Global patterns and ecological drivers of taxonomic and phylogenetic endemism in angiosperm genera

Endemism of lineages lies at the core of understanding variation in community composition among geographic regions because it reflects how speciation,extinction,and dispersal have influenced current distributions.Here,we investigated geographic patterns and ecological drivers of taxonomic and phylogenetic endemism of angiosperm genera across the world.We identify centers of paleo-endemism and neo-endemism of angiosperm genera,and show that they are mostly located in the Southern Hemisphere in tropical and subtropical regions,particularly in Asia and Australia.Different categories of phylogenetic endemism centers can be differentiated using current climate conditions.Current climate,historical climate change,and geographic variables together explained~80%of global variation in taxonomic and phylogenetic endemism,while 42-46%,1%,and 15%were independently explained by these three types of variables,respectively.Thus our findings show that past climate change,current climate,and geography act together in shaping endemism,which are consistent with the findings of previous studies that higher temperature and topographic heterogeneity promote endemism.Our study showed that many centers of phylogenetic endemism of angiosperms,including regions in Amazonia,Venezuela,and west-central tropical Africa that have not previously been identified as biodiversity hotspots,are missed by taxon-based measures of endemism,indicating the importance of including evolutionary history in biodiversity assessment.

Geographic patterns of taxonomic and phylogenetic β-diversity of angiosperm genera in regional floras across the world

Beta diversity(β-diversity)is the scalar between local(α)and regional(γ)diversity.Understanding geographic patterns ofβ-diversity is central to ecology,biogeography,and conservation biology.A full understanding of the origin and maintenance of geographic patterns ofβ-diversity requires exploring both taxonomic and phylogeneticβ-diversity,as well as their respective turnover and nestedness components,and exploring phylogenetic p-diversity at different evolutionary depths.In this study,we explore and map geographic patterns ofβ-diversity for angiosperm genera in regional floras across the world.We examine both taxonomic and phylogeneticβ-diversity and their constituent components,and both tip-weighted and basal-weighted phylogeneticβ-diversity,and relate them to latitude.On the one hand,our study found that the global distribution ofβ-diversity is highly heterogeneous.This is the case for both taxonomic and phylogeneticβ-diversity,and for both tip-weighted and basal-weighted phylogeneticβ-diversity.On the other hand,our study found that there are highly consistent geographic patterns among different metrics ofβ-diversity.In most cases,metrics ofβ-diversity are negatively associated with latitude,particularly in the Northern Hemisphere.Different metrics of taxonomicβ-diversity are strongly and positively correlated with their counterparts of phylogeneticβ-diversity.

Xingxueanthus: An Enigmatic Jurassic Seed Plant and Its Implications for the Origin of Angiospermy

The origin of angiosperms has been tantalizing botanists for centuries. Despite the efforts of palaeobotanists, most of the pre-Cretaceous angiosperms are regarded either non-convincing or misdated. The applications of SEM and LM （light microscope） enable us to recognize a coalified fossil plant, Xingxueanthus sinensis gen. et sp. nov., from the Haifanggou Formation （Middle Jurassic, 〉160 Ma） in western Liaoning, China. Xingxueanthus is an ＂inflorescence＂ with more than 20 female units spirally arranged. Each female unit is situated in the axii of a bract. The female unit is composed of an ovule-container and a style-like projection at the top. There is a vertical column bearing several ovules in the ovule-container. The general morphology and the internal structure of Xingxueanthus distinguish itself from any known fossil and extant gymnosperms, and its structures are more comparable to those of angiosperms. Xingxueanthus, if taken as a gymnosperm, would represent a new class, demonstrate an evolutionarily advanced status of ovule-protection in gymnosperms never seen before, and provide new insights into the origin of angiospermy. Alternatively, if taken as an angiosperm, together with Schmeissneria, it would increase the diversity of Jurassic angiosperms, which has been underestimated for a long time, and suggest a much earlier origin of angiospermy than currently accepted.

An Undercover Angiosperm from the Jurassic of China

Searching for early angiosperms is a riveting activity in botany because it helps to resolve the phyiogenetic relationships among seed plants and among angiosperms themselves. One of the challenges for this job is what the target fossils look like. Most possibly early angiosperms may elude our scrutiny with gymnospermous appearances. This possibility becomes a reality in a Jurassic plant, Solaranthus gen. nov, which bears a peltaspermalean appearance and enclosed ovules. According to knowledge available hitherto, the latter feature makes it an angiosperm. However, such a feature is more likely to be eclipsed by its gymnospermous appearance. The early age and unexpected character assemblage of Solaranthus urge for a fresh look on the assumed-simple relationship between angiosperms and gymnosperms. Its resemblance to the order Peltaspermales favors the Mostly Male Theory.

Late Cretaceous Aquatic Angiosperms from Jiayin,Heilongjiang,Northeast China

Three taxa of Late Cretaceous aquatic angiosperms, Queruexia angulata （Lesq.） Krysht., Cobbania corrugata （Lesq.） Stockey et al. and Nelumbites cf. extenuinervis Upchurch et al. from Jiayin of Heilongjiang, NE China, are described in detail. Among them, Cobbania and Nelumbites from the Upper Cretaceous in China are reported for the first time. The aquatic angiosperm assemblage of Queruexia-Cobbania-Nelumbites appears to imply a seasonal, warm and moist environment in the Jiayin area during the Santonian-Campanian time.

A Dichocarpum-like Angiosperm from the Early Cretaceous of China

The Yixian Formation（the Early Cretaceous） of China has yielded a diverse group of early angiosperms, revealing the charm of angiosperms from the formation is far from finishing. Here we report a fossil angiosperm, Nothodichocarpum gen. et sp. nov, with physically connected female parts, male parts, branches, and leaves with pinnate reticulate venation from the Yixian Formation of Liaoning, China. In addition to the previous reports, this report underscores the diversity of angiosperms in the Early Cretaceous Yixian Formation and earlier origin of angiosperms. The morphological variations in the reproductive parts in different stages allow us to infer the development of this early angiosperm. This fossil plant demonstrates a unique character assemblage that sheds new light on the origin and evolution of carpels.

A Whole Plant Herbaceous Angiosperm from the Middle Jurassic of China

In contrast to woody habit with secondary growth, truthful herbaceous habit lacking secondary growth is restricted to angiosperms among seed plants. Although angiosperms might have occurred as early as in the Triassic and herbaceous habit theoretically may have been well adopted by pioneer angiosperms, pre-Cretaceous herbs are missing hitherto, leaving the origin of herbs and evolution of herbaceous angiosperms mysterious. Here we report Juraherba bodae gen. et sp. nov, a whole plant herbaceous angiosperm, from the Middle Jurassic （〉164 Ma） at Daohugou Village, Inner Mongolia, China, a fossil Lagerst^itten that is worldwide famous for various fossil finds. The angiospermous affinity of Juraherba is ensured by its enclosed ovules/seeds. The plant is small but complete, with physically connected hairy root, stem, leaves, and fructifications. The Middle Jurassic age recommends Juraherba as the earliest record of herbaceous seed plants, demanding a refresh look at the evolutionary history of angiosperms.

Mid-Cretaceous Hothouse Climate and the Expansion of Early Angiosperms

The remarkable transition of early angiosperms from a small to a dominant group characterized the terrestrial ecosystem of the Cretaceous. This transition was instigated and promoted by environmental changes. Mid-Cretaceous is characterized by major geological events that affected the global environment. δ^18O, palaeothermometer TEX86, and other climatic indices from marine sediments suggest rapid temperature increase during mid-Cretaceous despite occasional short cooling events. Simultaneously, terrestrial deposits in East Asia changed from coal-bearing to shale, then to red beds and evaporites. Plant assemblages and other paleoclimate indicators point to rapid aridification for midCretaceous terrestrial environments. In addition, the wildfires were frequently spread all over the earth by the numerous charcoal evidence during the Mid-Cretaceous. Thus, we speculate that the seasonally dry and hot conditions of mid-Cretaceous created a fiery hothouse world. Early angiosperms increased in abundance and diversity and evolved from a few aquatic species to terrestrial herbaceous and then to the diversified flora of today. Angiosperms showed rapid physiological evolution in vein density and leaf area that improved photosynthesis and water absorption. These ecophysiological changes made early angiosperms well adapted to the hot and dry environment in mid-Cretaceous. Moreover, these physiological changes facilitated the fire–angiosperm cycles in mid-Cretaceous that likely further stimulated the early angiosperm evolution.

A Novel Angiosperm from the Early Cretaceous and Its Implications for Carpel-Deriving

The Yixian Formation （Lower Cretaceous） of China is famous for its fossils of early angiosperms, and these fossils have shed otherwise unavailable light on the evolution of angiosperms. The seeds in Archaefructus and Nothodichocarpum are inserted along the dorsal of the fruits while those in Sinocarpus are along the ventral of the fruits, suggesting different Bau-plans and pathways deriving the carpels in these plants of the Early Cretaceous. Adding further fossil evidence, here we report a novel fossil angiosperm, Neofructus lingyuanensis gen. et sp. nov, with its seeds inserted on both ventral and dorsal sides of the fruits documented through light microscopic and SEM observations, suggesting a novel way forming gynoecium in the Yixian Formation. These fossil angiosperms indicate that angiosperm gynoecia in the Yixian Formation （the Barremian to Aptian） are derived in obviously different ways, implying an evolutionary scenario for angiosperms quite different from formerly assumed.

A Biased, Misleading Review on Early Angiosperms

A recently published review by Herendeen?et al.?is misleading, self-centered, self-praising, and self-conflicting. They excluded the famous early angiosperm?Archaefructus?from their list of exemplar angiosperms, which contained only fossil plants they published themselves, leaving the impression that they were only authoritative on the origin and early history of angiosperms. Their 57-year-old “No Angiosperms Until the Cretaceous” conception does not reflect the truth about the origin and early history of angiosperms. Reinforcing such vapidly repeated statement does not help resolving any problem in science but leads to no solution for the origin of angiosperms. The authors tried to establish a criterion identifying a fossil angiosperm but their own exemplar angiosperm?Monetianthus?overturns their own criterion. Apparently, such a review does not positively contribute much to science.

Comparative Studies of Tracheary Element Structure of Some Gymnosperms with Angiosperms

Tissues of the pinna and rachis of Cycas diannaensis and pinna, rachis, and root of Cycas taiwaniana, rachis of Cycas szechuanensis, stem of Metasequoia glyptostroboides (Taxodiaceae), stems of Chamaecyparis obtusa (Sieb.et Zucc.) Endl cv. Tetragona (Cupressaceae), and leaves and stems of Michelia alba and Michelia figo and stems of Amygdalus persica (angiosperms) were compared using the scanning electron microscopy. In all species of these gymnosperms, their many tracheary elemnts have perforations in end walls and lateral walls. These structures are the same as vessels of angiosperms;therefore, these tracheary elements are vessel elements. Many types of vessels were found in cycads: pitted vessels in M. glyptostroboides, spiral and pitted vessels in Chamaecyparis obtusa cv. Tetragona. The development and structural characteristics of vessels of cycads, the two other gymnosperms, and the angiosperms were identical. Some characters such as extent of incline of perforation plate in the end wall showed that vessel characters of some angiosperms were more primitive than the cycads or M. glyptostroboides and C. obtusa cv. Tetragona. Many of the vessel elements of the angiosperms were band shaped, without end walls, and had only two lateral walls and other two margins;the end was acuate or with an arc margin;the end of some vessel elements was acute with no perforations, many perforations located only in lateral wall. Such results are rarely reported in previous work. In all species, perforations were seen only in tracheae, and the walls of parenchyma cells only had a thin primary wall and without perforation. Analysis and discussion to the experimental measures which were observed and research of the structure of vessel or tracheid, pointed out that several measures all could be used and the Jeffrey’ method effects were better. Comparing the vessels of cycads, Taxodiaceae and Cupressaceae helps us to understand the mechanism in which these most primitive or more primitive extant gymnosperms were adapted to harsh environments and to understand these species’ evolutionary extent, and has the significance to the studies of plant anatomy, plant systematics and plant evolution.

Origin of Angiosperms and Their Diversification in the Cretaceous

The dominating hypothesis stated that angiosperms originated in the Early Cretaceous, there were no pre-Cretaceous angiosperms, and carpels (the basic units of gynoecium) were derived from former megasporophylls bearing ovules/seeds along their margins through longitudinally folding and enrolling. However, there are increasing evidences of pre-Cretaceous angiosperms, the assumed megasporophyll actually does not exist, and the Cretaceous-only history of angiosperms appears much shorter than suggested by molecular clocks. Here I will integrate new knowledge of living and fossil plants to give a plausible explanation for the origin and early evolution of angiosperms. Several lines of evidence indicate that the ancestor of angiosperms may well have been present in the Triassic. The former gap between angiosperms and gymnosperms is artificial. Some Triassic fossils playing a role intermediate between angiosperms and gymnosperms seem to favor the Unifying Theory.

Nanjinganthus is an angiosperm,isn't it?

Nanjinganthus is an Early Jurassic angiosperm recognized based on the study of over 200 specimens.However,some other authors have misinterpreted these fossils.Here the authors try to remedy the problems,by pointing out the logical pitfalls in these publications and underscoring a long-used,workable criterion for early angiosperms.The paper explains the cons and pros of this criterion,hoping to bring palaeobotany and plant taxonomy back to a consistent and practical track.Nanjinganthus is an angiosperm.

Inference of phylogenetic relationships among key angiosperm lineages using a compatibility method on a molecular data set

Phylogenetic relationships among the five key angiosperm lineages, Ceratophyllum, Chloranthaceae, eudicots, magnoliids, and monocots, have resisted resolution despite several large-scale analyses sampling taxa and characters extensively and using various analytical methods. Meanwhile, compatibility methods, which were explored together with parsimony and likelihood methods during the early development stage of phylogenetics, have been greatly under-appreciated and not been used to analyze the massive amount of sequence data to recon-struct the basal angiosperm phylogeny. In this study, we used a compatibility method on a data set of eight genes (mitochondrial atp1, matR, and nad5, plastid atpB, matK, rbcL, and rpoC2, and nuclear 18S rDNA) gathered in an earlier study. We selected two sets of characters that are compatible with more of the other characters than a random character would be with at probabilities of pM<0.1 and pM<0.5 respectively. The resulting data matrices were subjected to parsimony and likelihood bootstrap analyses. Our unrooted parsimony analyses showed that Cerato-phyllum was immediately related to eudicots, this larger lineage was immediately related to magnoliids, and monocots were closely related to Chloranthaceae. All these relationships received 76%–96% bootstrap support. A likelihood analysis of the 8 gene pM<0.5 compatible site matrix recovered the same topology but with low support. Likelihood analyses of other compatible site matrices produced different topologies that were all weakly sup-ported. The topology reconstructed in the parsimony analyses agrees with the one recovered in the previous study using both parsimony and likelihood methods when no character was eliminated. Parts of this topology have also been recovered in several earlier studies. Hence, this topology plausibly reflects the true relationships among the five key angiosperm lineages.

Nuclear phylogenomics of angiosperms and insights into their relationships and evolution

Angiosperms(flowering plants) are by far the most diverse land plant group with over 300,000 species. The sudden appearance of diverse angiosperms in the fossil record was referred to by Darwin as the “abominable mystery,”hence contributing to the heightened interest in angiosperm evolution. Angiosperms display wide ranges of morphological, physiological,and ecological characters, some of which have probably influenced their species richness. The evolutionary analyses of these characteristics help to address questions of angiosperm diversification and require well resolved phylogeny. Following the great successes of phylogenetic analyses using plastid sequences,dozens to thousands of nuclear genes from next-generation sequencing have been used in angiosperm phylogenomic analyses, providing well resolved phylogenies and new insights into the evolution of angiosperms. In this review we focus on recent nuclear phylogenomic analyses of large angiosperm clades, orders, families,and subdivisions of some families and provide a summarized Nuclear Phylogenetic Tree of Angiosperm Families. The newly established nuclear phylogenetic relationships are highlighted and compared with previous phylogenetic results. The sequenced genomes of Amborella,Nymphaea, Chloranthus, Ceratophyllum, and species of monocots, Magnoliids, and basal eudicots, have facilitated the phylogenomics of relationships among five major angiosperms clades. All but one of the 64 angiosperm orders were included in nuclear phylogenomics with well resolved relationships except the placements of several orders. Most families have been included with robust and highly supported placements, especially for relationships within several large and important orders and families.Additionally, we examine the divergence time estimation and biogeographic analyses of angiosperm on the basis of the nuclear phylogenomic frameworks and discuss the differences compared with previous analyses. Furthermore,we discuss the implications of nuclear phylogenomic analyses on ancestral reconstruction of morphological, physiological, and ecological characters of angiosperm groups, limitations of current nuclear phylogenomic studies, and the taxa that require future attention.

Global multifaceted biodiversity patterns,centers,and conservation needs in angiosperms

The Convention on Biological Diversity seeks to conserve at least 30%of global land and water areas by 2030,which is a challenge but also an opportunity to better preserve biodiversity,including flowering plants(angiosperms).Herein,we compiled a large database on distributions of over 300,000 angiosperm species and the key functional traits of 67,024 species.Using this database,we constructed biodiversity-environment models to predict global patterns of taxonomic,phylogenetic,and functional diversity in terrestrial angiosperms and provide a comprehensive mapping of the three diversity facets.We further evaluated the current protection status of the biodiversity centers of these diversity facets.Our results showed that geographical patterns of the three facets of plant diversity exhibited substantial spatial mismatches and nonoverlapping conservation priorities.Idiosyncratic centers of functional diversity,particularly of herbaceous species,were primarily distributed in temperate regions and under weaker protection compared with other biodiversity centers of taxonomic and phylogenetic facets.Our global assessment of multifaceted biodiversity patterns and centers highlights the insufficiency and unbalanced conservation among the three diversity facets and the two growth forms(woody vs.herbaceous),thus providing directions for guiding the future conservation of global plant diversity.

Angiosperm-wide analysis of fruit and ovary evolution aided by a new nuclear phylogeny supports association of the same ovary type with both dry and fleshy fruits

Fruit functions in seed protection and dispersal and belongs to many dry and fleshy types,yet their evolutionary pattern remains unclear in part due to uncertainties in the phylogenetic relationships among several orders and families.Thus we used nuclear genes of 502 angiosperm species representing 231 families to reconstruct a well supported phylogeny,with resolved relationships for orders and families with previously uncertain placements.Using this phylogeny as a framework,molecular dating supports a Triassic origin of the crown angiosperms,followed by the emergence of most orders in the Jurassic and Cretaceous and their rise to ecological dominance during the Cretaceous Terrestrial Revolution.The robust phylogeny allowed an examination of the evolutionary pattern of fruit and ovary types,revealing a trend of parallel carpel fusions during early diversifications in eudicots,monocots,and magnoliids.Moreover,taxa in the same order or family with the same ovary type can develop either dry or fleshy fruits with strong correlations between specific types of dry and fleshy fruits;such associations of ovary,dry and fleshy fruits define several ovaryfruit"modules"each found in multiple families.One of the frequent modules has an ovary containing multiple ovules,capsules and berries,and another with an ovary having one or two ovules,achenes(or other single-seeded dry fruits)and drupes.This new perspective of relationships among fruit types highlights the closeness of specific dry and fleshy fruit types,such as capsule and berry,that develop from the same ovary type and belong to the same module relative to dry and fleshy fruits of other modules(such as achenes and drupes).Further analyses of gene families containing known genes for ovary and fruit development identified phylogenetic nodes with multiple gene duplications,supporting a possible role of whole-genome duplications,in combination with climate changes and animal behaviors,in angiosperm fruit and ovary diversification.

Genome-scale angiosperm phylogenies based on nuclear,plastome,and mitochondrial datasets

Angiosperms dominate the Earth’s ecosystems and provide most of the basic necessities for human life.The major angiosperm clades comprise 64 orders,as recognized by the APGⅣclassification.However,the phylogenetic relationships of angiosperms remain unclear,as phylogenetic trees with different topologies have been reconstructed depending on the sequence datasets utilized,from targeted genes to transcriptomes.Here,we used currently available de novo genome data to reconstruct the phylogenies of 366 angiosperm species from 241 genera belonging 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 phylogenetic relationships were largely consistent with previously constructed phylogenies based on sequence variations in each genome type.However,there were major inconsistencies in the phylogenetic relationships of the five Mesangiospermae lineages when different genomes were examined.We discuss ways to address these inconsistencies,which could ultimately lead to the reconstruction of a comprehensive angiosperm tree of life.The angiosperm phylogenies presented here provide a basic framework for further updates and comparisons.These phylogenies can also be used as guides to examine the evolutionary trajectories among the three genome types during lineage radiation.

A novel protein domain is important for photosystem Ⅱ complex assembly and photoautotrophic growth in angiosperms

Photosystem Ⅱ(PSⅡ)is a multi-subunit protein complex of the photosynthetic electron transport chain that is vital to photosynthesis.Although the structure,composition,and function of PSⅡ have been extensively studied,its biogenesis mechanism remains less understood.Thylakoid rhodanese-like(TROL)provides an anchor for leaf-type ferredoxin:NADP^(+)oxidoreductase.Here,we report the chacterizaton of a second type of TROL protein,TROL2,encoded by seed plant genomes whose function has not previously been reported.We show that TROL2 is a PSⅡ assembly cofactor with essential roles in the establishment of photoautotrophy.TROL2 contains a 45-amino-acid domain,termed the chlorotic lethal seedling(CLS)domain,that is both necessary and sufficient for TROL2 function in PSⅡ assembly and photoautotrophic growth.Phylogenetic analyses suggest that TROL2 may have arisen from ancestral TROL1 via gene duplication before the emergence of seed plants and acquired the CLS domain via evolution of the sequence encoding its N-terminal portion.We further reveal that TROL2(or CLS)forms an assembly cofactor complex with the intrinsic thylakoid membrane protein LOW PSⅡ ACCUMULATION2 and interacts with small PSⅡ subunits to facilitate PSⅡ complex assembly.Collectively,our study not only shows that TROL2(CLS)is essential for photoautotrophy in angiosperms but also reveals its mechanistic role in PSⅡ complex assembly,shedding light on the molecular and evolutionary mechanisms of photosynthetic complex assemblyin angiosperms.

山西省被子植物5个新记录种

【目的】丰富山西省被子植物种质资源信息,促进中条山生物多样性和森林生态系统研究。【方法】在大量野外植被调查工作基础上,通过标本鉴定、资料查阅和专家咨询,对中条山植物标本、典型特征照片进行整理。【结果】小酸模(Rumex acetosella L.)、伏毛银莲花(Anemone narcissiflora subsp.protracta(Ulbrich) Ziman&Fedoronczuk)、弯曲碎米荠(Cardamine flexuosa With.)、卢氏凤仙花(Impatiens lushiensis Y. L. Chen)、小酸浆(Physalis minima L.)等5种被子植物在山西未有分布记录。【结论】该5种植物隶属于5科5属,为山西省被子植物分布新记录,新记录发现不仅丰富了山西省被子植物种质资源信息,而且对研究中条山生物多样性和森林生态系统具有重要意义。