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Reply to Caetano-Anollés et al. comment on “Empirical genome evolution models root the tree of life”

Harish, Ajith LU and Kurland, Charles LU (2018) In Biochimie 149. p.137-138
Abstract

We recently analyzed the robustness of competing evolution models developed to identify the root of the Tree of Life: 1) An empirical Sankoff parsimony (ESP) model (Harish and Kurland, 2017), which is a nonstationary and directional evolution model; and 2) An a priori ancestor (APA) model (Kim and Caetano-Anollés, 2011) that is a stationary and reversible evolution model. Both Bayesian model selection tests as well as maximum parsimony analyses demonstrate that the ESP model is, overwhelmingly, the better model. Moreover, we showed that the APA model is not only sensitive to artifacts, but also that the underlying assumptions are neither empirically grounded nor biologically realistic.

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author
and
organization
publishing date
type
Contribution to journal
publication status
published
subject
keywords
Evolution, Phylogenomics, Proteome, Selection, Tree of life
in
Biochimie
volume
149
pages
2 pages
publisher
Elsevier
external identifiers
  • pmid:29631014
  • scopus:85046778769
ISSN
0300-9084
DOI
10.1016/j.biochi.2018.04.002
language
English
LU publication?
yes
id
1e165fe3-45a7-4418-b61a-d11c7e7eaf31
date added to LUP
2018-05-21 14:56:30
date last changed
2024-03-01 19:17:25
@article{1e165fe3-45a7-4418-b61a-d11c7e7eaf31,
  abstract     = {{<p>We recently analyzed the robustness of competing evolution models developed to identify the root of the Tree of Life: 1) An empirical Sankoff parsimony (ESP) model (Harish and Kurland, 2017), which is a nonstationary and directional evolution model; and 2) An a priori ancestor (APA) model (Kim and Caetano-Anollés, 2011) that is a stationary and reversible evolution model. Both Bayesian model selection tests as well as maximum parsimony analyses demonstrate that the ESP model is, overwhelmingly, the better model. Moreover, we showed that the APA model is not only sensitive to artifacts, but also that the underlying assumptions are neither empirically grounded nor biologically realistic.</p>}},
  author       = {{Harish, Ajith and Kurland, Charles}},
  issn         = {{0300-9084}},
  keywords     = {{Evolution; Phylogenomics; Proteome; Selection; Tree of life}},
  language     = {{eng}},
  month        = {{06}},
  pages        = {{137--138}},
  publisher    = {{Elsevier}},
  series       = {{Biochimie}},
  title        = {{Reply to Caetano-Anollés et al. comment on “Empirical genome evolution models root the tree of life”}},
  url          = {{http://dx.doi.org/10.1016/j.biochi.2018.04.002}},
  doi          = {{10.1016/j.biochi.2018.04.002}},
  volume       = {{149}},
  year         = {{2018}},
}