Folding and unfolding phylogenetic trees and networks

Phylogenetic networks are rooted, labelled directed acyclic graphs which are commonly used to represent reticulate evolution. There is a close relationship between phylogenetic networks and multi-labelled trees (MUL-trees). Indeed, any phylogenetic network $N$ can be "unfolded" to obtain a MUL-tree $U(N)$ and, conversely, a MUL-tree $T$ can in certain circumstances be "folded" to obtain a phylogenetic network $F(T)$ that exhibits $T$. In this paper, we study properties of the operations $U$ and $F$ in more detail. In particular, we introduce the class of stable networks, phylogenetic networks $N$ for which $F(U(N))$ is isomorphic to $N$, characterise such networks, and show that they are related to the well-known class of tree-sibling networks.We also explore how the concept of displaying a tree in a network $N$ can be related to displaying the tree in the MUL-tree $U(N)$. To do this, we develop a phylogenetic analogue of graph fibrations. This allows us to view $U(N)$ as the analogue of the universal cover of a digraph, and to establish a close connection between displaying trees in $U(N)$ and reconcilingphylogenetic trees with networks

Virtual discussions to support climate risk decision making on farms

Climate variability represents a significant risk to farming enterprises. Effective extension of climate information may improve climate risk decision making and adaptive management responses to climate variability on farms. This paper briefly reviews current agricultural extension approaches and reports stakeholder responses to new web-based virtual world ‘discussion-support’ tools developed for the Australian sugar cane farming industry. These tools incorporate current climate science and sugar industry better management practices, while leveraging the social-learning aspects of farming, to provide a stimulus for discussion and climate risk decision making. Responses suggest that such virtual world tools may provide effective support for climate risk decision making on Australian sugar cane farms. Increasing capacity to deliver such tools online also suggests potential to engage large numbers of farmers globally

Locating a Tree in a Phylogenetic Network in Quadratic Time

International audienceA fundamental problem in the study of phylogenetic networks is to determine whether or not a given phylogenetic network contains a given phylogenetic tree. We develop a quadratic-time algorithm for this problem for binary nearly-stable phylogenetic networks. We also show that the number of reticulations in a reticulation visible or nearly stable phylogenetic network is bounded from above by a function linear in the number of taxa

How much information is needed to infer reticulate evolutionary histories?

Phylogenetic networks are a generalization of evolutionary trees and are an important tool for analyzing reticulate evolutionary histories. Recently, there has been great interest in developing new methods to construct rooted phylogenetic networks, that is, networks whose internal vertices correspond to hypothetical ancestors, whose leaves correspond to sampled taxa, and in which vertices with more than one parent correspond to taxa formed by reticulate evolutionary events such as recombination or hybridization. Several methods for constructing evolutionary trees use the strategy of building up a tree from simpler building blocks (such as triplets or clusters), and so it is natural to look for ways to construct networks from smaller networks. In this article, we shall demonstrate a fundamental issue with this approach. Namely, we show that even if we are given all of the subnetworks induced on all proper subsets of the leaves of some rooted phylogenetic network, we still do not have all of the information required to completely determine that network. This implies that even if all of the building blocks for some reticulate evolutionary history were to be taken as the input for any given network building method, the method might still output an incorrect history. We also discuss some potential consequences of this result for constructing phylogenetic networks

Progress on outbound tourism expenditure research: A review

This study aims to identify how the paradigm of outbound tourism expenditure (OTE) research transforms from economic to social concern. It also explicates the evolution of OTE from an advocacy platform to a sustainability platform. This study adopts a hybrid of narrative and systematic reviews to study OTE as a complex social phenomenon. This hybrid review is complemented by a thematic review and semantic network analysis on gaps and future directions of relevant studies. The results reveal that the paradigm of OTE research is directed from economic toward social thinking. This study proposes an application of socially related antecedent configurations, social theories, pragmatic methods, and various scales of study contexts as promising solutions to address the complexity and heterogeneity of OTE. The study concludes that the conceptual structure of OTE is premised on a sustainability platform, which is influenced by socio-cultural, environmental, economic, and political issues. This study provides a road map that enlightens the current state of OTE, prevailing topics, and pathways for further research

The Development of Virtual World Tools to Enhance Learning and Real World Decision Making in the Australian Sugar Farming Industry

In farming, the outcome of critical decisions to enhance productivity and profitability and so ensure the viability of farming enterprises is often influenced by seasonal conditions and weather events over the growing season. This paper reports on a project that uses cutting-edge advances in digital technologies and their application in learning environments to develop and evaluate a web-based virtual ‘discussion-support’ system for improved climate risk management in Australian sugar farming systems. Customized scripted video clips (machinima) are created in the Second Life virtual world environment. The videos use contextualized settings and lifelike avatar actors to model conversations about climate risk and key farm operational decisions relevant to the real-world lives and practices of sugarcane farmers. The tools generate new cognitive schema for farmers to access and provide stimuli for discussions around how to incorporate an understanding of climate risk into operational decision-making. They also have potential to provide cost-effective agricultural extension which simulates real world face-to-face extension services but is accessible anytime anywhere

Gene expression profiling of noninvasive primary urothelial tumours using microarrays

At present, the mechanism leading to bladder cancer is still poorly understood, and our knowledge about early events in tumorigenesis is limited. This study describes the changes in gene expression occurring during the neoplastic transition from normal bladder urothelium to primary Ta tumours. Using DNA microarrays, we identified novel differentially expressed genes in Ta tumours compared to normal bladder, and genes that were altered in high-grade tumours. Among the mostly changed genes between normal bladder and Ta tumours, we found genes related to the cytoskeleton (keratin 7 and syndecan 1), and transcription (high mobility group AT-hook 1). Altered genes in high-grade tumours were related to cell cycle (cyclin-dependent kinase 4) and transcription (jun d proto-oncogene). Furthermore, we showed the presence of high keratin 7 transcript expression in bladder cancer, and Western blotting analysis revealed three major molecular isoforms of keratin 7 in the tissues. These could be detected in urine sediments from bladder tumour patients

Hyaluronan Export through Plasma Membranes Depends on Concurrent K+ Efflux by Kir Channels

Hyaluronan is synthesized within the cytoplasm and exported into the extracellular matrix through the cell membrane of fibroblasts by the MRP5 transporter. In order to meet the law of electroneutrality, a cation is required to neutralize the emerging negative hyaluronan charges. As we previously observed an inhibiting of hyaluronan export by inhibitors of K+ channels, hyaluronan export was now analysed by simultaneously measuring membrane potential in the presence of drugs. This was done by both hyaluronan import into inside-out vesicles and by inhibition with antisense siRNA. Hyaluronan export from fibroblast was particularly inhibited by glibenclamide, ropivacain and BaCl2 which all belong to ATP-sensitive inwardly-rectifying Kir channel inhibitors. Import of hyaluronan into vesicles was activated by 150 mM KCl and this activation was abolished by ATP. siRNA for the K+ channels Kir3.4 and Kir6.2 inhibited hyaluronan export. Collectively, these results indicated that hyaluronan export depends on concurrent K+ efflux

Progenitor-Derivative Relationships of Hordeum Polyploids (Poaceae, Triticeae) Inferred from Sequences of TOPO6, a Nuclear Low-Copy Gene Region

Polyploidization is a major mechanism of speciation in plants. Within the barley genus Hordeum, approximately half of the taxa are polyploids. While for diploid species a good hypothesis of phylogenetic relationships exists, there is little information available for the polyploids (4×, 6×) of Hordeum. Relationships among all 33 diploid and polyploid Hordeum species were analyzed with the low-copy nuclear marker region TOPO6 for 341 Hordeum individuals and eight outgroup species. PCR products were either directly sequenced or cloned and on average 12 clones per individual were included in phylogenetic analyses. In most diploid Hordeum species TOPO6 is probably a single-copy locus. Most sequences found in polyploid individuals phylogenetically cluster together with sequences derived from diploid species and thus allow the identification of parental taxa of polyploids. Four groups of sequences occurring only in polyploid taxa are interpreted as footprints of extinct diploid taxa, which contributed to allopolyploid evolution. Our analysis identifies three key species involved in the evolution of the American polyploids of the genus. (i) All but one of the American tetraploids have a TOPO6 copy originating from the Central Asian diploid H. roshevitzii, the second copy clustering with different American diploid species. (ii) All hexaploid species from the New World have a copy of an extinct close relative of H. californicum and (iii) possess the TOPO6 sequence pattern of tetraploid H. jubatum, each with an additional copy derived from different American diploids. Tetraploid H. bulbosum is an autopolyploid, while the assumed autopolyploid H. brevisubulatum (4×, 6×) was identified as allopolyploid throughout most of its distribution area. The use of a proof-reading DNA polymerase in PCR reduced the proportion of chimerical sequences in polyploids in comparison to Taq polymerase