Evolutionary Genomics Of Hybridization Between Populus Alba And P.tremula

Populus alba and P.tremula are widely distributed in Eurasia,accompanied with the formation of hybrid zones between them.Given their wide distributions and hybridization is common among Populus species,the two species provide an ideal system to study hybrid zones,hybrid incompatibility,genome divergence and gene flow during evolutionary hybridization process.In this study,we collected and sequenced 63 individuals from 13 populations of P.alba,P.tremula and their hybrid offspring P.× canescens in China.Then we downloaded the published genome data for 44 individuals of P.tremula and P.tremuloides that are distributed in Europe and North America,respectively.We combined these publicly available data with our genome dataset to examine the evolutionary processes and hybridization between the two species.The results are summarized as follows.(1)Our population genomic analyses suggested that P.alba diverged first and P.tremuloides is sister to P.tremula.The Chinese populations of P.tremula has the lowest genetic diversity(??=0.0016)and negative values of Tajima's D(-0.61),suggesting that there was a founder effect during its evolutionary history.P.alba showed a high level of inbreeding with the average ROH(Run of Homozygosity)length of 52.47 Mb.Although P.tremula and P.tremuloides share the most recent common ancestor,the largest scale of IBD(Identity by Decent)was found between P.alba and P.tremula,suggesting the widespread gene flow between these two non-sister species.Individuals of P.× canescens were confirmed as hybrids(F1 or backcrosses)between P.alba and P.tremula without independent genetic features.(2)We used PSMC and Fastsimcoal25 software to reconstruct the demographic history of four groups(P.alba,P.tremula in China and Europe,respectively,and P.tremuloides)identified by population structure analyses.The results suggested that P.alba diverged with the common ancestor of P.tremula and P.tremuloides around 6.5 million years ago(Mya),followed by a later divergence betwwen P.tremula and P.tremuloides approximately 1.1 Mya.The interspecific divergence between the two groups of P.tremula populations dated back to 0.9 Mya.We detected a widespread gene flow between P.alba and P.tremula.The gene flow occurred at least two times,which occurred between P.alba and the ancestor of the two groups of P.tremula,and between P.alba and the Chinese P.tremula populations.(3)Based on the genome-wide sequencing and analyses of P.alba,P.tremula and their hybrids P.× canescens,we found that most of the hybrid individuals were F1(5/9),threes as backcrosses with P.alba,and one as backcross with P.tremula.In addition,by investigating the sites that were fixed in either of its parental species and the frequency of these sites in the hybrid offspring,we identified 157 hybrid incompatible candidate sites with 18 non-synonymous mutations located in 11 coding genes.Among them,two genes are associated with the meiosis and the development of the seeds while another two ones are related to innate immune system that may be involved in the hybrid incompatibility caused by the interaction of the alleles in different loci after hybridization.(4)Genome divergence during speciation is a dynamic process,which is affected by various factors,including gene flow.We found that the gene flow between P.alba and P.tremula can significantly reduce the interspecific divergence(FST and DXY),but the recent gene flow between the Chinese P.tremula populations and P.alba did not affect their difference,which may result from reproductive isolation strengthened by selection.In addition,gene flow between the two groups of P.tremula populations reduced their differentiation greatly because of the lack of reproductive barriers.Gene flow occurs in all regions across the genomes,and the FST increased at the regions related to the environmental selection.(5)The specific gene flow regions of P.alba and P.tremula are mainly related to stress resistance,and are significantly enriched in genes such as POD gene family and innate immune response.These genes may help Populus species resist the biotic and abiotic stress.In addition,the direction of gene flow is mostly from P.tremula to P.alba,but the reverse is also existed.These results improve our understanding of how Populus species adapt to the diverse environments.