Elevational patterns of seed plants and the driving mechanisms in the Himalaya.

The Himalaya is an important biodiversity hotspot on earth, which is of great significance to study the elevational gradients in plant diversity and its influencing factors for further revealing the formation of biodiversity and conservation. In this study, we measured the elevational range of 11886 seed plant species and different growth-forms (7918 herbaceous species, 2587 shrub species, and 1388 tree species) in the Himalaya. Using the optimal fitted regression models, we found that species richness and phylogenetic diversity of seed plants in the Himalaya mainly showed unimodal curves with the increases of elevation. The species richness and phylogenetic diversity of all species, trees, shrubs and herbaceous species reached the maximum value at the elevation of about 2000, 1000, 1600 and 3000 m, respectively. The results of partial regression and hierarchical partitioning analysis showed that climate and topography together drove the elevational gradient in plant diversity. Among these, mean annual temperature and annual precipitation contributed greatly to the elevational pattern, while surface area ratio and topographic heterogeneity had little influence. Compared with all species and herbaceous species, the elevational gradients of trees and shrubs plants were affected to a greater extent by the interaction between climate and topography.

Proteome and Interactome Linked to Metabolism, Genetic Information Processing, and Abiotic Stress in Gametophytes of Two Woodferns.

Ferns and lycophytes have received scant molecular attention in comparison to angiosperms. The advent of high-throughput technologies allowed an advance towards a greater knowledge of their elusive genomes. In this work, proteomic analyses of heart-shaped gametophytes of two ferns were performed: the apomictic Dryopteris affinis ssp. affinis and its sexual relative Dryopteris oreades. In total, a set of 218 proteins shared by these two gametophytes were analyzed using the STRING database, and their proteome associated with metabolism, genetic information processing, and responses to abiotic stress is discussed. Specifically, we report proteins involved in the metabolism of carbohydrates, lipids, and nucleotides, the biosynthesis of amino acids and secondary compounds, energy, oxide-reduction, transcription, translation, protein folding, sorting and degradation, and responses to abiotic stresses. The interactome of this set of proteins represents a total network composed of 218 nodes and 1792 interactions, obtained mostly from databases and text mining. The interactions among the identified proteins of the ferns D. affinis and D. oreades, together with the description of their biological functions, might contribute to a better understanding of the function and development of ferns as well as fill knowledge gaps in plant evolution.

Specialized herbivory in fossil leaves reveals convergent origins of nyctinasty.

Plants can move in various complex ways in response to external stimuli.1,2 These mechanisms include responses to environmental triggers, such as tropic responses to light or gravity and nastic responses to humidity or contact.3 Nyctinasty, the movements involving circadian rhythmic folding at night and opening at daytime of plant leaves or leaflets, has attracted the attention of scientists and the public for centuries.4,5 In his canonical work entitled The Power of Movement in Plants, Charles Darwin carried out pioneering observations to document the diverse range of movements in plants.6 His systematic examination of plants showing "sleep [folding] movements of leaves" led him to conclude that the legume family (Fabaceae) includes many more nyctinastic species than all other families combined.3 Darwin also found that a specialized motor organ, the pulvinus, is responsible for most sleep movements of plant leaves, although differential cell division and the hydrolysis of glycosides and phyllanthurinolactone also facilitate nyctinasty in some plants.7,8 However, the origin, evolutionary history, and functional benefits of foliar sleep movements remain ambiguous owing to the lack of fossil evidence for this process. Here, we document the first fossil evidence of foliar nyctinasty based on a symmetrical style of insect feeding damage (Folifenestra symmetrica isp. nov.) in gigantopterid seed-plant leaves from the upper Permian (∼259-252 Ma) of China. The pattern of insect damage indicates that the host leaves were attacked when mature but folded. Our finding reveals that foliar nyctinasty extends back to the late Paleozoic and evolved independently among various plant lineages.

A novel cupulate seed plant, Xadzigacalix quatsinoensis gen. et sp. nov., provides new insight into the Mesozoic radiation of gymnosperms.

PREMISE: Anatomically preserved evidence for a novel clade of gymnosperms emphasizes diversity of seed plants immediately prior to the appearance of angiosperm fossils in the paleontological record. METHODS: Cupulate seeds from the Early Cretaceous Apple Bay locality (Vancouver Island) are described from serial cellulose acetate peels and three-dimensional reconstruction. Phylogenetic context is assessed through the comparative analysis of gymnosperm seed producing fructifications and maximum parsimony analysis of a revised morphological data set for seed plant phylogeny. RESULTS: Xadzigacalix quatsinoensis gen. et sp. nov. is characterized by an orthotropous ovule with an elongated micropyle and complex integument, enclosed within a radial cupule. The micropylar canal is elongated; and the nucellus extends into the micropyle to seal the post pollination ovule. Except at the apex of the micropyle, the seed is completely enclosed by a parenchymatous cupule with ca. 20 axially elongated secretory ducts. The cupulate seed is produced upon a triangular woody stele, consisting of a parenchymatous pith surrounded by radially aligned tracheids. The stele produces three short terete traces that terminate within the base of the cupule as transfusion tissue at the seed chalaza. CONCLUSIONS: Organography, vascularization, nature of the integument and nucellus, and configuration of the micropylar canal distinguish Xadzigacalix quatsinoensis from all other gymnosperm clades. Cladistic analyses suggest the new plant may have affinities with gnetophytes or angiosperms. These results are complemented with a critical re-evaluation of ovulate structures for Mesozoic gymnosperms, providing new insight into plant diversity immediately antecedent to the explosive diversification of flowering plants.

Two new species and a new combination from Zhejiang, East China.

As the supplement of the flora of Zhejiang, East China, two new species were described with illustrations. Cerastiumhuadingense Y.F.Lu, W.Y.Xie & X.F.Jin (Caryophyllaceae) differs from C.qingliangfengicum in having sterile stems absent, leaves sessile, petals slightly longer than sepals, and stamens slightly shorter than sepals. Ixeridiumdimorphifolium Y.L.Xu, Y.F.Lu & X.Cai (Asteraceae) differs from I.beauverdianum in having plant stoloniferous, basal leaves dimorphic, involucre 8‒10 mm long, inner phyllaries 8, and florets 7‒10. Paraphlomissetulosa C.Y.Wu & H.W.Li (Lamiaceae) was reviewed and morphological characters of the corolla and stamens of its type and the specimens collected in the field survey were critically examined. With barbate anthers and strongly divergent anther cells, Paraphlomissetulosa was transferred to Sinopogonanthera, and S.setulosa (C.Y.Wu & H.W.Li) H.W.Zhang & X.F.Jin was consequently combined.

Taxon sampling and alternative hypotheses of relationships in the euphyllophyte plexus that gave rise to seed plants: insights from an Early Devonian radiatopsid.

An abrupt transition in the fossil record separates Early Devonian euphyllophytes with a simple structure from a broad diversity of structurally complex Middle-Late Devonian plants. Morphological evolution and phylogeny across this transition are poorly understood due to incomplete sampling of the fossil record. We document a new Early Devonian radiatopsid and integrate it in analyses addressing euphyllophyte relationships. Anatomically preserved Emsian fossils (402-394 Ma) from the Battery Point Formation (Gaspé, Quebec, Canada) are studied in serial sections. The phylogenetic analysis is based on a matrix of 31 taxa and 50 characters emphasising vegetative morphology (41 discrete, nine continuous). The new plant, Kenrickia bivena gen. et sp. nov., is one of very few structurally complex euphyllophytes documented in the Early Devonian. Inclusion of Kenrickia overturns previously established phylogenetic relationships among Radiatopses, reiterating the need for increased density of Early Devonian taxon sampling. Kenrickia is recovered as the sister lineage to all other radiatopsids, a clade in which paraphyletic Stenokoleales led to a lignophyte clade where archaeopterids and seed plants fall into sister clades. Our results shed light on early euphyllophyte relationships and evolution, indicating early exploration of structural complexity by multiple lineages and reiterating the potential of a single origin of secondary growth in euphyllophytes.

Ancient noeggerathialean reveals the seed plant sister group diversified alongside the primary seed plant radiation.

Noeggerathiales are enigmatic plants that existed during Carboniferous and Permian times, ∼323 to 252 Mya. Although their morphology, diversity, and distribution are well known, their systematic affinity remained enigmatic because their anatomy was unknown. Here, we report from a 298-My-old volcanic ash deposit, an in situ, complete, anatomically preserved noeggerathialean. The plant resolves the group's affinity and places it in a key evolutionary position within the seed plant sister group. Paratingia wuhaia sp. nov. is a small tree producing gymnospermous wood with a crown of pinnate, compound megaphyllous leaves and fertile shoots each with Ω-shaped vascular bundles. The heterosporous (containing both microspores and megaspores), bisporangiate fertile shoots appear cylindrical and cone-like, but their bilateral vasculature demonstrates that they are complex, three-dimensional sporophylls, representing leaf homologs that are unique to Noeggerathiales. The combination of heterospory and gymnospermous wood confirms that Paratingia, and thus the Noeggerathiales, are progymnosperms. Progymnosperms constitute the seed plant stem group, and Paratingia extends their range 60 My, to the end of the Permian. Cladistic analysis resolves the position of the Noeggerathiales as the most derived members of a heterosporous progymnosperm clade that are the seed plant sister group, altering our understanding of the relationships within the seed plant stem lineage and the transition from pteridophytic spore-based reproduction to the seed. Permian Noeggerathiales show that the heterosporous progymnosperm sister group to seed plants diversified alongside the primary radiation of seed plants for ∼110 My, independently evolving sophisticated cone-like fertile organs from modified leaves.

Evolution of stomatal closure to optimize water-use efficiency in response to dehydration in ferns and seed plants.

Plants control water-use efficiency (WUE) by regulating water loss and CO2 diffusion through stomata. Variation in stomatal control has been reported among lineages of vascular plants, thus giving rise to the possibility that different lineages may show distinct WUE dynamics in response to water stress. Here, we compared the response of gas exchange to decreasing leaf water potential among four ferns and nine seed plant species exposed to a gradually intensifying water deficit. The data collected were combined with those from 339 phylogenetically diverse species obtained from previous studies. In well-watered angiosperms, the maximum stomatal conductance was high and greater than that required for maximum WUE, but drought stress caused a rapid reduction in stomatal conductance and an increase in WUE in response to elevated concentrations of abscisic acid. However, in ferns, stomata did not open beyond the optimum point corresponding to maximum WUE and actually exhibited a steady WUE in response to dehydration. Thus, seed plants showed improved photosynthetic WUE under water stress. The ability of seed plants to increase WUE could provide them with an advantage over ferns under drought conditions, thereby presumably increasing their fitness under selection pressure by drought.

Evolution and patterning of the ovule in seed plants.

The ovule and its developmental successor, the seed, together represent a highly characteristic feature of seed plants that has strongly enhanced the reproductive and dispersal potential of this diverse group of taxa. Ovules encompass multiple tissues that perform various roles within a highly constrained space, requiring a complex cascade of genes that generate localized cell proliferation and programmed cell death during different developmental stages. Many heritable morphological differences among lineages reflect relative displacement of these tissues, but others, such as the second (outer) integuments of angiosperms and Gnetales, represent novel and apparently profound and independent innovations. Recent studies, mostly on model taxa, have considerably enhanced our understanding of gene expression in the ovule. However, understanding its evolutionary history requires a comparative and phylogenetic approach that is problematic when comparing extant angiosperms not only with phylogenetically distant extant gymnosperms but also with taxa known only from fossils. This paper reviews ovule characters across a phylogenetically broad range of seed plants in a dynamic developmental context. It discusses both well-established and recent theories of ovule and seed evolution and highlights potential gaps in comparative data that will usefully enhance our understanding of evolutionary transitions and developmental mechanisms.

The Complete Mitogenome of Elymus sibiricus and Insights Into Its Evolutionary Pattern Based on Simple Repeat Sequences of Seed Plant Mitogenomes.

The most intriguing characteristics of plant mitochondrial genomes (mitogenomes) include their high variation in both sequence and structure, the extensive horizontal gene transfer (HGT), and the important role they play in hypoxic adaptation. However, the investigation of the mechanisms of hypoxic adaptation and HGT in plant mitochondria remains challenging due to the limited number of sequenced mitogenomes and non-coding nature of the transferred DNA. In this study, the mitogenome of Elymus sibiricus (Gramineae, Triticeae), a perennial grass species native to the Qinghai-Tibet plateau (QTP), was de novo assembled and compared with the mitogenomes of eight Gramineae species. The unique haplotype composition and higher TE content compared to three other Triticeae species may be attributed to the long-term high-altitude plateau adaptability of E. sibiricus. We aimed to discover the connection between mitogenome simple sequence repeats (SSRs) (mt-SSRs) and HGT. Therefore, we predicted and annotated the mt-SSRs of E. sibiricus along with the sequencing of 87 seed plants. The clustering result based on all of the predicted compound mitogenome SSRs (mt-c-SSRs) revealed an expected synteny within systematic taxa and also inter-taxa. The mt-c-SSRs were annotated to 11 genes, among which "(ATA)3agtcaagtcaag (AAT)3" occurred in the nad5 gene of 8 species. The above-mentioned results further confirmed the HGT of mitogenomes sequences even among distant species from the aspect of mt-c-SSRs. Two genes, nad4 and nad7, possessed a vast number of SSRs in their intron regions across the seed plant mitogenomes. Furthermore, five pairs of SSRs developed from the mitogenome of E. sibiricus could be considered as potential markers to distinguish between the species E. sibiricus and its related sympatric species E. nutans.

Buried deep beyond the veil of extinction: Euphyllophyte relationships at the base of the spermatophyte clade.

PREMISE OF THE STUDY: The deep origin and early evolution of seed plants (spermatophytes) are poorly understood. Starting in the Early Devonian, euphyllophytes diversified rapidly into several groups. Two of these groups, progymnospems and Stenokoleales, along with satellite taxa, have been involved in discussions of seed plant origins. Because these early lineages are extinct, the key to the origin and early evolution of seed plants lies in the fossil record. Decades-long paleobotanical work has produced data on the diversity and anatomy of fossil species, which now provide a foundation for exploring seed plant origins in a phylogenetic context. METHODS: We address phylogenetic relationships between early seed plants, aneurophytalean progymnosperms, Stenokoleales, and several Devonian species of uncertain affinities using parsimony analyses that include 28 anatomically preserved species (the most comprehensive taxon sampling to date) and 49 morphoanatomical characters (including nine continuous characters). KEY RESULTS: Our analyses recover monophyletic seed plants, Stenokoleales, and aneurophytes, with the latter placed as sister to a clade (termed the bilateral clade) that includes the former two. When added in the analysis, continuous characters based on anatomy improve phylogenetic resolution. CONCLUSIONS: Our results support the groups defined by traditional taxonomy, resolve Stenokoleales nested among the lignophytes, and indicate that seed plants may share a closer ancestor with Stenokoleales than with aneurophytes. Additionally, our trees suggest a Givetian minimum age for the seed plant ancestor, a late Emsian minimum age for the Stenokoleales, and early Emsian minimum ages for lignophytes, the bilateral clade, and the aneurophyte ancestor.

Further study of Late Devonian seed plant Cosmosperma polyloba: its reconstruction and evolutionary significance.

BACKGROUND: The earliest seed plants in the Late Devonian (Famennian) are abundant and well known. However, most of them lack information regarding the frond system and reconstruction. Cosmosperma polyloba represents the first Devonian ovule in China and East Asia, and its cupules, isolated synangiate pollen organs and pinnules have been studied in the preceding years. RESULTS: New fossils of Cosmosperma were obtained from the type locality, i.e. the Leigutai Member of the Wutong Formation in Fanwan Village, Changxing County, Zhejiang Province, South China. The collection illustrates stems and fronds extensively covered in prickles, as well as fertile portions including uniovulate cupules and anisotomous branches bearing synangiate pollen organs. The stems are unbranched and bear fronds helically. Fronds are dimorphic, displaying bifurcate and trifurcate types, with the latter possibly connected to fertile rachises terminated by pollen organs. Tertiary and quaternary rachises possessing pinnules are arranged alternately (pinnately). The cupule is uniovulate and the ovule has four linear integumentary lobes fused in basal 1/3. The striations on the stems and rachises may indicate a Sparganum-type cortex. CONCLUSIONS: Cosmosperma further demonstrates diversification of frond branching patterns in the earliest seed plants. The less-fused cupule and integument of this plant are considered primitive among Devonian spermatophytes with uniovulate cupules. We tentatively reconstructed Cosmosperma with an upright, semi-self-supporting habit, and the prickles along stems and frond rachises were interpreted as characteristics facilitating supporting rather than defensive structures.

Latisemenia longshania, gen. et sp. nov., a new Late Devonian seed plant from China.

The earliest known ovules in the Late Devonian (Famennian) are borne terminally on fertile branches and are typically enclosed in a cupule. Among these ovules are some that have terete integumentary lobes with little or no fusion. Here, we report a new taxon, Latisemenia longshania, from the Famennian of South China, which bears cupulate ovules that are terminal as well as opposite on the fertile axis. Each ovule has four broad integumentary lobes, which are extensively fused to each other and also to the nucellus. The cupule is uniovulate, and the five flattened cupule segments of each terminal ovule are elongate cuneate and shorter than the ovule. Associated but not attached pinnules are laminate and Sphenopteris-like, with an entire or lobate margin. Latisemenia is the earliest known plant with ovules borne on the side of the fertile axis and may foreshadow the diverse ovule arrangements found among younger seed plant lineages that emerge in the Carboniferous. Following the telome theory, Latisemenia demonstrates derived features in both ovules and cupules, and the shape and fusion of integumentary lobes suggest effective pollination and protection to the nucellus. Along with other recent discoveries from China, Latisemenia extends the palaeogeographic range of the earliest seed plants.

MADS goes genomic in conifers: towards determining the ancestral set of MADS-box genes in seed plants.

BACKGROUND AND AIMS: MADS-box genes comprise a gene family coding for transcription factors. This gene family expanded greatly during land plant evolution such that the number of MADS-box genes ranges from one or two in green algae to around 100 in angiosperms. Given the crucial functions of MADS-box genes for nearly all aspects of plant development, the expansion of this gene family probably contributed to the increasing complexity of plants. However, the expansion of MADS-box genes during one important step of land plant evolution, namely the origin of seed plants, remains poorly understood due to the previous lack of whole-genome data for gymnosperms. METHODS: The newly available genome sequences of Picea abies, Picea glauca and Pinus taeda were used to identify the complete set of MADS-box genes in these conifers. In addition, MADS-box genes were identified in the growing number of transcriptomes available for gymnosperms. With these datasets, phylogenies were constructed to determine the ancestral set of MADS-box genes of seed plants and to infer the ancestral functions of these genes. KEY RESULTS: Type I MADS-box genes are under-represented in gymnosperms and only a minimum of two Type I MADS-box genes have been present in the most recent common ancestor (MRCA) of seed plants. In contrast, a large number of Type II MADS-box genes were found in gymnosperms. The MRCA of extant seed plants probably possessed at least 11-14 Type II MADS-box genes. In gymnosperms two duplications of Type II MADS-box genes were found, such that the MRCA of extant gymnosperms had at least 14-16 Type II MADS-box genes. CONCLUSIONS: The implied ancestral set of MADS-box genes for seed plants shows simplicity for Type I MADS-box genes and remarkable complexity for Type II MADS-box genes in terms of phylogeny and putative functions. The analysis of transcriptome data reveals that gymnosperm MADS-box genes are expressed in a great variety of tissues, indicating diverse roles of MADS-box genes for the development of gymnosperms. This study is the first that provides a comprehensive overview of MADS-box genes in conifers and thus will provide a framework for future work on MADS-box genes in seed plants.

Pinaceae-like reproductive morphology in Schizolepidopsis canicularis sp. nov. from the Early Cretaceous (Aptian-Albian) of Mongolia.

PREMISE OF THE STUDY: Seed cone scales assigned to the genus Schizolepidopsis are widespread in Late Triassic to Cretaceous Eurasian deposits. They have been linked to the conifer family Pinaceae based on associated vegetative remains, but their exact affinities are uncertain. Recently discovered material from the Early Cretaceous of Mongolia reveals important new information concerning Schizolepidopsis cone scales and seeds, and provides support for a relationship between the genus and extant Pinaceae. METHODS: Specimens were collected from Early Cretaceous (probable Aptian-Albian) lignite deposits in central Mongolia. Lignite samples were disaggregated, cleaned in hydrofluoric acid, and washed in water. Specimens were selected for further study using light and electron microscopy. KEY RESULTS: Schizolepidopsis canicularis seed cones consist of loosely arranged, bilobed ovulate scales subtended by a small bract. A single inverted seed with an elongate micropyle is borne on each lobe of the ovulate scale. Each seed has a wing formed by the separation of the adaxial surface of the ovulate scale. CONCLUSIONS: Schizolepidopsis canicularis produced winged seeds that formed in a manner that is unique to Pinaceae among extant conifers. We do not definitively place this species in Pinaceae pending more complete information concerning its pollen cones and vegetative remains. Nevertheless, this material suggests that Schizolepidopsis may be important for understanding the early evolution of Pinaceae, and may potentially help reconcile the appearance of the family in the fossil record with results based on phylogenetic analyses of molecular data.