On the size distribution of live genera

This article deals with the theoretical size (number of species) distribution of live genera, arising from a simple model of macroevolution in which speciations and extinctions are assumed to occur independently and at random, and in which new genera are formed by the random splitting of existing genera. Mathematically, the distribution is that of the state of a homogeneous birth-and-death process after an exponentially distributed time. An ordinary differential equation for the generating function of the distribution is derived and solved and a recurrence relation for computing the probabilities in the distribution presented. Some properties of the distribution, including asymptotic behaviour, are examined and the distribution of the time since establishment of a genus of a given size derived. Fitting the distribution to empirical taxon size distributions by maximum likelihood is discussed and two examples are presented.     

Random generation of RNA secondary structures according to native distributions

Background

Random biological sequences are a topic of great interest in genome analysis since, according to a powerful paradigm, they represent the background noise from which the actual biological information must differentiate. Accordingly, the generation of random sequences has been investigated for a long time. Similarly, random object of a more complicated structure like RNA molecules or proteins are of interest.

Results

In this article, we present a new general framework for deriving algorithms for the non-uniform random generation of combinatorial objects according to the encoding and probability distribution implied by a stochastic context-free grammar. Briefly, the framework extends on the well-known recursive method for (uniform) random generation and uses the popular framework of admissible specifications of combinatorial classes, introducing weighted combinatorial classes to allow for the non-uniform generation by means of unranking. This framework is used to derive an algorithm for the generation of RNA secondary structures of a given fixed size. We address the random generation of these structures according to a realistic distribution obtained from real-life data by using a very detailed context-free grammar (that models the class of RNA secondary structures by distinguishing between all known motifs in RNA structure). Compared to well-known sampling approaches used in several structure prediction tools (such as SFold) ours has two major advantages: Firstly, after a preprocessing step in time for the computation of all weighted class sizes needed, with our approach a set of m random secondary structures of a given structure size n can be computed in worst-case time complexity while other algorithms typically have a runtime in . Secondly, our approach works with integer arithmetic only which is faster and saves us from all the discomforting details of using floating point arithmetic with logarithmized probabilities.

Conclusion

A number of experimental results shows that our random generation method produces realistic output, at least with respect to the appearance of the different structural motifs. The algorithm is available as a webservice at http://wwwagak.cs.uni-kl.de/NonUniRandGen and can be used for generating random secondary structures of any specified RNA type. A link to download an implementation of our method (in Wolfram Mathematica) can be found there, too.     

Discontinuous DNA variation in the evolution of plant species

The four genera,Clarkia, Nicotiana, Lathyrus andAllium have widely different geographical distributions and evolutionary patterns, but the nucleardna amounts of species within each genus occur in groups at intervals of approximately 2 or 4 picograms. Diploids with different basic chromosome numbers, and polyploids, can occur in the same group. When anydna group of one genus is paired with the nearestdna group of another genus all other groups of both genera pair exactly in so far as they have a common range of DNA amounts. Hence thedna groups of the four genera are associated in larger groups, or nodes, separated by 2 or 4 picograms forming a progression over all four genera, implying there are favoured, discontinuous,dna amounts, either arisingde novo or subsequently within a continuously varying distribution.     

Topological classification and enumeration of RNA structures by genus

To an RNA pseudoknot structure is naturally associated a topological surface, which has its associated genus, and structures can thus be classified by the genus. Based on earlier work of Harer–Zagier, we compute the generating function $\mathbf{D}_{g,\sigma }(z)=\sum _{n}\mathbf{d}_{g,\sigma }(n)z^n$ for the number $\mathbf{d}_{g,\sigma }(n)$ of those structures of fixed genus $g$ and minimum stack size $\sigma $ with $n$ nucleotides so that no two consecutive nucleotides are basepaired and show that $\mathbf{D}_{g,\sigma }(z)$ is algebraic. In particular, we prove that $\mathbf{d}_{g,2}(n)\sim k_g\,n^{3(g-\frac{1}{2})} \gamma _2^n$ , where $\gamma _2\approx 1.9685$ . Thus, for stack size at least two, the genus only enters through the sub-exponential factor, and the slow growth rate compared to the number of RNA molecules implies the existence of neutral networks of distinct molecules with the same structure of any genus. Certain RNA structures called shapes are shown to be in natural one-to-one correspondence with the cells in the Penner–Strebel decomposition of Riemann’s moduli space of a surface of genus $g$ with one boundary component, thus providing a link between RNA enumerative problems and the geometry of Riemann’s moduli space.     

Climate change‐driven extinctions of tree species affect forest functioning more than random extinctions

Aim

Climate change affects forest functioning not only through direct physiological effects such as modifying photosynthesis and growing season lengths, but also through indirect effects on community composition related to species extinctions and colonizations. Such indirect effects remain poorly explored in comparison with the direct ones. Biodiversity–ecosystem functioning (BEF) studies commonly examine the effects of species loss by eliminating species randomly. However, species extinctions caused by climate change will depend on the species’ vulnerability to the new environmental conditions, thus occurring in a specific, non‐random order. Here, we evaluated whether successive tree species extinctions, according to their vulnerability to climate change, impact forest functions differently than random species losses.

Location

Eleven temperate forests across a gradient of climatic conditions in central Europe.

Methods

We simulated tree community dynamics with a forest succession model to study the impact of species loss on the communities’ aboveground biomass, productivity and temporal stability. Tree species were removed from the local pool (1) randomly, and according to (2) their inability to be recruited under a warmer climate or (3) their increased mortality under drier conditions.

Results

Results showed that non‐random species loss (i.e., based on their vulnerability to warmer or drier conditions) changed forest functioning at a different rate, and sometimes direction, than random species loss. Furthermore, directed extinctions, unlike random, triggered tipping points along the species loss process where forest functions were strongly impacted. These tipping points occurred after fewer extinctions in forests located in the coldest areas, where ecosystem functioning relies on fewer species.

Main conclusions

We showed that the extinction of species in a deterministic and mechanistically motivated order, in this case the species vulnerability to climate change, strengthens the selection effect of diversity on ecosystem functioning. BEF studies exploring the impact of species loss on ecosystem functioning using random extinctions thus possibly underestimate the potential effect of biodiversity loss when driven by a directional force, such as climate change.

     

Two new genera of Indian Umbelliferae/Apiaceae

Two new monotypic genera are proposed:Karnataka, based uponSchultzia? benthamii C. B. Clarke (=K. benthamii) from southern Peninsular India andKedarnatha, based onK. sanctuarii, recently obtained from the Himalaya. Neither genus appears to be closely related to other apioid genera of our area.     

When size makes a difference: allometry, life-history and morphological evolution of capuchins (Cebus) and squirrels (Saimiri) monkeys (Cebinae, Platyrrhini)

Background

How are morphological evolution and developmental changes related? This rather old and intriguing question had a substantial boost after the 70s within the framework of heterochrony (changes in rates or timing of development) and nowadays has the potential to make another major leap forward through the combination of approaches: molecular biology, developmental experimentation, comparative systematic studies, geometric morphometrics and quantitative genetics. Here I take an integrated approach combining life-history comparative analyses, classical and geometric morphometrics applied to ontogenetic series to understand changes in size and shape which happen during the evolution of two New World Monkeys (NWM) sister genera.

Results

Cebus and Saimiri share the same basic allometric patterns in skull traits, a result robust to sexual and ontogenetic variation. If adults of both genera are compared in the same scale (discounting size differences) most differences are small and not statistically significant. These results are consistent using both approaches, classical and geometric Morphometrics. Cebus is a genus characterized by a number of peramorphic traits (adult-like) while Saimiri is a genus with paedomorphic (child like) traits. Yet, the whole clade Cebinae is characterized by a unique combination of very high pre-natal growth rates and relatively slow post-natal growth rates when compared to the rest of the NWM. Morphologically Cebinae can be considered paedomorphic in relation to the other NWM. Geometric morphometrics allows the precise separation of absolute size, shape variation associated with size (allometry), and shape variation non-associated with size. Interestingly, and despite the fact that they were extracted as independent factors (principal components), evolutionary allometry (those differences in allometric shape associated with intergeneric differences) and ontogenetic allometry (differences in allometric shape associated with ontogenetic variation within genus) are correlated within these two genera. Furthermore, morphological differences produced along these two axes are quite similar. Cebus and Saimiri are aligned along the same evolutionary allometry and have parallel ontogenetic allometry trajectories.

Conclusion

The evolution of these two Platyrrhini monkeys is basically due to a size differentiation (and consequently to shape changes associated with size). Many life-history changes are correlated or may be the causal agents in such evolution, such as delayed on-set of reproduction in Cebus and larger neonates in Saimiri.     

Malignant gastrointestinal stromal tumor presenting with hemoperitoneum in puerperium: report of a case with review of the literature

Background

Leiomysarcoma of intravascular origin is an exceedingly rare entity of malignant soft tissue tumors. They are most frequently encountered in the retroperitoneum arising from the inferior vena cava and are scarcely found to arise from vessels of the extremities. These tumors were analysed with particular reference to treatment outcome and prognosis. The aim of this article is to broaden the knowledge of the clinical course of this rare malignancy.

Method

During 2000 and 2009 twelve patients were identified with an intravascular origin of a leiomyosarcoma. Details regarding the clinical course, follow-up and outcome were assessed with focus on patient survival, tumor relapse and metastases and treatment outcome. 3 year survival probability was calculated using Kaplan-Meier method.

Results

Vascular leiomyosarcomas accounted for 0.7% of all malignant soft tissue tumors treated at our soft tissue sarcoma reference center. The mean follow up period was 38 months. Tumor relapse was encountered in six patients. 6 patients developed metastatic disease. The three year survival was 57%.

Conclusion

Vascular leiomysarcoma is a rare but aggressive tumor entity with a high rate of local recurrence and metastasis.     

Viruses and thyroiditis: an update

Background

Despite the demonstration that geminiviruses, like many other single stranded DNA viruses, are evolving at rates similar to those of RNA viruses, a recent study has suggested that grass-infecting species in the genus Mastrevirus may have co-diverged with their hosts over millions of years. This "co-divergence hypothesis" requires that long-term mastrevirus substitution rates be at least 100,000-fold lower than their basal mutation rates and 10,000-fold lower than their observable short-term substitution rates. The credibility of this hypothesis, therefore, hinges on the testable claim that negative selection during mastrevirus evolution is so potent that it effectively purges 99.999% of all mutations that occur.

Results

We have conducted long-term evolution experiments lasting between 6 and 32 years, where we have determined substitution rates of between 2 and 3 × 10^-4 substitutions/site/year for the mastreviruses Maize streak virus (MSV) and Sugarcane streak Réunion virus (SSRV). We further show that mutation biases are similar for different geminivirus genera, suggesting that mutational processes that drive high basal mutation rates are conserved across the family. Rather than displaying signs of extremely severe negative selection as implied by the co-divergence hypothesis, our evolution experiments indicate that MSV and SSRV are predominantly evolving under neutral genetic drift.

Conclusion

The absence of strong negative selection signals within our evolution experiments and the uniformly high geminivirus substitution rates that we and others have reported suggest that mastreviruses cannot have co-diverged with their hosts.     

An ethnobotanical study of medicinal plants in Wayu Tuka District,East Welega Zone of Oromia Regional State,West Ethiopia

Background

Himalayan forests are the most important source of medicinal plants and with useful species for the local people. Kedarnath Wildlife Sanctuary (KWLS) is situated in the interior part of the Garhwal Himalayan region. The presented study was carried out in Madhmeshwar area of KWLS for the ecological status of medicinal plants and further focused on the ethnomedicinal uses of these plants in the study area.

Methods

Ecological information about ethnomedicinal plants were collected using random quadrats in a random sampling technique along an altitudinal gradient in the KWLS. Information on medicinal properties of plants encountered in the present study was generated by questionnaire survey and was also compared with relevant literature.

Results

A total of 152 medicinally important plant species were reported, in which 103 were found herbs, 32 shrubs and 17 were tree species which represented 123 genera of 61 families. A total of 18 plant species fell into the rare, endangered (critically endangered) and vulnerable status categories.

Conclusion

The present study documented the traditional uses of medicinal plants, their ecological status and importance of these plants in the largest protected area of Garhwal Himalaya. This study can serve as baseline information on medicinal plants and could be helpful to further strengthen the conservation of this important resource.     

Variation of secondary metabolite levels in maize seedling roots induced by inoculation with Azospirillum, Pseudomonas and Glomus consortium under field conditions

Background and aims

Many plant-beneficial microorganisms can influence secondary plant metabolism, but whether these effects add up when plants are co-inoculated is unclear. This issue was assessed, under field conditions, by comparing the early impacts of seed inoculation on secondary metabolite profiles of maize at current or reduced mineral fertilization levels.

Methods

Maize seeds were inoculated singly with selected strains from bacterial genera Pseudomonas and Azospirillum or mycorrhizal genus Glomus, or with these strains combined two by two or all three together. At 16?days, maize root methanolic extracts were analyzed by RP-HPLC and secondary metabolites (phenolics, flavonoids, xanthones, benzoxazionoids, etc.) identified by LC/MS.

Results

Inoculation did not impact on plant biomass but resulted in enhanced total root surface, total root volume and/or root number in certain inoculated treatments, at reduced fertilization. Inoculation led to qualitative and quantitative modifications of root secondary metabolites, particularly benzoxazinoids and diethylphthalate. These modifications depended on fertilization level and microorganism(s) inoculated. The three selected strains gave distinct results when used alone, but unexpectedly all microbial consortia gave somewhat similar results.

Conclusions

The early effects on maize secondary metabolism were not additive, as combining strains gave effects similar to those of Glomus alone. This is the first study demonstrating and analyzing inoculation effects on crop secondary metabolites in the field.     

Interpreting the ash trend within ombrotrophic bog profiles: atmospheric dust depositions vs. mineralization processes. The Etang de la Gruère case study

Introduction

Ash peaks along ombrotrophic bog profiles may arise from several different processes. In a recent paper, Leifeld and co-authors (Plant Soil 341:349–361, 2011) argued that ash peaks along the Etang de la Gruère (EGr) peat bog profiles are signs of previous periods of higher peat decomposition rather that an indication of periods of elevated dust inputs.

Aims and methods

Here we question the approach and scrutinize results using published data on several peat cores from EGr, demonstrating that peaks in ash content at EGr are very reproducible when cores are carefully collected (e.g., using the Wardenaar corer), and age dated (using ²¹⁰Pb and ¹⁴C).

Results

Data clearly show that variations in ash content along bog profiles cannot be attributed simply, or exclusively, to differences in organic matter mineralization rate, and that averaging the ash contents and normalizing to a single ash peak leads to losses in valuable information and defeats the purpose of detailed paleoenvironmental reconstructions.

Conclusions

Comparing results obtained using sensitive spectroscopic and isotopic tools with the ash content profiles at EGr shows clearly that the distribution of ash and/or acid-insoluble ash cannot be used as a surrogate for the intensity of processes including organic matter mineralization, decomposition and/or humification.     

New taxa of Leguminosae-Caesalpinioideae from Bahia,Brazil

Brodriguesia santosii, gen. & sp. nov., from the coastal rain forest of Bahia, is described, illustrated and compared with nearly related genera of the tribe Detarieae. In addition, three new species, Arapatiella emarginata (the second species of the genus), Swartzia oblata, S. pinheiroana and one new variety, Goniorrhachis marginata var. bahiana, are presented.     

Same-strand overlapping genes in bacteria: compositional determinants of phase bias

Background

Same-strand overlapping genes may occur in frameshifts of one (phase 1) or two nucleotides (phase 2). In previous studies of bacterial genomes, long phase-1 overlaps were found to be more numerous than long phase-2 overlaps. This bias was explained by either genomic location or an unspecified selection advantage. Models that focused on the ability of the two genes to evolve independently did not predict this phase bias. Here, we propose that a purely compositional model explains the phase bias in a more parsimonious manner. Same-strand overlapping genes may arise through either a mutation at the termination codon of the upstream gene or a mutation at the initiation codon of the downstream gene. We hypothesized that given these two scenarios, the frequencies of initiation and termination codons in the two phases may determine the number for overlapping genes.

Results

We examined the frequencies of initiation- and termination-codons in the two phases, and found that termination codons do not significantly differ between the two phases, whereas initiation codons are more abundant in phase 1. We found that the primary factors explaining the phase inequality are the frequencies of amino acids whose codons may combine to form start codons in the two phases. We show that the frequencies of start codons in each of the two phases, and, hence, the potential for the creation of overlapping genes, are determined by a universal amino-acid frequency and species-specific codon usage, leading to a correlation between long phase-1 overlaps and genomic GC content.

Conclusion

Our model explains the phase bias in same-strand overlapping genes by compositional factors without invoking selection. Therefore, it can be used as a null model of neutral evolution to test selection hypotheses concerning the evolution of overlapping genes.

Reviewers

This article was reviewed by Bill Martin, Itai Yanai, and Mikhail Gelfand.     

Contribution to the phylogeny and a new species of <Emphasis Type="Italic">Coccodiella</Emphasis> (Phyllachorales)

Coccodiella is a genus of plant-parasitic species in the family Phyllachoraceae (Phyllachorales, Ascomycota), i.e., tropical tar spot fungi. Members of the genus Coccodiella are tropical in distribution and are host-specific, growing on plant species belonging to nine host plant families. Most of the known species occur on various genera and species of the Melastomataceae in tropical America. In this study, we describe the new species C. calatheae from Panama, growing on Calathea crotalifera (Marantaceae). We obtained ITS, nrLSU, and nrSSU sequence data from this new species and from other freshly collected specimens of five species of Coccodiella on members of Melastomataceae from Ecuador and Panama. Phylogenetic analyses allowed us to confirm the placement of Coccodiella within Phyllachoraceae, as well as the monophyly of the genus. The phylogeny of representative species within the family Phyllachoraceae, including Coccodiella spp., graminicolous species of Phyllachora and taxa with erumpent to superficial stroma from several host families, suggests that the genus Phyllachora might be polyphyletic. Furthermore, tar spot fungi with superficial or erumpent perithecia seem to be restricted to the family Phyllachoraceae, independently of the host plant. We also discuss the biodiversity and host-plant patterns of species of Coccodiella worldwide.     

Difference in capacity of physiological integration between two ecotypes of Leymus chinensis underlies their different performance

Background and aims

Physiological integration can enhance the performance of clonal plants, but whether this differs between ecotypes and whether such difference is underlying their distribution have scarcely been addressed. We aimed to determine whether physiological integration differs between ecotypes and whether an ecotype with a wider distribution shows a greater capacity of physiological integration.

Methods

A garden experiment was conducted with ramet pairs of both ecotypes (grey-green and yellow-green ecotype) of a typical rhizomatous clonal plant, Leymus chinensis, using rhizome connection (connected vs. disconnected) and ecotype as factors. Physiological and biomass features were measured and compared to assess the effects of physiological integration for both ecotypes.

Results

Physiological integration enhanced the maximum net photosynthetic rate, apparent quantum efficiency, respiration rate, water use efficiency, and chlorophyll content of ramets no matter whether they were subject to nutrient-poor or -rich soil, as long as they were connected to other ramets. Moreover, such an effect on photosynthetic capacity and water use efficiency was larger for the grey-green ecotype than for the yellow-green ecotype.

Conclusions

The results suggested that grey-green ecotype has significantly greater capacity of physiological integration than yellow-green ecotype, which was assumed to be one of the underlying mechanisms of the wider distribution of the former in nature.     

Addressing the effect of social life cycle assessments

Purpose

In the recently published ??Guidelines for social life cycle assessment of products??, it is stated that the ultimate objective of developing the social life cycle assessment (SLCA) is to promote improvements of social conditions for the stakeholders in the life cycle. This article addresses how the SLCA should be developed so that its use promotes these improvements.

Methods

Hypotheses of how the use of SLCA can promote improvement of social conditions in the life cycle are formulated, after which theories and empirical findings from relevant fields of research are used to address the validity of these hypotheses.

Results

Three in some cases potentially overlapping SLCA approaches are presented, assumed to create a beneficial effect in the life cycle in different ways. However, empirical and theoretical findings show that the beneficial effects proposed to arise from the use of each of these three approaches may all be problematic. Some of these problems may be mitigated through methodological modifications.

Conclusions

Given the significant problems in relation to creating an effect through the use of the SLCAs, and given the significant practical problems in applying the SLCAs, it is questioned whether the development of SLCA is a fruitful approach for improving social conditions in the product life cycle.