Gorges partition diversity within New Zealand flathead Galaxias populations.

Understanding the landscape factors governing population connectivity in riverine ecosystems represents an ongoing challenge for freshwater biologists. We used DNA sequence analysis to test the hypothesis that major geomorphological features underpin freshwater-limited fish diversity in a tectonically dynamic region of New Zealand. Phylogeographic analysis of 101 Galaxias depressiceps cytochrome b sequences, incorporating 55 localities from southern New Zealand, revealed 26 haplotypes, with only one shared among rivers. We detect strong hierarchical genetic differentiation both among and within river systems. Genetic structuring is particularly pronounced across the Taieri River system (63 individuals from 35 sites, 18 haplotypes), with 92% of variation partitioned among locations. Distinctive within-river genetic clusters are invariably associated with major subcatchment units, typically isolated by substantial gorges. The anomalous distribution of a single lineage across a major drainage divide is consistent with local, tectonically driven headwater capture. We conclude that major landscape features such as gorges can strongly partition riverine fish diversity and constrain freshwater biodiversity.

Integrating kelp genomic analyses and geological data to reveal ancient earthquake impacts.

Detached buoyant kelp can disperse thousands of kilometres at sea and can colonize newly available shores in the wake of disturbances that wipe out competitors. Localized earthquake uplift can cause extirpation of intertidal kelp populations followed by recolonization. Sources of recolonizing kelp can be detectable in genomic structure of contemporary populations. Our field observations combined with LiDAR mapping identified a previously unrecognized zone of uplifted rocky coastline in a region that is slowly subsiding. Intertidal kelp (Durvillaea antarctica) on the uplifted section of coast is genetically distinctive from nearby populations, with genomic signatures most similar to that of kelp 300 km to the south. Genetic divergence between these locations suggests reproductive isolation for thousands of years. Combined geological and genetic data suggest that this uplift event occurred during one of four major earthquakes between 6000 and 2000 years ago, with one of the younger events most likely. Extirpation of the pre-existing kelp required sudden uplift of approximately 2 metres, precluding several small incremental uplift events. Our results show the power of integrating biological (genomic) analyses with geological data to understand ancient geological processes and their ecological impacts.

Geological controls on evolution of evaporative precipitates on soil-free substrates and ecosystems, southern New Zealand.

Soil-free bare substrates have formed by natural and human-induced processes in a semi-arid rain shadow, in the lee of actively rising mountains. These substrates have developed evaporative salt encrustations with a wide range of minerals controlled by local substrate permeability and mineralogy. Many of these small (hectare scale) sites also host endemic salt-tolerant ecosystems that are currently endangered by weed incursion. This study characterises the differing mineralogy and geochemistry of these rare ecosystem-hosting substrates. Impermeable substrates, especially clay-rich schist basement, are dominated by NaCl from marine aerosols in rain. The high Na at these sites further enhances impermeability of substrates by promoting surficial clay mobility, so that even Pleistocene-Recent sediments derived from schist basement develop evaporative crusts. The Na/Cl ratio of some of these substrates, especially sediments, has been increased by alteration of albite. However, mineralogically similar greywacke-derived sediments do not develop saline encrustations. Penetration of rainwater into substrates facilitates water-rock interaction reactions that yield entirely different evaporative salt mineralogy, as the NaCl component is overshadowed by constituents dissolved from the rocks. Schist basement and limestone-rich substrates develop carbonate-dominated evaporites, especially calcite, and associated waters are typically supersaturated with respect to carbonate minerals. Some sulphate-rich evaporites form where rock pyrite has been oxidised. Hydrothermally altered schist basement is locally enriched in Mg-bearing carbonates, sulphides and gold. Bare substrates on these sites are variably permeable and develop evaporative salts with carbonates, sulphates, ferric oxyhydroxide (some arsenic-bearing), and minor brucite, after extensive water-rock interaction. Most of the sites are alkaline, and pH locally exceeds 10, as a result of the combinations of evaporative processes and water-rock interactions. The specialist plants have evolved to tolerate the relatively high salinities and pH of these chemically distinctive sites.

Parallel recolonizations generate distinct genomic sectors in kelp following high-magnitude earthquake disturbance.

Large-scale disturbance events have the potential to drastically reshape biodiversity patterns. Notably, newly vacant habitat space cleared by disturbance can be colonized by multiple lineages, which can lead to the evolution of distinct spatial "sectors" of genetic diversity within a species. We test for disturbance-driven sectoring of genetic diversity in intertidal southern bull kelp, Durvillaea antarctica (Chamisso) Hariot, following the high-magnitude 1855 Wairarapa earthquake in New Zealand. Specifically, we use genotyping-by-sequencing (GBS) to analyse fine-scale population structure across the uplift zone and apply machine learning to assess the fit of alternative recolonizaton models. Our analysis reveals that specimens from the uplift zone carry distinctive genomic signatures potentially linked to post-earthquake recolonization processes. Specifically, our analysis identifies two parapatric spatial-genomic sectors of D. antarctica at Turakirae Head, which experienced the most dramatic uplift. Based on phylogeographical modelling, we infer that bull kelp in the Wellington region was probably a source for recolonization of the heavily uplifted Turakirae Head coastline, via two parallel, eastward recolonization events. By identifying multiple parapatric genotypic sectors within a recently recolonized coastal region, the current study provides support for the hypothesis that competing lineage expansions can generate striking spatial structuring of genetic diversity, even in highly dispersive taxa.

Concordant phylogeographic responses to large-scale coastal disturbance in intertidal macroalgae and their epibiota.

Major ecological disturbance events can provide opportunities to assess multispecies responses to upheaval. In particular, catastrophic disturbances that regionally extirpate habitat-forming species can potentially influence the genetic diversity of large numbers of codistributed taxa. However, due to the rarity of such disturbance events over ecological timeframes, the genetic dynamics of multispecies recolonization processes have remained little understood. Here, we use single nucleotide polymorphism (SNP) data from multiple coastal species to track the dynamics of cocolonization events in response to ancient earthquake disturbance in southern New Zealand. Specifically, we use a comparative phylogeographic approach to understand the extent to which epifauna (with varying ecological associations with their macroalgal hosts) share comparable spatial and temporal recolonization patterns. Our study reveals concordant disturbance-related phylogeographic breaks in two intertidal macroalgal species along with two associated epibiotic species (a chiton and an isopod). By contrast, two codistributed species, one of which is an epibiotic amphipod and the other a subtidal macroalga, show few, if any, genetic effects of palaeoseismic coastal uplift. Phylogeographic model selection reveals similar post-uplift recolonization routes for the epibiotic chiton and isopod and their macroalgal hosts. Additionally, codemographic analyses support synchronous population expansions of these four phylogeographically similar taxa. Our findings indicate that coastal paleoseismic activity has driven concordant impacts on multiple codistributed species, with concerted recolonization events probably facilitated by macroalgal rafting. These results highlight that high-resolution comparative genomic data can help reconstruct concerted multispecies responses to recent ecological disturbance.

Northward range extension for Durvillaea poha bull kelp: Response to tectonic disturbance?

Understanding the forces that shape species distributions is increasingly important in a fast-changing world. Although major disturbance events can adversely affect natural populations, they can also present new opportunities, for example by opening up habitat for colonization by other lineages. Following extensive geographic sampling, we use genomic data to infer a range extension following disturbance for an ecologically important intertidal macroalgal species. Specifically, we genotyped 288 southern bull kelp (Durvillaea) plants from 28 localities across central New Zealand. All specimens from the North Island were expected to be D. antarctica, but unexpectedly 10 samples from four sites were identified as D. poha. Extensive sampling from the northern South Island (105 samples at five locations) confirmed the absence of D. poha north of the Kaikoura Peninsula. The North Island specimens of D. poha therefore reveal a biogeographic disjunction, some 150 km northeast of the nearest (South Island) population of this species. Based on strong geographic correspondence between these North Island samples and historic disturbance, we infer that tectonic upheaval, particularly earthquake-generated landslides, likely extirpated local D. antarctica and created an opportunity for a northward range expansion event by D. poha. Close phylogenomic relationships between this new North Island population and South Island samples support a geologically recent northward expansion, rather than a deeper evolutionary origin. These findings indicate the potential of large-scale disturbances to facilitate sudden biogeographic range expansions, and they emphasize the ability of genomic analyses with fine-scale sampling to reveal long-lasting signatures of past disturbance, dispersal, and colonization.

The genomic footprint of coastal earthquake uplift.

Theory suggests that catastrophic earth-history events can drive rapid biological evolution, but empirical evidence for such processes is scarce. Destructive geological events such as earthquakes can represent large-scale natural experiments for inferring such evolutionary processes. We capitalized on a major prehistoric (800 yr BP) geological uplift event affecting a southern New Zealand coastline to test for the lasting genomic impacts of disturbance. Genome-wide analyses of three co-distributed keystone kelp taxa revealed that post-earthquake recolonization drove the evolution of novel, large-scale intertidal spatial genetic 'sectors' which are tightly linked to geological fault boundaries. Demographic simulations confirmed that, following widespread extirpation, parallel expansions into newly vacant habitats rapidly restructured genome-wide diversity. Interspecific differences in recolonization mode and tempo reflect differing ecological constraints relating to habitat choice and dispersal capacity among taxa. This study highlights the rapid and enduring evolutionary effects of catastrophic ecosystem disturbance and reveals the key role of range expansion in reshaping spatial genetic patterns.

Crossing the front: contrasting storm-forced dispersal dynamics revealed by biological, geological and genetic analysis of beach-cast kelp.

The subtropical front (STF) generally represents a substantial oceanographic barrier to dispersal between cold-sub-Antarctic and warm-temperate water masses. Recent studies have suggested that storm events can drastically influence marine dispersal and patterns. Here we analyse biological and geological dispersal driven by two major, contrasting storm events in southern New Zealand, 2017. We integrate biological and physical data to show that a severe southerly system in July 2017 disrupted this barrier by promoting movement of substantial numbers of southern sub-Antarctic Durvillaea kelp rafts across the STF, to make landfall in mainland NZ. By contrast, a less intense easterly storm (Cyclone Cook, April 2017) resulted in more moderate dispersal distances, with minimal dispersal between the sub-Antarctic and mainland New Zealand. These quantitative analyses of approximately 200 freshly beach-cast kelp specimens indicate that storm intensity and wind direction can strongly influence marine dispersal and landfall outcomes.

Characterisation of acid mine drainage in a high rainfall mountain environment, New Zealand.

The Stockton coal mine lies at 700-1100 m above sea level in a mountainous orographic precipitation zone on the West Coast of the South Island of New Zealand. Rainfall exceeds 6000 mm/year and arrives with frequent flood events that can deliver > 200 mm/day. Streams vary in discharges by up to two orders of magnitude over a time scale of hours. Pyritic waste rock at the mine interacts chemically with even the most intense rainfall, and almost all runoff is acidic to some degree. In the most intense rain event recorded in this study (> 10 mm/hour), dilution of acid mine drainage (AMD) occurred and pH rose from 3 to >5 over several hours, with stream discharge at a monitoring point rising from <0.5 to >100 cumecs. However, most rain events of similar magnitude are less intense, longer duration, and only raise AMD pH to ~4 with similar high discharges. Results presented here for Stockton confirm that it is the intensity of rain events on the hourly scale, rather than the total amount of rainwater delivered to the site, that governs the amount and composition of AMD generated during flood events. Stream discharge loads of dissolved iron and aluminium range from ~20 to 1000 kg/hour. Dissolved sulfate and acidity loads are typically ~500 kg/hour but can exceed 20 tonnes/hour in rain events. First flush effects observable elsewhere around the world involving peak metal loads following dry periods or seasonal changes are not obvious at Stockton due to the high and variable rainfall environment. Dissolved Fe concentrations may be limited in runoff waters by precipitation of jarosite and schwertmannite, especially when rainfall is sufficiently intense to raise pH to 4 or higher. These minerals are widespread in the exposed waste rock on site. Likewise, precipitation of alunite may occur as pH rises in rain events, but no field evidence for this has been observed.

Processes of attenuation of dissolved arsenic downstream from historic gold mine sites, New Zealand.

Mine and processing sites in the mesothermal gold deposits of the Reefton gold field, New Zealand, generate extremely high dissolved As concentrations (up to 59 mg/L). Attenuation of these waters takes place by at least one of the three mechanisms: (1) precipitation of the secondary arsenic mineral scorodite, (2) chemisorption onto iron oxyhydroxide (HFO) and (3) dilution with regional catchment water. The presence and effectiveness of these mechanisms vary among the three studied catchments. A strong physiochemical control on arsenic attenuation was identified due to a chemical gradient within the gold field itself and processing methods, which can generate site specific arsenic minerals, such as arsenolite. Precipitation of scorodite only occurs in the presence of dissolving arsenolite, which is a roasting by-product present at two of the studied sites. Abundant HFO is generated in the pyritic mesothermal part of the gold field, and here chemisorption onto HFO is the dominant attenuation process. In the non-pyritic part of the gold field, HFO is mainly produced as a result of ankerite dissolution but only where sufficiently exposed mineralised rock is present. In the absence of significant adsorption sites, dissolved As is attenuated only via less effective dilution and ecosystem guidelines are exceeded over kilometres downstream from the mineralised zone until drainage waters are diluted by regional catchment water. Catchment morphology was identified as a major control on dilution. Despite the presence of strong As point sources upstream, mine-related As contributes <10% to the regional As river load in all three catchments. On a regional scale As mobility across a wide range of pH regimes reveals a strong control of scorodite, which has already been observed locally.

Does fish ecology predict dispersal across a river drainage divide?

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.

Geological dates and molecular rates: fish DNA sheds light on time dependency.

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.

ATR-IR spectroscopic study of antimonate adsorption to iron oxide.

Antimonate ions adsorb to iron oxides in mining contexts, but the nature of the adsorbed antimonate species has not frequently been investigated. In this study, ATR-IR spectroscopy was used to reveal that the adsorption of Sb(OH)6- ion from aqueous solutions onto an amorphous iron oxide particle film is accompanied by changes in the Sb(OH)6- spectrum and the loss of OH stretching absorptions from iron oxide surface hydroxyl groups. These spectral changes upon adsorption imply an inner-sphere surface interaction with the formation of Sb-O-Fe bonds as well as some outer-sphere adsorption. The corresponding results from solutions of antimonate in D2O confirm that chemisorption occurs. The dependence of antimonate adsorption on pH in the range from 8 to 3 follows that expected for anions on iron oxide considering its pH-dependent surface charge, with the greatest amount of adsorbed antimonate at pH 3. The study of adsorption/desorption kinetics showed a more rapid desorption of adsorbed antimonate under alkaline conditions. This trend is expected from the pH dependence of the antimonate charge and iron oxide surface charge, but it might be partly due to the fact that high pH favors hydrolysis of antimonate oligomers formed on the iron oxide surface from adsorption under acidic conditions.

An empirical test of freshwater vicariance via river capture.

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.

Geological dates and molecular rates: rapid divergence of rivers and their biotas.

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.