Deep evolutionary histories can play an important role in assembling species into communities, but few studies have explored the effects of deep evolutionary histories on species assembly of angiosperms (flowering plants). Here we explore patterns of family divergence and diversification times (stem and crown ages, respectively) and phylogenetic fuses for angiosperm assemblages in 100?×?100?km grid cells across geographic and ecological gradients in China. We found that both family stem and crown ages of angiosperm assemblages are older in southeastern China with warm and humid climates than in northwestern China with cold and dry climates; these patterns are stronger for family stem ages than for family crown ages; families in colder and drier climates are more closely related across the family-level angiosperm phylogeny; and family phylogenetic fuses are, on average, longer for angiosperm assemblages in warm and humid climates than in cold and dry climate. We conclude that the fact that deep evolutionary histories, which were measured as family stem and crown ages and family phylogenetic fuses in this study, have shown strong geographic and ecological patterns suggests that deep evolutionary histories of angiosperms have profound effects on assembling angiosperm species into ecological communities.

Hemiptera is the largest order of non-holometabolous insects. Recent phylogenetic studies have contributed greatly to our understanding of the phylogeny of the group. However, parts of the hemipteran tree remain unclear. In this study, we have sequenced transcriptomes from five sternorrhynchan species, four exemplars from Aphididae, and one from Monophlebidae. The addition of published transcriptome data produced alignments of >105?000 amino acids from 224 hemipteran taxa in 30 superfamilies covering all suborder and infraorder clades. The data confirmed the Sternorrhyncha superfamily relationship of Aleyrodoidea?+?(Psylloidea?+?[Coccoidea?+?Aphidoidea]). In addition, phylogenomic analyses supported a basal split of Sternorrhyncha and the remaining hemipteran lineages. The Fulgoromorpha formed a sister clade to Cicadomorpha, with strong support. Therefore, our results supported the monophyly of Auchenorrhyncha. The Coleorrhyncha was robustly resolved as a sister group of Auchenorrhyncha, contrary to the concept of the Heteropterodea. Within Heteroptera, the Enicocephalomorpha, Dipsocoromorpha, and Gerromorpha were resolved as the earliest branching groups, while the Nepomorpha, Leptopodomorpha, Cimicomorpha, and Pentatomomorpha were the successive sister groups to the remaining clades in the series. The Cimicomorpha and Pentatomomorpha were sister groups that occupied the most apical branches of the heteropteran tree. Although some phylogenetic estimates yielded conflicting hypotheses for superfamily relationships of Cicadomorpha, Four-cluster Likelihood Mapping (FcLM) analyses revealed a greater phylogenetic signal for the relationship of Membracoidea?+?(Cicadoidea?+?Cercopoidea).

Many species of the subfamily Polygonoideae are economically important. However, phylogenetic relationships and taxonomic treatments of these species remain disputed. In this study, we used highly orthologous nuclear genes and plastome sequence variation extracted from transcriptomes from 98 species of 26 genera of Polygonaceae mainly from the subfamily Polygonoideae to construct a robust phylogeny. We discerned six successively diverged and well-defined clades and both nuclear and plastome phylogenies are highly consistent with each other in this subfamily. Phylogenetic relationships between all clades and subclades were well resolved within Polygonoideae. Our analyses revealed that the shrub tribe Atraphaxideae and the herbal genera Polygonum, Persicaria, and Fallopia are polyphyletic. The sampled species of Polygonoideae started to diversify around the Cretaceous/Tertiary boundary (70?Ma) when the global climate exhibited large oscillations. Further origins of more herbal and woody species were found to have clearly increased during later climatic oscillations. We found that woody habits, especially shrubs, originated multiple times from ancestral herbs in this subfamily. Local dry climates may have favored such habit shifts from ancestral herbs. Our results deepen our understanding of evolutionary diversification of Polygonoideae.

The fern family Polypodiaceae, with over 1600 species, is not only one of the most species-rich families of ferns, but also a major contributor to the vascular epiphytic diversity throughout the tropics. Although the vast majority of species belonging to this family prefer to grow as epiphytes, several species colonize successfully rheophytic, lithophytic, and even terrestrial habitats. Here, we explore the hypothesis that non-epiphytic habitat preferences, including terrestrial growth, evolved secondarily with epiphytes being the plesiomorphic habitat preference. The results of phylogenetic analyses, based on dense taxon sampling and four chloroplast DNA regions, were integrated with divergence time estimates and ancestral character state reconstructions to test these predictions. Both fossils and secondary calibration data were incorporated to obtain divergence time estimations. The results support the prediction of multiple transitions from epiphytic/lithophytic to terrestrial/rheophytic habitats occurring mainly in the Microsoreae lineage. The change in niche preferences coincides with niche colonization opportunities created by climatic fluctuations and geographical changes during the Oligocene and Miocene periods.

Medicago is a genus of legumes (Fabaceae) that resemble common clovers with pinnately trifoliate leaves and spirally coiled seed pods, and Medicago sativa is a famous forage crop throughout the world. In this study, we systematically assembled the complete plastid genomes of 18 Medicago species, representing 35 Medicago accessions, whose genome size ranged from ~119 to 125?kb, and identified one novel inverted repeat (IR) in two accessions of Medicago soleirolii (PI537242 and PI537243), albeit of no IRs in the most accessions. We built a phylogenetic tree based on common protein-coding sequences of 55 Medicago accessions in 38 species, which were placed into five clades with a divergence since 9.37 million years ago. Global alignment revealed independent genome evolution events, including eight inversions in nine species and four intron losses (ILs) in 10 species, among which four inversions and two ILs have not been reported previously. Within 109–111 unique genes, ndhA, rpl2, and ycf3 were under positive selection in 54 Medicago accessions. Finally, by aligning chloroplast genes against the nuclear genome assembly of M. sativa cultivar “Zhongmu No.1”, we found that a large number of chloroplast gene fragments were horizontally transferred to nuclear chromosomes in alfalfa, especially on the chr3:47518422–48722257 coordinates of chromosome 3. Our comprehensive exploration of Medicago chloroplast genomes provided insights for the understanding of Medicago diversity and their genomic evolution events.

A significant fraction of higher plants in China are threatened due to dramatic landscape transformation and increasing climate change. However, the conservation effectiveness of threatened higher plants (THPs) and their response to climate change are still underexplored to date. Based on the latest list of THPs in China, we obtained 102?593 occurrence records with latitude and longitude for 3858 THPs. By integrating the distribution patterns of three biodiversity indexes (i.e., species richness, species complementarity, and weighted endemism) and 10 plant categories, we identified hotspots for THPs and calculated the conservation effectiveness of nature reserves. We then selected 1959 THPs to project the shift of species richness and range sizes under climate change (representative concentration pathway [RCP] 2.6 and RCP 8.5). In total, 16 hotspot areas covering 7.38% of Chinese land area and containing 91.73% of THPs were identified. Current nature reserves protected 35.05% of hotspots, 73.07% of all THPs, and 56.64% of narrow-ranged species. By the 2070s, the species richness of THPs were predicted to decrease in Southeast and Central China, and 42.42% (RCP 2.6) and 51.40% (RCP 8.5) of the 1959 THPs would confront habitat contraction. Future conservation efforts should focus on the conservation gaps and carry out targeted conservation for THPs with narrow distribution range. In order to cope with climate change, the hotspots with relatively low species loss can serve as important areas to contain current species diversity and the areas with high species gain offer opportunities for ex-situ conservation of THPs.

Diversification rates are critically important for understanding patterns of species richness among clades. However, the effects of climatic niche width on plant diversification rates remain to be elucidated. Based on the phylogenetic, climatic, and distributional information of angiosperms in China, a total of 26?906 species from 182 families were included in this study. We aimed to test relationships between diversification rate and climatic niche width and climatic niche width related variables (including climatic niche divergence, climatic niche position, geographic extent, and climatic niche evolutionary rate) using phylogenetic methods. We found that climatic niche divergence had the largest unique contribution to the diversification rate, while the unique effects of climatic niche width, climatic niche position, geographic extent, and climatic niche evolutionary rate on the diversification rate were negligible. We also observed that the relationship between diversification rate and climatic niche divergence was significantly stronger than the null assumption (artefactual relationship between diversification and clade-level climatic niche width by sampling more species). Our study supports the hypothesis that wider family climatic niche widths explain faster diversification rates through a higher climatic niche divergence rather than through higher geographic extent, higher climatic niche evolutionary rate, or separated climatic niche position. Hence, the results provide a potential explanation for large-scale diversity patterns within families of plants.

Over-harvesting, habitat loss and fragmentation, and biological invasions have led to a sharp decline in wild medicinal plants population in China, where they are an essential component of traditional medicine and used widely. The current national list of protected medicinal materials, the State Key-protected Wild Medicinal Species List (SKPWMSL), which has not been revised for 30 years, is in urgent need of an update. This study proposes a new scoring system with seven indicators that set the conservation priorities of threatened medicinal plants. The advantages of our approach include: (i) quantitative methods with high repeatability and comparability; and (ii) consideration of the evolutionary history of medicinal species. After assessing 911 threatened medicinal angiosperms in China, we identified 112 species as key medicinal plants for conservation priority (KMPCP). We suggest promoting the SKPWMSL with KMPCP as a supplement and update. Meanwhile, our scoring system will improve the future setting of conservation priority and can be extended to other countries or regions.

Bats provide an excellent casestudy for studying evolution due to their remarkable flight and echolocation capabilities. In this study, we sought to understand the phenotypic evolution of key traits in Rhinolophidae (horseshoe bats) using phylogenetic comparative methods. We aimed to test the phylogenetic signals of traits, and evaluated the best-fit evolutionary models given the data for each trait considering different traits may evolve under different models (i.e., Brownian Motion [BM], Ornstein-Uhlenbeck [OU], and Early Burst [EB]) and reconstruct ancestral character states. We examined how phenotypic characters are associated with echolocation calls and minimum detectable prey size. We measured 34 traits of 10 Asian rhinolophids species (187 individuals). We found that the majority of traits showed a high phylogenetic signal based on Blomberg′s K and Pagel′s λ, but each trait may evolve under different evolutionary models. Sella traits were shown to evolve under stabilizing selection based on OU models, indicating sella traits have the tendency to move forward along the branches toward some medial value in equilibrium. Our findings highlight the importance of sella characters in association with echolocation call emissions in Rhinolophidae, as calls are important for spatial cognition and also influence dietary preferences. Minimum detectable prey size in Rhinolophidae was associated with call frequency, bandwidth, call duration, wingspan, and wing surface area. Ultimately, understanding trait evolution requires sensitivity due to the differential selective pressures which may apply to different characteristics.