Geography and the Environment Shape the Landscape Genetics of the Vulnerable Species Ulmus lamellosa in Northern China

A comprehensive understanding of the pattern of genetic variation among populations and adaptations to environmental heterogeneity is very important for conservation and genetic improvement. Forest tree species are ideal resources for understanding population genetic differentiation and detecting signatures of selection due to their adaptations to heterogeneous landscapes. Ulmus lamellosa is a tree species that is endemic to northern China. In this study, using restriction-site-associated DNA sequencing (RAD-seq) data, 12,179 single-nucleotide polymorphisms were identified across 51 individuals from seven populations. There was a high level of genetic diversity and population differentiation in U. lamellosa. Population genetic structure analyses revealed a significant genetic structure related to the configuration of the mountains. Additionally, we found that the isolation-by-distance pattern explained the genetic differentiation best, and environmental heterogeneity also played a role in shaping the landscape genetics of this species inhabiting mountain ecosystems. The FST-based outlier and genotype–environment association approaches were used to explore the genomic signatures of selection and local adaptation and detected 317 candidate outlier loci. Precipitation seasonality (coefficient of variation), precipitation in the driest month, and enhanced vegetation index were important determinants of adaptive genetic variation. This study provides abundant genetic resources for U. lamellosa and insights into the genetic variation patterns among populations.