On finding lowest common ancestors: Simplification and parallelization

Lack of support for Deuterostomia prompts reinterpretation of the first Bilateria

Science Advances ◽

10.1126/sciadv.abe2741 ◽

2021 ◽

Vol 7 (12) ◽

pp. eabe2741

Author(s):

Paschalia Kapli ◽

Paschalis Natsidis ◽

Daniel J. Leite ◽

Maximilian Fursman ◽

Nadia Jeffrie ◽

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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.

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A case of hyalinosis cutis et mucosae (lipoid proteinosis of Urbach and Wiethe) with common ancestors in four remote generations.

Journal of Medical Genetics ◽

10.1136/jmg.12.1.110 ◽

1975 ◽

Vol 12 (1) ◽

pp. 110-112 ◽

Cited By ~ 8

Author(s):

R C Juberg ◽

P R Winder ◽

L L Turk

Keyword(s):

Lipoid Proteinosis ◽

Hyalinosis Cutis Et Mucosae ◽

Common Ancestors

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An integrated information-based similarity measurement of gene ontology terms

Computer Science and Information Systems ◽

10.2298/csis141130053z ◽

2015 ◽

Vol 12 (4) ◽

pp. 1235-1253 ◽

Cited By ~ 1

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.

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