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The use of environmental DNA (eDNA) to determine the presence and distribution of aquatic organisms has become an important tool to monitor and investigate freshwater communities. The successful application of this method in the field, however, is dependent on the effectiveness of positive DNA verification, which is influenced by site-specific environmental parameters. Factors affecting eDNA concentrations in aquatic ecosystems include flow conditions, and the presence of substances that possess DNA-binding properties or inhibitory effects. In this study we investigated the influence of different environmental parameters on the detection success of eDNA using the invasive goby Neogobius melanostomus. In a standardized laboratory setup, different conditions of flow, sediment-properties, and fish density were compared, as well as different potential natural inhibitors such as algae, humic substances, and suspended sediment particles. The presence of sediment was mainly responsible for lower eDNA detection in the water samples, regardless of flow-through or standing water conditions and a delayed release of eDNA was detected in the presence of sediment. Humic substances had the highest inhibitory effect on eDNA detection followed by algae and siliceous sediment particles. The results of our study highlight that a successful application of eDNA methods in field surveys strongly depends on site-specific conditions, such as water flow conditions, sediment composition, and suspended particles. All these factors should be carefully considered when sampling, analyzing, and interpreting eDNA detection results.

Many freshwater mussel species are highly endangered. Knowledge of their occurrence and distribution is a crucial prerequisite for their conservation. The use of environmental DNA (eDNA) is a relatively new approach and an effective tool to detect the presence of target species in freshwater environments. This study aimed to establish a molecular identification tool for eDNA for the endangered thick-shelled river mussel Unio crassus Philipsson in Retzius, 1788 and to analyze the relationships between mussel abundance, stream discharge, sampling distance, and freshwater mollusk DNA signal (detectability and DNA quantity) by using binary logistic and linear regression modeling. We additionally correlated turbidity and mollusk DNA detectability. We developed a species-specific eDNA detection system in silico and tested the efficiency and species specificity on water samples collected downstream of extant populations of different sizes (100–42,000 individuals) in Bavaria, Germany. This system allowed detection of very small U. crassus populations over long distances (>3 km) and excluded amplification of DNA from other potentially co-occurring species. Signal strength was most strongly associated with population size and distance of sampling point from mussel population. Additionally, a negative correlation with stream turbidity was evident. This species-specific tool may help in screening of streams for target species that are otherwise difficult to monitor. [ABSTRACT FROM AUTHOR]

Targeted capture coupled with high‐throughput sequencing can be used to gain information about nuclear sequence variation at hundreds to thousands of loci. Divergent reference capture makes use of molecular data of one species to enrich target loci in other (related) species. This is particularly valuable for nonmodel organisms, for which often no a priori knowledge exists regarding these loci. Here, we have used targeted capture to obtain data for 809 nuclear coding DNA sequences (CDS) in a nonmodel organism, the Eurasian lynx Lynx lynx, using baits designed with the help of the published genome of a related model organism (the domestic cat Felis catus). Using this approach, we were able to survey intraspecific variation at hundreds of nuclear loci in L. lynx across the species' European range. A large set of biallelic candidate SNPs was then evaluated using a high‐throughput SNP genotyping platform (Fluidigm), which we then reduced to a final 96 SNP‐panel based on assay performance and reliability; validation was carried out with 100 additional Eurasian lynx samples not included in the SNP discovery phase. The 96 SNP‐panel developed from CDS performed very successfully in the identification of individuals and in population genetic structure inference (including the assignment of individuals to their source population). In keeping with recent studies, our results show that genic SNPs can be valuable for genetic monitoring of wildlife species. [ABSTRACT FROM AUTHOR]

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The article focuses on a study which analyzes the effects of preservation methods on DNA quality of the insect model species Ips typographus, one of the beetle species which are most commonly used in biodiversity studies. Microsatellite genotyping errors were also compared in this study. The preservation solutions included acetic acid, formalin and sodium benzoate. The results show that mean DNA quantity of solutions extracted from bodies varied widely among different treatments.

We report the isolation and characterization of microsatellite markers for the eastern green lizard ( Lacerta viridis) usable for noninvasive samples. Ten polymorphic loci were obtained by screening 3000 recombinant clones and tested on 39 noninvasive DNA samples of individuals from different locations of the Danube area, Germany. Allelic richness ranged from three to nine alleles, the observed heterozygosity from 0.33 to 0.80, and the expected heterozygosity from 0.36 to 0.85. Our 10 loci, along with another 12 loci previously described, deliver effective analytical tools to analyse the genetic variability and to assess the social structure of eastern green lizard populations. [ABSTRACT FROM AUTHOR]