Testing Hypotheses of Molecular Evolution

Abstract

This chapter lifts the uncertainty quantification of the previous chapters up to the level of molecular evolution hypotheses. A relatively recent rival to the neutral theory of molecular evolution is explained in terms of how its predictions differ. The exercises at the end of the chapter give readers experience with quantifying the extent to which sequence data support one evolutionary hypothesis more than another.

In applying mathematics to subjects such as physics or statistics we make tentative assumptions about the real world which we know are false but which we believe may be useful nonetheless. – George E. P. Box¹

Is it of the slightest use to reject a hypothesis until we have some idea of what to put in its place? … There has not been a single date in the history of the law of gravitation when a modern significance test would not have rejected all laws and left us with no law.

– Sir Harold Jeffreys²

“Science and Statistics,” Journal of the American Statistical Association [25], copyright Ⓒ American Statistical Association, reprinted by permission of Taylor & Francis Ltd, http://www.tandfonline.com on behalf of American Statistical Association.

Theory of Probability (Oxford University Press) [63, §7.22]. Reproduced with permission of the Licensor through PLSclear.