ESTIMATING PHYLOGENIES FROM LACUNOSE DISTANCE MATRICES - ADDITIVE IS SUPERIOR TO ULTRAMETRIC ESTIMATION

Lapointe and Kirsch (1995) have recently explored the possibility of r econstructing phylogenetic trees from lacunose distance matrices. They have shown that missing cells can be estimated using the ultrametric property of distances, and that reliable trees can be derived from suc h filled matrices. Here, we extend their work by introducing a novel w ay to estimate distances based on the four-point condition of additive matrices. A simulation study was designed to assess whether the addit ive procedure is superior to the ultrametric one in recovering distanc es randomly deleted from complete distance matrices. Our results clear ly indicate that the topologies and branch lengths of the trees derive d from matrices which were estimated additively are better recovered t han those of trees derived from matrices estimated ultrametrically; th e original distances are also better recovered with the additive proce dure. Except in the case of small matrices with many missing cells for which both methods perform equally well, the additive is generally su perior to the ultrametric method for estimating missing cells in dista nce matrices prior to phylogenetic reconstruction.