Science in Siberia: Scientists learn about a historically large population of the Baikal seal

The Baikal seal is one of few preserved, exclusively freshwater, pinniped species. The pending issue is how and when they reached their current habitat, i.e. the rift Lake Baikal, more than three thousand kilometres away from the Arctic Ocean. According to one hypothesis, the Baikal seal reached the Siberian lake through the Angara—Yenisei river system. According to another hypothesis, it may have come along the Lena River, which is believed to have had a runoff from Lake Baikal.

The article is published in the journal Genes. The project included: Alla Lapidus, Professor in the Department of Cytology and Histology at St Petersburg University, Director of the Centre for Algorithmic Biotechnology at the Institute of Translational Biomedicine at St Petersburg University; and Mikhail Rayko, Senior Research Associate at the Centre for Algorithmic Biotechnology at St Petersburg University.

The most plausible current view suggests that migration routes of the Baikal seal led from the Arctic waters. This hypothesis is supported by several Arctic adaptations of the modern pagophilic species: breeding on ice; the white natal fur of pups, providing camouflage on snow-covered ice; the ability to spend considerable time and cover long distances underwater, considering the chance to be trapped under the thick ice; and the instinct to breathe from pockets of exhaled air that accumulates under the ice. Similar behaviour is typical for the Baikal seal’s Arctic relatives, i.e. the ringed seal (Pusa hispida) and the Caspian seal (Pusa caspica).

To explore the demographic history and genetic diversity of this species, the scientists generated a de novo chromosome-length assembly. The projects involved many Russian and foreign research organisations. Among them are the following: St Petersburg University; ITMO University (St Petersburg); the Institute of Molecular and Cellular Biology at the Siberian Branch of the Russian Academy of Sciences (Novosibirsk); DNA Zoo consortium (the USA); Novosibirsk State University; Baikal Branch of the Russian Research Institute of Fisheries and Oceanography (Ulan-Ude); the Skolkovo Institute of Science and Technology (Moscow); A P Ershov Institute of Informatics Systems of the Siberian Branch of the Russian Academy of Sciences (Novosibirsk); and Cambridge (Great Britain) to name just a few.

‘A chromosome assembly is a sequence consisting of unique small reads, where, ideally, each sequence corresponds to a biological chromosome. It also includes shorter DNA fragments that cannot be reliably attributed to any chromosome. This type of assembly may contain gaps, yet it is accurate enough for population studies,’ says Aliya Yakupova at the ITMO University.

Before generating a chromosome-length assembly, scientists sequenced the samples to get the reads, i.e. short sequences of DNA nucleotides. For whole genome sequencing, scientists used primary fibroblast cell lines of one male (PUSI1m) and one female (PUSI1f) Baikal seal, obtained from the Novosibirsk Cell Line Collection, located at the Institute of Molecular and Cell Biology of the Siberian Branch of the Russian Academy of Sciences. Sequencing was also carried out at the Institute of Molecular and Cell Biology of the Siberian Branch of the Russian Academy of Sciences.

After analysing the genetic data, the scientists put forward a hypothesis that there had been a historically large population of the Baikal seal, compared to the modern population size. ‘Demographic reconstruction has revealed higher values of effective population size in some time intervals in the past. We can assume that it reached its peak in the period from 4 million to 800 thousand years ago,’ says Aliya Yakupova. ‘Based on the time intervals of the peak of the population during the reconstruction and the data of geological studies, we also assume that this happened before the formation of Lake Baikal.’

Yet, this is just a hypothesis. The scientists used a PSMC-based reconstruction of the historical demography, i.e. Pairwise Sequential Markov Coalescence (PSMC) analysis. The results of the PSMC-based reconstruction are interpretation-dependent. However, it is impossible to reliably calibrate timescale and population size relying only on the events in the past. Additionally, it is difficult to understand why the population size has changed. It is impossible to say whether the population size has become smaller or some of the individuals migrated and the subgroup became a separate species.

The scientists also studied the heterozygosity of the Baikal seal and its Arctic relatives. Heterozygosity in diploid organisms means the simultaneous presence of two different alleles of the same gene in an individual. This affects the traits of individuals. It is generally accepted that genetic diversity, along with other factors, contributes to better survival of species.

‘We have found that the average heterozygosity of the studied individuals of the Baikal seal is relatively low, yet it does not differ much from the heterozygosity of other pinnipeds. However, according to the results of the analysis of demographic history, the Baikal seal showed a significantly more severe decline in population size relative to other species. This could be due to the difference in environmental conditions encountered by the earlier populations of Baikal seals, as ice sheets changed during glacial—interglacial cycles. We connect this period to the time of migration to Lake Baikal, which occurred ~3—0.3 million years ago, after which the population stabilised, indicating balanced habitat conditions,’ the scientists said in their article.

According to recent estimates, the population size of the Baikal seal ranges from 82,500 to 115,000 individuals. Such calculations are quite difficult to make, since the animals spend a lot of time under water. This shows that there are enough resources for the Baikal seals in Baikal Lake. In comparison, the population of the ringed seal, whose range covers the entire Arctic Ocean and the northern parts of the Atlantic Ocean and the Pacific Ocean, is estimated to reach about 1.5 million individuals.

The population size of Baikal seals is influenced by the presence and thickness of ice. It is also sensitive to anthropogenic factors, such as overfishing, which is part of the diet of seals, pollution of the lake, and viruses of terrestrial animals.

‘The closest relative of the Baikal seal is the ringed seal, which inhabits the Arctic Ocean and several sub-Arctic seas, such as the Baltic Sea. Ringed seals have a similar association with ice, the same structure of snow lairs, and the same structure of snow dens, and can maintain breathing holes through at least 1.8 m of ice. These two species are estimated to have diverged 1.15–1.7 million years ago. However, such a hypothesis could be verified only after whole genome sequencing of the ringed seal and the Caspian seal,’ the scientists write.