Development and implementation of eco-genomic tools for aquatic ecosystem biomonitoring: the SYNAQUA French-Swiss program

The effectiveness of environmental protection measures is based on the early identification and diagnosis of anthropogenic pressures. Similarly, restoration actions require precise monitoring of changes in the ecological quality of ecosystems, in order to highlight their effectiveness. Monitoring the ecological quality relies on bioindicators, which are organisms revealing the pressures exerted on the environment through the composition of their communities. Their implementation, based on the morphological identification of species, is expensive because it requires time and experts in taxonomy. Recent genomic tools should provide access to reliable and high-throughput environmental monitoring by directly inferring the composition of bioindicators’ communities from their DNA (metabarcoding). The French-Swiss program SYNAQUA (INTERREG France-Switzerland 2017–2019) proposes to use and validate the tools of environmental genomic for biomonitoring and aims ultimately at their implementation in the regulatory bio-surveillance. SYNAQUA will test the metabarcoding approach focusing on two bioindicators, diatoms, and aquatic oligochaetes, which are used in freshwater biomonitoring in France and Switzerland. To go towards the renewal of current biomonitoring practices, SYNAQUA will (1) bring together different actors: scientists, environmental managers, consulting firms, and biotechnological companies, (2) apply this approach on a large scale to demonstrate its relevance, (3) propose robust and reliable tools, and (4) raise public awareness and train the various actors likely to use these new tools. Biomonitoring approaches based on such environmental genomic tools should address the European need for reliable, higher-throughput monitoring to improve the protection of aquatic environments under multiple pressures, guide their restoration, and follow their evolution.     

Local Arctic air pollution: Sources and impacts

Local emissions of Arctic air pollutants and their impacts on climate, ecosystems and health are poorly understood. Future increases due to Arctic warming or economic drivers may put additional pressures on the fragile Arctic environment already affected by mid-latitude air pollution. Aircraft data were collected, for the first time, downwind of shipping and petroleum extraction facilities in the European Arctic. Data analysis reveals discrepancies compared to commonly used emission inventories, highlighting missing emissions (e.g. drilling rigs) and the intermittent nature of certain emissions (e.g. flaring, shipping). Present-day shipping/petroleum extraction emissions already appear to be impacting pollutant (ozone, aerosols) levels along the Norwegian coast and are estimated to cool and warm the Arctic climate, respectively. Future increases in shipping may lead to short-term (long-term) warming (cooling) due to reduced sulphur (CO₂) emissions, and be detrimental to regional air quality (ozone). Further quantification of local Arctic emission impacts is needed.     

‘Natural’ disaster? A retrospect into the causes of the late-2004 typhoon disaster in Eastern Luzon, Philippines

Between 14 November and 4 December 2004, four successive tropical depressions and typhoons lashed the Eastern coast of Luzon in the Philippines. Heavy rainfall triggered massive landslides and devastating flash floods, which brought tremendous damage and killed more than 1600 people. Immediately after the disaster, there was a media and political consensus to incrimate ‘extraordinary’ natural phenomena and widespread deforestation as responsible for the catastrophe. We argue that the tragedy that befell the municipalities of General Nakar, Infanta and Real, among other devastated areas, is enmeshed in a deeper tangle of causal factors that are political, socio-economic and demographic in nature. These factors include unmanaged population growth, difficult access to land and resources, corruption within the government, and power of the elite.     

Prenatal diagnosis of trisomy 9. Six cases and a review of the literature

Six prenatally diagnosed cases of trisomy 9 are reported and 22 previously reported cases are reviewed; the difficulty of genetic counselling for such cases and the variation in the percentage of trisomic cells in different tissues, thus making accurate diagnosis of trisomy 9 difficult, are emphasized. In addition to karyotyping results, ultrasound findings are important in achieving diagnoses. Finally, a course of action when prenatal trisomy 9 is detected is proposed.     

Validating graph-based connectivity models with independent presence–absence and genetic data sets

Habitat connectivity is a key objective of current conservation policies and is commonly modeled by landscape graphs (i.e., sets of habitat patches [nodes] connected by potential dispersal paths [links]). These graphs are often built based on expert opinion or species distribution models (SDMs) and therefore lack empirical validation from data more closely reflecting functional connectivity. Accordingly, we tested whether landscape graphs reflect how habitat connectivity influences gene flow, which is one of the main ecoevolutionary processes. To that purpose, we modeled the habitat network of a forest bird (plumbeous warbler [Setophaga plumbea]) on Guadeloupe with graphs based on expert opinion, Jacobs’ specialization indices, and an SDM. We used genetic data (712 birds from 27 populations) to compute local genetic indices and pairwise genetic distances. Finally, we assessed the relationships between genetic distances or indices and cost distances or connectivity metrics with maximum-likelihood population-effects distance models and Spearman correlations between metrics. Overall, the landscape graphs reliably reflected the influence of connectivity on population genetic structure; validation R² was up to 0.30 and correlation coefficients were up to 0.71. Yet, the relationship among graph ecological relevance, data requirements, and construction and analysis methods was not straightforward because the graph based on the most complex construction method (species distribution modeling) sometimes had less ecological relevance than the others. Cross-validation methods and sensitivity analyzes allowed us to make the advantages and limitations of each construction method spatially explicit. We confirmed the relevance of landscape graphs for conservation modeling but recommend a case-specific consideration of the cost-effectiveness of their construction methods. We hope the replication of independent validation approaches across species and landscapes will strengthen the ecological relevance of connectivity models.     

The development of aquaculture on the northern coast of Manila Bay (Philippines): an analysis of long-term land-use changes and their causes

This study documents the event chronology and causes of land-use change in a deltaic region of the Philippines since the beginnings of aquaculture in the late nineteenth century. Satellite images and topographic maps spanning the period 1972–2013 were processed to map fishponds and the natural habitats over which they have encroached. Historical archives were consulted and interviews were conducted to understand the historical exploitation of local natural resources and the reasons behind the recorded land changes. Results showed that aquaculture developed in the late nineteenth century and expanded subsequently across the landscape under a succession of forcing factors. The global market, for example, played an early role but a number of land-use changes were also a direct response to changing environmental constraints and natural hazards. These cumulative events have promoted continuous gain in favor of aquaculture, to the detriment of other land-use options.