East Asian wild grapes show a high level of species diversity and have been widely recognized as important germplasm resources of wine, table grapes, and resistance to biotic and abiotic stresses for the grape industry. However, the deeper phylogenetic relationships and drivers of diversification of East Asian Vitis remain poorly understood. Hybridization and introgression events of East Asian Vitis are not well investigated, particularly at the genome-wide scale. The phylogenetic relationships of East Asian Vitis are herein explored using nuclear and plastid genome data based on target enrichment (Hyb-Seq). Seven major clades are recognized for East Asian Vitis based on the nuclear phylogenetic trees, but there is topological incongruence between concatenated and coalescent analyses. Furthermore, significant cytonuclear discordance is observed within East Asian Vitis. Species network analyses identified several hybridization events within East Asian Vitis. These interspecific hybridization events may have caused the topological discordances and relatively low support detected in our analyses. Ecological niche modeling shows that most of the diversification of East Asian Vitis species is driven by temperature and precipitation environmental variables. Sympatric parallel diversifications of major clades also may have facilitated the rich diversity in East Asian Vitis.

Accurate species delimitation is crucial for biodiversity conservation. The Acer series Campestria comprises four species, A. campestre L., A. miyabei Maxim., A. miaotaiense P. C. Tsoong, and A. yangjuechi Fang & P. L. Chiu. To clarify controversies over the taxonomic status of the latter three endangered species, we undertook phylogenomic, morphological, and niche differentiation analyses in series Campestria. Our coalescent species tree of 544 and 77 single-copy nuclear genes supported series Campestria as monophyletic, with A. yangjuechi having the closest relationship with A. miaotaiense. However, in the plastome-derived tree based on 64 protein coding sequences, the four species did not cluster together, and each of them grouped with some other sympatric Acer species. Given this nuclear-cytoplasmic conflict, we hypothesize that A. yangjuechi have been subject to nuclear gene introgression and plastid (pt) capture involving another sympatric maple, that is, A. amplum Rehder. Principal component analysis and machine learning based on morphological data could not separate A. yangjuechi and A. miaotaiense, but they both could be clearly distinguished from A. miyabei. Moreover, the niche overlap tests of the two more widespread species, A. miyabei and A. miaotaiense, showed they clearly occupy distinct niches. Overall, we conclude that A. miyabei and A. miaotaiense are distinct species, while A. yangjuechi (endemic to Mt. Tianmu/East China) should be treated as a subspecies of A. miaotaiense. Our study points out that multiple lines of phylogenomic, morphological, and ecological evidence prove highly useful in species delimitation. Additionally, our results should help to inform conservation measures for endangered species of the genus Acer/series Campestria in East Asia.

The study of genomic structural evolution associated with accelerated evolutionary rates that result in avoidance of meltdown and increase biodiversity is becoming ever more possible as the number of available plastomes increases. To more comprehensively analyze rate heterogeneity among monocots and within Poaceae, we sequenced plastomes from four Poaceae species, combined them with publicly available data from ~200 plastomes, and conducted comparative analyses to quantify the pattern of rate heterogeneity between different lineages, functional groups, and periods of evolutionary time. We compared structural differences across the Poaceae to quantify how changes in plastome size correspond to different genomic subunits and the evolution of IR–SC junction boundaries. The substitution rates among ancestral Poaceae were inferred to be exceptionally rapid compared to other monocots but slowed after divergence into extant lineages, which could not be sufficiently explained by positive selection. As such, rapid rates in the ancestral lineage leading to Poaceae might be more closely linked to large-scale structural changes like the loss of ycf1 and ycf2. The total increase in plastome size across Poaceae was positively correlated with the total length of intergenic spacers, tandem repeats, and dispersed repeats as well as large single copy, and inverted repeats (IRs). The continuous evolution of IR–SC junction boundaries was asynchronous with sizes of total genome and subunits across Poaceae. Future work is needed to better understand what factors in ancestral Poaceae evolved to harness such rapid rates of plastome evolution, avoid a mutational meltdown, and escape the stagnation of strong purifying selection as well as if these factors could be utilized to synthetically control rates.

Tetraploid emmer wheat (Triticum turgidum L., BBAA) is the founder progenitor of bread wheat, providing the valuable genetic resource and gene pool for wheat improvement. However, the evolutionary trajectory of tetraploid wheat, especially the evolutionary fate of different types of genes has not been well studied. In this study, the rate of non-synonymous substitution (d_N) and synonymous substitution (d_S) was calculated by comparing the orthologs between the wild emmer and cultivated durum wheat at the whole genome and subgenome levels to obtain the positively selected genes (PSGs) and negatively selected genes (NSGs). Then, mutation rate, gene length, exon number, GC content, codon bias, and expression level were comprehensively investigated and compared between the PSGs and NSGs. Within both wild emmer and cultivated durum wheat, PSGs between A and B subgenome displayed shorter gene and exon lengths as well as fewer exon numbers compared with NSGs, whereas from wild emmer to cultivated durum wheat, PSGs showed longer gene length and more exon numbers. Furthermore, PSGs displayed much higher expression levels and stronger codon usage bias, but lower genetic diversity compared with NSGs. Finally, two PSGs TdER1-6B, and TdLC7-2A, were found to play the crucial roles in regulating grain width and plant height of tetraploid wheat, respectively. This study systematically investigated the evolutionary, structural, and functional difference between PSGs and NSGs in tetraploid wheat, which will contribute to a better understanding of the selective mode and evolutionary trajectory during wheat domestication and evolution.

Camellia contains tea, oil camellia, and camellias which benefit people globally. Its infrageneric classification is, however, controversial and unstable, and former phylogenetic analyses failed to yield robust and consistent trees. Here, we aimed to reconstruct a robust phylogenetic tree, date all clades and discuss the evolutionary history of Camellia. Emphasizing the taxonomically comprehensive sampling rather than more DNA data, orthologous nuclear RPB2 introns 11–15 and 23, and waxy were sequenced for 99 taxa of Camellia to reconstruct its phylogenetic history. Ten clades are identified in Camellia: Camellia II, Camelliopsis, Corallina, Furfuracea, Heterogenea, Paracamellia, Piquetia, Stereocarpus, Thea and Yellow camellias II. Camellia grijsii and C. shensiensis are not closely related with other oil camellias that form the clade Paracamellia. Sections Camelliopsis and Theopsis together form the clade Camelliopsis, while clade Furfuracea consists of sect. Furfuracea and C. hongkongensis. Camellia connata is separated from C. lanceolata but nested in the clade Heterogenea, and C. longissima is nested in the clade Thea, suggesting a new germplasm for tea breeding. Molecular dating using four fossil calibration points suggests that the crown age of Camellia is 39.5 Ma with clade Corallina probably the earliest infrageneric clade to diversify and the most widespread clade, Paracamellia, the latest. Our findings provide new insights into the phylogenetic relationships, systematics and evolutionary history of Camellia.

Functional traits impact species interactions, community composition, and ecosystem functioning. However, few studies have focused on the diversification and phylogenetic correlation of multiple functional traits over geological time. We conducted phylogenetic comparative analysis for boreal forest understory species in northeast China to examine the diversification and phylogenetic correlation in several functional traits: leaf area (LA), leaf carbon content (LCC), leaf dry matter content (LDMC), leaf nitrogen content (LNC), plant height (PH), and specific leaf area (SLA). Phylogenetic signals showed that there were very low levels of phylogenetic niche conservatism (PNC) in understory leaf-related traits and plant height, suggesting divergence of functional traits for the co-occurring understory species. The disparity through time analyses (DTT) indicated that trait disparities mainly originated during recent divergence events and there were no differences in the observed trait disparities compared with that expected under Brownian motion. Furthermore, we found both positive and negative phylogenetic correlations among the measured functional traits. The very low levels of PNC suggest that these functional traits diverged among co-occurring understory species, and that those species are distantly phylogenetically related. The phylogenetic correlations among traits may be caused by both positively and negatively correlated adaptions that correspond to resource acquisition strategies. This study provides evidence that divergence in functional traits may reflect understory adaptions to boreal conditions.

Determining the mechanisms that drive phenotypic and genetic divergence by species has been a central topic in evolutionary biology for many years. However, the relative contributions of isolation by distance (IBD) and environment factors to species divergence are largely unknown in perennial herbs in East Asia. In this study, we collected population genetic samples of the cold-tolerant perennial herb Notopterygium oviforme R. H. Shan in central China. We integrated the population transcriptomes, whole chloroplast genomes, genotyping-by-sequencing, microsatellite markers, and ecological factors to determine the relative contributions of geography, climate, and soil factors to genetic, chemical, and phenotypic divergence. A clear genetic distinction was identified between the West Qinling and East Qinling Mountains geographical groups of N. oviforme based on various molecular datasets. Interestingly, obvious niche conservation might have been responsible for the similarity of most of the leaf functional traits in the two groups. Multiple matrix regression with randomization analysis showed that the spatial intraspecific divergence pattern was mainly due to IBD rather than isolation by environment. In addition, transcriptomic expression divergence and some ecological factors have played key roles in intraspecific lineage differentiation. Approximate Bayesian Computation showed that both lineages have experienced historical population expansion and recent range contraction. Molecular dating suggested that intraspecific divergence was closely associated with dramatic uplifts of the Qinling Mountains in East Asia. These results demonstrate that geographical, geological, and environmental factors together shaped cryptic intraspecific diversification and shifts in the population dynamics of the perennial cold-tolerant herb N. oviforme.

Southeast China is one of the core areas of the Sino-Japanese floristic region and a hotspot of biodiversity in East Asia. This region has been considered as both a museum and a cradle of woody genera in China. Why a region with highly stable topography and climate could be a cradle of species diversity remains unclear. In this study, the phylogeographic pattern and genetic structure of Wikstroemia monnula, an endemic species to southeast China, were analyzed by sequencing four chloroplast DNA fragments (4679 bp in total) of 836 individuals from 39 populations. Extremely high diversity and endemism of chlorotypes were found. Out of 54 chlorotypes, 51 (94.44%) were private, with genetic diversity index (H_T) near 1 (H_T = 0.992), and 96.51% of the genetic variation occurring among populations, indicating that this species has undergone strong intraspecific differentiation and very limited migration. The correlational analysis showed that the population differentiation of W. monnula was driven not only via isolation by distance (IBD), but more importantly via isolation by environment (IBE). A significant phylogeographic structure was not found (N_ST = 0.979, G_ST = 0.833, P > 0.05); however, the spatial pattern of the sublineages of chlorotypes was largely consistent with the biogeographic boundaries on a smaller scale in the region. These results suggest that habitat heterogeneity in southeast China not only promoted speciation on a long time-scale, but still continues to impact population differentiation in recent times.

Grapevine is one of the most economically important crops in the world. Although long terminal repeat (LTR) retrotransposons are thought to have played an important role in plants, its distribution in grapevine is not clear. Here, we identified genome-wide intact LTR retrotransposons in a total of six high-quality grapevine genomes from Vitis vinifera L., Vitis sylvestris C.C. Gmel., Vitis riparia Michx. and Vitis amurensis Rupr. with an average of 2938 per genome. Among them, the Copia superfamily (particularly for Ale) is a major component of the LTR retrotransposon in grapevine. Insertion time and copy number analysis revealed that the expansion of 70% LTR retrotransposons concentrating on approximately 2.5 Ma was able to drive genome size variation. Phylogenetic tree and syntenic analyses showed that most LTR retrotransposons in these genomes formed and evolved after species divergence. Furthermore, the function and expression of genes inserted by LTR retrotransposons in V. vinifera (Pinot noir) and V. riparia were explored. The length and expression of genes related to starch metabolism and quinone synthesis pathway in Pinot noir and environmental adaptation pathway in V. riparia were significantly affected by LTR retrotransposon insertion. The results improve the understanding of LTR retrotransposons in grapevine genomes and provide insights for its potential contribution to grapevine trait evolution.

Although mechanical isolation mediated by shared pollinators has been considered as a classic model of pollinator-mediated floral isolation in Pedicularis, a superdiverse genus in Hengduan Mountains, southwest China, there has been no empirical study of interspecific pollen flow between closely related species. We examined reproductive barriers at six different stages between Pedicularis cranolopha and Pedicularis tricolor, two sister species. The two sister species were geographically isolated from each other based on our field survey and the records of herbarium specimens. Translocation experiments showed that flowering phenology partly overlapped and bumblebee pollinators did not discriminate between flowers of the two species. Bumblebee interspecific moves could mediate interspecific pollination as traced using fluorescent powder, in which pollen analogs placed on one species were transferred to the stigmas of the other species in experimental plots containing both species. Heterospecific pollen tubes grew in the style as well as conspecific pollen in hand-pollination experiments. Reciprocal hybridization between the two species could produce (partially) viable seeds, suggesting weak post-pollination barriers. Our results showed that geographic isolation was an important barrier of two species, and the total reproductive isolation between two species was incomplete when without geographical isolation. The formation of Big Snow Mountains could introduce an important pre-zygotic reproductive barrier between the two sister species of Pedicularis; such geographical isolation could be responsible for allopatric speciation, giving a clue to understanding the rapid radiation on mountain areas.