The marginal likelihood is commonly used for comparing different evolutionary models in Bayesian phylogenetics and is the central quantity used in computing Bayes Factors for comparing model fit. A ...popular method for estimating marginal likelihoods, the harmonic mean (HM) method, can be easily computed from the output of a Markov chain Monte Carlo analysis but often greatly overestimates the marginal likelihood. The thermodynamic integration (TI) method is much more accurate than the HM method but requires more computation. In this paper, we introduce a new method, stepping stone sampling (SS), which uses importance sampling to estimate each ratio in a series (the "stepping stones") bridging the posterior and prior distributions. We compare the performance of the SS approach to the TI and HM methods in simulation and using real data. We conclude that the greatly increased accuracy of the SS and TI methods argues for their use instead of the HM method, despite the extra computation needed.
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BFBNIB, DOBA, IZUM, KILJ, NMLJ, NUK, PILJ, PNG, SAZU, SIK, UILJ, UKNU, UL, UM, UPUK
Evolutionary biologists have adopted simple likelihood models for purposes of estimating ancestral states and evaluating character independence on specified phylogenies; however, for purposes of ...estimating phylogenies by using discrete morphological data, maximum parsimony remains the only option. This paper explores the possibility of using standard, well-behaved Markov models for estimating morphological phylogenies (including branch lengths) under the likelihood criterion. An important modification of standard Markov models involves making the likelihood conditional on characters being variable, because constant characters are absent in morphological data sets. Without this modification, branch lengths are often overestimated, resulting in potentially serious biases in tree topology selection. Several new avenues of research are opened by an explicitly model-based approach to phylogenetic analysis of discrete morphological data, including combined-data likelihood analyses (morphology + sequence data), likelihood ratio tests, and Bayesian analyses.
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BFBNIB, DOBA, IZUM, KILJ, NMLJ, NUK, PILJ, PNG, SAZU, SIK, UILJ, UKNU, UL, UM, UPUK
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•Nine chloroplast genomes of chlorophycean green algae were sequenced and characterized.•The genomes exhibited variation in size and non-coding content.•Gene content was similar ...across all genomes.•Phylogenetic analysis of 56 genes indicated bias on nucleotide and codon level.•Conflict between nt and aa analyses is largely due to Arg, Leu, and Ser codon usage.
Chloroplast sequence data are widely used to infer phylogenies of plants and algae. With the increasing availability of complete chloroplast genome sequences, the opportunity arises to resolve ancient divergences that were heretofore problematic. On the flip side, properly analyzing large multi-gene data sets can be a major challenge, as these data may be riddled with systematic biases and conflicting signals. Our study contributes new data from nine complete and four fragmentary chloroplast genome sequences across the green algal order Sphaeropleales. Our phylogenetic analyses of a 56-gene data set show that analyzing these data on a nucleotide level yields a well-supported phylogeny – yet one that is quite different from a corresponding amino acid analysis. We offer some possible explanations for this conflict through a range of analyses of modified data sets. In addition, we characterize the newly sequenced genomes in terms of their structure and content, thereby further contributing to the knowledge of chloroplast genome evolution.
Background:
The 2019 community-acquired pneumonia guidelines recommend using recent respiratory cultures and locally validated epidemiology plus risk factor assessment to determine empirical coverage ...of methicillin-resistant Staphylococcus aureus (MRSA) and Pseudomonas aeruginosa.
Objective:
To develop a methodology for evaluating local epidemiology and validating local risk factors for P aeruginosa and MRSA.
Methods:
This multicenter, retrospective cohort evaluated adult patients admitted for pneumonia. Risk factors for MRSA and P aeruginosa were evaluated using multivariable logistic regression and reported as adjusted odds ratios (aORs).
Results:
There were 10 723 cases evaluated. Lung abscess/empyema had the highest odds associated with MRSA (aOR = 4.24; P < 0.0001), followed by influenza (aOR = 2.34; P = 0.01), end-stage renal disease (ESRD; aOR = 2.09; P = 0.006), illicit substance use (aOR = 1.7; P = 0.007), and chronic obstructive pulmonary disease (COPD; aOR = 1.26; P = 0.04). For P aeruginosa, the highest odds were in bronchiectasis (aOR = 6.13; P < 0.0001), lung abscess/empyema (aOR = 3.36; P = 0.005), and COPD (aOR = 1.84; P < 0.0001). Isolated COPD without other risk factors did not pose an increased risk of either organism.
Conclusion and Relevance:
Influenza, ESRD, lung abscess/empyema, and illicit substance use were local risk factors for MRSA. Bronchiectasis and lung abscess/empyema were risk factors for Pseudomonas. COPD was associated with MRSA and Pseudomonas. However, isolated COPD had similar rates of MRSA and Pseudomonas pneumonia compared with the total population. This study established a feasible methodology for evaluating local risk factors.
BEAGLE 3 Ayres, Daniel L.; Cummings, Michael P.; Baele, Guy ...
Systematic biology,
11/2019, Letnik:
68, Številka:
6
Journal Article
Recenzirano
Odprti dostop
BEAGLE is a high-performance likelihood-calculation library for phylogenetic inference. The BEAGLE library defines a simple, but flexible, application programming interface (API), and includes a ...collection of efficient implementations for calculation under a variety of evolutionary models on different hardware devices. The library has been integrated into recent versions of popular phylogenetics software packages including BEAST and MrBayes and has been widely used across a diverse range of evolutionary studies. Here, we present BEAGLE 3 with new parallel implementations, increased performance for challenging data sets, improved scalability, and better usability. We have added new OpenCL and central processing unit-threaded implementations to the library, allowing the effective utilization of a wider range of modern hardware. Further, we have extended the API and library to support concurrent computation of independent partial likelihood arrays, for increased performance of nucleotide-model analyses with greater flexibility of data partitioning. For better scalability and usability, we have improved how phylogenetic software packages use BEAGLE in multi-GPU (graphics processing unit) and cluster environments, and introduced an automated method to select the fastest device given the data set, evolutionary model, and hardware. For application developers who wish to integrate the library, we also have developed an online tutorial. To evaluate the effect of the improvements, we ran a variety of benchmarks on state-of-the-art hardware. For a partitioned exemplar analysis, we observe run-time performance improvements as high as 5.9-fold over our previous GPU implementation. BEAGLE 3 is free, open-source software licensed under the Lesser GPL and available at https://beagle-dev.github.io.
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BFBNIB, DOBA, IZUM, KILJ, NMLJ, NUK, PILJ, PNG, SAZU, SIK, UILJ, UKNU, UL, UM, UPUK
PREMISE OF THE STUDY:
Estimating phylogenetic relationships in relatively recent evolutionary radiations is challenging, especially if short branches associated with recent divergence result in ...multiple gene tree histories. We combine anchored enrichment next‐generation sequencing with species tree analyses to produce a robust estimate of phylogenetic relationships in the genus Protea (Proteaceae), an iconic radiation in South Africa.
METHODS:
We sampled multiple individuals within 59 out of 112 species of Protea and 6 outgroup species for a total of 163 individuals, and obtained sequences for 498 low‐copy, orthologous nuclear loci using anchored phylogenomics. We compare several approaches for building species trees, and explore gene tree–species tree discrepancies to determine whether poor phylogenetic resolution reflects a lack of informative sites, incomplete lineage sorting, or hybridization.
KEY RESULTS:
Phylogenetic estimates from species tree approaches are similar to one another and recover previously well‐supported clades within Protea, in addition to providing well‐supported phylogenetic hypotheses for previously poorly resolved intrageneric relationships. Individual gene trees are markedly different from one another and from species trees. Nonetheless, analyses indicate that differences among gene trees occur primarily concerning clades supported by short branches.
CONCLUSIONS:
Species tree methods using hundreds of nuclear loci provided strong support for many previously unresolved relationships in the radiation of the genus Protea. In cases where support for particular relationships remains low, these appear to arise from few informative sites and lack of information rather than strongly supported disagreement among gene trees.
Phylogenetic inference is fundamental to our understanding of most aspects of the origin and evolution of life, and in recent years, there has been a concentration of interest in statistical ...approaches such as Bayesian inference and maximum likelihood estimation. Yet, for large data sets and realistic or interesting models of evolution, these approaches remain computationally demanding. High-throughput sequencing can yield data for thousands of taxa, but scaling to such problems using serial computing often necessitates the use of nonstatistical or approximate approaches. The recent emergence of graphics processing units (GPUs) provides an opportunity to leverage their excellent floating-point computational performance to accelerate statistical phylogenetic inference. A specialized library for phylogenetic calculation would allow existing software packages to make more effective use of available computer hardware, including GPUs. Adoption of a common library would also make it easier for other emerging computing architectures, such as field programmable gate arrays, to be used in the future. We present BEAGLE, an application programming interface (API) and library for high-performance statistical phylogenetic inference. The API provides a uniform interface for performing phylogenetic likelihood calculations on a variety of compute hardware platforms. The library includes a set of efficient implementations and can currently exploit hardware including GPUs using NVIDIA CUDA, central processing units (CPUs) with Streaming SIMD Extensions and related processor supplementary instruction sets, and multicore CPUs via OpenMP. To demonstrate the advantages of a common API, we have incorporated the library into several popular phylogenetic software packages. The BEAGLE library is free open source software licensed under the Lesser GPL and available from http://beagle-lib.googlecode.com. An example client program is available as public domain software.
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BFBNIB, DOBA, IZUM, KILJ, NMLJ, NUK, PILJ, PNG, SAZU, SIK, UILJ, UKNU, UL, UM, UPUK
Lanchester's models of combat have been invoked to explain the mechanics of group fighting in social animals. Specifically, Lanchester's square law posits that the fighting ability of the group is ...proportional to the square of the number of combatants. Although used to explain a variety of ecological phenomena, the models have not been thoroughly tested. We tested the Lanchester models using group battles between colonies of the termite
. Our main goals were to determine if mortality rates fit the Lanchester models, and if so, whether the behavioural mechanisms underlying a group's success match those used in deriving the model. We initiated battles between pairs of colonies with different ratios of fighters and recorded deaths over time. We found that the numerically larger army has an advantage, but that the advantage is not as pronounced as predicted by Lanchester's square law. We also video-recorded battles to analyse individual behaviour, which did not support the mechanisms invoked by Lanchester. Instead, the killing power of an individual is increased by the presence of nest-mates, giving the larger group a disproportionate advantage. Although the behavioural mechanisms leading to the advantage may differ, our results still support some of the proposed ecological phenomena.
It is of great practical importance to compare and combine data from different studies in order to carry out appropriate and more powerful statistical inference. We propose a partition based measure ...to quantify the compatibility of two datasets using their respective posterior distributions. We further propose an information gain measure to quantify the information increase (or decrease) in combining two datasets. These measures are well calibrated and efficient computational algorithms are provided for their calculations. We use examples in a benchmark dose toxicology study, a six cities pollution data and a melanoma clinical trial to illustrate how these two measures are useful in combining current data with historical data and missing data.
The construction of evolutionary trees is now a standard part of exploratory sequence analysis. Bayesian methods for estimating trees have recently been proposed as a faster method of incorporating ...the power of complex statistical models into the process. Researchers who rely on comparative analyses need to understand the theoretical and practical motivations that underlie these new techniques, and how they differ from previous methods. The ability of the new approaches to address previously intractable questions is making phylogenetic analysis an essential tool in an increasing number of areas of genetic research.
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DOBA, IJS, IZUM, KILJ, NUK, PILJ, PNG, SAZU, UILJ, UKNU, UL, UM, UPUK
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