Mountain- and brown hare genetic polymorphisms to survey local adaptations and conservation status of the heath hare (Lepus timidus sylvaticus, Nilsson 1831)

Abstract

We provide the first whole genome sequences from three specimens of the mountain hare subspecies the heath hare (Lepus timidus sylvaticus), along with samples from two mountain hares (Lepus timidus timidus) and two brown hares (Lepus europaeus) from Sweden. The heath hare has a unique grey winter pelage as compared to other mountain hares (white) and brown hares (mostly brown), and face regional extinction, likely due to competitive exclusion from the non-native brown hare. Whole genome resequencing from the seven hare specimens were mapped to the Lepus timidus pseudoreference genome and used for detection of 11,363,883 polymorphic nucleotide positions. The data presented here could be useful for addressing local adaptations and conservation status of mountain hares and brown hares in Sweden, including unique subspecies.

High quality genome assembly of the brown hare (Lepus europaeus) with chromosome-level scaffolding

“…Consequently, a lot of work has been already done in terms of population genetics, evolution and genomics of mountain hares [e.g. (Ferreira et al , 2021; Gaertner et al ., 2022; Giska et al ., 2022; Levanen et al ., 2018b; Marques et al ., 2020; Melo-Ferreira et al ., 2009; Michell et al ., 2022; Pohjoismaki et al ., 2021; Smith et al ., 2017)]. However, a high-quality reference genome will allow us to peer deeper into genome structure and chromosome evolution, which will be particularly interesting in the context of genetic introgression (Juric et al , 2016) and maintenance of species boundaries.…”

“…The mountain hare has shown resilience during the past warm periods of the Holocene (Smith et al , 2017), diverging also to more temperate climate-adapted subspecies (Giska et al , 2022), such as the Irish hare ( L. t. hibernicus Bell) and the heath hare ( L. t. sylvaticus Nilsson), which quite likely represent relatively old evolutionary lineages, genetically distinguishable from the widespread nominal subspecies (Giska et al ., 2022; Michell et al , 2022). In addition, post-glacial contact with other congeneric hare species has resulted in recurrent hybridization and genetic introgression (Levanen et al , 2018b; Melo-Ferreira et al , 2009), some of which has apparently adaptive significance (Giska et al , 2019; Giska et al ., 2022; Pohjoismaki et al , 2021).…”

“…In addition, post-glacial contact with other congeneric hare species has resulted in recurrent hybridization and genetic introgression (Levanen et al , 2018b; Melo-Ferreira et al , 2009), some of which has apparently adaptive significance (Giska et al , 2019; Giska et al ., 2022; Pohjoismaki et al , 2021). Besides the fact that especially the geographically restricted, relic-like subspecies are highly threatened (Caravaggi et al , 2017; Thulin et al , 2021) and thus interesting in the context of conservation genetics, hares provide ample opportunities to study local adaptations (Giska et al ., 2022; Michell et al ., 2022), genomic introgression (Giska et al ., 2019; Levanen et al ., 2018b; Pohjoismaki et al ., 2021) and genetic constituents of species boundaries (Gaertner et al , 2022). These studies benefit greatly from the increased availability of genomic information.…”

Chromosome-level reference genome assembly for the mountain hare (Lepus timidus)

“…The mountain hare has shown resilience during the past warm periods of the Holocene (Smith et al, 2017), diverging also to more temperate climate-adapted subspecies (Giska et al, 2022). Notable examples include the Irish hare (L. t. hibernicus Bell) and the heath hare (L. t. sylvaticus Nilsson), which are likely relatively old evolutionary lineages that are genetically distinct from the widespread nominal subspecies (Giska et al, 2022;Michell et al, 2022). In addition, post-glacial contact with other congeneric hare species has resulted in recurrent hybridization and genetic introgression (Melo-Ferreira et al, 2009;Levänen, Thulin, et al, 2018), which appears to have adaptive significance (Giska et al, 2019;Pohjoismäki et al, 2021;Giska et al, 2022).…”

“…It is worth noting that Linné did not formally designate a type specimen for the mountain hare, and the type locality has been later decided to be Uppsala in Sweden (Angerbjörn & Schai-Braun, 2022). The Swedish hares belong to the same larger, geographically connected Fennoscandian population as our specimen (Levänen, Thulin, et al, 2018;Michell et al, 2022). This is important because sampling from or near the type locality is considered desirable for the representativeness of the reference genome assembly (Lawniczak et al, 2022).…”