A PQ Framework for Reconstructions of Common Ancestors and Phylogeny

2006 ◽  
pp. 141-155
Author(s):  
Laxmi Parida
Keyword(s):  
Common Ancestors

scholarly journals Lack of support for Deuterostomia prompts reinterpretation of the first Bilateria

2021 ◽  
Vol 7 (12) ◽  
pp. eabe2741
Author(s):  
Paschalia Kapli ◽  
Paschalis Natsidis ◽  
Daniel J. Leite ◽  
Maximilian Fursman ◽  
Nadia Jeffrie ◽  
...  
Keyword(s):  
Systematic Error ◽  
Tree Reconstruction ◽  
Simulation Experiments ◽  
Animal Evolution ◽  
Phylogenetic Studies ◽  
Branch Lengths ◽  
Molecular Phylogenetic ◽  
Common Ancestors

The bilaterally symmetric animals (Bilateria) are considered to comprise two monophyletic groups, Protostomia (Ecdysozoa and the Lophotrochozoa) and Deuterostomia (Chordata and the Xenambulacraria). Recent molecular phylogenetic studies have not consistently supported deuterostome monophyly. Here, we compare support for Protostomia and Deuterostomia using multiple, independent phylogenomic datasets. As expected, Protostomia is always strongly supported, especially by longer and higher-quality genes. Support for Deuterostomia, however, is always equivocal and barely higher than support for paraphyletic alternatives. Conditions that cause tree reconstruction errors—inadequate models, short internal branches, faster evolving genes, and unequal branch lengths—coincide with support for monophyletic deuterostomes. Simulation experiments show that support for Deuterostomia could be explained by systematic error. The branch between bilaterian and deuterostome common ancestors is, at best, very short, supporting the idea that the bilaterian ancestor may have been deuterostome-like. Our findings have important implications for the understanding of early animal evolution.

scholarly journals An integrated information-based similarity measurement of gene ontology terms

2015 ◽  
Vol 12 (4) ◽  
pp. 1235-1253 ◽  
Author(s):  
Shu-Bo Zhang ◽  
Jian-Huang Lai
Keyword(s):  
Gene Ontology ◽  
Semantic Similarity ◽  
Semantic Information ◽  
Gene Expression Dataset ◽  
Similarity Measurement ◽  
Depth Information ◽  
Go Terms ◽  
Validation Experiments ◽  
Integrated Information ◽  
Common Ancestors

Measuring the semantic similarity between pairs of terms in Gene Ontology (GO) can help to compare genes that can not be compared by other computational methods. In this study, we proposed an integrated information-based similarity measurement (IISM) to calculate the semantic similarity between two GO terms by taking into account multiple common ancestors that they share, and aggregating the semantic information and depth information of the non-redundant common ancestors. Our method searches for non-redundant common ancestors in an effective way. Validation experiments were conducted on both gene expression dataset and pathway dataset, and the experimental results suggest the superiority of our method against some existing methods.

Inferring a Tree from Lowest Common Ancestors with an Application to the Optimization of Relational Expressions

1981 ◽  
Vol 10 (3) ◽  
pp. 405-421 ◽  
Author(s):  
A. V. Aho ◽  
Y. Sagiv ◽  
T. G. Szymanski ◽  
J. D. Ullman
Keyword(s):  
Common Ancestors

Nearest Common Ancestors: A Survey and a New Algorithm for a Distributed Environment

2004 ◽  
Vol 37 (3) ◽  
pp. 441-456 ◽  
Author(s):  
Stephen Alstrup ◽  
Cyril Gavoille ◽  
Haim Kaplan ◽  
Theis Rauhe
Keyword(s):  
Distributed Environment ◽  
Common Ancestors

On Finding Lowest Common Ancestors in Trees

1976 ◽  
Vol 5 (1) ◽  
pp. 115-132 ◽  
Author(s):  
A. V. Aho ◽  
J. E. Hopcroft ◽  
J. D. Ullman
Keyword(s):  
Common Ancestors

Actions of Molecules which Regulate Hemopoiesis on Endothelial Cells: Memoirs of Common Ancestors?

1994 ◽  
Vol 190 (9-10) ◽  
pp. 834-839 ◽  
Author(s):  
F. Bussolino ◽  
E. Bocchietto ◽  
F. Silvagno ◽  
R. Soldi ◽  
M. Arese ◽  
...  
Keyword(s):  
Endothelial Cells ◽  
Common Ancestors
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