Proposed minimal standards for the description of genera, species and subspecies of the Pasteurellaceae

Principles and guidelines are presented to ensure a solid scientific standard of papers dealing with the taxonomy of taxa of Pasteurellaceae Pohl 1981. The classification of the Pasteurellaceae is in principle based on a polyphasic approach. DNA sequencing of certain genes is very important for defining the borders of a taxon. However, the characteristics that are common to all members of the taxon and which might be helpful for separating it from related taxa must also be identified. Descriptions have to be based on as many strains as possible (inclusion of at least five strains is highly desirable), representing different sources with respect to geography and ecology, to allow proper characterization both phenotypically and genotypically, to establish the extent of diversity of the cluster to be named. A genus must be monophyletic based on 16S rRNA gene sequence-based phylogenetic analysis. Only in very rare cases is it acceptable that monophyly can not be achieved by 16S rRNA gene sequence comparison. Recently, the monophyly of genera has been confirmed by sequence comparison of housekeeping genes. In principle, a new genus should be recognized by a distinct phenotype, and characters that separate the new genus from its neighbours should be given clearly. Due to the overall importance of accurate classification of species, at least two genotypic methods are needed to show coherence and for separation at the species level. The main criterion for the classification of a novel species is that it forms a monophyletic group based on 16S rRNA gene sequence-based phylogenetic analysis. However, some groups might also include closely related species. In these cases, more sensitive tools for genetic recognition of species should be applied, such as DNA-DNA hybridizations. The comparison of housekeeping gene sequences has recently been used for genotypic definition of species. In order to separate species, phenotypic characters must also be identified to recognize them, and at least two phenotypic differences from existing species should be identified if possible. We recommend the use of the subspecies category only for subgroups associated with disease or similar biological characteristics. At the subspecies level, the genotypic groups must always be nested within the boundaries of an existing species. Phenotypic cohesion must be documented at the subspecies level and separation between subspecies and related species must be fully documented, as well as association with particular disease and host. An overview of methods previously used to characterize isolates of the Pasteurellaceae has been given. Genotypic and phenotypic methods are separated in relation to tests for investigating diversity and cohesion and to separate taxa at the level of genus as well as species and subspecies.

Diversification in the South American Pampas: the genetic and morphological variation of the widespread Petunia axillaris complex (Solanaceae)

Understanding the spatiotemporal distribution of genetic variation and the ways in which this distribution is connected to the ecological context of natural populations is fundamental for understanding the nature and mode of intraspecific and, ultimately, interspecific differentiation. The Petunia axillaris complex is endemic to the grasslands of southern South America and includes three subspecies: P.a.axillaris, P.a.parodii and P.a.subandina. These subspecies are traditionally delimited based on both geography and floral morphology, although the latter is highly variable. Here, we determined the patterns of genetic (nuclear and cpDNA), morphological and ecological (bioclimatic) variation of a large number of P.axillaris populations and found that they are mostly coincident with subspecies delimitation. The nuclear data suggest that the subspecies are likely independent evolutionary units, and their morphological differences may be associated with local adaptations to diverse climatic and/or edaphic conditions and population isolation. The demographic dynamics over time estimated by skyline plot analyses showed different patterns for each subspecies in the last 100000years, which is compatible with a divergence time between 35000 and 107000years ago between P.a.axillaris and P.a.parodii, as estimated with the IMa program. Coalescent simulation tests using Approximate Bayesian Computation do not support previous suggestions of extensive gene flow between P.a.axillaris and P.a.parodii in their contact zone.

Beyond the tree of texts: Building an empirical model of scribal variation through graph analysis of texts and stemmata

Stemmatology, or the reconstruction of the transmission history of texts, is a field that stands particularly to gain from digital methods. Many scholars already take stemmatic approaches that rely heavily on computational analysis of the collated text (e.g. Robinson and O’Hara 1996; Salemans 2000; Heikkilä 2005; Windram et al. 2008 among many others). Although there is great value in computationally assisted stemmatology, providing as it does a reproducible result and allowing access to the relevant methodological process in related fields such as evolutionary biology, computational stemmatics is not without its critics. The current state-of-the-art effectively forces scholars to choose between a preconceived judgment of the significance of textual differences (the Lachmannian or neo-Lachmannian approach, and the weighted phylogenetic approach) or to make no judgment at all (the unweighted phylogenetic approach). Some basis for judgment of the significance of variation is sorely needed for medieval text criticism in particular. By this, we mean that there is a need for a statistical empirical profile of the text-genealogical significance of the different sorts of variation in different sorts of medieval texts. The rules that apply to copies of Greek and Latin classics may not apply to copies of medieval Dutch story collections; the practices of copying authoritative texts such as the Bible will most likely have been different from the practices of copying the Lives of local saints and other commonly adapted texts. It is nevertheless imperative that we have a consistent, flexible, and analytically tractable model for capturing these phenomena of transmission. In this article, we present a computational model that captures most of the phenomena of text variation, and a method for analysis of one or more stemma hypotheses against the variation model. We apply this method to three ‘artificial traditions’ (i.e. texts copied under laboratory conditions by scholars to study the properties of text variation) and four genuine medieval traditions whose transmission history is known or deduced in varying degrees. Although our findings are necessarily limited by the small number of texts at our disposal, we demonstrate here some of the wide variety of calculations that can be made using our model. Certain of our results call sharply into question the utility of excluding ‘trivial’ variation such as orthographic and spelling changes from stemmatic analysis.

Topology and Link quality-aware Geographical opportunistic routing in wireless ad-hoc networks

Opportunistic routing (OR) takes advantage of the broadcast nature and spatial diversity of wireless transmission to improve the performance of wireless ad-hoc networks. Instead of using a predetermined path to send packets, OR postpones the choice of the next-hop to the receiver side, and lets the multiple receivers of a packet to coordinate and decide which one will be the forwarder. Existing OR protocols choose the next-hop forwarder based on a predefined candidate list, which is calculated using single network metrics. In this paper, we propose TLG - Topology and Link quality-aware Geographical opportunistic routing protocol. TLG uses multiple network metrics such as network topology, link quality, and geographic location to implement the coordination mechanism of OR. We compare TLG with well-known existing solutions and simulation results show that TLG outperforms others in terms of both QoS and QoE metrics.

Cultural Legacies and Political Preferences: The Failure of Separatism in the Swiss Jura

The study of secession generally stresses the causal influence of cultural identities, political preferences, or ecological factors. Whereas these different views are often considered to be mutually exclusive, this paper proposes a two-stage model in which they are complementary. We posit that cultural identities matter for explaining secessionism, but not because of primordial attachments. Rather, religious and linguistic groups matter because their members are imbued with cultural legacies that lead to distinct political preferences – in this case preferences over welfare statism. Further, ecological constraints such as geography and topography affect social interaction with like-minded individuals. On the basis of both these political preferences and ecological constraints, individuals then make rational choices about the desirability of secession. Instrumental considerations are therefore crucial in explaining the decision to secede, but not in a conventional pocketbook manner. To examine this theory, we analyze the 2013 referendum on the secession of the Jura Bernois region from the Canton of Berne in Switzerland, using municipal level census and referendum data. The results lend support to the theory and suggest one way in which the politics of identity, based on factors like language and religion, can be fused with the politics of interest (preferences for more or less state intervention into the polity and economy) to better understand group behavior.