Knowledge of DNA evolution is central to our understanding of biological history, but how fast does DNA change? Previously, pedigree and ancient DNA studies--focusing on evolution in the short term--have yielded molecular rate estimates substantially faster than those based on deeper phylogenies. It has recently been suggested that short-term, elevated molecular rates decay exponentially over 1-2 Myr to long-term, phylogenetic rates, termed "time dependency of molecular rates." This transition has potential to confound molecular inferences of demographic parameters and dating of many important evolutionary events. Here, we employ a novel approach--geologically dated changes in river drainages and isolation of fish populations--to document rates of mitochondrial DNA change over a range of temporal scales. This method utilizes precise spatiotemporal disruptions of linear freshwater systems and hence avoids many of the limitations associated with typical DNA calibration methods involving fossil data or island formation. Studies of freshwater-limited fishes across the South Island of New Zealand have revealed that genetic relationships reflect past, rather than present, drainage connections. Here, we use this link between drainage geology and genetics to calibrate rates of molecular evolution across nine events ranging in age from 0.007 Myr (Holocene) to 5.0 Myr (Pliocene). Molecular rates of change in galaxiid fishes from calibration points younger than 200 kyr were faster than those based on older calibration points. This study provides conclusive evidence of time dependency in molecular rates as it is based on a robust calibration system that was applied to closely related taxa, and analyzed using a consistent and rigorous methodology. The time dependency observed here appears short-lived relative to previous suggestions (1-2 Myr), which has bearing on the accuracy of molecular inferences drawn from processes operating within the Quaternary and mechanisms invoked to explain the decay of rates with time.

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The Otago and Alpine schists of the South Island of New Zealand form a young (<200 Ma), lithologically monotonous, metasedimentary belt with exposures ranging from unmetamorphosed graywackes to amphibolite facies rocks. The belt contains abundant orogenic gold deposits, including the 125-t Au Macraes deposit. As such, the schist belt is an ideal geologic setting for investigation of the sources of metals and fluids responsible for formation of metamorphic rock-hosted gold deposits.A large suite of samples representative of the lithologic and metamorphic variation in the Otago and Alpine schists was collected and analyzed for a comprehensive suite of elements. The aim was to identify any rock type or metamorphic setting that may be depleted in the suite of ore-forming elements (Au, Ag, As, Sb, Hg, Mo, and W) relative to unmetamorphosed protoliths, perhaps representing the source for the enrichments observed in the Otago ore deposits. Gold, Ag, As, Sb, Hg, Mo, and W were found to have significantly lower concentrations in higher grade metamorphic rocks compared to unmetamorphosed protolith samples. These were the only elements in a suite of 12 major and 50 trace elements to show systematic depletions with metamorphic grade. Investigation of the trace element chemistry of sulfide minerals indicates that the whole-rock depletions are caused by the disappearance between greenschist and amphibolite facies conditions of pyrite, galena, sphalerite, and cobaltite, the major host phases for the ore-forming elements. More than 95 percent of upper greenschist and amphibolite facies samples are significantly depleted in the ore-forming elements. Such regional-scale depletions require pervasive, grain-boundary fluid flow throughout these rocks. The leaching is most likely to have been caused by metamorphic fluid produced by dehydration reactions at the greenschist-amphibolite boundary.The suite of elements depleted in mid-to high-grade Otago and Alpine schists is almost identical to those enriched in the orogenic gold deposits in Otago. Furthermore, the vertical zonation in depletions is similar to the vertical zonation in enrichments that occurs in the Otago deposits. Mass-balance calculations suggest that 2 metric tons (t) Au and 24,000 t As was leached from 1 km 3 of amphibolite facies rock and that the Macraes deposit could have been formed by leaching of a 5-× 5-× 5-km cube of amphibolite facies rock. We propose that the orogenic gold deposits in Otago, such as Macraes, were formed directly from metal-rich metamorphic fluid produced during prograde metamorphism at depth. The contribution of other fluid and metal sources in the formation of these deposits, such as magmatic fluids, cannot be ruled out, but there is no direct evidence to support their involvement. Infiltration of meteoric water, such as occurs currently in the Southern Alps of New Zealand may have contributed to the formation of the late-stage deposits that formed at shallow level during uplift of the Otago schists.

River capture is a geomorphological process through which stream sections are displaced from one catchment to another, and it may represent a dominant facilitator of interdrainage transfer and cladogenesis in freshwater-limited taxa. However, few studies have been conducted in a manner to explicitly test the biological significance of river capture. Here we present a multispecies phylogeographical analysis to test whether the nonmigratory fish fauna of the Von River (South Island, New Zealand) is the product of a well-documented, Late Quaternary capture of a section of the Oreti River (Southland drainage). Specifically, we predict that nonmigratory fishes of the Von River will exhibit closer genetic affinities with those of Southland, rather than those of the Clutha system, into which the Von River presently drains. Mitochondrial DNA phylogeography (control region and cytochrome b sequence data) and analysis of nuclear orthologues of mtDNA sequences indicate that 'flathead'Galaxias of the Von River (n = 31, three sites) have greatest genetic affinities with those of Southland (Galaxias 'southern', n = 216, 38 sites), rather than with those of the Clutha River (Galaxias sp. 'D', n = 73, 32 sites). Likewise, Von River 'roundhead'Galaxias (n = 52, four sites) have greatest genetic affinities with those of Southland drainages (Galaxias gollumoides, n = 223, 58 sites), rather than with those of the Clutha River (Galaxias pullus, Galaxias anomalus, Galaxias gollumoides of the Nevis tributary; n = 68, 32 sites). These findings are consistent with our predictions that genetic affinities of the nonmigratory fish fauna in the Von River would reflect past, rather than present, drainage connections. Consequently, river capture is responsible for the nonmigratory fish fauna of the Von River. In a broader context, river capture has frequently influenced the distribution of genetic lineages among catchments in New Zealand freshwater-limited fish, and its biogeographical significance may have been underestimated in other regions.

River capture is potentially a key geomorphological driver of range expansion and cladogenesis in freshwater-limited taxa. While previous studies of freshwater fish, in particular, have indicated strong relationships between historical river connections and phylogeographic pattern, their analyses have been restricted to single taxa and geological hypotheses were typically constructed a posteriori. Here we assess the broader significance of river capture among taxa by testing multiple species for the genetic signature of a recent river capture event in New Zealand. During the Quaternary an upper tributary of the Clarence River system was diverted into the headwaters of the Wairau River catchment. Mitochondrial DNA (control region and cytochrome b) sequencing of two native galaxiid fishes (Galaxias vulgaris and Galaxias divergens) supports headwater exchange: populations from the Clarence and Wairau Rivers are closely related sister-groups, whereas samples from the geographically intermediate Awatere River are genetically divergent. The upland bully Gobiomorphus breviceps (Eleotridae), in contrast, lacks a genetic signature of the capture event. We hypothesize that there is an increased likelihood of observing genetic signatures from river capture events when they facilitate range expansion, as is inferred for the two galaxiid taxa studied here. When river capture merely translocates genetic lineages among established populations, by contrast, we suggest that the genetic signature of capture is less likely to be retained, as might be inferred for G. breviceps. Rates of molecular evolution calibrated against this recent event were elevated relative to traditional estimates, consistent with the contribution of polymorphisms to branch lengths at shallow phylogenetic levels prior to fixation by purifying selection and drift.

We used DNA analysis of the freshwater Galaxias vulgaris complex (Pisces: Galaxiidae) to test a geological hypothesis of drainage evolution in South Island, New Zealand. Geological evidence suggests that the presently north-flowing Nevis River branch of the Clutha/Kawarau River system (Otago) once flowed south into the Nokomai branch of the Mataura system (Southland). The flow reversal is thought to have resulted from fault and fold activity associated with post-Miocene uplift. Mitochondrial DNA sequence data (control region and cytochrome b genes; 76 individuals; maximum divergence 7.1%) corroborate this geomorphological hypothesis: The Nevis River retains a freshwater fish species (Galaxias gollumoides; five sites; 10 haplotypes) that is otherwise restricted to Southland (nine sites; 15 haplotypes). There is no indication that the Nevis River lineage of G. gollumoides lives elsewhere in the Clutha/ Kawarau system (> 30 sites). Likewise, two widespread Clutha lineages (G. 'sp D'; G. anomalus-G. pullus) are apparently absent from the Nevis (> 30 sites). In particular, G. 'sp D' lives throughout much of the Clutha (12 sites, 23 haplotypes), including a tributary of the Kawarau, but is absent from the Nevis itself. Conventional molecular clock calibrations (based on a minimum Nevis-Mataura haplotype divergence of 3.0%) indicate that the Nevis flow reversal may have occurred in the early-mid Pleistocene, which is roughly consistent with geological data. The broad phylogeographic structure evident in the Clutha system is consistent with the sedentary nature of nonmigratory galaxiids. Our study reinforces the value of combining biological and geological data for the formulation and testing of historical hypotheses.

Obligate freshwater taxa are frequently distributed among catchments isolated by marine and terrestrial barriers. Such distributions can arise through vicariant changes in drainage geometry, or dispersal via intermittent freshwater connections. We employed two adjacent rivers in southern New Zealand to test for interdrainage dispersal while controlling for historical drainage geometry, and analyzed four ecologically distinct freshwater-limited fish taxa to assess any relationship with habitat preference. Individuals from the Mararoa and Oreti catchments (n >100 per species) were sequenced for a minimum of 1297 bp of mitochondrial DNA (cytochrome b and control region). Phylogeographic relationships were consistent with ecological expectations of interdrainage dispersal capability, with the two obligate riverine taxa each exhibiting reciprocal monophyly between catchments, whereas the two facultative swamp dwellers revealed paraphyletic relationships, one of which shared a haplotype between catchments.Statistical phylogeography, accommodating taxon-specific mutation rates and the known age of the last major riverine connection between these catchments, rejected complete isolation of populations for one of the swamp dwellers. Therefore, dispersal across a young (145-240 kyr) drainage divide is inferred for one species, and can be predicted to some extent by species ecology. Moreover, our study highlights the importance of historical drainage geometry when assessing the causes of contemporary genetic structuring in freshwater taxa.