Adam N. H. Smith

Shearwater Foraging in the Southern Ocean: The Roles of Prey Availability and Winds

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°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.

Geographical variation in Hector's dolphin: Recognition of new subspecies of Cephalorhynchus hectori

Abstract 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 reproductively. A morphological study of skull and mandible features was undertaken to examine variation between the most genetically distinct population, occurring on the west coast of the North Island, and the populations around the South Island. Univariate and principal component analyses demonstrate that the North Island population can be differentiated from the southern populations on the basis of several skeletal characters. These characters, plus the genetic evidence of haplotype differences and absence of gene‐flow between populations, enable us to formally describe the North Island population of Hectors dolphin as a new subspecies, C. hectori maui, and the nominate South Island populations as C. hectori hectori.

Incorporating the intraspecific occupancy–abundance relationship into zero-inflated models

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.

Measuring the ecological impact of long-term flow disturbance on the macroinvertebrate community in a large Mediterranean climate river

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 July) for both drift and benthic fauna. Our results showed little difference between the low- and high-flow assemblages using common measures of diversity (i.e., species richness and Shannon diversity) and a measure of environmental tolerance (Hilsenhoff biotic index). Yet when we employed a multivariate measure of community similarity (i.e., non-metric multidimensional scaling) and associated statistical tests, we found significant assemblage differences between the low- and high-flow sections of the river. This study suggests that flow disturbance of this sort is likely to alter the macroinvertebrate community in ways that are not easily observed using common ecological metrics.

Temperate marine protected area provides recruitment subsidies to local fisheries

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.

Residency and movement patterns of an apex predatory shark (Galeocerdo cuvier) at the Galapagos Marine Reserve

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.

Shrinkage estimates of covariance matrices to improve the performance of multivariate cumulative sum control charts

Abstract 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.

Marine reserves indirectly affect fine-scale habitat associations, but not overall densities, of small benthic fishes

Abstract 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.

New tools for diet analyses: nanopore sequencing of metagenomic DNA from stomach contents to quantify diet in an invasive population of rats

Background Using 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. Results We 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. Conclusions This 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.

EWMA-type scheme for monitoring location parameter using auxiliary information

Abstract 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.