Climatic fluctuations, geographic features, and evolutionary forces: Shaping high genomic diversity and local adaptation in Muntiacus reevesi

Abstract

Aim

Genetic diversity is crucial for species adaptability. Understanding the mechanisms behind its formation and maintenance is essential for effective conservation. Recent studies have demonstrated that despite experiencing severe population bottlenecks, Muntiacus reevesi retains high genetic diversity and continues its northward migration, indicative of ongoing adaptive evolution. However, our comprehension of this phenomenon remains incomplete. The objective of this study is to explore the mechanisms underlying the formation of high genetic diversity and the genomic characteristics associated with local adaptation, using M. reevesi as a case study.

Location

Southern China.

Methods

We analysed resequencing data from 62 genomes and identified 29,124,081 high-quality single-nucleotide polymorphisms (SNPs). We used population genetics, demographic history, population differentiation, gene flow analysis software, and genotype-environment association (GEA) models to assess the factors that have contributed to high genetic diversity and environmental adaptability in the historical climate and geographical context.

Results

The study identified that during Pleistocene climatic fluctuations, M. reevesi diverged into eastern (DB and WJW populations) and western lineages (WL, BA, and QL populations), all displayed high genetic diversity. Historically, M. reevesi maintained large effective populations, but contemporary human-induced threats have led to a significant decline. Population differentiation models suggest distinct expansion pathways for eastern and western lineages, resulting in population admixture, with mountain corridors facilitating gene flow and maintaining high genetic diversity. Additionally, environmental-genotype analysis revealed local adaptation in the QL-BA population, highlighting candidate adaptive genes (ME3 and PRKG1) potentially linked to cold adaptation and foraging behaviour.

Conclusion

This study enhances our understanding of the mechanisms behind the high genetic diversity and environmental adaptability of M. reevesi, offering insights into how bottleneck populations maintain diversity, crucial for biogeographic research and conservation strategies for similar species.