Growth of brown trout in the wild predicted by embryo stress reaction in the laboratory.

Laboratory studies on embryos of salmonids, such as the brown trout (Salmo trutta), have been extensively used to study environmental stress and how responses vary within and between natural populations. These studies are based on the implicit assumption that early life-history traits are relevant for stress tolerance in the wild. Here we test this assumption by combining two data sets from studies on the same 60 families. These families had been experimentally produced from wild breeders to determine, in separate samples, (1) stress tolerances of singly kept embryos in the laboratory and (2) growth of juveniles during 6 months in the wild. We found that growth in the wild was well predicted by the larval size of their full sibs in the laboratory, especially if these siblings had been experimentally exposed to a pathogen. Exposure to the pathogen had not caused elevated mortality among the embryos but induced early hatching. The strength of this stress-induced change of life history was a significant predictor of juvenile growth in the wild: the stronger the response in the laboratory, the slower the growth in the wild. We conclude that embryo performance in controlled environments can be a useful predictor of juvenile performance in the wild

Matching commercial thrips predating phytoseids with the highly diversified climatic conditions of different strawberry production systems

Flower inhabiting thrips (Order: Thysanoptera) are a major threat to fruit quality in strawberry production around the world. As chemical control is often inefficient, alternative control measures are of broad and current interest. Their fast reproduction makes predatory mites highly suitable for thrips control in a crop with a relatively short cropping season like strawberry. However, climatic conditions of strawberry production can differ strongly depending on the production system (glasshouse, plastic tunnel, open field, etc.) and the time span of cultivation (depending mostly on planting date and the type of cultivar: summer-or everbearing). As predatory mites typically display a temperature-dependent life history and the current commercially available thrips predating phytoseids vary in geographic origin, one can assume that under certain climatic conditions some species will be more applicable than others. The goal of this study is to determine which species are suitable for which climatic conditions. Therefore all (Belgian) production systems and time spans are categorized into three climate types, simulated in the laboratory. The population build-up of seven predatory mite species (A. degenerans, A. montdorensis, A. andersoni, A. limonicus, A. swirskii, N. cucumeris and E. gallicus) were assessed for each of these climatic conditions. Under the coldest condition (A), the in West-Europe indigenous E. gallicus was the only species with a significant population build up. When moderate conditions (B) were simulated E. gallicus, N. cucumeris and A. limonicus were most successful. The warmest regime (C) was most adequate for E. gallicus and A. swirskii

Perspectives on the clonal persistence of presumed ‘ghost’ genomes in unisexual or allopolyploid taxa arising via hybridization

Although hybridization between non-sibling species rarely results in viable or fertile offspring, it occasionally produces self-perpetuating or sexually-parasitic lineages in which ancestral genomes are inherited clonally and thus may persist as 'ghost species' after ancestor extinction. Ghost species have been detected in animals and plants, for polyploid and diploid organisms, and across clonal, semi-clonal, and even sexual reproductive modes. Here we use a detailed investigation of the evolutionary and taxonomic status of a newly-discovered, putative ghost lineage (HX) in the fish genus Hypseleotris to provide perspectives on several important issues not previously explored by other studies on ghost species, but relevant to ongoing discussions about their detection, conservation, and artificial re-creation. Our comprehensive genetic (allozymes, mtDNA) and genomic (SNPs) datasets successfully identified a threatened sexual population of HX in one tiny portion of the extensive distribution displayed by two hemi-clonal HX-containing lineages. We also discuss what confidence should be placed on any assertion that an ancestral species is actually extinct, and how to assess whether any putative sexual ancestor represents a pure remnant, as shown here, or a naturally-occurring resurrection via the crossing of compatible clones or hemi-clones.P. J. Unmack, M. Adams, J. Bylemans, C. M. Hardy, M. P . Hammer, A. George

eDNA metabarcoding biodiversity of freshwater fish in the Alpine area

Environmental DNA (eDNA) based methods are proving to be a promising tool for freshwater fish biodiversity assessment in Europe within the Water Framework Directive (WFD, 2000/60/EC) especially for large rivers and lakes where current fish monitoring techniques have known shortcomings. Many freshwater fish are experiencing critical population declines with risk of local or global extinction because of intense anthropogenic pressure and this can have serious consequences on freshwater ecosystem functioning and diversity. Within the EU project Eco-AlpsWater, advanced high throughput sequencing (HTS) techniques are used to improve the traditional WFD monitoring approaches by using environmental DNA (eDNA) collected in Alpine waterbodies. An eDNA metabarcoding approach specifically designed to measure freshwater fish biodiversity in Alpine lakes and rivers has been extensively evaluated by using mock samples within an intercalibration test. This eDNA method was validated and used to study fish biodiversity of eight lakes and six rivers of the Alpine region including four EC countries (Austria, France, Italy, Slovenia) and Switzerland. More in detail, this metabarcoding approach, based on HTS sequencing of a section of the 12S rRNA gene, was used to assess freshwater fish biodiversity and their distribution in the different habitats. These data represent the first attempt to provide a comprehensive description of freshwater fish diversity in different ecosystems of the Alpine area confirming the applicability of eDNA metabarcoding analyses for the biomonitoring of fish inhabiting Alpine and perialpine lakes and rivers

The value of quantitative environmental DNA analyses for the management of invasive and endangered native fish

1. Environmental DNA (eDNA) monitoring is a useful tool for species detection but its use in addressing management questions remains scarce. One factor limiting the use of eDNA as a routine monitoring tool is uncertainty around the potential of eDNA data to estimate species abundance. While several confounding factors limit the ability of eDNA data to estimate absolute abundances at large spatial and temporal scales, eDNA data have the potential to estimate relative species abun- dances patterns at smaller scales, and this information can assist management. 2. Environmental DNA and conventional monitoring surveys were conducted in the Abercrombie River catchment (Australia) where an incursion of the invasive red- fin perch (Perca fluviatulis) threatens the survival of a population of endangered Macquarie perch (Macquaria australasica). Species-specific assays were used to quantify eDNA concentrations from water samples and estimate the relative abundance of both species. Electrofishing and fyke netting surveys were used to validate key observations from the eDNA survey. 3. Environmental DNA of both species was detected at all sites except one, where redfin perch DNA was not detected. Between species comparisons of eDNA con- centrations revealed a clear negative relationship between the eDNA concen- trations of both species, consistent with other evidence of redfin perch having a negative impact on Macquarie perch populations. Between site comparisons of redfin perch eDNA concentrations showed evidence of a novel incursion of the species in the upper reaches of the Abercrombie River and conventional monitor- ing in the following year confirmed the pattern of increased redfin perch abun- dances from downstream to upstream sites. 4. Relative comparisons of eDNA concentrations of aquatic species can be used to assess species interactions and reveal unexpected species abundance patterns (e.g. allowing inferences of novel incursions of invasive species). This informa- tion is critical to evaluate current, and design future, management strategies. Consequently, while deriving absolute species abundances from quantitative eDNA data may remain challenging, the use of quantitative eDNA surveys can provide relative abundance patterns valuable to the conservation and manage- ment of invasive and endangered species. 5. The quantitative nature of eDNA survey data has been debated extensively in the current literature because of potential confounding influences. Current study results show that these confounding influences may be less problematic at small spatial scales and quantitative eDNA data can be effective to monitor relative spe- cies abundances patterns

Novel universal primers for metabarcoding environmental DNA surveys of marine mammals and other marine vertebrates

Metabarcoding studies using environmental DNA (eDNA) and high‐throughput sequencing (HTS) are rapidly becoming an important tool for assessing and monitoring marine biodiversity, detecting invasive species, and supporting basic ecological research. Several barcode loci targeting teleost fish and elasmobranchs have previously been developed, but to date primer sets focusing on other marine megafauna, such as marine mammals, have received less attention. Similarly, there have been few attempts to identify potentially “universal” barcode loci which may be informative across multiple marine vertebrate orders. Here we describe the design and validation of two new sets of primers targeting hypervariable regions of the vertebrate mitochondrial 12S and 16S rRNA genes, which have conserved priming sites across virtually all cetaceans, pinnipeds, elasmobranchs, boney fish, sea turtles, and birds, and amplify fragments with consistently high levels of taxonomically diagnostic sequence variation. “In silico” validation using the OBITOOLS software showed our new barcode loci outperformed most existing vertebrate barcode loci for taxon detection and resolution. We also evaluated sequence diversity and taxonomic resolution of the new barcode loci in 680 complete marine mammal mitochondrial genomes demonstrating that they are effective at resolving amplicons for most taxa to the species level. Finally, we evaluated the performance of the primer sets with eDNA samples from aquarium communities with known species composition. These new primers will potentially allow surveys of complete marine vertebrate communities in single HTS metabarcoding assessments, simplifying workflows, reducing costs, and increasing accessibility to a wider range of investigators