Analyzing and reconstructing reticulation networks under timing constraints

Reticulation networks are now frequently used to model the history of life for various groups of organisms whose evolutionary past is likely to include reticulation events like horizontal gene transfer or hybridization. However, the reconstructed networks are rarely guaranteed to be temporal. If a reticulation network is temporal, then it satisfies the two biologically motivated timing constraints of instantaneously occurring reticulation events and successively occurring speciation events. On the other hand, if a reticulation network is not temporal, it is always possible to resolve this issue by adding a number of additional unsampled or extinct taxa. In the first half of the paper, we show that deciding whether a given number of additional taxa is sufficient to transform a non-temporal reticulation network into a temporal one is an NP-complete problem. As one is often given a set of gene trees instead of a network in the context of hybridization, this motivates the second half of the paper which provides an algorithm for reconstructing a temporal hybridization network that simultaneously explains the ancestral history of two trees or indicates that no such network exists. We highlight two practical applications of this algorithm and illustrate the second application on a grass data set

Quartet compatibility and the quartet graph

A collection P of leaf-labelled trees is compatible if there exists a single leaf-labelled tree that displays each of the trees in P. Despite its difficulty, determining the compatibility of P is a fundamental task in evolutionary biology. Attractive characterizations in terms of chordal graphs have been previously given for this problem as well as for the problems of (i) determining if there is a unique tree that displays each of the trees in P, that is 'P is definitive and (ii) determining if there is a tree that displays P and has the property that every other tree that displays P is a refinement of it, that is 'P identifies a leaf-labelled tree. In this paper, we describe new characterizations of each of these problems in terms of edge colourings. Furthermore, for an arbitrary leaf-labelled tree 'T, we also determine the minimum number of 'quartets' required to identify 'T, thus correcting a previously published result

Neighborhoods of trees in circular orderings

In phylogenetics, a common strategy used to construct an evolutionary tree for a set of species X is to search in the space of all such trees for one that optimizes some given score function (such as the minimum evolution, parsimony or likelihood score). As this can be computationally intensive, it was recently proposed to restrict such searches to the set of all those trees that are compatible with some circular ordering of the set X. To inform the design of efficient algorithms to perform such searches, it is therefore of interest to find bounds for the number of trees compatible with a fixed ordering in the neighborhood of a tree that is determined by certain tree operations commonly used to search for trees: the nearest neighbor interchange (nni), the subtree prune and regraft (spr) and the tree bisection and reconnection (tbr) operations. We show that the size of such a neighborhood of a binary tree associated with the nni operation is independent of the tree’s topology, but that this is not the case for the spr and tbr operations. We also give tight upper and lower bounds for the size of the neighborhood of a binary tree for the spr and tbr operations and characterize those trees for which these bounds are attained

The comparative clinical course of pregnant and non-pregnant women hospitalised with influenza A(H1N1)pdm09 infection

Introduction: The Influenza Clinical Information Network (FLU-CIN) was established to gather detailed clinical and epidemiological information about patients with laboratory confirmed A(H1N1)pdm09 infection in UK hospitals. This report focuses on the clinical course and outcomes of infection in pregnancy.Methods: A standardised data extraction form was used to obtain detailed clinical information from hospital case notes and electronic records, for patients with PCR-confirmed A(H1N1)pdm09 infection admitted to 13 sentinel hospitals in five clinical 'hubs' and a further 62 non-sentinel hospitals, between 11th May 2009 and 31st January 2010.Outcomes were compared for pregnant and non-pregnant women aged 15-44 years, using univariate and multivariable techniques.Results: Of the 395 women aged 15-44 years, 82 (21%) were pregnant; 73 (89%) in the second or third trimester. Pregnant women were significantly less likely to exhibit severe respiratory distress at initial assessment (OR?=?0.49 (95% CI: 0.30-0.82)), require supplemental oxygen on admission (OR?=?0.40 (95% CI: 0.20-0.80)), or have underlying co-morbidities (p-trend <0.001). However, they were equally likely to be admitted to high dependency (Level 2) or intensive care (Level 3) and/or to die, after adjustment for potential confounders (adj. OR?=?0.93 (95% CI: 0.46-1.92). Of 11 pregnant women needing Level 2/3 care, 10 required mechanical ventilation and three died.Conclusions: Since the expected prevalence of pregnancy in the source population was 6%, our data suggest that pregnancy greatly increased the likelihood of hospital admission with A(H1N1)pdm09. Pregnant women were less likely than non-pregnant women to have respiratory distress on admission, but severe outcomes were equally likely in both groups

The care and support needs of residential care home residents with comorbid cancer and dementia: A qualitative review and ethnographic study.

Background: Prevalence of cancer and dementia are strongly related to age. In the UK, 70% of care home residents have dementia. By 2040, older people (aged 65+) will account for 77% of all people living with cancer. Residents with only one of these conditions may have complex care needs. Having comorbid cancer and dementia (CCD) is likely to bring further challenges. This is the first research project to examine the care and support needs of people with CCD living in residential care homes and areas for improvement. Aims: To explore: (1) The care and support needs of people with CCD living in residential care homes. (2) What constitutes good care for people with CCD, their family/supporters, and residential care home staff. (3) Potential barriers and facilitators to providing good care for people with CCD. Methods: (1) Literature review to examine implications for cancerrelated care for people with dementia living in residential care homes. (2) Interviews with 5‐10 men and women with CCD, their family members/ supporters, and residential care home staff. (3) Ethnographic observations of 5‐10 people with CCD to further explore barriers and facilitators to good care. Results: Emergent findings from the literature review will be presented, and their implications for supporting people with CCD living in residential care homes discussed. Conclusions: Findings from this study will help improve the care and support of people with CCD and will contribute to a wider programme of research exploring the cancer care needs of people with dementia across a variety of care settings

A Note on Encodings of Phylogenetic Networks of Bounded Level

Driven by the need for better models that allow one to shed light into the question how life's diversity has evolved, phylogenetic networks have now joined phylogenetic trees in the center of phylogenetics research. Like phylogenetic trees, such networks canonically induce collections of phylogenetic trees, clusters, and triplets, respectively. Thus it is not surprising that many network approaches aim to reconstruct a phylogenetic network from such collections. Related to the well-studied perfect phylogeny problem, the following question is of fundamental importance in this context: When does one of the above collections encode (i.e. uniquely describe) the network that induces it? In this note, we present a complete answer to this question for the special case of a level-1 (phylogenetic) network by characterizing those level-1 networks for which an encoding in terms of one (or equivalently all) of the above collections exists. Given that this type of network forms the first layer of the rich hierarchy of level-k networks, k a non-negative integer, it is natural to wonder whether our arguments could be extended to members of that hierarchy for higher values for k. By giving examples, we show that this is not the case

Generalized Buneman pruning for inferring the most parsimonious multi-state phylogeny

Accurate reconstruction of phylogenies remains a key challenge in evolutionary biology. Most biologically plausible formulations of the problem are formally NP-hard, with no known efficient solution. The standard in practice are fast heuristic methods that are empirically known to work very well in general, but can yield results arbitrarily far from optimal. Practical exact methods, which yield exponential worst-case running times but generally much better times in practice, provide an important alternative. We report progress in this direction by introducing a provably optimal method for the weighted multi-state maximum parsimony phylogeny problem. The method is based on generalizing the notion of the Buneman graph, a construction key to efficient exact methods for binary sequences, so as to apply to sequences with arbitrary finite numbers of states with arbitrary state transition weights. We implement an integer linear programming (ILP) method for the multi-state problem using this generalized Buneman graph and demonstrate that the resulting method is able to solve data sets that are intractable by prior exact methods in run times comparable with popular heuristics. Our work provides the first method for provably optimal maximum parsimony phylogeny inference that is practical for multi-state data sets of more than a few characters.Comment: 15 page

Emergence of hyperons in failed supernovae: trigger of the black hole formation

We investigate the emergence of strange baryons in the dynamical collapse of a non-rotating massive star to a black hole by the neutrino-radiation hydrodynamical simulations in general relativity. By following the dynamical formation and collapse of nascent proto-neutron star from the gravitational collapse of a 40Msun star adopting a new hyperonic EOS table, we show that the hyperons do not appear at the core bounce but populate quickly at ~0.5-0.7 s after the bounce to trigger the re-collapse to a black hole. They start to show up off center owing to high temperatures and later prevail at center when the central density becomes high enough. The neutrino emission from the accreting proto-neutron star with the hyperonic EOS stops much earlier than the corresponding case with a nucleonic EOS while the average energies and luminosities are quite similar between them. These features of neutrino signal are a potential probe of the emergence of new degrees of freedom inside the black hole forming collapse.Comment: 11 pages, 3 figures, accepted for publication in ApJ