Confirmation in sociobiology: Comments on Barbara Horan's ‘functional explanations in sociobiology’

Responses

Confirmation in sociobiology: Comments on Barbara Horan's functional explanations in sociobiology     

Tree diversity,congruence and endemism: Himalaya ‘The land of diversity’

Trees are acknowledged as most valued gift of nature and saviour of earth, enhancing and protecting landscapes, ecosystems and production systems. An authentic database of tree flora missing from local to global scale has immense value. Formulation of conservation and management policies are difficult owing to huge variation in number of species, lack of tree cover and quantification of tree diversity. To endow with a pragmatic groundwork for quantification of tree diversity of IHR, we had published an inventory of 1466 tree species (Angiosperms and Gymnosperms) along with their taxonomically vetted scientific name, distributional range, phenological attributes (leaf persistence and flower colour), use value, congruence, endemism and threatened species. One more database on tree diversity of Western Himalaya was also published with an annotated list of tree flora compiled from unrestricted literature and e-floras related to the regions. The present paper is an attempt to bring out the overall representation of tree flora of IHR, its distributional pattern, congruence, and endemism criterion in Western and Eastern Himalaya along with correlation between the regions as well as states.

     

Low genetic diversity and functional constraint of miRNA genes participating pollen–pistil interaction in rice

Key message

In this study, we sequenced and analyzed the expression and evolution of rice miRNA genesparticipating pollen-pistil interaction that is crucial to rice yield.

Abstract

Pollen–pistil interaction is an essential reproductive process for all flowering plants. While microRNAs (miRNAs) are important noncoding small RNAs that regulate mRNA levels in eukaryotic cells, there is little knowledge about which miRNAs involved in the early stages of pollen–pistil interaction in rice and how they evolve under this conserved process. In this study, we sequenced the small RNAs in rice from unpollinated pistil (R0), pistil from 5 min and 15 min after pollination, respectively, to identify known and novel miRNAs that are involved in this process. By comparing the corresponding mRNA-seq dataset, we identified a group of miRNAs with strong negative expression pattern with their target genes. Further investigation of all miRNA loci (MIRNAs) across 1083 public rice accessions revealed significantly reduced genetic diversity in MIRNAs with strong negative expression of their targets when comparing to those with little or no impact on targets during pollen–pistil interaction. Annotation of targets suggested that those MIRNAs with strong impact on targets were pronounced in cell wall related processes such as xylan metabolism. Additionally, plant conserved miRNAs, such as those with functions in gibberellic acid, auxin and nitrate signaling, were also with strong negative expression of their targets. Overall, our analyses identified key miRNAs participating pollen–pistil interaction and their evolutionary patterns in rice, which can facilitate the understanding of molecular mechanisms associated with seed setting.

     

Phylogenetic relationships ofBacteria based on comparative sequence analysis of elongation factor Tu and ATP-synthase β-subunit genes

Comparative sequence analyses were performed on 14 genes encoding bacterial elongation factors EF-Tu and 7 genes encoding the -subunit of bacterial F₁F₀ type ATP-synthases. The corresponding predicted amino acid sequences were compared with published primary structures of homologous molecules. Phylogenetic trees were reconstructed from both data sets of aligned protein sequences and from an equivalent selection of 16S rRNA sequences by applying distance matrix and maximum parsimony methods. The EF-Tu data were in very good agreement with the rRNA data, although the resolution within the EF-Tu tree was reduced at certain phylogenetic levels. The resolution power of the ATPase -subunit sequence data were more reduced than those of the EF-Tu data. In comparison with the 16S rRNA tree there are minor differences in the order of adjacent branchings within the ATPase -subunit tree.     

‘Fine’ and ‘coarse’ mycorrhizal fungi on red clover plants in acid soils: Root colonization and plant responses

Three sterilized acid soils were inoculated with inocula of vesicular-arbuscular mycorrhizal fungi. Soils were limed and/or P fertilized to produce different fertility levels. Most inocula consisted of mixtures of fine + coarse type endophytes. Red clover (Trifolium pratense L.) was seeded in pots and grown in a glasshouse for 4 months. Root colonization by VAM fungi, the relative infection byGlomus tenue compared to that by coarse VAM fungi and the effect of inoculation on red clover growth and mineral nutrition (P, K, Ca and Mg) were studied. Spores were also checked and tentatively identified.Results showed that root colonization by VAM fungi was higher than 50% in most cases, the lower values being found in the soil with the highest P content. Inocula containingG. mosseae + G. tenue infected plant roots only in limed (pH>5.7) soils. A study of the relative colonization by fine and coarse endophytes showed that the competitive ability againstG. tenue followed the orderG. fasiculatum > G. mosseae > G. epigaeum > G. macrocarpum, although soil properties and fertility were crucial factors.Glomus lacteum was tentatively identified in two of the three experimental soils. The inoculum in whichGlommus tenue was most infective was also the most efficient in improving plant growth and nutrient uptake. The effect of inoculation on P and Mg uptake followed a similar pattern.     

The ‘masking effect’ of silviculture on substrate-induced plant diversity in oak-hornbeam forests from northern France

Traditional measures of plant diversity from phytosociological relevés are used to compare floristical richness and diversity between different oak-hornbeam forest stands of Thiérache (Northern France). Five sets of physiognomically similar forests are distinguished according to the geological substrate: schists and sandstones, loess on schists, loess on calcareous rocks, jurassic limestones, cretaceous marls and clays. Plant species diversity is investigated at two scale levels: a phytocoenotic level and a synusial one which is supposed to partly avoid a possible silviculture-related bias. Two pools of sets may be distinguished: a calcareous and a non-calcareous one. The calcareous shows the highest floristical diversity, and the non-calcareous one the highest phytosociological richness. For each inter-pool pair of sets, plant species diversity is significantly different at the phytocoenotic level as well as at the level of herbaceous or shrubby synusiae, but not at the arborescent one. Through the coppice-with-standards practice, silviculture was the main determining factor for arborescent synusiae while the herbaceous and shrubby synusiae, which support the major part of the diversity, remained strongly influenced by the substrate. It is suggested that silviculture has got a masking effect on plant species diversity within oak-hornbeam managed forests by making uniform tree layers that outshine the understory vegetation diversity.     

Comparison of ‘ignition’ and ‘extraction’ methods for the determination of organic phosphate in rocks and soils

Summary Ignition markedly increased the solubility in dilute acid of iron- and aluminium-bound inorganic phosphate in samples of weathered New Zealand greywacke rock. This observation supports the view that ignition methods may sometimes overestimate the total organic phosphate of soils.     

Synergism of thidiazuron and benzyladenine in axillary shoot formation depends on sequence of application in Miscanthus X ogiformis ‘Giganteus’

Shoots of Miscanthus X ogiformis Honda Giganteus transferred from medium with benzyladenine (BA) to thidiazuron (TDZ) formed significantly more axillary shoots than shoots grown continuously on either medium, or transferred from TDZ to BA. Shoot formation on axillary shoots transferred from BA-containing media to media with kinetin or isopentenyladenine (2iP) or transferred from media with TDZ, kinetin or 2iP to media with BA, corresponded to the number of shoots formed in the previous subculture. Shoot formation on shoots transferred from medium containing BA to media containing combinations of BA and/or TDZ increased with increasing concentrations of TDZ in the first subculture, whereas shoot formation in the second and third subculture depended on the BA concentration. When shoots were transferred from media with BA to media with TDZ, the time for shoot formation, as well as shoot size, indicate that the combined effect of BA and TDZ is expressed only during the early phase of the subculture. The results suggest that adenine- and phenylurea-type cytokinins have a common binding site in the plant cell, and a model is proposed.Abbreviations BA 6-benzyladenine - CBP cytokinin-binding protein - 2iP isopentenyladenine - KIN kinetin - MS Murashige & Skoog - TDZ thidiazuron     

Reply to: Comment on ‘neutron imaging reveals internal plant water dynamics’

Background

Our recent publication (Warren et al., Plant Soil 366:683–693, 2013) described how pulses of deuterium oxide (D₂O) or H₂O combined with neutron radiography can be used to indicate root water uptake and hydraulic redistribution in maize. This technique depends on the large inherent differences in neutron cross-section between D and H atoms resulting in strong image contrast.

Scope and Conclusions

However, as illustrated by Carminati and Zarebanadkouki (2013) there can be a change in total water content without a change in contrast simply by a change in the relative proportions of D₂O and H₂O. We agree with their premise and detailed calculations (Zarebanadkouki at al. 2012, 2013), and present further evidence that mixing of D₂O and H₂O did not confound evidence of hydraulic redistribution in our study.     

Presence of unique repeated insertion sequences in nodulation genes of Rhizobium ‘hedysari’

Cloning and sequencing of DNA from a symbiotic large plasmid in Rhizobium hedysari strain IS 123 required for its nodulation of the mediterranean legume crop Hedysarum coronarium (sulla) and complementation studies of nod^- mutant derivatives led to the characterization of a 30-kb region containing common and host-specific nod genes. This DNA region also contained at least six copies of a novel insertion sequence-like structure, some of which appeared to have suffered deletions. This 0.8 kb novel element carries two 17-bp flanking inverted repeats and an open reading frame showing homology with a transposase from Staphylococcus aureus. Hybridization studies revealed that several strains of Rhizobium hedysari carry this element in various copy number. The six copies in strain IS 123 appear clustered specifically within the pSym nod region.The significance of this IS element in rhizobia and its possible use as a probe for taxonomic and phylogenetic studies of Rhizobiaceae is addressed.     

Endangered species diversity ‘hot spots’ in Russia and centers of endemism

Geographic distributions of all 125 endangered and threatened animals and all 70 endangered flowering plant species were compiled and mapped by administrative territory (republics, states, provinces, and districts) of the Russian Federation, based on distributional data in the official Red Data Books of the R.S.F.S.R. [Eliseev et al. (eds) (1985) Red Book of the R.S.F.S.R.: Animals. Rosleskhoz Publishing, Moscow; Golovanov et al. (eds). (1988). Red Book of the R.S.F.S.R.: Plants. Rosagprom Publishing, Moscow]. Territories were ranked using an algorithm that gives highest rank to the single territory with the greatest number of endangered species present, then iteratively assigns the next highest rank to the territory containing the greatest number of species not found in a territory of higher rank. This algorithm minimizes the number of territories necessary to include one population of each endangered species, but may designate very low rank to a territory that holds high numbers of endangered species if many of those species are found in a territory of higher rank. When different sets of species were used to determine territory rank with this algorithm the only significant correlation between rank lists was between ranks generated when all species are used and when only species endemic to single territories were used. Mountainous territories on Russia's southern borders held the greatest numbers of endangered species and were highly ranked whether or not species occurring outside of Russia were excluded from the ranking algorithm. The Maritime state, Krasnodar state, Dagestan republic, Sakhalin province and the Jewish province all are centers of endangered species diversity that together contain 50 or more of endangered species for multiple taxonomic groups; this was the Dobson et al. [(1997) Science 275: 550–553] definition of an endangered species hot spot. These are all mountainous territories on Russia's southern border. Precise territorial ranking within the mountainous southern regions of the Southern Far East, Caucasus, and Altai/Sayan regions of southern Siberia was highly influenced by species endemic to single territories.     

Partial resistance to powdery mildew in German spring wheat ‘Naxos’ is based on multiple genes with stable effects in diverse environments

Powdery mildew is one of the most important wheat diseases in temperate regions of the world. Resistance breeding is considered to be an economical and environmentally benign way to control this disease. The German spring wheat cv. 'Naxos' exhibits high levels of partial and race non-specific resistance to powdery mildew in the field and is a valuable source in resistance breeding. The main objective of the present study was to map the genetic factors behind the resistance in Naxos, based on a population of recombinant inbred lines (RIL) from a cross with the susceptible CIMMYT breeding line SHA3/CBRD. Powdery mildew severity was evaluated in six field trials in Norway and four field trials in China. The major quantitative trait locus (QTL) with resistance from Naxos was detected close to the Pm3 locus on 1AS in all environments, and explained up to 35% of the phenotypic variation. Naxos was shown to carry another major QTL on 2DL and minor ones on 2BL and 7DS. QTL with resistance from SHA3/CBRD were detected on 1RS, 2DLc, 6BL and 7AL. The QTL on the 1B/1R translocation showed highly variable effects across environments corresponding to known virulence differences against Pm8. SHA3/CBRD was shown to possess the Pm3 haplotype on 1AS, but none of the known Pm3a-g alleles. The RIL population did not provide any evidence to suggest that the Pm3 allele of SHA3/CBRD acted as a suppressor of Pm8.     

Mode of inheritance and genetic diversity of BaMMV resistance of exotic barley germplasms carrying genes different from ‘ym4’

Summary In order to obtain information about the mode of inheritance of BaMMV resistance in germplasms carrying genes different from the German gene ym4 f₁-tests for resistance as well as F₂-segregation analyses of crosses to susceptible German cultivars were carried out by mechanical inoculation in the greenhouse. In the f₁ the majority of plants of each combination tested reacted susceptible to BaMMV while in the F₂ a good fit to a segregation of 1r:3s or 7r:9s was observed. Therefore, the results of these tests revealed that the BaMMV resistance of all the varieties tested is inherited either by a single or by two recessive genes. By testing intercrosses of these resistant varieties segregation of BaMMV-susceptile plants was observed in the majority of combinations, revealing a high degree of genetic diversity in the barley gene pool.Dedicated to Professor Dr. Wolfgang Schnell on the occasion of his 80th birthday     

Effects of habitat complexity on forest beetle diversity: do functional groups respond consistently?

We examined the responses of a beetle assemblage to habitat complexity differences within a single habitat type, Sydney sandstone ridgetop woodland, using pitfall and flight‐intercept trapping. Six habitat characters (tree canopy cover, shrub canopy cover, ground herb cover, soil moisture, amount of leaf litter, and amount of logs, rocks and debris) were scored between 0 and 3 using ordinal scales to reflect habitat complexity at survey sites. Pitfall trapped beetles were more species rich and of different composition in high complexity sites, compared with low complexity sites. Species from the Staphylinidae (Aleocharinae sp. 1 and sp. 2), Carabidae (Pamborus alternans Latreille), Corticariidae (Cartodere Thomson sp. 1) and Anobiidae (Mysticephala Ford sp. 1) were most clearly responsible for the compositional differences, preferring high complexity habitat. Affinities between general functional groupings of pitfall‐trapped beetles and habitat variables were not clear at a low taxonomic resolution (family level). The composition and species richness of flight‐intercept‐trapped beetles were similar in high and low complexity sites. Our study demonstrates that discrete responses of the various functional groups of beetles are strongly associated with their feeding habits, indicated by differing habitat components from within overall composite habitat complexity measures. Although habitat preferences by beetle species may often reflect their foraging habits, clarification of the causal mechanisms underpinning the relationships between habitat complexity and beetles are critical for the development of general principles linking habitat, functional roles and diversity.     

Pleurotus eryngii species complex: sequence analysis and phylogeny based on partial EF1α and RPB2 genes

The Pleurotus eryngii species complex comprises at least six varieties (var. eryngii (DC.: Fr) Quel., ferulae Lanzi, elaeoselini Venturella et?al., nebrodensis (Inzenga) Sacc., tingitanus Lewinsohn et?al. and tuoliensis C.J. Mou). This species is unique among the genus Pleurotus because in nature it is found in association with certain species of the Apiaceae (Umbelliferae) and Asteraceae (Compositae) families. Sequences of partial regions of the translation elongation factor (EF1α) and RNA polymerase II (RPB2) genes were analyzed in order to detect nucleotide polymorphisms that might unequivocally distinguish varieties eryngii, ferulae, elaeoselini and nebrodensis. A phylogenetic analysis was also performed with an aim to establish phylogenetic relationships among those. Sequence analysis of the partial EF1α and RPB2 genes contained nucleotide polymorphisms able to unequivocally distinguish variety nebrodensis from the rest. However, distinction among eryngii, elaeoselini and ferulae was achieved only through the RPB2 gene. The phylogenetic analyses from the combined data sets (EF1α and RPB2) indicated that P. eryngii is a monophyletic group and that varieties eryngii, elaeoselini and ferulae are closely related. P. eryngii var. nebrodensis was placed in a distinct clade clearly differentiated from the other varieties but still monophyletic with the P. eryngii complex. The limited nucleotide variation in partial EF1α and RPB2 among varieties eryngii, ferulae and elaeoselini supports the placement of these groups as varieties and not species within the complex.