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Terrestrial orchids are a group of genetically understudied, yet culturally and economically important plants. The Orchidinae tribe contains many species that produce edible tubers that are used for the production of traditional delicacies collectively called 'salep'. Overexploitation of wild orchids in the Eastern Mediterranean and Western Asia threatens to drive many of these species to extinction, but cost‐effective tools for monitoring their trade are currently lacking. Here we present a custom bait kit for target enrichment and sequencing of 205 novel genetic markers that are tailored to phylogenomic applications in Orchidinae s.l. A subset of 31 markers capture genes putatively involved in the production of glucomannan, a water‐soluble polysaccharide that gives salep its distinctive properties. We tested the kit on 73 taxa native to the area, demonstrating universally high locus recovery irrespective of species identity, that exceeds the total sequence length obtained with alternative kits currently available. Phylogenetic inference with concatenation and coalescent approaches was robust and showed high levels of support for most clades, including some which were previously unresolved. Resolution for hybridizing and recently radiated lineages remains difficult, but could be further improved by analysing multiple haplotypes and the non‐exonic sequences captured by our kit, with the promise to shed new light on the evolution of enigmatic taxa with a complex speciation history. Offering a step‐up from traditional barcoding and universal markers, the genome‐wide custom loci targeted by Orchidinae‐205 are a valuable new resource to study the evolution, systematics and trade of terrestrial orchids. [ABSTRACT FROM AUTHOR]

Clupeiform fishes are ecologically and economically important species contributing to industrial and artisanal fisheries worldwide. They represent key links in food webs, influencing the dynamic between trophic levels. The dietary interactions of these species are poorly studied in many regions, yet essential for fisheries management. To elucidate the role of these species in food webs of the Southern Brazilian Bight pelagic fisheries, we used metabarcoding analysis of fish stomach contents of Clupeiformes and possible predators. Onboard sampling from March to September 2016 allowed for processing of 87 stomach samples representing 31 species (including 12 samples representing three species of Clupeiformes). Links between trophic levels showed the predominance of Sardinella brasiliensis and Engraulis anchoita as important dietary items of a large range of fishes (28 species belonging to 18 families) and representing the majority of the total prey read abundance assigned to clupeiform fishes (~46% and ~32%, respectively). Opisthonema oglinum contributed to the diet of 16 species in 13 families and ~18% of total read abundance of clupeiform fishes as prey. The appearance of multiple clupeiform taxa in the diet of predators that are not commonly associated with pelagic prey indicates that ecosystem‐based fisheries management should not be separated between pelagic and demersal fisheries. The diet of Clupeiformes revealed an unexpectedly large diversity of fish species and a low proportion of invertebrates (<5% of clupeiform prey reads). This was likely due to a combination of both a limitation of the metabarcoding method (primer bias and low success of invertebrate taxonomic identification) as well as a contribution of early life stages (ichthyoplankton) to the diet of these fishes. The potential role of clupeiform fish populations as a constraint to the recruitment from the ichthyoplanktonic phase of other ecologically or commercially important fishes should be considered as an important direction for future studies. [ABSTRACT FROM AUTHOR]

Introductions of invasive non-native species often have severe effects on environments and can lead to the collapse of local populations. Freshwater systems are highly biodiverse habitats that are particularly sensitive to the introduction of non-native species, which is recognized as one of the leading causes of animal extinctions worldwide. Effective management firstly depends on the early detection of incipient invasions and subsequent rapid response. Here, we focus on the cryptic and difficult-to-detect amphipod, Crangonyx pseudogracilis, which is already established in several countries in Europe, and C. floridanus, which was recently found in the UK and Ireland. Their exact distribution is relatively unknown, and their morphological similarities to each other makes them taxonomically difficult to distinguish. To obtain better insights on the actual distribution of both species, we developed and validated species-specific assays for the detection of environmental DNA traces from both C. floridanus and C. pseudogracilis. Next, we analysed a large number of eDNA samples collected from several freshwater systems in Ireland where the presence of both alien species is known, and from unknown sites in Belgium, Netherlands, France, and Norway (countries where only C. pseudogracilis has previously been recorded). Using qPCR analyses, we successfully detected eDNA from both C. pseudogracilis and C. floridanus in the known locations in Ireland. Sites investigated in Belgium, Netherlands, France, and Norway were negative for the presence of both species. The qPCR based detection of freshwater amphipods from aquatic eDNA is a cost-effective and sensitive method to monitor establishment and spread of invasive species as well as species of conservation priority. Based on our results, we recommend that eDNA surveys can be used as a powerful tool for stakeholders, including ecologists, especially in at-risk areas to detect potential early invasion of these species. [ABSTRACT FROM AUTHOR]

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