Extremely low nucleotide polymorphism in Pinus krempfii Lecomte, a unique flat needle pine endemic to Vietnam

Pinus krempfii Lecomte is a morphologically and ecologically unique pine, endemic to Vietnam. It is regarded as vulnerable species with distribution limited to just two provinces: Khanh Hoa and Lam Dong. Although a few phylogenetic studies have included this species, almost nothing is known about its genetic features. In particular, there are no studies addressing the levels and patterns of genetic variation in natural populations of P. krempfii. In this study, we sampled 57 individuals from six natural populations of P. krempfii and analyzed their sequence variation in ten nuclear gene regions (approximately 9 kb) and 14 mitochondrial (mt) DNA regions (approximately 10 kb). We also analyzed variation at seven chloroplast (cp) microsatellite (SSR) loci. We found very low haplotype and nucleotide diversity at nuclear loci compared with other pine species. Furthermore, all investigated populations were monomorphic across all mitochondrial DNA (mtDNA) regions included in our study, which are polymorphic in other pine species. Population differentiation at nuclear loci was low (5.2%) but significant. However, structure analysis of nuclear loci did not detect genetically differentiated groups of populations. Approximate Bayesian computation (ABC) using nuclear sequence data and mismatch distribution analysis for cpSSR loci suggested recent expansion of the species. The implications of these findings for the management and conservation of P. krempfii genetic resources were discussed.

克氏松（Pinus krempfii Lecomte）是一种在形态学与生态学上均具独特性的松树，为越南特有物种。该物种被列为易危物种，分布范围仅局限于庆和省与林同省两省境内。尽管已有少量系统发育研究纳入该物种，但目前学界对其遗传特征仍知之甚少。尤为关键的是，目前尚无任何研究探讨克氏松天然种群的遗传变异水平与模式。本研究从克氏松的6个天然种群中采集了57份个体样本，对其10个核基因区域（总长约9 kb）与14个线粒体（mt）DNA区域（总长约10 kb）的序列变异进行了分析。此外，本研究还对7个叶绿体（cp）微卫星（SSR）位点的变异进行了检测。与其他松属物种相比，本研究发现核基因位点的单倍型多样性与核苷酸多样性均处于极低水平。进一步而言，本研究涵盖的所有线粒体DNA（mtDNA）区域在所有被测种群中均呈单态性，而这类区域在其他松属物种中通常表现为多态性。核基因位点的种群分化程度较低（5.2%）但具有统计学显著性。然而，对核基因位点的群体结构分析并未检测到存在遗传分化的种群类群。基于核基因序列数据的近似贝叶斯计算（ABC）以及针对cpSSR位点的错配分布分析结果均表明，该物种曾经历过近期的种群扩张事件。本研究最后讨论了上述研究结果对克氏松遗传资源的管理与保护工作的启示。