Molecular Ecology (2007) 16, 127–138 doi: 10.1111/j.1365-294X.2006.03132.x © 2006 The Authors Journal compilation © 2006 Blackwell Publishing Ltd Blackwell Publishing Ltd The genetic effective and adult census size of an Australian population of tiger prawns (Penaeus esculentus) JENNIFER R. OVENDEN,* DAVID PEEL,*‡ RAEWYN STREET,* ANTHONY J. COURTNEY,* SIMON D. HOYLE,*§ SAMANTHA L. PEEL * and HEATHER PODLICH †¶ *Molecular Fisheries Laboratory, Queensland Department of Primary Industries and Fisheries, Floor 6, North Tower, Queensland Biosciences Precinct, University of Queensland, St Lucia, Queensland 4072 Australia, †School of Land and Food Sciences, University of Queensland, St Lucia Queensland 4072 Australia Abstract This study compares estimates of the census size of the spawning population with genetic estimates of effective current and long-term population size for an abundant and commer- cially important marine invertebrate, the brown tiger prawn (Penaeus esculentus). Our aim was to focus on the relationship between genetic effective and census size that may provide a source of information for viability analyses of naturally occurring populations. Samples were taken in 2001, 2002 and 2003 from a population on the east coast of Australia and tem- poral allelic variation was measured at eight polymorphic microsatellite loci. Moments- based and maximum-likelihood estimates of current genetic effective population size ranged from 797 to 1304. The mean long-term genetic effective population size was 9968. Although small for a large population, the effective population size estimates were above the threshold where genetic diversity is lost at neutral alleles through drift or inbreeding. Simulation studies correctly predicted that under these experimental conditions the genetic estimates would have non-infinite upper confidence limits and revealed they might be overestimates of the true size. We also show that estimates of mortality and variance in family size may be derived from data on average fecundity, current genetic effective and census spawning population size, assuming effective population size is equivalent to the number of breeders. This work confirms that it is feasible to obtain accurate estimates of current genetic effective population size for abundant Type III species using existing genetic marker technology. Keywords: census, DNA microsatellites, genetic effective population size, Penaeus esculentus, spawning population size Received 13 May 2006; revision accepted 21 August 2006 Introduction Effective population size is arguably the most important genetic parameter in evolutionary biology (Waples 2002; p. 147). It is the number of breeding individuals in an ideal population that would lead to the same amount of change in a given genetic measure due to genetic drift (Hedrick 2000). Current (or short-term) effective size is most commonly calculated from the rate of allele frequency change (variance effective size) or the probability that two alleles can be traced back to the same gene in a common ancestor (inbreeding effective size; Waples 2002). It describes the rate of genetic drift, the rate of loss of diversity at neutral alleles and the rate of increase of inbreeding that may occur in threatened or fragmented populations (Frankham 1995). Along with other population genetics parameters, effective population size estimates can be used to guide management scenarios in naturally occurring populations. Frankham et al. (2002) estimated that the population size should be much greater than an effective size of 50 to retain reproductive fitness. Populations of freshwater species have been shown to approach this ( Jorde & Ryman 1996; Correspondence: Dr Jennifer Ovenden, Fax: +61 7 3346 2727; E-mail: jennifer.ovenden@dpi.qld.gov.au ‡Present address: CSIRO Mathematical and Information Sciences, GPO Box 1538, Hobart, Tasmania 7001, Australia. §Present address: Secretariat of the Pacific Community, BP D5, 98848 Noumea Cedex, New Caledonia. ¶Present address: College of Business and Public Administration, Drake University, Des Moines, IA, USA.