Genomic Insights into Lagomorph Evolution and Introgression

Lagomorphs, comprising rabbits, hares and pikas, represent a globally distributed mammalian order notable for rapid diversification, ecological specialisation and a rich fossil record. Recent genome-scale studies have transformed our understanding of their evolutionary history by revealing patterns of divergence, demographic change and interspecific gene flow. High-quality reference assemblies and phylogenomic analyses have clarified deep splits between the two families—Leporidae and Ochotonidae—while palaeogenomic data from extinct lineages have refined the placement of enigmatic taxa. Whole-genome resequencing has illuminated the extent and timing of hybridisation events, demonstrating that introgression has been both ancient and ongoing, with adaptive exchanges of genes involved in immunity, metabolic function and environmental adaptation. Such insights are reshaping conservation strategies and informing how lagomorphs may respond to future environmental change.

Research from Nature Portfolio

Ancient DNA recovered from the extinct Sardinian pika has yielded a partial mitochondrial genome that refines its position as an independent sister lineage to extant pikas, indicating a divergence around thirty million years ago and highlighting the power of palaeogenomics to resolve long-standing phylogenetic uncertainties. In brown hares, targeted sequencing of candidate loci combined with mitochondrial genotyping has shown that hybridisation with mountain hares contributes crucial functional diversity, notably alleles of a thermogenic uncoupling protein and immune-related genes, suggesting adaptive benefits in novel environments. Investigations of the Iberian hare have demonstrated that post-glacial range expansion underlies asymmetric mitochondrial introgression from mountain to Iberian species, fitting a neutral demographic model and emphasising the role of population dynamics in shaping genome-wide patterns of admixture.

Genomic Insights into Lagomorph Evolution and Introgression publication trend

The graph below shows the total number of articles in genomic insights into lagomorph evolution and introgression across all publications each year (not limited to Nature Index journals).

Technical terms

Introgression: Incorporation of genetic material from one species into another through hybridisation and backcrossing.

Hybridisation: Interbreeding between individuals from genetically distinct populations or species.

Mitogenome: The complete mitochondrial genome, often used to infer maternal lineage and divergence times.

Phylogenomic analysis: Reconstruction of evolutionary relationships using genome-scale sequence data.

Chromosome-scale genome assembly: Genome reconstruction in which sequences are organised into full chromosome-length scaffolds for high contiguity and accuracy.

References

1. Ancient DNA re-opens the question of the phylogenetic position of the Sardinian pika Prolagus sardus (Wagner, 1829), an extinct lagomorph. Scientific Reports (2023).
2. Hybridization with mountain hares increases the functional allelic repertoire in brown hares. Scientific Reports (2021).
3. Range expansion underlies historical introgressive hybridization in the Iberian hare. Scientific Reports (2017).
4. Chromosome-scale genome assembly of Lepus oiostolus (Lepus, Leporidae). Scientific Data (2024).
5. The Legacy of Recurrent Introgression during the Radiation of Hares. Systematic Biology (2020).
6. Out of Tibet: Genomic Perspectives on the Evolutionary History of Extant Pikas. Molecular Biology and Evolution (2020).