On the Construction of “Optimal” Phylogenetic Trees

1983 ◽  
Vol 38 (1-2) ◽  
pp. 156-158 ◽  
Author(s):  
Geert De Soete
Keyword(s):  
Phylogenetic Tree ◽  
Iterative Algorithm ◽  
Phylogenetic Trees ◽  
Data Set ◽  
Dissimilarity Data

An iterative algorithm for constructing the optimal phylogenetic tree from a given set o f dissimilarity data is described. The procedure is applied for illustrative purposes an a data set com piled by Fitch and Margoliash.

Comparing the fit of stratigraphic and morphologic data in phylogenetic analysis

Paleobiology ◽  
1997 ◽  
Vol 23 (1) ◽  
pp. 1-19 ◽  
Author(s):  
William C. Clyde ◽  
Daniel C. Fisher
Keyword(s):  
Phylogenetic Analysis ◽  
Phylogenetic Tree ◽  
Phylogenetic Trees ◽  
Ad Hoc ◽  
Retention Indices ◽  
Significant Loss ◽  
Phylogenetic Hypothesis ◽  
Data Set ◽  
Phylogenetic Hypotheses ◽  
Morphologic Data

Stratigraphic data are compared to morphologic data in terms of their fit to phylogenetic hypotheses for 29 data sets taken from the literature. Stratigraphic fit is measured using MacClade's stratigraphic character, which tracks the number of independent discrepancies between observed order and the order of occurrence that would be expected on the basis of a given phylogenetic hypothesis. Acceptance of a phylogenetic hypothesis despite such discrepancies requires ad hoc hypotheses concerning differential probabilities of preservation and recovery. These stratigraphic ad hoc hypotheses are treated as logically equivalent to morphologic ad hoc hypotheses of homoplasy. The retention index is used to compare the number of stratigraphic and morphologic ad hoc hypotheses required by given phylogenetic hypotheses. Each data set is subjected to five analyses, varying in the constraints imposed on the structure of the phylogenetic tree against which fit is measured. Analyses 1–4 compare the stratigraphic and morphologic retention indices using phylogenetic trees consistent with the morphologically most-parsimonious cladogram reported in the original study. Analysis 5 compares retention indices using the overall (stratigraphically and morphologically) most-parsimonious phylogenetic tree, which may be, but is not necessarily, consistent with the reported cladogram. Proceeding from Analysis 1 to Analysis 5, stratigraphic data are allowed greater influence in determining the structure of phylogenetic trees, with the trees in Analysis 1 derived without reference to the stratigraphic character and the trees in Analysis 5 derived from full interaction of stratigraphic and morphologic characters. Morphologic and stratigraphic retention indices for these 29 studies cannot be statistically distinguished in comparisons 3–5, suggesting very similar degrees of fit. The values of these retention indices are high, indicating a generally high level of congruence under these phylogenetic hypotheses. Significant gains (49%) in stratigraphic fit can be realized without significant loss (4%) in morphologic fit as the stratigraphic and morphologic evidence are both allowed to participate in constraining the structure of phylogenetic hypotheses. These results suggest that arguments based on alleged “noisiness” of stratigraphic data offer inadequate grounds for ignoring stratigraphic order in phylogenetic analysis. In terms of congruence, stratigraphic and morphologic data perform about equally well.

scholarly journals Graph Splitting: A Graph-Based Approach for Superfamily-Scale Phylogenetic Tree Reconstruction

2019 ◽  
Author(s):  
Motomu Matsui ◽  
Wataru Iwasaki
Keyword(s):  
Phylogenetic Tree ◽  
Phylogenetic Trees ◽  
Triosephosphate Isomerase ◽  
Rna World ◽  
Rapid Evolution ◽  
Poor Performance ◽  
Multiple Sequence ◽  
Data Set ◽  
Protein Superfamily ◽  
Tim Barrel

Abstract A protein superfamily contains distantly related proteins that have acquired diverse biological functions through a long evolutionary history. Phylogenetic analysis of the early evolution of protein superfamilies is a key challenge because existing phylogenetic methods show poor performance when protein sequences are too diverged to construct an informative multiple sequence alignment (MSA). Here, we propose the Graph Splitting (GS) method, which rapidly reconstructs a protein superfamily-scale phylogenetic tree using a graph-based approach. Evolutionary simulation showed that the GS method can accurately reconstruct phylogenetic trees and be robust to major problems in phylogenetic estimation, such as biased taxon sampling, heterogeneous evolutionary rates, and long-branch attraction when sequences are substantially diverge. Its application to an empirical data set of the triosephosphate isomerase (TIM)-barrel superfamily suggests rapid evolution of protein-mediated pyrimidine biosynthesis, likely taking place after the RNA world. Furthermore, the GS method can also substantially improve performance of widely used MSA methods by providing accurate guide trees.

scholarly journals Consequences of Recombination on Traditional Phylogenetic Analysis

Genetics ◽  
2000 ◽  
Vol 156 (2) ◽  
pp. 879-891 ◽  
Author(s):  
Mikkel H Schierup ◽  
Jotun Hein
Keyword(s):  
Phylogenetic Tree ◽  
Phylogenetic Trees ◽  
Branch Length ◽  
Population Data ◽  
Recent Common Ancestor ◽  
Data Sets ◽  
Data Set ◽  
Most Recent Common Ancestor ◽  
Total Branch Length ◽  
Viral Sequences

Abstract We investigate the shape of a phylogenetic tree reconstructed from sequences evolving under the coalescent with recombination. The motivation is that evolutionary inferences are often made from phylogenetic trees reconstructed from population data even though recombination may well occur (mtDNA or viral sequences) or does occur (nuclear sequences). We investigate the size and direction of biases when a single tree is reconstructed ignoring recombination. Standard software (PHYLIP) was used to construct the best phylogenetic tree from sequences simulated under the coalescent with recombination. With recombination present, the length of terminal branches and the total branch length are larger, and the time to the most recent common ancestor smaller, than for a tree reconstructed from sequences evolving with no recombination. The effects are pronounced even for small levels of recombination that may not be immediately detectable in a data set. The phylogenies when recombination is present superficially resemble phylogenies for sequences from an exponentially growing population. However, exponential growth has a different effect on statistics such as Tajima's D. Furthermore, ignoring recombination leads to a large overestimation of the substitution rate heterogeneity and the loss of the molecular clock. These results are discussed in relation to viral and mtDNA data sets.

scholarly journals APRIMORAMENTOS DA SOLUÇÃO PARALELA BASEADA EM OPERAÇÕES COLETIVAS PARA O BOOTSTRAP DA RECONSTRUÇÃO DE ÁRVORES FILOGENÉTICAS NO PHYML 3.0

2021 ◽  
Vol 12 (3) ◽  
pp. 39-52
Author(s):  
Martha Ximena Torres Delgado
Keyword(s):  
Phylogenetic Tree ◽  
Statistical Method ◽  
Phylogenetic Trees ◽  
Evolutionary Relationships ◽  
Performance Tests ◽  
Memory Consumption ◽  
Data Set ◽  
Parallel Implementations ◽  
Point To Point

Phylogenetics determines the evolutionary relationships between groups of species, through a phylogenetic tree. PhyML is among the main programs for the reconstruction of phylogenetic trees. Bootstrap is a statistical method used to measure the confidence of a given data set, which is usually applied in the analysis of inferred phylogenetic trees. In PhyML this method has two MPI parallel implementations: with point-to-point operations and collective operations. The second version is more efficient than the first, however it has a limitation on the number of bootstrap to be used due to the increase in memory consumption. In order to solve this problem, three proposals were developed. The objectives of this work were to carry out the validation of these versions together with performance tests. The validation showed that the proposed solutions present results equivalent to the point-to-point version. In the performance simulations, two solutions were shown to be superior to the point-to-point version, with the best one achieving gains of 28.46% and 39.64% for 32 and 64 processes, respectively. Therefore, the enhancements allow alternatives to the point-to-point version without limitingmemory.

scholarly journals Computing nearest neighbour interchange distances between ranked phylogenetic trees

2021 ◽  
Vol 82 (1-2) ◽  
Author(s):  
Lena Collienne ◽  
Alex Gavryushkin
Keyword(s):  
Cancer Research ◽  
Computational Complexity ◽  
Phylogenetic Tree ◽  
Shortest Path ◽  
Phylogenetic Trees ◽  
Shortest Paths ◽  
Nearest Neighbour ◽  
Tree Inference ◽  
Subtree Prune And Regraft ◽  
Comparison Algorithms

AbstractMany popular algorithms for searching the space of leaf-labelled (phylogenetic) trees are based on tree rearrangement operations. Under any such operation, the problem is reduced to searching a graph where vertices are trees and (undirected) edges are given by pairs of trees connected by one rearrangement operation (sometimes called a move). Most popular are the classical nearest neighbour interchange, subtree prune and regraft, and tree bisection and reconnection moves. The problem of computing distances, however, is $${\mathbf {N}}{\mathbf {P}}$$ N P -hard in each of these graphs, making tree inference and comparison algorithms challenging to design in practice. Although anked phylogenetic trees are one of the central objects of interest in applications such as cancer research, immunology, and epidemiology, the computational complexity of the shortest path problem for these trees remained unsolved for decades. In this paper, we settle this problem for the ranked nearest neighbour interchange operation by establishing that the complexity depends on the weight difference between the two types of tree rearrangements (rank moves and edge moves), and varies from quadratic, which is the lowest possible complexity for this problem, to $${\mathbf {N}}{\mathbf {P}}$$ N P -hard, which is the highest. In particular, our result provides the first example of a phylogenetic tree rearrangement operation for which shortest paths, and hence the distance, can be computed efficiently. Specifically, our algorithm scales to trees with tens of thousands of leaves (and likely hundreds of thousands if implemented efficiently).

scholarly journals Techniques for the verification of minimal phylogenetic trees illustrated with ten mammalian haemoglobin sequences

1980 ◽  
Vol 187 (1) ◽  
pp. 65-74 ◽  
Author(s):  
D Penny ◽  
M D Hendy ◽  
L R Foulds
Keyword(s):  
Amino Acid ◽  
Phylogenetic Tree ◽  
Protein Sequence ◽  
Phylogenetic Trees ◽  
Sequence Data ◽  
Protein Sequences ◽  
Nucleotide Sequences ◽  
Amino Acid Sequences ◽  
Minimal Tree ◽  
Protein Sequence Data

We have recently reported a method to identify the shortest possible phylogenetic tree for a set of protein sequences [Foulds Hendy & Penny (1979) J. Mol. Evol. 13. 127–150; Foulds, Penny & Hendy (1979) J. Mol. Evol. 13, 151–166]. The present paper discusses issues that arise during the construction of minimal phylogenetic trees from protein-sequence data. The conversion of the data from amino acid sequences into nucleotide sequences is shown to be advantageous. A new variation of a method for constructing a minimal tree is presented. Our previous methods have involved first constructing a tree and then either proving that it is minimal or transforming it into a minimal tree. The approach presented in the present paper progressively builds up a tree, taxon by taxon. We illustrate this approach by using it to construct a minimal tree for ten mammalian haemoglobin alpha-chain sequences. Finally we define a measure of the complexity of the data and illustrate a method to derive a directed phylogenetic tree from the minimal tree.

scholarly journals Analysis of SARS-CoV-2 nucleocapsid protein sequence variations in ASEAN countries

2021 ◽  
Author(s):  
Mochammad Rajasa Mukti Negara ◽  
Ita Krissanti ◽  
Gita Widya Pradini
Keyword(s):  
Phylogenetic Tree ◽  
Phylogenetic Trees ◽  
Protein Sequences ◽  
Reference Sequence ◽  
N Protein ◽  
Asean Country ◽  
Sequence Variations ◽  
Complete Sequences ◽  
Asean Countries ◽  
Global Initiative

BACKGROUND Nucleocapsid (N) protein is one of four structural proteins of SARS-CoV-2  which is known to be more conserved than spike protein and is highly immunogenic. This study aimed to analyze the variation of the SARS-CoV-2 N protein sequences in ASEAN countries, including Indonesia. METHODS Complete sequences of SARS-CoV-2 N protein from each ASEAN country were obtained from Global Initiative on Sharing All Influenza Data (GISAID), while the reference sequence was obtained from GenBank. All sequences collected from December 2019 to March 2021 were grouped to the clade according to GISAID, and two representative isolates were chosen from each clade for the analysis. The sequences were aligned by MUSCLE, and phylogenetic trees were built using MEGA-X software based on the nucleotide and translated AA sequences. RESULTS 98 isolates of complete N protein genes from ASEAN countries were analyzed. The nucleotides of all isolates were 97.5% conserved. Of 31 nucleotide changes, 22 led to amino acid (AA) substitutions; thus, the AA sequences were 94.5% conserved. The phylogenetic tree of nucleotide and AA sequences shows similar branches. Nucleotide variations in clade O (C28311T); clade GR (28881–28883 GGG>AAC); and clade GRY (28881–28883 GGG>AAC and C28977T) lead to specific branches corresponding to the clade within both trees. CONCLUSIONS The N protein sequences of SARS-CoV-2 across ASEAN countries are highly conserved. Most isolates were closely related to the reference sequence originating from China, except the isolates representing clade O, GR, and GRY which formed specific branches in the phylogenetic tree.

Can the Cambrian explosion be inferred through molecular phylogeny?

Development ◽  
1994 ◽  
Vol 1994 (Supplement) ◽  
pp. 15-25
Author(s):  
Hervé Philippe ◽  
Anne Chenuil ◽  
André Adoutte
Keyword(s):  
Phylogenetic Trees ◽  
18S Rrna ◽  
Phylogenetic Reconstruction ◽  
Cambrian Explosion ◽  
Bootstrap Support ◽  
Time Interval ◽  
Short Time Interval ◽  
Data Set ◽  
Molecular Phylogenetic ◽  
Animal Phyla

Most of the major invertebrate phyla appear in the fossil record during a relatively short time interval, not exceeding 20 million years (Myr), 540-520 Myr ago. This rapid diversification is known as the `Cambrian explosion'. In the present paper, we ask whether molecular phylogenetic reconstruction provides confirmation for such an evolutionary burst. The expectation is that the molecular phylogenetic trees should take the form of a large unresolved multifurcation of the various animal lineages. Complete 18S rRNA sequences of 69 extant representatives of 15 animal phyla were obtained from data banks. After eliminating a major source of artefact leading to lack of resolution in phylogenetic trees (mutational saturation of sequences), we indeed observe that the major lines of triploblast coelomates (arthropods, molluscs, echinoderms, chordates...) are very poorly resolved i.e. the nodes defining the various clades are not supported by high bootstrap values. Using a previously developed procedure consisting of calculating bootstrap proportions of each node of the tree as a function of increasing amount of nucleotides (Lecointre, G., Philippe, H. Le, H. L. V. and Le Guyader, H. (1994) Mol. Phyl. Evol., in press) we obtain a more informative indication of the robustness of each node. In addition, this procedure allows us to estimate the number of additional nucleotides that would be required to resolve confidently the currently uncertain nodes; this number turns out to be extremely high and experimentally unfeasible. We then take this approach one step further: using parameters derived from the above analysis, assuming a molecular clock and using palaeontological dates for calibration, we establish a relationship between the number of sites contained in a given data set and the time interval that this data set can confidently resolve (with 95% bootstrap support). Under these assumptions, the presently available 18S rRNA database cannot confidently resolve cladogenetic events separated by less than about 40 Myr. Thus, at the present time, the potential resolution by the palaeontological approach is higher than that by the molecular one.

INFERRING PHYLOGENETIC RELATIONSHIPS AVOIDING FORBIDDEN ROOTED TRIPLETS

2006 ◽  
Vol 04 (01) ◽  
pp. 59-74 ◽  
Author(s):  
YING-JUN HE ◽  
TRINH N. D. HUYNH ◽  
JESPER JANSSON ◽  
WING-KIN SUNG
Keyword(s):  
Approximation Algorithms ◽  
Phylogenetic Tree ◽  
Phylogenetic Trees ◽  
Evolutionary History ◽  
Phylogenetic Network ◽  
Evolutionary Relationships ◽  
Large Set ◽  
Tree Network ◽  
History Of ◽  
Overlapping Sets

To construct a phylogenetic tree or phylogenetic network for describing the evolutionary history of a set of species is a well-studied problem in computational biology. One previously proposed method to infer a phylogenetic tree/network for a large set of species is by merging a collection of known smaller phylogenetic trees on overlapping sets of species so that no (or as little as possible) branching information is lost. However, little work has been done so far on inferring a phylogenetic tree/network from a specified set of trees when in addition, certain evolutionary relationships among the species are known to be highly unlikely. In this paper, we consider the problem of constructing a phylogenetic tree/network which is consistent with all of the rooted triplets in a given set [Formula: see text] and none of the rooted triplets in another given set [Formula: see text]. Although NP-hard in the general case, we provide some efficient exact and approximation algorithms for a number of biologically meaningful variants of the problem.

Visualizing Speciation in Artificial Cichlid Fish

2006 ◽  
Vol 12 (2) ◽  
pp. 243-257 ◽  
Author(s):  
Ross Clement
Keyword(s):  
Phylogenetic Tree ◽  
Phylogenetic Trees ◽  
Cichlid Fish ◽  
Natural Consequence ◽  
Open Problems ◽  
Visualization System ◽  
Low Level ◽  
Wide Range ◽  
Level Information ◽  
History Of

The Cichlid Speciation Project (CSP) is an ALife simulation system for investigating open problems in the speciation of African cichlid fish. The CSP can be used to perform a wide range of experiments that show that speciation is a natural consequence of certain biological systems. A visualization system capable of extracting the history of speciation from low-level trace data and creating a phylogenetic tree has been implemented. Unlike previous approaches, this visualization system presents a concrete trace of speciation, rather than a summary of low-level information from which the viewer can make subjective decisions on how speciation progressed. The phylogenetic trees are a more objective visualization of speciation, and enable automated collection and summarization of the results of experiments. The visualization system is used to create a phylogenetic tree from an experiment that models sympatric speciation.

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