Metabolic pathways variability and sequence/networks comparisons

Background  

In this work a simple method for the computation of relative similarities between homologous metabolic network modules is presented. The method is similar to classical sequence alignment and allows for the generation of phenotypic trees amenable to be compared with correspondent sequence based trees. The procedure can be applied to both single metabolic modules and whole metabolic network data without the need of any specific assumption.     

Pollinators visit related plant species across 29 plant–pollinator networks

Understanding the evolution of specialization in host plant use by pollinators is often complicated by variability in the ecological context of specialization. Flowering communities offer their pollinators varying numbers and proportions of floral resources, and the uniformity observed in these floral resources is, to some degree, due to shared ancestry. Here, we find that pollinators visit related plant species more so than expected by chance throughout 29 plant–pollinator networks of varying sizes, with “clade specialization” increasing with community size. As predicted, less versatile pollinators showed more clade specialization overall. We then asked whether this clade specialization varied with the ratio of pollinator species to plant species such that pollinators were changing their behavior when there was increased competition (and presumably a forced narrowing of the realized niche) by examining pollinators that were present in at least three of the networks. Surprisingly, we found little evidence that variation in clade specialization is caused by pollinator species changing their behavior in different community contexts, suggesting that clade specialization is observed when pollinators are either restricted in their floral choices due to morphological constraints or innate preferences. The resulting pollinator sharing between closely related plant species could result in selection for greater pollinator specialization.     

Angiosperm origin and early stages of seed plant evolution deduced from rRNA sequence comparisons

Summary Complete or partial nucleotide sequences of five different rRNA species, coded by nuclear (18S, 5.8S, and 5S) or chloroplast genomes (5S, 4.5S) from a number of seed plants were determined. Based on the sequence data, the phylogenetic dendrograms were built by two methods, maximum parsimony and compatibility. The topologies of the trees for different rRNA species are not fully congruent, but they share some common features. It may be concluded that both gymnosperms and angiosperms are monophyletic groups. The data obtained suggest that the divergence of all the main groups of extant gymnosperms occurred after the branching off of the angiosperm lineage. As the time of divergence of at least some of these gymnosperm taxa is traceable back to the early Carboniferous, it may be concluded that the genealogical splitting of gymnosperm and angiosperm lineages occurred before this event, at least 360 million years ago, i.e., much earlier than the first angiosperm fossils were dated. Ancestral forms of angiosperms ought to be searched for among Progymnospermopsida. Genealogical relationships among gymnosperm taxa cannot be deduced unambiguously on the basis of rRNA data. The only inference may be that the taxon Gnetopsida is an artificial one, andGnetum andEphedra belong to quite different lineages of gymnosperms. As to the phylogenetic position of the two Angiospermae classes, extant monocotyledons seem to be a paraphyletic group located near the root of the angiosperm branch; it emerged at the earliest stages of angiosperm evolution. We may conclude that either monocotyledonous characters arose independently more than once in different groups of ancient Magnoliales or that monocotyledonous forms rather than dicotyledonous Magnoliales were the earliest angiosperms. Judging by the rRNA trees, Magnoliales are the most ancient group among dicotyledons. The most ancient lineage among monocotyledons leads to modern Liliaceae.     

Size-dependent species richness: trends within plant communities and across latitude

We examine how species richness and species‐specific plant density (number of species and number of individuals per species, respectively) vary within community size frequency distributions and across latitude. Communities from Asia, Africa, Europe, and North, Central and South America were studied (60°4′N–41°4′S latitude) using the Gentry data base. Log–log linear stem size (diameter) frequency distributions were constructed for each community and the species richness and species‐specific plant density within each size class were determined for each frequency distribution. Species richness in the smallest stem size class correlated with the Y‐intercepts (β‐values) of the regression curves describing each log–log linear size distributions. Two extreme community types were identified (designated as type A and type B). Type A communities had steep size distributions (i.e. large β‐values), log–log linear species‐richness size distributions, low species‐specific plant density distributions, and a small size class (2–4 cm) containing the majority of all species but rarely conspecifics of the dominant tree species. Type B communities had shallow size distributions (i.e. small β‐values), more or less uniform (and low) size class species‐ richness and species‐specific density distributions and size‐dominant species resident in the smallest size class. Type A communities were absent in the higher latitudes but increased in number towards the equator, i.e. in the smallest size class, species richness increased (and species‐specific density decreased) towards the tropics. Based on our survey of type A and type B communities (and their intermediates), species richness evinces size‐dependent and latitudinal trends, i.e. species richness increased with decreasing body size and most species increasingly reside in the smallest plant size class towards the tropics. Across all latitudes, a trade‐off exists between the number of species and the number of individuals per species residing in the smaller size classes.     

Studies of the transferability of microsatellites derived from Triticum tauschii to hexaploid wheat and to diploid related species using amplification,hybridization and sequence comparisons

Hexaploid wheat (Triticum aestivum L em Thell) is derived from a complex hybridization procedure involving three diploid species carrying the A, B and D genomes, respectively. We recently isolated microsatellites from a T. tauschii library enriched for various motifs and evaluated the transferability of these markers to several diploid species carrying the A, B or D genomes. All of the primer pairs amplifying more than one locus on bread wheat and half of those giving D-genome-specific loci gave an amplification product on A-and/or B-diploid species. All of the markers giving a single amplification product for T. tauschii and no amplification on the other diploid species were D-genome-specific at the hexaploid level. The non-specific microsatellite markers (which gave an amplification product on diploid species carrying the A, B or D genome) gave either a complex amplification pattern on bread wheat (with several bands) or generated a single band which mapped to the D genome. Southern blot hybridizations with probes corresponding to the microsatellite flanking regions gave a signal on all diploid and hexaploid species, whatever the specificity of the microsatellite. The patterns observed on bread wheat were generally in accordance with those observed for diploid species, with slight rearrangements. This suggests that the specificity of microsatellite markers is probably due to mutations in microsatellite flanking regions rather than sequence elimination during polyploidization events and that genome stringency is higher at the polyploid than at the diploid level.     

microRNA target predictions across seven Drosophila species and comparison to mammalian targets

microRNAs are small noncoding genes that regulate the protein production of genes by binding to partially complementary sites in the mRNAs of targeted genes. Here, using our algorithm PicTar, we exploit cross-species comparisons to predict, on average, 54 targeted genes per microRNA above noise in Drosophila melanogaster. Analysis of the functional annotation of target genes furthermore suggests specific biological functions for many microRNAs. We also predict combinatorial targets for clustered microRNAs and find that some clustered microRNAs are likely to coordinately regulate target genes. Furthermore, we compare microRNA regulation between insects and vertebrates. We find that the widespread extent of gene regulation by microRNAs is comparable between flies and mammals but that certain microRNAs may function in clade-specific modes of gene regulation. One of these microRNAs (miR-210) is predicted to contribute to the regulation of fly oogenesis. We also list specific regulatory relationships that appear to be conserved between flies and mammals. Our findings provide the most extensive microRNA target predictions in Drosophila to date, suggest specific functional roles for most microRNAs, indicate the existence of coordinate gene regulation executed by clustered microRNAs, and shed light on the evolution of microRNA function across large evolutionary distances. All predictions are freely accessible at our searchable Web site http://pictar.bio.nyu.edu.     

Genetic diversity across natural populations of three montane plant species from the Western Ghats, India revealed by intersimple sequence repeats

We analysed genetic diversity across the natural populations of three montane plant species in the Western Ghats, India; Symplocos laurina, Gaultheria fragrantissima and Eurya nitida using intersimple sequence repeat (ISSR) markers. These markers revealed genetic diversity within the populations of these plants from Nilgiri and also between two populations of S. laurina from Nilgiri and Amboli. Genetic variation within and between populations was analysed using various parameters such as total heterozygosity (HT), heterozygosity within population (HS), diversity between populations (DST), coefficient of population differentiation (GST), genetic distance (D) and gene flow (Nm). Total heterozygosity (HT) was higher for S. laurina (0.238) than for G. fragrantissima (0.172) and E. nitida (0.182). Two populations of S. laurina, separated by > 1000 km, showed a high within-population variation (53.7%) and a low gene flow (Nm = 0.447). upgma phenograms depicted a tendency of accessions to group according to their geographical locations in all the three plant species. The insight gained into the genetic structure of these plant populations might have implications in developing in situ and ex situ conservation strategies.     

Co-evolutionary networks of genes and cellular processes across fungal species

Background  

The introduction of measures such as evolutionary rate and propensity for gene loss have significantly advanced our knowledge of the evolutionary history and selection forces acting upon individual genes and cellular processes.     

Plant-associated bacterial populations on native and invasive plant species: comparisons between 2 freshwater environments

Plant-microbial interactions have been well studied because of the ecological importance of such relationships in aquatic systems. However, general knowledge regarding the composition of these biofilm communities is still evolving, partly as a result of several confounding factors that are attributable to plant host properties and to hydrodynamic conditions in aquatic environments. In this study, the occurrences of various bacterial phylogenetic taxa on 2 native plants, i.e., mayapple (Podophyllum peltatum L.) and cow parsnip (Heracleum maximum Bartram), and on an invasive species, i.e., garlic mustard (Alliaria petiolata (M. Bieb.) Cavara & Grande), were quantitatively examined using nucleic acid staining and fluorescence in situ hybridization. The plants were incubated in triplicates for about a week within the Kalamazoo River and Pierce Cedar Creek as well as in microcosms. The bacterial groups targeted for enumeration are known to globally occur in relatively high abundance and are also ubiquitously distributed in freshwater environments. Fluorescence in situ hybridization analyses of the bacterioplankton assemblages revealed that the majority of bacterial cells that hybridized with the different probes were similar between the 2 sites. In contrast, the plant-associated populations while similar on the 3 plants incubated in Kalamazoo River, their representations were highest on the 2 native plants relative to the invasive species in Pierce Cedar Creek. Overall, our results further suggested that epiphytic bacterial assemblages are probably under the influences of and probably subsequently respond to multiple variables and conditions in aquatic milieus.     

Acceptability and suitability of seven plant species for the mealybug Phenacoccus parvus

Survival, development and fecundity of cohorts of the mealybug Phenacoccus parvus Morrison were measured over one generation on seven plant species representing four plant families. Survival, development and fecundity were not significantly higher on the mealybug's principal field host, the weed Lantana camara L. (Verbenaceae), than on other plant species including Lycopersicon esculentum Miller (tomato) and Solanum melongena L. (eggplant). The acceptability of the leaves of the seven plant species to P. parvus first instar crawlers was measured on hatching, after active walking and after food deprivation. Lantana camara was the highest ranked plant species for all treatments. The number of crawlers settling on lower ranked plant species increased with the level of food deprivation.     

Constrained preferences in nitrogen uptake across plant species and environments

Knowledge of determining factors for nitrogen uptake preferences and how they are modified in changing environments are critical to understand ecosystem nitrogen cycling and to predict plant responses to future environmental changes. Two ¹⁵N tracer experiments utilizing a unique differential labelled nitrogen source were employed in both African savannas and greenhouse settings. The results demonstrated that nitrogen uptake preferences were constrained by the climatic conditions. As mainly indicated by root δ¹⁵N signatures at 1:1 ammonium/nitrate ratio, in the drier environments, plants preferred nitrate and in the wetter environments they preferred ammonium. Nitrogen uptake preferences were different across different ecosystems (e.g. from drier to wetter environments) even for the same species. More significantly, our experiments showed that the plant progeny continued to exhibit the same nitrogen preference as the parent plants in the field, even when removed from their native environment and the nitrogen source was changed dramatically. The climatic constraint of nitrogen uptake preference is likely influenced by ammonium/nitrate ratios in the native habitats of the plants. The constancy in nitrogen preference has important implications in predicting the success of plant communities in their response to climate change, to seed bank use and to reforestation efforts.     

High-resolution bioclimatic dataset derived from future climate projections for plant species distribution modeling

Species distribution modeling is playing an increasingly prominent role in ecology and global change biology, owing to its potential to predict species range shifts, biodiversity losses, and biological invasion risks for future climates. Such models are now well-established as important tools for biological conservation. However, the lack of high-resolution data for future climate scenarios has seriously limited their application, particularly because of the scale gap between general circulation models (GCMs) and species distribution models (SDMs). A recently introduced change-factor downscaling technique provides a convenient way to build high-resolution datasets from GCM projections. Here, we present a high-resolution (10’ × 10’) global bioclimatic dataset (BioPlant) for plant species distribution. The 15 bioclimatic variables we select are considered those most eco-physiologically relevant. They can be easily calculated from climatic variables common to all GCM projections. In addition to the traditional classes of variables regarding temperature and precipitation, the BioPlant dataset emphasizes the interactions between temperature and precipitation, particularly within plant growing seasons. A preliminary visual analysis shows that variations among GCMs are more significant on a species range scale than on a global scale. Thus, the formerly advocated ensemble modeling method should be applied not only to different SDMs, but also to various GCMs. Statistic analysis suggests that divergent behavior among GCM variations for temperature class variables and classes of precipitation variables requires special attention. Our dataset may provide a common platform for ensemble modeling, and can serve as an example to develop higher-resolution regional datasets.     

Allozyme and DNA sequence comparisons of nine species of Encephalartos (Zamiaceae)

Phylogenetic relationships between Encephalartos altensteinii Lehmann, E. arenarius R.A. Dyer, E. horridus (Jacquin) Lehmann, E. latifrons Lehmann, E. lehmannii Lehmann, E. longifolius (Jacquin) Lehmann, E. princeps R.A. Dyer and E. trispinosus (Hooker) R.A. Dyer were studied, using E. ferox Bertoloni f. as outgroup. Three continuous and one discontinuous buffer systems were used and gene products of 14 enzyme coding loci were examined by horizontal starch gel-electrophoresis. Genetic variation was studied in a cultivated population of E. lehmannii and the average heterozygosity value for this population is 13.5%, which falls within the range reported for other cycad species. Fixed allele differences between the species studied was not found at any of the loci studied, which suggest that these species are closely related. DNA sequence analysis of rbcL and ITS 1 & 2 genes (1428 and 895 basepairs, respectively) confirmed the close genetic relationships between these taxa. According to ITS and rbcL sequences E. altensteinii and E. princeps are sibling taxa which form a sister group to E. arenarius, E. horridus, E. latifrons, E. lehmannii, E. longifolius, and E. trispinosus. The genetic distances between both groups were 0.12-0.47% for ITS and 0.08-0.16% for rbcL DNA. The results indicate recent (probably pleistocenic) speciation for this group of cycads, and the relationships are discussed with reference to affinities based on morphology and distribution.     

Purification and sequence of a non-opioid peptide derived from ovine proenkephalin: implications for possible species specific processing

A non-enkephalin containing pentadeca peptide derived from ovine adrenal proenkephalin has been purified and sequenced. The sequence of the peptide is: Phe-Ala-Glu-Pro-Leu-Pro-Ser-Glu-Glu-Glu-Gly-Glu-Ser-Tyr-Ser (preproenkephalin 237-251) representing the amino portion of peptide B (preproenkephalin 237-268). The sequence is identical to bovine preproenkephalin 237-251, differing from the corresponding human sequence at positions 240 and 244. This peptide can be generated by a processing event common to other opioid peptides and is present in chromaffin granules in significant amounts. The presence of this peptide in substantial quantities suggests a possible difference in proenkephalin processing between the bovine and ovine adrenal medulla.     

Meaningful traits for grouping plant species across arid ecosystems

Grouping species may provide some degree of simplification to understand the ecological function of plants on key ecosystem processes. We asked whether groups of plant species based on morpho-chemical traits associated with plant persistence and stress/disturbance resistance reflect dominant plant growth forms in arid ecosystems. We selected twelve sites across an aridity gradient in northern Patagonia. At each site, we identified modal size plants of each dominant species and assessed specific leaf area (SLA), plant height, seed mass, N and soluble phenol concentration in green and senesced leaves at each plant. Plant species were grouped according with plant growth forms (perennial grasses, evergreen shrubs and deciduous shrubs) and plant morphological and/or chemical traits using cluster analysis. We calculated mean values of each plant trait for each species group and plant growth form. Plant growth forms significantly differed among them in most of the morpho-chemical traits. Evergreen shrubs were tall plants with the highest seed mass and soluble phenols in leaves, deciduous shrubs were also tall plants with high SLA and the highest N in leaves, and perennial grasses were short plants with high SLA and low concentration of N and soluble phenols in leaves. Grouping species by the combination of morpho-chemical traits yielded 4 groups in which species from one growth form prevailed. These species groups differed in soluble phenol concentration in senesced leaves and plant height. These traits were highly correlated. We concluded that (1) plant height is a relevant synthetic variable, (2) growth forms adequately summarize ecological strategies of species in arid ecosystems, and (3) the inclusion of plant morphological and chemical traits related to defenses against environmental stresses and herbivory enhanced the potential of species grouping, particularly within shrubby growth forms.