Reference genomes illuminate the colonisation histories, adaptation and hybridisation of two hare species

In June 2024, a research group from the University of Eastern Finland launched a new project under the BGE-ERGA umbrella. The project takes advantage of the natural experiment currently taking place in Finland, where the brown hare,  a temperate climate-adapted species and a recent arrival in the region, is expanding its distribution range with the help of climate change, at the expense of the cold-adapted mountain hare. 

The brown hare (Lepus europaeus) and the mountain hare (Lepus timidus) had their genomes sequenced as part of the ERGA Pilot Project.

While the two species hybridise and the hybrids are fertile, the gene flow between the species is highly unidirectional from mountain hares to brown hares. The factors causing this directionality as well as its consequences for the two hare species remain poorly understood. It seems likely that the brown hares outbreed mountain hares while obtaining locally adapted gene variants from these. Led by Prof. Jaakko Pohjoismäki, the project aims to showcase the utility of reference-quality genome assemblies in aiding and enabling detailed dissection of species’ colonisation histories, and the genetic impact of hybridisation and adaptation.

The distribution as well as the habitat use of mountain hares and brown hares overlaps in Finland. Despite the peaceful coexistence of the individuals in the wild, brown hares are expanding their range at the expense of the mountain hares. Game camera photos from a previous study on the species interactions. The trap was used for catching and tagging the hares for satellite tracking. Note the GPS collar on the mountain hare. Courtesy of the UEF hare research group.

To understand the genomic consequences of the species hybridization, pinpoint genomic regions under selection and reveal ancestral makeup as well as origins of the Finnish brown hare population, the group, in collaboration with researchers from CIBIO, Portugal, gathered genotype by sequencing datasets from a geographically representative sample of 200 mountain hares and 200 brown hares. As comparative “parental” populations, sequencing data was obtained from four brown hare populations (Germany, Austria, Pyrenees, and Hungary) and five mountain hare populations (Sweden, Ural Mountains, and the Russian Far East: Kolyma, Magadan, and Primorsky Krai).

The reference genome assemblies previously generated by the research group for the brown hare and the mountain hare as part of the ERGA Pilot Project are essential for the analysis as they facilitate SNP calling, recognition of linked variants, and the precise identification of the genes under selection. Data have already revealed hybridization patterns, genomic ancestry, and possible subpopulation structures among the two hare species. The group is currently investigating possible sex-linked biases in the introgression pattern, which might allow identification of possible male-related incompatibilities in the hybrids, as well as trying to pinpoint genes under selection.

A fertile first-generation hybrid between mountain hare and brown hare, confirmed by genotyping. Such hybrids seem to come with a cost to the mountain hare while potentially benefitting the local adaptation of brown hares. The background fence belongs to private property and is not related to keeping animals captive. Game camera photo, UEF hare research group.

Understanding the dynamics of the unique genetic interaction between the two hare species not only teaches us about the evolutionary processes of local adaptation in species range expansion but also provides valuable insight for informed conservation efforts for the mountain hare. This project is funded by the Horizon Europe program, with additional previous support from the Research Council of Finland (the xHARES consortium, grant no. 329264), and Portuguese FCT, Fundação para a Ciência e a Tecnologia (doi: 10.54499/PTDC/BIA-EVL/1307/2020), to the Portuguese collaborators. We also thank BGE-ERGA for providing a collaborative platform that made this research possible.

Chromosomal-level reference genome assemblies enable detailed analysis of species hybridisation, as these preliminary results of the presented study demonstrate. Upper panel: Example of mountain hare chromosomal segments in the genome of a brown hare individual from the Oulu region in Finland. The chromosomes appear in reverse alphabetical order from top to bottom. The Y-chromosome has been excluded as it lacks recombination. The red regions are homozygous, and the yellow regions are heterozygous with mountain hare genomic sequence. Lower panel: A closeup of the red section of chromosome 18, showing example gene loci in this region. Read more about the two genomes here. Image by Zsófia Fekete. Image by Zsófia Fekete.

About the Author

Prof. Jaakko Pohjoismäki is part of the ERGA Finland and participates in the ERGA Sampling and Sample Processing Committee, as well as its executive board. Besides the mitochondrial biology research group, he has led the hare research at the University of Eastern Finland since 2013 (https://uefconnect.uef.fi/en/hare-research/).