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.

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.

scholarly journals Model checking software for phylogenetic trees using distribution and database methods

2013 ◽  
Vol 10 (3) ◽  
pp. 16-30 ◽  
Author(s):  
José Ignacio Requeno ◽  
José Manuel Colom
Keyword(s):  
Model Checking ◽  
Phylogenetic Tree ◽  
Dna Sequence ◽  
Phylogenetic Trees ◽  
Computation Time ◽  
Biological Properties ◽  
Traditional Model ◽  
Temporal Logics ◽  
Memory Consumption ◽  
Speed Up

Summary Model checking, a generic and formal paradigm stemming from computer science based on temporal logics, has been proposed for the study of biological properties that emerge from the labeling of the states defined over the phylogenetic tree. This strategy allows us to use generic software tools already present in the industry. However, the performance of traditional model checking is penalized when scaling the system for large phylogenies. To this end, two strategies are presented here. The first one consists of partitioning the phylogenetic tree into a set of subgraphs each one representing a subproblem to be verified so as to speed up the computation time and distribute the memory consumption. The second strategy is based on uncoupling the information associated to each state of the phylogenetic tree (mainly, the DNA sequence) and exporting it to an external tool for the management of large information systems. The integration of all these approaches outperforms the results of monolithic model checking and helps us to execute the verification of properties in a real phylogenetic tree.

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.

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.

Evolutionary relationships in Oxytropis species, as estimated from the nuclear ribosomal internal transcribed spacer (ITS) sequences point to multiple expansions into the Arctic

Botany ◽  
2012 ◽  
Vol 90 (8) ◽  
pp. 770-779 ◽  
Author(s):  
Annie Archambault ◽  
Martina V. Strömvik
Keyword(s):  
North American ◽  
Internal Transcribed Spacer ◽  
Phylogenetic Trees ◽  
Its Region ◽  
Its Sequences ◽  
The Arctic ◽  
Evolutionary Relationships ◽  
Data Set ◽  
The North ◽  
North American Arctic

Species of the genus Oxytropis are distributed in the northern hemisphere, especially in alpine and arctic areas. Although comprehensive taxonomic treatments exist for local floras, an understanding of the evolutionary relationships is lacking for the genus as a whole. To determine if different ancestral Oxytropis species colonized the North American Arctic separately, as suggested by taxonomy, we sequenced the nuclear ribosomal internal transcribed spacer (ITS) region from 16 Oxytropis specimens, including four species that were used in a previous transcriptome study. In addition, 81 other Oxytropis ITS sequences were retrieved from public sequence databases and included in the analysis. The whole data set was analyzed using phylogenetic trees and statistical parsimony networks. Results show that all Oxytropis ITS sequences are very similar. Furthermore, at least six lineages evolved from different temperate ancestors to colonize the North American Arctic. This pattern is believed to be typical of the arctic flora. Additionally, the sequence relationship analyses confirm that the subgenus Phacoxytropis may be ancestral in Oxytropis.

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.

Using Great Ape Phylogeny to Teach Evolutionary Thinking

2016 ◽  
Vol 78 (3) ◽  
pp. 263-265
Author(s):  
Susan Offner
Keyword(s):  
Phylogenetic Tree ◽  
Phylogenetic Trees ◽  
Great Apes ◽  
Evolutionary Relationships ◽  
Great Ape ◽  
General Skill

A simple phylogenetic tree of the great apes provides many important teaching opportunities, both in the general skill of reading phylogenetic trees and in using them to explore evolutionary relationships.

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 Aminoacyl-tRNA Synthetases, the Genetic Code, and the Evolutionary Process

2000 ◽  
Vol 64 (1) ◽  
pp. 202-236 ◽  
Author(s):  
Carl R. Woese ◽  
Gary J. Olsen ◽  
Michael Ibba ◽  
Dieter Söll
Keyword(s):  
Genetic Code ◽  
Phylogenetic Trees ◽  
Genetic Material ◽  
Evolutionary Process ◽  
Group Iv ◽  
Evolutionary Relationships ◽  
Evolutionary Stage ◽  
Trna Synthetases ◽  
Aminoacyl Trna Synthetases ◽  
The Individual

SUMMARY The aminoacyl-tRNA synthetases (AARSs) and their relationship to the genetic code are examined from the evolutionary perspective. Despite a loose correlation between codon assignments and AARS evolutionary relationships, the code is far too highly structured to have been ordered merely through the evolutionary wanderings of these enzymes. Nevertheless, the AARSs are very informative about the evolutionary process. Examination of the phylogenetic trees for each of the AARSs reveals the following. (i) Their evolutionary relationships mostly conform to established organismal phylogeny: a strong distinction exists between bacterial- and archaeal-type AARSs. (ii) Although the evolutionary profiles of the individual AARSs might be expected to be similar in general respects, they are not. It is argued that these differences in profiles reflect the stages in the evolutionary process when the taxonomic distributions of the individual AARSs became fixed, not the nature of the individual enzymes. (iii) Horizontal transfer of AARS genes between Bacteria and Archaea is asymmetric: transfer of archaeal AARSs to the Bacteria is more prevalent than the reverse, which is seen only for the “gemini group.” (iv) The most far-ranging transfers of AARS genes have tended to occur in the distant evolutionary past, before or during formation of the primary organismal domains. These findings are also used to refine the theory that at the evolutionary stage represented by the root of the universal phylogenetic tree, cells were far more primitive than their modern counterparts and thus exchanged genetic material in far less restricted ways, in effect evolving in a communal sense.

Sign in / Sign up

Export Citation Format

Share Document