scholarly journals Bayesian inference of ancestral dates on bacterial phylogenetic trees

2018 ◽  
Author(s):  
Xavier Didelot ◽  
Nicholas J Croucher ◽  
Stephen D Bentley ◽  
Simon R Harris ◽  
Daniel J Wilson
Keyword(s):  
Phylogenetic Trees ◽  
Single Species ◽  
R Package ◽  
Bacterial Genomes ◽  
Phylogenetic Methods ◽  
Bacterial Genomics ◽  
Wide Range ◽  
Genomic Studies ◽  
Dated Phylogeny ◽  
Phylogenetic Method

ABSTRACTThe sequencing and comparative analysis of a collection of bacterial genomes from a single species or lineage of interest can lead to key insights into its evolution, ecology or epidemiology. The tool of choice for such a study is often to build a phylogenetic tree, and more specifically when possible a dated phylogeny, in which the dates of all common ancestors are estimated. Here we propose a new Bayesian methodology to construct dated phylogenies which is specifically designed for bacterial genomics. Unlike previous Bayesian methods aimed at building dated phylogenies, we consider that the phylogenetic relationships between the genomes have been previously evaluated using a standard phylogenetic method, which makes our methodology much faster and scalable. This two-steps approach also allows us to directly exploit existing phylogenetic methods that detect bacterial recombination, and therefore to account for the effect of recombination in the construction of a dated phylogeny. We analysed many simulated datasets in order to benchmark the performance of our approach in a wide range of situations. Furthermore, we present applications to three different real datasets from recent bacterial genomic studies. Our methodology is implemented in a R package called BactDating which is freely available for download at https://github.com/xavierdidelot/BactDating.

scholarly journals RevGadgets: an R Package for visualizing Bayesian phylogenetic analyses from RevBayes

2021 ◽  
Author(s):  
Carrie M. Tribble ◽  
William A. Freyman ◽  
Jun Ying Lim ◽  
Michael J. Landis ◽  
Joëlle Barido-Sottani ◽  
...  
Keyword(s):  
Open Source ◽  
Phylogenetic Analyses ◽  
R Package ◽  
Epidemiological Studies ◽  
Use Cases ◽  
Software Packages ◽  
Phylogenetic Methods ◽  
Wide Range ◽  
Publication Quality

1. Statistical phylogenetic methods are the foundation for a wide range of evolutionary and epidemiological studies. However, as these methods grow increasingly complex, users often encounter significant challenges with summarizing, visualizing, and communicating their key results. 2. We present RevGadgets, an R package for creating publication-quality figures from the results of a large variety of phylogenetic analyses performed in RevBayes (and other phylogenetic software packages). 3. We demonstrate how to use RevGadgets through a set of vignettes that cover the most common use cases that researchers will encounter. 4. RevGadgets is an open-source, extensible package that will continue to evolve in parallel with RevBayes, helping researchers to make sense of and communicate the results of a diverse array of analyses.

scholarly journals sangeranalyseR: simple and Interactive Processing of Sanger Sequencing Data in R

2021 ◽  
Author(s):  
Kuan-Hao Chao ◽  
Kirston Barton ◽  
Sarah Palmer ◽  
Robert Lanfear
Keyword(s):  
Open Source ◽  
Phylogenetic Trees ◽  
Input Data ◽  
Sanger Sequencing ◽  
R Package ◽  
Command Line ◽  
Sequencing Data ◽  
Fasta Format ◽  
Online Documentation ◽  
Wide Range

Abstract sangeranalyseR is feature-rich, free, and open-source R package for processing Sanger sequencing data. It allows users to go from loading reads to saving aligned contigs in a few lines of R code by using sensible defaults for most actions. It also provides complete flexibility for determining how individual reads and contigs are processed, both at the command-line in R and via interactive Shiny applications. sangeranalyseR provides a wide range of options for all steps in Sanger processing pipelines including trimming reads, detecting secondary peaks, viewing chromatograms, detecting indels and stop codons, aligning contigs, estimating phylogenetic trees, and more. Input data can be in either ABIF or FASTA format. sangeranalyseR comes with extensive online documentation and outputs aligned and unaligned reads and contigs in FASTA format, along with detailed interactive HTML reports. sangeranalyseR supports the use of colourblind-friendly palettes for viewing alignments and chromatograms. It is released under an MIT licence and available for all platforms on Bioconductor (https://bioconductor.org/packages/sangeranalyseR) and on Github (https://github.com/roblanf/sangeranalyseR).

scholarly journals BloodGen3Module: Blood transcriptional module repertoire analysis and visualization using R

2021 ◽  
Author(s):  
Darawan Rinchai ◽  
Jessica Roelands ◽  
Mohammed Toufiq ◽  
Wouter Hendrickx ◽  
Matthew C Altman ◽  
...  
Keyword(s):  
Transcript Abundance ◽  
R Package ◽  
Supplementary Information ◽  
Illustrative Case ◽  
Bioinformatic Tools ◽  
Transcriptional Module ◽  
Wide Range ◽  
Downstream Analysis ◽  
Computing Module ◽  
Parallel Workflow

Abstract Motivation We previously described the construction and characterization of generic and reusable blood transcriptional module repertoires. More recently we released a third iteration (“BloodGen3” module repertoire) that comprises 382 functionally annotated gene sets (modules) and encompasses 14,168 transcripts. Custom bioinformatic tools are needed to support downstream analysis, visualization and interpretation relying on such fixed module repertoires. Results We have developed and describe here a R package, BloodGen3Module. The functions of our package permit group comparison analyses to be performed at the module-level, and to display the results as annotated fingerprint grid plots. A parallel workflow for computing module repertoire changes for individual samples rather than groups of samples is also available; these results are displayed as fingerprint heatmaps. An illustrative case is used to demonstrate the steps involved in generating blood transcriptome repertoire fingerprints of septic patients. Taken together, this resource could facilitate the analysis and interpretation of changes in blood transcript abundance observed across a wide range of pathological and physiological states. Availability The BloodGen3Module package and documentation are freely available from Github: https://github.com/Drinchai/BloodGen3Module Supplementary information Supplementary data are available at Bioinformatics online.

scholarly journals Linking morphological and molecular sources to disentangle the case of Xylodon australis

2020 ◽  
Vol 10 (1) ◽  
Author(s):  
Javier Fernández-López ◽  
M. Teresa Telleria ◽  
Margarita Dueñas ◽  
Mara Laguna-Castro ◽  
Klaus Schliep ◽  
...  
Keyword(s):  
New Zealand ◽  
Phylogenetic Analyses ◽  
Single Species ◽  
R Package ◽  
Molecular Data ◽  
Historical Collections ◽  
Close Relationship ◽  
Kinship Relations ◽  
History Of ◽  
Different Sources

AbstractThe use of different sources of evidence has been recommended in order to conduct species delimitation analyses to solve taxonomic issues. In this study, we use a maximum likelihood framework to combine morphological and molecular traits to study the case of Xylodon australis (Hymenochaetales, Basidiomycota) using the locate.yeti function from the phytools R package. Xylodon australis has been considered a single species distributed across Australia, New Zealand and Patagonia. Multi-locus phylogenetic analyses were conducted to unmask the actual diversity under X. australis as well as the kinship relations respect their relatives. To assess the taxonomic position of each clade, locate.yeti function was used to locate in a molecular phylogeny the X. australis type material for which no molecular data was available using morphological continuous traits. Two different species were distinguished under the X. australis name, one from Australia–New Zealand and other from Patagonia. In addition, a close relationship with Xylodon lenis, a species from the South East of Asia, was confirmed for the Patagonian clade. We discuss the implications of our results for the biogeographical history of this genus and we evaluate the potential of this method to be used with historical collections for which molecular data is not available.

scholarly journals Assessing evidence for adaptive evolution in two hearing-related genes important for high-frequency hearing in echolocating mammals

2021 ◽  
Author(s):  
Hui Wang ◽  
Hanbo Zhao ◽  
Yujia Chu ◽  
Jiang Feng ◽  
Keping Sun
Keyword(s):  
Adaptive Evolution ◽  
Hair Cells ◽  
High Frequency ◽  
Phylogenetic Trees ◽  
Outer Hair Cells ◽  
Functional Domain ◽  
Coding Region ◽  
Selective Pressures ◽  
Wide Range ◽  
Different Parts

Abstract High-frequency hearing is particularly important for echolocating bats and toothed whales. Previously, studies of the hearing-related genes Prestin, KCNQ4, and TMC1 documented that adaptive evolution of high-frequency hearing has taken place in echolocating bats and toothed whales. In this study, we present two additional candidate hearing-related genes, Shh and SK2, that may also have contributed to the evolution of echolocation in mammals. Shh is a member of the vertebrate Hedgehog gene family and is required in the specification of the mammalian cochlea. SK2 is expressed in both inner and outer hair cells, and it plays an important role in the auditory system. The coding region sequences of Shh and SK2 were obtained from a wide range of mammals with and without echolocating ability. The topologies of phylogenetic trees constructed using Shh and SK2 were different; however, multiple molecular evolutionary analyses showed that those two genes experienced different selective pressures in echolocating bats and toothed whales compared to non-echolocating mammals. In addition, several nominally significant positively selected sites were detected in the non-functional domain of the SK2 gene, indicating that different selective pressures were acting on different parts of the SK2 gene. This study has expanded our knowledge of the adaptive evolution of high-frequency hearing in echolocating mammals.

scholarly journals Global phylogeography of a pantropical mangrove genus Rhizophora

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Koji Takayama ◽  
Yoichi Tateishi ◽  
Tadashi Kajita
Keyword(s):  
Phylogenetic Trees ◽  
Nuclear Dna ◽  
Divergence Time ◽  
Long Distance ◽  
F1 Hybrid ◽  
The Pacific ◽  
Comprehensive Picture ◽  
Dated Phylogeny ◽  
Stochastic Mapping ◽  
Historical Scenario

AbstractRhizophora is a key genus for revealing the formation process of the pantropical distribution of mangroves. In this study, in order to fully understand the historical scenario of Rhizophora that achieved pantropical distribution, we conducted phylogeographic analyses based on nucleotide sequences of chloroplast and nuclear DNA as well as microsatellites for samples collected worldwide. Phylogenetic trees suggested the monophyly of each AEP and IWP lineages respectively except for R. samoensis and R. × selala. The divergence time between the two lineages was 10.6 million years ago on a dated phylogeny, and biogeographic stochastic mapping analyses supported these lineages separated following a vicariant event. These data suggested that the closure of the Tethys Seaway and the reduction in mangrove distribution followed by Mid-Miocene cooling were key factors that caused the linage diversification. Phylogeographic analyses also suggested the formation of the distinctive genetic structure at the AEP region across the American continents around Pliocene. Furthermore, long-distance trans-pacific dispersal occurred from the Pacific coast of American continents to the South Pacific and formed F1 hybrid, resulting in gene exchange between the IWP and AEP lineages after 11 million years of isolation. Considering the phylogeny and phylogeography with divergence time, a comprehensive picture of the historical scenario behind the pantropical distribution of Rhizophora is updated.

scholarly journals Sequence data from isolated lichen-associated melanized fungi enhance delimitation of two new lineages within Chaetothyriomycetidae

2021 ◽  
Vol 20 (7) ◽  
pp. 911-927
Author(s):  
Lucia Muggia ◽  
Yu Quan ◽  
Cécile Gueidan ◽  
Abdullah M. S. Al-Hatmi ◽  
Martin Grube ◽  
...  
Keyword(s):  
Sequence Data ◽  
Single Species ◽  
Sister Group ◽  
Asexual Propagation ◽  
Dna Sequence Data ◽  
Wide Range ◽  
The Family ◽  
Rock Inhabiting Fungi ◽  
Stable Habitat

AbstractLichen thalli provide a long-lived and stable habitat for colonization by a wide range of microorganisms. Increased interest in these lichen-associated microbial communities has revealed an impressive diversity of fungi, including several novel lineages which still await formal taxonomic recognition. Among these, members of the Eurotiomycetes and Dothideomycetes usually occur asymptomatically in the lichen thalli, even if they share ancestry with fungi that may be parasitic on their host. Mycelia of the isolates are characterized by melanized cell walls and the fungi display exclusively asexual propagation. Their taxonomic placement requires, therefore, the use of DNA sequence data. Here, we consider recently published sequence data from lichen-associated fungi and characterize and formally describe two new, individually monophyletic lineages at family, genus, and species levels. The Pleostigmataceae fam. nov. and Melanina gen. nov. both comprise rock-inhabiting fungi that associate with epilithic, crust-forming lichens in subalpine habitats. The phylogenetic placement and the monophyly of Pleostigmataceae lack statistical support, but the family was resolved as sister to the order Verrucariales. This family comprises the species Pleostigma alpinum sp. nov., P. frigidum sp. nov., P. jungermannicola, and P. lichenophilum sp. nov. The placement of the genus Melanina is supported as a lineage within the Chaetothyriales. To date, this genus comprises the single species M. gunde-cimermaniae sp. nov. and forms a sister group to a large lineage including Herpotrichiellaceae, Chaetothyriaceae, Cyphellophoraceae, and Trichomeriaceae. The new phylogenetic analysis of the subclass Chaetothyiomycetidae provides new insight into genus and family level delimitation and classification of this ecologically diverse group of fungi.

scholarly journals MUREN: a robust and multi-reference approach of RNA-seq transcript normalization

2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Yance Feng ◽  
Lei M. Li
Keyword(s):  
Biological Significance ◽  
Housekeeping Genes ◽  
R Package ◽  
Data Sets ◽  
Statistical Regression ◽  
Rna Seq ◽  
Least Trimmed Squares ◽  
Standard Data ◽  
Wide Range ◽  
Multiple References

Abstract Background Normalization of RNA-seq data aims at identifying biological expression differentiation between samples by removing the effects of unwanted confounding factors. Explicitly or implicitly, the justification of normalization requires a set of housekeeping genes. However, the existence of housekeeping genes common for a very large collection of samples, especially under a wide range of conditions, is questionable. Results We propose to carry out pairwise normalization with respect to multiple references, selected from representative samples. Then the pairwise intermediates are integrated based on a linear model that adjusts the reference effects. Motivated by the notion of housekeeping genes and their statistical counterparts, we adopt the robust least trimmed squares regression in pairwise normalization. The proposed method (MUREN) is compared with other existing tools on some standard data sets. The goodness of normalization emphasizes on preserving possible asymmetric differentiation, whose biological significance is exemplified by a single cell data of cell cycle. MUREN is implemented as an R package. The code under license GPL-3 is available on the github platform: github.com/hippo-yf/MUREN and on the conda platform: anaconda.org/hippo-yf/r-muren. Conclusions MUREN performs the RNA-seq normalization using a two-step statistical regression induced from a general principle. We propose that the densities of pairwise differentiations are used to evaluate the goodness of normalization. MUREN adjusts the mode of differentiation toward zero while preserving the skewness due to biological asymmetric differentiation. Moreover, by robustly integrating pre-normalized counts with respect to multiple references, MUREN is immune to individual outlier samples.

scholarly journals Tandem Repeats in Bacillus: Unique Features and Taxonomic Distribution

2021 ◽  
Vol 22 (10) ◽  
pp. 5373
Author(s):  
Juan A. Subirana ◽  
Xavier Messeguer
Keyword(s):  
Tandem Repeats ◽  
Bacterial Species ◽  
Individual Species ◽  
Large Set ◽  
Bacterial Genomes ◽  
Rna Molecules ◽  
Variable Sequence ◽  
Repeat Size ◽  
Genomic Studies ◽  
Dna Tandem Repeats

Little is known about DNA tandem repeats across prokaryotes. We have recently described an enigmatic group of tandem repeats in bacterial genomes with a constant repeat size but variable sequence. These findings strongly suggest that tandem repeat size in some bacteria is under strong selective constraints. Here, we extend these studies and describe tandem repeats in a large set of Bacillus. Some species have very few repeats, while other species have a large number. Most tandem repeats have repeats with a constant size (either 52 or 20–21 nt), but a variable sequence. We characterize in detail these intriguing tandem repeats. Individual species have several families of tandem repeats with the same repeat length and different sequence. This result is in strong contrast with eukaryotes, where tandem repeats of many sizes are found in any species. We discuss the possibility that they are transcribed as small RNA molecules. They may also be involved in the stabilization of the nucleoid through interaction with proteins. We also show that the distribution of tandem repeats in different species has a taxonomic significance. The data we present for all tandem repeats and their families in these bacterial species will be useful for further genomic studies.

A review of the Afrotropical sand tampan, Ornithodoros savignyi: a complex species.

2021 ◽  
Vol 16 (036) ◽  
Author(s):  
Roxanne Albertha Charles
Keyword(s):  
Species Complex ◽  
Single Species ◽  
Biological Molecules ◽  
Soft Tick ◽  
Complex Species ◽  
Lake Chad ◽  
Ornithodoros Savignyi ◽  
Morphological Studies ◽  
Biological Studies ◽  
Wide Range

Abstract The sand tampan, Ornithodoros savignyi (Audouin, 1827), is an economically important soft tick of the Afrotropics parasitising a wide range of livestock and humans. These ticks are known to inflict painful bites which may be fatal in susceptible hosts. Historically thought to be a single species, Ornithodoros savignyi is now considered to be a complex of four tick subspecies based on molecular and morphological studies. They include Ornithodoros (Ornithodoros) kalahariensis, O. (O.) pavimentosus, O. (O.) noorsveldensis and O. (O.) savignyi. As such there may be significant implications for previous biological studies conducted on this tick. Therefore, for the purposes of this review, sand tampan toxicosis and potentially useful biological molecules have been discussed for O. (O.) savignyi sensu lato since most reported work was based on ticks collected from the Kalahari and Lake Chad region. An overview of the host range and vector biology for the O. (O.) savignyi species complex will also be examined.

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