralline algae can grow as either upright, genicu- late forms with nodal decalcification that provides some flexibility to the thallus, or crustose, non-geniculate forms appressed to the substrate, which may be rock, animal, another alga or a marine plant. Some species have been shown to provide specific chemical cues which trigger set- tling of invertebrate larvae (e.g. Roberts, 2001). Members of the order are also important constituents of reefs (van den Hoek et al., 1995), where they are thought to provide structural reinforcement at wave-exposed sites. Unattached or free-living non-geniculate corallines, known as rhodo- liths or mae ¨rl, form extensive beds on soft sediments, occurring worldwide over wide latitudinal and depth ranges (Foster, 2001; Steller et al., 2003). These beds are known to support a rich diversity of associated species including rare, unusual and endemic species. Recent studies have revealed that these benthic communities are vulnera- ble to damage from human activities. They are easily impacted by a number of different anthropogenic activities such as harvesting, trawling and anchoring, activities that reduce water quality, and the creation of coastal structures that influence current flow such as breakwaters and mari- nas (Barbera et al., 2003; Steller et al., 2003). Taxonomy of non-geniculate coralline algae often rests on reproductive characters such as the structure of 1055-7903/$ - see front matter Ó 2007 Elsevier Inc. All rights reserved. doi:10.1016/j.ympev.2007.12.016 * Corresponding author. Fax: +64 3 479 5276. E-mail address: judy.broom@otago.ac.nz (J.E.S. Broom). www.elsevier.com/locate/ympev Available online at www.sciencedirect.com Molecular Phylogenetics and Evolution 46 (2008) 958–973