Summary
A chromosome-level reference genome and resequencing data from 80 Saimaa ringed seals show extremely limited Y-chromosomal diversity compared with other ringed seals. The bioRxiv preprint estimates that the population retains about 1% of the broader Y-chromosomal diversity and 5% of mitochondrial diversity.
A new chromosome-level reference genome has enabled researchers to examine the previously poorly understood paternal genetic history of the highly endangered Saimaa ringed seal (Pusa saimensis). In a bioRxiv preprint posted on September 16, 2026, the team combined the reference assembly, including a curated Y chromosome, with whole-genome resequencing data from 80 individuals.
The analysis estimates that the contemporary Saimaa population retains about 5% of the mitochondrial diversity found across non-Saimaa ringed seals, but only approximately 1% of their Y-chromosomal diversity. The comparison points to especially narrow variation in the population’s paternal lineages.
A reference genome that includes the Y chromosome
A reference genome is an assembled genetic framework against which DNA sequences from other individuals can be mapped and compared. Assemblies that resolve individual chromosomes, including sex chromosomes, make it easier to study variation in regions that may be incomplete or difficult to analyse in less detailed references.
The researchers assembled a chromosome-level genome for the Saimaa ringed seal and curated its Y chromosome. They then checked whether the sex chromosomes behaved as expected when sequencing data from males and females were mapped to the assembly.
The test used read depth, meaning the number of sequencing reads covering a particular genomic region. Male individuals showed the expected two-fold increase in coverage across the pseudoautosomal region of the X chromosome and exclusive coverage of the Y chromosome. These patterns supported the accuracy of the assembled sex chromosomes and enabled reliable molecular sex determination.
The result provides more than a sequence for identifying genes. It also creates a framework for tracing sex-specific population history. In mammals, mitochondrial DNA generally follows maternal lineages, while the Y chromosome follows paternal lineages. Comparing the two can reveal whether genetic histories have been shared or have differed between these inheritance paths.
Saimaa lineages are distinct and unusually limited
Phylogenetic analyses found that both the Y-chromosomal and mitochondrial haplotypes of Saimaa ringed seals form distinct monophyletic clades relative to Baltic, Lake Ladoga and Arctic ringed seals. In this context, a monophyletic clade is a group of sampled genetic lineages that share a distinct evolutionary branch. The pattern is consistent with the species’ long evolutionary isolation from other ringed seal populations.
The diversity estimates show that this isolation is reflected differently in the two genomes. Saimaa seals retain an estimated 5% of the mitochondrial diversity observed across non-Saimaa ringed seals, compared with approximately 1% of Y-chromosomal diversity. Because the values are relative estimates, they describe the amount of diversity retained in the Saimaa population compared with the broader comparison group rather than a percentage of individual genes in each seal.
The authors connect the population’s low size and genetic diversity with its unique evolutionary history and intense persecution over the last century. The new reference genome gives conservation researchers a way to monitor maternal and paternal lineages separately, while also supporting comparisons of Y-chromosome evolution among pinnipeds and other mammals.
The work is presented as a bioRxiv preprint. Its central contribution is the genomic resource and the accompanying estimate of present-day lineage diversity; the supplied study summary does not quantify the separate contributions of long-term isolation, persecution and later demographic changes to the different mitochondrial and Y-chromosomal values.