Taxic Revisions

Parsimony analysis provides a straightforward way of assessing homology on a tree: a state shared by two terminals comprises homologous similarity if optimization attributes that state to all the stem species lying between those terminals. Three-taxon statements (3ts), although seemingly "exact" in that each either fits a tree or does not, do not provide a satisfactory assessment of homology, because that assessment can be internally contradictory and because 3ts systematically exclude homologous resemblance in reversed states. Modified 3ts analysis (m3ta), a method in which both plesiomorphic and apomorphic states of "paired homologue" (PH) characters (those other than presence/absence data) are regarded as "informative" (able to distinguish groups), can (obviously) group by symplesiomorphy and so form paraphyletic groups unless data are clocklike enough. Patterson's pattern analysis (ppa) has the same shortcoming, to which it adds the drawback that only characters fitting the tree perfectly are used, a restriction that can easily lead to discarding most of the structure in the data. Revised m3ta (rm3ta), a method in which plesiomorphic states are not taken as informative, can also form paraphyletic groups, because it cannot apply reversals as apomorphies. The idea that knowledge of phylogeny has been derived from classifications does not imply that nonevolutionary methods should be employed for classification, but instead means that systematic methods must be logically capable of phylogenetic interpretation. Neither m3ta nor rm3ta satisfies that requirement because of their contradictory assessments of homology.     

Bacterial Communities in the Rhizosphere of Biofuel Crops Grown on Marginal Lands as Evaluated by 16S rRNA Gene Pyrosequences

Microbes are key components of the soil environment and are important contributors to the sustainability of agricultural systems, which is especially significant for biofuel crops growing on marginal lands. We studied bacterial communities in the rhizosphere of five biofuel crops cultivated in four locations in Michigan to determine which factors were correlated to changes in the structure of those communities. Three of these sites were marginal lands in that two were not suitable for conventional agriculture and one was regulated as a brownfield due to prior industrial pollution. Bacterial community composition and structure were assessed by 454 sequencing of the 16S rRNA gene. A total of 387,111 sequences were used for multivariate statistical analysis and to test for correlation between community structure and environmental variables such as plant species, soil attributes, and location. The most abundant bacterial phyla found in the rhizosphere of all crops were Acidobacteria, Proteobacteria, Actinobacteria, and Verrucomicrobia. Bacterial communities grouped by location rather than by crop and their structures were correlated to soil attributes, principally pH, organic matter, and nutrients. The effect of plant species was low but significant, and interactions between locations, plant species, and soil attributes account for most of the explained variation in the structure of bacterial communities, showing a complex relationship between bacterial populations and their environment. Bacterial diversity was higher in the agricultural sites compared to adjacent forest sites, indicating that the cultivation of those biofuel crops increased the rRNA diversity.     

Short-term effects on sheep pastureland due to grazing abandonment in a Western Mediterranean island ecosystem: A multidisciplinary approach

Changes of pasture communities consequent to management practices resulting from land abandonment considerably affect the structure and function of the ecosystem. This study analyses the consequences of grazing abandonment in terms of plant and soil microbial diversity and fertility, on a Mediterranean upland sheep pasture, over a short period (five years). Grazing was experimentally excluded by fencing ten 10×10 m permanent plots within an area that had supported grazing until 2000, by 0.23 sheep ha^?1. Plant and soil microbial communities and physicochemical parameters were monitored within the fenced and unfenced control plots, during three sampling times from 2000 (before the fencing) to 2005. Grazing cessation notably altered the floral composition, with an average dissimilarity of 96.7% between the vegetation communities, over five years. No significant change occurred in the control plots that were grazed throughout the sampling period. This work highlighted that, over a short term, the structural change in the specific plant composition affected only the grass species, confirming that grazing favours the small-sized species over the annual species. Further, it was evident that species groups of conservational and phytogeographic interest, like the endemic and Mediterranean-Atlantic species, tended to disappear with pasture abandonment and were substituted by more widespread species throughout the Mediterranean or even the world. Pasture abandonment was accompanied by an increase of soil pH and a decrease in soil organic matter and soil nitrogen. The microbial parameters recorded at three different sampling times revealed a substantial effect of the plant community, or the time of grazing abandonment, on soil microbial abundance and diversity. Considerable importance is given to the consequences of pasture abandonment on the conservation of plant and microbial diversity and on soil fertility.     

The power of potential natural vegetation (and of spatial‐temporal scale): a response to Carrión & Fernández (2009)

A commentary by Carrión & Fernández (Journal of Biogeography, 2009, 36 , 2202–2203) compared Holocene pollen records with models of potential natural vegetation (PNV) proposed in the phytosociological literature and concluded that the predicted PNV resulted from anthropogenic disturbance. However, the authors misinterpreted PNV, leading to two serious flaws in their assumptions: (1) PNV is not defined as a pre‐anthropic or climax plant community; and (2) PNV is not a concept restricted to the phytosociological method. Therefore we criticize the conclusions expressed in the commentary, and we stress the need for an interdisciplinary approach based on multi‐temporal and multi‐spatial scales to achieve a modern framework for the study of plant communities.     

Sequence analysis of Escherichia coli O157:H7 bacteriophage ΦV10 and identification of a phage-encoded immunity protein that modifies the O157 antigen

Bacteriophage ΦV10 is a temperate phage, which specifically infects Escherichia coli O157:H7. The nucleotide sequence of the ΦV10 genome is 39 104 bp long and contains 55 predicted genes. ΦV10 is closely related to two previously sequenced phages, the Salmonella enterica serovar Anatum (Group E1) phage ɛ15 and a prophage from E. coli APEC O1. The attachment site of ΦV10, like those of its two closest relatives, overlaps the 3' end of guaA in the host chromosome. ΦV10 encodes an O -acetyltransferase, which modifies the O157 antigen. This modification is sufficient to block ΦV10 superinfection, indicating that the O157 antigen is most likely the ΦV10 receptor.     

ACPA fine-specificity profiles in early rheumatoid arthritis patients do not correlate with clinical features at baseline or with disease progression

Introduction

Autoantibodies against citrullinated peptides/proteins (ACPA) are found in approximately 75% of the sera of patients with rheumatoid arthritis (RA). The RA-specific ACPA are frequently present prior to disease onset and their presence associates with a more erosive disease course. ACPA can therefore be used to aid the diagnosis and prognosis of RA. Recently, it became clear that ACPA are very heterogeneous, both in an individual patient and among different patients. The aim of this study was to investigate whether clinically meaningful ACPA profiles exist in early RA patients.

Methods

Twenty citrullinated peptides and the corresponding non-citrullinated control peptides were immobilized on microarray sensor chips. Sera from 374 early arthritis patients were analyzed by surface plasmon resonance imaging (iSPR) of biomolecular interactions on the sensor chip.

Results

Cluster analysis of the reactivities with the citrullinated peptides, after subtraction of the reactivities with the corresponding control peptides confirmed the heterogeneity of the ACPA response in RA and revealed 12 distinct ACPA profiles. The association of the 5 most frequent profiles with clinical features at diagnosis and during the disease course was examined, showing no statistically significant associations.

Conclusions

Compared to the detection of ACPA in RA sera by CCP-based assays, ACPA profiling in early arthritis patients did not reveal associations with disease activity and progression scores.     

Are all pastures eligible for conservation? A phytosociological survey of the Sardinian–Corsican Province as a basic tool for the Habitats Directive

A consistent vegetation classification is an essential tool for conservation and monitoring purposes, also for semi-natural habitats such as pastures and hay meadows that are linked to traditional land use and generally considered crucial to maintain biodiversity within agricultural systems. Indeed, these habitats can be strongly affected by land abandonment or agriculture intensification. Despite their importance in the framework of the EU Habitats Directive (43/92/EEC), information on distribution, species composition, and conservation status is still lacking for many regions. To fill these gaps, we investigated from a phytosociological point of view the sheep pastures of the North-Western Sardinian trachy-basaltic sector. Three main communities were described as new: (i) perennial montane (meso-supratemperate) cattle and sheep pastures (Loto alpini-Festucetum morisianae); (ii) mixed (annual and perennial) Mediterranean (lower Thermomediterranean to lower supratemperate) sheep pastures (Ornithogalo corsici-Poetum bulbosae); and (iii) annual ploughed subnitrophilous Mediterranean and Temperate pastures (Cynosuro polybracteati-Vulpietum ligusticae). As the first two host numerous endemic taxa and show a peculiar floristic composition, we assign them a higher conservation value, testified also by their classification in two new syntaxa: Danthonio decumbentis-Caricenion insularis (Molinio-Arrhenatheretea) and Ornithogalo corsici-Trifolienion subterranei (Poetea bulbosae), respectively.     

Comparing aye-aye (Daubentonia madagascariensis) presence and distribution between degraded and non-degraded forest within Ranomafana National Park, Madagascar

The aye-aye is considered the most widely distributed lemur in Madagascar; however, the effect of forest quality on aye-aye abundance is unknown. We compared aye-aye presence across degraded and non-degraded forest at Ranomafana National Park, Madagascar. We used secondary signs (feeding sites, high activity sites) as indirect cues of aye-aye presence and Canarium trees as an indicator of resource availability. All 3 measured variables indicated higher aye-aye abundance within non-degraded forest; however, the differences across forest type were not significant. Both degraded and non-degraded forests showed a positive correlation between feeding sites and high activity sites. We found that Canarium, an important aye-aye food source, was rare and had limited dispersal, particularly across degraded forest. This preliminary study provides baseline data for aye-aye activity and resource utilization across degraded and non-degraded forests.