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Quantifying the Error of Secondary vs. Distant Primary Calibrations in a Simulated Environment.

Authors
  • Powell, Christopher Lowell Edward1
  • Waskin, Sydney1
  • Battistuzzi, Fabia Ursula1, 2
  • 1 Department of Biological Sciences, Oakland University, Rochester, MI, United States. , (United States)
  • 2 Center for Data Science and Big Data Analytics, Oakland University, Rochester, MI, United States. , (United States)
Type
Published Article
Journal
Frontiers in Genetics
Publisher
Frontiers Media SA
Publication Date
Jan 01, 2020
Volume
11
Pages
252–252
Identifiers
DOI: 10.3389/fgene.2020.00252
PMID: 32265987
Source
Medline
Keywords
Language
English
License
Unknown

Abstract

Using calibrations to obtain absolute divergence times is standard practice in molecular clock studies. While the use of primary (e.g., fossil) calibrations is preferred, this approach can be limiting because of their rarity in fast-growing datasets. Thus, alternatives need to be explored, such as the use of secondary (molecularly-derived) calibrations that can anchor a timetree in a larger number of nodes. However, the use of secondary calibrations has been discouraged in the past because of concerns in the error rates of the node estimates they produce with an apparent high precision. Here, we quantify the amount of errors in estimates produced by the use of secondary calibrations relative to true times and primary calibrations placed on distant nodes. We find that, overall, the inaccuracies in estimates based on secondary calibrations are predictable and mirror errors associated with primary calibrations and their confidence intervals. Additionally, we find comparable error rates in estimated times from secondary calibrations and distant primary calibrations, although the precision of estimates derived from distant primary calibrations is roughly twice as good as that of estimates derived from secondary calibrations. This suggests that increasing dataset size to include primary calibrations may produce divergence times that are about as accurate as those from secondary calibrations, albeit with a higher precision. Overall, our results suggest that secondary calibrations may be useful to explore the parameter space of plausible evolutionary scenarios when compared to time estimates obtained with distant primary calibrations. Copyright © 2020 Powell, Waskin and Battistuzzi.

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