A duplicate gene rooting of seed plants and the phylogenetic position of flowering plants

Flowering plants represent the most significant branch in the tree of land plants, with respect to the number of extant species, their impact on the shaping of modern ecosystems and their economic importance. However, unlike so many persistent phylogenetic problems that have yielded to insights from DNA sequence data, the mystery surrounding the origin of angiosperms has deepened with the advent and advance of molecular systematics. Strong statistical support for competing hypotheses and recent novel trees from molecular data suggest that the accuracy of current molecular trees requires further testing. Analyses of phytochrome amino acids using a duplicate gene-rooting approach yield trees that unite cycads and angiosperms in a clade that is sister to a clade in which Gingko and Cupressophyta are successive sister taxa to gnetophytes plus Pinaceae. Application of a cycads + angiosperms backbone constraint in analyses of a morphological dataset yields better resolved trees than do analyses in which extant gymnosperms are forced to be monophyletic. The results have implications both for our assessment of uncertainty in trees from sequence data and for our use of molecular constraints as a way to integrate insights from morphological and molecular evidence.     

Gene conversion and the evolution of euryarchaeal chaperonins: a maximum likelihood-based method for detecting conflicting phylogenetic signals

Recombination is well known as a complicating factor in the interpretation of molecular phylogenies. Here we describe a maximum likelihood sliding window method based on a likelihood ratio test for scanning DNA sequence alignments for regions of incongruent phylogenetic signals, such as those influenced by recombination. Using this method, we identify several instances of gene conversion between paralogous chaperonin genes in euryarchaeote Archaea, many of which are not detected by two other widely used methods. In the Thermococcus/Pyrococcus lineage, where a gene duplication producing a and b paralogues predates the divergence of Thermococcus strains KS-1 and KS-8, gene conversion has homogenized portions of the a and b genes in KS-8 since the divergence of these two strains. A region near the 3′ end of the a and b paralogues in the methanogen Methanobacterium thermoautotrophicum also appears to have undergone gene conversion. We apply the method to two additional test data sets, the argF gene of Neisseria and a set of actin paralogues in maize, and show that it successfully identifies all the recombinant regions that were previously detected with other methods. Our approach is relatively insensitive to the presence of divergent sequences in the alignment, making it ideal for detecting recombination between both closely and distantly related genes.     

The evolution of embryogeny in seed plants and the developmental origin and early history of endosperm

For almost a century, the formation of endosperm from a second and distinctive fertilization event has been viewed as a unique feature of flowering plants. However, until recently, the evolutionary origin of this unique embryo-nourishing entity remained a mystery. Based upon comparative developmental analysis of reproduction among basal angiosperms and their closest extant relatives, the Gnetales (Ephedra, Gnetum, and Welwitschia), it is possible to construct an explicit hypothesis of the events that led to the evolutionary establishment of double fertilization and endosperm. The formulation of this historical record is derived entirely from and dependent upon the determination of reproductive features that are likely to have characterized the common ancestors of angiosperms and Gnetales. Current evidence is most congruent with the concept that a process of double fertilization first evolved in a common ancestor of the Gnetales and angiosperms. Initially, however, the second fertilization product was diploid and yielded a supernumerary embryo. Subsequent to the divergence of the angiosperm lineage from its closest relatives (which include the Gnetales), modification of the development of the supernumerary embryo (derived from the second fertilization event) led to the establishment of an embryo-nourishing endosperm. Comparative analysis of patterns of embryogeny within Gnetales and angiosperms establishes that embryo development in the ancestors of flowering plants (with a rudimentary process of double fertilization) was ab initio cellular, and not free nuclear, as had previously been assumed. Thus, it is likely that the earliest flowering plants displayed an ab initio cellular pattern of endosperm development, whose expression was inherited from that of the supernumerary embryo of the ancestors of flowering plants.     

Occurrence and phylogenetic significance of cytokinesis-related callose in green algae, bryophytes, ferns and seed plants

 In order to investigate the occurrence of callose in dividing cells, we cultivated a selection of 30 organisms (the prokaryotic cyanobacterium Anabaena and eukaryotic green algae, bryophytes, ferns and seed plants) under defined conditions in the laboratory. Samples from these photoautotrophs, which are members of the evolutionary 'green lineage' leading from freshwater algae to land plants, were analysed by fluorescence microscopy. The β-1,3-glucan callose was identified by its staining properties with aniline blue and sirofluor. With the exception of the prokaryotic cyanobacterium, all of the eukaryotic organisms studied were capable of producing wound-induced callose. No callose was detected during cytokinesis of dividing cells of unicellular green algae (and Anabaena). However, in all of the multicellular green algae and land plants (embryophytes) investigated, callose was identified in newly made septae by an intense yellow fluorescence. The formation of wound callose was never detected in cells with callose in the newly formed septae. Additional experiments verified that no fixation-induced artefacts occurred. Our results show that callose is a regular component of developing septae in juvenile cells during cytokinesis in multicellular green algae and embryophytes. The implications of our results with respect to the evolutionary relationships between extant charophytes and land plants are discussed. Received: 15 September 2000 / Revision received: 23 October 2000 / Accepted: 23 October 2000     

Identifying the most noxious invasive plants in China: role of geographical origin, life form and means of introduction

In a heterogenous world, invasive plants often differ in noxiousness and nature of impacts, and there is a difference between strong and weak invaders. That knowing which invaders are most noxious and their nature of impacts is of great value to invasive ecology and management. Here we show that in China the most notorious invasive plants are with a perennial life cycle, clonal growth ability and from the American continent. They often form monocultural populations in land and water, replacing almost all other plants, and are mainly distributed in Central and South China. Following are some accidentally introduced annuals. Annuals from the American continent are often common, dominant or in monocultural populations in ruderal and agricultural habitats whereas those from Eurasia are highly noxious only in agricultural habitats. Annuals are not restricted in distribution and could spread fast to all of the country. There are also two perennial grasses from Europe and Mediterranean area and four intentionally introduced annuals from South America that were identified in this study. Factors that may account for these patterns include relatedness between invasives and natives, vegetative propagation, and plant strategies. The invasive plants identified in this study have caused significant negative impacts to native biodiversity, environment, economics and agriculture, with different groups being different in their extent and nature of impacts.     

The origin of the coelom in Brachiopoda and its phylogenetic significance

The origin of the mesoderm and the subsequent formation of the coelom in the larvae of the brachiopod species Notosaria nigricans and Calloria inconspicua is documented in detail at the ultrastructural level. During gastrulation, the blastocoel is completely displaced by the invaginating archenteron. Initial mesoderm formation was observed in late wedge-shaped to early three-lobed stages in both species. Proliferation of mesodermal cells from the archenteral epithelium mainly occurs in the dorsolateral (C. inconspicua) and caudolateral (N. nigricans) parts of the archenteral wall. Thus, a compact mesodermal cell mass pushes its way towards the subepidermal basal lamina. During further development of the larva, the mesoderm is separated from the archenteral epithelium by an extracellular matrix secreted frontad from behind. As a result, a single coelomic anlage is formed. The initial mesoderm in both species is of archenteral/endodermal origin. Considering endodermal origin as the crucial character for enterocoely, coelom formation through proliferation of a compact, endodermally derived mesodermal cell mass in Brachiopoda is clearly identified as enterocoely. Endodermal origin of mesoderm and, therefore, of the coelomic epithelium is hypothesised as a synapomorphy of Brachiopoda and Deuterostomia. As a consequence: (1) Brachiopoda and Deuterostomia are considered sister groups, (2) Brachiopoda group within Radialia and (3) lophophorates (”Tentaculata”) remain as a paraphyletic grouping. Accepted: 26 November 1999     

The MADS-box floral homeotic gene lineages predate the origin of seed plants: Phylogenetic and molecular clock estimates

Flower development in angiosperms is controlled in part by floral homeotic genes, many of which are members of the plant MADS-box regulatory gene family. The evolutionary history of these developmental genes was reconstructed using 74 loci from 15 dicot, three monocot, and one conifer species. Molecular clock estimates suggest that the different floral homeotic gene lineages began to diverge from one another about 450–500 mya, around the time of the origin of land plants themselves. Received: 31 January 1997 / Accepted: 9 April 1997     

Molecular genetic tools to infer the origin of forest plants and wood

Most forest tree species exhibit high levels of genetic diversity that can be used to trace the origin of living plants or their products such as timber and processed wood. Recent progress to isolate DNA not only from living tissue but also from wood and wood products offers new opportunities to test the declared origin of material such as seedlings for plantation establishment or timber. However, since most forest tree populations are weakly differentiated, the identification of genetic markers to differentiate among spatially isolated populations is often difficult and time consuming. Two important fields of “forensic” applications are described: Molecular tools are applied to test the declared origin of forest reproductive material used for plantation establishment and of internationally traded timber and wood products. These applications are illustrated taking examples from Germany, where mechanisms have been developed to improve the control of the trade with forest seeds and seedlings, and from the trade with wood of the important Southeast Asian tree family Dipterocarpaceae. Prospects and limitations of the use of molecular genetic methods to conclude on the origin of forest plants, wood, and wood products are discussed.     

Monitoring the presence and expression of transgenes in living plants

A range of bio- and nanotechnologies have been developed that could be adapted towards monitoring the presence and expression of transgenes, in real time and in the field, in plants of agronomic and ecological importance. Transgene escape from crop hosts to wild relatives or landraces is one example in which monitoring might be useful, depending on the ecological impact of the transgene. In addition, there might be non-biosafety-related practical reasons to monitor transgene expression. Transgenes can be tagged with green fluorescent protein and imaged or measured using instruments designed to detect fluorescence signals on the plant. In addition, nanotechnologies using aptamers, quantum dots and molecular beacons are rapidly evolving and could also be used for post hoc (after transformation) in vivo monitoring. These nanotechnologies have the benefit of being useful on a post hoc basis.     

Within- and between-species patterns of allocation to pulp and seed in vertebrate dispersed plants

Non-uniform scaling of pulp and seed mass has been shown to alter dispersal probabilities in vertebrate dispersed species. Since dispersal in tropical forests is strongly linked to establishment success, processes determining allocation to pulp and seed are likely to impact on parental fitness, and therefore should be under the control of natural selection. In this study I examine size-dependent dry mass allocation pattern to pulp and seed mass both among and within 20 fruit-producing plant species of tropical rainforest in northeast Queensland, Australia. Reduced major axis analyses using mean values for each species showed significant isometry, indicating that at the community level, plant species that employ vertebrates as a means of seed dispersal tend to allocate an equivalent mean relative proportion of the overall dry weight investment in fruit to pulp. However, identical analyses conducted for each species separately revealed that relationships within individual species do not reflect the inter-specific relationship. These results imply two influences on dry mass allocation to fruit components; the first (within-species allometry) determines how fruits vary within each species. The second (between-species allometry) operates in a similar manner across species to produce equal ratios of mean pulp and seed mass independent of within-species allometries.     

Analysis of FRET signals in the presence of free donors and acceptors

A method for spectral analysis of Förster resonance energy transfer (FRET) signals is presented, taking into consideration both the contributions of unpaired donor and acceptor fluorophores and the influence of incomplete labeling of the interacting partners. It is shown that spectral analysis of intermolecular FRET cannot yield accurate values of the Förster energy transfer efficiency E, unless one of the interactors is in large excess and perfectly labeled. Instead, analysis of donor quenching yields a product of the form Ef_dp_a, where f_d is the fraction of donor-type molecules participating in donor-acceptor complexes and p_a is the labeling probability of the acceptor. Similarly, analysis of sensitized emission yields a product involving Ef_a. The analysis of intramolecular FRET (e.g., of tandem constructs) yields the product Ep_a. We use our method to determine these values for a tandem construct of cyan fluorescent protein and yellow fluorescent protein and compare them with those obtained by standard acceptor photobleaching and fluorescence lifetime measurements. We call the method lux-FRET, since it relies on linear unmixing of spectral components.     

Annual variability in seed production by woody plants and the masting concept: reassessment of principles and relationship to pollination and seed dispersal

By analyzing 296 published and unpublished data sets describing annual variation in seed output by 144 species of woody plants, this article addresses the following questions. Do plant species naturally fall into distinct groups corresponding to masting and nonmasting habits? Do plant populations generally exhibit significant bimodality in annual seed output? Are there significant relationships between annual variability in seed production and pollination and seed dispersal modes, as predicted from economy of scale considerations? We failed to identify distinct groups of species with contrasting levels of annual variability in seed output but did find evidence that most polycarpic woody plants seem to adhere to alternating supra-annual schedules consisting of either high or low reproduction years. Seed production was weakly more variable among wind-pollinated taxa than animal-pollinated ones. Plants dispersed by mutualistic frugivores were less variable than those dispersed by either inanimate means or animals that predominantly behave as seed predators. We conclude that there are no objective reasons to perpetuate the concept of mast fruiting in the ecological literature as a shorthand to designate a distinct biological phenomenon. Associations between supra-annual variability in seed output and pollination and seed dispersal methods suggest the existence of important reproductive correlates that demand further investigation.     

Targeted gene disruption in the development of mouse models to elucidate the role of receptor guanylyl cyclase signaling pathways in physiological function

The physiological role of receptor guanylyl cyclases (GCs), which transduce a signal via the generation of intracellular cyclic GMP, has been somewhat speculative since there are few specific inhibitors that discriminate among various receptor isoforms. Although the natriuretic peptide receptors have been thought to regulate cardiovascular and renal function, the exact contribution of the receptor subtypes has not been clarified. The normal role of the heat-stable enterotoxin receptor guanylyl cyclase remains undefined, and several orphan members of the family await the identification of ligands as well as function. Targeted gene disruption, familiarly known as gene knockout, has emerged during the past decade as a powerful technique for probing the function of gene products, and has been used to develop animal models of inherited human diseases. We are just beginning to apply gene targeting technology to the guanylyl cyclase receptor family. Reviewed here is the information gained to date from the targeted disruption of several members of the guanylyl cyclase receptor family, their ligands, or effector molecules.     

Synthesis of spontaneous interferon by mouse peritoneal cells in vitro. I. Attempts to elucidate the origin of spontaneous interferon.

Interferon-like substance has been obtained in the media of mice 129/AoBoy peritoneal cell cultures after incubation at 26 degrees C. The substance showed characteristics that permitted it to be accepted as an interferon. Looking for the presence (in the media or in the sera) of infectious agents responsible for this event experiments were performed that excluded this possibility. Peritoneal cells cultures in media without calf sera (MEM, PBS) produced spontaneous interferon, too. In the same medium the peritoneal cells from various mouse strains differed in the capacity to spontaneous interferon formation. Finally it was found that the level of this interferon was raised with the age of mice.     

Progress in understanding the origin and functions of carotenoid hydroxylases in plants

The dihydroxy xanthophylls lutein (beta,epsilon-carotene-3,3'-diol) and zeaxanthin (beta,beta-carotene-3,3'-diol) are well known for their critical roles in photosystem structure and adaptation of plants to high light stress. As a group, carotenoid hydroxylases catalyze the formation of lutein and zeaxanthin from their corresponding cyclic carotene precursors. Carotenoid beta-ring hydroxylases (beta-hydroxylases) have been isolated and characterized from various organisms and have invariably been shown to be non-heme di-iron monooxygenases. The presence of an epsilon-ring specific hydroxylase (epsilon-hydroxylase) was genetically demonstrated by isolation of mutants at the LUT1 locus in Arabidopsis. This review focuses on progress in understanding the molecular and biochemical nature of the epsilon-hydroxylase and the in vivo overlapping functions of the various carotenoid beta- and epsilon-hydroxylases in Arabidopsis.