<scp>TNT</scp> version 1.5, including a full implementation of phylogenetic morphometrics

TLDR

Version 1.5 of TNT fully integrates landmark data into phylogenetic analysis. TNT reconstructs ancestral shapes by minimizing the summed differences between ancestor and descendant shapes across all branches, allowing landmark data to be analyzed alone or with standard characters using all existing commands and rescaling options. These algorithms make searches for landmark data tens to hundreds of times faster—up to 3 T times faster, where T is the number of taxa—making phylogenetic analysis of landmarks feasible on standard personal computers.

Abstract

Version 1.5 of the computer program TNT completely integrates landmark data into phylogenetic analysis. Landmark data consist of coordinates (in two or three dimensions) for the terminal taxa; TNT reconstructs shapes for the internal nodes such that the difference between ancestor and descendant shapes for all tree branches sums up to a minimum; this sum is used as tree score. Landmark data can be analysed alone or in combination with standard characters; all the applicable commands and options in TNT can be used transparently after reading a landmark data set. The program continues implementing all the types of analyses in former versions, including discrete and continuous characters (which can now be read at any scale, and automatically rescaled by TNT). Using algorithms described in this paper, searches for landmark data can be made tens to hundreds of times faster than it was possible before (from T to 3T times faster, where T is the number of taxa), thus making phylogenetic analysis of landmarks feasible even on standard personal computers.