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Mol Biol Evol. 2015 Jul;32(7):1907-12. doi: 10.1093/molbev/msv075. Epub 2015 Mar 25.

A Protocol for Diagnosing the Effect of Calibration Priors on Posterior Time Estimates: A Case Study for the Cambrian Explosion of Animal Phyla.

Author information

1
Department of Biological Sciences, Oakland University.
2
Department of Molecular Biology and Genetics, College of Human Ecology, Cornell University.
3
Institute for Genomics and Evolutionary Medicine, Temple University.
4
Institute for Genomics and Evolutionary Medicine, Temple University Department of Biology, Temple University Center for Genomic Medicine and Research, King Abdulaziz University, Jddah, Saudi Arabia s.kumar@temple.edu.

Abstract

We present a procedure to test the effect of calibration priors on estimated times, which applies a recently developed calibration-free approach (RelTime) method that produces relative divergence times for all nodes in the tree. We illustrate this protocol by applying it to a timetree of metazoan diversification (Erwin DH, Laflamme M, Tweedt SM, Sperling EA, Pisani D, Peterson KJ. 2011. The Cambrian conundrum: early divergence and later ecological success in the early history of animals. Science 334:1091-1097.), which placed the divergence of animal phyla close to the time of the Cambrian explosion inferred from the fossil record. These analyses revealed that the two maximum-only calibration priors in the pre-Cambrian are the primary determinants of the young divergence times among animal phyla in this study. In fact, these two maximum-only calibrations produce divergence times that severely violate minimum boundaries of almost all of the other 22 calibration constraints. The use of these 22 calibrations produces dates for metazoan divergences that are hundreds of millions of years earlier in the Proterozoic. Our results encourage the use of calibration-free approaches to identify most influential calibration constraints and to evaluate their impact in order to achieve biologically robust interpretations.

KEYWORDS:

Cambrian explosion; RelTime; animal divergence times; calibration points; molecular clocks

PMID:
25808541
PMCID:
PMC4476164
DOI:
10.1093/molbev/msv075
[Indexed for MEDLINE]
Free PMC Article

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