Effects of Geological and Environmental Events on the Diversity and Genetic Divergence of Four Closely Related Pines: Pinus koraiensis, P. armandii, P. griffithii, and P. pumila

Abstract

The effects of mountain uplift and environmental oscillations on nucleotide variability and species divergence remain largely unknown in East Asia. In this study, based on multiple nuclear DNA markers, we investigated the levels and patterns of nucleotide diversity and interspecific divergence in four closely related pines in China, i.e., Pinus koraiensis, P. armandii, P. griffithii, and P. pumila. The four pine taxa shared low levels of nucleotide polymorphisms at the species level. P. pumila had the highest silent nucleotide diversity (πsil = 0.00661) whereas P. griffithii had the lowest (πsil = 0.00175), while the levels of genetic polymorphism in P. armandii (πsil = 0.00508) and P. koraiensis (πsil = 0.00652) were intermediate between the other two species. Population genetic structure analysis showed that variations primarily existed within populations of the four pine species, presumably due to habitat fragmentation or the island-like distributions of Pinus species. Population divergence (FST) analysis showed that the genetic divergence between P. griffithii and P. koraiensis was much greater than that between P. koraiensis and the other two pines species. Isolation-with-migration analysis suggested that asymmetric gene flow had occurred between any two pairs of pine species. Phylogenetic analyses indicated that the four allied species split into two groups about 1.37 million years ago, where P. armandii and P. pumila were closer and clustered as sister species, whereas P. koraiensis and P. griffithii were clustered on another branch. Our results and those obtained in previous studies suggest that mountain uplift and geological climate oscillations may have led to the patterns of genetic divergence and nucleotide variations in these four pine species.

Phenotypic Variability and Genetic Diversity in a Pinus koraiensis Clonal Trial in Northeastern China

“…The average number of alleles and effective alleles per locus (Na, 4.67 ± 0.43; Ne, 2.916 ± 0.18) and the mean He (0.62 ± 0.02) and uHe (0.63 ± 0.02) were higher compared to the diversity parameters reported for Pinus thunbergii [ 75 ]. However, the values determined in this study were higher compared to results reported by [ 76 , 77 ], which analyzed the mating system in a complete P. koraiensis population containing seeds, male and female trees using 14 SSR markers. Our results corroborated previous studies [ 78 , 79 ], which indicated higher genetic diversity in Chinese natural Korean pine populations compared to that of other populations in the Russian region.…”

Genetic Diversity and Population Differentiation of Pinus koraiensis in China

“…Pinus koraiensis (Sieb. et Zucc), commonly known as Korean pine, is a perennial evergreen tree in the Pinaceae family with five needles per fascicle [1][2][3]. It is an ancient and valued forest tree in East Asia, and natural forests of this species have undergone long-term succession and are described as tertiary forest [4].…”

Evolutionary legacy of a forest plantation tree species (Pinus armandii): Implications for widespread afforestation

“…PCR fragments were separated on an ABI 3730 xl DNA Sequencer and individually assessed using GENEMAPPER v4.0 (Applied Biosystems). In addition, following the protocols of Jia et al (2018), one chloroplast (cpDNA) fragment, ycf1 , and two nuclear fragments, AGP 6 and LFY , were successfully amplified and sequenced for 466, 201, and 44 individuals, respectively. Following on from STRUCTURE results that separated out three geographic lineages (Figure 2), we selected between two and five individuals from each lineage, making 12 in total, for chloroplast genome sequencing; these together covered the full geographic range of P. armandii (Table ).…”