Alain F. Zuur

Modelling of essential fish habitat based on remote sensing, spatial analysis and GIS

We review the variety of existing modelling approaches applied to species habitat mapping and we discuss issues arising from the availability and nature of sampled biological data and corresponding ecological and environmental habitat descriptors, as well as the different spatial analysis approaches that are selected according to specific hypotheses. We focus on marine species habitat mapping, presenting an overview of work on modelling fish habitat carried out through a European Communities Policy-Support Action, EnviEFH ‘Environmental Approach to Essential Fish Habitat (EFH) Designation’ (2005–2008). The selection of the appropriate habitat model is dataset-specific and the resulting EFH maps are often similar in spite of using different models. Derived EFH maps are based on either environmental ranges (used as minimum and maximum environmental habitat descriptors) or probability of occurrence values. We apply model outputs to regions larger than sampled areas making use of the capacity of satellite data to cover wide areas.

A review of cephalopod—environment interactions in European Seas

Cephalopods are highly sensitive to environmental conditions and changes at a range of spatial and temporal scales. Relationships documented between cephalopod stock dynamics and environmental conditions are of two main types: those concerning the geographic distribution of abundance, for which the mechanism is often unknown, and those relating to biological processes such as egg survival, growth, recruitment and migration, where mechanisms are sometimes known and in a very few cases demonstrated by experimental evidence. Cephalopods seem to respond to environmental variation both ‘actively’ (e.g. migrating to areas with more favoured environmental conditions for feeding or spawning) and ‘passively’ (growth and survival vary according to conditions experienced, passive migration with prevailing currents). Environmental effects on early life stages can affect life history characteristics (growth and maturation rates) as well as distribution and abundance. Both large-scale atmospheric and oceanic processes and local environmental variation appear to play important roles in species–environment interactions. While oceanographic conditions are of particular significance for mobile pelagic species such as the ommastrephid squids, the less widely ranging demersal and benthic species may be more dependent on other physical habitat characteristics (e.g. substrate and bathymetry). Coastal species may be impacted by variations in water quality and salinity (related to rainfall and river flow). Gaps in current knowledge and future research priorities are discussed. Key research goals include linking distribution and abundance to environmental effects on biological processes, and using such knowledge to provide environmental indicators and to underpin fishery management.

Long-term changes in deep-water fish populations in the northeast Atlantic: a deeper reaching effect of fisheries?

A severe scarcity of life history and population data for deep-water fishes is a major impediment to successful fisheries management. Long-term data for non-target species and those living deeper than the fishing grounds are particularly rare. We analysed a unique dataset of scientific trawls made from 1977 to 1989 and from 1997 to 2002, at depths from 800 to 4800 m. Over this time, overall fish abundance fell significantly at all depths from 800 to 2500 m, considerably deeper than the maximum depth of commercial fishing (approx. 1600 m). Changes in abundance were significantly larger in species whose ranges fell at least partly within fished depths and did not appear to be consistent with any natural factors such as changes in fluxes from the surface or the abundance of potential prey. If the observed decreases in abundance are due to fishing, then its effects now extend into the lower bathyal zone, resulting in declines in areas that have been previously thought to be unaffected. A possible mechanism is impacts on the shallow parts of the ranges of fish species, resulting in declines in abundance in the lower parts of their ranges. This unexpected phenomenon has important consequences for fisheries and marine reserve management, as this would indicate that the impacts of fisheries can be transmitted into deep offshore areas that are neither routinely monitored nor considered as part of the managed fishery areas.

A protocol for conducting and presenting results of regression-type analyses

Summary Scientific investigation is of value only insofar as relevant results are obtained and communicated, a task that requires organizing, evaluating, analysing and unambiguously communicating the significance of data. In this context, working with ecological data, reflecting the complexities and interactions of the natural world, can be a challenge. Recent innovations for statistical analysis of multifaceted interrelated data make obtaining more accurate and meaningful results possible, but key decisions of the analyses to use, and which components to present in a scientific paper or report, may be overwhelming. We offer a 10-step protocol to streamline analysis of data that will enhance understanding of the data, the statistical models and the results, and optimize communication with the reader with respect to both the procedure and the outcomes. The protocol takes the investigator from study design and organization of data (formulating relevant questions, visualizing data collection, data exploration, identifying dependency), through conducting analysis (presenting, fitting and validating the model) and presenting output (numerically and visually), to extending the model via simulation. Each step includes procedures to clarify aspects of the data that affect statistical analysis, as well as guidelines for written presentation. Steps are illustrated with examples using data from the literature. Following this protocol will reduce the organization, analysis and presentation of what may be an overwhelming information avalanche into sequential and, more to the point, manageable, steps. It provides guidelines for selecting optimal statistical tools to assess data relevance and significance, for choosing aspects of the analysis to include in a published report and for clearly communicating information.

Long-term population trends of endangered Hawaiian waterbirds

We analyzed long-term winter survey data (1956–2007) for three endangered waterbirds endemic to the Hawaiian Islands, the Hawaiian moorhen (Gallinula chloropus sandvicensis), Hawaiian coot (Fulica alai), and Hawaiian stilt (Himantopus mexicanus knudseni). Time series were analyzed by species–island combinations using generalized additive models, with alternative models compared using Akaike information criterion (AIC). The best model included three smoothers, one for each species. Our analyses show that all three of the endangered Hawaiian waterbirds have increased in population size over the past three decades. The Hawaiian moorhen increase has been slower in more recent years than earlier in the survey period, but Hawaiian coot and stilt numbers still exhibit steep increases. The patterns of population size increase also varied by island, although this effect was less influential than that between species. In contrast to earlier studies, we found no evidence that rainfall affects counts of the target species. Significant population increases were found on islands where most wetland protection has occurred (Oahu, Kauai), while weak or no increases were found on islands with few wetlands or less protection (Hawaii, Maui). Increased protection and management, especially on Maui where potential is greatest, would likely result in continued population gains, increasing the potential for meeting population recovery goals.

Proximate causes and possible adaptive functions of mast seeding and barren flower shows in spinifex grasses (Triodia spp.) in arid regions of Australia

Mast seeding, the intermittent production of large synchronised seed crops among plant populations, is a phenomenon that occurs at exceptionally long intervals in spinifex grasses (Triodia spp.) from arid regions of Australia. This is despite the reliance of these fire-sensitive plants on seeds for post-fire regeneration, and that spinifex grasslands rate among Australia’s most flammable ecosystems. The proximate causes and possible adaptive functions of masting in seven species of spinifex from arid regions within the 350-mm rainfall isohyet were investigated. Specifically, the seed set percentages of 79 specimens collected between 1947 and 2012 were related to the following environmental covariates: antecedent rainfall over 6, 12 and 36 months, relative humidity, and the number of days above 40°C and below 0°C during anthesis. Given the potential importance of seeding events for post-fire regeneration, it was also investigated whether masting in Triodia could represent a fire-related form of environmentally predictive masting, by testing whether high-yield years corresponded to years of increased fire occurrence. Examination of the dataset showed that 43% of specimens contained completely aborted inflorescences (0% seed fill), while seed set ranged from 2 to 69% in the remaining specimens. High levels of insect activity were also found, with 42% of specimens showing evidence of insect occupation. Statistical analyses showed that the main environmental driver of seed set was high precipitation over the previous 12 months, and that high-yield years were strongly related to years of increased fire likelihood. The number of days over 40°C was a weakly significant driver of yield, while the remaining covariates were not significant. It is hypothesised that intermittent reproduction by Triodia is a fire-related form of environmentally predictive masting, which maximises chances of post-fire regeneration by satiating seed predators during flammable periods (i.e. after heavy rain years). Furthermore, it is suggested that non-viable flower crops after initial low rainfalls may have an adaptive function, by diluting pre-dispersal seed predator densities with ‘decoy’ ovules that do not mature and lead to the starvation of developing larvae.

Time series analysis of Hawaiian waterbirds

Surveys to monitor changes in population size over time are of interest for a variety of research questions and management goals. For example, population biologists require survey data collected over time to test hypotheses concerning the patterns and mechanisms of population regulation or to evaluate the effects on population size of interactions caused by competition and predation. Resource managers use changes in population size to (i) evaluate the effectiveness of management actions that are designed to increase or decrease numbers, (ii) monitor changes in indicator species, and (iii) quantify the effects of environmental change. Monitoring population size over time is particularly important to species conservation, where population decline is one key to identifying species that are at risk of extinction.

Investigating the effects of rice farming on aquatic birds with mixed modelling

Ecologists are frequently interested in describing differences among the ecological communities that occur in habitats with different characteristics. In an ideal world, experimental methods would standardise situations such that each habitat variable could be altered separately in order to investigate their individual effects. This approach works well in simple ecosystems that can be replicated at small spatial scales. Unfortunately, the world is not always simple and many situations cannot be experimentally manipulated. Investigating specific applied questions, in particular, often can be done only at the spatial scales at which the applied phenomena occur and within the logistical constraints imposed by the system under study. In such cases, one is often left with the choice between collecting “messy” data that are difficult to analyse or avoiding the research questions entirely. In this chapter, we investigate just such a case, in which applied ecological questions were of interest, but experimental influence over the system was not possible.

A modelling framework to optimize timing of haulout counts for estimating harbour seal ( Phoca vitulina ) abundance

The time of year and day, the state of the tide and prevailing environmental conditions significantly influence seal haulout behaviour. Understanding these effects is fundamentally important in deriving accurate estimates of harbour seal abundance from haulout data. We present a modelling approach to assess the influence of these variables on seals’ haulout behaviour and, by identifying the combination of covariates during which seal abundance is highest, predict the optimal time and conditions for future surveys. Count data of harbour seals at haulouts in southwest Ireland collected during 2003-2005 were included in mixed additive models together with environmental covariates, including season, time of day and weather conditions. The models show maximum abundance at haulout sites occurred during midday periods during August and in late afternoon/early evening during September. Accurate national and local population estimates are essential for the effective monitoring of the conservation status of the species and for the identification, management and monitoring of Special Areas of Conservation (SAC) in accordance with the EU Habitats Directive. Our model based approach provides a useful tool for optimising the timing of harbour seal surveys in Ireland and the modelling framework is useful for predicting optimal survey periods for other protected, endangered or significant species worldwide.

Incorporating Temporal Correlation in Seal Abundance Data with MCMC

Common or harbour seals (Phoca vitulina L.) are semi-aquatic mammals that spend time onshore at terrestrial sites where they haul-out to rest, breed, moult, engage in social activity, and escape predation (Fig.23.1).