TECHNICAL NOTE Identification of seventeen microsatellite markers for conservation genetic studies of the endemic anemonefish, Amphiprion mccullochi Martin H. van der Meer • Michael G. Gardner • Jean-Paul A. Hobbs • G. P. Jones • Lynne van Herwerden Received: 25 August 2011 / Accepted: 28 August 2011 / Published online: 14 September 2011 Ó Springer Science+Business Media B.V. 2011 Abstract Endemic species at remote islands have a high risk of extinction because they often exhibit ecological, biological and genetic traits that make them particularly vulnerable to disturbances. McCulloch’s anemonefish (Amphiprion mccullochi) is endemic to a few oceanic reefs off Australia’s east coast and is an habitat specialist. Using 454 shotgun sequencing, we developed and evaluated primers for seventeen independent microsatellite loci to reveal gene flow, population genetic structure and genetic diversity across three isolated reefs. Observed and expected heterozygosities ranged from 0.556 to 1 and 0.543 to 0.907, respectively, in 30 Lord Howe Island individuals. When cross tested with the close relative, Amphiprion akindynos, amplification was successful with high levels of polymor- phism. These loci will therefore be useful in studies of A. mccullochi, A. akindynos and possibly other closely related anemonefish. Keywords Coral reef fish Á Island endemics Á Genetic diversity Á Cross-species amplification Remote offshore islands usually contain high numbers of endemic species (Gillespie et al. 2008), which makes them a high conservation priority (Gillespie et al. 2008). Conserving endemics is challenging because of their high extinction risk due to small population size, ecological specialisation, limited dispersal and low genetic diversity (McKinney 1997; Frankham 1998). The McCulloch’s anemonefish (Amphiprion mccullochi) has arguably the smallest geographic range size of any anemonefish (ende- mic to offshore Australian waters, Coleman 1980) and is a habitat specialist living on a single host anemone, Entac- maea quadricolor (Fautin and Allen 1992). To date, gene flow, population genetic structure and genetic diversity of A. mccullochi have not been examined. This paper describes the development of 17 polymorphic microsatellite markers for A. mccullochi using 454 shotgun pyrosequenc- ing on a Roche GS-FLX (Australain Genome Research Facility, AGRF, Brisbane, Australia). Genomic DNA was extracted using a Qiagen Gentra Puregene extraction protocol and was RNAse treated. The DNA (1 lg) was shotgun sequenced on 12.5% of a Roche GS-FLX (Australian Genome Research Facility, AGRF, Brisbane, Australia) following Gardner et al. (2011). The resulting sequences (totalling 114,272 reads, average sequence length of 350, total GC content of 40.08%) were screened for pure di to hexanucleotide microsatellite loci with six or more repeats. QDD v1.3 (Meglecz et al. 2009) identified 7,224 (6.32% of sequences) microsatellite loci, M. H. van der Meer (&) Á L. van Herwerden Molecular Ecology and Evolution Laboratory, Australian Tropical Sciences and Innovation Precinct, James Cook University, Townsville 4811, Australia e-mail: martinhvandermeer@gmail.com M. H. van der Meer Á J.-P. A. Hobbs Á G. P. Jones Á L. van Herwerden School of Marine and Tropical Biology, James Cook University, Townsville 4811, Australia M. G. Gardner School of Biological Sciences, Flinders University, GPO Box 2100, Adelaide, SA 5001, Australia M. G. Gardner Australian Centre for Evolutionary Biology and Biodiversity, University of Adelaide, Adelaide, SA 5005, Australia J.-P. A. Hobbs Á G. P. Jones ARC Centre of Excellence for Coral Reef Studies, James Cook University, Townsville 4811, Australia 123 Conservation Genet Resour (2012) 4:247–250 DOI 10.1007/s12686-011-9517-1