Reticulate Species Diversification Of The Genus Picea

Spruces(Picea)are important components of the forests in the Northern Hemisphere.The genus Picea(spruces)includes around 34 species and varieties with eight taxa in America,three in Europe,and remaining 23 in Asia.Due to the large effective population size,long generation time,radiative diversification and frequent interspecific hybridization and introgression,it is difficult to construct phylogenies of the genus Picea by using traditional method.In this study,we carried out genome-scale phylogenetic analyses of Picea species using transcriptome data from 26 species(varieties),including 15 from Asia,three from Europe,and eight from North America.(1)Genome-scale phylogenies of the genus Picea.Phylogenetic analyses used three datasets.The first dataset consisted of the nuclear gene orthologs,and we referred to it as the genome-scale ortholog dataset(GOD).The second dataset consisted of the nuclear genome Single Nucleotide Polymorphisms(SNPs),referred as the N-SNP dataset.The third dataset consisted of the chloroplast genome SNPs or C-SNP.Four major lineages,comprising three to 11 species/varieties each,largely consistent with morphological evidence,were recovered across the coalescent nuclear and plastome phylogenies.However,both phylogenies contradicted each other with respect to inter-lineage relationships.Nuclear and chloroplast genome phylogenies contradicted each other in their placements of lineage I and IV.(2)Widespread shared polymorphisms and tests of the non-bifurcating relationship.Non-bifurcating divergence because of introgressive hybridizations between assumed sister taxa and the third one is continuously reported for closely related species in conifers and other plants.We aimed to test the genus Picea non-bifurcating hypothesis between them based on genomic data.Firstly,we used identity-by-descent(IBD)blocks to detect polymorphisms shared between lineages,under the algorithm from BEAGLE.Secondly,basing on the presence of between-lineage IBD blocks,we further tested the possible gene flow between the identified major lineages using the ABBA-BABA approach.Ultimately,we identified numerous polymorphisms shared between both within-lineage species and four major lineages.ABBA-BABA tests rejected the bifurcating divergences between lineages according to phylogenetic relationships from the nuclear genome-scale data and those randomly hypothesis,thus violating the bifurcating divergence model.Gene flow occurred more frequently between lineages distributed in the same continent than in the disjunct continents.To sum up,our results underscore the widespread introgression and non-bifurcating diversification even between deep lineages of conifers.