Phylogenetic test of the molecular clock and linearized trees.

TLDR

The authors aim to estimate divergence times of species or groups using molecular data by developing a method that constructs a linearized tree under a molecular clock assumption. They introduce two molecular‑clock tests—the two‑cluster test for lineages from an interior node and the branch‑length test for root‑to‑tip deviations—eliminate sequences with extreme rates, and then build a linearized tree assuming rate constancy. Applying these methods to hominoid mitochondrial DNA and drosophilid Adh gene sequences demonstrates their utility for estimating divergence times.

Abstract

To estimate approximate divergence times of species or species groups with molecular data, we have developed a method of constructing a linearized tree under the assumption of a molecular clock. We present two tests of the molecular clock for a given topology: two-cluster test and branch-length test. The two-cluster test examines the hypothesis of the molecular clock for the two lineages created by an interior node of the tree, whereas the branch-length test examines the deviation of the branch length between the tree root and a tip from the average length. Sequences evolving excessively fast or slow at a high significance level may be eliminated. A linearized tree will then be constructed for a given topology for the remaining sequences under the assumption of rate constancy. We have used these methods to analyze hominoid mitochondrial DNA and drosophilid Adh gene sequences.