Abstract
Motivation
The Robinson–Foulds (RF) metric is widely used by biologists, linguists and chemists to quantify similarity between pairs of phylogenetic trees. The measure tallies the number of ...bipartition splits that occur in both trees—but this conservative approach ignores potential similarities between almost-identical splits, with undesirable consequences. ‘Generalized’ RF metrics address this shortcoming by pairing splits in one tree with similar splits in the other. Each pair is assigned a similarity score, the sum of which enumerates the similarity between two trees. The challenge lies in quantifying split similarity: existing definitions lack a principled statistical underpinning, resulting in misleading tree distances that are difficult to interpret. Here, I propose probabilistic measures of split similarity, which allow tree similarity to be measured in natural units (bits).
Results
My new information-theoretic metrics outperform alternative measures of tree similarity when evaluated against a broad suite of criteria, even though they do not account for the non-independence of splits within a single tree. Mutual clustering information exhibits none of the undesirable properties that characterize other tree comparison metrics, and should be preferred to the RF metric.
Availability and implementation
The methods discussed in this article are implemented in the R package ‘TreeDist’, archived at https://dx.doi.org/10.5281/zenodo.3528123.
Supplementary information
Supplementary data are available at Bioinformatics online.
Phylogenetic analysis aims to establish the true relationships between taxa. Different analytical methods, however, can reach different conclusions. In order to establish which approach best ...reconstructs true relationships, previous studies have simulated datasets from known tree topologies, and identified the method that reconstructs the generative tree most accurately. On this basis, researchers have argued that morphological datasets should be analysed by Bayesian approaches, which employ an explicit probabilistic model of evolution, rather than parsimony methods-with implied weights parsimony sometimes identified as particularly inaccurate. Accuracy alone, however, is an inadequate measure of a tree's utility: a fully unresolved tree is perfectly accurate, yet contains no phylogenetic information. The highly resolved trees recovered by implied weights parsimony in fact contain as much useful information as the more accurate, but less resolved, trees recovered by Bayesian methods. By collapsing poorly supported groups, this superior resolution can be traded for accuracy, resulting in trees as accurate as those obtained by a Bayesian approach. By contrast, equally weighted parsimony analysis produces trees that are less resolved and less accurate, leading to less reliable evolutionary conclusions.
Near-infrared spectroscopy (NIRS) has potential as a non-invasive brain monitor in a wide range of clinical scenarios. In the last decade, there has been a rapid expansion of clinical experience ...using NIRS to monitor cerebral oxygenation, particularly in cardiac surgery, where there is some evidence that NIRS-guided brain protection protocols might lead to a reduction in peri-operative neurological complications. There are no data to support the wider application of NIRS to monitor cerebral oxygenation during routine anaesthesia and surgery, and its application in brain injury, where it might be expected to have a key monitoring role, is as yet undefined. Technological developments, including the introduction of broadband and time-resolved spectrometers that are capable of reliably measuring changes in oxidized cytochrome c oxidase, offer real potential for a single NIRS-based device to provide multi-site, regional monitoring of cerebral metabolic status as well as oxygenation and haemodynamics.
Abstract
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.
The quest for advanced designer adsorbents for air filtration and monitoring hazardous trace gases has recently been more and more driven by the need to ensure clean air in indoor, outdoor, and ...industrial environments. How to increase safety with regard to personal protection in the event of hazardous gas exposure is a critical question for an ever‐growing population spending most of their lifetime indoors, but is also crucial for the chemical industry in order to protect future generations of employees from potential hazards. Metal–organic frameworks (MOFs) are already quite advanced and promising in terms of capacity and specific affinity to overcome limitations of current adsorbent materials for trace and toxic gas adsorption. Due to their advantageous features (e.g., high specific surface area, catalytic activity, tailorable pore sizes, structural diversity, and range of chemical and physical properties), MOFs offer a high potential as adsorbents for air filtration and monitoring of hazardous trace gases. Three advanced topics are considered here, in applying MOFs for selective adsorption: (i) toxic gas adsorption toward filtration for respiratory protection as well as indoor and cabin air, (ii) enrichment of hazardous gases using MOFs, and (iii) MOFs as sensors for toxic trace gases and explosives.
Filtration, enrichment, and sensing of toxic gases and vapors using metal–organic frameworks (MOFs) are currently studied by many researchers. To meet increasing demands regarding air quality and safety issues, new functional materials are required. MOFs show great potential to overcome the drawbacks of state‐of‐the‐art materials in regard to air filtration and monitoring of hazardous trace gases.
Does international trade make all parties better off? We study the relationship between food security and the international trade of fish and seafood between developing and developed countries. ...Specifically, we look at and discuss the evolution of trade flows – values, quantities, and prices – between developing and developed countries. The picture that emerges suggests that the quantity of seafood exported from developing countries to developed countries is close to the quantity of seafood imported by developing countries from developed countries. What takes place is a quality exchange: developing countries export high-quality seafood in exchange for lower quality seafood.
• There are two theories about how allocation of metabolic products occurs. The allometric biomass partitioning theory (APT) suggests that all plants follow common allometric scaling rules. The ...optimal partitioning theory (OPT) predicts that plants allocate more biomass to the organ capturing the most limiting resource.
• Whole-plant harvests of mature and juvenile tropical deciduous trees, evergreen trees, and lianas and model simulations were used to address the following knowledge gaps: (1) Do mature lianas comply with the APT scaling laws or do they invest less biomass in stems compared to trees? (2) Do juveniles follow the same allocation patterns as mature individuals? (3) Is either leaf phenology or life form a predictor of rooting depth?
• It was found that: (1) mature lianas followed the same allometric scaling laws as trees; (2) juveniles and mature individuals do not follow the same allocation patterns; and (3) mature lianas had shallowest coarse roots and evergreen trees had the deepest.
• It was demonstrated that: (1) mature lianas invested proportionally similar biomass to stems as trees and not less, as expected; (2) lianas were not deeper-rooted than trees as had been previously proposed; and (3) evergreen trees had the deepest roots, which is necessary to maintain canopy during simulated dry seasons.
Abstract
“Rogue” taxa of uncertain affinity can confound attempts to summarize the results of phylogenetic analyses. Rogues reduce resolution and support values in consensus trees, potentially ...obscuring strong evidence for relationships between other taxa. Information theory provides a principled means of assessing the congruence between a set of trees and their consensus, allowing rogue taxa to be identified more effectively than when using ad hoc measures of tree quality. A basic implementation of this approach in R recovers reduced consensus trees that are better resolved, more accurate, and more informative than those generated by existing methods. Consensus trees; information theory; phylogenetic software; Rogue taxa.
RNA modifications have been historically considered as fine-tuning chemo-structural features of infrastructural RNAs, such as rRNAs, tRNAs, and snoRNAs. This view has changed dramatically in recent ...years, to a large extent as a result of systematic efforts to map and quantify various RNA modifications in a transcriptome-wide manner, revealing that RNA modifications are reversible, dynamically regulated, far more widespread than originally thought, and involved in major biological processes, including cell differentiation, sex determination, and stress responses. Here we summarize the state of knowledge and provide a catalog of RNA modifications and their links to neurological disorders, cancers, and other diseases. With the advent of direct RNA-sequencing technologies, we expect that this catalog will help prioritize those RNA modifications for transcriptome-wide maps.
Starfish, graptolites and humans look as different as can be, yet are more closely related to each other than to any other phylum. Disc-shaped Cambrian fossils join the dots between these disparate ...body plans to plot out their evolutionary origins.
Starfish, graptolites and humans look as different as can be, yet are more closely related to each other than to any other phylum. Disc-shaped Cambrian fossils join the dots between these disparate body plans to plot out their evolutionary origins.
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