Accounting for false mortality in telemetry tag applications

Deaths of animals in the wild are rarely observed directly, which often limits understanding of survival rates. Telemetry transmitters offer field ecologists the opportunity to observe mortality events in cases as the absence of animal movement. When observations of mortality are based on factors such as the absence of animal movement, live individuals can be mistaken for dead, resulting in biased estimates of survival. Additionally, tag failure or emigration might also influence estimates of survival in telemetry studies. Failing to account for mis-classification, tag failure, and emigration rates can result in overestimates of mortality rates by up two-fold, even when the data are corrected for obviously mistaken entries. We use a multi-state capture–recapture model with a misclassification parameter in estimating both the rate of permanent emigration and/or tag failure and the rate at which individuals are mistakenly identified as dead. We use this method on an annual telemetry survey of three species of native fish in the Murray river, Australia: Murray cod (Maccullochella peelii), trout cod (Maccullochella macquariensis) and golden perch (Macquaria ambigua). Evidence for higher mortality rates in the first year post-implantation occurred for Murray cod and golden perch, which is likely an effect of tagging and/or the transmitter, or transmitters shedding. Using simulations, we confirm that our model approach is robust to a broad range of misclassification and transmitter failure rates. With these simulations we also demonstrate that misclassification models that do not account for emigration will likely be erroneous if live and dead animals have different probabilities of detection. These findings will have a broad interest to ecologists wishing to account for multiple sources of misclassification error in capture-mark-recapture studies, with the caveat that the specifics of the approach are dependent on species, transmitter types and other aspects of experimental design which may or may not be amenable to the misclassification framework

Optimal scales to observe habitat dynamics: A coral reef example

A new technique to estimate the characteristic length scales (CLSs) of real ecological systems provides an objective means to identify the optimal scale(s) of observation to best detect underlying dynamical trends. Application of the technique to natural systems has focused on identifying appropriate scales to measure the dynamics of species as descriptors of community and ecosystem dynamics. However, ecosystem monitoring is often based not on assessing single species, but on species assemblages, functional groups, or habitat types. We asked whether the concept of CLSs based on dynamic interactions among species could be extended to examine interactions among habitat types and thus to identify optimal scales for observing habitat dynamics. A time series of three spatial maps of benthic habitats on a Caribbean coral reef was constructed from aerial photographs, Compact Airborne Spectrographic Imager (CASI) images, and IKONOS satellite images, providing the short time sequence required for this technique. We estimated the CLS based on the dynamics of three distinct habitat types: dense stands of seagrass, sparse stands of seagrass, and Montastrea patch reefs. Despite notable differences in the areal extent of and relative change in these habitats over the 21-year observation period, analyses based on each habitat type indicated a similar CLS of similar to 300 m. We interpret the consistency of CLSs among habitats to indicate that the dynamics of the three habitat types are linked. The results are encouraging, and they indicate that CLS techniques can be used to identify the appropriate scale at which to monitor ecosystem trends on the basis of the dynamics of only one of a disparate suite of habitat types

Distributions of young cephalopods in the tropical waters of Western Australia over two consecutive summers

Cephalopod paralarvae and juveniles were sampled with light traps deployed at the surface and deeper in the southern NW Shelf and on Ningaloo Reef off Western Australia during two consecutive summers. One cross shelf transect (Exmouth) was sampled in the late spring and summers of 1997/1998 (summer 1) and 1998/1999 (summer 2), and a second cross shelf transect (Thevenard) and a longshore transect (Ningaloo) along the Ningaloo Reef were sampled in summer 2. Species captured in the order of abundance were octopods, Photololigo sp., Sepioteuthis lessoniana, and Sthenoteuthis oualaniensis. Most were captured in shallow traps except for Photololigo sp., which was common in both shallow and deep traps with larger animals found in deeper water. The presence of Idiosepius pygmaeus in deep water off Ningaloo Reef revealed the species to be eurytopic, inhabiting a wider range of habitats than previously known. Photololigo sp. and S. lessoniana were more abundant inshore, and octopods were especially abundant on mid-depth stations of the Exmouth transect, probably because of the turbulent mixing and increased productivity there. Fewer S. oualaniensis were caught during the first summer on the Ningaloo transect (n = 5) than during the second summer (n = 79)

New insights into the cardiorespiratory physiology of weaned southern elephant seals (Mirounga leonina)

Southern elephant seal (Mirounga leonina) pups must strike a balance between conserving energy during their post-weaning fast and simultaneously developing diving abilities to attain nutritional independence. Little is known about environmental influences on cardiorespiratory patterns, hence energy use, throughout the 6 week fast. Continuous heart rates were recorded for free-ranging, newly weaned southern elephant seals using heart rate time-depth recorders for 5-9 days at Sub-Antarctic Macquarie Island, during October 1994 (n = 1), 1995 (n = 4) and 1996 (n = 1). Daytime observations of respiration and behaviour were made throughout. We present the first instance of synchronous heart rate traces recorded simultaneously for individual weaners. Generalized additive models revealed that a sinusoidal pattern of diurnal heart rate elevation and nocturnal depression was evident in all seals and, on at least one occasion, a conspicuous break in this pattern coincided with an extreme cold weather event. Seals in this study were capable of considerable cardiorespiratory control and regularly demonstrated bradycardia during periods of resting apnoea. Apnoeic duration ranged from 33 to 291 s (mean 134 s). Apnoeic heart rates (mean 67 ± 15 beats min(-1), range 40-114 beats min(-1)) were on average 19.7% lower than those exhibited during periods of eupnoea (mean 83 ± 15 beats min(-1), range 44-124 beats min(-1)). The early development of the cardiorespiratory response is characterized by arrhythmic heart and respiration rates. The strong temporal patterns observed are being driven by the opposing requirements of maximizing time spent fasting in order to develop diving capabilities and of maximizing departure mass. This pilot study has highlighted a potentially large effect of ambient weather conditions on newly weaned southern elephant seal cardiorespiratory activity. Given the increasing westerlies and more erratic and increasing storminess associated with the Southern Annular Mode predicted in the Southern Ocean, the patterns observed here warrant further investigation

Assessing the viability of estimating baleen whale abundance from tourist vessels

Many populations of southern hemisphere baleen whales are recovering and are again becoming dominant consumers in the Southern Ocean. Key to understanding the present and future role of baleen whales in Southern Ocean ecosystems is determining their abundance on foraging grounds. Distance sampling is the standard method for estimating baleen whale abundance but requires specific logistic requirements which are rarely achieved in the remote Southern Ocean. We explore the potential use of tourist vessel-based sampling as a cost-effective solution for conducting distance sampling surveys for baleen whales in the Southern Ocean. We used a dataset of tourist vessel locations from the southwest Atlantic sector of the Southern Ocean and published knowledge from Southern Ocean sighting surveys to determine the number of tourist vessel voyages required for robust abundance estimates. Second, we simulated the abundance and distributions of four baleen whale species for the study area and sampled them with both standardized line transect surveys and non-standardized tourist vessel-based surveys, then compared modeled abundance and distributions from each survey to the original simulation. For the southwest Atlantic, we show that 12-22 tourist vessel voyages are likely required to estimate abundance for humpback and fin whales, with relative estimates for blue, sei, Antarctic minke, and southern right whales. Second, we show tourist vessel-based surveys outperformed standardized line transect surveys at reproducing simulated baleen whale abundances and distribution. These analyses suggest tourist vessel-based surveys are a viable method for estimating baleen whale abundance in remote regions. For the southwest Atlantic, the relatively cost-effective nature of tourist vessel-based survey and regularity of tourist vessel voyages could allow for annual and intra-annual estimates of abundance, a fundamental improvement on current methods, which may capture spatiotemporal trends in baleen whale movements on forging grounds. Comparative modeling of sampling methods provided insights into the behavior of general additive model-based abundance modeling, contributing to the development of detailed guidelines of best practices for these approaches. Through successful engagement with tourist company partners, this method has the potential to characterize abundance across a variety of marine species and spaces globally, and deliver high-quality scientific outcomes relevant to management organizations.publishedVersio

Krill biomass estimation : sampling and measurement variability

FB is funded by an EPSRC studentship (grant code: EP/R513337/1).Krill are the subject of growing commercial fisheries and therefore fisheries management is necessary to ensure long-term sustainability. Krill catch limits, set by Commission for the Conservation of Antarctic Marine Living Resources, are based on absolute krill biomass, estimated from acoustic-trawl surveys. In this work, we develop a method for determining an error budget for acoustic-trawl surveys of krill which includes sampling and measurement variability. We use our error budget method to examine the sensitivity of biomass estimates to parameters in acoustic target strength (TS) models, length frequency distribution and length to wetmass relationships derived from net data. We determined that the average coefficient of variation (CV) of estimated biomass was 17.7% and the average CV due from scaling acoustic observations to biomass density was 5.3%. We found that a large proportion of the variability of biomass estimates is due to the krill orientation distribution, a parameter in the TS model. Orientation distributions with narrow standard deviations were found to emphasise the results of nulls in the TS to length relationship, which has to potential to lead to biologically implausible results.Publisher PDFPeer reviewe

Spatial link between Adélie penguin foraging effort and krill swarm abundance and distribution

Understanding how predator foraging behaviour is influenced by the distribution and abundance of prey is a fundamental challenge in marine foraging ecology. This is particularly relevant in Southern Ocean ecosystems where the relationships between select predator species and Antarctic krill (Euphausia superba) can inform ecosystem conservation and precautionary fisheries management. In this study, we examine the spatial associations between krill swarm characteristics and Adélie penguin (Pygoscelis adeliae) foraging effort at Béchervaise Island, a long-term monitoring site in East Antarctica. Spatially integrating two years of regional-scale krill acoustic data with contemporaneous horizontal and vertical movement information from chick-rearing adult Adélie penguins, we assessed how penguin foraging effort changed in relation to krill swarm abundance and distribution across the survey area. Our findings show that penguin diving effort was focused in areas with a high number of krill swarms, yet they did not focus their effort in areas with high krill biomass. These results suggest the spatial organisation of Adélie penguin foraging effort can provide an indication of krill presence (and/or availability) but may not reflect krill abundance. We discuss our results in the context of penguin foraging strategies, capturing single krill within the water column rather than the engulfment feeding strategy of larger marine mammals such as whales. Our work substantially improves understanding of penguin-krill dynamics in East Antarctica and provides a greater level of nuance regarding the utility of Adélie penguins as indicator species under CCAMLR’s Ecosystem Monitoring Programme (CEMP). Understanding these predator-prey linkages will become increasingly important for managing any expanding krill fisheries in the region or changes in the prey field under future climate change scenarios. Thus, our results can be interpreted alongside other ecological indicators to support management of the East Antarctic sector of the Southern Ocean ecosystem

An octameric PqiC toroid stabilises the outer-membrane interaction of the PqiABC transport system

The E. coli Paraquat Inducible (Pqi) Pathway is a putative Gram-negative phospholipid transport system. The pathway comprises three components: an integral inner membrane protein (PqiA), a periplasmic spanning MCE family protein (PqiB) and an outer membrane lipoprotein (PqiC). Interactions between all complex components, including stoichiometry, remain uncharacterised; nevertheless, once assembled into their quaternary complex, the trio of Pqi proteins are anticipated to provide a continuous channel between the inner and outer membranes of diderms. Here, we present X-ray structures of both the native and a truncated, soluble construct of the PqiC lipoprotein, providing insight into its biological assembly, and utilise neutron reflectometry to characterise the nature of the PqiB-PqiC-membrane interaction. Finally, we employ phenotypic complementation assays to probe specific PqiC residues, which imply the interaction between PqiB and PqiC is less intimate than previously anticipated.</p