# Genome‐Wide SNP Data and Species Distribution Modeling Reveal Population Structure and Conservation Implications of Primula wilsonii (Primulaceae)

## TL;DR

This study uses genetic data and climate modeling to understand the population structure and conservation needs of a rare alpine plant in Southwest China.

## Contribution

The integration of genome-wide SNP data and species distribution modeling provides new insights into the conservation of plants with extremely small populations.

## Key findings

- Population genetic analysis revealed two major clusters with low genetic diversity and one highly differentiated population.
- Demographic history suggests expansion 0.88 Ma followed by sustained contraction since 45 ka.
- Species distribution models indicate range contraction during the Last Glacial Maximum and future refugia in the Hengduan Mountains.

## Abstract

Integrating population genetics with species distribution models provides powerful insights into species' evolutionary trajectories under climatic and geological contexts, and informs evidence‐based conservation strategies for endangered species. In this study, we characterized the population genetic structure of
Primula wilsonii
, a plant species with extremely small populations (PSESP) endemic to the mountains of Southwest China, to provide insights for the conservation of alpine endangered plants. Double‐digest restriction‐site associated DNA sequencing (ddRAD‐seq) generated 18,313 neutral and unlinked single‐nucleotide polymorphisms (SNPs) from 30 individuals across seven populations. Population genetic analysis revealed that these populations formed two major clusters. All populations exhibited low levels of genetic diversity (He = 0.00184–0.00271; π = 0.00176–0.00292), with one population (MG1) showing high genetic differentiation (F
ST > 0.7) from the other populations, possibly reflecting long‐term geographic isolation resulting in a small effective population size (Ne). Demographic history analysis indicated an expansion around 0.88 Ma, followed by sustained contraction since approximately 45 ka with low Ne levels maintained. Species distribution models further suggested range contraction from the Last Glacial Maximum to the mid‐Holocene and persistence of suitable refugia in the Hengduan Mountains under future warming scenarios. In conclusion, our results indicated that complex topography and Quaternary climatic oscillations have shaped a hierarchical genetic structure with deeply isolated lineages. We therefore recommend delineating at least three independent management units, consistent with patterns of genetic structure, differentiation, and demographic history. These findings highlight the importance of integrating genetic and environmental evidence in the conservation of
P. wilsonii
and other PSESPs.

This study investigates the genetic erosion and conservation of
Primula wilsonii
, a plant species with extremely small populations in Southwest China. Using genomic sequencing and species distribution models, the research identifies distinct genetic clusters, low genetic diversity, and significant genetic differentiation among populations, in the text of complex topography and climatic oscillations. The findings highlight the need for targeted conservation efforts.