Phylogenetic Reconstruction Based on Synteny Block and Gene Adjacencies

Abstract Gene order can be used as an informative character to reconstruct phylogenetic relationships between species independently from the local information present in gene/protein sequences. PhyChro is a reconstruction method based on chromosomal rearrangements, applicable to a wide range of eukaryotic genomes with different gene contents and levels of synteny conservation. For each synteny breakpoint issued from pairwise genome comparisons, the algorithm defines two disjoint sets of genomes, named partial splits, respectively, supporting the two block adjacencies defining the breakpoint. Considering all partial splits issued from all pairwise comparisons, a distance between two genomes is computed from the number of partial splits separating them. Tree reconstruction is achieved through a bottom-up approach by iteratively grouping sister genomes minimizing genome distances. PhyChro estimates branch lengths based on the number of synteny breakpoints and provides confidence scores for the branches. PhyChro performance is evaluated on two data sets of 13 vertebrates and 21 yeast genomes by using up to 130,000 and 179,000 breakpoints, respectively, a scale of genomic markers that has been out of reach until now. PhyChro reconstructs very accurate tree topologies even at known problematic branching positions. Its robustness has been benchmarked for different synteny block reconstruction methods. On simulated data PhyChro reconstructs phylogenies perfectly in almost all cases, and shows the highest accuracy compared with other existing tools. PhyChro is very fast, reconstructing the vertebrate and yeast phylogenies in <15 min.

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Phylogenetic reconstruction based on synteny block and gene adjacencies

10.1101/840942 ◽

2019 ◽

Author(s):

Guénola Drillon ◽

Raphaël Champeimont ◽

Francesco Oteri ◽

Gilles Fischer ◽

Alessandra Carbone

Keyword(s):

Chromosomal Rearrangements ◽

Phylogenetic Reconstruction ◽

Simulated Data ◽

Synteny Block ◽

Reconstruction Method ◽

Reconstruction Methods ◽

Wide Range ◽

Genomic Markers ◽

Tree Topologies ◽

Almost All

AbstractGene order can be used as an informative character to reconstruct phylogenetic relationships-between species independently from the local information present in gene/protein sequences.PhyChro is a reconstruction method based on chromosomal rearrangements, applicable to a wide range of eukaryotic genomes with different gene contents and levels of synteny conservation. For each synteny breakpoint issued from pairwise genome comparisons, the algorithm defines two disjoint sets of genomes, named partial splits, respectively supporting the two block adjacencies defining the breakpoint. Considering all partial splits issued from all pairwise comparisons, a distance between two genomes is computed from the number of partial splits separating them. Tree reconstruction is achieved through a bottom-up approach by iteratively grouping sister genomes minimizing genome distances. PhyChro estimates branch lengths based on the number of synteny breakpoints and provides confidence scores for the branches.PhyChro performance isevaluatedon two datasets of 13 vertebrates and 21 yeast genomes by using up to 130 000 and 179 000 breakpoints respectively, a scale of genomic markers that has been out of reach until now. PhyChro reconstructs very accurate tree topologies even at known problematic branching positions. Its robustness has been benchmarked for different synteny block reconstruction methods. On simulated data PhyChro reconstructs phylogenies perfectly in almost all cases, and shows the highest accuracy compared to other existing tools. PhyChro is very fast, reconstructing the vertebrate and yeast phylogenies in less than 15 min.AvailabilityPhyChro will be freely available under the BSD license after [email protected]

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Mitochondrial Architecture Rearrangements Produce Asymmetrical Nonadaptive Mutational Pressures That Subvert the Phylogenetic Reconstruction in Isopoda

Genome Biology and Evolution ◽

10.1093/gbe/evz121 ◽

2019 ◽

Vol 11 (7) ◽

pp. 1797-1812 ◽

Cited By ~ 6

Author(s):

Dong Zhang ◽

Hong Zou ◽

Cong-Jie Hua ◽

Wen-Xiang Li ◽

Shahid Mahboob ◽

...

Keyword(s):

Life Histories ◽

Phylogenetic Reconstruction ◽

Mitochondrial Genomes ◽

Data Sets ◽

Long Branch Attraction ◽

Mitochondrial Data ◽

Gc Skew ◽

Limited Applicability ◽

Phylogenetic Hypotheses ◽

Almost All

Abstract The phylogeny of Isopoda, a speciose order of crustaceans, remains unresolved, with different data sets (morphological, nuclear, mitochondrial) often producing starkly incongruent phylogenetic hypotheses. We hypothesized that extreme diversity in their life histories might be causing compositional heterogeneity/heterotachy in their mitochondrial genomes, and compromising the phylogenetic reconstruction. We tested the effects of different data sets (mitochondrial, nuclear, nucleotides, amino acids, concatenated genes, individual genes, gene orders), phylogenetic algorithms (assuming data homogeneity, heterogeneity, and heterotachy), and partitioning; and found that almost all of them produced unique topologies. As we also found that mitogenomes of Asellota and two Cymothoida families (Cymothoidae and Corallanidae) possess inversed base (GC) skew patterns in comparison to other isopods, we concluded that inverted skews cause long-branch attraction phylogenetic artifacts between these taxa. These asymmetrical skews are most likely driven by multiple independent inversions of origin of replication (i.e., nonadaptive mutational pressures). Although the PhyloBayes CAT-GTR algorithm managed to attenuate some of these artifacts (and outperform partitioning), mitochondrial data have limited applicability for reconstructing the phylogeny of Isopoda. Regardless of this, our analyses allowed us to propose solutions to some unresolved phylogenetic debates, and support Asellota are the most likely candidate for the basal isopod branch. As our findings show that architectural rearrangements might produce major compositional biases even on relatively short evolutionary timescales, the implications are that proving the suitability of data via composition skew analyses should be a prerequisite for every study that aims to use mitochondrial data for phylogenetic reconstruction, even among closely related taxa.

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Ultra-fast accurate reconstruction of spiking activity from calcium imaging data

Journal of Neurophysiology ◽

10.1152/jn.00934.2017 ◽

2018 ◽

Vol 119 (5) ◽

pp. 1863-1878 ◽

Cited By ~ 6

Author(s):

Vahid Rahmati ◽

Knut Kirmse ◽

Knut Holthoff ◽

Stefan J. Kiebel

Keyword(s):

Calcium Imaging ◽

Reconstruction Method ◽

Imaging Data ◽

Decay Kinetics ◽

Experimental Conditions ◽

Model Free ◽

Reconstruction Methods ◽

Wide Range ◽

Fast Processing ◽

Spiking Activity

Calcium imaging provides an indirect observation of the underlying neural dynamics and enables the functional analysis of neuronal populations. However, the recorded fluorescence traces are temporally smeared, thus making the reconstruction of exact spiking activity challenging. Most of the established methods to tackle this issue are limited in dealing with issues such as the variability in the kinetics of fluorescence transients, fast processing of long-term data, high firing rates, and measurement noise. We propose a novel, heuristic reconstruction method to overcome these limitations. By using both synthetic and experimental data, we demonstrate the four main features of this method: 1) it accurately reconstructs both isolated spikes and within-burst spikes, and the spike count per fluorescence transient, from a given noisy fluorescence trace; 2) it performs the reconstruction of a trace extracted from 1,000,000 frames in less than 2 s; 3) it adapts to transients with different rise and decay kinetics or amplitudes, both within and across single neurons; and 4) it has only one key parameter, which we will show can be set in a nearly automatic way to an approximately optimal value. Furthermore, we demonstrate the ability of the method to effectively correct for fast and rather complex, slowly varying drifts as frequently observed in in vivo data. NEW & NOTEWORTHY Reconstruction of spiking activities from calcium imaging data remains challenging. Most of the established reconstruction methods not only have limitations in adapting to systematic variations in the data and fast processing of large amounts of data, but their results also depend on the user’s experience. To overcome these limitations, we present a novel, heuristic model-free-type method that enables an ultra-fast, accurate, near-automatic reconstruction from data recorded under a wide range of experimental conditions.

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Evaluation of phylogenetic reconstruction methods using bacterial whole genomes: a simulation based study

Wellcome Open Research ◽

10.12688/wellcomeopenres.14265.2 ◽

2018 ◽

Vol 3 ◽

pp. 33 ◽

Cited By ~ 18

Author(s):

John A. Lees ◽

Michelle Kendall ◽

Julian Parkhill ◽

Caroline Colijn ◽

Stephen D. Bentley ◽

...

Keyword(s):

Maximum Likelihood ◽

Phylogenetic Reconstruction ◽

Simulated Data ◽

Real Data ◽

Tree Topology ◽

Computational Time ◽

Advantages And Disadvantages ◽

Phylogenetic Reconstructions ◽

Reconstruction Methods ◽

True Tree

Background: Phylogenetic reconstruction is a necessary first step in many analyses which use whole genome sequence data from bacterial populations. There are many available methods to infer phylogenies, and these have various advantages and disadvantages, but few unbiased comparisons of the range of approaches have been made. Methods: We simulated data from a defined 'true tree' using a realistic evolutionary model. We built phylogenies from this data using a range of methods, and compared reconstructed trees to the true tree using two measures, noting the computational time needed for different phylogenetic reconstructions. We also used real data from Streptococcus pneumoniae alignments to compare individual core gene trees to a core genome tree. Results: We found that, as expected, maximum likelihood trees from good quality alignments were the most accurate, but also the most computationally intensive. Using less accurate phylogenetic reconstruction methods, we were able to obtain results of comparable accuracy; we found that approximate results can rapidly be obtained using genetic distance based methods. In real data we found that highly conserved core genes, such as those involved in translation, gave an inaccurate tree topology, whereas genes involved in recombination events gave inaccurate branch lengths. We also show a tree-of-trees, relating the results of different phylogenetic reconstructions to each other. Conclusions: We recommend three approaches, depending on requirements for accuracy and computational time. For the most accurate tree, use of either RAxML or IQ-TREE with an alignment of variable sites produced by mapping to a reference genome is best. Quicker approaches that do not perform full maximum likelihood optimisation may be useful for many analyses requiring a phylogeny, as generating a high quality input alignment is likely to be the major limiting factor of accurate tree topology. We have publicly released our simulated data and code to enable further comparisons.

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Family-Joining: A Fast Distance-Based Method for Constructing Generally Labeled Trees

Molecular Biology and Evolution ◽

10.1093/molbev/msw123 ◽

2016 ◽

Vol 33 (10) ◽

pp. 2720-2734 ◽

Cited By ~ 2

Author(s):

Prabhav Kalaghatgi ◽

Nico Pfeifer ◽

Thomas Lengauer

Keyword(s):

Simulated Data ◽

Information Criterion ◽

Bootstrap Support ◽

Evolutionary Relationships ◽

Distance Threshold ◽

Labeled Trees ◽

Wide Range ◽

Branching Points ◽

Cross Validation Error ◽

Almost All

Abstract The widely used model for evolutionary relationships is a bifurcating tree with all taxa/observations placed at the leaves. This is not appropriate if the taxa have been densely sampled across evolutionary time and may be in a direct ancestral relationship, or if there is not enough information to fully resolve all the branching points in the evolutionary tree. In this article, we present a fast distance-based agglomeration method called family-joining (FJ) for constructing so-called generally labeled trees in which taxa may be placed at internal vertices and the tree may contain polytomies. FJ constructs such trees on the basis of pairwise distances and a distance threshold. We tested three methods for threshold selection, FJ-AIC, FJ-BIC, and FJ-CV, which minimize Akaike information criterion, Bayesian information criterion, and cross-validation error, respectively. When compared with related methods on simulated data, FJ-BIC was among the best at reconstructing the correct tree across a wide range of simulation scenarios. FJ-BIC was applied to HIV sequences sampled from individuals involved in a known transmission chain. The FJ-BIC tree was found to be compatible with almost all transmission events. On average, internal branches in the FJ-BIC tree have higher bootstrap support than branches in the leaf-labeled bifurcating tree constructed using RAxML. 36% and 25% of the internal branches in the FJ-BIC tree and RAxML tree, respectively, have bootstrap support greater than 70%. To the best of our knowledge the method presented here is the first attempt at modeling evolutionary relationships using generally labeled trees.

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Explaining predictive models using Shapley values and non-parametric vine copulas

Dependence Modeling ◽

10.1515/demo-2021-0103 ◽

2021 ◽

Vol 9 (1) ◽

pp. 62-81

Author(s):

Kjersti Aas ◽

Thomas Nagler ◽

Martin Jullum ◽

Anders Løland

Keyword(s):

Traditional Approach ◽

Simulated Data ◽

Real Data ◽

Data Sets ◽

Data Set ◽

Wide Range ◽

Shapley Values ◽

Non Gaussian ◽

Vine Copula ◽

Vine Copulas

Abstract In this paper the goal is to explain predictions from complex machine learning models. One method that has become very popular during the last few years is Shapley values. The original development of Shapley values for prediction explanation relied on the assumption that the features being described were independent. If the features in reality are dependent this may lead to incorrect explanations. Hence, there have recently been attempts of appropriately modelling/estimating the dependence between the features. Although the previously proposed methods clearly outperform the traditional approach assuming independence, they have their weaknesses. In this paper we propose two new approaches for modelling the dependence between the features. Both approaches are based on vine copulas, which are flexible tools for modelling multivariate non-Gaussian distributions able to characterise a wide range of complex dependencies. The performance of the proposed methods is evaluated on simulated data sets and a real data set. The experiments demonstrate that the vine copula approaches give more accurate approximations to the true Shapley values than their competitors.

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Evaluation of phylogenetic reconstruction methods using bacterial whole genomes: a simulation based study

Wellcome Open Research ◽

10.12688/wellcomeopenres.14265.1 ◽

2018 ◽

Vol 3 ◽

pp. 33 ◽

Cited By ~ 7

Author(s):

John A. Lees ◽

Michelle Kendall ◽

Julian Parkhill ◽

Caroline Colijn ◽

Stephen D. Bentley ◽

...

Keyword(s):

Maximum Likelihood ◽

Phylogenetic Reconstruction ◽

Simulated Data ◽

Real Data ◽

Tree Topology ◽

Computational Time ◽

Advantages And Disadvantages ◽

Phylogenetic Reconstructions ◽

Reconstruction Methods ◽

True Tree

Background: Phylogenetic reconstruction is a necessary first step in many analyses which use whole genome sequence data from bacterial populations. There are many available methods to infer phylogenies, and these have various advantages and disadvantages, but few unbiased comparisons of the range of approaches have been made. Methods: We simulated data from a defined “true tree” using a realistic evolutionary model. We built phylogenies from this data using a range of methods, and compared reconstructed trees to the true tree using two measures, noting the computational time needed for different phylogenetic reconstructions. We also used real data from Streptococcus pneumoniae alignments to compare individual core gene trees to a core genome tree. Results: We found that, as expected, maximum likelihood trees from good quality alignments were the most accurate, but also the most computationally intensive. Using less accurate phylogenetic reconstruction methods, we were able to obtain results of comparable accuracy; we found that approximate results can rapidly be obtained using genetic distance based methods. In real data we found that highly conserved core genes, such as those involved in translation, gave an inaccurate tree topology, whereas genes involved in recombination events gave inaccurate branch lengths. We also show a tree-of-trees, relating the results of different phylogenetic reconstructions to each other. Conclusions: We recommend three approaches, depending on requirements for accuracy and computational time. Quicker approaches that do not perform full maximum likelihood optimisation may be useful for many analyses requiring a phylogeny, as generating a high quality input alignment is likely to be the major limiting factor of accurate tree topology. We have publicly released our simulated data and code to enable further comparisons.

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Phylo SI: a new genome-wide approach for prokaryotic phylogeny

Nucleic Acids Research ◽

10.1093/nar/gkt1138 ◽

2013 ◽

Vol 42 (4) ◽

pp. 2391-2404 ◽

Cited By ~ 14

Author(s):

Anton Shifman ◽

Noga Ninyo ◽

Uri Gophna ◽

Sagi Snir

Keyword(s):

Phylogenetic Signal ◽

Phylogenetic Reconstruction ◽

Simulated Data ◽

High Sensitivity ◽

Life Forms ◽

Data Sets ◽

Genome Wide ◽

Gene Order Conservation ◽

History Of ◽

Prokaryotic Evolution

Abstract The evolutionary history of all life forms is usually represented as a vertical tree-like process. In prokaryotes, however, the vertical signal is partly obscured by the massive influence of horizontal gene transfer (HGT). The HGT creates widespread discordance between evolutionary histories of different genes as genomes become mosaics of gene histories. Thus, the Tree of Life (TOL) has been questioned as an appropriate representation of the evolution of prokaryotes. Nevertheless a common hypothesis is that prokaryotic evolution is primarily tree-like, and a routine effort is made to place new isolates in their appropriate location in the TOL. Moreover, it appears desirable to exploit non–tree-like evolutionary processes for the task of microbial classification. In this work, we present a novel technique that builds on the straightforward observation that gene order conservation (‘synteny’) decreases in time as a result of gene mobility. This is particularly true in prokaryotes, mainly due to HGT. Using a ‘synteny index’ (SI) that measures the average synteny between a pair of genomes, we developed the phylogenetic reconstruction tool ‘Phylo SI’. Phylo SI offers several attractive properties such as easy bootstrapping, high sensitivity in cases where phylogenetic signal is weak and computational efficiency. Phylo SI was tested both on simulated data and on two bacterial data sets and compared with two well-established phylogenetic methods. Phylo SI is particularly efficient on short evolutionary distances where synteny footprints remain detectable, whereas the nucleotide substitution signal is too weak for reliable sequence-based phylogenetic reconstruction. The method is publicly available at http://research.haifa.ac.il/ssagi/software/PhyloSI.zip.

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Super RaSE: Super Random Subspace Ensemble Classification

Journal of Risk and Financial Management ◽

10.3390/jrfm14120612 ◽

2021 ◽

Vol 14 (12) ◽

pp. 612

Author(s):

Jianan Zhu ◽

Yang Feng

Keyword(s):

Simulated Data ◽

Real Data ◽

Classification Problem ◽

R Package ◽

Ensemble Classification ◽

Data Sets ◽

Random Subspace ◽

Base Classifier ◽

Wide Range ◽

Random Subspace Ensemble

We propose a new ensemble classification algorithm, named super random subspace ensemble (Super RaSE), to tackle the sparse classification problem. The proposed algorithm is motivated by the random subspace ensemble algorithm (RaSE). The RaSE method was shown to be a flexible framework that can be coupled with any existing base classification. However, the success of RaSE largely depends on the proper choice of the base classifier, which is unfortunately unknown to us. In this work, we show that Super RaSE avoids the need to choose a base classifier by randomly sampling a collection of classifiers together with the subspace. As a result, Super RaSE is more flexible and robust than RaSE. In addition to the vanilla Super RaSE, we also develop the iterative Super RaSE, which adaptively changes the base classifier distribution as well as the subspace distribution. We show that the Super RaSE algorithm and its iterative version perform competitively for a wide range of simulated data sets and two real data examples. The new Super RaSE algorithm and its iterative version are implemented in a new version of the R package RaSEn.

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A Robust Phylogeny of the Oropendolas: Polyphyly Revealed by Mitochondrial Sequence Data

The Auk ◽

10.1093/auk/119.2.335 ◽

2002 ◽

Vol 119 (2) ◽

pp. 335-348 ◽

Cited By ~ 4

Author(s):

J. Jordan Price ◽

Scott M. Lanyon

Keyword(s):

Sequence Data ◽

Phylogenetic Reconstruction ◽

Species Level ◽

Species Relationships ◽

Base Pairs ◽

Phylogenetic Information ◽

Multiple Exemplars ◽

Reconstruction Methods ◽

Mitochondrial Cytochrome B ◽

Wide Range

Abstract We present a robust, fully resolved phylogeny for the oropendolas that will serve as a basis for comparative studies in this group. We sequenced 2,011 base pairs (bp) of the mitochondrial cytochrome-b and ND2 genes from 22 individuals to reconstruct relationships between recognized species and subspecies and to assess variation within polytypic taxa. A single phylogenetic tree was produced despite the use of a wide range of weighting schemes and phylogenetic reconstruction methods. Our data provide strong evidence that oropendolas are polyphyletic, with two distinct groups within a larger clade of oropendolas and caciques. We confirm the monophyly of recognized species, but indicate that some within-species relationships do not conform to recognized subspecies limits. Our findings thus demonstrate the importance of including multiple exemplars from each taxon of interest. The two genes provided complimentary and equally effective phylogenetic information for comparisons within the oropendolas, but exhibited lower resolution in comparisons above the species level.

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