179 research outputs found
Progress on Constructing Phylogenetic Networks for Languages
In 2006, Warnow, Evans, Ringe, and Nakhleh proposed a stochastic model
(hereafter, the WERN 2006 model) of multi-state linguistic character evolution
that allowed for homoplasy and borrowing. They proved that if there is no
borrowing between languages and homoplastic states are known in advance, then
the phylogenetic tree of a set of languages is statistically identifiable under
this model, and they presented statistically consistent methods for estimating
these phylogenetic trees. However, they left open the question of whether a
phylogenetic network -- which would explicitly model borrowing between
languages that are in contact -- can be estimated under the model of character
evolution. Here, we establish that under some mild additional constraints on
the WERN 2006 model, the phylogenetic network topology is statistically
identifiable, and we present algorithms to infer the phylogenetic network. We
discuss the ramifications for linguistic phylogenetic network estimation in
practice, and suggest directions for future research.Comment: 16 pages, 2 figure
First impressions and perceived roles: Palestinian perceptions on foreign aid
This paper summarizes some results of a wider research on foreign aid that was conducted in the West Bank and Gaza Strip in 2010. It seeks to describe the impressions and feelings of Palestinian aid beneficiaries as well as the roles and functions they attached to foreign aid. To capture and measure local perceptions on Western assistance a series of individual in depth interviews and few focus group interviews were conducted in the Palestinian territories. The interview transcripts were processed by content analysis. As research results show â from the perspective of aid beneficiaries â foreign aid is more related to human dignity than to any economic development. All this implies that frustration with the ongoing Israeli-Palestinian conflict inevitably embraces the donor policies and practices too
PhyloNet: a software package for analyzing and reconstructing reticulate evolutionary relationships
<p>Abstract</p> <p>Background</p> <p>Phylogenies, i.e., the evolutionary histories of groups of taxa, play a major role in representing the interrelationships among biological entities. Many software tools for reconstructing and evaluating such phylogenies have been proposed, almost all of which assume the underlying evolutionary history to be a tree. While trees give a satisfactory first-order approximation for many families of organisms, other families exhibit evolutionary mechanisms that cannot be represented by trees. Processes such as horizontal gene transfer (HGT), hybrid speciation, and interspecific recombination, collectively referred to as <it>reticulate evolutionary events</it>, result in <it>networks</it>, rather than trees, of relationships. Various software tools have been recently developed to analyze reticulate evolutionary relationships, which include SplitsTree4, LatTrans, EEEP, HorizStory, and T-REX.</p> <p>Results</p> <p>In this paper, we report on the PhyloNet software package, which is a suite of tools for analyzing reticulate evolutionary relationships, or <it>evolutionary networks</it>, which are rooted, directed, acyclic graphs, leaf-labeled by a set of taxa. These tools can be classified into four categories: (1) evolutionary network representation: reading/writing evolutionary networks in a newly devised compact form; (2) evolutionary network characterization: analyzing evolutionary networks in terms of three basic building blocks â trees, clusters, and tripartitions; (3) evolutionary network comparison: comparing two evolutionary networks in terms of topological dissimilarities, as well as fitness to sequence evolution under a maximum parsimony criterion; and (4) evolutionary network reconstruction: reconstructing an evolutionary network from a species tree and a set of gene trees.</p> <p>Conclusion</p> <p>The software package, PhyloNet, offers an array of utilities to allow for efficient and accurate analysis of evolutionary networks. The software package will help significantly in analyzing large data sets, as well as in studying the performance of evolutionary network reconstruction methods. Further, the software package supports the proposed eNewick format for compact representation of evolutionary networks, a feature that allows for efficient interoperability of evolutionary network software tools. Currently, all utilities in PhyloNet are invoked on the command line.</p
Inference of reticulate evolutionary histories by maximum likelihood: the performance of information criteria
Background: Maximum likelihood has been widely used for over three decades to infer phylogenetic trees from
molecular data. When reticulate evolutionary events occur, several genomic regions may have conflicting
evolutionary histories, and a phylogenetic network may provide a more adequate model for representing the
evolutionary history of the genomes or species. A maximum likelihood (ML) model has been proposed for this
case and accounts for both mutation within a genomic region and reticulation across the regions. However, the
performance of this model in terms of inferring information about reticulate evolution and properties that affect
this performance have not been studied.
Results: In this paper, we study the effect of the evolutionary diameter and height of a reticulation event on its
identifiability under ML. We find both of them, particularly the diameter, have a significant effect. Further, we find
that the number of genes (which can be generalized to the concept of "non-recombining genomic regions") that
are transferred across a reticulation edge affects its detectability. Last but not least, a fundamental challenge with
phylogenetic networks is that they allow an arbitrary level of complexity, giving rise to the model selection
problem. We investigate the performance of two information criteria, the Akaike Information Criterion (AIC) and the
Bayesian Information Criterion (BIC), for addressing this problem. We find that BIC performs well in general for
controlling the model complexity and preventing ML from grossly overestimating the number of reticulation
events.
Conclusion: Our results demonstrate that BIC provides a good framework for inferring reticulate evolutionary
histories. Nevertheless, the results call for caution when interpreting the accuracy of the inference particularly for
data sets with particular evolutionary features
Efficiently Calculating Evolutionary Tree Measures Using SAT
We develop techniques to calculate important measures in evolutionary biology by encoding to CNF formulas and using powerful SAT solvers. Comparing evolutionary trees is a necessary step in tree reconstruction algorithms, locating recombination and lateral gene transfer, and in analyzing and visualizing sets of trees. We focus on two popular comparison measures for trees: the hybridization number and the rooted subtree-prune-and-regraft (rSPR) distance. Both have recently been shown to be NP-hard, and effcient algorithms are needed to compute
and approximate these measures. We encode these as a Boolean formula such that two trees have hybridization number k (or rSPR distance k) if and only if the corresponding formula is satisfiable. We use state-of-the-art SAT solvers to determine if the formula encoding the measure has a satisfying assignment. Our encoding also provides a rich
source of real-world SAT instances, and we include a comparison of several recent solvers (minisat, adaptg2wsat, novelty+p, Walksat, March KS and SATzilla).Postprint (authorâs final draft
Using Interviews in CER Projects: Options, Considerations, and Limitations
Interviews can be a powerful chemistry education research tool. Different from an assessment score or Likert-scale survey number, interviews can provide the researcher with a way to examine and describe what we cannot see, aspects such as feelings, thoughts, or explanations of thinking or behavior. Most people have no doubt seen countless interviews on TV news and talk shows. These sessions might convey interviewing as a spontaneous, easy, and straightforward process. However, using interviews as a meaningful research tool requires considerable thought, preparation, and practice. This chapter provides a general introduction to the use of interviews as a tool within a chemistry education research context. The chapter provides a general introduction to the use of interviews as a research tool including how to plan, conduct, and analyze interviews. It highlights important considerations for designing and conducting fruitful interviews, provides examples of different ways in which interviews have been used effectively in chemistry education research, and supplies additional references for the reader who wants to delve more deeply into particular topics
Dynamic Models of Language Evolution: The Linguistic Perspective
Language is probably the key defining characteristic of humanity, an immensely powerful tool which provides its users with an infinitely expressive means of representing their complex thoughts and reflections, and of successfully communicating them to others. It is the foundation on which human societies have been built and the means through which humanityâs unparalleled intellectual and technological achievements have been realized. Although we have a natural intuitive understanding of what a language is, the specification of a particular language is nevertheless remarkably difficult, if not impossible, to pin down precisely. All languages contain many separate yet integral systems which work interdependently to allow the expression of our thoughts and the interpretation of othersâ expressions: each has, for instance, a set of basic meaningless sounds (e.g. [e], [l], [s]) which can be combined to make different meaningful words and parts of words (e.g. else, less, sell, -less ); these meaningful units can be combined to make complex words (e.g. spinelessness, selling ), and the words themselves can then be combined in very many complex ways into phrases, clauses and an infinite number of meaningful sentences; finally each of these sentences can be interpreted in dramatically different ways, depending on the contexts in which it is uttered and on who is doing the interpretation. Languages can be analysed at any of these different levels, which make up many of the sub-fields of linguistics, and the primary job of linguistic theorists is to try to explain the rules which best explain these complex combinations
Understanding interactions in face-to-face and remote undergraduate science laboratories
This paper reviews the ways in which interactions have been studied, and the findings of such studies, in science
education in both face-to-face and remote laboratories. Guided by a systematic selection process, 27 directly
relevant articles were analysed based on three categories: the instruments used for measuring interactions, the
research findings on student interactions, and the theoretical frameworks used in the studies of student
interactions. In face-to-face laboratories, instruments for measuring interactions and the characterisation of the
nature of interactions were prominent. For remote laboratories, the analysis of direct interactions was found to be
lacking. Instead, studies of remote laboratories were mainly concerned with their practical scope. In addition, it is
found that only a limited number of theoretical frameworks have been developed and applied in the research
design. Existent theories are summarised and possible theoretical frameworks that may be implemented in studies
of interactions in undergraduate laboratories are proposed. Finally, future directions for research on the interrelationship between student interactions and laboratory learning are suggested
Profiles of Volatile Biomarkers Detect Tuberculosis from Skin
Tuberculosis (TB) is an infectious disease that threatens >10Â million people annually. Despite advances in TB diagnostics, patients continue to receive an insufficient diagnosis as TB symptoms are not specific. Many existing biodiagnostic tests are slow, have low clinical performance, and can be unsuitable for resource-limited settings. According to the World Health Organization (WHO), a rapid, sputum-free, and cost-effective triage test for real-time detection of TB is urgently needed. This article reports on a new diagnostic pathway enabling a noninvasive, fast, and highly accurate way of detecting TB. The approach relies on TB-specific volatile organic compounds (VOCs) that are detected and quantified from the skin headspace. A specifically designed nanomaterial-based sensors array translates these findings into a point-of-care diagnosis by discriminating between active pulmonary TB patients and controls with sensitivity above 90%. This fulfills the WHO's triage test requirements and poses the potential to become a TB triage test
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