Molecular phenotyping uncovers differences in basic housekeeping functions among closely related species of hares (Lepus spp., Lagomorpha: Leporidae)

Abstract

Speciation is a fundamental evolutionary process, which results in genetic differentiation of populations and manifests as discrete morphological, physiological and behavioral differences. Each species has had its own evolutionary trajectory, formed by many types of selection pressures and random drift, making the association of genetic differences between the species with the phenotypic differences extremely difficult. In the present study, we have used an in vitro model to analyze in depth the genetic and gene regulation differences between fibroblasts of two closely related mammals, the arctic/subarctic mountain hare (Lepus timidus Linnaeus) and the temperate steppe-climate adapted brown hare (Lepus europaeus Pallas). We discovered the existence of a species-specific expression pattern of 1,623 genes, manifesting in differences in cell growth, respiration, and metabolism. Interspecific differences in the housekeeping functions of fibroblast cells suggest speciation acts on fundamental processes, even in these two interfertile species. Our results help to understand the molecular constituents of a species difference on cellular level, which could contribute to the maintenance of the species boundary

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

“…As example, we sent living cell suspensions from Joensuu, Finland to the ZFMK biobank in Bonn, Germany, over regular airmail in ambient temperature. It is worth to point out that the obtained genome scaffolded to 23 autosomes, X and Y chromosomes, as expected for the species, showing no evidence of karyotypic dri] caused by cell culture, dispelling possible concerns for the use of cell lines for such work (Gaertner et al, 2022).…”

“…Consequently, a lot of work has been already done in terms of populaSon geneScs, evoluSon 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 evoluSon, which will be parScularly interesSng in the context of geneSc introgression (Juric et al, 2016) and maintenance of species boundaries.…”

“…The collecSon locaSon is remote wilderness, dominated by boreal Taiga Forest (Figure 1A) and devoid of brown hares, which in Finland are dependent on man-made environments (Levanen et al, 2018a). Further analysis of the coding part of the genome and mitochondrial DNA haplotyping showed no ancestral admixture with brown hares (Gaertner et al, 2022).…”

“…The fibroblast cell line (LT1) was isolated from the specimen as described earlier (Gaertner et al, 2022) and is deposited under voucher number ZFMK-TIS-69753 into the biobank of the Stiftung Leibniz-Institut zur Analyse des Biodiversitätswandels, Zoological Research Museum Alexander König (ZFMK), Bonn, Germany.…”

“…In addiSon, postglacial contact with other congeneric hare species has resulted in recurrent hybridizaSon and geneSc introgression (Levanen et al, 2018b;Melo-Ferreira et al, 2009), some of which has apparently adapSve 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 interesSng in the context of conservaSon geneScs, hares provide ample opportuniSes to study local adaptaSons (Giska et al, 2022;Michell et al, 2022), genomic introgression (Giska et al, 2019;Levanen et al, 2018b;Pohjoismaki et al, 2021) and geneSc consStuents of species boundaries (Gaertner et al, 2022). These studies benefit greatly from the increased availability of genomic informaSon.…”