Population genetics, phylogenomics and hybrid speciation of Juglans in China determined from whole chloroplast genomes, transcriptomes, and genotyping-by-sequencing (GBS)

摘要

Genomic data are a powerful tool for elucidating the processes involved in the evolution and divergence of species. The speciation and phylogenetic relationships among ChineseJuglansremain unclear. Here, we used results from phylogenomic and population genetic analyses, transcriptomics, Genotyping-By-Sequencing (GBS), and whole chloroplast genomes (Cp genome) data to infer processes of lineage formation among the five native Chinese species of the walnut genus (Juglans,Juglandaceae), a widespread, economically important group. We found that the processes of isolation generated diversity during glaciations, but that the recent range expansion ofJ.regia, probably from multiple refugia, led to hybrid formation both within and between sections of the genus. In southern China, human dispersal ofJ.regiabrought it into contact withJ.sigillata, which we determined to be an ecotype ofJ.regiathat is now maintained as a landrace. In northern China, walnut hybridized with a distinct lineage ofJ.mandshuricato formJ.hopeiensis, a controversial taxon (considered threatened) that our data indicate is a horticultural variety. Comparisons among whole chloroplast genomes and nuclear transcriptome analyses provided conflicting evidence for the timing of the divergence of ChineseJuglanstaxa.J. cathayensisandJ. mandshuricaare poorly differentiated based our genomic data. Reconstruction ofJuglansevolutionary history indicate that episodes of climatic variation over the past 4.5 to 33.80 million years, associated with glacial advances and retreats and population isolation, have shaped Chinese walnut demography and evolution, even in the presence of gene flow and introgression.