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Finnish hare genomes help to understand local adaptation and the formation of species

Jaakko Pohjoismäki, Professor in molecular biology and genetics, Department of Environmental and Biological Sciences, University of Eastern Finland

There are six to eight species of hares in Europe, depending on one’s view on the certain subspecies and the geographical boundaries of the subcontinent. Two of the species, the mountain hare (Lepus timidus) and the brown hare (Lepus europaeus), are widespread and extend their range also to the Nordic countries, including Finland.

As evident from the name, mountain hares are adapted to cold and snowy environments, having wide snowshoe feet and white winter pelage. In the barren winter landscapes of the high north, mountain hares can feed on twigs and saplings of local willow and birch species that are low in nutrients but full of harmful chemicals, which render the plants inedible for most plant-eaters. Consequently, mountain hares dominate the higher latitudes and mountainous regions of Europe, as well as exist as ice age relict populations in the British Isles.

The brown hare is in contrast a more temperate climate adapted species, originating from the open grasslands of southwestern Eurasia and relying much on herbaceous plants also in their winter diet. Therefore, it is not surprising that the species has benefitted from the agriculture and cattle induced changes in the European landscape. During the last couple of decades, the brown hare’s distribution has been expanding northward with increasing speed, a change largely explained by the climate change driven shortening of the snow-covered season. This range expansion brings brown hares increasingly in contact with the mountain hares, whose numbers are simultaneously decreasing. The plight of the mountain hare is both due to increased predation because of camouflage mismatch during shortened winters but also because of direct competition by the brown hares. In southwestern Finland the situation is exemplified by the gradual extinction of the mountain hare populations on the mainland, whereas the populations on the Finnish Archipelago islands, not yet colonized by brown hares, are still thriving.

Although the species have slightly different habitat preferences, mountain hares and brown hares coexist in many places in Finland, including urban areas. Photo by Mervi Kunnasranta.

One aspect of the competition is highly intimate, as the two species can pair and produce fertile hybrid offspring. Curiously, this interaction is one-sided as the brown hare seems to be able to obtain locally adapted gene variants from the mountain hare whereas for the mountain hare hybridization appears to be a dead-end. While this unidirectionality can be driven by demographic factors or mate competition, our research group in the University of Eastern Finland has been interested in investigating whether genetic compatibility could help  explain the phenomenon. This is particularly interesting as these mechanisms could give an insight into speciation mechanisms at the genome level. 

At some stage of their history, species originate from the same ancestral population but develop following independent evolutionary trajectories, where their genetic makeup is independently moulded by local selective pressures and random genetic drift. Through time, the genetic differences accumulate from population differences to species differences, such as we see them in both the phenotype and the genotype of mountain hares and brown hares, separated from their common ancestor some three million years ago. Although the schoolbook definition of species as “ a group of individuals that actually or potentially interbreed in nature” emphasizes the reproductive isolation between them, the reproductive isolation can be governed by many mechanisms. One of these is genetic compatibility, allowing the embryonic development and birth of viable, fertile hybrids. As the incompatibilities develop gradually during evolution, they are not dichotomous and can exhibit substantial variation.

The mountain hare – brown hare couple is especially interesting as the large lifestyle differences reflect significant differences in how their bodies function, including some basic cellular processes. Because of their adaptation to the harsh winter conditions, mountain hares are more prepared for resource conservation compared to brown hares. This shows also in the life history strategy of the two species, with mountain hares resourcing more into ageing rather than reproduction, especially compared to the brown hares. Consequently, mountain hares are longer lived (up to 18 years!) but have lower reproductive capacity than brown hares. This difference is also seen at the cellular level. Brown hare fibroblast cells grow and migrate faster than those of mountain hares, a difference that is explained by the differences in the relative lengths of certain cell cycle phases. Similarly, mountain hare cells have certain interesting and specialized biochemical pathways, which probably enable cold adaptation with the expense of having fewer resources to anabolic metabolism - that is, fewer resources that allow them to build-up more complex molecules from simpler ones. It can well be that certain types of adaptations are not permissive for changes caused by the genes from another species. In this context, the brown hare would represent a genetically flexible species, capable of incorporating mountain hare genetic components as a part of its normal physiological processes, whereas the incorporation of brown hare features into mountain hare background will cause a breakdown of the hybrids.

While the Mountain hare's snowshoe feet are a highly characteristic adaptation to the long snow covered season, the narrow hind feet of the brown hares can cause major difficulties for the animals to move and find food when the snow is soft and deep. Photos by Jaakko Pohjoismäki.

Our group has generated the reference genomes for both the brown hare and the mountain hare as a part of the ERGA pilot project. For us, these genomes are akin to the Rosetta stone, allowing us to decipher the exact nature and the information content of any gene in the two species. They enable us to pinpoint the genes underlying the observed species differences and experimentally test the role of individual genes in any cellular process. This is particularly interesting when trying to understand metabolic adaptation, the evolution of life history strategies and how these contribute to the compatibility of the hybridization.

Mountain hare and brown hare species pair in Finland represents an exciting natural experiment, which – with the help of the species genomes – allows us to understand broader evolutionary processes. They also vividly exemplify how climate change is reforming animal populations and effects the species interactions. The brown hare has already experienced and will continue to benefit from human impacts on the environment. Only time will reveal the resilience of its arctic cousin in confronting the challenges that lie ahead.


The annotated genome assembly of the brown hare has been published and is openly available (Read the publication pre-print). The mountain hare genome has been assembled and is currently undergoing the annotation process.


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