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.

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.

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.

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.

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.

Evolutionary history shapes variation of wood density of tree species across the world

The effect of evolutionary history on wood density variation may play an important role in shaping variation in wood density,but this has largely not been tested.Using a comprehensive global dataset including 27,297 measurements of wood density from 2621 tree species worldwide,we test the hypothesis that the legacy of evolutionary history plays an important role in driving the variation of wood density among tree species.We assessed phylogenetic signal in different taxonomic(e.g.,angiosperms and gymnosperms)and ecological(e.g.,tropical,temperate,and boreal)groups of tree species,explored the biogeographical and phylogenetic patterns of wood density,and quantified the relative importance of current environmental factors(e.g.,climatic and soil variables)and evolutionary history(i.e.,phylogenetic relatedness among species and lineages)in driving global wood density variation.We found that wood density displayed a significant phylogenetic signal.Wood density differed among different biomes and climatic zones,with higher mean values of wood density in relatively drier regions(highest in subtropical desert).Our study revealed that at a global scale,for angiosperms and gymnosperms combined,phylogeny and species(representing the variance explained by taxonomy and not direct explained by long-term evolution process)explained 84.3%and 7.7%of total wood density variation,respectively,whereas current environment explained 2.7%of total wood density variation when phylogeny and species were taken into account.When angiosperms and gymnosperms were considered separately,the three proportions of explained variation are,respectively,84.2%,7.5%and 6.7%for angiosperms,and 45.7%,21.3%and 18.6%for gymnosperms.Our study shows that evolutionary history outpaced current environmental factors in shaping global variation in wood density.

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.

Climatic correlates of phylogenetic relatedness of woody angiosperms in forest communities along a tropical elevational gradient in South America

Aims This study assesses the relationship between phylogenetic relat-edness of angiosperm tree species and climatic variables in local forests distributed along a tropical elevational gradient in South America.In particular,this paper addresses two questions:Is phylo-genetic relatedness of plant species in communities related to tem-perature variables more strongly than to water variables for tropical elevational gradients?Is phylogenetic relatedness of plant species in communities driven by extreme climatic conditions(e.g.minimum temperature(MT)and water deficit)more strongly than by climatic seasonal variability(e.g.temperature seasonality and precipitation seasonality)?Methods I used a set of 34 angiosperm woody plant assemblages along an elevational gradient in the Andes within less than 5 degrees of the equator.Phylogenetic relatedness was quantified as net relatedness index(NRI)and nearest taxon index(NTI)and was related to major climatic variables.Correlation analysis and structure equation modeling approach were used to assess the relationships between phylogenetic relatedness and climatic variables.Important Findings Phylogenetic relatedness of angiosperm woody species in the local forest communities is more strongly associated with temperature-related variables than with water-related variables,is positively cor-related with mean annual temperature(MAT)and MT,and is related with extreme cold temperature more strongly than with seasonal temperature variability.NTI was related with elevation,MAT and MT more strongly than was NRI.Niche convergence,rather than niche conservatism,has played a primary role in driving community assem-bly in local forests along the tropical elevational gradient examined.Negative correlations of phylogenetic relatedness with elevation and higher correlations of phylogenetic relatedness with elevation and temperature for NTI than for NRI indicate that evolution of cold toler-ance at high elevations in tropical regions primarily occurred at recent(terminal)phylogenetic nodes widely distributed among major clades.

An Early Fossil Flower of Angiosperms From Northeast China

In the last two decades, paleobotanists paid attention to seeking and studying fossils of angiosperm flowers. In particular, the Cretaceous and Tertiary flowers discovered from Sweden and North America are well-preserved, some as three-dimensional charcoal fossils. Such valuable specimens provided more important details of floral structure, insect-and wind-pollination mechanisms of early angiosperms. Based on the

Intercontinental comparison of phylogenetic relatedness in introduced plants at the transition from naturalization to invasion:A case study on the floras of South Africa and China

Invasive species may pose significant threats to biodiversity and ecosystem structure and functioning.The number of introduced species that have become invasive is substantial and is rapidly increasing.Identifying potentially invasive species and preventing their expansion are of critical importance in invasion ecology.Phylogenetic relatedness between invasive and native species has been used in predicting invasion success.Previous studies on the phylogenetic relatedness of plants at the transition from naturalization to invasion have shown mixed results,which may be because different methods were used in different studies.Here,I use the same method to analyze two comprehensive data sets from South Africa and China,using two phylogenetic metrics reflecting deep and shallow evolutionary histories,to address the question whether the probability of becoming invasive is higher for naturalized species distantly related to the native flora.My study suggests that the probability of becoming invasive is higher for naturalized species closely related to the native flora.The finding of my study is consistent with Darwin's preadaptation hypothesis.

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.

Global patterns of taxonomic and phylogenetic diversity of flowering plants: Biodiversity hotspots and coldspots

Species diversity of angiosperms(flowering plants) varies greatly among regions.Geographic patterns of variation in species diversity are shaped by the interplay of ecological and evolutionary processes.Here,using a comprehensive data set for regional angiosperm floras across the world,we show geographic patterns of taxonomic(species) diversity,phylogenetic diversity,phylogenetic dispersion,and phylogenetic deviation(i.e.,phylogenetic diversity after accounting for taxonomic diversity) across the world.Phylogenetic diversity is strongly and positively correlated with taxonomic diversity;as a result,geographic patterns of taxonomic and phylogenetic diversity across the world are highly similar.Areas with high taxonomic and phylogenetic diversity are located in tropical regions whereas areas with low taxonomic and phylogenetic diversity are located in temperate regions,particularly in Eurasia and North America,and in northern Africa.Similarly,phylogenetic dispersion is,in general,higher in tropical regions and lower in temperate regions.However,the geographic pattern of phylogenetic deviation differs substantially from those of taxonomic and phylogenetic diversity and phylogenetic dispersion.As a result,hotspots and coldspots of angiosperm diversity identified based on taxonomic and phylogenetic diversity and phylogenetic dispersion are incongruent with those identified based on phylogenetic deviations.Each of these metrics may be considered when selecting areas to be protected for their biodiversity.

Patterns of phylogenetic relatedness of non-native plants across the introduction-naturalization-invasion continuum in China

Human activities have caused the exchange of species among different parts of the world.When introduced species become naturalized and invasive,they may cause great negative impacts on the environment and human societies,and pose significant threats to biodiversity and ecosystem structure.Knowledge on phylogenetic relatedness between native and non-native species and among non-native species at different stages of species invasion may help for better understanding the drivers of species invasion.Here,I analyze a comprehensive data set including both native and non-native angiosperm species in China to determine phylogenetic relatedness of introduced species across a full invasion continuum(from introduction through naturalization to invasion).This study found that(1) introduced plants are a phylogenetically clustered subset of overall(i.e.native plus non-native) angiosperm flora,(2) naturalized plants are a phylogenetically clustered subset of introduced plants,and(3) invasive plants are a phylogenetically clustered subset of naturalized plants.These patterns hold regardless of spatial scales examined(i.e.national versus provincial scale) and whether basal-or tip-weighted metric of phylogenetic relatedness is considered.These findings are consistent with Darwin's preadaptation hypothesis.

Dramatic impact of metric choice on biogeographical regionalization

For a quantitative biogeographical regionalization,the choice of an appropriate dissimilarity index to measure pairwise distances is crucial.Several different metrics have been used,but there is no specific study to test the impact of metric choice on biogeographical regionalization.We herein applied a hierarchical cluster analysis on the mean nearest taxon distance(MNTD)and the phylogenetic turnover component of the SФrensen dissimilarity index(pβsim)pairwise distances to generate two schemes of phylogenetic regio nalization of the Chinese flora,and then evaluated the effect of metric choice.Floristic regionalization based on MNTD was influenced by richness differences,but regionalization based on pβsim can clearly reflect the evolutionary history of the Chinese flora.We provided a brief description of the five regions identified by pβsim,and the regionalization can help develop strategies to effectively conserve the taxa and floristic regions with different origins and evolutionary histories.

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.

Monocotyledon-like Leaves from the Middle Jurassic of East Siberia(Russia)

Leaf fragments of Herbifolia antiqua A.Frolov et Enushchenko gen.et sp.nov.from the Middle Jurassic(Aalenian)of the Irkutsk Coal Basin(Eastern Siberia,Russia)are reported.The following features are characteristic of H.antiqua gen.et sp.nov.:the presence of leaf sheaths,linear smooth-edged leaves with parallel venation,anastomoses between the veins,anomocytic stomata,rhomb-shaped ordinary epidermal cells.Such a combination of characters is widespread in modern monocotyledonous plants and is absent in fossil and modern cryptogam and gymnosperms.Due to the lack of evidence of an enclosed ovule in H.antiqua gen.et sp.nov.,we attribute it to a typological angiosperm,based on its unique leaf structure characteristic of monocotyledons.The leaf epidermal structure of Herbifolia gen.nov.is most similar to those of modern Asparagales and Liliales.

An edible fruit from the Jurassic of China

Frugivory is an important ecological tie between animals and angiosperms.It plays an important role in the evolution of food webs and energy flow networks in the ecosystem.However,little is known about how old this relationship can be due to lack of relevant fossil evidence.Here,the authors report a fossil fruit,Jurafructus gen.nov.,a putative angiosperm from the Middle-Late Jurassic(>164 Ma)of Daohugou Village,Inner Mongolia,China,which provides the currently earliest evidence of frugivory.The fossil is a more or less three-dimensionally preserved coalified drupe that has been damaged by animals in two different ways.The pericarp,in addition to the seed coat surrounding parenchyma seed contents,is suggestive of an angiospermous affinity,as such a 3+3 structure is distinct from a three-layered seed coat in gymnosperms.The seed possesses a distal micropyle,attached on the base of the pericarp,suggestive of a former orthotropous ovule in the gynoecium.The damaged pericarp of Jurafructus suggests that firugivory can be dated back to the Middle-Late Jurassic.Apparently,the ecological relationship between angiosperms and animals extends deep into the fossil record.

Androecium of Archaefructus,the Late Jurassic Angioperms from Western Liaoning,China

Androecium of the earliest known flowering plant Archaefructus liaoningensis was found from the Upper Jurassic Jianshangou Formation of western Liaoning, China. The androecium consists of numerous stamens bearing in pair on the reproductive axes below conduplicate carpels. The stamens are composed of a short filament and basifixed anther for each. Monosulcate pollen in situ are found from the anthers. The characters of the androecium reveals that Archaefructus are probably protandrous, and the paired stamens and monosulcate pollen appear to indicate that Archaefructus, as primitive angiosperms,might be derived from extinct seed -ferns during the Older Mesozoic. Archaefructus is considered Late Jurassic in age.

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.