Species divergence and environmental adaptation of <i>Picea asperata</i> complex at the whole genome level

To study the interspecific differentiation characteristics of species originating from recent radiation, the genotyping-by-sequencing (GBS) technique was used to explore the kinship, population structure, gene flow, genetic variability, genotype-environment association and selective sweeps of <i>Picea asperata</i> complex with similar phenotypes from a genome-wide perspective. The following results were obtained: 14 populations of <i>P. asperata</i> complex could be divided into 5 clades; <i>P. wilsonii</i> and <i>P. neoveitchii</i> diverged earlier and were more distantly related to the remaining 6 spruce species. Various geological events have promoted the species differentiation of <i>P. asperata</i> complex. There were four instances of gene flow among <i>P. koraiensis</i>, <i>P. meyeri</i>, <i>P. asperata</i>, <i>P. crassifolia</i> and <i>P. mongolica</i>. The population of <i>P. mongolica</i> had the highest level of nucleotide diversity, and <i>P. neoveitchii</i> may have experienced a bottleneck recently. Genotype-environment association found that a total of 20,808 genes were related to the environmental variables, which enhanced the adaptability of spruce in different environments. Genes that were selectively swept in the <i>P. asperata</i> complex were primarily associated with plant stress resistance. Among them were some genes involved in plant growth and development, heat stress, circadian rhythms and flowering. In addition to the commonly selected genes, different spruce species also displayed unique genes subjected to selective sweeps that improved their adaptability to different habitats. Understanding the interspecific gene flow and adaptive evolution of <i>Picea</i> species is beneficial to further understanding the species relationships of spruce and can provide a basis for studying spruce introgression and functional genomics.