TY - JOUR
T1 - No evidence for phylostratigraphic bias impacting inferences on patterns of gene emergence and evolution
AU - Domazet-Lošo, Tomislav
AU - Carvunis, Anne Ruxandra
AU - Albà, M. Mar
AU - Šestak, Martin Sebastijan
AU - Bakarić, Robert
AU - Neme, Rafik
AU - Tautz, Diethard
AU - Kim, Yuseob
N1 - Funding Information:
We thank B. Moyers for discussion and for providing analysis files, as well as G. Abrusán, M. Calderwood, H. Carter, J. Castresana, B. Charloteaux, J. Kreisberg, A. McLysaght and M. Domazet-Lošo for discussion, comments, and suggestions on the manuscript. We thank the following funding organizations for support of our work: TD-L: City of Zagreb and Adris Foundation grants; A-RC: National Institute of Health (NIH) grant K99 GM108865; MA: grant BFU2015-65235-P from MINECO/FEDER, EU; DT: ERC grant NewGenes, 322564.
Publisher Copyright:
© The Author 2017.
PY - 2017/4/1
Y1 - 2017/4/1
N2 - 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.
AB - 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.
KW - BLAST
KW - Gene age estimation
KW - Genome analysis
KW - Phylostratigraphy
UR - http://www.scopus.com/inward/record.url?scp=85018947967&partnerID=8YFLogxK
U2 - 10.1093/molbev/msw284
DO - 10.1093/molbev/msw284
M3 - Article
C2 - 28087778
AN - SCOPUS:85018947967
SN - 0737-4038
VL - 34
SP - 843
EP - 856
JO - Molecular Biology and Evolution
JF - Molecular Biology and Evolution
IS - 4
ER -