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  No evidence for phylostratigraphic bias impacting inferences on patterns of gene emergence and evolution

Domazet-Lošo, T., Carvunis, A.-R., Albà, M. M., Šestak, M. S., Bakarić, R., Neme, R., et al. (2017). No evidence for phylostratigraphic bias impacting inferences on patterns of gene emergence and evolution. Molecular Biology and Evolution, 34(4), 843-856. Retrieved from http://dx.doi.org/10.1093/molbev/msw284.

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Item Permalink: http://hdl.handle.net/11858/00-001M-0000-002E-8FDF-0 Version Permalink: http://hdl.handle.net/11858/00-001M-0000-002E-8FE0-A
Genre: Journal Article

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 Creators:
Domazet-Lošo, Tomislav1, Author              
Carvunis, Anne-Ruxandra1, Author
Albà, M. Mar1, Author
Šestak, Martin Sebastijan1, Author
Bakarić, Robert, Author              
Neme, Rafik2, Author              
Tautz, Diethard2, Author              
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1External, ou_persistent22              
2Department Evolutionary Genetics, Max Planck Institute for Evolutionary Biology, Max Planck Society, ou_1445635              

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Free keywords: BLAST; gene age estimation; genome analysis; phylostratigraphy
 Abstract: Phylostratigraphy is a computational framework for dating the emergence of DNA and protein sequences in a phylogeny. It has been extensively applied to make inferences on patterns of genome evolution, including patterns of disease gene evolution, ontogeny and de novo gene origination. Phylostratigraphy typically relies on BLAST searches along a species tree, but new simulation studies have raised concerns about the ability of BLAST to detect remote homologues and its impact on phylostratigraphic inferences. Here, we re-assessed these simulations. We found that, even with a possible overall BLAST false negative rate between 11–15%, the large majority of sequences assigned to a recent evolutionary origin by phylostratigraphy is unaffected by technical concerns about BLAST. Where the results of the simulations did cast doubt on previously reported findings, we repeated the original analyses but now excluded all questionable sequences. The originally described patterns remained essentially unchanged. These new analyses strongly support phylostratigraphic inferences, including: genes that emerged after the origin of eukaryotes are more likely to be expressed in the ectoderm than in the endoderm or mesoderm in Drosophila, and the de novo emergence of protein-coding genes from non-genic sequences occurs through proto-gene intermediates in yeast. We conclude that BLAST is an appropriate and sufficiently sensitive tool in phylostratigraphic analysis that does not appear to introduce significant biases into evolutionary pattern inferences.

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Language(s): eng - English
 Dates: 2017-01-122017-04
 Publication Status: Published in print
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Title: Molecular Biology and Evolution
Source Genre: Journal
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Pages: - Volume / Issue: 34 (4) Sequence Number: - Start / End Page: 843 - 856 Identifier: ISBN: 0737-4038