Whole-genome Speciation Of Medicago Archiducis-nicolai And M.ruthenica

Speciation,the fundamental phenomenon underlying biodiversity,continues to be a central focus within evolutionary studies.Over the last two decades,numerous studies have revealed that speciation happens between contacting populations far more frequently than previously thought.Many of these investigations have demonstrated that divergence between closely related species occurred in the presence of gene flow,with hybrids occurred in the contacting regions.Under such circumstances,populations living in their respective local environments experience different selective pressures and are therefore adapted to distinct environments.However,how genomic divergence originates and accumulates in the face of gene flow during ecological adaptation remains poorly understood.Closely related species that have adapted to distinct environments but that also inhabit overlapping ranges are an ideal system to evaluate these key issues.Here,we combine population genomics and species distribution models to examine genomic divergences between two sister plant species,Medicago archiducis-nicolai and M.ruthenica,that occur in northern China and the northeast Qinghai–Tibet Plateau,respectively,with overlapping distributions in the border of the two regions.The main research results and conclusions are summarized as follows:(1)A total of 113 individuals collected from 70 sites(of which 36 individuals from 9 sites were sympatrically distributed)of the two species were sequenced,which generated a total of 570.8 Gb of whole-genome sequencing data.After mapping to the reference genome of M.ruthenica,performing genetic variation detection and filtering.A total of ～5 million high-quality SNPs were obtained for subsequent analysis.(2)Based on the high-quality SNP data set,PCA,genome-wide SNP phylogenetic tree,chloroplast genome phylogenetic tree,and population structure analysis were performed.The results indicated that the two species were genetically well separated,but 10 admixed individuals in the sympatric sites and seven admixed M.archiducis-nicolai individuals found in northern Sichuan province were identified.Further analysis showed that the hybrids in the sympatric sites were produced by recent hybridization,while the hybrids in northern Sichuan were formed from ancient hybridization events.(3)Using species distribution models,the potential distribution areas of these two species were simulated in the present and various historical periods.The results showed that the predicted current distributions of both species are highly consistent with their actual distribution,indicating that the used model had a relatively high degree of accuracy.In the past different historical periods,the distribution range of these two species had changed to some extent compared to the present,but there has always been an area of contacts between the two species.(4)The coalescent simulation models showed that M.archiducis-nicolai and M.ruthenica began to diverge about 1.73 million years ago,accompanied by continuous gene flow during the differentiation process,and the level of gene flow was higher in the recent period.This result is consistent with the species distribution models,in which the two species were not completely geographically isolated in various past periods,which may have maintained the gene flow between the two species.In addition,the divergence time of the two species coincided with the Quaternary period,and the climatic oscillations during the Quaternary have promoted the divergence of the two species.(5)Based on the sliding-window based FST method,590 FST outlier windows were identified between the two genomes,which were further merged into 455 genomic differentiation islands,including 583 genes.These islands were scattered throughout the genome,while some showed local aggregation,and the DXY of the islands was significantly higher than that of the genome background,indicating that the sorting of ancestral polymorphisms and gene flow acted together on the formation of genomic islands.(6)A total of 869 positively selected genes were identified by HKA and XP-CLR,of which 215 were located in genomic islands,accounting for 37% of the number of genes within islands.Functional enrichment and annotation of the detected positively selected genes found that many GO terms related to environmental adaptation,organ development and reproductive isolation were enriched,and the functions of homologous genes of many positive selection genes were related to drought,cold and salt stress response.This result suggests that these selected genes may have enhanced the adaptability of the two species to their respective environments.In summary,these results suggest that past climatic changes may have triggered initial interspecific divergence between M.archiducis-nicolai and M.ruthenica.Despite climatic oscillations during the Quaternary,continuous contact and gene flow between the two species has been maintained since divergence.Both disruptive selection under gene flow and divergent sorting of ancient polymorphisms may have contributed to the generation of genomic islands of divergence.In addition,numerous genes were identified both within and outside genomic islands with positive selection signatures that are likely associated with adaptations to distinct environmental conditions and reproductive isolation.These results reveal that climate fluctuations together with ecological adaptation had promoted and has maintained the interspecific divergence between the two sister species.Given the importance of Mediago as a forage species,these findings provide a genetic basis for de novo domestication of these wild species as well as valuable genetic resources for molecular breeding research on alfalfa.