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18 septembre 2018

Metabarcoding by capture using a single COI probe (MCSP) to identify and quantify fish species in ichthyoplankton swarms [PLOS One]

Subject Areas : sequence databases, larvae, taxonomy, polymerase chain reaction, sequence alignment, probe hybridization, DNA extraction, genomic databases

The ability to determine the composition and relative frequencies of fish species in large ichthyoplankton swarms could have extremely important ecological applications However, this task is currently hampered by methodological limitations. We proposed a new method for Amazonian species based on hybridization capture of the COI gene DNA from a distant species (Danio rerio), absent from our study area (the Amazon basin). The COI sequence of this species is approximately equidistant from all COI of Amazonian species available. By using this sequence as probe we successfully facilitated the simultaneous identification of fish larvae belonging to the order Siluriformes and to the Characiformes represented in our ichthyoplankton samples.(...)

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17 septembre 2018

Herbarium genomics retraces the origins of C4-specific carbonic anhydrase in Andropogoneae (Poaceae) [Botany Letters]

Guillaume Besnard, Jan Hackel, Sophie Manzi

Natural history collections are traditionally used for taxonomic research, but their relevance can extend into studies of molecular evolution as illustrated here using the example of C4 photosynthesis. This complex trait boosts growth in open and warm conditions and evolved numerous times, providing multiple comparisons among C3 and C4 relatives. Previous genomic studies relied on comparisons of model species which are often separated by long-time divergence. The large C4 group Andropogoneae (Poaceae) was usually compared to relatively distant C3 taxa. Early-diverging C4 Andropogoneae and closely related C3 taxa are known but are difficult to collect and hence have not been sequenced yet. We show here that genome scans generated from herbarium samples can be used to retrace the evolution of βca genes, which encode beta carbonic anhydrase, an enzyme of the C4 pathway.(...)

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14 septembre 2018

Epidemiological tracing of Batrachochytrium salamandrivorans identifies widespread infection and associated mortalities in private amphibian collections [Scientific Reports]

The amphibian chytrid fungus Batrachochytrium salamandrivorans (Bsal) infects newts and salamanders (urodele amphibians), in which it can cause fatal disease. This pathogen has caused dramatic fire salamander population declines in Belgium, the Netherlands and Germany since its discovery in 2010. Thought to be native to Asia, it has been hypothesised that Bsal was introduced to Europe with the importation of infected amphibians for the commercial pet trade. Following the discovery of Bsal in captive amphibians in the United Kingdom in 2015, we used contact-tracing to identify epidemiologically-linked private amphibian collections in Western Europe.(...)

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14 septembre 2018

Classifying drivers of global forest loss [Science]

Global maps of forest loss depict the scale and magnitude of forest disturbance, yet companies, governments, and nongovernmental organizations need to distinguish permanent conversion (i.e., deforestation) from temporary loss from forestry or wildfire. Using satellite imagery, we developed a forest loss classification model to determine a spatial attribution of forest disturbance to the dominant drivers of land cover and land use change over the period 2001 to 2015. Our results indicate that 27% of global forest loss can be attributed to deforestation through permanent land use change for commodity production. The remaining areas maintained the same land use over 15 years ; in those areas, loss was attributed to forestry (26%), shifting agriculture (24%), and wildfire (23%). Despite corporate commitments, the rate of commodity-driven deforestation has not declined. To end deforestation, companies must eliminate 5 million hectares of conversion from supply chains each year.

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14 septembre 2018

A continental system for forecasting bird migration [Science]

Billions of animals cross the globe each year during seasonal migrations, but efforts to monitor them are hampered by the unpredictability of their movements. We developed a bird migration forecast system at a continental scale by leveraging 23 years of spring observations to identify associations between atmospheric conditions and bird migration intensity. Our models explained up to 81% of variation in migration intensity across the United States at altitudes of 0 to 3000 meters, and performance remained high in forecasting events 1 to 7 days in advance (62 to 76% of variation was explained). Avian migratory movements across the United States likely exceed 500 million individuals per night during peak passage. Bird migration forecasts will reduce collisions with buildings, airplanes, and wind turbines ; inform a variety of monitoring efforts ; and engage the public.

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