Combinatorial characterization of a certain class of words and a conjectured connection with general subclasses of phylogenetic tree-child networks
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ABSTRACT:
SUBMITTER: Pons M
PROVIDER: S-EPMC8575882 | biostudies-literature |
REPOSITORIES: biostudies-literature
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Project description:MOTIVATION: The presence of reticulate evolutionary events in phylogenies turn phylogenetic trees into phylogenetic networks. These events imply in particular that there may exist multiple evolutionary paths from a non-extant species to an extant one, and this multiplicity makes the comparison of phylogenetic networks much more difficult than the comparison of phylogenetic trees. In fact, all attempts to define a sound distance measure on the class of all phylogenetic networks have failed so far. Thus, the only practical solutions have been either the use of rough estimates of similarity (based on comparison of the trees embedded in the networks), or narrowing the class of phylogenetic networks to a certain class where such a distance is known and can be efficiently computed. The first approach has the problem that one may identify two networks as equivalent, when they are not; the second one has the drawback that there may not exist algorithms to reconstruct such networks from biological sequences. RESULTS: We present in this article a distance measure on the class of semi-binary tree-sibling time consistent phylogenetic networks, which generalize tree-child time consistent phylogenetic networks, and thus also galled-trees. The practical interest of this distance measure is 2-fold: it can be computed in polynomial time by means of simple algorithms, and there also exist polynomial-time algorithms for reconstructing networks of this class from DNA sequence data. AVAILABILITY: The Perl package Bio::PhyloNetwork, included in the BioPerl bundle, implements many algorithms on phylogenetic networks, including the computation of the distance presented in this article. SUPPLEMENTARY INFORMATION: Some counterexamples, proofs of the results not included in this article, and some computational experiments are available at Bioinformatics online.
| S-EPMC2718672 | biostudies-literature
Project description:Learning to read involves associating abstract visual shapes with familiar meanings. Embodiment theories suggest that word meaning is at least partially represented in distributed sensorimotor networks in the brain (Barsalou, 2008; Pulvermueller, 2013). We explored how reading comprehension develops by tracking when and how printed words start activating these "semantic" sensorimotor representations as children learn to read. Adults and children aged 7-10 years showed clear category-specific cortical specialization for tool versus animal pictures during a one-back categorisation task. Thus, sensorimotor representations for these categories were in place at all ages. However, co-activation of these same brain regions by the visual objects' written names was only present in adults, even though all children could read and comprehend all presented words, showed adult-like task performance, and older children were proficient readers. It thus takes years of training and expert reading skill before spontaneous processing of printed words' sensorimotor meanings develops in childhood.
| S-EPMC4271739 | biostudies-literature
Project description:Child stunting in Latin America and the Caribbean (LAC) decreased from 22.9% in 1990 to 9.6% in 2017. While stunting rates in the region were falling, access to electricity and refrigeration were on the rise. Despite a large body of evidence surrounding the effects of refrigeration on food consumption, and separately of the importance of food consumption for child health and nutrition, surprisingly few studies explore the potential effects of refrigeration on child nutrition. We studied the relationship between refrigeration and child nutrition outcomes using rich panel data for 1298 low-income households with children younger than 12 months at baseline in El Alto, Bolivia. We estimated the effects of refrigerator ownership on diet and nutrition outcomes using a difference-in-difference approach. Owning a refrigerator was associated with increased food expenditures and improved child nutrition. We found evidence that households that acquired a refrigerator were more likely to buy food that requires refrigeration, and children in households that acquired refrigerators were 0.17 standard deviations taller for their age after 2 years. We also found that refrigeration was associated with a 0.26 standard deviation decline in BMI-for-age, an effect driven by increased height rather than lower weight. These results suggest that refrigeration may play a role in explaining reductions in undernutrition observed in low- and middle-income countries in recent decades.
| S-EPMC7988856 | biostudies-literature
Project description:The genus Flaveria has been extensively used as a model to study the evolution of C4 photosynthesis as it contains both C3 and C4 species as well as a number of species that exhibit intermediate types of photosynthesis. The current phylogenetic tree of the Flaveria genus contains 21 of the 23 known Flaveria species and has been constructed using a combination of morphologicial data and three non-coding DNA sequences (nuclear encoded ETS, ITS and chloroplast encoded trnl-F). However, recent studies have suggested that phylogenetic trees inferred using a small number of molecular sequences may often be incorrect. Moreover, studies in other genera have often shown substantial differences between trees inferred using morphological data and those using molecular sequence. To provide new insight into the phylogeny of the genus Flaveria we utilize RNA-Seq data to construct a multi-gene concatenated phylogenetic tree of 17 Flaveria species. Furthermore, we use this new data to identify 14 C4 specific non-synonymous mutation sites, 12 of which (86%) can be independently verified by public sequence data. We propose that the data collection method provided in this study can be used as a generic method for facilitating phylogenetic tree reconstruction in the absence of reference genomes for the target species.
2015-01-08 | GSE54339 | GEO
Project description:The genus Flaveria has been extensively used as a model to study the evolution of C4 photosynthesis as it contains both C3 and C4 species as well as a number of species that exhibit intermediate types of photosynthesis. The current phylogenetic tree of the Flaveria genus contains 21 of the 23 known Flaveria species and has been constructed using a combination of morphologicial data and three non-coding DNA sequences (nuclear encoded ETS, ITS and chloroplast encoded trnl-F). However, recent studies have suggested that phylogenetic trees inferred using a small number of molecular sequences may often be incorrect. Moreover, studies in other genera have often shown substantial differences between trees inferred using morphological data and those using molecular sequence. To provide new insight into the phylogeny of the genus Flaveria we utilize RNA-Seq data to construct a multi-gene concatenated phylogenetic tree of 17 Flaveria species. Furthermore, we use this new data to identify 14 C4 specific non-synonymous mutation sites, 12 of which (86%) can be independently verified by public sequence data. We propose that the data collection method provided in this study can be used as a generic method for facilitating phylogenetic tree reconstruction in the absence of reference genomes for the target species. 18 Flaveria sample including 11 species are sequenced, other three samples were also sequenced as out-group. In all, 21 samples.
2015-01-08 | E-GEOD-54339 | biostudies-arrayexpress
Project description:The shapes of evolutionary trees are influenced by the nature of the evolutionary process but comparisons of trees from different processes are hindered by the challenge of completely describing tree shape. We present a full characterization of the shapes of rooted branching trees in a form that lends itself to natural tree comparisons. We use this characterization to define a metric, in the sense of a true distance function, on tree shapes. The metric distinguishes trees from random models known to produce different tree shapes. It separates trees derived from tropical versus USA influenza A sequences, which reflect the differing epidemiology of tropical and seasonal flu. We describe several metrics based on the same core characterization, and illustrate how to extend the metric to incorporate trees' branch lengths or other features such as overall imbalance. Our approach allows us to construct addition and multiplication on trees, and to create a convex metric on tree shapes which formally allows computation of average tree shapes.
| S-EPMC5790134 | biostudies-literature
Project description:Phylogenetic analyses often produce large numbers of trees. Mapping trees' distribution in "tree space" can illuminate the behavior and performance of search strategies, reveal distinct clusters of optimal trees, and expose differences between different data sources or phylogenetic methods-but the high-dimensional spaces defined by metric distances are necessarily distorted when represented in fewer dimensions. Here, I explore the consequences of this transformation in phylogenetic search results from 128 morphological data sets, using stratigraphic congruence-a complementary aspect of tree similarity-to evaluate the utility of low-dimensional mappings. I find that phylogenetic similarities between cladograms are most accurately depicted in tree spaces derived from information-theoretic tree distances or the quartet distance. Robinson-Foulds tree spaces exhibit prominent distortions and often fail to group trees according to phylogenetic similarity, whereas the strong influence of tree shape on the Kendall-Colijn distance makes its tree space unsuitable for many purposes. Distances mapped into two or even three dimensions often display little correspondence with true distances, which can lead to profound misrepresentation of clustering structure. Without explicit testing, one cannot be confident that a tree space mapping faithfully represents the true distribution of trees, nor that visually evident structure is valid. My recommendations for tree space validation and visualization are implemented in a new graphical user interface in the "TreeDist" R package. [Multidimensional scaling; phylogenetic software; tree distance metrics; treespace projections.].
| S-EPMC9366458 | biostudies-literature
Project description:Leishmania infantum is the etiological agent of zoonotic visceral leishmaniasis. In endemic areas, canine infections are considered the main source of infection for human populations. Therefore, any control of human leishmaniasis must include the control of canine infections. Chemotherapy of leishmaniasis is inadequate and canine immunoprophylaxis has important limitations. Reports on the response of infected dogs are abundant but no clear picture of immune events has emerged. To shed some light on these shortcomings the specific IgG subclass response was followed in 20 Beagle dogs experimentally infected with L. infantum using monoclonal antibodies (MAb) specific for canine IgG1, IgG2, IgG3 and IgG4, along with ELISA and flow cytometry. Results showed that parasitic infection elicits a general response of all IgG subclasses, with a predominant IgG1 response and without any evidence of IgG1/IgG2 dichotomy. These findings suggest that the inconsistent results reported previously could be related to the lack of specific reagents and not to the actual differences in the immune response of infected animals. Differential IgG subclass reactivity in ELISA and cytometry and the analysis of the reacting antigens could facilitate the diagnosis and prognosis of the disease and provide a useful tool for adequate therapeutics and vaccine development against leishmaniasis.
| S-EPMC7606601 | biostudies-literature
Project description:The vast majority of methods available for sequence comparison rely on a first sequence alignment step, which requires a number of assumptions on evolutionary history and is sometimes very difficult or impossible to perform due to the abundance of gaps (insertions/deletions). In such cases, an alternative alignment-free method would prove valuable. Our method starts by a computation of a generalized suffix tree of all sequences, which is completed in linear time. Using this tree, the frequency of all possible words with a preset length L-L-words--in each sequence is rapidly calculated. Based on the L-words frequency profile of each sequence, a pairwise standard Euclidean distance is then computed producing a symmetric genetic distance matrix, which can be used to generate a neighbor joining dendrogram or a multidimensional scaling graph. We present an improvement to word counting alignment-free approaches for sequence comparison, by determining a single optimal word length and combining suffix tree structures to the word counting tasks. Our approach is, thus, a fast and simple application that proved to be efficient and powerful when applied to mitochondrial genomes. The algorithm was implemented in Python language and is freely available on the web.
| S-EPMC3444837 | biostudies-literature
Project description:BACKGROUND AND OBJECTIVES:Whole-genome sequencing is becoming popular as a tool for understanding outbreaks of communicable diseases, with phylogenetic trees being used to identify individual transmission events or to characterize outbreak-level overall transmission dynamics. Existing methods to infer transmission dynamics from sequence data rely on well-characterized infectious periods, epidemiological and clinical metadata which may not always be available, and typically require computationally intensive analysis focusing on the branch lengths in phylogenetic trees. We sought to determine whether the topological structures of phylogenetic trees contain signatures of the transmission patterns underlying an outbreak. METHODOLOGY:We use simulated outbreaks to train and then test computational classifiers. We test the method on data from two real-world outbreaks. RESULTS:We show that different transmission patterns result in quantitatively different phylogenetic tree shapes. We describe topological features that summarize a phylogeny's structure and find that computational classifiers based on these are capable of predicting an outbreak's transmission dynamics. The method is robust to variations in the transmission parameters and network types, and recapitulates known epidemiology of previously characterized real-world outbreaks. CONCLUSIONS AND IMPLICATIONS:There are simple structural properties of phylogenetic trees which, when combined, can distinguish communicable disease outbreaks with a super-spreader, homogeneous transmission and chains of transmission. This is possible using genome data alone, and can be done during an outbreak. We discuss the implications for management of outbreaks.
| S-EPMC4097963 | biostudies-literature