Reply to Phillips et al.

Summary Phillips et al. [1] reply to our finding that genetic divergence between subterranean metacrangonyctid amphipods from opposite shores of the Atlantic is congruent with vicariance by plate tectonics [2]. They highlight three presumed shortcomings in our analyses: first, the third codon positions of the mitochondrial genes used to reconstruct the metacrangonyctid phylogeny are saturated and consequently should be excluded from the analysis; second, substitution rates across the tree do not fit an uncorrelated lognormally distributed (UCLD) clock, and implementation of a random local clock (RLC) model would be more appropriate; third, the two dates that we used to calibrate the tree are fairly recent compared to the overall tree length, while the inclusion of a deep fossil calibrator could have improved dating. However, much of the criticism of Phillips et al. applies more to their modification of our data set than to the original data themselves. Specifically, their addition of several highly divergent taxa — driven by the necessity to include taxa encompassing the new deep calibration node they propose — largely alters the properties of our original data matrix. We maintain that third codon position saturation and deviation from lognormal rates largely apply to the new and not to the original data set. We also have some concerns about the fossil calibration used by Phillips et al. [1].