Orographic and climatic oscillations have played crucial roles in shaping the nucleotide diversity and evolutionary history of many species across the Northern Hemisphere. In this study, based on 10 nuclear loci and a chloroplast DNA marker, we analyzed the nucleotide polymorphisms and demographic history of the endangered conifer species Pinus bungeana in Northwest China and investigated the phylogenetic relationships between P. bungeana and two related species, that is, Pinus gerardiana and Pinus squamata. We found that P. bungeana exhibited an extremely low level of nucleotide diversity (π sil = 0.00159). Demographic simulations based on DIYABC analysis showed that P. bungeana underwent demographic expansion and contraction during the Miocene. According to ecological niche modeling, we found that this species survived in situ during the glacial period and was not restricted to southern refugia. We speculate that P. bungeana may have experienced widespread population shrinkage from the Last Interglacial to the Last Glacial Maximum due to geological or climatic events. Isolation-with-migration analysis revealed that the divergence (~2.4-4.2 Ma) among P. bungeana and its related species was significantly associated with the Qinghai-Tibetan Plateau uplift events in the mid-tolate Tertiary period. Species tree analyses suggested that these three related Pinus species formed a monophyletic clade with high bootstrap support. These results suggest that the Miocene-Pliocene and Pleistocene geological and climatic fluctuations might have profoundly affected the nucleotide diversity and demography of this psychrotolerant conifer species in western China.

Chloroplasts are semiautonomous organelles found in photosynthetic plants. The major functions of chloroplasts include photosynthesis and carbon fixation, which are mainly regulated by its circular genomes. In the highly conserved chloroplast genome, the chloroplast transfer RNA genes (cp tRNA) play important roles in protein translation within chloroplasts. However, the evolution of cp tRNAs remains unclear. Thus, in the present study, we investigated the evolutionary characteristics of chloroplast tRNAs in five Adoxaceae species using 185 tRNA gene sequences. In total, 37 tRNAs encoding 28 anticodons are found in the chloroplast genome in Adoxaceae species. Some consensus sequences are found within the Ψ‐stem and anticodon loop of the tRNAs. Some putative novel structures were also identified, including a new stem located in the variable region of tRNATyr in a similar manner to the anticodon stem. Furthermore, phylogenetic and evolutionary analyses indicated that synonymous tRNAs may have evolved from multiple ancestors and frequent tRNA duplications during the evolutionary process may have been primarily caused by positive selection and adaptive evolution. The transition and transversion rates are uneven among different tRNA isotypes. For all tRNAs, the transition rate is greater with a transition/transversion bias of 3.13. Phylogenetic analysis of cp tRNA suggested that the type I introns in different taxa (including eukaryote organisms and cyanobacteria) share the conserved sequences “U‐U‐x2‐C” and “U‐x‐G‐x2‐T,” thereby indicating the diverse cyanobacterial origins of organelles. This detailed study of cp tRNAs in Adoxaceae may facilitate further investigations of the evolution, phylogeny, structure, and related functions of chloroplast tRNAs.