Comparative Analysis Of Speciation And Driving Forces Of Pinus Henryi Based Mitochondria And Simplified Genome

Pinus henryi,a rare pinus plant endemic to the Qinba Mountains in China,mainly distributed in Qinling Mountains,Daba Mountains,Wushan Mountains and Wuling Mountains.P.henryi located in the transitional distribution area of Pinus tabuliformis Carr.and Pinus massoniana Lamb.There are still serious differences in the classification status of P.henryi in different studies,and no clear conclusion has been reached so far.This paper analyzes the phylogeny,hybridization,historical dynamics,and ecological differentiation driving force of P.henryi and the other 2 related species.Based on the rich markers of the nuclear genome and the lineage sorting characteristics of the mitochondrial genome,the speciation and the species formation of P.henryi are reproduced.In the process of differentiation,the ecological adaptation model of P.henryi was constructed.(1)Phylogenetic analysis reveals the independent species status of P.henryi and the genetic mixing phenomenon of related species.The analysis based on nuclear genome showed that the individuals of P.henryi clustered well in the results.Which suggested that P.henryi should be classified as an independent species,but the genetic distance between P.henryi and P.tabulaeformis was closer than that of P.massoniana.At the same time,genome mixing from P.tabulaeformis and P.massoniana was detected.The different populations of P.henryi have been traced in the stratification of mitochondrial populations.Two uniparental and one mixed P.henryi intraspecific lineages have been sorted.Meanwhile,the genetic structure showed that the P.henryi populations with complete P.tabulaeformis gene type to transitional form of P.massoniana gene type.(2)Hybridization and gene flow calculations confirmed the paleo-hybridization events and mixed gene flow events during the differentiation of P.henryi,and explained the phenomenon of genetic mixing in phylogeny and population analysis.In the nuclear genome hybridization test result,f3 was negative,and the Z-score was 20.0776.There were hybrid events originating from P.tabulaeformis and P.massoniana.We further determined the approximate time of the hybridization event.Recent gene flow analysis revealed that the main recent gene flow originated from P.tabulaeformis.In the mixed gene flow event,the ancient gene flow event from P.massoniana was successfully detected with the extremely limited variable inheritance of P.henryi drift.The above results mutually confirmed the paleo-hybridization event of P.henryi and the recent gene flow event of P.tabulaeformis.(3)The dynamic analysis of population history repeats the differentiation process from the perspectives of species differentiation time,population size,distribution range,and historical events.P.tabulaeformis and P.massoniana roughly differentiated at 12.78 mys ago,and crossed around 5.15 mys ago,resulting in the original hybrid of P.henryi.After that,a long-term gene return from P.tabulaeformis to P.henryi made the genetic structure of P.henryi continue to change.The effective population size of P.henryi continued to shrink at the same times.Because the P.tabulaeformis population divided by the Qinling Mountains at 0.70 mys ago,the gene flow of the P.tabulaeformis drastically reduced,and finally formed the now severely P.tabulaeformis species,whose distribution range showed a trend of approaching and merging with the P.tabulaeformis.(4)Analysis of niche and driving force a consistent model of species differentiation and ecological adaptation of P.henryi was established from the perspectives of niche,ecological difference factors,differentiation driving force,and adaptability sites.Due to the narrow distribution range of the effective population size among the 19 bioclimatic factors,the average level of most factors is between P.tabulaeformis and P.massoniana,the main peak coincides with the lateral peak of P.massoniana,and the mean value of factors such as BIO2,BIO3 and BIO17 was equal to that of P.massoniana.Bio3,Bio9 and Bio15 were the key climatic factors for the differential distribution of P.henryi.The difference in population allele frequency between P.henryi and P.tabulaeformis was mainly due to migration,diffusion and gene flow events.59.70% of the difference in neutral sites can be explained by migration factors.The interpretation rate of selected sites by different models even reached81.24.%-81.77%.Geographical differences(45.96%)contribute more to gene frequency differences than environmental differences(29.24%).The co-explanatory rate of migration factors and geographical differences factors reached 76.34% in neutral sites,and between64.80% and 90.42% in the selected sites of different models.A total of 8459 possible selected sites were screened,of which 673 sites were related to the environment,and 11 sites were verified in 3 different models.This research restores the differentiation process and ecological driving force of P.henryi.The new theorys of double-wing hybrid model and unequal backcross phenomenon provide a case for the study of species differentiation and the exploration of species adaptation mechanisms.