An eDNA assay for Irish Petromyzon marinus and Salmo trutta and field validation in running water.

This pilot study presents an environmental DNA (eDNA) assay for sea lamprey Petromyzon marinus and brown trout Salmo trutta, two species of economic and conservation importance in the Republic of Ireland. The results demonstrate the effectiveness of eDNA for assessing presence of low-abundance taxa (here, P. marinus) for environmental managers, and they highlight the potential for assessing relative abundance of rare or invasive freshwater species.

Rapid, economical single-nucleotide polymorphism and microsatellite discovery based on de novo assembly of a reduced representation genome in a non-model organism: a case study of Atlantic cod Gadus morhua.

By combining next-generation sequencing technology (454) and reduced representation library (RRL) construction, the rapid and economical isolation of over 25 000 potential single-nucleotide polymorphisms (SNP) and >6000 putative microsatellite loci from c. 2% of the genome of the non-model teleost, Atlantic cod Gadus morhua from the Celtic Sea, south of Ireland, was demonstrated. A small-scale validation of markers indicated that 80% (11 of 14) of SNP loci and 40% (6 of 15) of the microsatellite loci could be amplified and showed variability. The results clearly show that small-scale next-generation sequencing of RRL genomes is an economical and rapid approach for simultaneous SNP and microsatellite discovery that is applicable to any species. The low cost and relatively small investment in time allows for positive exploitation of ascertainment bias to design markers applicable to specific populations and study questions.

Kin-biased distribution in brown trout: an effect of redd location or kin recognition?

A wide range of animals have been reported to show kin-biased behaviours, such as reduced aggressiveness and increased food sharing among relatives. However, less is known about whether wild animals also associate with relatives under natural conditions, which is a prerequisite to facilitate kin-biased behaviours and hence kin selection. We tested, by means of microsatellite polymorphism, correlations between pair-wise relatedness and pair-wise metric distance in wild brown trout (Salmo trutta L.) under natural conditions in two streams. Our data show that young-of-the-year as well as older trout found close together also had a higher genetic relatedness in one of the two streams, whereas no relationship was found in the other stream. Very few half and full siblings were found in the second stream and under these conditions it is unlikely that kin-biased behaviours will receive positive selection. We discuss the underlying mechanisms for the observed structure and we specifically address the issue of whether the grouping of related individuals could reflect dispersal from the same spawning redds, or if it reflects active association with relatives, possibly conferring kin-selected advantages.