Fossils and plant phylogeny

Botany and geogenomics: Constraining geological hypotheses in the neotropics with large-scale genetic data derived from plants

Decades of empirical research have revealed how the geological history of our planet shaped plant evolution by establishing well-known patterns (e.g., how mountain uplift resulted in high rates of diversification and replicate radiations in montane plant taxa). This follows a traditional approach where botanical data are interpreted in light of geological events. In this synthesis, I instead describe how by integrating natural history, phylogenetics, and population genetics, botanical research can be applied alongside geology and paleontology to inform our understanding of past geological and climatic processes. This conceptual shift aligns with the goals of the emerging field of geogenomics. In the neotropics, plant geogenomics is a powerful tool for the reciprocal exploration of two long standing questions in biology and geology: how the dynamic landscape of the region came to be and how it shaped the evolution of the richest flora. Current challenges that are specific to analytical approaches for plant geogenomics are discussed. I describe the scale at which various geological questions can be addressed from biological data and what makes some groups of plants excellent model systems for geogenomics research. Although plant geogenomics is discussed with reference to the neotropics, the recommendations given here for approaches to plant geogenomics can and should be expanded to exploring long-standing questions on how the earth evolved with the use of plant DNA.

Quantifying the effects of exceptional fossil preservation on the global availability of phylogenetic data in deep time

Fossil deposits with exceptional preservation ("lagerstätten") provide important details not typically preserved in the fossil record, such that they hold an outsized influence on our understanding of biodiversity and evolution. In particular, the potential bias imparted by this so-called "lagerstätten effect" remains a critical, but underexplored aspect of reconstructing evolutionary relationships. Here, we quantify the amount of phylogenetic information available in the global fossil records of 1,327 species of non-avian theropod dinosaurs, Mesozoic birds, and fossil squamates (e.g., lizards, snakes, mosasaurs), and then compare the influence of lagerstätten deposits on phylogenetic information content and taxon selection in phylogenetic analyses to other fossil-bearing deposits. We find that groups that preserve a high amount of phylogenetic information in their global fossil record (e.g., non-avian theropods) are less vulnerable to a "lagerstätten effect" that leads to disproportionate representation of fossil taxa from one geologic unit in an evolutionary tree. Additionally, for each taxonomic group, we find comparable amounts of phylogenetic information in lagerstätten deposits, even though corresponding morphological character datasets vary greatly. Finally, we unexpectedly find that ancient sand dune deposits of the Late Cretaceous Gobi Desert of Mongolia and China exert an anomalously large influence on the phylogenetic information available in the squamate fossil record, suggesting a "lagerstätten effect" can be present in units not traditionally considered lagerstätten. These results offer a phylogenetics-based lens through which to examine the effects of exceptional fossil preservation on biological patterns through time and space, and invites further quantification of evolutionary information in the rock record.

The role of paleontological data in bryophyte systematics

Systematics reconstructs tempo and mode in biological evolution by resolving the phylogenetic fabric of biodiversity. The staggering duration and complexity of evolution, coupled with loss of information (extinction), render exhaustive reconstruction of the evolutionary history of life unattainable. Instead, we sample its products-phenotypes and genotypes-to generate phylogenetic hypotheses, which we sequentially reassess and update against new data. Current consensus in evolutionary biology emphasizes fossil integration in total-evidence analyses, requiring in-depth understanding of fossils-age, phenotypes, and systematic affinities-and a detailed morphological framework uniting fossil and extant taxa. Bryophytes present a special case: deep evolutionary history but sparse fossil record and phenotypic diversity encompassing small dimensional scales. We review how these peculiarities shape fossil inclusion in bryophyte systematics. Paucity of the bryophyte fossil record, driven primarily by phenotypic (small plant size) and ecological constraints (patchy substrate-hugging populations), and incomplete exploration, results in many morphologically isolated, taxonomically ambiguous fossil taxa. Nevertheless, instances of exquisite preservation and pioneering studies demonstrate the feasibility of including bryophyte fossils in evolutionary inference. Further progress will arise from developing extensive morphological matrices for bryophytes, continued exploration of the fossil record, re-evaluation of previously described fossils, and training specialists in identification and characterization of bryophyte fossils, and in bryophyte morphology.

Decoding family-level features for modern and fossil leaves from computer-vision heat maps

PREMISE

Angiosperm leaves present a classic identification problem due to their morphological complexity. Computer-vision algorithms can identify diagnostic regions in images, and heat map outputs illustrate those regions for identification, providing novel insights through visual feedback. We investigate the potential of analyzing leaf heat maps to reveal novel, human-friendly botanical information with applications for extant- and fossil-leaf identification.

METHODS

We developed a manual scoring system for hotspot locations on published computer-vision heat maps of cleared leaves that showed diagnostic regions for family identification. Heat maps of 3114 cleared leaves of 930 genera in 14 angiosperm families were analyzed. The top-5 and top-1 hotspot regions of highest diagnostic value were scored for 21 leaf locations. The resulting data were viewed using box plots and analyzed using cluster and principal component analyses. We manually identified similar features in fossil leaves to informally demonstrate potential fossil applications.

RESULTS

The method successfully mapped machine strategy using standard botanical language, and distinctive patterns emerged for each family. Hotspots were concentrated on secondary veins (Salicaceae, Myrtaceae, Anacardiaceae), tooth apices (Betulaceae, Rosaceae), and on the little-studied margins of untoothed leaves (Rubiaceae, Annonaceae, Ericaceae). Similar features drove the results from multivariate analyses. The results echo many traditional observations, while also showing that most diagnostic leaf features remain undescribed.

CONCLUSIONS

Machine-derived heat maps that initially appear to be dominated by noise can be translated into human-interpretable knowledge, highlighting paths forward for botanists and paleobotanists to discover new diagnostic botanical characters.

Pollination features and floral volatiles of Gymnospermium scipetarum (Berberidaceae)

The discovery of few isolated populations of Gymnospermium scipetarum (since now considered as an amphi-Adriatic endemic) in the S-Apennines prompted to investigate, also for conservation purposes, some aspects of its reproductive biology. We aim: (1) to determine if insects play an important role in pollination; (2) to describe the pollinator community; (3) to detect floral scent composition. Experiments of insect exclusion were carried out in the field using 24 flowering individuals: one raceme was capped whereas the nearest one was used as control to ascertain differences in seed set. Pollinator community was detected during the blooming phase of two consecutive flowering seasons by visual observation; insect identification was made at the highest possible taxonomic resolution with the help of digital photographs. In order to determine the chemical composition of the volatiles, we used SPME sampling of cultivated plants. Mann-Whitney U test reveals significant differences for treatment in mean seed set with very low values for capped flowers, thus clearly indicating as insects are crucial for successful pollination. During the 42 h of observations we detected 326 visitors belonging to only three guilds: 79% were Diptera, 20% Hymenoptera and 1% Coleoptera. We identified overall 36 floral organic compounds with only two compounds common to the other studied Berberidaceae. Ambrox was never identified before in the floral scents of any angiosperm. The presence in the scent of several aldehydes and one ketone (benzophenone) could be related to the detected dominance of muscoid flies as pollinators. Floral morphology and composition of the pollinators community indicate a generalist pollination behaviour probably related to its phenology and habitat preference. The possibility of being pollinated also by muscoid flies can be considered an advantage for the reproductive fitness of the species, since these Diptera are abundant in the mountain pastures surrounding the forest habitat of Gymnospermium.

Origin, evolution, and divergence of plant class C GH9 endoglucanases

BACKGROUND

Glycoside hydrolases of the GH9 family encode cellulases that predominantly function as endoglucanases and have wide applications in the food, paper, pharmaceutical, and biofuel industries. The partitioning of plant GH9 endoglucanases, into classes A, B, and C, is based on the differential presence of transmembrane, signal peptide, and the carbohydrate binding module (CBM49). There is considerable debate on the distribution and the functions of these enzymes which may vary in different organisms. In light of these findings we examined the origin, emergence, and subsequent divergence of plant GH9 endoglucanases, with an emphasis on elucidating the role of CBM49 in the digestion of crystalline cellulose by class C members.

RESULTS

Since, the digestion of crystalline cellulose mandates the presence of a well-defined set of aromatic and polar amino acids and/or an attributable domain that can mediate this conversion, we hypothesize a vertical mode of transfer of genes that could favour the emergence of class C like GH9 endoglucanase activity in land plants from potentially ancestral non plant taxa. We demonstrated the concomitant occurrence of a GH9 domain with CBM49 and other homologous carbohydrate binding modules, in putative endoglucanase sequences from several non-plant taxa. In the absence of comparable full length CBMs, we have characterized several low strength patterns that could approximate the CBM49, thereby, extending support for digestion of crystalline cellulose to other segments of the protein. We also provide data suggestive of the ancestral role of putative class C GH9 endoglucanases in land plants, which includes detailed phylogenetics and the presence and subsequent loss of CBM49, transmembrane, and signal peptide regions in certain populations of early land plants. These findings suggest that classes A and B of modern vascular land plants may have emerged by diverging directly from CBM49 encompassing putative class C enzymes.

CONCLUSION

Our detailed phylogenetic and bioinformatics analysis of putative GH9 endoglucanase sequences across major taxa suggests that plant class C enzymes, despite their recent discovery, could function as the last common ancestor of classes A and B. Additionally, research into their ability to digest or inter-convert crystalline and amorphous forms of cellulose could make them lucrative candidates for engineering biofuel feedstock.

Evolutionary history of the cobalamin-independent methionine synthase gene family across the land plants

Plants are successful paleopolyploids. The wide diversity of land plants is driven strongly by their gene duplicates undergoing distinct evolutionary fates after duplication. We used genomic resources from 35 model plant species to unravel the evolutionary fate of gene copies (paralogs) of the cobalamin-independent methionine synthase (metE) gene family across the land plants. To explore genealogical relationships and characterize positive selection as a driving force in the evolution of metE paralogs within a single species, we carried out complementary analyses on genomic data of 32 genotypes of soybean. The size of the metE gene family remained small across the land plants; most of the studied species possessed 1-6 paralogs. Gene products were either cytosolic or chloroplastic; this dual subcellular distribution arose early during the divergence of the land plants and reached all extant lineages. Biased gene loss and gene retention events took place multiple times; recurrent evolution remodeled redundant metE paralogs to recover and maintain the dual subcellular distribution of MetE. Shared whole-genome duplication events gave rise to the metE paralogs of both soybean and Medicago truncatula. In soybean, the ancestral paralog pair GlymaPP2A encoded a cytosolic isoform of MetE, was under strong purifying selection, and retained high levels of expression across eight RNA-seq expression libraries. The daughters GlymaPP1 and GlymaPP2B showed accelerated rates of evolution, accumulated many sites predicted to be under positive selection, and possessed low levels of expression. Our results suggest that the metE paralogs of soybean follow Ohno's neofunctionalization model of gene duplicate evolution.

Fossil record of Ephedra in the Lower Cretaceous (Aptian), Argentina

Fossil plants from the Lower Cretaceous (upper Aptian) of the La Cantera Formation, Argentina, are described. The fossils studied represent a leafy shooting system with several orders of articulated and striated axes and attached leaves with unequivocal ephedroid affinity. We also found associated remains of ovulate cones with four whorls of sterile bracts, which contain two female reproductive units (FRU). Ovulate cone characters fit well within the genus Ephedra. Special characters in the ovulate cones including an outer seed envelope with two types of trichomes, allowed us to consider our remains as a new Ephedra species. Abundant dispersed ephedroid pollen obtained from the macrofossil-bearing strata also confirms the abundance of Ephedraceae in the basin. The co-occurrence of abundant fossil of Ephedra (adapted to dry habitats) associated with thermophilic cheirolepideacean conifer pollen (Classopollis) in the unit would suggest marked seasonality at the locality during the Early Cretaceous. Furthermore, the floristic association is linked to dry sensitive rocks in the entire section. The macro- and microflora from San Luis Basin are similar in composition to several Early Cretaceous floras from the Northern Gondwana floristic province, but it may represent one of the southernmost records of an arid biome in South America.

A tree of life based on ninety-eight expressed genes conserved across diverse eukaryotic species

Rapid advances in DNA sequencing technologies have resulted in the accumulation of large data sets in the public domain, facilitating comparative studies to provide novel insights into the evolution of life. Phylogenetic studies across the eukaryotic taxa have been reported but on the basis of a limited number of genes. Here we present a genome-wide analysis across different plant, fungal, protist, and animal species, with reference to the 36,002 expressed genes of the rice genome. Our analysis revealed 9831 genes unique to rice and 98 genes conserved across all 49 eukaryotic species analysed. The 98 genes conserved across diverse eukaryotes mostly exhibited binding and catalytic activities and shared common sequence motifs; and hence appeared to have a common origin. The 98 conserved genes belonged to 22 functional gene families including 26S protease, actin, ADP–ribosylation factor, ATP synthase, casein kinase, DEAD-box protein, DnaK, elongation factor 2, glyceraldehyde 3-phosphate, phosphatase 2A, ras-related protein, Ser/Thr protein phosphatase family protein, tubulin, ubiquitin and others. The consensus Bayesian eukaryotic tree of life developed in this study demonstrated widely separated clades of plants, fungi, and animals. Musa acuminata provided an evolutionary link between monocotyledons and dicotyledons, and Salpingoeca rosetta provided an evolutionary link between fungi and animals, which indicating that protozoan species are close relatives of fungi and animals. The divergence times for 1176 species pairs were estimated accurately by integrating fossil information with synonymous substitution rates in the comprehensive set of 98 genes. The present study provides valuable insight into the evolution of eukaryotes.

Two early eudicot fossil flowers from the Kamikitaba assemblage (Coniacian, Late Cretaceous) in northeastern Japan

Two new fossil taxa referable to the basal eudicot grade are described from the Kamikitaba locality (ca. 89 MYBP, early Coniacian: Late Cretaceous) of the Futaba Group in Japan. These charcoalified mesofossils exhibit well-preserved three-dimensional structure and were analyzed using synchrotron-radiation X-ray microtomography to document their composition and internal structure. Cathiaria japonica sp. nov. is represented by infructescence segments that consist of an axis bearing three to four fruits. The capsular fruits are sessile and dehiscent and consist of a gynoecium subtended by a bract. No perianth parts are present. The gynoecium is monocarpellate containing two pendulous seeds. The carpel is ascidiate in the lower half and conduplicate in the upper part, and the style is deflected abaxially with a large, obliquely decurrent stigma. Pollen grains are tricolpate with a reticulate exine. The morphological features of Cathiaria are consistent with an assignment to the Buxaceae s. l. (including Didymelaceae). Archaestella verticillatus gen. et sp. nov. is represented by flowers that are small, actinomorphic, pedicellate, bisexual, semi-inferior, and multicarpellate. The floral receptacle is cup shaped with a perigynous perianth consisting of several tepals inserted around the rim. The gynoecium consists of a whorl of ten conduplicate, laterally connate but distally distinct carpels with a conspicuous dorsal bulge, including a central cavity. The styles are short, becoming recurved with a ventrally decurrent stigma. Seeds are ca. 10 per carpel, marginal, pendulous from the broad, oblique summit of the locule. Pollen grains are tricolpate with a reticulate exine pattern, suggesting a relationship to eudicots. The morphological features of Archaestella indicate a possible relationship to Trochodendraceae in the basal grade of eudicots. The fossil currently provides the earliest record of the family and documents the presence of Trochodendraceae in eastern Eurasia during the middle part of the Late Cretaceous.

Yuhania: a unique angiosperm from the Middle Jurassic of Inner Mongolia, China

Despite increasing claims of pre-Cretaceous angiosperms, whether there really are angiosperms in the Jurassic is apparently still an open question for many people before further evidence is available. This question can only be answered by studying more Jurassic plant fossils. Here we report a fossil angiosperm, Yuhania daohugouensis gen. et sp. nov, from the Middle Jurassic of Inner Mongolia, China. The plant includes connected stem, leaves, flowers, aggregate fruits, fruitlets, and seeds within fruitlets. The leaves are helically arranged along the curving stem, linear in shape, with 5-6 parallel veins. The aggregate fruit is pedicellate, composed of over 20 carpels/fruitlets helically arranged. Each fruitlet encloses a seed. The reproductive organs in various stages are found in the same plant, allowing us to understand the development of Yuhania. The occurrence of Yuhania in the Middle Jurassic re-confirms the Jurassic history for angiosperms that has been suggested by other independent research and adds to the on-going study on the early evolution of angiosperms.

Diversification of C(4) grasses (Poaceae) does not coincide with their ecological dominance

PREMISE OF THE STUDY

The radiation of a lineage and its rise to ecological dominance are distinct phenomena and driven by different processes. For example, paleoecological data has been used to show that the Cretaceous angiosperm radiation did not coincide with their rise to dominance. Using a phylogenetic approach, we here explored the evolution of C4 grasses and evaluated whether the diversification of this group and its rise to ecological dominance in the late Miocene were decoupled.

METHODS

We assembled a matrix including 675 grass species of the PACMAD clade and 2784 characters (ITS and ndhF) to run a molecular dating analysis using three fossils as reference calibrations. We coded species as C3 vs. C4 and reconstructed ancestral states under maximum likelihood. We used the program BiSSE to test whether rates of diversification are correlated with photosynthetic pathway and whether the radiation of C4 lineages preceded or coincided with their rise to ecological dominance from ∼10 Ma.

KEY RESULTS

C4 grass lineages first originated around 35 Ma at the time of the Eocene-Oligocene transition. Accelerated diversification of C4 lineages did not coincide with their rise to ecological dominance.

CONCLUSIONS

C4-dominated grasslands have expanded only since the Late Miocene and Pliocene. The initial diversification of their biotic elements can be tracked back as far as the Eocene-Oligocene transition. We suggest that shifts in taxonomic diversification and ecological dominance were stimulated by different factors, as in the case of the early angiosperms in the Cretaceous.

Gene duplication as a major force in evolution

Gene duplication is an important mechanism for acquiring new genes and creating genetic novelty in organisms. Many new gene functions have evolved through gene duplication and it has contributed tremendously to the evolution of developmental programmes in various organisms. Gene duplication can result from unequal crossing over, retroposition or chromosomal (or genome) duplication. Understanding the mechanisms that generate duplicate gene copies and the subsequent dynamics among gene duplicates is vital because these investigations shed light on localized and genomewide aspects of evolutionary forces shaping intra-specific and inter-specific genome contents, evolutionary relationships, and interactions. Based on whole-genome analysis of Arabidopsis thaliana, there is compelling evidence that angiosperms underwent two whole-genome duplication events early during their evolutionary history. Recent studies have shown that these events were crucial for creation of many important developmental and regulatory genes found in extant angiosperm genomes. Recent studies also provide strong indications that even yeast (Saccharomyces cerevisiae), with its compact genome, is in fact an ancient tetraploid. Gene duplication can provide new genetic material for mutation, drift and selection to act upon, the result of which is specialized or new gene functions. Without gene duplication the plasticity of a genome or species in adapting to changing environments would be severely limited. Whether a duplicate is retained depends upon its function, its mode of duplication, (i.e. whether it was duplicated during a whole-genome duplication event), the species in which it occurs, and its expression rate. The exaptation of preexisting secondary functions is an important feature in gene evolution, just as it is in morphological evolution.

A Callixylon (Archaeopteridales, Progymnospermopsida) trunk with preserved secondary phloem from the Late Devonian of Morocco

PREMISE OF THE STUDY

During the Devonian, the evolution of secondary phloem produced by a bifacial vascular cambium was a key innovation that increased the ability of plants within the lignophyte clade to redistribute photosynthates and other organic compounds throughout their body. Unraveling the secondary phloem anatomy of the first arborescent lignophytes is crucial to understand the evolution of this tissue and the physiology of early trees.

METHODS

A 10 cm wide stem of Callixylon with preserved secondary phloem from the Famennian of Morocco is described using thin-sections.

KEY RESULTS

The secondary phloem of this Callixylon zalesskyi-type of stem is composed of fibers, sclereids, rays, axial parenchyma, and putative sieve cells. Fibers differentiate early and are relatively abundant in the inner phloem. In the older phloem, fibers are arranged in tangential bands alternating with extensive layers of axial parenchyma. Changes between the young and old phloem involve the periclinal division and radial elongation of the axial parenchyma cells. The presence of fibers in the inner, presumably functional phloem, combined with evidence for rhythmicity in the production of different phloem cell types are documented for the first time in detail in an archaeopteridalean progymnosperm. No periderm was observed within the preserved seven millimeters of bark tissues.

CONCLUSIONS

The secondary phloem anatomy supports a close affinity of archaeopteridalean progymnosperms with both aneurophytalean progymnosperms and seed plants. The production of secondary phloem might have provided an advantage to these first arborescent lignophytes over other types of Devonian early trees, especially in dry conditions.

Importance of plant integrity in crop research, breeding, and production

Plant integrity looks like a "very easy and expanded topic," but the reality is totally different. Thanks to the very high specialization of scientists, we are losing a holistic view of plants and are making mistakes in our research due to this drawback. It is necessary to sense a plant in their whole complexity--in both roots and shoot, as well as throughout their life cycles. Only such an integrated approach can allow us to reach correct interpretations of our experimental results.

Natural stilbenoids: distribution in the plant kingdom and chemotaxonomic interest in Vitaceae

Stilbenoids, a family of polyphenols known for the complexity of their structure and for their diverse biological activities, occur with a limited but heterogeneous distribution in the plant kingdom. The most prominent stilbene containing plant family, the Vitaceae, represented by the famous wine producing grape vines Vitis vinifera L., is one of the richest sources of novel stilbenes currently known, together with other families, such as Dipterocarpaceae, Gnetaceae and Fabaceae. This review focuses on the distribution of stilbenes and 2-arylbenzofuran derivatives in the plant kingdom, the chemical structure of stilbenes in the Vitaceae family and their taxonomic implication.

A lower Cretaceous (Valanginian) seed cone provides the earliest fossil record for Picea (Pinaceae)

PREMISE OF STUDY

Sequence analyses for Pinaceae have suggested that extant genera diverged in the late Mesozoic. While the fossil record indicates that Pinaceae was highly diverse during the Cretaceous, there are few records of living genera. This description of an anatomically preserved seed cone extends the fossil record for Picea A. Dietrich (Pinaceae) by ∼75 Ma.

METHODS

The specimen was collected from the Apple Bay locality of Vancouver Island (Lower Cretaceous, Valanginian) and is described from anatomical sections prepared using cellulose acetate peels. Cladistic analyses of fossil and extant pinaceous seed cones employed parsimony ratchet searches of an anatomical and morphological matrix.

KEY RESULTS

This new seed cone has a combination of characters shared only with the genus Picea A. Dietr. and is thus described as Picea burtonii Klymiuk et Stockey sp. nov. Bisaccate pollen attributable to Picea is found in the micropyles of several ovules, corroborating the designation of this cone as an early spruce. Cladistic analyses place P. burtonii with extant Picea and an Oligocene representative of the genus. Furthermore, our analyses indicate that Picea is sister to Cathaya Chun et Kuang, and P. burtonii helps to establish a minimum date for this node in hypotheses of conifer phylogeny.

CONCLUSIONS

As an early member of the extant genus Picea, this seed cone extends the fossil record of Picea to the Valanginian Stage of the Early Cretaceous, ca. 136 Ma, thereby resolving a ghost lineage predicted by molecular divergence analyses, and offers new insight into the evolution of Pinaceae.

Deconstruction of the (paleo)polyploid grapevine genome based on the analysis of transposition events involving NBS resistance genes

Plants have followed a reticulate type of evolution and taxa have frequently merged via allopolyploidization. A polyploid structure of sequenced genomes has often been proposed, but the chromosomes belonging to putative component genomes are difficult to identify. The 19 grapevine chromosomes are evolutionary stable structures: their homologous triplets have strongly conserved gene order, interrupted by rare translocations. The aim of this study is to examine how the grapevine nucleotide-binding site (NBS)-encoding resistance (NBS-R) genes have evolved in the genomic context and to understand mechanisms for the genome evolution. We show that, in grapevine, i) helitrons have significantly contributed to transposition of NBS-R genes, and ii) NBS-R gene cluster similarity indicates the existence of two groups of chromosomes (named as Va and Vc) that may have evolved independently. Chromosome triplets consist of two Va and one Vc chromosomes, as expected from the tetraploid and diploid conditions of the two component genomes. The hexaploid state could have been derived from either allopolyploidy or the separation of the Va and Vc component genomes in the same nucleus before fusion, as known for Rosaceae species. Time estimation indicates that grapevine component genomes may have fused about 60 mya, having had at least 40–60 mya to evolve independently. Chromosome number variation in the Vitaceae and related families, and the gap between the time of eudicot radiation and the age of Vitaceae fossils, are accounted for by our hypothesis.

The evolution of seeds

The evolution of the seed represents a remarkable life-history transition for photosynthetic organisms. Here, we review the recent literature and historical understanding of how and why seeds evolved. Answering the 'how' question involves a detailed understanding of the developmental morphology and anatomy of seeds, as well as the genetic programs that determine seed size. We complement this with a special emphasis on the evolution of dormancy, the characteristic of seeds that allows for long 'distance' time travel. Answering the 'why' question involves proposed hypotheses of how natural selection has operated to favor the seed life-history phenomenon. The recent flurry of research describing the comparative biology of seeds is discussed. The review will be divided into sections dealing with: (1) the development and anatomy of seeds; (2) the endosperm; (3) dormancy; (4) early seed-like structures and the transition to seeds; and (5) the evolution of seed size (mass). In many cases, a special distinction is made between angiosperm and gymnosperm seeds. Finally, we make some recommendations for future research in seed biology.

Diversity and evolution of floral structure among early diverging lineages in the Ericales

This is a combination of review and original data on floral structure and diversity in the two earliest diverging lineages of the Ericales, i.e. the balsaminoids, comprising Balsaminaceae, Marcgraviaceae and Tetrameristaceae, and the polemonioids, comprising Fouquieriaceae and Polemoniaceae. Each clade is strongly supported in molecular studies, while structural synapomorphies have largely been lacking. For the balsaminoid families, we compare floral morphology, anatomy and histology among selected taxa and find that the entire clade is strongly supported by the shared presence of nectariferous tissue in the floral periphery, thread-like structures on anthers, truncate stigmas, secretion in the ovary, as well as mucilage cells, raphides and tannins in floral tissues. A possible sister group relationship between Balsaminaceae and Tetrameristaceae is supported by the shared presence of post-genital fusion of filaments and ovary and a star-shaped stylar canal. For polemonioids, we document unexpected diversity of floral features in Polemoniaceae, partly providing structural links to Fouquieriaceae. Features include cochlear and quincuncial corolla aestivation, connective protrusions, ventrifixed anthers and nectariferous tissue in the base of the ovary. In addition, we outline future directions for research on floral structure in the Ericales and briefly discuss the general importance of structural studies for our understanding of plant phylogeny and evolution.

Nystroemiaceae, a new family of Permian gymnosperms from China with an unusual combination of features

Nystroemiaceae is proposed as a new family of gymnosperms from the Permian of Cathaysia that adds to the diversity of gymnosperms known from this critical time in seed plant evolution. This family is characterized by bifurcating and highly branched pinnate ovuliferous organs bearing bicornute ovules (seeds) and entire leaves with anastomozing veins that are born on complex and modern-looking branching systems with clear axillary branching. The reconstruction is based on numerous large specimens from two localities in North China, in which the different plant parts are attached to each other. The ovulate structures show some apparently plesiomorphic (primitive) character states more typical of early seed plants, whereas the leaves and branches show the clearly apomorphic (derived) character states of broad-leaved gymnosperms.

Rosid radiation and the rapid rise of angiosperm-dominated forests

The rosid clade (70,000 species) contains more than one-fourth of all angiosperm species and includes most lineages of extant temperate and tropical forest trees. Despite progress in elucidating relationships within the angiosperms, rosids remain the largest poorly resolved major clade; deep relationships within the rosids are particularly enigmatic. Based on parsimony and maximum likelihood (ML) analyses of separate and combined 12-gene (10 plastid genes, 2 nuclear; >18,000 bp) and plastid inverted repeat (IR; 24 genes and intervening spacers; >25,000 bp) datasets for >100 rosid species, we provide a greatly improved understanding of rosid phylogeny. Vitaceae are sister to all other rosids, which in turn form 2 large clades, each with a ML bootstrap value of 100%: (i) eurosids I (Fabidae) include the nitrogen-fixing clade, Celastrales, Huaceae, Zygophyllales, Malpighiales, and Oxalidales; and (ii) eurosids II (Malvidae) include Tapisciaceae, Brassicales, Malvales, Sapindales, Geraniales, Myrtales, Crossosomatales, and Picramniaceae. The rosid clade diversified rapidly into these major lineages, possibly over a period of <15 million years, and perhaps in as little as 4 to 5 million years. The timing of the inferred rapid radiation of rosids [108 to 91 million years ago (Mya) and 107-83 Mya for Fabidae and Malvidae, respectively] corresponds with the rapid rise of angiosperm-dominated forests and the concomitant diversification of other clades that inhabit these forests, including amphibians, ants, placental mammals, and ferns.

Early Cretaceous mesofossils from Portugal and eastern North America related to the Bennettitales-Erdtmanithecales-Gnetales group

Four new genera and six new species of fossil seed (Buarcospermum tetragonium, Lignierispermum maroneae, Lobospermum glabrum, L. rugosum, L. stampanonii, Rugonella trigonospermum) are described from five Early Cretaceous mesofossil floras from Portugal and eastern North America. The four genera are distinguished by differences in size, shape, and details of seed anatomy, but all are unusual in having an outer seed envelope with a distinctive anatomical structure that surrounds the nucellus and the integument. The integument is extended apically into a long, narrow micropylar tube. The four new genera are part of a diverse, but previously unrecognized, complex of extinct plants that was widespread in Early Cretaceous vegetation and that coexisted in similar habitats with early angiosperms. The distinctive structure of these seeds, and the strong similarities to other fossil seeds (Ephedra, Ephedripites, Erdtmanispermum, Raunsgaardispermum, and some Bennettitales) already known from the Early Cretaceous, suggests that this newly recognized complex of extinct plants, together with Bennettitales, Erdtmanithecales, and Gnetales (the BEG group), is phylogenetically closely related.

Different gymnosperm outgroups have (mostly) congruent signal regarding the root of flowering plant phylogeny

We examined multiple plastid genes from a diversity of gymnosperm lineages to explore the consistency of signal among different outgroups for rooting flowering plant phylogeny. For maximum parsimony (MP), most outgroups attach on a branch of the underlying ingroup tree that leads to Amborella. Maximum likelihood (ML) analyses either root angiosperms on a nearby branch or find split support for these neighboring root placements, depending on the outgroup. The inclusion of two species of Hydatellaceae, recently recognized as an ancient line of angiosperms, does not aid in inference of the root. Cost profiles for placing the root in suboptimal locations are highly correlated across most outgroup comparisons, even comparing MP and ML profiles. Those for Gnetales are the most deviant of all those considered. This divergent outgroup either attaches on a long eudicot branch with moderate bootstrap support in MP analyses or supports no particular root location in ML analysis. Removing the most rapidly evolving sites in rate classifications based on two divergent angiosperm root placements with Gnetales yields strongly conflicting root placements in MP analysis, despite substantial overlap in the estimated sets of conservative sites. However, the generally high consistency in rooting signal among distantly related gymnosperm clades suggests that the long branch connecting angiosperms to their extant relatives may not interfere substantially with inference of the angiosperm root.

Bennettitales from the Grisethorpe Bed (Middle Jurassic) at Cayton Bay, Yorkshire, UK

Middle Jurassic fossil plants from the Grisethorpe Bed at Cayton Bay and Grisethorpe Bay, Yorkshire, UK, are preserved in a soft claystone, and plant mesofossils recovered by sieving reveal excellent details of external structure. Studies of these mesofossils complement previous work on macrofossils from the Grisethorpe Bed and allow the plant fossils in this classic flora to be studied in a similar way to those preserved in Cretaceous mesofloras. Bennettitales, a key group in discussions of how angiosperms may be related to other seed plants, are especially well represented among mesofossils from the Grisethorpe Bed. Abundant bennettitalean leaves, scale leaves, and fragments of pollen and ovulate organs provide new information on these extinct plants. In particular, a specimen of Williamsoniella coronata (presumed aborted) shows only weak differentiation between interseminal scales and ovules and provides further evidence of homology between these structures.

Floral variation and floral genetics in basal angiosperms

Recent advances in phylogeny reconstruction and floral genetics set the stage for new investigations of the origin and diversification of the flower. We review the current state of angiosperm phylogeny, with an emphasis on basal lineages. With the surprising inclusion of Hydatellaceae with Nymphaeales, recent studies support the topology of Amborella sister to all other extant angiosperms, with Nymphaeales and then Austrobaileyales as subsequent sisters to all remaining angiosperms. Notable modifications from most recent analyses are the sister relationships of Chloranthaceae with the magnoliids and of Ceratophyllaceae with eudicots. We review "trends" in floral morphology and contrast historical, intuitive interpretations with explicit character-state reconstructions using molecular-based trees, focusing on (1) the size, number, and organization of floral organs; (2) the evolution of the perianth; (3) floral symmetry; and (4) floral synorganization. We provide summaries of those genes known to affect floral features that contribute to much of floral diversity. Although most floral genes have not been investigated outside of a few model systems, sufficient information is emerging to identify candidate genes for testing specific hypotheses in nonmodel plants. We conclude with a set of evo-devo case studies in which floral genetics have been linked to variation in floral morphology.

Is the anthophyte hypothesis alive and well? New evidence from the reproductive structures of Bennettitales

Bennettitales is an extinct group of seed plants with reproductive structures that are similar in some respects to both Gnetales and angiosperms, but systematic relationships among the three clades remain controversial. This study summarizes characters of bennettitalean plants and presents new evidence for the structure of cones and seeds that help clarify relationships of Bennettitales to flowering plants, Gnetales, and other potential angiosperm sister groups. Bennettitales have simple mono- or bisporangiate cones. Seeds are borne terminally on sporophylls. They have a unique structure that includes a nucellus with a solid apex, no pollen chamber, and a single integument, and they are clearly not enclosed by a cupule or other specialized structures. Such features differ substantially from Gnetales, flowering plants, and the seed fern Caytonia, providing no compelling evidence for the origin of the angiospermous carpel. Cladistic tests were performed to assess the strength of the "anthophyte hypothesis" and possible relationships of Bennettitales, Gnetales, and Caytonia to flowering plants. Our results do not support the anthophyte hypothesis for the origin of angiosperms by a transformation of fertile organs that were already aggregated into a cone or flower-like structure. However, the anthophyte topology of the seed plant tree continues to be supported by morphological analyses of living and extinct taxa.

Phylogenetic relationships among seed plants: Persistent questions and the limits of molecular data

Trees inferred from DNA sequence data provide only limited insight into the phylogeny of seed plants because the living lineages (cycads, Ginkgo, conifers, gnetophytes, and angiosperms) represent fewer than half of the major lineages that have been detected in the fossil record. Nevertheless, phylogenetic trees of living seed plants inferred from sequence data can provide a test of relationships inferred in analyses that include fossils. So far, however, significant uncertainty persists because nucleotide data support several conflicting hypotheses. It is likely that improved sampling of gymnosperm diversity in nucleotide data sets will help alleviate some of the analytical issues encountered in the estimation of seed plant phylogeny, providing a more definitive test of morphological trees. Still, rigorous morphological analyses will be required to answer certain fundamental questions, such as the identity of the angiosperm sister group and the rooting of crown seed plants. Moreover, it will be important to identify approaches for incorporating insights from data that may be accurate but less likely than sequence data to generate results supported by high bootstrap values. How best to weigh evidence and distinguish among hypotheses when some types of data give high support values and others do not remains an important problem.

Evolution of developmental mechanisms in plants

As our understanding of developmental mechanisms in flowering plant species has become more advanced, an appreciation of the need to understand how distinct plant morphologies are generated has grown. This has led to an awareness of the key morphological differences in distinct land plant groups and to an assessment of the major innovations that occurred during land plant evolution. Recent advances demonstrate how developmental toolkits have been recruited for related purposes in different land plant groups, but the limited number of examples highlights both the infancy of the field and the difficulty of working with non-flowering plants.

Insect-damaged fossil leaves record food web response to ancient climate change and extinction

Plants and herbivorous insects have dominated terrestrial ecosystems for over 300 million years. Uniquely in the fossil record, foliage with well-preserved insect damage offers abundant and diverse information both about producers and about ecological and sometimes taxonomic groups of consumers. These data are ideally suited to investigate food web response to environmental perturbations, and they represent an invaluable deep-time complement to neoecological studies of global change. Correlations between feeding diversity and temperature, between herbivory and leaf traits that are modulated by climate, and between insect diversity and plant diversity can all be investigated in deep time. To illustrate, I emphasize recent work on the time interval from the latest Cretaceous through the middle Eocene (67-47 million years ago (Ma)), including two significant events that affected life: the end-Cretaceous mass extinction (65.5 Ma) and its ensuing recovery; and globally warming temperatures across the Paleocene-Eocene boundary (55.8 Ma). Climatic effects predicted from neoecology generally hold true in these deep-time settings. Rising temperature is associated with increased herbivory in multiple studies, a result with major predictive importance for current global warming. Diverse floras are usually associated with diverse insect damage; however, recovery from the end-Cretaceous extinction reveals uncorrelated plant and insect diversity as food webs rebuilt chaotically from a drastically simplified state. Calibration studies from living forests are needed to improve interpretation of the fossil data.

Phylogeny of Extant and Fossil Juglandaceae Inferred from the Integration of Molecular and Morphological Data Sets

It is widely acknowledged that integrating fossils into data sets of extant taxa is imperative for proper placement of fossils, resolution of relationships, and a better understanding of character evolution. The importance of this process has been further magnified because of the crucial role of fossils in dating divergence times. Outstanding issues remain, including appropriate methods to place fossils in phylogenetic trees, the importance of molecules versus morphology in these analyses, as well as the impact of potentially large amounts of missing data for fossil taxa. In this study we used the angiosperm clade Juglandaceae as a model for investigating methods of integrating fossils into a phylogenetic framework of extant taxa. The clade has a rich fossil record relative to low extant diversity, as well as a robust molecular phylogeny and morphological database for extant taxa. After combining fossil organ genera into composite and terminal taxa, our objectives were to (1) compare multiple methods for the integration of the fossils and extant taxa (including total evidence, molecular scaffolds, and molecular matrix representation with parsimony [MRP]); (2) explore the impact of missing data (incomplete taxa and characters) and the evidence for placing fossils on the topology; (3) simulate the phylogenetic effect of missing data by creating "artificial fossils"; and (4) place fossils and compare the impact of single and multiple fossil constraints in estimating the age of clades. Despite large and variable amounts of missing data, each of the methods provided reasonable placement of both fossils and simulated "artificial fossils" in the phylogeny previously inferred only from extant taxa. Our results clearly show that the amount of missing data in any given taxon is not by itself an operational guideline for excluding fossils from analysis. Three fossil taxa (Cruciptera simsonii, Paleoplatycarya wingii, and Platycarya americana) were placed within crown clades containing living taxa for which relationships previously had been suggested based on morphology, whereas Polyptera manningii, a mosaic taxon with equivocal affinities, was placed firmly as sister to two modern crown clades. The position of Paleooreomunnea stoneana was ambiguous with total evidence but conclusive with DNA scaffolds and MRP. There was less disturbance of relationships among extant taxa using a total evidence approach, and the DNA scaffold approach did not provide improved resolution or internal support for clades compared to total evidence, whereas weighted MRP retained comparable levels of support but lost crown clade resolution. Multiple internal minimum age constraints generally provided reasonable age estimates, but the use of single constraints provided by extinct genera tended to underestimate clade ages.

Embryological evidence for developmental lability during early angiosperm evolution

Recent advances in angiosperm phylogeny reconstruction, palaeobotany and comparative organismic biology have provided the impetus for a major re-evaluation of the earliest phases of the diversification of flowering plants. We now know that within the first fifteen million years of angiosperm history, three major lineages of flowering plants-monocotyledons, eumagnoliids and eudicotyledons-were established, and that within this window of time, tremendous variation in vegetative and floral characteristics evolved. Here I report on a novel type of embryo sac (angiosperm female gametophyte or haploid egg-producing structure) in Amborella trichopoda, the sole member of the most ancient extant angiosperm lineage. This is the first new pattern of embryo sac structure to be discovered among angiosperms in well over half a century. This discovery also supports the emerging view that the earliest phases of angiosperm evolution were characterized by an extensive degree of developmental experimentation and structural lability, and may provide evidence of a critical link to the gymnospermous ancestors of flowering plants.

A re-examination of the root cortex in wetland flowering plants with respect to aerenchyma

AIMS

We review literature and present new observations on the differences among three general patterns of aerenchyma origin and their systematic distributions among the flowering plants, and we clarify terminology on root aerenchyma.

SCOPE

From our own previous works and some new observations, we have analysed the root cortex in 85 species of 41 families in 21 orders of flowering plants that typically grow in wetlands to determine the characteristic patterns of aerenchyma.

FINDINGS

A developmental and structural pattern that we term expansigeny, as manifested by honeycomb aerenchyma, is characteristic of all aquatic basal angiosperms (the Nymphaeales) and basal monocots (the Acorales). Expansigenous aerenchyma develops by expansion of intercellular spaces into lacunae by cell division and cell expansion. Schizogeny and lysigeny, so often characterized in recent reviews as the only patterns of root cortex lacunar formation, are present in most wetland plants, but are clearly not present in the most basal flowering plants.

CONCLUSION

We conclude that expansigeny is the basic type of aerenchyma development in roots of flowering plants and that the presence of expansigenous honeycomb aerenchyma in root cortices was fundamental to the success of the earliest flowering plants found in wetland environments.

Rise from the ashes - the reconstruction of charcoal fossil flowers

The fossil record provides a unique opportunity to study the evolutionary history and past diversity of life. Without making use of palaeontological data, a comprehensive understanding of the phylogeny and present diversity of life would remain elusive. Angiosperms (flowering plants) are the largest and most diverse group of land plants. Our understanding of their evolution has in recent years profited immensely from the discovery and study of three-dimensionally preserved fossil flowers. Descriptions of such fossil flowers are in many respects equivalent to those of extant plants. Here, I provide background information about this type of angiosperm fossils and give special attention to the techniques used to reconstruct their three-dimensional shape and organization.

When Earth started blooming: insights from the fossil record

Recent palaeobotanical studies have greatly increased the quantity and quality of information available about the structure and relationships of Cretaceous angiosperms. Discoveries of extremely well preserved Cretaceous flowers have been especially informative and, combined with results from phylogenetic analyses of extant angiosperms (based mainly on molecular sequence data), have greatly clarified important aspects of early angiosperm diversification. Nevertheless, many questions still persist. The phylogenetic origin of the group itself remains as enigmatic as ever and, in some cases, newly introduced techniques from molecular biology have given confusing results. In particular, relationships between the five groups of extant seed plants remain uncertain, and it has sometimes proved difficult to reconcile estimates of the time of divergence between extant lineages made using a 'molecular clock' with the fossil record. One result, however, is becoming increasingly clear: a great deal of angiosperm diversity is extinct. Some groups of angiosperms were evidently more diverse in the past than they are today. In other cases, fossils defy assignment to extant groups at the family level or below. This raises the possibility that evolutionary conclusions based solely upon extant taxa that are merely relics of groups that were once much more diverse might be misled by the effects of extinction. It also introduces the possibility that some early enigmatic fossils might represent lineages that diverged from the main line of angiosperm evolution below the most recent common ancestor of all extant taxa. These, and other questions, are among those that need to be addressed by future palaeobotanical research.

Phylogeny and evolution of ferns (monilophytes) with a focus on the early leptosporangiate divergences

The phylogenetic structure of ferns (= monilophytes) is explored here, with a special focus on the early divergences among leptosporangiate lineages. Despite considerable progress in our understanding of fern relationships, a rigorous and comprehensive analysis of the early leptosporangiate divergences was lacking. Therefore, a data set was designed here to include critical taxa that were not included in earlier studies. More than 5000 bp from the plastid (rbcL, atpB, rps4) and the nuclear (18S rDNA) genomes were sequenced for 62 taxa. Phylogenetic analyses of these data (1) confirm that Osmundaceae are sister to the rest of the leptosporangiates, (2) resolve a diverse set of ferns formerly thought to be a subsequent grade as possibly monophyletic (((Dipteridaceae, Matoniaceae), Gleicheniaceae), Hymenophyllaceae), and (3) place schizaeoid ferns as sister to a large clade of "core leptosporangiates" that includes heterosporous ferns, tree ferns, and polypods. Divergence time estimates for ferns are reported from penalized likelihood analyses of our molecular data, with constraints from a reassessment of the fossil record.

The origin and diversification of angiosperms

The angiosperms, one of five groups of extant seed plants, are the largest group of land plants. Despite their relatively recent origin, this clade is extremely diverse morphologically and ecologically. However, angiosperms are clearly united by several synapomorphies. During the past 10 years, higher-level relationships of the angiosperms have been resolved. For example, most analyses are consistent in identifying Amborella, Nymphaeaceae, and Austrobaileyales as the basalmost branches of the angiosperm tree. Other basal lineages include Chloranthaceae, magnoliids, and monocots. Approximately three quarters of all angiosperm species belong to the eudicot clade, which is strongly supported by molecular data but united morphologically by a single synapomorphy-triaperturate pollen. Major clades of eudicots include Ranunculales, which are sister to all other eudicots, and a clade of core eudicots, the largest members of which are Saxifragales, Caryophyllales, rosids, and asterids. Despite rapid progress in resolving angiosperm relationships, several significant problems remain: (1) relationships among the monocots, Chloranthaceae, magnoliids, and eudicots, (2) branching order among basal eudicots, (3) relationships among the major clades of core eudicots, (4) relationships within rosids, (5) relationships of the many lineages of parasitic plants, and (6) integration of fossils with extant taxa into a comprehensive tree of angiosperm phylogeny.

The plant tree of life: an overview and some points of view

We provide a brief overview of this special issue on the plant tree of life, describing its history and the general nature of its articles. We then present our estimate for the overall topology and, for land plants, divergence times of the plant tree of life. We discuss several major controversies and unsolved problems in resolving portions of this tree. We conclude with a few thoughts about the prospects for obtaining a comprehensive, robustly resolved, and accurately dated plant tree of life and the importance of such a grand endeavor.

The evolution of plant development

The last decade has witnessed a resurgence in the study of the evolution of plant development, combining investigations in systematics, developmental morphology, molecular developmental genetics, and molecular evolution. The integration of phylogenetic studies, structural analyses of fossil and extant taxa, and molecular developmental genetic information allows the formulation of explicit and testable hypotheses for the evolution of morphological characters. These comprehensive approaches provide opportunities to dissect the evolution of major developmental transitions among land plants, including those associated with apical meristems, the origins of the root/shoot dichotomy, diversification of leaves, and origin and subsequent modification of flower structure. The evolution of these major developmental innovations is discussed within both phylogenetic and molecular genetic contexts. We conclude that it is the combination of these approaches that will lead to the greatest understanding of the evolution of plant development.

Fossil evidence and phylogeny: the age of major angiosperm clades based on mesofossil and macrofossil evidence from Cretaceous deposits

The fossil record has played an important role in the history of evolutionary thought, has aided the determination of key relationships through mosaics, and has allowed an assessment of a number of ecological hypotheses. Nonetheless, expectations that it might accurately and precisely mirror the progression of taxa through time seem optimistic in light of the many factors potentially interfering with uniform preservation. In view of these limitations, attempts to use the fossil record to corroborate phylogenetic hypotheses based on extensive comparisons among extant taxa may be misplaced. Instead we suggest a method-minimum age node mapping-for combining reliable fossil evidence with hypotheses of phylogeny. We use this methodology in conjunction with a phylogeny for angiosperms to assess timing in the history of major angiosperm clades. This method places many clades both with and without fossil records in temporal perspective, reveals discrepancies among clades in propensities for preservation, and raises some interesting questions about angiosperm evolution. By providing a context for understanding the gaps in the angiosperm fossil record this technique lends credibility and support to the remainder of the angiosperm record and to its applications in understanding a variety of aspects of angiosperm history. In effect, this methodology empowers the fossil record.