Cymbidium(Orchidaceae:Epidendroideae),with around 60 species,is widely-distributed across South-east Asia,providing a nice system for studying the processes that underlie patterns of biodiversity in the region.However,phylogenetic relationships of Cymbidium have not been well resolved,hampering in-vestigations of species diversification and the biogeographical history of this genus.In this study,we construct a plastome phylogeny of 56 Cymbidium species,with four well-resolved major clades,which provides a framework for biogeographical and diversification rate analyses.Molecular dating and biogeographical analyses show that Cymbidium likely originated in the region spanning northern Indo-Burma to the eastern Himalayas during the early Miocene(～21.10 Ma).It then rapidly diversified into four major clades in East Asia within approximately a million years during the middle Miocene.Cymbidium spp.migration to the adjacent regions(Borneo,Philippines,and Sulawesi)primarily occurred during the Pliocene-Pleistocene period.Our analyses indicate that the net diversification rate of Cymbidium has decreased since its origin,and is positively associated with changes in temperature and monsoon in-tensity.Favorable hydrothermal conditions brought by monsoon intensification in the early Miocene possibly contributed to the initial rapid diversification,after which the net diversification rate was reduced with the cooling climate after the middle Miocene.The transition from epiphytic to terrestrial habits may have enabled adaptation to cooler environments and colonization of northern niches,yet without a significant effect on diversification rates.This study provides new insights into how monsoon activity and temperature changes affected the diversification dynamics of plants in Southeast Asia.

Pseudosasa gracilis(Poaceae:Bambusoideae)is a temperate woody bamboo species endemic to South-central China with a narrow distribution.Previous phylogenetic studies revealed an unexpected,iso-lated phylogenetic position of Ps.gracilis.Here we conducted phylogenomic analysis by sampling pop-ulations of Ps.gracilis and its sympatric species Ps.nanunica and Sinosasa polytricha reflecting different genomic signals,by deep genome skimming.Integrating molecular evidence from chloroplast genes and genome-wide SNPs,we deciphered the phylogenetic relationships of Ps.gracilis.Both plastid and nuclear data indicate that Ps.gracilis is more closely related to Sinosasa,which is discordant with the taxonomic treatment.To further explore this molecular-morphological conflict,we screened 411"perfect-copy"syntenic genes to reconstruct phylogenies using both the concatenation and coalescent methods.We observed extensive discordance between gene trees and the putative species tree.A significant hy-bridization event was detected based on 411 genes from the D subgenome,showing Ps.gracilis was a hybrid descendant between Sinosasa longiligulata and Ps.nanunica,with 63.56％and 36.44％inheritance probabilities of each parent.Moreover,introgression events were detected in the C subgenome between Ps.gracilis and S.polytricha in the same distribution region.Our findings suggest that sympatric hy-bridization and introgression play a crucial role in the origin of Ps.gracilis.By providing an empirical example of bamboo of hybrid origin using comprehensive analyses based on genomic data from different inheritance systems and morphological characters,our study represents a step forward in understanding of reticulate evolution of bamboos.

Here,we infer the historical biogeography and evolutionary diversification of the genus Lilium.For this purpose,we used the complete plastomes of 64 currently accepted species in the genus Lilium(14 plastomes were newly sequenced)to recover the phylogenetic backbone of the genus and a time-calibrated phylogenetic framework to estimate biogeographical history scenarios and evolutionary diversification rates of Lilium.Our results suggest that ancient climatic changes and geological tectonic activities jointly shaped the distribution range and drove evolutionary radiation of Lilium,including the Middle Miocene Climate Optimum(MMCO),the late Miocene global cooling,as well as the successive uplift of the Qinghai-Tibet Plateau(QTP)and the strengthening of the monsoon climate in East Asia during the late Miocene and the Pliocene.This case study suggests that the unique geological and cli-matic events in the Neogene of East Asia,in particular the uplift of QTP and the enhancement of monsoonal climate,may have played an essential role in formation of uneven distribution of plant di-versity in the Northern Hemisphere.

为明确国家二级保护植物半枫荷与近缘类群的系统发育关系,分析叶绿体基因的适应性进化.该研究利用22个物种的24条叶绿体基因组序列构建最大似然树和贝叶斯树,探讨半枫荷及其近缘类群的系统发育关系,并通过不同模型检测半枫荷与近缘类群的叶绿体编码基因的变异位点与选择压力间的关系.结果表明:(1)半枫荷叶绿体基因组具有133个基因,包括蛋白质编码基因88个(其中11个具有内含子)、tRNA基因37个、rRNA基因8个.(2)半枫荷及其近缘属蕈树属、枫香树属8个物种的叶绿体基因组在序列长度、基因数量及组成、GC含量等方面相对保守,反向重复区与小单拷贝区边界高度保守.小单拷贝区和大单拷贝区的变异程度较高,而反向重复区的变异程度较低.(3)半枫荷与蕈树属、枫香树属物种聚成蕈树科分支,并可划分为3个亚分支,亚分支间或物种间可能存在杂交或不完全谱系分选.(4)适应性进化结果显示,在不同模型下蕈树科分支的物种在ndhA等叶绿体基因受选择约束(纯化选择),位点模型也检测到10个基因的28个位点P大于0.99,这些编码基因变异可能与蕈树科植物适应性分化有关.该研究结果支持半枫荷隶属于蕈树科,蕈树科内物种的叶绿体基因可能存在适应性进化,这为同名异物类药材的资源保护和民族药的创新研发提供了参考资料.

Creating a multi-gene alignment matrix for phylogenetic analysis using organelle genomes involves aligning single-gene datasets manually,a process that can be time-consuming and prone to errors.The HomBlocks pipeline has been created to eliminate the inaccuracies arising from manual operations.The processing of a large number of sequences,however,remains a time-consuming task.To conquer this challenge,we develop a speedy and efficient method called Organelle Genomes for Phylogenetic Analysis(ORPA).ORPA can quickly generate multiple sequence alignments for whole-genome comparisons by parsing the result files of NCBI BLAST,completing the task just in 1 min.With increasing data volume,the efficiency of ORPA is even more pronounced,over 300 times faster than HomBlocks in aligning 60 high-plant chloroplast genomes.The phylogenetic tree outputs from ORPA are equivalent to HomBlocks,indicating its outstanding efficiency.Due to its speed and accuracy,ORPA can identify species-level evolutionary conflicts,providing valuable insights into evolutionary cognition.

Widespread species that inhabit diverse environments possess large population sizes and exhibit a high capacity for environmental adaptation,thus enabling range expansion.In contrast,narrow-range species are confined to restricted geographical areas and are ecologically adapted to narrow environmental conditions,thus limiting their ability to expand into novel environments.However,the genomic mechanisms underlying the differentiation between closely related species with varying distribution ranges remain poorly understood.The Niviventer niviventer species complex(NNSC),consisting of highly abundant wild rats in Southeast Asia and China,offers an excellent opportunity to investigate these questions due to the presence of both widespread and narrow-range species that are phylogenetically closely related.In the present study,we combined ecological niche modeling with phylogenetic analysis,which suggested that sister species cannot be both widespread and dominant within the same geographical region.Moreover,by assessing heterozygosity,linkage disequilibrium decay,and Tajima's D analysis,we found that widespread species exhibited higher genetic diversity than narrow-range species.In addition,by exploring the"genomic islands of speciation",we identified 13 genes in highly divergent regions that were shared by the two widespread species,distinguishing them from their narrow-range counterparts.Functional annotation analysis indicated that these genes are involved in nervous system development and regulation.The adaptive evolution of these genes likely played an important role in the speciation of these widespread species.

Roscoea is an alpine or subalpine genus from the pan-tropical family Zingiberaceae,which consists of two disjunct groups in geography,namely the"Chinese"clade and the"Himalayan"clade.Despite extensive research on the genus,Roscoea species remain poorly defined and relationships between these species are not well resolved.In this study,we used plastid genomes of nine species and one variety to resolve phylogenetic relationships within the"Chinese"clade of Roscoea and as DNA super barcodes for species discrimination.We found that Roscoea plastid genomes ranged in length from 163,063 to 163,796 bp,and encoded 113 genes,including 79 protein-coding genes,30 tRNA genes,four rRNA genes.In addition,expansion and contraction of the IR regions showed obvious infraspecific conservatism and interspecific differentiation.Plastid phylogenomics revealed that species belonging to the"Chinese"clade of Roscoea can be divided into four distinct subclades.Furthermore,our analysis supported the independence of R.cautleoides var.pubescens,the recovery of Roscoea pubescens Z.Y.Zhu,and a close relationship between R.humeana and R.cautloides.When we used the plastid genome as a super barcode,we found that it possessed strong discriminatory power(90％)with high support values.Intergenic regions provided similar resolution,which was much better than that of protein-coding regions,hypervariable regions,and DNA universal barcodes.However,plastid genomes could not completely resolve Roscoea phylogeny or definitively discriminate species.These limitations are likely related to the complex history of Roscoea speciation,poorly defined species within the genus,and the maternal inheritance of plastid genomes.

Angiosperms dominate the Earth's ecosystems and provide most of the basic necessities for human life.The major angiosperm clades com-prise 64 orders,as recognized by the APG IV classification.However,the phylogenetic rela-tionships of angiosperms remain unclear,as phy-logenetic trees with different topologies have been reconstructed depending on the sequence datasets utilized,from targeted genes to tran-scriptomes.Here,we used currently available de novo genome data to reconstruct the phylogenies of 366 angiosperm species from 241 genera be-longing to 97 families across 43 of the 64 orders based on orthologous genes from the nuclear,plastid,and mitochondrial genomes of the same species with compatible datasets.The phyloge-netic relationships were largely consistent with previously constructed phylogenies based on se-quence variations in each genome type.However,there were major inconsistencies in the phyloge-netic relationships of the five Mesangiospermae lineages when different genomes were examined.We discuss ways to address these incon-sistencies,which could ultimately lead to the re-construction of a comprehensive angiosperm tree of life.The angiosperm phylogenies presented here provide a basic framework for further up-dates and comparisons.These phylogenies can also be used as guides to examine the evolu-tionary trajectories among the three genome types during lineage radiation.

Establishing how lineages with similar traits are phylogenetically related remains critical for un-derstanding the origin of biodiversity on Earth.Floral traits in plants are widely used to explore phylogenetic relationships and to delin-eate taxonomic groups.The subtribe Swertiinae(Gentianaceae)comprises more than 350 species with high floral diversity ranging from rotate to tubular corollas and possessing diverse nec-taries.Here we performed phylogenetic analysis of 60 species from all 15 genera of the subtribe Swertiinae sensu Ho and Liu,representing the range of floral diversity,using data from the nu-clear and plastid genomes.Extensive topological conflicts were present between the nuclear and plastome trees.Three of the 15 genera repre-sented by multiple species are polyphyletic in both trees.Key floral traits including corolla type,absence or presence of lobe scales,nectary type,nectary position,and stigma type are randomly distributed in the nuclear and plastome trees without phylogenetic correlation.We also re-vealed the likely ancient hybrid origin of one large clade comprising 10 genera with diverse floral traits.These results highlight the complex evo-lutionary history of this subtribe.The phylogenies constructed here provide a basic framework for further exploring the ecological and genetic mechanisms underlying both species diversifi-cation and floral diversity.

Gene duplications provide evolutionary potentials for generating novel functions,while polyploidization or whole genome duplication (WGD) doubles the chromosomes initially and results in hundreds to thousands of retained duplicates.WGDs are strongly supported by evidence commonly found in many species-rich lineages of eukaryotes,and thus are considered as a major driving force in species diversification.We performed comparative genomic and phylogenomic analyses of 59 public genomes/transcriptomes and 46 newly sequenced transcriptomes covering major lineages of angiosperms to detect large-scale gene duplication events by surveying tens of thousands of gene family trees.These analyses confirmed most of the previously reported WGDs and provided strong evidence for novel ones in many lineages.The detected WGDs supported a model of exponential gene loss during evolution with an estimated half-life of approximately 21.6 million years,and were correlated with both the emergence of lineages with high degrees of diversification and periods of global climate changes.The new datasets and analyses detected many novel WGDs widely spread during angiosperm evolution,uncovered preferential retention of gene functions in essential cellular metabolisms,and provided clues for the roles of WGD in promoting angiosperm radiation and enhancing their adaptation to environmental changes.