Double fertilization in Gnetum gnemon (Gnetaceae): its bearing on the evolution of sexual reproduction within the Gnetales and the anthophyte clade

The fertilization process in Gnetum is critical to our understanding of the evolution of sexual reproduction within the Gnetales, a monophyletic group of nonfiowering seed plants that are the closest living relatives to flowering plants. Although much is known about the fertilization process in Ephedra, which is basal within the Gnetales, little is known about sexual reproduction in the derived sister groups Gnetum and Welwitschia. Ovules of Gnetum gnemon were collected at various stages after hand pollination and processed for light, fluorescence, and electron microscopy. Approximately 5 d after pollination, pollen tubes reach sexually mature female gametophytes, which are coenocytic. At that time, a binucleate sperm cell is found within each pollen tube. Within 7 d of pollination, double fertilization events occur when each of two sperm nuclei released from a pollen tube fuses with a separate, undifferentiated female nucleus within the free nuclear female gametophyte, which lacks differentiated egg cells. The products of double fertilization are two viable zygotes; endosperm is not formed. The lack of differentiated egg cells in Gnetum gnemon is unparalleled among land plants and the documentation of a regularly occurring process of double fertilization is congruent with the hypothesis that a rudimentary process of double fertilization evolved in a common ancestor of angiosperms and Gnetales.     

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.     

Evolution of follistatin in teleosts revealed through phylogenetic, genomic and expression analyses

Follistatin (Fst) inhibits transforming growth factor-β (TGF-B) proteins and is a known regulator of amniote myogenesis. Here, we used phylogenetic, genomic and experimental approaches to study its evolution in teleosts. Phylogenetic analyses suggested that one fst gene (fst1) is common to euteleosts, but a second gene (fst2) is conserved specifically within the Ostariophysi. Zebrafish fst1/2 respectively appear on chromosomes 5 and 10 in two genomic regions, each with conserved synteny to a single region in tetrapods. Interestingly, other teleosts have two corresponding chromosomal regions with a similar repertoire of paralogues. Phylogenetic reconstruction clustered these gene duplicates into two sister clades branching from tetrapod sequences. We suggest that an ancestral fst-containing chromosome was duplicated during the teleost whole genome duplication, but that fst2 was lost in lineages external to the Ostariophysi. We show that Fst1 of teleosts/mammals has evolved under strong purifying selection, but the N-terminal of Fst2 may have evolved under positive selection. Furthermore, the tissue-specific expression of zebrafish fst2 was restricted to fewer tissues compared to its paralogue and the single fst1 orthologue of Atlantic salmon (Salmo salar). Zebrafish fst1/2 may have subfunctionalized relative to non-duplicated vertebrate lineages, as several regions in the fst promoter of tetrapods were conserved with one paralogue, but not both. Finally, we examined the embryonic expression of fst1 in a teleost outside the Ostariophysi (Atlantic salmon). During segmentation, fst1 was expressed in the anterior somite compartment but was excluded from muscle progenitors that strongly expressed myogenic regulatory factors (MRFs). Later, fst1 was expressed in myogenic progenitors of the pectoral fin buds and also within the pax7 ⁺ cell layer external to the myotome. Electronic supplementary material The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

A hardware interpretation of the evolution of the genetic code

A quantitative rationale for the evolution of the genetic code is developed considering the principle of minimal hardware. This principle defines an optimal code as one that minimizes for a given amount of information encoded, the product of the number of physical devices used by the average complexity of each device. By identifying the number of different amino acids, number of nucleotide positions per codon and number of base types that can occupy each such position with, respectively, the amount of information, number of devices and the complexity, we show that optimal codes occur for 3, 7 and 20 amino acids with codons having a single, two and three base positions per codon, respectively. The advantage of a code of exactly 4 symbols is deduced, as well as a plausible evolutionary pathway from a code of doublets to triplets. The present day code of 20 amino acids encoded by 64 codons is shown to be the most optimal in an absolute sense. Using a tetraplet code further evolution to a code in which there would be 55 amino acids is in principle possible, but such a code would deviate slightly more than the present day code from the minimal hardware configuration. The change from a triplet code to a tetraplet code would occur at about 32 amino acids. Our conclusions are independent of, but consistent with, the observed physico-chemical properties of the amino acids and codon structures. These correlations could have evolved within the constrains imposed by the minimal hardware principle.     

The evolution of large brain size in birds is related to social,not genetic,monogamy

There are several hypotheses suggesting that social complexity, including pair bonding, is important in the evolution of increased brain size. I examined whether genetic or social monogamy was related to large brain size in birds. Recent work has indicated that the length and strength of pair bonds are associated with large brain size. I tested several hypotheses for the evolution of large brain size in 42 species of bird by including life history variables in a regression model. A test on 100 phylogenetic trees revealed no phylogenetic signal in brain size. Controlling for body size, a principal components analysis was run on the life history variables and degrees of extra‐pair paternity. The main principal component (PC1) was regressed on brain size revealing a strong, positive association. Social, but not genetic, monogamy was positively related to brain size. Large brain size is related to the selective pressures of procuring extra‐pair copulations whilst maintaining a social partnership. However, other life history variables also loaded positively and significantly on brain size. These results indicate that the evolution of large brain size in birds was driven by several important selective pressures. © 2014 The Linnean Society of London, Biological Journal of the Linnean Society, 2014, 111 , 668–678.     

Immunolocalization of the PmSUC1 sucrose transporter in Plantago major flowers and reporter-gene analyses of the PmSUC1 promoter suggest a role in sucrose release from the inner integument

This paper presents a detailed analysis of the PmSUC1 gene from plantago major, of its promoter activity in Arabidopsis, and of the tissue specific localization of the encoded protein in Plantago. PmSUC1 promoter activity was detected in the innermost layer of the inner integument (the endothel) of Arabidopsis plants expressing the gene of the green fluorescent protein (GFP) under the control of the PmSUC1 promoter. This promoter activity was confirmed with a PmSUC1-specific antiserum that identified the PmSUC1 protein in the endothel of Plantago and of Arabidopsis plants expressing the PmSUC1 gene under the control of its own promoter. PmSUC1 promoter activity and PmSUC1 protein were also detected in pollen grains during maturation inside the anthers and in pollen tubes during and after germination. These results demonstrate that PmSUC1 is involved in sucrose partitioning to the young embryo and to the developing pollen and growing pollen tube. In the innermost cell layer of the inner integument, a tissue that delivers nutrients to the endosperm and the embryo, PmSUC1 may catalyze the release of sucrose into the apoplast.     

On the origin and evolution of the genetic code

Two ideas have essentially been used to explain the origin of the genetic code: Crick's frozen accident and Woese's amino acid-codon specific chemical interaction. Whatever the origin and codon-amino acid correlation, it is difficult to imagine the sudden appearance of the genetic code in its present form of 64 codons coding for 20 amino acids without appealing to some evolutionary process. On the contrary, it is more reasonable to assume that it evolved from a much simpler initial state in which a few triplets were coding for each of a small number of amino acids. Analysis of genetic code through information theory and the metabolism of pyrimidine biosynthesis provide evidence that suggests that the genetic code could have begun in an RNA world with the two letters A and U grouped in eight triplets coding for seven amino acids and one stop signal. This code could have progressively evolved by making gradual use of letters G and C to end with 64 triplets coding for 20 amino acids and three stop signals. According to proposed evidence, DNA could have appeared after the four-letter structure was already achieved. In the newborn DNA world, T substituted U to get higher physicochemical and genetic stability.     

中国干旱区柽柳科植物种子形态特征及其系统学意义

对中国干旱区柽柳科（Ｔａｍａｒｉｃａｃｅａｅ）植物３属７代表种的种子形态及种皮表面亚显微结构进行了观察,表明种子形态及种皮表面亚显微结构可为本科植物的分类提供有价值的信息。根据种子表皮毛着生的类型并结合外部形态特征可初步得出以下结论：（１）表皮毛可分为Ⅰ型表皮毛和Ⅱ型表皮毛,前者着生于种子表面,包括红砂属（ＲｅａｕｍｕｒｉａＬ．）和柽柳属（ＴａｍａｒｉｘＬ．）植物的一些种类;后者着生于种子顶端的芒柱上,包括柽柳属一些种类和水柏枝属（ＭｙｒｉｃａｒｉａＤｅｓｖ．）植物。（２）表皮毛的演化趋势是由Ⅰ型表皮毛向Ⅱ型表皮毛转化。（３）红砂属处于本科的原始地位,水柏枝属较为进化,柽柳属是联系两者的中间环节,本属内亦存在许多过渡类型。     

The evolution of the scalation pattern in temnospondyl amphibians

In most Palaeozoic temnospondyls, thin round-oval scales covering the flanks and the back of the trunk can be distinguished from ventral, elongate gastral scales arranged in a chevron pattern. The extensive growth series of the temnospondyl Sclerocephalus reveals that the morphology of the gastral scales in small larvae corresponds to the round-oval scales of the rest of the body. During subsequent ontogeny, the gastral scales differentiate and attain a spindle-shaped morphology. The tapering end of each gastral scale fits into a dorsal groove on the medial adjacent scale. This arrangement allowed telescoping of the scales and thus provided a high degree of flexibility. In the ontogenetically most advanced specimens of Sclerocephalus the gastral scales attain a rhomboid outline, and the articulation by well-defined facets has reduced the flexibility between them. In most temnospondyls, the gastral scales retain the 'juvenile' spindle-shape or the 'larval' round-oval shape, which can be interpreted as a paedomorphic trait. This suggests that the different types of gastral scales in temnospondyls, as well as the scales of the back and the flanks, can be traced back to the same Anlage of round-oval scales that differentiated early in ontogeny. In the Mesozoic, a complete reduction of dermal scalation occurred independently in distinct dissorophoid, capitosauroid, and trematosauroid temnospondyls. This reduction was probably the result of several factors unique to each group, such as cutaneous respiration, the demand for greater mobility, and the decreased importance of belly protection in fully aquatic temnospondyls.  © 2007 The Linnean Society of London, Zoological Journal of the Linnean Society , 2007, 150 , 815–834.     

On the molecular mechanism of the evolution of genetic code alterations

Alterations to the standard genetic code have been found in both prokaryotes and eukaryotes. This finding demolished the central dogma of molecular biology, postulated by Crick in 1968, of an immutable and universal genetic code, and raised the question of how organisms survive genetic code alterations. Recent studies suggest that genetic code alterations are driven by selection using a mechanism that requires translational ambiguity. In C. albicans, the leucine CUG codon is decoded as serine through structural alterations of the translational machinery, in particular, of Ser-tRNA_CAG, which has dual identity and novel decoding properties. Here, we review the molecular mechanism of CUG reassignment, focusing on the structural change of the translational machinery and on the impact that such alteration had on the evolution of the Candida albicans genome. Published in Russian in Molekulyarnaya Biologiya, 2006, Vol. 40, No. 4, pp. 634–639. The text was submitted by the authors in English.     

Non-random pre-transcriptional evolution in HIV-1. A refutation of the foundational conditions for neutral evolution

The complete base sequence of HIV-1 virus and GP120 ENV gene were analyzed to establish their distance to the expected neutral random sequence. An especial methodology was devised to achieve this aim. Analyses included: a) proportion of dinucleotides (signatures); b) homogeneity in the distribution of dinucleotides and bases (isochores) by dividing both segments in ten and three sub-segments, respectively; c) probability of runs of bases and No-bases according to the Bose-Einstein distribution. The analyses showed a huge deviation from the random distribution expected from neutral evolution and neutral-neighbor influence of nucleotide sites. The most significant result is the tremendous lack of CG dinucleotides (p < 10(-50) ), a selective trait of eukaryote and not of single stranded RNA virus genomes. Results not only refute neutral evolution and neutral neighbor influence, but also strongly indicate that any base at any nucleotide site correlates with all the viral genome or sub-segments. These results suggest that evolution of HIV-1 is pan-selective rather than neutral or nearly neutral.     

Recruitment trade-offs and the evolution of dispersal mechanisms in plants

In this study we place seed size vs. seed number trade-offs in the context of plant dispersal ability. The objective was to suggest explanations for the evolution of different seed dispersal mechanisms, in particular fleshy fruits, wind dispersal and the maintenance of unassisted dispersal. We suggest that selection for improved dispersal may act either by increasing the intercept of a dispersal curve (log seed number vs. distance) or by flattening the slope of the curve. 'Improved dispersal' is defined as a marginal increase in the number of recruits sited at some (arbitrary) distance away from the parent plant. Increasing the intercept of the dispersal curve, i.e. producing more seeds, is associated with a reduction in seed size, which in turn affects the recruitment ability, provided that this ability is related to seed size. If recruitment is related to seed size there will be a recruitment cost of evolving increased seed production. On the other hand, a flattening of the slope by evolving dispersal attributes is likely to be associated with a fecundity cost. An exception is wind dispersal where smaller (and hence more numerous) seeds may lead to more efficient dispersal. We derive two main predictions: If recruitment is strongly related to seed size, selection for improved dispersal acts on the slope of the dispersal curve, i.e. by favouring evolution of dispersal attributes on seeds or fruits. If, on the other hand, recruitment is only weakly related to seed size (or not related, or negatively related), selection for improved dispersal favours increased seed production. Despite its simplicity, the model suggests explanations for (i) why so many plant species lack special seed dispersal attributes, (ii) differences in dispersal spectra among plant communities, and (iii) adaptive radiation in seed size and dispersal attributes during angiosperm evolution. This revised version was published online in July 2006 with corrections to the Cover Date.     

Molecular evolution of the sex peptide network in Drosophila

Successful reproduction depends on interactions between numerous proteins beyond those involved directly in gamete fusion. Although such reproductive proteins evolve in response to sexual selection pressures, how networks of interacting proteins arise and evolve as reproductive phenotypes change remains an open question. Here, we investigated the molecular evolution of the ‘sex peptide network’ of Drosophila melanogaster, a functionally well‐characterized reproductive protein network. In this species, the peptide hormone sex peptide (SP) and its interacting proteins cause major changes in female physiology and behaviour after mating. In contrast, females of more distantly related Drosophila species do not respond to SP. In spite of these phenotypic differences, we detected orthologs of all network proteins across 22 diverse Drosophila species and found evidence that most orthologs likely function in reproduction throughout the genus. Within SP‐responsive species, we detected the recurrent, adaptive evolution of several network proteins, consistent with sexual selection acting to continually refine network function. We also found some evidence for adaptive evolution of several proteins along two specific phylogenetic lineages that correspond with increased expression of the SP receptor in female reproductive tracts or increased sperm length, respectively. Finally, we used gene expression profiling to examine the likely degree of functional conservation of the paralogs of an SP network protein that arose via gene duplication. Our results suggest a dynamic history for the SP network in which network members arose before the onset of robust SP‐mediated responses and then were shaped by both purifying and positive selection.