# Geographic isolation shapes the genetic landscape of the threatened karst-endemic plant Malania oleifera (Ximeniaceae)

## TL;DR

This study explores how geographic isolation affects the genetic diversity of the endangered Malania oleifera plant in China's karst forests.

## Contribution

The study provides new insights into the genetic structure and population history of Malania oleifera, emphasizing the role of geographic isolation.

## Key findings

- Genetic diversity is moderate, with Guangxi populations showing higher nucleotide diversity than Yunnan populations.
- Geographic isolation is the main driver of genetic differentiation, as shown by a strong isolation-by-distance pattern.
- Demographic analysis suggests a sharp decline in population size around 30,000 years ago due to climatic changes.

## Abstract

Malania oleifera Chun & S.K. Lee is a rare and endangered tree species endemic to the karst forests of southwestern China. Its seeds are rich in nervonic acid, a compound of significant ecological and economic value. However, habitat fragmentation, overharvesting, and climate change have imposed severe survival pressures on this species, leading to a risk of genetic diversity loss. In this study, we employed genotyping-by-sequencing (GBS) to investigate the genome-wide genetic diversity and population structure of 89 individuals from 16 natural populations. A total of 332,551 high-quality single nucleotide polymorphisms (SNPs) were obtained. The results showed moderate genetic diversity, with populations in Guangxi exhibiting significantly higher nucleotide diversity than those in Yunnan. Population structure analyses identified six genetic clusters that corresponded closely to their geographic distribution, indicating that geographic isolation is the main driver of genetic differentiation. Mantel tests revealed a highly significant positive correlation between genetic and geographic distances but no correlation with environmental distance, representing a typical isolation-by-distance (IBD) pattern. Redundancy analysis (RDA) identified 4,361 SNPs significantly associated with environmental variables suggesting potential local adaptation signals. Demographic reconstruction revealed that M. oleifera began a sharp and continuous decline in effective population size approximately 30 kya, likely triggered by climatic fluctuations during the Last Glacial Maximum. These findings provide valuable insights for the conservation, restoration, and regional management of this ecologically and economically important species.