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Genome size variation is of fundamental biological importance and has been a longstanding puzzle in evolutionary biology. Several hypotheses for genome size evolution including neutral, maladaptive, and adaptive models have been proposed, but the relative importance of these models remains controversial. Primulina is a genus that is highly diversified in the Karst region of southern China, where genome size variation and the underlying evolutionary mechanisms are poorly understood. We reconstructed the phylogeny of Primulina using DNA sequences for 104 species and determined the genome sizes of 101 species. We examined the phylogenetic signal in genome size variation, and tested the fit to different evolutionary models and for correlations with variation in latitude and specific leaf area (SLA). The results showed that genome size, SLA and latitudinal variation all displayed strong phylogenetic signals, but were best explained by different evolutionary models. Furthermore, significant positive relationships were detected between genome size and SLA and between genome size and latitude. Our study is the first to investigate genome size evolution on such a comprehensive scale and in the Karst region flora. We conclude that genome size in Primulina is phylogenetically conserved but its variation among species is a combined outcome of both neutral and adaptive evolution.

The flowering plants that dominate modern vegetation possess leaf gas exchange potentials that far exceed those of all other living or extinct plants. The great divide in maximal ability to exchange CO₂ for water between leaves of nonangiosperms and angiosperms forms the mechanistic foundation for speculation about how angiosperms drove sweeping ecological and biogeochemical change during the Cretaceous. However, there is no empirical evidence that angiosperms evolved highly photosynthetically active leaves during the Cretaceous. Using vein density (DV) measurements of fossil angiosperm leaves, we show that the leaf hydraulic capacities of angiosperms escalated several-fold during the Cretaceous. During the first 30 million years of angiosperm leaf evolution, angiosperm leaves exhibited uniformly low vein DV that overlapped the DV range of dominant Early Cretaceous ferns and gymnosperms. Fossil angiosperm vein densities reveal a subsequent biphasic increase in DV. During the first mid-Cretaceous surge, angiosperm DV first surpassed the upper bound of DV limits for nonangiosperms. However, the upper limits of DV typical of modern megathermal rainforest trees first appear during a second wave of increased DV during the Cretaceous-Tertiary transition. Thus, our findings provide fossil evidence for the hypothesis that significant ecosystem change brought about by angiosperms lagged behind the Early Cretaceous taxonomic diversification of angiosperms.

A near-perfect mimetic association between a mecopteran insect species and a ginkgoalean plant species from the late Middle Jurassic of northeastern China recently has been discovered. The association stems from a case of mixed identity between a particular plant and an insect in the laboratory and the field. This confusion is explained as a case of leaf mimesis, wherein the appearance of the multilobed leaf of Yimaia capituliformis (the ginkgoalean model) was accurately replicated by the wings and abdomen of the cimbrophlebiid Juracimbrophlebia ginkgofolia (the hangingfly mimic). Our results suggest that hangingflies developed leaf mimesis either as an antipredator avoidance device or possibly as a predatory strategy to provide an antiherbivore function for its plant hosts, thus gaining mutual benefit for both the hangingfly and the ginkgo species. This documentation of mimesis is a rare occasion whereby exquisitely preserved, co-occurring fossils occupy a narrow spatiotemporal window that reveal likely reciprocal mechanisms which plants and insects provide mutual defensive support during their preangiospermous evolutionary histories.

Many studies have shown that individuals from invasive populations of many different plant species grow larger than individuals from native populations and that this difference has a genetic basis. This increased vigor in invasive populations is thought to be due to life history tradeoffs, in which selection favors the loss of costly defense traits, thereby freeing resources that can be devoted to increased growth or fecundity. Despite the theoretical importance of such allocation shifts for invasions, there have been no efforts to understand apparent evolutionary shifts in defensegrowth allocation mechanistically. Real location of nitrogen (N) to photosynthesis is likely to play a crucial role in any growth increase; however, no study has been conducted to explore potential evolutionary changes in N allocation of introduced plants. Here, we show that introduced Ageratina adenophora. a noxious invasive plant throughout the subtropics, appears to have evolved increased N allocation to photosynthesis (growth) and reduced allocation to cell walls, resulting in poorer structural defenses. Our results provide a potential mechanism behind the commonly observed and genetically based increase in plant growth and vigor when they are introduced to new ranges.

1. Plant diversity loss can alter higher trophic-level communities via non-random species interactions, which in turn may cascade to affect key ecosystem functions. These non-random linkages might be best captured by patterns of phylogenetic diversity, which take into account co-evolutionary dependencies. However, lack of adequate phylogenetic data of higher trophic levels hampers our mechanistic understanding of biodiversity relationships in species-rich ecosystems. 2. We used DNA barcoding to generate data on the phylogenetic diversity of lepidopteran caterpillars in a large-scale forest biodiversity experiment in subtropical China. We analysed how different metrics of lepidopteran phylogenetic diversity (Faith's PD, MPD, MNTD) and taxonomic diversity were influenced by multiple components of tree diversity (taxonomic, functional, phylogenetic). 3. Our data from six sampling periods represent 7,204 mitochondrial cytochrome c oxidase subunit I (COI) sequences of lepidopteran larvae, clustered into 461 molecular operational taxonomic units. Lepidopteran abundance, the effective number of species (irrespective of the focus on rare or common species) and Faith's PD and MPD (reflecting basal evolutionary splits), but not MNTD (reflecting recent evolutionary splits), significantly increased with experimentally manipulated tree species richness. Lepidopteran MNTD decreased with increasing tree MNTD. Path analyses showed that tree phylogenetic and functional diversity explained part, but not all of the effects of tree species richness on lepidopteran diversity. Importantly, tree diversity effects on lepidopteran diversity were to a large extent indirect, operating via changes in lepidopteran abundance. 4. Synthesis. Our study shows that evolutionary dependencies determine the response of herbivore communities to changes in host plant diversity. Incorporating a wider range of diversity metrics both at the level of producers and consumers can thus help to develop a more comprehensive understanding of the functional consequences of biodiversity change across trophic levels. Moreover, the dependence of trophic linkages on herbivore abundances underlines the need to address the consequences of current declines in insect abundances for ecosystem structure and functioning.

Background Members of the plant-specific SPL gene family (squamosa promoter-binding protein -like) contain the SBP conserved domain and are involved in the regulation of plant growth and development, including the development of plant flowers and plant epidermal hair, the plant stress response, and the synthesis of secondary metabolites. This family has been identified in various plants. However, there is no systematic analysis of the SPL gene family at the genome-wide level of wheat. Results In this study, 56 putative TaSPL genes were identified using the comparative genomics method; we renamed them TaSPL001 - TaSPL056 on their chromosomal distribution. According to the un-rooted neighbor joining phylogenetic tree, gene structure and motif analyses, the 56 TaSPL genes were divided into 8 subgroups. A total of 81 TaSPL gene pairs were designated as arising from duplication events and 64 interacting protein branches were identified as involve in the protein interaction network. The expression patterns of 21 randomly selected TaSPL genes in different tissues (roots, stems, leaves and inflorescence) and under 4 treatments (abscisic acid, gibberellin, drought and salt) were detected by quantitative real-time polymerase chain reaction (qRT-PCR). Conclusions The wheat genome contains 56 TaSPL genes and those in same subfamily share similar gene structure and motifs. TaSPL gene expansion occurred through segmental duplication events. Combining the results of transcriptional and qRT-PCR analyses, most of these TaSPL genes were found to regulate inflorescence and spike development. Additionally, we found that 13 TaSPLs were upregulated by abscisic acid, indicating that TaSPL genes play a positive role in the abscisic acid-mediated pathway of the seedling stage. This study provides comprehensive information on the SPL gene family of wheat and lays a solid foundation for elucidating the biological functions of TaSPLs and improvement of wheat yield.

Background Polyploidization and introgression are major events driving plant genome evolution and influencing crop breeding. However, the mechanisms underlying the higher-order chromatin organization of subgenomes and alien chromosomes are largely unknown. Results We probe the three-dimensional chromatin architecture of Aikang 58 (AK58), a widely cultivated allohexaploid wheat variety in China carrying the 1RS/1BL translocation chromosome. The regions involved in inter-chromosomal interactions, both within and between subgenomes, have highly similar sequences. Subgenome-specific territories tend to be connected by subgenome-dominant homologous transposable elements (TEs). The alien 1RS chromosomal arm, which was introgressed from rye and differs from its wheat counterpart, has relatively few inter-chromosome interactions with wheat chromosomes. An analysis of local chromatin structures reveals topologically associating domain (TAD)-like regions covering 52% of the AK58 genome, the boundaries of which are enriched with active genes, zinc-finger factor-binding motifs, CHH methylation, and 24-nt small RNAs. The chromatin loops are mostly localized around TAD boundaries, and the number of gene loops is positively associated with gene activity. Conclusions The present study reveals the impact of the genetic sequence context on the higher-order chromatin structure and subgenome stability in hexaploid wheat. Specifically, we characterized the sequence homology-mediated inter-chromosome interactions and the non-canonical role of subgenome-biased TEs. Our findings may have profound implications for future investigations of the interplay between genetic sequences and higher-order structures and their consequences on polyploid genome evolution and introgression-based breeding of crop plants.

The colonization of terrestrial environments by rooted vascular plants had far-reaching impacts on the Earth system. However, the belowground structures of early vascular plants are rarely documented, and thus the plant–soil interactions in early terrestrial ecosystems are poorly understood. Here we report the earliest rooted paleosols (fossil soils) in Asia from Early Devonian deposits of Yunnan, China. Plant traces are extensive within the soil and occur as complex network-like structures, which are interpreted as representing long-lived, belowground rhizomes of the basal lycopsid Drepanophycus. The rhizomes produced large clones and helped the plant survive frequent sediment burial in well-drained soils within a seasonal wet–dry climate zone. Rhizome networks contributed to the accumulation and pedogenesis of floodplain sediments and increased the soil stabilizing effects of early plants. Predating the appearance of trees with deep roots in the Middle Devonian, plant rhizomes have long functioned in the belowground soil ecosystem. This study presents strong, direct evidence for plant–soil interactions at an early stage of vascular plant radiation. Soil stabilization by complex rhizome systems was apparently widespread, and contributed to landscape modification at an earlier time than had been appreciated.

Summary Sesame (Sesamum indicum L.) is an important oil crop renowned for its high oil content and quality. Recently, genome assemblies for five sesame varieties including two landraces (S. indicum cv. Baizhima and Mishuozhima) and three modern cultivars (S. indicum var. Zhongzhi13, Yuzhi11 and Swetha), have become available providing a rich resource for comparative genomic analyses and gene discovery. Here, we employed a reference‐assisted assembly approach to improve the draft assemblies of four of the sesame varieties. We then constructed a sesame pan‐genome of 554.05 Mb. The pan‐genome contained 26 472 orthologous gene clusters; 15 409 (58.21%) of them were core (present across all five sesame genomes), whereas the remaining 41.79% (11 063) clusters and the 15 890 variety‐specific genes were dispensable. Comparisons between varieties suggest that modern cultivars from China and India display significant genomic variation. The gene families unique to the sesame modern cultivars contain genes mainly related to yield and quality, while those unique to the landraces contain genes involved in environmental adaptation. Comparative evolutionary analysis indicates that several genes involved in plant‐pathogen interaction and lipid metabolism are under positive selection, which may be associated with sesame environmental adaption and selection for high seed oil content. This study of the sesame pan‐genome provides insights into the evolution and genomic characteristics of this important oilseed and constitutes a resource for further sesame crop improvement.