Molecular Ecology (2006) 15, 1083–1093 doi: 10.1111/j.1365-294X.2006.02852.x © 2006 Blackwell Publishing Ltd Blackwell Publishing Ltd Biogeographic history of an Australian freshwater shrimp, Paratya australiensis (Atyidae): the role life history transition in phylogeographic diversification B. D. COOK, A. M. BAKER,* T. J. PAGE, S. C. GRANT, J. H. FAWCETT, D. A. HURWOOD * and J. M. HUGHES Cooperative Research Centre for Freshwater Ecology, Centre for Riverine Landscapes, Griffith University, Nathan, Queensland 4111, Australia Abstract The widespread distribution of the freshwater shrimp Paratya australiensis in eastern Australia suggests that populations of this species have been connected in the past. Amphidromy is ancestral in these shrimps, although many extant populations are known to be restricted to freshwater habitats. In this study, we used a fragment of the cytochrome c oxidase I mitochondrial DNA (mtDNA) gene to examine diversity within P. australiensis and to assess the relative importance of amphidromy in its evolutionary history. We hypothesized that if transitions from an amphidromous to a freshwater life history were important, then we would find a number of divergent lineages restricted to single or groups of nearby drainages. Alternatively, if amphidromy was maintained within the species historically, we expected to find lineages distributed over many drainages. We assumed that the only way for divergence to occur within amphidromous lineages was if dispersal was limited to between nearby estuaries, which, during arid periods in the earth’s history, became isolated from one another. We found nine highly divergent mtDNA lineages, estimated to have diverged from one another in the late Miocene/early Pliocene, when the climate was more arid than at present. Despite this, the geographic distribution of lineages and haplotypes within lineages did not support the notion of a stepping-stone model of dispersal between estuaries. We conclude that the extensive divergence has most likely arisen through a number of independent amphidromy–freshwater life history transitions, rather than via historical isolation of amphidromy populations. We also found evidence for extensive movement between coastal and inland drainages, supporting the notion that sec- ondary contact between lineages may have occurred as a result of drainage rearrangements. Finally, our data indicate that P. australiensis is likely a complex of cryptic species, some of which are widely distributed, and others geographically restricted. Keywords: 28S, amphidromy–freshwater transition, ancestral polymorphism, COI, cryptic species Received 22 January 2005; revision received 3 June 2005; accepted 22 November 2005 Introduction The widespread distribution of many freshwater species throughout geographically isolated river habitats implies that some form of connectivity has existed between those habitats. Life history strategy and earth history are the principal mechanisms that determine levels of connectivity among populations of freshwater taxa, and recent phylo- geographic studies have examined their relative importance in the biogeographic history of various aquatic species (e.g. Jerry & Baverstock 1998; McGlashan & Hughes 2000; Ponniah & Hughes 2004). For some freshwater species, various forms of diadromy (i.e. migration between freshwater and estuarine/marine habitats) is a strategy Correspondence: Jane M. Hughes, Fax: 07-3735-7615; E-mail: jane.hughes@griffith.edu.au *Present address: School of Natural Resource Sciences, Queensland University of Technology, Gardens Point Campus, Queensland 4001, Australia.