On Sackin's original proposal: The variance of the leaves' depths as a phylogenetic balance index
Abstract Background: The Sackin index S of a rooted phylogenetic tree, defined as the sum of its leaves' depths, is one of the most popular balance indices in phylogenetics, and Sackin's 1972 paper is usually cited as the source for this index. However, what Sackin actually proposed in his paper as a measure of the imbalance of a rooted tree was not the sum of its leaves' depths, but their "variation". This proposal was later implemented as the variance of the leaves' depths by Kirkpatrick and Slatkin, where moreover they posed the problem of finding a closed formula for its expected value under the Yule model. Nowadays, Sackin's original proposal seems to have passed into oblivion in the phylogenetics literature, replaced by the index bearing his name, which, in fact, was introduced a decade later by Sokal.Results: In this paper we study the properties of the variance of the leaves' depths, V, as a balance index. Firstly, we prove that the rooted trees with n leaves and maximum V value are exactly the combs with n leaves. But although V achieves its minimum value on every space BT_n of bifurcating rooted phylogenetic trees with n< 184 leaves at the so-called "maximally balanced trees" with n leaves, this property fails for almost every n>= 184. We provide then an algorithm that finds in O(n) time the trees in BT_n with minimum V value. Secondly, we obtain closed formulas for the expected V value of a bifurcating rooted tree with any number n of leaves under the Yule and the uniform models and, as a by-product of the computations leading to these formulas, we also obtain closed formulas for the variance of the Sackin index and the total cophenetic indexof a bifurcating rooted tree, as well as of their covariance, under the uniform model, thus filling this gap in the literature.Conclusions: The phylogenetics crowd has been wise in preferring as a balance index the sum S(T) of the leaves’ depths of a phylogenetic tree T over their variance V (T), because the latter does not seem to capture correctly the notion of balance of large bifurcating rooted trees. But for bifurcating trees up to 183 leaves, V is a valid and useful balance index.
