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

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.

RelTime Rates Collapse to a Strict Clock When Estimating the Timeline of Animal Diversification

“…1 b ). This unambiguously demonstrates that the discrepancy between the results of Battistuzzi et al (2015) and Erwin et al (2011) cannot have been caused by the calibrations used by Erwin et al (2011). Instead, the disparity in relative clade ages must be a consequence of the fundamentally different way in which RelTime and Phylobayes calculate rates of evolution.…”

“…*Note: Battistuzzi et al (2015) described their root calibration as a gamma density with mean = 1,000 Ma and SD = 1,000 Myr. This gamma density has shape parameter = 1, and it is thus an exponential distribution of mean = 1,000 Ma.…”

Molecular clocks and the early evolution of metazoan nervous systems

“…Another important improvement has come in best practices for choosing calibration points. Methods that test for consistency among calibration points allow one to identify outliers that can strongly bias divergence time estimates [68,69]. Simulation Runnegar [50] Wray et al [53] Gu [111] Ayala et al…”

“…Not imposing hard maximum bounds on calibration points is particularly important [63,78], and instead using minimum and soft maximum constraints [79]. Also important is using cross-validation to identify calibration points that are inconsistent with the rest, and which can have a disproportionate impact if they are among the deeper calibration points [80].…”

“…The four studies that obtained the shallowest protostome-deuterostome divergence times [54,59,81,82] are all likely to be significant underestimates for technical reasons that are now better understood [56,69,77,78]. Some of the studies that obtained very deep divergence time estimates [53,55] were based on approaches that either do not allow for the rate variation among branches or used unrealistic sequence divergence models, and are consequently likely to be significant overestimates [54,74,83].…”