Biodiversity on the brink: Evaluating a transdisciplinary research collaboration

Global biodiversity is facing an extinction crisis. Australia has one of the highest terrestrial species extinction rates in the world. Scientists, policy advisors and governments have recommended that the issue be addressed at a landscape-scale, while noting that there are significant knowledge gaps that are hampering implementation of such an approach. From 2011–2015, the Australian Government funded a transdisciplinary research program, the Landscapes and Policy Hub, to meet this need. Transdisciplinary research is widely acknowledged as essential to address the complexity of contemporary environmental problems. Given that such research programs are in their infancy, it is important to evaluate their efficacy and provide an empirical basis for improving their design. This paper presents an evaluation of the strategies fostering transdisciplinarity adopted by the Landscapes and Policy Hub. A heavy emphasis on communication, with skilled knowledge brokering, regular face-to-face meetings using participatory activities and shared field engagements enhanced transdisciplinary interaction between researchers and research users. However, establishing a fully integrated interdisciplinary research program remained a challenge. Efforts to enable shared conceptual frameworks to emerge through adaptive application of theory in practice could have been balanced with increased effort at the outset for researchers and research users to collaboratively formulate shared research questions, leading to the establishment of teams that could address these questions through cross-mobilisation of interdisciplinary expertise.     

Improved two‐stage group sequential procedures for testing a secondary endpoint after the primary endpoint achieves significance

In two‐stage group sequential trials with a primary and a secondary endpoint, the overall type I error rate for the primary endpoint is often controlled by an α‐level boundary, such as an O'Brien‐Fleming or Pocock boundary. Following a hierarchical testing sequence, the secondary endpoint is tested only if the primary endpoint achieves statistical significance either at an interim analysis or at the final analysis. To control the type I error rate for the secondary endpoint, this is tested using a Bonferroni procedure or any α‐level group sequential method. In comparison with marginal testing, there is an overall power loss for the test of the secondary endpoint since a claim of a positive result depends on the significance of the primary endpoint in the hierarchical testing sequence. We propose two group sequential testing procedures with improved secondary power: the improved Bonferroni procedure and the improved Pocock procedure. The proposed procedures use the correlation between the interim and final statistics for the secondary endpoint while applying graphical approaches to transfer the significance level from the primary endpoint to the secondary endpoint. The procedures control the familywise error rate (FWER) strongly by construction and this is confirmed via simulation. We also compare the proposed procedures with other commonly used group sequential procedures in terms of control of the FWER and the power of rejecting the secondary hypothesis. An example is provided to illustrate the procedures.     

On the Estimation of Heritability from Unbalanced Data

The distribution and moments, of ANOVA estimator of heritability are given under unbalanced random model. These expressions are used to investigate the effect of unbalancedness on the bias and variance/MSE of the estimator and also the validity of certain approximations for its variance, numerically. The computed results reveal that the unbalancedness increases both the bias and variance/MSE of the estimator and the Smith-approximation for the variance of the estimator provides better accuracy.     

Marine ecosystem services: Linking indicators to their classification

There is a multitude of ecosystem service classifications available within the literature, each with its own advantages and drawbacks. Elements of them have been used to tailor a generic ecosystem service classification for the marine environment and then for a case study site within the North Sea: the Dogger Bank. Indicators for each of the ecosystem services, deemed relevant to the case study site, were identified. Each indicator was then assessed against a set of agreed criteria to ensure its relevance and applicability to environmental management. This paper identifies the need to distinguish between indicators of ecosystem services that are entirely ecological in nature (and largely reveal the potential of an ecosystem to provide ecosystem services), indicators for the ecological processes contributing to the delivery of these services, and indicators of benefits that reveal the realized human use or enjoyment of an ecosystem service. It highlights some of the difficulties faced in selecting meaningful indicators, such as problems of specificity, spatial disconnect and the considerable uncertainty about marine species, habitats and the processes, functions and services they contribute to.     

Polyphasic characterization of Delftia acidovorans ESM-1, a facultative methylotrophic bacterium isolated from rhizosphere of Eruca sativa

In this study, one bacterial strain, ESM-1, was isolated from rhizosphere of Eruca sativa, growing in Al Hofouf, Saudia Arabia, after enrichment with methanol as a sole carbon and energy source in a batch culture. ESM-1 was characterized by a polyphasic approach. The strain was identified as Delftia acidovorans at similarity level of 99.9% of the 16S rRNA gene sequences. Results of the Biolog Gen III MicroPlate test system showed that strain ESM-1 reacted positively to 47 (50%) including the one-carbon compound formic acid, and partially positive to 6 (∼6.4%) out of the 94 different the traits examined. The total cellular fatty acids composition of the strain ESM-1 was (C_16:1ω7c/C_16:1ω6c) and C_16:0) and matched that of Delftia acidovorans at a similarity index of 0.9, providing a robustness to the ESM-1 identification. Furthermore, ESM-1 displayed a complex polar lipid profile consisting of phosphatidylethanolamine, phosphatidylglycerol, glycolipid, aminolipid, in addition to uncharacterized lipids. The DNA G+C content of the strain was 66.6 mol%. Phylogenetic analyses based on 16S rRNA gene sequences showed that the strain ESM1-1 was clearly clustered within the Delftia clade and constructed a monophyletic subcluster with Delftia acidovorans NBRC14950. The results addressed that ESM-1 is a facultative methylotrophic bacterium indigenous to Al Hofouf region and opens the door for potential biotechnological applications (e.g., bioremediation) of this strain, in future. Additionally, these findings assure that the total cellular fatty acid analysis and 16S rRNA gene are reliable tool for bacterial characterization and identification.     

Functional role of phenylacetic acid from metapleural gland secretions in controlling fungal pathogens in evolutionarily derived leaf-cutting ants

Fungus-farming ant colonies vary four to five orders of magnitude in size. They employ compounds from actinomycete bacteria and exocrine glands as antimicrobial agents. Atta colonies have millions of ants and are particularly relevant for understanding hygienic strategies as they have abandoned their ancestors'' prime dependence on antibiotic-based biological control in favour of using metapleural gland (MG) chemical secretions. Atta MGs are unique in synthesizing large quantities of phenylacetic acid (PAA), a known but little investigated antimicrobial agent. We show that particularly the smallest workers greatly reduce germination rates of Escovopsis and Metarhizium spores after actively applying PAA to experimental infection targets in garden fragments and transferring the spores to the ants'' infrabuccal cavities. In vitro assays further indicated that Escovopsis strains isolated from evolutionarily derived leaf-cutting ants are less sensitive to PAA than strains from phylogenetically more basal fungus-farming ants, consistent with the dynamics of an evolutionary arms race between virulence and control for Escovopsis, but not Metarhizium. Atta ants form larger colonies with more extreme caste differentiation relative to other attines, in societies characterized by an almost complete absence of reproductive conflicts. We hypothesize that these changes are associated with unique evolutionary innovations in chemical pest management that appear robust against selection pressure for resistance by specialized mycopathogens.     

Ecological indicators to capture the effects of fishing on biodiversity and conservation status of marine ecosystems

IndiSeas (“Indicators for the Seas”) is a collaborative international working group that was established in 2005 to evaluate the status of exploited marine ecosystems using a suite of indicators in a comparative framework. An initial shortlist of seven ecological indicators was selected to quantify the effects of fishing on the broader ecosystem using several criteria (i.e., ecological meaning, sensitivity to fishing, data availability, management objectives and public awareness). The suite comprised: (i) the inverse coefficient of variation of total biomass of surveyed species, (ii) mean fish length in the surveyed community, (iii) mean maximum life span of surveyed fish species, (iv) proportion of predatory fish in the surveyed community, (v) proportion of under and moderately exploited stocks, (vi) total biomass of surveyed species, and (vii) mean trophic level of the landed catch. In line with the Nagoya Strategic Plan of the Convention on Biological Diversity (2011–2020), we extended this suite to emphasize the broader biodiversity and conservation risks in exploited marine ecosystems. We selected a subset of indicators from a list of empirically based candidate biodiversity indicators initially established based on ecological significance to complement the original IndiSeas indicators. The additional selected indicators were: (viii) mean intrinsic vulnerability index of the fish landed catch, (ix) proportion of non-declining exploited species in the surveyed community, (x) catch-based marine trophic index, and (xi) mean trophic level of the surveyed community. Despite the lack of data in some ecosystems, we also selected (xii) mean trophic level of the modelled community, and (xiii) proportion of discards in the fishery as extra indicators. These additional indicators were examined, along with the initial set of IndiSeas ecological indicators, to evaluate whether adding new biodiversity indicators provided useful additional information to refine our understanding of the status evaluation of 29 exploited marine ecosystems. We used state and trend analyses, and we performed correlation, redundancy and multivariate tests. Existing developments in ecosystem-based fisheries management have largely focused on exploited species. Our study, using mostly fisheries independent survey-based indicators, highlights that biodiversity and conservation-based indicators are complementary to ecological indicators of fishing pressure. Thus, they should be used to provide additional information to evaluate the overall impact of fishing on exploited marine ecosystems.