Population genomics provides new insights into the genetic variation patterns, population demographic history, and high-altitude adaptation of Sophora moorcroftiana

Abstract

Background: Sophora moorcroftiana, a key stone shrub in Xizang (Tibet), has significant ecological and economic value. However, its populations face severe degradation. Understanding key evolutionary drivers of genetic variation within and among populations is critical for conserving and managing this species. Previous studies indicate a strong genetic structure correlated with altitude, but limited knowledge exists about the drivers of its geographic structure and evolutionary history. To address this, we conducted genomic research on 225 samples from 15 populations of S. moorcroftiana.

Results: Populations of S. moorcroftiana exhibited distinct population structure, divided into four subpopulations. Subpopulation P1 (Gongbu Jiangda County, Nyingchi) showed the greatest genetic differentiation from other populations (average Fst = 0.2477), with the lowest genetic diversity (Pi = 1.1 × 10^-4) and the smallest effective population size. P2, in the lower altitude area (Nyingchi), had larger genetic differentiation from the mid-altitude P3 (Fst = 0.168) and the high-altitude P4 (Fst = 0.227), with lower genetic diversity and effective population size. P3 and P4 had smaller genetic differentiation, with P3 having the largest genetic diversity and effective population size, followed by P4. D-statistics and Treemix revealed predominant gene flow from lower to higher altitude populations, with geographic proximity enhancing genetic sharing. SMC + + analyses suggested that the subpopulations experienced severe bottlenecks, genetic drift, and population expansion due to glacial-interglacial cycles and geological events. Partial Mantel tests revealed that the genetic variation distribution of S. moorcroftiana populations was more influenced by geographic isolation. Through genotype-environment association analysis, 90 single nucleotide polymorphisms (SNPs) were found to be significantly associated with environmental factors, of which 55 SNPs were annotated to genes, involving 20 genes.

Conclusions: The uplift of the plateau and intense climatic fluctuations during the Quaternary have profoundly impacted the genetic structure and geographic distribution of species in the region. The current genetic distribution characteristics were shaped by the subsequent influences of geography, environment, and gene flow. These findings provide a theoretical basis for the utilization of genetic resources, the formulation and implementation of conservation strategies for S. moorcroftiana, and the exploration of its adaptation mechanisms to the plateau environment.

Keywords: Sophora moorcroftiana; Genotype–environment association (GEA); Genotyping–by–sequencing (GBS); Isolation by distance (IBD); Single nucleotide polymorphism (SNP).