An individual-based model of the early life history of mackerel (Scomber scombrus) in the eastern North Atlantic, simulating transport, growth and mortality

The main purpose of this paper is to provide the core description of the modelling exercise within the Shelf Edge Advection Mortality And Recruitment (SEAMAR) programme. An individual-based model (IBM) was developed for the prediction of year-to-year survival of the early life-history stages of mackerel (Scomber scombrus) in the eastern North Atlantic. The IBM is one of two components of the model system. The first component is a circulation model to provide physical input data for the IBM. The circulation model is a geographical variant of the HAMburg Shelf Ocean Model (HAMSOM). The second component is the IBM, which is an i-space configuration model in which large numbers of individuals are followed as discrete entities to simulate the transport, growth and mortality of mackerel eggs, larvae and post-larvae. Larval and post-larval growth is modelled as a function of length, temperature and food distribution; mortality is modelled as a function of length and absolute growth rate. Each particle is considered as a super-individual representing 10 super(6) eggs at the outset of the simulation, and then declining according to the mortality function. Simulations were carried out for the years 1998-2000. Results showed concentrations of particles at Porcupine Bank and the adjacent Irish shelf, along the Celtic Sea shelf-edge, and in the southern Bay of Biscay. High survival was observed only at Porcupine and the adjacent shelf areas, and, more patchily, around the coastal margin of Biscay. The low survival along the shelf-edge of the Celtic Sea was due to the consistently low estimates of food availability in that area.

Simulation of mackerel (Scomber scombrus) recruitment with an individual-based model and comparison with field data

An individual-based model (IBM) for the simulation of year-to-year survival during the early life-history stages of the north-east Atlantic stock of mackerel (Scomber scombrus) was developed within the EU funded Shelf-Edge Advection, Mortality and Recruitment (SEAMAR) programme. The IBM included transport, growth and survival and was used to track the passive movement of mackerel eggs, larvae and post-larvae and determine their distribution and abundance after approximately 2 months of drift. One of the main outputs from the IBM, namely distributions and numbers of surviving post-larvae, are compared with field data as recruit (age-0/age-1 juveniles) distribution and abundance for the years 1998, 1999 and 2000. The juvenile distributions show more inter-annual and spatial variability than the modelled distributions of survivors; this may be due to the restriction of using the same initial egg distribution for all 3 yr of simulation. The IBM simulations indicate two main recruitment areas for the north-east Atlantic stock of mackerel, these being Porcupine Bank and the south-eastern Bay of Biscay. These areas correspond to areas of high juvenile catches, although the juveniles generally have a more widespread distribution than the model simulations. The best agreement between modelled data and field data for distribution (juveniles and model survivors) is for the year 1998. The juvenile catches in different representative nursery areas are totalled to give a field abundance index (FAI). This index is compared with a model survivor index (MSI) which is calculated from the total of survivors for the whole spawning season. The MSI compares favourably with the FAI for 1998 and 1999 but not for 2000; in this year, juvenile catches dropped sharply compared with the previous years but there was no equivalent drop in modelled survivors.

Mighty small: Observing and modeling individual microbes becomes big science

Progress in microbiology has always been driven by technological advances, ever since Antonie van Leeuwenhoek discovered bacteria by making an improved compound microscope. However, until very recently we have not been able to identify microbes and record their mostly invisible activities, such as nutrient consumption or toxin production on the level of the single cell, not even in the laboratory. This is now changing with the rapid rise of exciting new technologies for single-cell microbiology (1, 2), which enable microbiologists to do what plant and animal ecologists have been doing for a long time: observe who does what, when, where, and next to whom. Single cells taken from the environment can be identified and even their genomes sequenced. Ex situ, their size, elemental, and biochemical composition, as well as other characteristics can be measured with high-throughput and cells sorted accordingly. Even better, individual microbes can be observed in situ with a range of novel microscopic and spectroscopic methods, enabling localization, identification, or functional characterization of cells in a natural sample, combined with detecting uptake of labeled compounds. Alternatively, they can be placed into fabricated microfluidic environments, where they can be positioned, exposed to stimuli, monitored, and their interactions controlled “in microfluido.” By introducing genetically engineered reporter cells into a fabricated landscape or a microcosm taken from nature, their reproductive success or activity can be followed, or their sensing of their local environment recorded.

Quantifying ecosystem-level consequences of ocean acidification and warming by scaling up individual level responses of a predator snail and its trophic interactions

Understanding long‐term, ecosystem‐level impacts of climate change is challenging because experimental research frequently focuses on short‐term, individual‐level impacts in isolation. We address this shortcoming first through an interdisciplinary ensemble of novel experimental techniques to investigate the impacts of 14‐month exposure to ocean acidification and warming (OAW) on the physiology, activity, predatory behaviour and susceptibility to predation of an important marine gastropod (Nucella lapillus). We simultaneously estimated the potential impacts of these global drivers on N. lapillus population dynamics and dispersal parameters. We then used these data to parameterize a dynamic bioclimatic envelope model, to investigate the consequences of OAW on the distribution of the species in the wider NE Atlantic region by 2100. The model accounts also for changes in the distribution of resources, suitable habitat and environment simulated by finely resolved biogeochemical models, under three IPCC global emissions scenarios. The experiments showed that temperature had the greatest impact on individual‐level responses, while acidification had a similarly important role in the mediation of predatory behaviour and susceptibility to predators. Changes in Nucella predatory behaviour appeared to serve as a strategy to mitigate individual‐level impacts of acidification, but the development of this response may be limited in the presence of predators. The model projected significant large‐scale changes in the distribution of Nucella by the year 2100 that were exacerbated by rising greenhouse gas emissions. These changes were spatially heterogeneous, as the degree of impact of OAW on the combination of responses considered by the model varied depending on local‐environmental conditions and resource availability. Such changes in macro‐scale distributions cannot be predicted by investigating individual‐level impacts in isolation, or by considering climate stressors separately. Scaling up the results of experimental climate change research requires approaches that account for long‐term, multiscale responses to multiple stressors, in an ecosystem context.

Long-term individual foraging site fidelity – why some gannets don’t change their spots

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Long-term individual foraging site fidelity – why some gannets don’t change their spots

Many established models of animal foraging assume that individuals are ecologically equivalent. However, it is increasingly recognized that populations may comprise individuals who differ consistently in their diets and foraging behaviors. For example, recent studies have shown that individual foraging site fidelity (IFSF, when individuals consistently forage in only a small part of their population's home range) occurs in some colonial breeders. Short‐term IFSF could result from animals using a win–stay, lose–shift foraging strategy. Alternatively, it may be a consequence of individual specialization. Pelagic seabirds are colonial central‐place foragers, classically assumed to use flexible foraging strategies to target widely dispersed, spatiotemporally patchy prey. However, tracking has shown that IFSF occurs in many seabirds, although it is not known whether this persists across years. To test for long‐term IFSF and to examine alternative hypotheses concerning its cause, we repeatedly tracked 55 Northern Gannets (Morus bassanus) from a large colony in the North Sea within and across three successive breeding seasons. Gannets foraged in neritic waters, predictably structured by tidal mixing and thermal stratification, but subject to stochastic, wind‐induced overturning. Both within and across years, coarse to mesoscale (tens of kilometers) IFSF was significant but not absolute, and foraging birds departed the colony in individually consistent directions. Carbon stable isotope ratios in gannet blood tissues were repeatable within years and nitrogen ratios were also repeatable across years, suggesting long‐term individual dietary specialization. Individuals were also consistent across years in habitat use with respect to relative sea surface temperature and in some dive metrics, yet none of these factors accounted for IFSF. Moreover, at the scale of weeks, IFSF did not decay over time and the magnitude of IFSF across years was similar to that within years, suggesting that IFSF is not primarily the result of win–stay, lose–shift foraging. Rather, we hypothesize that site familiarity, accrued early in life, causes IFSF by canalizing subsequent foraging decisions. Evidence from this and other studies suggests that IFSF may be common in colonial central‐place foragers, with far‐reaching consequences for our attempts to understand and conserve these animals in a rapidly changing environment.

Initial Examination of AltiKa's Individual Echoes

The AltiKa altimeter records the reflection of Ka-band radar pulses from the Earth’s surface, with the commonly used waveform product involving the summation of 96 returns to provide average echoes at 40 Hz. Occasionally there are one-second recordings of the complex individual echoes (IEs), which facilitate the evaluation of on-board processing and offer the potential for new processing strategies. Our investigation of these IEs over the ocean confirms the on-board operations, whilst noting that data quantization limits the accuracy in the thermal noise region. By constructing average waveforms from 32 IEs at a time, and applying an innovative subwaveform retracker, we demonstrate that accurate height and wave height information can be retrieved from very short sections of data. Early exploration of the complex echoes reveals structure in the phase information similar to that noted for Envisat’s IEs.