Molecular cytogenetic evidence for a high level of chromosome pairing among different genomes in Triticum aestivum–Thinopyrum intermedium hybrids

Intergeneric hybrids (ABDJJ^sS genomes) were made between Triticum aestivum cv. Chinese Spring (CS) and Thinopyrum intermedium. Genomic in situ hybridization (GISH) using genomic DNA probes from Pseudoroegneria libanotica (Hackel) D.R. Dewey (genome S, 2n = 14) was used to study chromosome pairing among J, J^s, S and wheat ABD genomes in the hybrids. It was shown that in the hexaploid (ABDJJ^sS) hybrids, high pairing occurred among wheat chromosomes and among Thinopyrum chromosomes. A closer relationship was observed among the three genomes of Th. intermedium than among the three genomes of T. aestivum. It was further discerned that S genome chromosomes paired with J- and J^s-genome chromosomes at a high frequency. The frequency of heterologous pairing between S and J or S and J^s chromosomes was higher than those between J and J^s chromosomes, indicating that the S-genome was more closely related with these two genomes. Our results provided direct molecular cytogenetic evidence for the hypothesis that S-genome chromosomes are genetically similar to the J-genome chromosomes and, therefore, genetic exchange between these genomes is possible. The discovery of a close relationship among S, J and J^s genomes provides valuable markers for molecular cytogenetic analyses using S-genomic DNA probes in monitoring the transfer of useful traits from Thinopyrum species into wheat. Received: 23 August 2000 / Accepted: 5 September 2000     

What genes make a tree a tree?

Woody growth is evolutionarily ancient, yet has been gained and lost multiple times in plant evolution and is readily enhanced or minimized in eudicot speciation. New molecular genetic and genomic studies in Populus and Arabidopsis that are defining the genes responsible for cambium function and woody growth suggest that the genes regulating woody growth are not unique to woody plants. Surprisingly, key genetic mechanisms originally characterized as regulating the meristematic cells of the shoot apical meristem are also expressed in the vascular cambium during woody growth. This has important implications for the development of Populus as a model species and illustrates why forest trees constitute a contrived group of plants that have more in common with herbaceous relatives than we foresters like to admit.     

Chromosome mapping of the large elaenia (Elaenia spectabilis): evidence for a cytogenetic signature for passeriform birds?

Among birds, Tyrannidae comprises one of the most diverse and species‐rich families. Although cytogenetic data have shown interesting results in this family, such as variations in the macrochromosome morphology and diploid number, only a few species have had their karyotypes described. In the present study, we report the characterization of the karyotype of Elaenia spectabilis (Passeriformes, Tyrannidae) by means of classical and molecular cytogenetics. The results show that syntenic groups of Gallus gallus (GGA) were conserved, except GGA1 and GGA4, which were divided into two different pairs each. However, the results obtained with Leucopternis albicollis probes revealed the occurrence of inversions in segments homologous to GGA1q, similar to those observed in other Passerifomes (Turdus), and one inversion in GGA1p. These results suggest that the centric fission in GGA1, as well as the inversions observed in segments homologous to GGA1q, appeared in the early history of Passeriformes because they could be detected in Oscine and Suboscine species. © 2015 The Linnean Society of London, Biological Journal of the Linnean Society, 2015, 115 , 391–398.     

The ligand-binding site of bovine beta-lactoglobulin: evidence for a function?

Ever since the fortuitous observation that beta-lactoglobulin (beta-Lg), the major whey protein in the milk of ruminants, bound retinol, the details of the binding have been controversial. beta-Lg is a lipocalin, like plasma retinol-binding protein, so that ligand association was expected to make use of the central cavity in the protein. However, an early crystallographic analysis and some of the more recent solution studies indicated binding elsewhere. We have now determined the crystal structures of the complexes of the trigonal form of beta-Lg at pH 7.5 with bound retinol (R=21.4% for 7329 reflections between 20 and 2.4 A resolution, R(free)=30.6%) and with bound retinoic acid (R=22.7% for 7813 reflections between 20 and 2.34 A resolution, R(free)=29.8%). Both ligands are found to occupy the central calyx in a manner similar to retinol binding in retinol-binding protein. We find no evidence of binding at the putative external binding site in either of these structural analyses. Further, competition between palmitic acid and retinol reveals only palmitate bound to the protein. An explanation is provided for the lack of ligand binding to the orthorhombic crystal form also obtained at pH 7.5. Finally, the possible function of beta-Lg is discussed in the light of its species distribution and similarity to other lipocalins.     

One size fits all? Molecular evidence for a commonly inherited petal identity program in Ranunculales

Petaloid organs are a major component of the floral diversity observed across nearly all major clades of angiosperms. The variable morphology and development of these organs has led to the hypothesis that they are not homologous but, rather, have evolved multiple times. A particularly notable example of petal diversity, and potential homoplasy, is found within the order Ranunculales, exemplified by families such as Ranunculaceae, Berberidaceae, and Papaveraceae. To investigate the molecular basis of petal identity in Ranunculales, we used a combination of molecular phylogenetics and gene expression analysis to characterize APETALA3 (AP3) and PISTILLATA (PI) homologs from a total of 13 representative genera of the order. One of the most striking results of this study is that expression of orthologs of a single AP3 lineage is consistently petal-specific across both Ranunculaceae and Berberidaceae. We conclude from this finding that these supposedly homoplastic petals in fact share a developmental genetic program that appears to have been present in the common ancestor of the two families. We discuss the implications of this type of molecular data for long-held typological definitions of petals and, more broadly, the evolution of petaloid organs across the angiosperms.     

The coup de grâce for the nested clade phylogeographic analysis?

Nested clade phylogeographic analysis (NCPA) has become a popular method for reconstructing the history of populations across species ranges. Ever since its invention in 1995, criticisms have been formulated, but the method, which has been regularly updated, continues to attract investigators. Molecular Ecology has published a large fraction of the literature on the topic — both pro and con. A recent study by Panchal and Beaumont (2007) finally allows a precise evaluation of the method by developing software that automates the somewhat complicated NCPA procedure. Using simulations of random-mating populations, Panchal and Beaumont find a high frequency of false-positives with their automated NCPA procedure (over 75%). These findings, which echo and amplify earlier warnings, appear serious enough to suggest to researchers to await further evaluation of the method. Although no other all-encompassing method such as the NCAP currently exists to evaluate phylogeographic data sets, researchers have many alternative methods to test ever more refined hypotheses.     

Masting in a temperate tree: Evidence for environmental prediction?

Many plant species produce large fruit crops in some years and then produce few or no fruits in others. Synchronous, inter‐annual variation in plant reproduction is known as ‘masting’ and its adaptive significance has yet to be fully resolved. For 8 consecutive years, I quantified every fruit produced by 22 females of a New Zealand tree species (Dysoxylum spectabile), which has an unusual habit of taking a full calendar year to mature fruits after flowering. Fruit production varied strongly among years and was tightly synchronized among trees. Annual variability in fruit production declined with total reproductive output, indicating trees with lower fecundity exhibited a stronger tendency to mast. Although unrelated to temperature, annual fruit production was positively related to precipitation during annual periods of fruit development, and negatively related to fruit production in the previous year. Seedlings had higher rates of survivorship in a wet, high‐seed year than in a dry, low‐seed year, suggesting that seedlings might be drought sensitive. Therefore, D. spectabile produced large fruit crops during periods of high rainfall prior to fruit maturation, which may enhance survivorship of drought‐intolerant seeds. Results were inconsistent with several hypotheses that are widely believed to be the most likely explanations for masting. Instead, results were consistent with the environmental prediction hypothesis, suggesting that this hypothesis may be more important than previously appreciated.     

Molecular analysis of the gene encoding α-lytic protease: evidence for a preproenzyme

A 1.7-kb EcoRI fragment containing the structural gene for α-lytic protease has been cloned from Lysobacter enzymogenes 495 chromosomal DNA: the first example of a gene cloned from this organism. The protein sequence deduced from the nucleotide sequence encoding this serine protease matches the published amino acid sequence [Olson et al., Nature 228 (1970) 438–442] precisely. Sequence analysis and S 1 mapping indicate that, like subtilisin [e.g. Wells et al., Nucleic Acids Res. 11 (1983) 7911–7925] α-lytic protease is synthesized as a pre-pro protein (41 kDa) that is subsequently processed to its mature extracellular form (20 kDa). This first finding of a large N-terminal protease precursor in a Gram-negative bacterial protease strengthens the hypothesis that large precursors may be a general property of extracellular bacterial proteases, and suggests that the N- or C-terminal location of the precursor segment may be significant.     

Pollination of Ravenala madagascariensis (Strelitziaceae) by lemurs in Madagascar: evidence for an archaic coevolutionary system?

Investigations of the floral biology of the traveler's tree (Ravenala madagascariensis) and the ecology of the ruffed lemur (Varecia variegata), both endemic to the island of Madagascar, suggest a plant-pollinator relationship. Ravenala exhibits many specializations for visitation by large nonflying animals: inflorescences placed below the crown of the plant and easily accessible to arboreal animals; large flowers enclosed in tough, protective bracts that require a strong pollinator to open; stiff, rodlike styles that withstand the rough handling of the visitors; and copious, sucrose-dominant nectar that provides a renewable reward for a sizable animal for a long time period. Our observations in the field also show that Varecia variegata: consistently and almost exclusively visit the flowers of Ravenala; carry pollen on their fur between flowers on the same plant and between conspecific plants; do not destroy the flowers while obtaining the nectar; and appear to be highly dependent on nectar as a food source during specific times of the year. The basal phylogenetic position of Ravenala in the family Strelitziaceae, as indicated by molecular sequence data, and the distribution of reproductive traits in the three extant genera are consistent with the hypothesis that pollination by nonflying mammals is an archaic system, whereas bird and bat pollination are derived.     

Is there a star tree paradox?

Concerns have been raised that posterior probabilities on phylogenetic trees can be unreliable when the true tree is unresolved or has very short internal branches, because existing methods for Bayesian phylogenetic analysis do not explicitly evaluate unresolved trees. Two recent papers have proposed that evaluating only resolved trees results in a "star tree paradox": when the true tree is unresolved or close to it, posterior probabilities were predicted to become increasingly unpredictable as sequence length grows, resulting in inflated confidence in one resolved tree or another and an increasing risk of false-positive inferences. Here we show that this is not the case; existing Bayesian methods do not lead to an inflation of statistical confidence, provided the evolutionary model is correct and uninformative priors are assumed. Posterior probabilities do not become increasingly unpredictable with increasing sequence length, and they exhibit conservative type I error rates, leading to a low rate of false-positive inferences. With infinite data, posterior probabilities give equal support for all resolved trees, and the rate of false inferences falls to zero. We conclude that there is no star tree paradox caused by not sampling unresolved trees.     

Extrapair paternity and egg hatchability in tree swallows: evidence for the genetic compatibility hypothesis?

Tree swallows (Tachycineta bicolor) show one of the highestlevels of extrapair paternity in birds, and there is evidencethat females have control over who fathers their offspring.However, it is unclear which benefits female tree swallows obtainfrom mating with multiple males. Using microsatellite DNA fingerprinting,we studied extrapair paternity in relation to nesting successand male, female, and offspring characteristics. More than 70%of all nests contained extrapair young, and more than half ofall offspring were extrapair. Within broods, the extrapair youngwere often fathered by several males. Despite screening allresident and some floater males, we could identify the biologicalfather of only 21% of all extrapair offspring. All identifiedextrapair males were close neighbors. Extrapair males did notdiffer from within-pair males in any of the measured characteristics,except that the former had larger cloacal protuberances than thelatter. Extrapair males were equally successful in gaining paternityin their own broods as males that did not father extra young.In nests with mixed paternity, extrapair young did not differfrom within-pair young in body size or mass. However, nestswith extrapair young had higher hatching success than nestswithout extrapair young. All examined unhatched eggs were fertilizedand thus hatch failure resulted from embryo mortality. The availabledata are in accordance with the genetic diversity and the geneticcompatibility hypothesis, but not with the good genes hypothesis.     

Archaea sister group of Bacteria? Indications from tree reconstruction artifacts in ancient phylogenies.

The 54-kDa signal recognition particle and the receptor SR alpha, two proteins involved in the cotranslational translocation of proteins, are paralogs. They originate from a gene duplication that occurred prior to the last universal common ancestor, allowing one to root the universal tree of life. Phylogenetic analysis using standard methods supports the generally accepted cluster of Archaea and Eucarya. However, a new method increasing the signal-to-noise ratio strongly suggests that this result is due to a long-branch attraction artifact, with the Bacteria evolving fastest. In fact, the Archaea/Eucarya sisterhood is recovered only by the fast-evolving positions. In contrast, the most slowly evolving positions, which are the most likely to retain the ancient phylogenetic signal, support the monophyly of prokaryotes. Such a eukaryotic rooting provides a simple explanation for the high similarity of Archaea and Bacteria observed in complete-genome analysis, and should prompt a reconsideration of current views on the origin of eukaryotes.     

Is Oligomeris (Resedaceae) indigenous to North America? Molecular evidence for a natural colonization from the Old World

Oligomeris linifolia constitutes one of the few examples of intercontinental disjunctions at the species level between the arid regions of the Old World and SW North America. The status of the American populations has been obscure, with some authors considering the populations to be introduced, whereas others believe them to be native. To clarify these conflicting opinions, we performed phylogeographic analyses using nuclear ribosomal ITS and plastid trnL-F and rps16 sequences to infer the origin of the disjunct American populations. Two independent molecular clock approaches based on ITS and cpDNA sequences (rbcL, matK, trnL-F) were used to estimate a divergence time of O. linifolia. Low levels of sequence divergence and estimates of relatively recent splits of Oligomeris lineages disagree with the vicariance hypotheses traditionally suggested to account for New-Old World disjunctions. In addition, significant genetic differentiation of American populations does not indicate a recent anthropogenic introduction. Morphological uniformity and the sharing of haplotypes between disjunct populations, together with the molecular clock results, suggest that a long-distance dispersal event from the Old Word to SW North America may have taken place during the Quaternary, in spite of limited dispersal mechanisms in Oligomeris.     

The BioImage Archive – Building a Home for Life-Sciences Microscopy Data

Despite the huge impact of data resources in genomics and structural biology, until now there has been no central archive for biological data for all imaging modalities. The BioImage Archive is a new data resource at the European Bioinformatics Institute (EMBL-EBI) designed to fill this gap. In its initial development BioImage Archive accepts bioimaging data associated with publications, in any format, from any imaging modality from the molecular to the organism scale, excluding medical imaging. The BioImage Archive will ensure reproducibility of published studies that derive results from image data and reduce duplication of effort. Most importantly, the BioImage Archive will help scientists to generate new insights through reuse of existing data to answer new biological questions, and provision of training, testing and benchmarking data for development of tools for image analysis. The archive is available at https://www.ebi.ac.uk/bioimage-archive/.     

Is there evidence for automatic imitation in a strategic context?

Over the past decade, a compelling number of studies reported that observing an action makes the imitation of that action more likely. The automatic character of human imitative behaviour was often claimed, but rarely tested. The demonstration of the absence of conscious control has been attempted in a recent report claiming that imitation can occur in the rock-paper-scissors (RPS) game, where strategic players should avoid imitating their opponents. This surprising result could serve as strong evidence that humans imitate each other unconsciously. We find, however, that this conclusion is problematic. In addition to reviewing the original methods, in this work, we also replicated the experiment with double the sample size. Thorough examination of the original analyses and the results of the present replication do not support the original conclusion. In our view, testing the theory of automatic imitation in RPS games is a potentially promising avenue of exploration, yet the interpretation of the data requires further understanding of the subsidiary effects controlling the behaviour of the players.