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15 juin 2018

An efficient and improved laboratory workflow and tetrapod database for larger scale eDNA studies [BioRxiv]

Background : The use of environmental DNA, "eDNA", for species detection via metabarcoding is growing rapidly and now, even terrestrial mammals can be monitored via "invertebrate-derived DNA" or "iDNA" from hematophagous invertebrates. We present a co-designed lab workflow and bioinformatic pipeline to mitigate the two most important risks of e/iDNA : sample contamination and taxonomic mis-assignment. These risks arise from the need for amplification to detect the trace amounts of DNA and the necessity of using short target regions due to DNA degradation. Findings : Here we present a high-throughput laboratory workflow that minimises these risks via a three-step strategy : (1) each sample is sequenced for two PCR replicates from each of two extraction replicates ; (2) we use a "twin-tagging", two-step PCR protocol ; (3) and a multi-marker approach targeting three mitochondrial loci : 12S, 16S and CytB. As a test, 1532 leeches were analysed from Sabah, Malaysian Borneo. Twin-tagging allowed us to detect and exclude chimeric sequences. The smallest DNA fragment (16S) amplified best for all samples but often at lower taxonomic resolution.(...)

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15 juin 2018

What is Speciation Genomics ? The roles of ecology, gene flow, and genomic architecture in the formation of species [Biological Journal of the Linnean Society]

Keywords : barrier loci, coalescence, ecological speciation, genome scans, genomic islands, lineage diversification, reproductive isolation, sympatric speciation

As is true of virtually every realm of the biological sciences, our understanding of speciation is increasingly informed by the genomic revolution of the past decade. Investigators can ask detailed questions relating to both the extrinsic (e.g. inter- and intra-population and ecological interactions) and intrinsic (e.g. genome content and architecture) forces that drive speciation. Technologies ranging from restriction-site associated DNA sequencing (RADseq), to whole genome sequencing and assembly, to transcriptomics, to CRISPR are revolutionizing the means by which investigators can both frame and test hypotheses of lineage diversification. Our review aims to examine both extrinsic and intrinsic aspects of speciation.(...)

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15 juin 2018

Consumption explains intraspecific variation in nutrient recycling stoichiometry in a desert fish [Ecology]

Keywords : Chihuahuan desert, desert spring, ecological stoichiometry, elemental phenotype, excretion, mosquitofish

Consumer‐driven nutrient recycling can have substantial effects on primary production and patterns of nutrient limitation in aquatic ecosystems by altering the rates as well as the relative supplies of the key nutrients nitrogen (N) and phosphorus (P). While variation in nutrient recycling stoichiometry has been well‐studied among species, the mechanisms that explain intraspecific variation in recycling N:P are not well‐understood. We examined the relative importance of potential drivers of variation in nutrient recycling by the fish Gambusia marshi among aquatic habitats in the Cuatro Ciénegas basin of Coahuila, Mexico.(...)

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15 juin 2018

The increasing disconnection of primary biodiversity data from specimens : How does it happen and how to handle it ? [Systematic Biology]

Keywords : rimary biodiversity data, specimen, observation, database, ancillary data, biodiversity occurrences, big data

Primary biodiversity data represent the fundamental elements of any study in systematics and evolution. They are, however, no longer gathered as they used to be and the mass-production of observation-based occurrences is overthrowing the collection of specimen-based occurrences. Although this change in practice is a major upheaval with significant consequences in the study of biodiversity, it remains understudied and has not attracted yet the attention it deserves. Analyzing 536 million occurrences from the Global Biodiversity Information Facility (GBIF) mediated data, we show that this spectacular change affects the 24 eukaryote taxonomic classes we targeted : from 1970 to 2016 the proportion of occurrences marked as traceable to tangible material (i.e. specimen-based occurrences) fell from 68 to 18% ; moreover, most of those specimen based-occurrences cannot be readily traced back to a specimen because the necessary information is missing. Ethical, practical or legal reasons responsible for this shift are known, and this situation appears unlikely to be reversed. Still, we urge scholars to acknowledge this dramatic change, embrace it and actively deal with it.(...)

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15 juin 2018

The economics of fishing the high seas [Science Advances]

While the ecological impacts of fishing the waters beyond national jurisdiction (the “high seas”) have been widely studied, the economic rationale is more difficult to ascertain because of scarce data on the costs and revenues of the fleets that fish there. Newly compiled satellite data and machine learning now allow us to track individual fishing vessels on the high seas in near real time. These technological advances help us quantify high-seas fishing effort, costs, and benefits, and assess whether, where, and when high-seas fishing makes economic sense. We characterize the global high-seas fishing fleet and report the economic benefits of fishing the high seas globally, nationally, and at the scale of individual fleets.(...)

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