Using Optical Water-Type Classification in Data-Poor Water Quality Assessment: A Case Study in the Torres Strait

For many years, local communities have expressed concerns that turbid plume waters from the Fly River in Papua New Guinea may potentially deliver mine-derived contaminants to the Torres Strait, an ecologically and culturally unique area north of the Australian mainland. Information on suspended sediment transport and turbidity patterns are needed in this data-limited region to identify and manage downstream ecosystems that may be at risk of exposure from the Fly River runoff. This study used MODIS satellite time series and a colour-classification approach to map optical water types around the data-poor Gulf of Papua and Torres Strait region. The satellite data were supported by field data, including salinity and suspended sediment measurements, and used together in qualitative water quality assessments to evaluate the habitats that are likely exposed to Fly River discharge and/or derived sediments. It showed that the Fly River influence in the Torres Strait region is largely limited to the north-east corner of the Torres Strait. The drivers of turbidity vary between locations, and it is impossible to fully separate direct riverine plume influence from wave and tidally driven sediment resuspension in the satellite maps. However, results indicate that coastal habitats located as far east as Bramble Cay and west to Boigu Island are located in an area that is most likely exposed to the Fly River discharge within the region, directly or through sediment resuspension. The area that is the most likely exposed is a relatively small proportion of the Torres Strait region, but encompasses habitats of high ecological importance, including coral reefs and seagrass meadows. Satellite data showed that the period of highest risk of exposure was during the south-east trade wind season and complemented recent model simulations in the region over larger spatial and temporal frames. This study did not evaluate transboundary pollution or the ecological impact on local marine resources, but other recent studies suggest it is likely to be limited. However, this study did provide long-term, extensive but qualitative, baseline information needed to inform future ecological risk mapping and to support decision making about management priorities in the region. This is important for ensuring the protection of the Torres Strait ecosystems, given their importance to Torres Strait communities and turtle and dugong populations, and the Torres Strait’s connectivity with the Great Barrier Reef Marine Park

Baseline assessment of coastal water quality, in Vanuatu, South Pacific: insights gained from in-situ sampling

Nearshore deterioration of water quality in Pacific coastal waters is a growing problem, associated with increasing urban and industrial sewage discharges, and agricultural runoff. Published water quality studies in the Pacific region are limited in both number and scope, making it difficult to resolve the extent of the issue or quantify the variability of water quality across Pacific islands and countries. This study collected water quality measurements over three years in the coastal waters around the Island of Efate (Vanuatu) with majority of work carried out in Port Vila, its capital. Port Vila is the key urban centre for Vanuatu where the increasing population and pollution inputs are placing substantial pressure on the coastal environment. Highest concentrations of dissolved nutrients and suspended sediments were measured adjacent or near the urban drains that enter the coastal areas along the capital's seafront, highlighting many of the issues around anthropogenic inputs are linked to the increasing urbanisation in Port Vila Bay. We provide baseline data that explores variability of coastal water quality and these types of datasets for Pacific islands are a first step towards facilitating development of long-term monitoring programmes and informing coastal zone management decision making

2017 Scientific Consensus Statement: land use impacts on the Great Barrier Reef water quality and ecosystem condition, Chapter 3: the risk from anthropogenic pollutants to Great Barrier Reef coastal and marine ecosystems

In this chapter, we applied an ecological risk assessment approach to assess the likelihood of exposure and potential risks from land-based pollutants to Great Barrier Reef coastal (floodplain wetlands and floodplains) and marine (coral reefs and seagrass meadows) ecosystems. Ecological risk is defined as the product of the likelihood of an effect occurring and the consequences if that effect was to occur

Assessing relative resilience potential of coral reefs to inform management

International audienceEcological resilience assessments are an important part of resilience-based management (RBM) and can help prioritize and target management actions. Use of such assessments has been limited due to a lack of clear guidance on the assessment process. This study builds on the latest scientific advances in RBM to provide that guidance from a resilience assessment undertaken in the Commonwealth of the Northern Mariana Islands (CNMI). We assessed spatial variation in ecological resilience potential at 78 forereef sites near the populated islands of the CNMI: Saipan, Tinian/Aguijan, and Rota. The assessments are based on measuring indicators of resilience processes and are combined with information on anthropogenic stress and larval connectivity. We find great spatial variation in relative resilience potential with many high resilience sites near Saipan (5 of 7) and low resilience sites near Rota (7 of 9). Criteria were developed to identify priority sites for six types of management actions (e.g., conservation, land-based sources of pollution reduction, and fishery management and enforcement) and 51 of the 78 sites met at least one of the sets of criteria. The connectivity simulations developed indicate that Tinian and Aguijan are each roughly 10 × the larvae source that Rota is and twice as frequent a destination. These results may explain the lower relative resilience potential of Rota reefs and indicates that actions in Saipan and Tinian/Aguijan will be important to maintaining supply of larvae. The process we describe for undertaking resilience assessments can be tailored for use in coral reef areas globally and applied to other ecosystems

Assessment of the relative risk of water quality to ecosystems of the Great Barrier Reef. A report to the Department of the Environment and Heritage Protection, Queensland Government, Brisbane - Report 13/28

A risk assessment method was developed and applied to the Great Barrier Reef (GBR) to provide robust and scientifically defensible information for policy makers and catchment managers on the key land-based pollutants of greatest risk to the health of the two main GBR ecosystems (coral reefs and seagrass beds). This information was used to inform management prioritisation for Reef Rescue 2 and Reef Plan 3. The risk assessment method needed to take account of the fact that catchment-associated risk will vary with distance from the river mouth, with coastal habitats nearest to river mouths most impacted by poor marine water quality. The main water quality pollutants of concern for the GBR are enhanced levels of suspended sediments, excess nutrients and pesticides added to the GBR lagoon from the adjacent catchments. Until recently, there has been insufficient knowledge about the relative exposure to and effects of these pollutants to guide effective prioritisation of the management of their sources

Principles to enable comprehensive national marine ecosystem status assessments from disparate data: The state of the marine environment in Kuwait

This paper presents an approach for preparing a comprehensive national marine ecosystem assessment and its application to the marine and coastal areas of the State of Kuwait. The approach is based on a set of principles to enable diverse data sources, of differing data quality and salience, to be combined into a single coordinated national assessment of marine ecosystem status to support the implementation of ecosystem-based management. The approach enables state assessments for multiple components of the marine ecosystem to be undertaken in a coordinated manner, using differing methods varying from quantitative to qualitative assessments depending on data and indicator availability. The marine ecosystem assessment is structured according to 6 major themes: i) Biodiversity, ii) Commercial Fisheries, iii) Food and Water Quality for Human Health, iv) Environmental Pollution, v) Eutrophication and Harmful Algal Blooms, and vi) Coastal Process and Oceanography. Comprehensive ecosystem assessments are an essential part of implementing the ecosystem approach, however detailed data directly related to clear, specified numerical management targets covering all aspects of a marine ecosystem are rarely available. The development of a State of the Marine Environment Report (SOMER) for Kuwait demonstrate that a coordinated comprehensive ecosystem assessment can be conducted using disparate data, and in relation to partially specified regulatory management objectives. The Kuwait SOMER highlighted the issues of coastal pollution, particularly sewage for human health and the environment. It shows that the rapid urbanization of Kuwait has led to significant changes in the ecology, with clear impacts on coral reef health, the availability of nesting locations for turtles and habitats for migratory birds. Long-term changes in nutrient input, via waste water and modified freshwater inputs is resulting in demonstrable impacts on a range of marine species and habitats within Kuwait marine waters. It also supports the move towards a regional approach required due to transboundary properties of many of the ecosystem components, drivers and pressures

Contribution of copy number variants to schizophrenia from a genome-wide study of 41,321 subjects

Copy number variants (CNVs) have been strongly implicated in the genetic etiology of schizophrenia (SCZ). However, genome-wide investigation of the contribution of CNV to risk has been hampered by limited sample sizes. We sought to address this obstacle by applying a centralized analysis pipeline to a SCZ cohort of 21,094 cases and 20,227 controls. A global enrichment of CNV burden was observed in cases (OR=1.11, P=5.7×10−15), which persisted after excluding loci implicated in previous studies (OR=1.07, P=1.7 ×10−6). CNV burden was enriched for genes associated with synaptic function (OR = 1.68, P = 2.8 ×10−11) and neurobehavioral phenotypes in mouse (OR = 1.18, P= 7.3 ×10−5). Genome-wide significant evidence was obtained for eight loci, including 1q21.1, 2p16.3 (NRXN1), 3q29, 7q11.2, 15q13.3, distal 16p11.2, proximal 16p11.2 and 22q11.2. Suggestive support was found for eight additional candidate susceptibility and protective loci, which consisted predominantly of CNVs mediated by non-allelic homologous recombination

No Reliable Association between Runs of Homozygosity and Schizophrenia in a Well-Powered Replication Study

It is well known that inbreeding increases the risk of recessive monogenic diseases, but it is less certain whether it contributes to the etiology of complex diseases such as schizophrenia. One way to estimate the effects of inbreeding is to examine the association between disease diagnosis and genome-wide autozygosity estimated using runs of homozygosity (ROH) in genome-wide single nucleotide polymorphism arrays. Using data for schizophrenia from the Psychiatric Genomics Consortium (n = 21,868), Keller et al. (2012) estimated that the odds of developing schizophrenia increased by approximately 17% for every additional percent of the genome that is autozygous (β = 16.1, CI(β) = [6.93, 25.7], Z = 3.44, p = 0.0006). Here we describe replication results from 22 independent schizophrenia case-control datasets from the Psychiatric Genomics Consortium (n = 39,830). Using the same ROH calling thresholds and procedures as Keller et al. (2012), we were unable to replicate the significant association between ROH burden and schizophrenia in the independent PGC phase II data, although the effect was in the predicted direction, and the combined (original + replication) dataset yielded an attenuated but significant relationship between Froh and schizophrenia (β = 4.86,CI(β) = [0.90,8.83],Z = 2.40,p = 0.02). Since Keller et al. (2012), several studies reported inconsistent association of ROH burden with complex traits, particularly in case-control data. These conflicting results might suggest that the effects of autozygosity are confounded by various factors, such as socioeconomic status, education, urbanicity, and religiosity, which may be associated with both real inbreeding and the outcome measures of interest

Gene expression imputation across multiple brain regions provides insights into schizophrenia risk

Transcriptomic imputation approaches combine eQTL reference panels with large-scale genotype data in order to test associations between disease and gene expression. These genic associations could elucidate signals in complex genome-wide association study (GWAS) loci and may disentangle the role of different tissues in disease development. We used the largest eQTL reference panel for the dorso-lateral prefrontal cortex (DLPFC) to create a set of gene expression predictors and demonstrate their utility. We applied DLPFC and 12 GTEx-brain predictors to 40,299 schizophrenia cases and 65,264 matched controls for a large transcriptomic imputation study of schizophrenia. We identified 413 genic associations across 13 brain regions. Stepwise conditioning identified 67 non-MHC genes, of which 14 did not fall within previous GWAS loci. We identified 36 significantly enriched pathways, including hexosaminidase-A deficiency, and multiple porphyric disorder pathways. We investigated developmental expression patterns among the 67 non-MHC genes and identified specific groups of pre- and postnatal expression

Age at first birth in women is genetically associated with increased risk of schizophrenia

Prof. Paunio on PGC:n jäsenPrevious studies have shown an increased risk for mental health problems in children born to both younger and older parents compared to children of average-aged parents. We previously used a novel design to reveal a latent mechanism of genetic association between schizophrenia and age at first birth in women (AFB). Here, we use independent data from the UK Biobank (N = 38,892) to replicate the finding of an association between predicted genetic risk of schizophrenia and AFB in women, and to estimate the genetic correlation between schizophrenia and AFB in women stratified into younger and older groups. We find evidence for an association between predicted genetic risk of schizophrenia and AFB in women (P-value = 1.12E-05), and we show genetic heterogeneity between younger and older AFB groups (P-value = 3.45E-03). The genetic correlation between schizophrenia and AFB in the younger AFB group is -0.16 (SE = 0.04) while that between schizophrenia and AFB in the older AFB group is 0.14 (SE = 0.08). Our results suggest that early, and perhaps also late, age at first birth in women is associated with increased genetic risk for schizophrenia in the UK Biobank sample. These findings contribute new insights into factors contributing to the complex bio-social risk architecture underpinning the association between parental age and offspring mental health.Peer reviewe