Mitochondrial DNA reveals how perch colonized the Baltic Sea

“As the saying goes, all roads lead to Rome - or in this case, (almost) all roads lead to the Baltic Sea region, which has also become a melting pot characterized by great genetic diversity” says Anti Vasemägi, professor at the Department of Aquatic Resources at SLU who led the study.

History written in DNA

Just 20,000 years ago, a massive kilometer thick ice sheet covered Northern Europe. The melting was quick in geological terms but from human perspective, it took a while. For example, melting of the ice sheet in Scandinavia took almost 6,000 years. As the ice melted, different species began to colonise the new areas, and this process is still ongoing. Thus, all species living today in Northern Europe are relatively recent colonisers; the question is when and where particular species arrived.

This is the core of the scientific fields called phylogenetics and phylogeography, which aim to understand the diversification patterns and their shared biogeographic histories. Due to the explosive development of new DNA sequencing technologies in recent decades, it is now possible to investigate genetic relationships among and within species using large-scale DNA sequence data covering the entire genomes. In addition, scientists have learned to better read the information hidden within genomes, which helps to more accurately understand how migrations, as well as good and bad times, have shaped genetic diversity.

The Baltic Sea Region as a Meeting Place for Divergent Maternal Lineages

To gain a deeper insight into the evolutionary history of the Eurasian perch, a widely distributed fish species, Swedish and Estonian scientists undertook, for the first time, comprehensive analyses using both mitochondrial and nuclear genomes.

"We identified a total of five distinct mitochondrial lineages, with the oldest occurring in Lake Balaton, Hungary," stated Vitalii Lichman, the study's first author and a doctoral student at the Estonian University of Life Sciences.

He highlighted that the relatively high mutation rate combined with maternal inheritance makes mitochondrial DNA as a powerful tool for exploring the evolutionary relationships among organisms within the same species.

 "By employing the molecular clock concept, we estimated that these five maternal lineages diverged from each another hundreds of thousands of years ago. Notably, three of the identified lineages were widely spread across the Baltic Sea region, with traces of these maternal lineages leading to Western, Central, and Eastern Europe. Thus, the Baltic Sea region is a meeting place for highly diverged maternal lineages of perch," he concluded.

Nuclear genomes of perch - “shaken and stirred”

In addition to analyzing the mitochondrial genomes, the scientists studied nearly a million single nucleotide polymorphisms (SNPs) present in the nuclear genome. This analysis provided evidence that Northern Europe serves not only as a convergence point for diverged maternal lineages but also as a genetic melting pot, where nuclear DNA has undergone extensive reshuffling following colonization.

These findings demonstrate how colonization can result to unexpected patterns; rather than diminishing genetic diversity, colonization can create hotspots of genetic diversity when organisms from different glacial refugia meet and subsequently hybridize.

The results of the study  "Whole-genome analysis reveals phylogenetic and demographic history of Eurasian perch" were published in the British Fisheries Society journal, Journal of Fish Biology. The project was supported by the Swedish Research Council and Estonian Research Council.