Molecular Ecology (2003) 12, 2387–2397 doi: 10.10.1046/j.1365-294X.2003.01921.x © 2003 Blackwell Publishing Ltd Blackwell Publishing Ltd. Oceanic interchange and nonequilibrium population structure in the estuarine dependent Indo-Pacific tasselfish, Polynemus sheridani STEPHEN F. CHENOWETH and JANE M. HUGHES Molecular Ecology Laboratory, Faculty of Environmental Sciences, Griffith University, Nathan, Queensland, Australia 4111 Abstract We assayed mtDNA haplotype [300 base pairs (bp) control region] geography and geneal- ogy in the Indo-Pacific tasselfish, Polynemus sheridani from its contiguous estuarine distri- bution across northern Australia (n = 169). Eight estuaries were sampled from three oceanographic regions (Timor Sea, Gulf of Carpentaria and the Coral Sea) to assess the impact of Pleistocene sea level changes on the historical connectivity among P. sheridani populations. Specifically, we investigated the genetic consequences of disruption to Indian-Pacific Ocean connectivity brought about by the closure of the Torres Strait. Overall there was significant population subdivision among estuaries (F ST = 0.161, Φ ST = 0.187). Despite a linear distribution, P. sheridani did not show isolation by distance over the entire sampled range because of genetic similarity of estuaries greater than 3000 km apart. How- ever, significant isolation by distance was detected between estuaries separated by less than 3000 km of coastline. Unlike many genetic studies of Indo–Pacific marine species, there was no evidence for an historical division between eastern and western populations. Instead, phylogeographical patterns were dominated by a starlike intraspecific phylogeny coupled with evidence for population expansion in both the Gulf of Carpentaria and the Coral Sea but not the Timor Sea. This was interpreted as evidence for recent west to east recolonization across of northern Australia following the last postglacial marine advance. We argue that although sufficient time has elapsed postcolonization for populations to approach gene flow-drift equilibrium over smaller spatial scales (< 3000 km), the signal of historical colonization persists to obscure the expected equilibrium pattern of isolation by distance over large spatial scales (> 3000 km). Keywords: biogeography, Indo-Pacific, isolation-by-distance, Polynemus sheridani, population structure, Torres Strait Received 25 March 2003; revision received 19 May 2003; accepted 3 June 2003 Introduction Recently, intraspecific phylogeographical studies have been used to examine the levels of historical connectivity between marine populations in the Indo-West Pacific. One pattern that has emerged among these studies is the presence of strong genetic differences between Indian and Pacific Ocean populations. This genetic divergence is manifested as either reciprocal monophyly between oceans (McMillan & Palumbi 1995; Lavery et al . 1996; Barber et al . 2002; Gopurenko & Hughes 2002), strong frequency differences of mono- phyletic lineages between oceans (indicating secondary intergradation) (Chenoweth et al . 1998a) or haplotype fre- quency differences between oceans (Williams & Benzie 1998; Benzie et al . 2002). The level of divergence among mtDNA clades within species is often compatible with Pleistocene divergence. A possible mechanism for divergence between the two oceans are the large fluctuations in sea level that were fre- quent during the Pleistocene (Rosen 1988; Palumbi 1996). Small changes in sea level can result in significant changes Correspondence and present address: Stephen F. Chenoweth, Department of Zoology and Entomology, Queensland University, St Lucia, Queensland, Australia 4072. Fax: + 61 7 3365 1655; E-mail: schenoweth@zen.uq.edu.au