It has been recently suggested that the C-value paradox, the lack of an obvious association between organismal complexity and genome size, can result simply from biases in insertion and deletion rates--the DNA loss hypothesis. This hypothesis has been heavily criticized, particularly because its evidence, a negative relationship between genome size and DNA loss rate, is based on a highly selective use of the available data. In this study it is show that even the even the most favorable interpretation of the data favoring the DNA loss hypothesis is largely an artifact of phylogenetic nonindependence, supporting the assertion made by other authors that the mechanisms underlying genome size evolution might be more complex than envisioned by the DNA loss hypothesis.