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501 results for “Phylogenetic tree”
Phylogenetic tree of S-protein genes of selected betacoronaviruses
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FIG. 1. — Phylogenetic tree using Bayesian inference with mitochondrial 16S in A review of the genus Coccoglypta Pilsbry, 1895 (Gastropoda: Pulmonata: Camaenidae)
FIG. 1. — Phylogenetic tree using Bayesian inference with mitochondrial 16S and CO1 genes. Numbers above or below branches indicate Bayesian posterior probabilities.
Fig. 2. Bayesian majority rule consensus tree reconstructed for 90 in Phylogenetic analysis and systematic position of two new species of the ant genus Crematogaster (Hymenoptera, Formicidae) from Southeast Asia
Fig. 2. Bayesian majority rule consensus tree reconstructed for 90 taxa using five genes (ArgK, CAD, LWRh, Top1, Wg) in a MrBayes analysis. Most of the outgroups are not shown. Above node numbers indicate posterior probability, bootstrap value for MP, and bootstrap value for ML. Data were partitioned by PartitionFinder v.1.1.1 and analyzed using a best fit model for each gene and codon position, with 10 million generations and a burn-in of 25 %.
Phylogenetic trees
<p>Phylogenetic trees from different matrix versions and under different treatments.</p>
Model trees and associated simulated nucleotide sequences for testing phylogenetic inference methods
<p>This repository contains 142 tar.gz archive files, each containing nucleotide sequence data that have been simulated using <a href="http://abacus.gene.ucl.ac.uk/software/indelible/"><em>INDELible</em></a> for testing alignment-free phylogenetic inference methods. These datasets were generated by using the results (trees and model parameters) of 142 phylogenomic analyses of real-case data as model (available <a href="https://zenodo.org/record/4034261">here</a>). Initial sequence length was 5 Mbs, and an indel rate of 0.01 was set with indel length drawn from [1, 50000] according to a Zipf distribution with parameter 1.5 (see <em>INDELible</em> <a href="http://abacus.gene.ucl.ac.uk/software/indelible/manual/model.shtml">manual</a>).</p> <p>Each archive contains the following files/directories:</p> <ul> <li><code>GTR.params.trees.tsv </code> a tab-delimited file summarizing the real-case GTR+Γ model parameters and the phylogenetic tree used to simulate the sequence dataset (gathered from <a href="https://zenodo.org/record/4034261">https://zenodo.org/record/4034261</a>)</li> <li><code>tax.tsv </code> a tab-delimited file containing the initial (col 1) and simplified (col 2) taxon names</li> <li><code>model.nwk </code> a <a href="https://evolution.genetics.washington.edu/phylip/newicktree.html">Newick</a>-formatted file containing the initial model tree (gathered from <code>GTR.params.trees.tsv</code>) with simplified leaf names (following <code>tax.tsv</code>)</li> <li><code>control.txt </code> the <em>INDELible</em> input file used to simulate the evolution of a sequence along the tree in <code>model.nwk</code></li> <li><code>seq/ </code> a directory containing the simulated sequences (one FASTA file per leaf in the tree in <code>model.nwk</code>)</li> </ul> <p>___</p> <p>Criscuolo A (2020) <em>On the transformation of MinHash-based uncorrected distances into proper evolutionary distances for phylogenetic inference</em>. F1000Research, 9:1309. <a href="https://doi.org/10.12688/f1000research.26930.1">doi:10.12688/f1000research.26930.1</a></p>
The genome assembly and annotation of Magnolia biondii Pamp., a phylogenetically, economically, and medicinally important ornamental tree species
<p><em>Magnolia biondii</em> Pamp. (Magnoliaceae, magnoliids) is a phylogenetically, economically, and medicinally important ornamental tree species widely grown and cultivated in the north-temperate regions of China. Contributing a genome sequence for <i>M</i>. <i>biondii</i> will help resolve phylogenetic uncertainty of magnoliids and further understand individual trait evolution in <i>Magnolia</i>. We assembled a chromosome-level reference genome of<i> M. biondii</i> using ~67, ~175, and ~154 Gb of raw DNA sequences generated by Pacific Biosciences Single-molecule Real-time sequencing, 10X genomics Chromium, and Hi-C scaffolding strategies, respectively. The final genome assembly was ∼2.22 Gb with a contig N50 of 269.11 Kb and a BUSCO complete gene ratio of 91.90%. About 89.17% of the genome length was organized to 19 chromosomes, resulting in a scaffold N50 of 92.86 Mb. The genome contained 48,319 protein-coding genes, accounting for 22.97% of the genome length, in contrast to 66.48% of the genome length for the repetitive elements. We confirmed a Magnoliaceae specific WGD event that might have probably occurred shortly after the split of Magnoliaceae and Annonaceae. Functional enrichment of the <i>Magnolia</i> specific and expanded gene families highlighted genes involved in biosynthesis of secondary metabolites, plant-pathogen interaction, and response to stimulus, which may improve ecological fitness and biological adaptability of the lineage. Phylogenomic analyses recovered a sister relationship of magnoliids and Chloranthaceae, which are sister to a clade comprising monocots and eudicots. The genome sequence of <i>M. biondii</i> could empower trait improvement, germplasm conservation, and evolutionary studies on rapid radiation of early angiosperms.</p>
Data from: Minimizing the average distance to a closest leaf in a phylogenetic tree
When performing an analysis on a collection of molecular sequences, it can be convenient to reduce the number of sequences under consideration while maintaining some characteristic of a larger collection of sequences. For example, one may wish to select a subset of high-quality sequences that represent the diversity of a larger collection of sequences. One may also wish to specialize a large database of characterized "reference sequences" to a smaller subset that is as close as possible on average to a collection of "query sequences" of interest. Such a representative subset can be useful whenever one wishes to find a set of reference sequences that is appropriate to use for comparative analysis of environmentally-derived sequences, such as for selecting "reference tree" sequences for phylogenetic placement of metagenomic reads. In this paper we formalize these problems in terms of the minimization of the Average Distance to the Closest Leaf (ADCL) and investigate algorithms to perform the relevant minimization. We show that the greedy algorithm is not effective, show that a variant of the Partitioning Among Medoids (PAM) heuristic gets stuck in local minima, and develop an exact dynamic programming approach. Using this exact program we note that the performance of PAM appears to be good for simulated trees, and is faster than the exact algorithm for small trees. On the other hand, the exact program gives solutions for all numbers of leaves less than or equal to the given desired number of leaves, while PAM only gives a solution for the pre-specified number of leaves. Via application to real data, we show that the ADCL criterion chooses chimeric sequences less often than random subsets, while the maximization of phylogenetic diversity chooses them more often than random. These algorithms have been implemented in publicly available software.
Data from: Phylogenetic tree estimation with and without alignment: new distance methods and benchmarking
Phylogenetic tree inference is a critical component of many systematic and evolutionary studies. The majority of these studies are based on the two-step process of multiple sequence alignment followed by tree inference, despite persistent evidence that the alignment step can lead to biased results. Here we present a two-part study that first presents PaHMM-Tree, a novel neighbour joining-based method that estimates pairwise distances without assuming a single alignment. We then use simulations to benchmark its performance against a wide-range of other phylogenetic tree inference methods, including the first comparison of alignment-free distance-based methods against more conventional tree estimation methods. Our new method for calculating pairwise distances based on statistical alignment provides distance estimates that are as accurate as those obtained using standard methods based on the true alignment. Pairwise distance estimates based on the two-step process tend to be substantially less accurate. This improved performance carries through to tree inference, where PaHMM-Tree provides more accurate tree estimates than all of the pairwise distance methods assessed. For close to moderately divergent sequence data we find that the two-step methods using statistical inference, where information from all sequences is included in the estimation procedure, tend to perform better than PaHMM-Tree, particularly full statistical alignment, which simultaneously estimates both the tree and the alignment. For deep divergences we find the alignment step becomes so prone to error that our distance-based PaHMM-Tree outperforms all other methods of tree inference. Finally, we find that the accuracy of alignment-free methods tends to decline faster than standard two-step methods in the presence of alignment uncertainty, and identify no conditions where alignment-free methods are equal to or more accurate than standard phylogenetic methods even in the presence of substantial alignment error.
Data from: A chloroplast tree for Viburnum (Adoxaceae) and its implications for phylogenetic classification and character evolution
Premise of the study: Despite recent progress, significant uncertainties remain concerning relationships among early-branching lineages within Viburnum (Adoxaceae). This has prohibited a new classification, and has hindered studies of character evolution and the increasing use of Viburnum in addressing a wide range of ecological and evolutionary questions. We hoped to resolve these issues by sequencing whole plastid genomes for representative species and combining these with molecular data previously obtained from an expanded taxon sample. Methods: We performed paired-end Illumina sequencing of plastid genomes of 22 Viburnum species, and combined these data with a 10-gene dataset to infer phylogenetic relationships for 113 species. We used the results to devise a comprehensive phylogenetic classification and to analyze the evolution of eight morphological characters that vary among early-branching lineages. Key results: With greatly increased levels of confidence in most of the early branches, we propose a phylogenetic classification of Viburnum, providing formal phylogenetic definitions for 30 clades, including 13 with ICN names, eight with previously proposed informal names, and nine newly proposed names for major branches. Our parsimony reconstructions of bud structure, leaf margins, inflorescence form, ruminate endosperm, extrafloral nectaries, glandular trichomes, palisade anatomy, and pollen exine showed varying levels of homoplasy, but collectively provided morphological support for some, though not all, of the major clades. Conclusions: Our study demonstrates the value of next generation plastid sequencing, the ease of creating a formal phylogenetic classification, and the utility of such a system in describing patterns of character evolution.
Data from: Simple chained guide trees give poorer multiple sequence alignments than inferred trees in simulation and phylogenetic benchmarks
Multiple sequence aligners typically work by progressively aligning the most closely related sequences or group of sequences according to guide trees. In PNAS, Boyce et al. report that alignments reconstructed using simple chained trees (i.e., comb-like topologies) with random leaf assignment performed better in protein structure-based benchmarks than those reconstructed using phylogenies estimated from the data as guide trees. The authors state that this result could turn decades of research in the field on its head. In light of this statement, it is important to check immediately whether their result holds under evolutionary criteria: recovery of homologous sequence residues and inference of phylogenetic trees from the alignments. We have done this and the results are entirely opposed to Boyce et al.'s findings.
Data from: Phylogenetic stability, tree shape, and character compatibility: a case study using early tetrapods
Phylogenetic tree shape varies as the evolutionary processes affecting a clade change over time. In this study, we examined an empirical phylogeny of fossil tetrapods during several time intervals, and studied how temporal constraints manifested in patterns of tree imbalance and character change. The results indicate that the impact of temporal constraints on tree shape is minimal and highlights the stability through time of the reference tetrapod phylogeny. Unexpected values of imbalance for Mississippian and Pennsylvanian time slices strongly support the hypothesis that the Carboniferous was a period of explosive tetrapod radiation. Several significant diversification shifts take place in the Mississippian and underpin increased terrestrialization among the earliest limbed vertebrates. Character incompatibility is relatively high at the beginning of tetrapod history, but quickly decreases to a relatively stable lower level, relative to a null distribution based on constant rates of character change. This implies that basal tetrapods had high, but declining, rates of homoplasy early in their evolutionary history, although the origin of Lissamphibia is an exception to this trend. The time slice approach is a powerful method of phylogenetic analysis and a useful tool for assessing the impact of combining extinct and extant taxa in phylogenetic analyses of large and speciose clades.
Data from: A parametric method for assessing diversification rate variation in phylogenetic trees
Phylogenetic hypotheses are frequently used to examine variation in rates of diversification across the history of a group. Patterns of diversification-rate variation can be used to infer underlying ecological and evolutionary processes responsible for patterns of cladogenesis. Most existing methods examine rate variation through time. Methods for examining differences in diversification among groups are more limited. Here we present a new method, parametric rate comparison (PRC), that explicitly compares diversification rates among lineages in a tree using a variety of standard statistical distributions. PRC can identify subclades of the tree where diversification-rates are at variance with the remainder of the tree. A randomization test can be used to evaluate how often such variance would appear by chance alone. The method also allows for comparison of diversification-rate among a priori defined groups. Further, the application of the PRC method is not restricted to monophyletic groups. We examined the performance of PRC using simulated data which showed that PRC has acceptable false positive rates and statistical power to detect rate variation. We apply the PRC method to the well-studied radiation of North American Plethodon salamanders, and support the inference that the large-bodied P. glutinosus clade has a higher historical rate of diversification compared to other Plethodon salamanders.
Data from: The efficacy of consensus tree methods for summarising phylogenetic relationships from a posterior sample of trees estimated from morphological data
Consensus trees are required to summarise trees obtained through MCMC sampling of a posterior distribution, providing an overview of the distribution of estimated parameters such as topology, branch lengths and divergence times. Numerous consensus tree construction methods are available, each presenting a different interpretation of the tree sample. The rise of morphological clock and sampled-ancestor methods of divergence time estimation, in which times and topology are co-estimated, has increased the popularity of the maximum clade credibility (MCC) consensus tree method. The MCC method assumes that the sampled, fully resolved topology with the highest clade credibility contains an adequate summary of the most probable clades, with parameter estimates from compatible sampled trees used to obtain the marginal distributions of parameters such as clade ages and branch lengths. Using both simulated and empirical data, we demonstrate that MCC trees, and trees constructed using the similar maximum a posteriori (MAP) method, often include poorly supported and incorrect clades when summarising diffuse posterior samples of trees. We demonstrate that the paucity of information in morphological datasets contributes to the inability of MCC and MAP trees to present an accurate summary of the posterior distribution. Conversely, majority-rule consensus (MRC) trees report a lower proportion of incorrect nodes when summarising the same posterior samples of trees. Thus, we advocate the use of MRC trees, in place of MCC or MAP trees, in attempts to summarise the results of Bayesian phylogenetic analyses of morphological data.
Data from: ggtree: an R package for visualization and annotation of phylogenetic trees with their covariates and other associated data
We present an r package, ggtree, which provides programmable visualization and annotation of phylogenetic trees. ggtree can read more tree file formats than other softwares, including newick, nexus, NHX, phylip and jplace formats, and support visualization of phylo, multiphylo, phylo4, phylo4d, obkdata and phyloseq tree objects defined in other r packages. It can also extract the tree/branch/node-specific and other data from the analysis outputs of beast, epa, hyphy, paml, phylodog, pplacer, r8s, raxml and revbayes software, and allows using these data to annotate the tree. The package allows colouring and annotation of a tree by numerical/categorical node attributes, manipulating a tree by rotating, collapsing and zooming out clades, highlighting user selected clades or operational taxonomic units and exploration of a large tree by zooming into a selected portion. A two-dimensional tree can be drawn by scaling the tree width based on an attribute of the nodes. A tree can be annotated with an associated numerical matrix (as a heat map), multiple sequence alignment, subplots or silhouette images. The package ggtree is released under the artistic-2.0 license. The source code and documents are freely available through bioconductor (http://www.bioconductor.org/packages/ggtree).
Data from: Testing Phylogenetic Methods with Tree Congruence: Phylogenetic Analysis of Polymorphic Morphological Characters in Phrynosomatid Lizards
Congruence between trees from separately analyzed data sets is a powerful approach for assessing the performance of phylogenetic methods but has been applied primarily to the analysis of molecular data. In this study, different methods for treating polymorphic characters were compared using morphological data from phrynosomatid lizards. Clades were identified that are both traditionally recognized and supported by recent molecular analyses, and species were sampled from these clades to make three RknownS phylogenies of eight species each. The ability of different methods to estimate these "known" phylogenies with a finite sample of characters was tested. The phylogenetic methods included eight parsimony methods for coding polymorphism, three distance approaches (UPGMA, neighbor joining, and Fitch-Margoliash) applied to two genetic distance measures (Nei's and the modified Cavalli-Sforza and Edwards chord distance), and continuous maximum likelihood. The effects of excluding polymorphic characters and character weighting (a priori and successive) were also tested. Among the different parsimony approaches, the fixed-only method (excluding all polymorphic characters) performed relatively poorly, whereas the frequency method (including all polymorphic characters) performed relatively well. However, frequency-based distance methods consistently outperformed parsimony, especially with a small sample size (n= 1 individual per species). These results agree closely with those from recent simulation studies of polymorphic data and argue against the common practices of excluding polymorphic morphological characters, ignoring the frequencies of traits within species, and the exclusive use of parsimony to analyze morphological data.
Data from: Comparing the rates of speciation and extinction between phylogenetic trees
Over the past decade or so it has become increasingly popular to use reconstructed evolutionary trees to investigate questions about the rates of speciation and extinction. Although the methodology of this field has grown substantially in its sophistication in recent years, here I'll take a step back to present a very simple model that is designed to investigate the relatively straightforward question of whether the tempo of diversification (speciation and extinction) differs between two or more phylogenetic trees, without attempting to attribute a causal basis to this difference. It is a likelihood method, and I demonstrate that it generally shows type I error that is close to the nominal level. I also demonstrate that parameter estimates obtained with this approach are largely unbiased. Since this method can be used to compare trees of unknown relationship, it will be particularly well-suited to problems in which a difference in diversification rate between clades is suspected, but in which these clades are not particularly closely related. Since diversification methods can easily take into account an incomplete sampling fraction, but missing lineages are assumed to be missing at random, this method is also appropriate for cases in which we've hypothesized a difference in the process of diversification between two or more focal clades, but in which many un-sampled groups separate the few of interest. The method of this study is by no means an attempt to replace more sophisticated models in which, for instance, diversification depends on the state of an observed or unobserved discrete or continuous trait. Rather, my intention is to provide a complementary approach for circumstances in which a simpler hypothesis is warranted and of biological interest.
Data from: Age-dependent and lineage-dependent speciation and extinction in the imbalance of phylogenetic trees
It is known that phylogenetic trees are more imbalanced than expected from a birth–death model with constant rates of speciation and extinction, and also that imbalance can be better fit by allowing the rate of speciation to decrease as the age of the parent species increases. If imbalance is measured in more detail, at nodes within trees as a function of the number of species descended from the nodes, age-dependent models predict levels of imbalance comparable to real trees for small numbers of descendent species, but predicted imbalance approaches an asymptote not found in real trees as the number of descendent species becomes large. Age-dependence must therefore be complemented by another process such as inheritance of different rates along different lineages, which is known to predict insufficient imbalance at nodes with few descendent species, but can predict increasing imbalance with increasing numbers of descendent species.
Data from: Tree imbalance causes a bias in phylogenetic estimation of evolutionary timescales using heterochronous sequences
Phylogenetic estimation of evolutionary timescales has become routine in biology, forming the basis of a wide range of evolutionary and ecological studies. However, there are various sources of bias that can affect these estimates. We investigated whether tree imbalance, a property that is commonly observed in phylogenetic trees, can lead to reduced accuracy or precision of phylogenetic timescale estimates. We analysed simulated data sets with calibrations at internal nodes and at the tips, taking into consideration different calibration schemes and levels of tree imbalance. We also investigated the effect of tree imbalance on two empirical data sets: mitogenomes from primates and serial samples of the African swine fever virus. In analyses calibrated using dated, heterochronous tips, we found that tree imbalance had a detrimental impact on precision and produced a bias in which the overall timescale was underestimated. A pronounced effect was observed in analyses with shallow calibrations. The greatest decreases in accuracy usually occurred in the age estimates for medium and deep nodes of the tree. In contrast, analyses calibrated at internal nodes did not display a reduction in estimation accuracy or precision due to tree imbalance. Our results suggest that molecular-clock analyses can be improved by increasing taxon sampling, with the specific aims of including deeper calibrations, breaking up long branches and reducing tree imbalance.
Data from: Mean and variance of phylogenetic trees
We describe the use of the Fréchet mean and variance in the Billera-Holmes-Vogtmann (BHV) treespace to summarize and explore the diversity of a set of phylogenetic trees. We show that the Fréchet mean is comparable to other summary methods, and, despite its stickiness property, is more likely to be binary than the majority-rules consensus tree. We show that the Fréchet variance is faster and more precise than commonly used variance measures. The Fréchet mean and variance are more theoretically justified, and more robust, than previous estimates of this type, and can be estimated reasonably efficiently, providing a foundation for building more advanced statistical methods and leading to applications such as mean hypothesis testing and outlier detection.
Data from: Detecting the dependence of diversification on multiple traits from phylogenetic trees and trait data
Species diversification may be determined by many different variables, including the traits of the diversifying lineages. The State-dependent Speciation and Extinction (SSE) framework contains methods to detect the dependence of diversification on these traits. For the analysis of traits with multiple states, MuSSE (Multiple-States dependent Speciation and Extinction) was developed. However, MuSSE and other state-dependent speciation and extinction models have been shown to yield false positives, because they cannot separate differential diversification rates from dependence of diversification on the observed traits. The recently introduced method HiSSE (Hidden- State dependent Speciation and Extinction) resolves this problem by allowing a hidden state to affect diversification rates. Unfortunately, HiSSE does not allow traits with more than two states, and, perhaps more interestingly, the simultaneous action of multiple traits on diversification. Here, we introduce an R package (SecSSE: Several examined and concealed States-dependent Speciation and Extinction) that combines the features of HiSSE and MuSSE to simultaneously infer state-dependent diversification across two or more examined (observed) traits or states while accounting for the role of a possible concealed (hidden) trait. Moreover, SecSSE also has improved functionality compared to its two 'parents'. First, it allows for an observed trait being in two or more states simultaneously, which is useful for example when a taxon is a generalist or when the exact state is not precisely known. Second, it provides the correct likelihood when conditioned on non-extinction, which has been incorrectly implemented in HiSSE and other SSE models. To illustrate our method we apply SecSSE to 7 previous studies that used MuSSE, and find that in 5 out of 7 cases, the conclusions drawn based on MuSSE were premature. We test with simulations whether SecSSE sacrifices statistical power to avoid the high type I error problem of MuSSE, but we find that this is not the case: for the majority of simulations where the observed traits affect diversification, SecSSE detects this.
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