RESEARCH ARTICLE Protection from ﬁshing alters the species composition of ﬁsh assemblages in a temperate-tropical transition zone Dianne L. Watson Euan S. Harvey Gary A. Kendrick Kim Nardi Marti J. Anderson Received: 16 January 2007 / Accepted: 2 July 2007 / Published online: 21 July 2007 Ó Springer-Verlag 2007 Abstract Closure of areas to ﬁshing is expected to result in an increase in the abundance of targeted species; how- ever, changes to populations of species not targeted by ﬁshermen will depend upon their role in the ecosystem and their relationship with targeted species. The effects of protection on targeted and non-targeted reef ﬁsh species at the Houtman Abrolhos Islands, Western Australia were studied using baited remote underwater stereo–video cameras. Video images were collected from shallow (8– 12 m) and deep (22–26 m) reef sites inside a Marine Protected Area (MPA) at each of three island groups and from three replicate ﬁshed locations at each of these groups that span a temperate-tropical transition area. The MPAs were established in 1994 and vary in size from 13.72 km 2 at the Pelsaert group in the south to 22.29 km 2 at the Easter group to 27.44 km 2 at the Wallabi group in the north. The relative abundances of 137 ﬁsh species from 42 families were recorded. Large differences in ﬁsh assemblage structure existed between MPA and ﬁshed locations, and also between shallow and deep regions. Targeted ﬁsh species Plectropomus leopardus, Lethrinus miniatus, Lethrinus nebulosus, Pagrus auratus and Glaucosoma hebraicum were more abundant inside MPAs than in areas open to ﬁshing. Their abundance inside MPAs was be- tween 1.13 and 8 times greater than their abundance at ﬁshed locations. For non-targeted ﬁsh species many were more abundant in areas open to ﬁshing, e.g. Coris auric- ularis, Thalassoma lutescens, Thalassoma lunare, Dascyl- lus trimaculatus, however others were conversely more abundant inside MPAs, e.g. Gymnothorax spp, Kyphosus sydneyanus, Scarus microhinos, Chromis westaustralis, Chaetodon spp. This study demonstrates that the removal of abundant targeted species from an ecosystem by ﬁshing can indirectly impact non-ﬁshed species and alter the tro- phic structure of ﬁsh assemblages. Introduction There is increasing scientiﬁc evidence demonstrating that the abundance, biomass and length of targeted ﬁsh species increase inside Marine Protected Areas (MPAs) relative to areas that remain open to ﬁshing (Russ and Alcala 1996; Babcock et al. 1999; Russ et al. 2005). These targeted ﬁsh species are often top-predators and their removal from the ecosystem by ﬁshing can affect other reef organisms by inﬂuencing processes such as herbivory, predation and competition (Babcock et al. 1999; Pinnegar et al. 2000; Willis and Anderson 2003). In protecting targeted ﬁsh species MPAs can also shield marine ecosystems against Communicated by G.F. Humphrey. Electronic supplementary material The online version of this article (doi:10.1007/s00227-007-0767-0) contains supplementary material, which is available to authorized users. D. L. Watson (&)  E. S. Harvey  G. A. Kendrick CRC for Coastal Zone, Estuary and Waterway Management, School of Plant Biology, The University of Western Australia, 35 Stirling Hwy, Crawley, Perth, WA 6009, Australia e-mail: dwatson@plants.uwa.edu.au K. Nardi Department of Fisheries, Western Australia, PO Box 1171, Geraldton, WA 6531, Australia M. J. Anderson Department of Statistics, University of Auckland, Private Bag 92019, Auckland, New Zealand 123 Mar Biol (2007) 152:1197–1206 DOI 10.1007/s00227-007-0767-0