Mitochondrial DNA (COI) analyses reveal that amphipod diversity is associated with environmental heterogeneity in deep-sea habitats MATTHEW A. KNOX,* IAN D. HOGG,* CONRAD A. PILDITCH,* ANNE-NINA LO ¨ RZ, † PAUL D. N. HEBERT ‡ and DIRK STEINKE ‡ *Department of Biological Sciences, University of Waikato, Private Bag 3105, Hamilton, New Zealand, †National Institute of Water and Atmospheric Research (NIWA) Ltd, Private Bag 14901, Wellington, New Zealand, ‡Biodiversity Institute of Ontario, University of Guelph, 50 Stone Road East, Guelph, ON, N1G 2W1, Canada Abstract The relationship between species diversity and environmental parameters is poorly understood for the mobile macrofauna of deep-sea habitats due to under-sampling and subsequent lack of accurate taxonomic information. To redress this, cytochrome oxi- dase c subunit I (COI) DNA sequences were used to estimate species diversity and to compare phoxocephalid amphipod assemblages among 20 stations encompassing a range of environmental conditions. Two regions, east (Chatham Rise) and west (Chal- lenger Plateau) of New Zealand were sampled to depths of 200–1200 m with an epibenthic sled. Using a comparison among identified morphospecies, we found a clear gap in sequence divergences between 6% and 13% and used a 6% threshold to designate molecular operational taxonomic units (MOTUs), as a surrogate to putative species. DNA sequences (n = 297) revealed high total diversity (n = 49 MOTUs), as well as high beta diversity (28 MOTUs found at single location only). Novel phoxo- cephalid MOTUs were found at most stations, especially on Challenger Plateau and the flanks of Chatham Rise. Analyses of interstation assemblages revealed a major split between regions, indicating minimal overlap in taxon distributions. A cluster of highly similar stations was identified, broadly distributed over the crest of Chatham Rise, in association with elevated food availability, probably resulting from higher sur- face productivity and relatively shallow depth. Accordingly, multivariate analysis revealed a strong correlation between phoxocephalid assemblages and food supply. This study highlights the value of molecular approaches, in particular COI sequences, for quantifying and comparing diversity in under-sampled and/or under-studied taxa. Keywords: biodiversity, continental shelf, DNA barcoding, New Zealand, Phoxocephalidae Received 25 March 2012; revision received 1 June 2012; accepted 6 June 2012 Introduction Determining and understanding changes in community structure and composition across environmental gradi- ents is an essential element of community ecology (Levin 1992). However, with an estimated 10 7 species in the deep sea (Grassle & Maciolek 1992), the vast major- ity of which await discovery and/or formal descriptions (Lo ¨ rz & Brandt 2003; Brandt & Berge 2007), compari- sons of deep-sea communities are frequently limited to a relatively small group of easily identified megafaunal taxa or to the analysis of higher taxonomic levels. Due to a lack of accurate taxonomic information, macrofauna are often overlooked despite their domination of bio- mass, especially at relatively shallow (200–4000 m) depths (Rex et al. 2006). To overcome this lack of taxo- nomic data, we utilize a molecular-based approach to assess diversity and community composition of phoxo- cephalid amphipods from a series of stations along the Correspondence: Matthew Knox, Fax: +64 7 838 4324; E-mail: mak14@waikato.ac.nz © 2012 Blackwell Publishing Ltd Molecular Ecology (2012) doi: 10.1111/j.1365-294X.2012.05729.x