Genetic variation and population structure in the New Zealand snapper

Fifteen proteins encoded by 23 gene loci were electrophoretically surveyed in two samples of snapper Chrysophrys auratus (Forster) from Wellington Harbour and the Hauraki Gulf. Between 17% and 26% of the loci examined were found to be polymorphic and the proportion of heterozygous loci per individual was 7.9% to 8.4%. Using Rogers’ genetic distance coefficient an overall similarity of 0.98 was calculated between the two samples.

Three polymorphic loci Est‐4, Gpi‐1, and Idh were examined in an additional 10 samples from around New Zealand. Two genetically distinct stocks were apparent: one along the west coast, the other along the east coast of the North Island. There was an indication of stock mixing at Ninety Mile Beach and in the Bay of Plenty and East Cape. The distribution of alleles at the Est‐4 locus revealed a third stock in Hawke Bay that is genetically more similar to the west coast than the east coast stock. Hydrological conditions in Hawke Bay are more similar to those of the west coast than to those of the north east coast of the North Island. Thus it is possible that Est‐4 alleles are selectively maintained in response to an environmental factor.     

Risks of shifting baselines highlighted by anecdotal accounts of New Zealand's snapper (Pagrus auratus) fishery

Anecdotal data sources may constitute an important component of the information available about an exploited species, as record keeping may not have occurred until after exploitation began. Here, we aimed to fill any gaps in the exploitative history of the sparid snapper (Pagrus auratus), using social and historical research methods. Social research consisted of interviews with recreational fishers, focusing on the most and largest snapper they had caught. In addition, the diary‐logs of two recreational fishers were analysed. Historical research consisted of investigation of old books, photos, archives and unpublished sources unconventional to fishery science. Interviews with fishers demonstrated no or weak trends in snapper abundance or size, and were likely impeded by a lack of ability to detect change in a fish stock that may still be considered abundant. The fishers’ perception of change, however, largely reflected recent experiences (last c. 10 years), when biomass is understood to have increased, and mostly did not consider experiences before the 1980s. Alternatively, diary‐logs of fisher catch rates produced a pattern that matched formal stock assessments of snapper biomass, suggesting declines in abundance up until the 1990s and an increase in biomass after that time. Historical research, although more qualitative, had the ability to investigate periods where formal records were not kept and described a fishery vastly different from the current one. Snapper were easily caught, in great abundance and in unusual locations. Localised depletion of snapper was first noticed in the early 20th century, despite spectacular catches of snapper occurring after that time. Snapper behaviour was also likely different, with visual sightings of snapper by onlookers a common occurrence. Although predictions from stock assessment models are consistent with that of the anecdotes listed here (i.e., high biomass in the past), these anecdotes are valuable as they explain lost biomass in a perspective meaningful to all. This perspective may be valuable for managers trying to consider the non‐financial value of a shared fishery but, if unrecognised, represents a shifting baseline.     

DNA identification of Pacific bluefin tuna (Thunnus orientalis) in the New Zealand fishery

Muscle samples were collected from 69 specimens identified as Pacific bluefin tuna (Thunnus orientalis) (Temminck and Schlegel, 1844) in the New Zealand Exclusive Economic Zone (EEZ) between 1990 and 2000. Identifications before 1996 were based on body size and colour of the caudal keel; later identifications were mostly based on the shape of abdominal cavity. The tissue samples were tested with a diagnostic mitochondrial DNA marker that distinguishes southern bluefin Thunnus maccoyii (Castelnau, 1872) and Pacific bluefin tuna T. orientalis; 59 specimens were confirmed as T. orientalis and 10 as T. maccoyii. Specimens recorded as Pacific bluefin tuna by the shape of the abdominal cavity were correctly identified as T. orientalis, and this character can be used to identify large specimens landed on tuna vessels. Some specimens recorded as Pacific bluefin tuna on the basis of colour and size were T. maccoyii; and early records of T. orientalis in New Zealand waters, based on these characters, are unreliable. Unusual colour patterns were reported in some specimens of T. orientalis but not T. maccoyii. The Pacific bluefin tuna T. orientalis accounted for less than 0.3% of the bluefin tuna catch in the New Zealand EEZ during the 1990s.     

Biochemical‐genetic and meristic evidence that blue and copper moki (Teleostei: Latridae: Latridopsis) are discrete species

Specimens of blue moki Latridopsis ciliaris (Forster in Bloch & Schneider, 1801) from New Zealand were shown to differ from specimens of copper moki Latridopsis forsteri (Castelnau, 1872) using two genetic methods—allozymes and muscle proteins. Allozyme techniques revealed fixed differences between blue and copper moki at 4 out of 15 loci. There was a genetic distance of 0.31–0.34 between population samples of the two colour morphs. The two morphs were also distinguished by iso‐electric focusing of muscle proteins. Meristic characters, counted in the specimens studied with genetic markers, revealed diagnostic markers in tubed lateral line scales and scales in the lower transverse series. It is concluded that specimens of blue moki from New Zealand and copper moki from New Zealand and Tasmania are valid species.     

Variability in invasion risk for ballast water exchange on the Scotian Shelf of eastern Canada

A semi-quantitative risk assessment model for dispersion of ballast water organisms in shelf seas is applied to the Scotian Shelf region of eastern Canada. The ballast water exchange process is simulated as the dispersion of tracer released into the surface layer of an ocean circulation model of the region. Circulation model variability is driven by wind stress from a cyclical year of forcing representing climatological storminess. Dispersion metrics related to invasion risk are developed and incorporated into a risk equation that computes the relative overall risk of invasion for ballast water exchange segments along vessel tracks crossing the shelf. Three hundred and sixty dispersion simulations are done for each segment of each of six tracks. Because the flow fields represent climatological variability in shelf circulation, the application of the risk assessment model captures the expected variability in invasion risk. Model results indicate that more than an order of magnitude variation in risk can exist along a given vessel track, and that tracks with offshelf segments provide a lower risk option compared to onshelf tracks. The model provides quantitative guidance to regulators regarding what is an acceptable trip diversion and can aid in numerous other management decisions.     

Oxygen and carbon isotope ratios in the martian atmosphere

Oxygen and carbon isotope ratios in the martian CO₂ are key values to study evolution of volatiles on Mars. The major problems in spectroscopic determinations of these ratios on Mars are uncertainties associated with: (1) equivalent widths of the observed absorption lines, (2) line strengths in spectroscopic databases, and (3) thermal structure of the martian atmosphere during the observation. We have made special efforts to reduce all these uncertainties. We observed Mars using the Fourier Transform Spectrometer at the Canada–France–Hawaii Telescope. While the oxygen and carbon isotope ratios on Mars were byproducts in the previous observations, our observation was specifically aimed at these isotope ratios. We covered a range of 6022 to 6308 cm⁻¹ with the highest resolving power of ν/δν=3.5×10⁵ and a signal-to-noise ratio of 180 in the middle of the spectrum. The chosen spectral range involves 475 lines of the main isotope, 184 lines of ¹³CO₂, 181 lines of CO¹⁸O, and 119 lines of CO¹⁷O. (Lines with strengths exceeding 10⁻²⁷ cm at 218 K are considered here.) Due to the high spectral resolution, most of the lines are not blended. Uncertainties of retrieved isotope abundances are in inverse proportion to resolving power, signal-to-noise ratio, and square root of the number of lines. Laboratory studies of the CO₂ isotope spectra in the range of our observation achieved an accuracy of 1% in the line strengths. Detailed observations of temperature profiles using MGS/TES and data on temperature variations with local time from two GCMs are used to simulate each absorption line at various heights in each part of the instrument field of view and then sum up the results. Thermal radiation of Mars' surface and atmosphere is negligible in the chosen spectral range, and this reduces errors associated with uncertainties in the thermal structure on Mars. Using a combination of all these factors, the highest accuracy has been achieved in measuring the CO₂ isotope ratios: ¹³C/¹²C = 0.978 ± 0.020 and ¹⁸O/¹⁶O = 1.018 ± 0.018 times the terrestrial standards. Heavy isotopes in the atmosphere are enriched by nonthermal escape and sputtering, and depleted by fractionation with solid-phase reservoirs. The retrieved ratios show that isotope fractionation between CO₂ and oxygen and carbon reservoirs in the solid phase is almost balanced by nonthermal escape and sputtering of O and C from Mars.     

Numerical estimation of effective diffusion coefficients for charged porous materials based on micro-scale analyses

In order to describe diffusive transport of solutes through a porous material, estimation of effective diffusion coefficients is required. It has been shown theoretically that in the case of uncharged porous materials the effective diffusion coefficient of solutes is a function of the pore morphology of the material and can be described by the tortuosity (tensor) (Bear, 1988 [1]). Given detailed information of the pore geometry at the micro-scale the tortuosity of different materials can be accurately estimated using homogenization procedures. However, many engineering materials (e.g., clays and shales) are characterized by electrical surface charges on particles of the porous material which strongly affect the (diffusive) transport properties of ions. For these type of materials, estimation of effective diffusion coefficients have been mostly based on phenomenological equations with no link to underlying micro-scale properties of these charged materials although a few recent studies have used alternative methods to obtain the diffusion parameters (Jougnot et al., 2009; Pivonka et al., 2009; Revil and Linde, 2006 2, 3 and 4). In this paper we employ a recently proposed up-scaled Poisson–Nernst–Planck type of equation (PNP) and its micro-scale counterpart to estimate effective ion diffusion coefficients in thin charged membranes. We investigate a variety of different pore geometries together with different surface charges on particles. Here, we show that independent of the charges on particles, a (generalized) tortuosity factor can be identified as function of the pore morphology only using the new PNP model. On the other hand, all electro-static interactions of ions and charges on particles can consistently be captured by the ratio of average concentration to effective intrinsic concentration in the macroscopic PNP equations. Using this formulation allows to consistently take into account electrochemical interactions of ions and charges on particles and so excludes any ambiguity generally encountered in phenomenological equations.     

Aquifer Storage Recovery (ASR) of chlorinated municipal drinking water in a confined aquifer

About 1.02 × 10⁶ m³ of chlorinated municipal drinking water was injected into a confined aquifer, 94–137 m below Roseville, California, between December 2005 and April 2006. The water was stored in the aquifer for 438 days, and 2.64 × 10⁶ m³ of water were extracted between July 2007 and February 2008. On the basis of Cl⁻ data, 35% of the injected water was recovered and 65% of the injected water and associated disinfection by-products (DBPs) remained in the aquifer at the end of extraction. About 46.3 kg of total trihalomethanes (TTHM) entered the aquifer with the injected water and 37.6 kg of TTHM were extracted. As much as 44 kg of TTHMs remained in the aquifer at the end of extraction because of incomplete recovery of injected water and formation of THMs within the aquifer by reactions with free-chlorine in the injected water. Well-bore velocity log data collected from the Aquifer Storage Recovery (ASR) well show as much as 60% of the injected water entered the aquifer through a 9 m thick, high-permeability layer within the confined aquifer near the top of the screened interval. Model simulations of ground-water flow near the ASR well indicate that (1) aquifer heterogeneity allowed injected water to move rapidly through the aquifer to nearby monitoring wells, (2) aquifer heterogeneity caused injected water to move further than expected assuming uniform aquifer properties, and (3) physical clogging of high-permeability layers is the probable cause for the observed change in the distribution of borehole flow. Aquifer heterogeneity also enhanced mixing of native anoxic ground water with oxic injected water, promoting removal of THMs primarily through sorption. A 3 to 4-fold reduction in TTHM concentrations was observed in the furthest monitoring well 427 m downgradient from the ASR well, and similar magnitude reductions were observed in depth-dependent water samples collected from the upper part of the screened interval in the ASR well near the end of the extraction phase. Haloacetic acids (HAAs) were completely sorbed or degraded within 10 months of injection.     

Utilization of a multicriteria least cost path model in an aquatic environment

A critical component of maintaining biodiversity in fragmented habitats is maintaining connectivity among the usable fragments. Least cost path (LCP) analysis is a tool that can be used for predicting the ability of an organism to move from one habitat patch to another, based on geographical features of the landscape and life history traits of the organism. While this analysis has been utilized for terrestrial habitats, it is rarely applied to aquatic environments. Aquatic hypoxic conditions occur when dissolved oxygen falls below 2 mg/L. These conditions can create barriers in the water column that can either force fish to leave a habitat, or avoid that habitat altogether. Using the lower St. Johns River (LSJR) estuary in Florida, USA, as a study system, the ability of an adult silver perch, Bairdiella chrysoura, to escape a large-scale hypoxic event was modeled using a multicriteria LCP approach. Criteria-specific cost grids were constructed based upon current speed, risk of predation, and whether oxygen levels in the habitat area were normoxic (>5.5 mg/L), or hypoxic (<2.0–1.5 mg/L) as a function of water depth for the LSJR. The criteria cost grids were combined using relative weighting to produce the multicriteria cost grid used to implement the LCP analysis. Three origin and destination point locations within the LSJR study area were selected for modeling whether or not a silver perch would be able to escape a hypoxic zone. Since the LCP model will always determine a LCP from the specified origin point location, ecologically relevant swimming capacities for silver perch under normoxic and hypoxic conditions were then applied to assess the model, and to determine whether the fish would be able to reach areas unimpacted by hypoxia. The LCP model and the swimming capacity results for this study predict that under normoxic conditions, fish movement was unimpeded. During the rapidly developing hypoxic event that was modeled, the results from the LCP model indicate that the fish could move outside the hypoxic zone, but when swimming capacities were applied to the model, the silver perch could not escape. Ecologically, the results of this study suggest that silver perch would experience high mortality under a rapidly developing hypoxic event. Additionally, the results of this study indicate that a LCP model can be applied to an aquatic habitat, as long as the cost grids incorporate relevant abiotic and biotic factors.