John McKinlay

Community fingerprinting in a sequencing world

Despite decreasing costs, generating large-scale, well-replicated and multivariate microbial ecology investigations with sequencing remains an expensive and time-consuming option. As a result, many microbial ecology investigations continue to suffer from a lack of appropriate replication. We evaluated two fingerprinting approaches - terminal restriction fragment length polymorphism (T-RFLP) and automated ribosomal intergenic spacer analysis (ARISA) against 454 pyrosequencing, by applying them to 225 polar soil samples from East Antarctica and the high Arctic. By incorporating local and global spatial scales into the dataset, our aim was to determine whether various approaches differed in their ability and hence utility, to identify ecological patterns. Through the reduction in the 454 sequencing data to the most dominant OTUs, we revealed that a surprisingly small proportion of abundant OTUs (< 0.25%) was driving the biological patterns observed. Overall, ARISA and T-RFLP had a similar capacity as sequencing to separate samples according to distance at a local scale, and to correlate environmental variables with microbial community structure. Pyrosequencing had a greater resolution at the global scale but all methods were capable of significantly differentiating the polar sites. We conclude fingerprinting remains a legitimate approach to generating large datasets as well as a cost-effective rapid method to identify samples for elucidating taxonomic information or diversity estimates with sequencing methods.

Functionally distinct adult assemblages within a single breeding stock of the sardine, Sardinops sagax: management units within a management unit

Distribution of Sardinops eggs from seven surveys off southern Western Australia (WA) were assessed to determine if there were separate concentrations of spawning adults. Ten year series (1989–1998) of both age compositions and gonadosomatic indices (GSIs), obtained from routine sampling of commercial catches, were also analysed to aid assessment of stock structure of Sardinops from three regions on the southern WA coast. The patterns in the distribution of Sardinops eggs provided evidence for the existence of distinct centres of spawning that were joined by intervening areas of less spawning activity. Together with regional differences in mean GSI and independence of age compositions between regions in 5 of the 10 years examined, these results indicate that there is not wide-scale mixing of mature age classes between the three regions. As first vulnerability occurs at time of maturity, these non-mixing assemblages are termed functionally distinct adult assemblages (FDAAs) and may persist due to fitness-related ties to localised areas of higher habitat suitability in a region of the world with an oligotrophic pelagic ecosystem. Alternatively, given that the interrelationships between pre-recruit Sardinops across the three regions are poorly understood, it is also possible that behavioural mechanisms, such as natal homing, may be involved in maintaining distinctness of the FDAAs. Regardless of the cause of non-mixing, when fisheries exploit spatially limited but disjunct parts of a single breeding stock, the exploited portions of the stock may in some cases also be considered as distinct for the purposes of management. Crown Copyright # 2002 Published by Elsevier Science B.V. All rights reserved.

New methods and technologies for regional-scale abundance estimation of land-breeding marine animals: application to Adelie penguin populations in East Antarctica

Land-breeding marine animals such as penguins, flying seabirds and pinnipeds are important components of marine ecosystems, and their abundance has been used extensively as an indication of ecosystem status and change. Until recently, many efforts to measure and monitor abundance of these species’ groups have focussed on smaller populations and spatial scales, and efforts to account for perception bias and availability bias have been variable and often ad hoc. We describe a suite of new methods, technologies and estimation procedures for cost-effective, large-scale abundance estimation within a general estimation framework and illustrate their application on large Adélie penguin populations in two regions of East Antarctica. The methods include photographic sample counts, automated cameras for collecting availability data, and bootstrap estimation to adjust counts for the sampling fraction, perception bias, and availability bias, and are applicable for a range of land-breeding marine species. The methods will improve our ability to obtain population data over large spatial and population scales within tight logistic, environmental and time constraints. This first application of the methods has given new insights into the biases and uncertainties in abundance estimation for penguins and other land-breeding marine species. We provide guidelines for applying the methods in future surveys.

Spatially Extensive Standardized Surveys Reveal Widespread, Multi-Decadal Increase in East Antarctic Adélie Penguin Populations

Seabirds are considered to be useful and practical indicators of the state of marine ecosystems because they integrate across changes in the lower trophic levels and the physical environment. Signals from this key group of species can indicate broad scale impacts or response to environmental change. Recent studies of penguin populations, the most commonly abundant Antarctic seabirds in the west Antarctic Peninsula and western Ross Sea, have demonstrated that physical changes in Antarctic marine environments have profound effects on biota at high trophic levels. Large populations of the circumpolar-breeding Adélie penguin occur in East Antarctica, but direct, standardized population data across much of this vast coastline have been more limited than in other Antarctic regions. We combine extensive new population survey data, new population estimation methods, and re-interpreted historical survey data to assess decadal-scale change in East Antarctic Adélie penguin breeding populations. We show that, in contrast to the west Antarctic Peninsula and western Ross Sea where breeding populations have decreased or shown variable trends over the last 30 years, East Antarctic regional populations have almost doubled in abundance since the 1980’s and have been increasing since the earliest counts in the 1960’s. The population changes are associated with five-year lagged changes in the physical environment, suggesting that the changing environment impacts primarily on the pre-breeding age classes. East Antarctic marine ecosystems have been subject to a number of changes over the last 50 years which may have influenced Adélie penguin population growth, including decadal-scale climate variation, an inferred mid-20th century sea-ice contraction, and early-to-mid 20th century exploitation of fish and whale populations.

Re-constructing historical Adélie penguin abundance estimates by retrospectively accounting for detection bias

Seabirds and other land-breeding marine predators are considered to be useful and practical indicators of the state of marine ecosystems because of their dependence on marine prey and the accessibility of their populations at breeding colonies. Historical counts of breeding populations of these higher-order marine predators are one of few data sources available for inferring past change in marine ecosystems. However, historical abundance estimates derived from these population counts may be subject to unrecognised bias and uncertainty because of variable attendance of birds at breeding colonies and variable timing of past population surveys. We retrospectively accounted for detection bias in historical abundance estimates of the colonial, land-breeding Adélie penguin through an analysis of 222 historical abundance estimates from 81 breeding sites in east Antarctica. The published abundance estimates were de-constructed to retrieve the raw count data and then re-constructed by applying contemporary adjustment factors obtained from remotely operating time-lapse cameras. The re-construction process incorporated spatial and temporal variation in phenology and attendance by using data from cameras deployed at multiple sites over multiple years and propagating this uncertainty through to the final revised abundance estimates. Our re-constructed abundance estimates were consistently higher and more uncertain than published estimates. The re-constructed estimates alter the conclusions reached for some sites in east Antarctica in recent assessments of long-term Adélie penguin population change. Our approach is applicable to abundance data for a wide range of colonial, land-breeding marine species including other penguin species, flying seabirds and marine mammals.

Abundance and richness of key Antarctic seafloor fauna correlates with modelled food availability

Most seafloor communities at depths below the photosynthesis zone rely on food that sinks through the water column. However, the nature and strength of this pelagic–benthic coupling and its influence on the structure and diversity of seafloor communities is unclear, especially around Antarctica where ecological data are sparse. Here we show that the strength of pelagic–benthic coupling along the East Antarctic shelf depends on both physical processes and the types of benthic organisms considered. In an approach based on modelling food availability, we combine remotely sensed sea-surface chlorophyll-a, a regional ocean model and diatom abundances from sediment grabs with particle tracking and show that fluctuating seabed currents are crucial in the redistribution of surface productivity at the seafloor. The estimated availability of suspended food near the seafloor correlates strongly with the abundance of benthic suspension feeders, while the deposition of food particles correlates with decreasing suspension feeder richness and more abundant deposit feeders. The modelling framework, which can be modified for other regions, has broad applications in conservation and management, as it enables spatial predictions of key components of seafloor biodiversity over vast regions around Antarctica.Combining data on sea-surface chlorophyll-a with a regional ocean model and diatom abundance from sediment grabs, the authors determine the strength of pelagic–benthic coupling across the George V region in East Antarctica.