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Reproductive biology was assessed in 106 female common dolphins (Delphinus delphis) examined post-mortem from stranding and bycatch events along the New Zealand coastline between 1997 and 2019. The average age (ASM) and length (LSM) at sexual maturity was estimated at 7.5 years and 183.5 cm, respectively. The total number of corpora in mature individuals increased with age and appeared to persist throughout life. Ovarian asymmetry was apparent, with the left ovary displaying higher rates of ovulation, and a maximum of 19 corpora recorded for a 24-year-old female. The estimated ovulation and annual pregnancy rates for mature females were 0.39 year−1 and 30%, respectively. Conception and calving occurred year-round, with a weak seasonal increase observed in late austral spring and early austral summer. As these data did not clearly show whether seasonality was present, the gestation, lactation, and resting periods were calculated as either 12.6 or 12.8 months based on the presence/absence of seasonality, respectively. Similarly, calving interval ranged from 3.15 to 3.2 years, depending upon whether seasonality was considered. The estimated LSM of the New Zealand population aligns with other populations globally, although the estimated ASM is younger by approximately 6 months. Other reproductive parameters align with Northern Hemisphere populations, although demonstrate variation, which may reflect adaptations to local conditions such as water temperature and prey availability. As the species is subject to anthropogenic impacts including pollution and bycatch, we suggest our findings be used as a baseline with which to monitor trends in population parameters.

To date, there remains no satisfactory solution for absent levels in random forest models. Absent levels are levels of a predictor variable encountered during prediction for which no explicit rule exists. Imposing an order on nominal predictors allows absent levels to be integrated and used for prediction. The ordering of predictors has traditionally been via class probabilities with absent levels designated the lowest order. Using a combination of simulated data and pathogen source-attribution models using whole-genome sequencing data, we examine how the method of ordering predictors with absent levels can (i) systematically bias a model, and (ii) affect the out-of-bag error rate. We show that the traditional approach is systematically biased and underestimates out-of-bag error rates, and that this bias is resolved by ordering absent levels according to the a priori hypothesis of equal class probability. We present a novel method of ordering predictors via principal coordinates analysis (PCO) which capitalizes on the similarity between pairs of predictor levels. Absent levels are designated an order according to their similarity to each of the other levels in the training data. We show that the PCO method performs at least as well as the traditional approach of ordering and is not biased.

Long-term evolution experiments have tested the importance of genetic and environmental factors in influencing evolutionary outcomes. Differences in phylogenetic history, recent adaptation to distinct environments and chance events, all influence the fitness of a population. However, the interplay of these factors on a population's evolutionary potential remains relatively unexplored. We tracked the outcome of 2000 generations of evolution of four natural isolates of Escherichia coli bacteria that were engineered to also create differences in shallow history by adding previously identified mutations selected in a separate long-term experiment. Replicate populations started from each progenitor evolved in four environments. We found that deep and shallow phylogenetic histories both contributed significantly to differences in evolved fitness, though by different amounts in different selection environments. With one exception, chance effects were not significant. Whereas the effect of deep history did not follow any detectable pattern, effects of shallow history followed a pattern of diminishing returns whereby fitter ancestors had smaller fitness increases. These results are consistent with adaptive evolution being contingent on the interaction of several evolutionary forces but demonstrate that the nature of these interactions is not fixed and may not be predictable even when the role of chance is small.

An exceptionally large coral Porites sp. has been identified and measured at Goolboodi (Orpheus Island), Great Barrier Reef (GBR). This coral was measured in March 2021 during citizen science research of coral reefs in the Palm Islands group. We conducted a literature review and consulted scientists to compare the size, age and health of the Porites with others in the GBR and internationally. This is the largest diameter Porites coral measured by scientists and the sixth highest coral measured in the GBR. The health of the Porites was assessed as very good with over 70% live coral cover and minor percentages of sponge, live coral rock and macroalgae. An estimated age of 421–438 years was calculated based on linear growth models. Manbarra Traditional Owners were consulted and suggested that the Porites be named Muga dhambi (big coral) to communicate traditional knowledge, language and culture to indigenous, tourists, scientists and students.

Effective management of wild populations of animals relies on having accurate methods for estimating their densities from field surveys. Surveying sharks and other highly mobile marine predators is particularly difficult, requiring specialised methods that can entail a range of potential biases. Recent simulation studies have suggested that non-instantaneous visual and video survey methods may overestimate densities of highly mobile fishes. A non-instantaneous method is one where each point in space is surveyed for a non-negligible period of time, rather than in an instantaneous ‘snapshot’, allowing animals to move into the survey space during the survey period. We conducted instantaneous and non-instantaneous surveys of sharks (Sphyrna lewini and Carcharhinus galapagensis) around Darwin and Wolf Islands (Galápagos Islands, Ecuador) using diver-operated stereo-video (stereo-DOV) systems with towed GPS. We provide the first empirical evidence of non-instantaneous bias and show that the degree of bias is negatively related to diver swimming speed. At a speed of 40 m min-1, the non-instantaneous method recorded twice as many sharks as the instantaneous method. The bias may be as high as 10 fold at slow speeds (23 m min-1) and negligible at very fast speeds (65 m min-1). Moreover, we used GPS data to produce fine-scale distribution maps, revealing high densities in areas of strong currents along the south-eastern sides of both islands. We recommend the use of stereo-DOV systems with GPS and fast swimming speeds for surveying highly mobile sharks, to produce more realistic estimates of densities on which to base management of these species.

Multivariate exponentially weighted moving average (MEWMA) control charts for individual monitoring require a priori knowledge of the in-control parameters. In practice, this assumption is not alwa...

Knowledge of population biological parameters can contribute to assessing the resilience of a population in the face of increasing anthropogenic pressures. Southern Hemisphere long-finned pilot whales (Globicephala melas edwardii) are susceptible to high rates of live stranding-related mortality. However, the biological parameters of this population largely are unknown. In this study, age, growth, allometry, and sexual dimorphism are described using teeth and external body measurements obtained from 515 male, 776 female, and 229 individuals of unknown sex, stranded on the New Zealand coastline between 1948 and 2017. Maximum ages of 31 and 38 years were estimated for males (n = 163) and females (n = 239), respectively. Females ranged in length from 160 to 500 cm (modal size class 400–449 cm) and males from 165 to 622 cm (modal size class 500–549 cm). Length-at-birth for both sexes was estimated at 170 cm using a logistic regression model. Growth models for both sexes indicated a preliminary rapid growth phase followed by a second phase of slower growth. For males, a two-phase growth model also indicated a moderate growth spurt around the average age at attainment of sexual maturity (ca.12–13 years). Asymptotic lengths were estimated at 570 and 438 cm for males and females, respectively. We found strong evidence of sexual size dimorphism, with males significantly larger than females for 13 of 14 external measurements. We also found sexual dimorphism with respect to shape, with males having proportionally longer pectoral fins, wider tail flukes, and taller dorsal fins, than females. Estimates of length-at-birth, maximum ages, and sexual shape dimorphism for G. m. edwardii differed from those previously reported for the North Atlantic subspecies (G. m. melas), which may indicate subspecies or population-level differences in morphology, longevity, and sociality.

Male reproductive biology is described for the Southern Hemisphere long-finned pilot whale (Globicephala melas edwardii), a subspecies that regularly mass strands along the New Zealand coastline. Ten mass stranding events sampled over a 7-year period enabled assessments of key life history parameters. Sexual maturation in immature, maturing, and mature males was assessed using morphological data and histological examination of testicular tissue. Variation was observed in the age (11–15 years) and length (450–490 cm) at which individuals attained sexual maturity. Using Bayesian cumulative logit regression models, we estimated the average age and length at the attainment of sexual maturity to be 13.5 years and 472 cm, respectively. Combined testes weight, combined testes length, an index of testicular development (combined testes weight/combined testes length), and mean seminiferous tubule diameter were all good indicators of sexual maturity status. Combined testes length was the best nonhistological indicator, and all testicular measures were found to be better indicators of sexual maturation for G. m. edwardii than age or total body length. Sexual maturity was attained before physical maturity (> 40 years and 570 cm), and at a younger age and smaller body length than previously reported for Globicephala melas melas in the North Atlantic. Given the ease of collection, minimal processing, and applicability to suboptimal material collected from stranding events, future studies should assess the value of testicular size as an indicator of sexual maturity in pilot whales and other cetacean species. Estimates of the average age and length at sexual maturity for G. m. edwardii provided in this study may be used to inform population models required for conservation management of the subspecies, which is subject to high levels of stranding-related mortality.

In this paper, we propose an efficient control chart for monitoring small shifts in a process mean for scenarios where the process variable is observed with a correlated auxiliary variable. The proposed chart, called an auxiliary homogeneously weighted moving average (AHWMA) chart, is a homogeneously weighted moving average type control chart that uses both the process and auxiliary variables in the form of a regression estimator to provide an efficient and unbiased estimate of the mean of the process variable. We provide the design structure of the chart and examine its performance in terms of its run length properties. Using a simulation study, we compare its run length performance with several existing methods for detecting a small shift in the process mean. Our simulation results show that the proposed chart is more efficient in detecting a small shift in the process mean than its competitors. We provide a detailed study of the chart's robustness to non-normal distributions and show that the chart may also be designed to be less sensitive to non-normality. We give some recommendations on the application of the chart when the process parameters are unknown and provide an example to show the implementation of the proposed new technique.

Novel tools and methods for monitoring marine environments can improve efficiency but must not compromise long-term data records. Quantitative comparisons between new and existing methods are therefore required to assess their compatibility for monitoring. Monitoring of shallow water coral reefs is typically conducted using diver-based collection of benthic images along transects. Diverless systems for obtaining underwater images (e.g. towed-cameras, remotely operated vehicles, autonomous underwater vehicles) are increasingly used for mapping coral reefs. Of these imaging platforms, towed-cameras offer a practical, low cost and efficient method for surveys but their utility for repeated measures in monitoring studies has not been tested. We quantitatively compare a towed-camera approach to repeated surveys of shallow water coral reef benthic assemblages on fixed transects, relative to benchmark data from diver photo-transects. Differences in the percent cover detected by the two methods was partly explained by differences in the morphology of benthic groups. The reef habitat and physical descriptors of the site—slope, depth and structural complexity—also influenced the comparability of data, with differences between the tow-camera and the diver data increasing with structural complexity and slope. Differences between the methods decreased when a greater number of images were collected per tow-camera transect. We attribute lower image quality (variable perspective, exposure and focal distance) and lower spatial accuracy and precision of the towed-camera transects as the key reasons for differences in the data from the two methods and suggest changes to the sampling design to improve the application of tow-cameras to monitoring.

Knowledge of population biological parameters can contribute to assessing the resilience of a population in the face of increasing anthropogenic pressures. Southern Hemisphere long-finned pilot whales (

Made available in DSpace on 2021-06-25T12:19:58Z (GMT). No. of bitstreams: 0 Previous issue date: 2020-09-24 Australian Government's National Environmental Science Program Australian Research Data Commons GorgonBarrow Island Gorgon Barrow Island Net Conservation Benefits Fund Baited remote underwater stereo-video systems (stereo-BRUVs) are a popular tool to sample demersal fish assemblages and gather data on their relative abundance and body size structure in a robust, cost-effective and non-invasive manner. Given the rapid uptake of the method, subtle differences have emerged in the way stereo-BRUVs are deployed and how the resulting imagery is annotated. These disparities limit the interoperability of datasets obtained across studies, preventing broadscale insights into the dynamics of ecological systems. We provide the first globally accepted guide for using stereo-BRUVs to survey demersal fish assemblages and associated benthic habitats. Information on stereo-BRUVs design, camera settings, field operations and image annotation are outlined. Additionally, we provide links to protocols for data validation, archiving and sharing. Globally, the use of stereo-BRUVs is spreading rapidly. We provide a standardized protocol that will reduce methodological variation among researchers and encourage the use of Findable, Accessible, Interoperable and Reusable workflows to increase the ability to synthesize global datasets and answer a broad suite of ecological questions. Univ Western Australia, UWA Oceans Inst, Perth, WA, Australia Univ Western Australia, Sch Biol Sci, Perth, WA, Australia Dept Biodivers Conservat & Attract, Marine Sci Program, Biodivers & Conservat Sci, Kensington, WA, Australia Curtin Univ, Sch Mol & Life Sci, Perth, WA, Australia Univ Tasmania, Inst Marine & Antarctic Studies, Hobart, Tas, Australia Silliman Univ, Angelo King Ctr Res & Environm Management, Dumaguete, Philippines NOAA Inouye Reg Ctr, NOAA Fisheries, Pacific Isl Fisheries Sci Ctr, Sci Operat Div, Honolulu, HI USA Univ Hawaii Manoa, Joint Inst Marine & Atmospher Res, Honolulu, HI 96822 USA South African Inst Aquat Biodivers, Grahamstown, South Africa Rhodes Univ, Dept Zool & Entomol, Grahamstown, South Africa Univ St Andrews, Ctr Res Ecol & Environm Modelling, Sch Math & Stat, St Andrews, Fife, Scotland Indian Ocean Marine Res Ctr, Australian Inst Marine Sci, Perth, WA, Australia Australian Inst Marine Sci, Townsville, Qld, Australia Govt Western Australia, Western Australian Fisheries & Marine Res Labs, Dept Primary Ind & Reg Dev, North Beach, WA, Australia NSW Dept Primary Ind, Fisheries Res, Taylors Beach, NSW, Australia Dept Environm & Water, Marine Sci Program, Sci & Corp Serv Div, Adelaide, SA, Australia Flinders Univ S Australia, Southern Shark Ecol Grp, Coll Sci & Engn, Bedford Pk, SA, Australia Deakin Univ, Sch Life & Environm Sci, Ctr Integrat Ecol, Warrnambool, Vic, Australia NSW Dept Primary Ind, Fisheries Res, Huskisson, NSW, Australia Coral Reef Res Fdn, Koror, Palau NSW Dept Primary Ind, Fisheries Res, Coffs Harbour, NSW, Australia Ctr Environm Fisheries & Aquaculture Sci, Lowestoft, Suffolk, England Sao Paulo State Univ, Elasmobranch Res Lab, Inst Biosci, Sao Vicente, SP, Brazil Massey Univ, Sch Nat & Computat Sci, Auckland, New Zealand Sao Paulo State Univ, Elasmobranch Res Lab, Inst Biosci, Sao Vicente, SP, Brazil

An Amendment to this paper has been published and can be accessed via a link at the top of the paper.

Coral reef ecosystems have suffered an unprecedented loss of habitat-forming hard corals in recent decades. While marine conservation has historically focused on passive habitat protection, demand for and interest in active restoration has been growing in recent decades. However, a disconnect between coral restoration practitioners, coral reef managers and scientists has resulted in a disjointed field where it is difficult to gain an overview of existing knowledge. To address this, we aimed to synthesise the available knowledge in a comprehensive global review of coral restoration methods, incorporating data from the peer-reviewed scientific literature, complemented with grey literature and through a survey of coral restoration practitioners. We found that coral restoration case studies are dominated by short-term projects, with 60% of all projects reporting less than 18 months of monitoring of the restored sites. Similarly, most projects are relatively small in spatial scale, with a median size of restored area of 100 m2. A diverse range of species are represented in the dataset, with 229 different species from 72 coral genera. Overall, coral restoration projects focused primarily on fast-growing branching corals (59% of studies), and report survival between 60 and 70%. To date, the relatively young field of coral restoration has been plagued by similar ‘growing pains’ as ecological restoration in other ecosystems. These include 1) a lack of clear and achievable objectives, 2) a lack of appropriate and standardised monitoring and reporting and, 3) poorly designed projects in relation to stated objectives. Mitigating these will be crucial to successfully scale up projects, and to retain public trust in restoration as a tool for resilience based management. Finally, while it is clear that practitioners have developed effective methods to successfully grow corals at small scales, it is critical not to view restoration as a replacement for meaningful action on climate change.

Fishing has had a profound impact on global reef shark populations, and the absence or presence of sharks is strongly correlated with national socio-economic conditions and reef governance. Decades of overexploitation have devastated shark populations, leaving considerable doubt as to their ecological status(1,2). Yet much of what is known about sharks has been inferred from catch records in industrial fisheries, whereas far less information is available about sharks that live in coastal habitats(3). Here we address this knowledge gap using data from more than 15,000 standardized baited remote underwater video stations that were deployed on 371 reefs in 58 nations to estimate the conservation status of reef sharks globally. Our results reveal the profound impact that fishing has had on reef shark populations: we observed no sharks on almost 20% of the surveyed reefs. Reef sharks were almost completely absent from reefs in several nations, and shark depletion was strongly related to socio-economic conditions such as the size and proximity of the nearest market, poor governance and the density of the human population. However, opportunities for the conservation of reef sharks remain: shark sanctuaries, closed areas, catch limits and an absence of gillnets and longlines were associated with a substantially higher relative abundance of reef sharks. These results reveal several policy pathways for the restoration and management of reef shark populations, from direct top-down management of fishing to indirect improvement of governance conditions. Reef shark populations will only have a high chance of recovery by engaging key socio-economic aspects of tropical fisheries.

Globally, coastal habitat restoration is growing in recognition as a viable management tool to repair and reinstate valuable coastal habitats and species, such as mangrove and macroalgae forests, salt marshes, seagrass meadows, shellfish and coral reefs (Aronson & Alexander (2013), Restoration Ecology, 293; Anthony et al. (2017) Nature Ecology and Evolution, 1420; TNC (2017) Caribbean: A revolution to save coral reefs in the Caribbean and beyond). In Australia, there is increasing interest and investment in coastal restoration and habitat conservation, particularly with respect to growing national concerns around habitat loss, coastal inundation and erosion, loss of fisheries and climate change (Maggini et al. (2013) Protecting and restoring habitat to help Australia's threatened species adapt to climate change; GBRMPA (2017) Reef summit sets new course of action for the Great Barrier Reef). This has led to new community of practices being formed for shellfish reef restoration (Shellfish Reef Restoration Network shellfishrestoration.org.au), seagrass restoration (Seagrass Restoration Network seagrassrestoration.net), and saltmarsh and mangrove (Saltmarsh and Mangrove Network, amsn.net.au) conservation. However, despite this interest, there has been no national coordination, network or society with coastal restoration as a primary focus. The inaugural Australian Coastal Restoration Symposium brought together 60 Australian restoration practitioners, researchers and managers at James Cook University, Townsville for three days from the 31st of August 2017. The symposium goals were to enhance collaboration and national coordination amongst coastal restoration projects and practitioners, as well as to connect researchers and practitioners working in the restoration space with one another. Three international keynote speakers shared their experiences and advice. Delegates were enthusiastic about continuing to meet at future symposiu, meetings and workshops, and noted the value of being able to connect, share project experiences and learnings, and collaborate. The Australian Coastal Restoration Network has been formed with the goal of meeting annually to continue to share knowledge and improve collaboration. View a video about the symposium by following this link – https://www.youtube.com/watch?v=lukSpo3mM-4

Control charts are statistical methods used to detect shifts in the location parameter of a process that is monitored over time. Here, we propose an improvement to the performance of the classical exponentially weighted moving average (EWMA) control charts, by making use of auxiliary information that is correlated with the process variable. We present an EWMA P and its modifications: EWMA-type control charts based on a product estimator where the location parameter of the process is monitored using an auxiliary variable. The charts are developed using different sampling schemes: simple random sampling, ranked set sampling (RSS) and median ranked set sampling (MRSS), and we evaluate their performance using average run length, and other performance measures such as extra quadratic loss and relative average run length. It is observed that the proposed control charts are performing better than the classical EWMA control chart in monitoring shifts in the location parameter of a process, especially when a strong negative correlation exists between the process and the auxiliary variables. They are particularly efficient in detecting small to moderate shifts in the process.

When conducting field studies, it is common for ecologists to choose the locations of sampling units arbitrarily at the time sampling occurs, rather than using a properly randomised sampling design. Unfortunately, this ‘haphazard’ sampling approach cannot provide formal statistical inference from the sample to the population without making untestable assumptions. Here, we argue that two recent technological developments remove the need for haphazard sampling in many situations. A general approach to simple randomised sampling designs is outlined, and some examples demonstrate that even complicated designs can be implemented easily using software that is widely used among ecologists. We consider that more rigorous, randomised sampling designs would strengthen the validity of the conclusions drawn from ecological studies, to the benefit of the discipline as a whole. This article is protected by copyright. All rights reserved.

The aesthetic appreciation of natural places is one of the most fundamental ways in which people relate to their environment. It provides wellbeing, an opportunity for recreation and reflection, a sense of place, and cultural enrichment. It also motivates people to take care of natural places and to conserve them for current and future appreciation. Aesthetically valuable places also support significant economic activity. However, there is little guidance available to assist environmental managers and policy-makers to consider and integrate aesthetic values into decision-making processes. In this study, we present an approach for developing robust and practical indicators of aesthetic value to enable environmental managers to consider, assess and report on aesthetic condition and trend. We demonstrate its utility using the case of the Great Barrier Reef, a region currently undergoing significant social, economic and environmental change and an area formally protected, in part, for its aesthetic values. A qualitative scoping study with 30 key informants identified over 180 potential qualities contributing to reef aesthetics. We tested five for their utility in capturing key aspects of the coral reef aesthetic: (i) coral cover, (ii) coral pattern, (iii) coral topography, (iv) fish abundance, and (v) visibility. We asked 1,417 online Australians to aesthetically rate 50 out of 181 underwater coral reef images that varied in relation to these five attributes. Coral topography, fish abundance, and visibility were significantly correlated with aesthetic ratings, whilst coral cover and coral pattern were not. We also tested for demographic patterns in aesthetic ratings. Our pilot study has demonstrated that readily measurable characteristics of coral reefs can provide useful indicators of aesthetic quality, opening up opportunities for coral reef managers and policymakers to assess and track changes in aesthetics in ways that are relevant to the public. There is considerable scope to further advance capacity for monitoring and managing aesthetic values of coral reefs through additional research that resolves nuances in the meanings associated with aesthetics in coral reef settings.

This paper presents a multivariate homogeneously weighted moving average (MHWMA) control chart for monitoring a process mean vector. The MHWMA control chart statistic gives a specific weight to the current observation, and the remaining weight is evenly distributed among the previous observations. We present the design procedure and compare the average run length (ARL) performance of the proposed chart with multivariate Chi-square, multivariate EWMA, and multivariate cumulative sum control charts. The ARL comparison indicates superior performance of the MHWMA chart over its competitors, particularly for the detection of small shifts in the process mean vector. Examples are also provided to show the application of the proposed chart. - 2013 IEEE. Scopus

The Waitematā Harbour is a drowned river valley in the south-west of the Hauraki Gulf, on the north east of New Zealand’s North Island. The central business district for the city of Auckland is situated on the southern shore of the central Waitematā Harbour and is New Zealand’s largest and fastest growing city. The Waitematā Harbour hosts a major international port, New Zealand’s primary naval base and international cruise terminal, as well as a large and committed community of recreational users. In comparison with the marine ecosystems surrounding many of the world’s coastal cities, the Waitematā Harbour and the Hauraki Gulf have experienced a relatively short period of human occupation. Nonetheless, rapid and widespread changes have occurred within these ecosystems. Habitat loss and declines in biodiversity as well as impacts on human activities such as safe swimming and recreational harvesting have motivated several conservation and restoration initiatives. Here, we review the natural and social context of the Waitematā Harbour and Hauraki Gulf, and summarise some of the pressures the region faces. Last, we present three case studies highlighting current participatory initiatives aimed at ensuring more sustainable management of the region’s marine ecosystems. The Waitematā Harbour and Hauraki Gulf have provided considerable ecological, social and economic wealth for the people of Auckland; accordingly, conserving these ecosystems and preserving future prosperity should be a collective priority for all sectors of society.

Many large, fishery‐targeted predatory species have attained very high relative densities as a direct result of protection by no‐take marine reserves. Indirect effects, via interactions with targeted species, may also occur for species that are not themselves targeted by fishing. In some temperate rocky reef ecosystems, indirect effects have caused profound changes in community structure, notably the restoration of predator–urchin–macroalgae trophic cascades. Yet, indirect effects on small benthic reef fishes remain poorly understood, perhaps because of behavioral associations with complex, refuge‐providing habitats. Few, if any, studies have evaluated any potential effects of marine reserves on habitat associations in small benthic fishes. We surveyed densities of small benthic fishes, including some endemic species of triplefin (Tripterygiidae), along with fine‐scale habitat features in kelp forests on rocky reefs in and around multiple marine reserves in northern New Zealand over 3 years. Bayesian generalized linear mixed models were used to evaluate evidence for (1) main effects of marine reserve protection, (2) associations with habitat gradients, including complexity, and (3) differences in habitat associations inside versus outside reserves. No evidence of overall main effects of marine reserves on species richness or densities of fishes was found. Both richness and densities showed strong associations with gradients in habitat features, particularly habitat complexity. In addition, some species exhibited reserve‐by‐habitat interactions, having different associations with habitat gradients inside versus outside marine reserves. Two species (Ruanoho whero and Forsterygion flavonigrum) showed stronger positive associations with habitat complexity inside reserves. These results are consistent with the presence of a behavioral risk effect, whereby prey fishes are more strongly attracted to habitats that provide refuge from predation in areas where predators are more abundant. This work highlights the importance of habitat structure and the potential for fishing to affect behavioral interactions and the interspecific dynamic attributes of community structure beyond simple predator–prey consumption and archetypal trophic cascades.

BackgroundUsing metagenomics to determine animal diet offers a new and promising alternative to current methods. Here we show that rapid and inexpensive diet quantification is possible through metagenomic sequencing with the portable Oxford Nanopore Technologies (ONT) MinION. Using an amplification-free approach, we profiled the stomach contents from wild-caught rats.ResultsWe conservatively identified diet items from over 50 taxonomic orders, ranging across nine phyla that include plants, vertebrates, invertebrates, and fungi. This highlights the wide range of taxa that can be identified using this simple approach. We calibrate the accuracy of this method by comparing the characteristics of reads matching the ground-truth host genome (rat) to those matching diet items, and show that at the family-level, false positive taxon assignments are approximately 97.5% accurate. We also suggest a way to mitigate for database biases in metagenomic approaches. Finally, we implement a constrained ordination analysis and show that we can identify the sampling location of an individual rat within tens of kilometres based on diet content alone.ConclusionsThis work establishes proof-of-principle for long-read metagenomic methods in quantitative diet analysis. We show that diet content can be quantified even with limited expertise, using a simple, amplification free workflow and a relatively inexpensive and accessible next generation sequencing method. Continued increases in the accuracy and throughput of ONT sequencing, along with improved genomic databases, suggests that a metagenomic approach to quantification of animal diets will become an important method in the future.

Multivariate cumulative sum control charts require knowledge of the in-control process covariance parameters. Here, we show that the performance of the multivariate cumulative sum control charts for individual-observation monitoring is affected by the estimation of parameters unless the Phase I sample size is large. When only a small Phase I sample size is available, we propose the use of a shrinkage estimate. The average run length performance of multivariate cumulative sum control charts obtained using the shrinkage estimate is superior to the other methods examined in this study. The improved performance of the control charts using the shrinkage estimate is also demonstrated via an illustrative case study of Bimetal data, in which measurements of four properties of bimetal brass and steel thermostats are monitored, and a shift in the multivariate centroid is detected earlier using the shrinkage-based method. - 2018 Elsevier Ltd Scopus

The utility of marine protected areas (MPAs) as a means of protecting exploited species and conserving biodiversity within MPA boundaries is supported by strong empirical evidence. However, the potential contribution of MPAs to fished populations beyond their boundaries is still highly controversial; empirical measures are scarce and modelling studies have produced a range of predictions, including both positive and negative effects. Using a combination of genetic parentage and relatedness analysis, we measured larval subsidies to local fisheries replenishment for Australasian snapper (Chrysophrys auratus: Sparidae) from a small (5.2 km2), well-established, temperate, coastal MPA in northern New Zealand. Adult snapper within the MPA contributed an estimated 10.6% (95% CI: 5.5–18.1%) of newly settled juveniles to surrounding areas (approx. 400 km2), with no decreasing trend in contributions up to 40 km away. Biophysical modelling of larval dispersal matched experimental data, showing larvae produced inside the MPA dispersed over a comparable distance. These results demonstrate that temperate MPAs have the potential to provide recruitment subsidies at magnitudes and spatial scales relevant to fisheries management. The validated biophysical model provides a cost-efficient opportunity to generalize these findings to other locations and climate conditions, and potentially informs the design of MPA networks for enhancing fisheries management.

Evaluating the effects of marine reserves on exploited species can be challengingbecause they occur within a context of natural spatial and temporal variation at many scales. For rigorous inferences to be made, such evaluations require monitoring programmes that are replicated at appropriate scales. We analysed monitoring data of snapper Pagrus auratus (Sparidae) in northeastern New Zealand, comprised of counts from baited-underwater-video surveys from inside and outside 3 marine reserves. Surveys were replicated at many levels, including areas inside and outside of marine reserves at 3 locations in 2 seasons, over a period of up to 14 yr, in an unbalanced design. The Bayesian modelling approach allowed the use of some familiar aspects of ANOVA, including mixed models of fixed and random effects, hierarchically nested structures, and variance decomposition, while allowing for overdispersion and excess zeros in the counts. Model selection and estimates of variance components revealed that protection by marine reserves was by far the strongest measured source of variation for relative densities of legal-sized snapper. The size of the effect varied across years among the 3 reserves, with relative densities between 7 and 20 times greater in reserves than in nearby areas. Other than the reserve effect, the temporal factors of season and year were generally more important than the spatial factors at explaining variation in counts. In particular, overall relative densities were ~2 to 3 times greater in autumn than in spring for legal-sized snapper, although the seasonal effect was also variable among locations and years. We consider that the Bayesian generalised linear mixed modelling approach, as used here, provides an extremely useful and flexible tool for estimating the effects of management actions and comparing them directly with other sources of spatial and temporal variation in natural systems.

Zero-inflated versions of standard distributions for count data are often required in order to account for excess zeros when modeling the abundance of organisms. Such distributions typically have as parameters lambda, the mean of the count distribution, and pi, the probability of an excess zero. Implementations of zero-inflated models in ecology typically model lambda using a set of predictor variables, and pi is fit either as a constant or with its own separate model. Neither of these approaches makes use of any relationship that might exist between pi and lambda. However, for many species, the rate of occupancy is closely and positively related to its average abundance. Here, this relationship was incorporated into the model for zero inflation by functionally linking pi to lambda, and was demonstrated in a study of snapper (Pagrus auratus) in and around a marine reserve. This approach has several potential practical advantages, including better computational performance and more straightforward model interpretation. It is concluded that, where appropriate, directly linking pi to lambda can produce more ecologically accurate and parsimonious statistical models of species abundance data.

The Feather River is a large flow-regulated river in the Central Valley of California. The Mediterranean climate of the area imposes a natural flow regime for the region that is characterized by predictable high flows in the winter and spring and low flows in the summer and fall. The Oroville Dam complex on the Feather River has created a permanent low-flow section of the river where a base flow is continuous year round but the natural annual variability of flow has been completely eliminated. We used this modified section of the river to examine the ecological impact that removing natural flow variability has on the macroinvertebrate assemblage and how we might measure such a change if it is present. Specifically, we examined whether biodiversity and community similarity differed between the low- and high-flow sections of the river for both benthic and drifting aquatic invertebrates. Using a modified Surber sampler we collected samples at three distinct time periods within a year (January, April, and Jul...

We applied a multivariate statistical modelling technique called boosted regression trees to derive relationships between environmental conditions and the distribution of the adult stage of the cyclopoid copepod Oithona similis in the Southern Ocean. Nearly 20 000 samples from the Southern Ocean Continuous Plankton Recorder survey (87% from East Antarctica) were used to model the probability of detection (presence) and relative abundance of adults of this zooplankton species in surface waters. We demonstrate that it is possible to obtain reasonable models for both the presence (area under the Receiver Operating Characteristic curve of 0.77) and relative abundance (28–35% variance explained) of adult O. similis between November and March in much of the Southern Ocean. No investigation was possible where the environmental characteristics were not well represented by the SO-CPR dataset, namely, the Argentine shelf, Weddell Sea, and the frontal region north of the Amundsen Sea, or under sea-ice. Our analyses support the hypothesis that adult O. similis abundance is related to environmental conditions in a broadly similar way throughout the Southern Ocean. Compared to a compilation of net-haul data from the literature, the abundance model explained 34% of the variance in surface concentrations of adult stages of this species, and 23–59% of the variance in depth-integrated abundance of copepodite and adult stages combined. The models show higher occurrence and elevated abundances in a broad circumpolar band between the Antarctic Polar Front and the southern boundary of the Antarctic Circumpolar Current (approximately 54–64°S). Evidence of diel vertical migration by adults of this species north of 65°S was found, with surface abundances 20% higher at night than during the day. There was no evidence of diel migration south of 65°S. Five potential “hotspots” of adult O. similis were identified: in the southern Scotia Sea, two areas off east Antarctica, in the frontal zone north of the Amundsen Sea, and a small area in the outer Bellingshausen Sea. We recommend that a database of all available net-haul data on Oithona similis in the Southern Ocean be created to facilitate further investigations on the circumpolar distribution of this species.

Currently, there is little professional consensus as to which ecological metrics should be used to measure restoration success in wetlands. Aquatic macroinvertebrate communities have many qualities to recommend them as useful metrics in this manner; yet, they have not been widely used to evaluate wetland restoration success. We examined the macroinvertebrate communities of four restored seasonal wetlands across a chronosequence of postrestoration age and compared them to a remnant natural wetland in the Central Valley of California. We examined two qualitatively different sets of aquatic macroinvertebrate metrics, general measures of community properties (abundance, richness, and diversity) and specific assemblage membership (nonmetric multidimensional scaling and permutational multivariate analysis of variance). Our results using these two different sets of metrics give us different answers. The general measures suggest that wetland macroinvertebrate communities converge on relatively stable values sometime after 10 years postrestoration. The specific assemblage results imply that the particular set of taxa found in restored wetlands is not predictable over the chronosequence we examined. Taken together, our results suggest that aquatic macroinvertebrate communities may be useful for measuring some aspects of restoration success but that there is unlikely to be a final aquatic community pattern indicating restoration success.

We investigated the neighbourhood-scale effect of weeding on native plants in Lance McCaskill Nature Reserve, Canterbury, New Zealand. The reserve is an unproductive basin of limestone debris. Originally set up to protect the Castle Hill buttercup, Ranunculus crithmifolius var. paucifolius , the reserve also offers protection for nationally endangered species: Myosotis colensoi and Lepidium sisymbrioides . Our aim was to investigate whether removal of introduced plants increased the cover of remaining native species. We removed introduced plants, by hand, every year for 6 years from half of the plots. We used nonparametric multivariate analysis to compare overall species cover.The results suggest that weeding does benefit the native plants in this area. There was a significant difference in the mean of the overall native species cover between the weeded and the non-weeded plots. For the ten species measured, the mean area covered per square metre was higher in the weeded plots than in the non-weeded plots...

The endemic New Zealand dolphin Cephalorhynchus hectori has been shown through genetic analyses to consist of four regional populations separated to various degrees both geographically and...

The potential effectiveness of marine protected areas (MPAs) as a conservation tool for large sharks has been questioned due to the limited spatial extent of most MPAs in contrast to the complex life history and high mobility of many sharks. Here we evaluated the movement dynamics of a highly migratory apex predatory shark (tiger shark Galeocerdo cuvier) at the Galapagos Marine Reserve (GMR). Using data from satellite tracking passive acoustic telemetry, and stereo baited remote underwater video, we estimated residency, activity spaces, site fidelity, distributional abundances and migration patterns from the GMR and in relation to nesting beaches of green sea turtles (Chelonia mydas), a seasonally abundant and predictable prey source for large tiger sharks. Tiger sharks exhibited a high degree of philopatry, with 93% of the total satellite-tracked time across all individuals occurring within the GMR. Large sharks (> 200 cm TL) concentrated their movements in front of the two most important green sea turtle-nesting beaches in the GMR, visiting them on a daily basis during nocturnal hours. In contrast, small sharks (< 200 cm TL) rarely visited turtle-nesting areas and displayed diurnal presence at a third location where only immature sharks were found. Small and some large individuals remained in the three study areas even outside of the turtle-nesting season. Only two sharks were satellite-tracked outside of the GMR, and following long-distance migrations, both individuals returned to turtle-nesting beaches at the subsequent turtle-nesting season. The spatial patterns of residency and site fidelity of tiger sharks suggest that the presence of a predictable source of prey and suitable habitats might reduce the spatial extent of this large shark that is highly migratory in other parts of its range. This highly philopatric behaviour enhances the potential effectiveness of the GMR for their protection.

International audience; BACKGROUND: Sooty (Puffinus griseus) and short-tailed (P. tenuirostris) shearwaters are abundant seabirds that range widely across global oceans. Understanding the foraging ecology of these species in the Southern Ocean is important for monitoring and ecosystem conservation and management. METHODOLOGY/PRINCIPAL FINDINGS: Tracking data from sooty and short-tailed shearwaters from three regions of New Zealand and Australia were combined with at-sea observations of shearwaters in the Southern Ocean, physical oceanography, near-surface copepod distributions, pelagic trawl data, and synoptic near-surface winds. Shearwaters from all three regions foraged in the Polar Front zone, and showed particular overlap in the region around 140 degrees E. Short-tailed shearwaters from South Australia also foraged in Antarctic waters south of the Polar Front. The spatial distribution of shearwater foraging effort in the Polar Front zone was matched by patterns in large-scale upwelling, primary production, and abundances of copepods and myctophid fish. Oceanic winds were found to be broad determinants of foraging distribution, and of the flight paths taken by the birds on long foraging trips to Antarctic waters. CONCLUSIONS/SIGNIFICANCE: The shearwaters displayed foraging site fidelity and overlap of foraging habitat between species and populations that may enhance their utility as indicators of Southern Ocean ecosystems. The results highlight the importance of upwellings due to interactions of the Antarctic Circumpolar Current with large-scale bottom topography, and the corresponding localised increases in the productivity of the Polar Front ecosystem.

Harbours are a focus of intensive and diverse activities and thus have a high potential to become centres of conflict between users. Reviewing the multiple uses associated with harbours provides important insights into maritime communities and the management of conflict. In this paper, seven international, multi-disciplinary groups provide their expert synthesis of individual harbours. After a detailed discussion experts from Sydney, Qingdao, Vigo, Auckland, Jakarta, Crete and Plymouth synthesised and shared their harbour’s characteristics, user conflicts and how such conflicts have been researched and managed. The paper addresses an omission of “conflict” in most of the research literature about harbours, and ports and scopes a research agenda that includes integration, risk appreciation and other approaches to these increasingly contentious maritime environments. This process provided an opportunity for global researchers to share the ways harbour conflicts are mitigated and the kinds of adaptations that are possible.

Ultrasound as a Diagnostic and Surgical Tool Edited by Dr. Douglas Gordon. (Based on the International Symposium held at the Royal College of Surgeons, London, December 5th and 6th, 1962.) Pp. xii + 413. (Edinburgh and London: E. and S. Livingstone, Ltd., 1964.) 63s. net.