Phylogenomic and ecological analyses reveal the spatiotemporal evolution of global pines

Abstract

How coniferous forests evolved in the Northern Hemisphere remains largely unknown. Unlike most groups of organisms that generally follow a latitudinal diversity gradient, most conifer species in the Northern Hemisphere are distributed in mountainous areas at middle latitudes. It is of great interest to know whether the midlatitude region has been an evolutionary cradle or museum for conifers and how evolutionary and ecological factors have driven their spatiotemporal evolution. Here, we investigated the macroevolution of Pinus, the largest conifer genus and characteristic of northern temperate coniferous forests, based on nearly complete species sampling. Using 1,662 genes from transcriptome sequences, we reconstructed a robust species phylogeny and reestimated divergence times of global pines. We found that ∼90% of extant pine species originated in the Miocene in sharp contrast to the ancient origin of Pinus, indicating a Neogene rediversification. Surprisingly, species at middle latitudes are much older than those at other latitudes. This finding, coupled with net diversification rate analysis, indicates that the midlatitude region has provided an evolutionary museum for global pines. Analyses of 31 environmental variables, together with a comparison of evolutionary rates of niche and phenotypic traits with a net diversification rate, found that topography played a primary role in pine diversification, and the aridity index was decisive for the niche rate shift. Moreover, fire has forced diversification and adaptive evolution of Pinus. Our study highlights the importance of integrating phylogenomic and ecological approaches to address evolution of biological groups at the global scale.

Morphological and Comparative Transcriptome Analysis of Three Species of Five-Needle Pines: Insights Into Phenotypic Evolution and Phylogeny

“…We observed that P. koraiensis and P. sibirica maintain relatively close genetic relationship compared with P. pumila . Similar results were reported in previous study of spatiotemporal evolution of global pines ( Jin et al, 2021 ). Furthermore, in subgroup II, P. pumila and P. parviflora were divided into the same group of five-needle pines, which may correspond to the traits of short needles among them.…”

Spatiotemporal Evolution of the Global Species Diversity of Rhododendron

“…Notably, the transcriptome-based phylogeny also shows a very high resolution of interspecific relationships, indicating that phylotranscriptomics is an economical and highly efficient approach for tree of life reconstruction at the species level, even for plant groups with recent evolutionary radiations like Rhododendron or with long generation times and slow molecular evolutionary rates like pines ( Jin et al 2021 ). It is generally recognized that transcriptome sequencing (RNA-seq) needs fresh samples, but actually silica-gel dried plant materials are also suitable for phylotranscriptomic studies according to our experience, because phylotranscriptomics uses OGs generated from RNA-seq and does not compare gene expression levels.…”

Divergence amid recurring gene flow: complex demographic histories for two North American pines (Pinus pungens and P. rigida) fit growing expectations among forest trees

“…Phenological traits have been linked to seasonal variation within species of North America (Jump and Penuelas 2005), and differences in seasonality requirements for P. pungens and P. rigida likely explain the observed phenological trait differences in seed size, reproductive age, timing of pollen release, and rates of seedling establishment across these two species (Zobel 1969; Della- Bianca 1990; Ledig et al 2015). Using niche and trait data, the phylogenetic inference of Jin et al (2021) identified precipitation seasonality (Bio15) and elevation as drivers of diversification in eastern North American pines. The results of our RDA corroborate these conclusions, as clear separation of species-level genetic differences was explained by Bio15 and elevation along axis 1 (Fig.…”