Single-strand conformation polymorphism (SSCP) analysis of the NADH IV region of the mitochondrial DNA (mtDNA) molecule in greenshell mussels (Perna canaliculus) indicated strong population genetic structuring in this endemic New Zealand species. A northern and a southern group were differentiated by frequency shifts in common haplotypes and by the occurrence of a unique southern haplotype at approximately 20% frequency. This split occurred south of Cook Strait (the body of water between the North and the South Island) at approximately 42 degrees S latitude. Northern populations were less genetically diverse than southern populations and mussels from the west coast of the South Island were most distinct from northern mussels. We hypothesize that the unique haplotype VIII originated in the lower South Island, and that its spread northwards was obstructed by the opening of Cook Strait approximately 15 000-16 000 years ago and the subsequent establishment of present-day surface water circulation patterns in Greater Cook Strait. We suggest that present-day strong tidal flows and turbulent mixing of water masses in Cook Strait, and intense up-welling on the east and west coasts in this region, represent a barrier to gene flow between mussels located in the North Island and northern South Island vs. mussels in most of the South Island and Stewart Island.

We highlight a novel molecular clock calibration system based on geologically dated river reversal and river capture events. Changes in drainage pattern may effect vicariant isolation of freshwater taxa, and thus provide a predictive framework for associated phylogeographic study. As a case in point, New Zealand's Pelorus and Kaituna rivers became geologically isolated from the larger Wairau River system 70 to 130 kyr BP. We conducted mitochondrial DNA phylogeographic analyses of two unrelated freshwater-limited fish taxa native to these river systems (Gobiomorphus breviceps, n = 63; Galaxias divergens, n = 95). Phylogenetic analysis of combined control region and cytochrome b sequences yielded reciprocally monophyletic clades of Pelorus-Kaituna and Wairau haplotypes for each species. Calibrated rates of molecular change based on this freshwater vicariant event are substantially faster than traditionally accepted rates for fishes but consistent with other recent inferences based on geologically young calibration points. A survey of freshwater phylogeographic literature reveals numerous examples in which the ages of recent evolutionary events may have been substantially overestimated through the use of "accepted" calibrations. We recommend that--wherever possible--biologists should start to reassess the conclusions of such studies by using more appropriate molecular calibrations derived from recent geological events.

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Tectonic movement at the boundary of the Indo-Australian and Pacific Plates during the Miocene and Pliocene is recognized as a driving force for invertebrate speciation in New Zealand. Two endemic freshwater crayfish (koura) species, Paranephrops planifrons White 1842 and Paranephrops zealandicus White 1842, represent good model taxa to test geological hypotheses because, due to their low dispersal capacity and life history, geographical restriction of populations may be caused by vicariant processes. Analysis of a mitochondrial DNA marker (cytochrome oxidase subunit I) reveals not two, but three major koura lineages. Contrary to expectation, the cryptic West Coast group appears to be more closely related to P. zealandicus than to P. planifrons and has diverged earlier than the final development (Late Pleistocene) of Cook Strait. Our date estimates suggest that koura lineage diversification probably coincided with early to mid-Alpine orogeny in the mid-Pliocene. Estimates of node ages and the phylogenies are inconsistent with both ancient Oligocene and recent postglacial Pleistocene range expansion, but suggest central to north colonization of North Island and west to east movement in South Island during mid- to late Pliocene. Crypsis and paraphyly of the West Coast group suggest that morphological characters presently used to classify koura species could be misleading.

Allozyme analysis of 35 populations of the endemic New Zealand greenshell mussel Perna canaliculus (Gmelin 1791) indicated an absence of genetic structuring, whereas mitochondrial DNA (mtDNA) single-strand conformation polymorphism (SSCP) analysis of 22 of the same populations indicated a pronounced genetic discontinuity between northern and southern mussels at ~42°S latitude. The present study examines the genetic structuring of a subset of 19 New Zealand mussel populations using the randomly amplified polymorphic DNA (RAPD) technique. A genetic discontinuity was observed between northern and southern populations, which resulted from significant allele frequency differences, but no absolute differences between populations of these regions. Southern populations were genetically more diverse than northern populations, with the west coast of the South Island being the most distinct from northern populations. The RAPD data are consistent with the mtDNA data, indicating that both studies have resolved the population structure of P. canaliculus at a higher level than previous allozyme studies. The location of the genetic discontinuity coincides with major hydrographic features at ~42°S latitude. We hypothesise that restricted gene flow (larval transport), a consequence of present day coastal surface circulation patterns, influences the population genetic structuring of this species, an effect which is relatively recent in geological time (within the last 12 000 yr).