Whole-genome analysis reveals phylogenetic and demographic history of Eurasian perch.

The contemporary diversity and distribution of species are shaped by their evolutionary and ecological history. This can be deciphered with the help of phylogenetic and demographic analysis methods, ideally combining and supplementing information from mitochondrial and nuclear genomes. In this study, we investigated the demographic history of Eurasian perch (Perca fluviatilis), a highly adaptable teleost with a distribution range across Eurasia.

Know your enemy - transcriptome of myxozoan reveals potential drug targets against proliferative kidney disease in salmonids.

The myxozoan Tetracapsuloides bryosalmonae is a widely spread endoparasite that causes proliferative kidney disease (PKD) in salmonid fish. We developed an in silico pipeline to separate transcripts of T. bryosalmonae from the kidney tissue of its natural vertebrate host, brown trout (Salmo trutta).

The strength and form of natural selection on transcript abundance in the wild.

Gene transcription variation is known to contribute to disease susceptibility and adaptation, but we currently know very little about how contemporary natural selection shapes transcript abundance. Here, we propose a novel analytical framework to quantify the strength and form of ongoing natural selection at the transcriptome level in a wild vertebrate. We estimated selection on transcript abundance in a cohort of a wild salmonid fish (Salmo trutta) affected by an extracellular myxozoan parasite (Tetracapsuloides bryosalmonae) through mark-recapture field sampling and the integration of RNA-sequencing with classical regression-based selection analysis.

Highly Continuous Genome Assembly of Eurasian Perch () Using Linked-Read Sequencing.

The Eurasian perch () is the most common fish of the Percidae family and is widely distributed across Eurasia. Perch is a popular target for professional and recreational fisheries, and a promising freshwater aquaculture species in Europe. However, despite its high ecological, economical and societal importance, the available genomic resources for are rather limited.

Less is more: extreme genome complexity reduction with ddRAD using Ion Torrent semiconductor technology.

Massively parallel sequencing a small proportion of the whole genome at high coverage enables answering a wide range of questions from molecular evolution and evolutionary biology to animal and plant breeding and forensics. In this study, we describe the development of restriction-site associated DNA (RAD) sequencing approach for Ion Torrent PGM platform. Our protocol results in extreme genome complexity reduction using two rare-cutting restriction enzymes and strict size selection of the library allowing sequencing of a relatively small number of genomic fragments with high sequencing depth.

Genetic and life-history changes associated with fisheries-induced population collapse.

Over the recent years, growing number of studies suggests that intensive size-selective fishing can cause evolutionary changes in life-history traits in the harvested population, which can have drastic negative effects on populations, ecosystems and fisheries. However, most studies to date have overlooked the potential role of immigration of fish with different phenotypes as an alternative plausible mechanism behind observed phenotypic trends. Here, we investigated the evolutionary consequences of intensive fishing simultaneously at phenotypic and molecular level in Eurasian perch ( L.