Calculation of evolutionary trees from sequence data.

Abstract

Evolutionary trees are usually calculated from comparisons of protein or nucleic acid sequences. from present-day organisms by use of algorithms that use only the difference matrix, where the difference matrix is constructed from the sequence differences between pairs of sequences from the organisms. The difference matrix alone cannot.define uniquely the correct position of the ancestor of the present-day organisms (root of the tree). Furthermore, methods using the difference matrix alone often fail to give the correct pattern of tree branching (topology) when the different sequences evolve at different rates. Only for equal rates of evolution can the difference matrix (when used with the so-called matrix method) yield exactly the correct topology and root. In this paper we present a method for calculating evolutionary trees from sequence data that uses, along with the difference matrix, the rate of evolution of the various sequences from their common ancestor. It is proven analytically that this method uniquely determines both the correct tree topology and root in theory for unequal rates of sequence evolution. How one would estimate an ancestral sequence to be used in the method is discussed in particular fox the 5S RNA sequences from prokaryotes and eukaryotes and for ferredoxin sequences. The recent proliferation of protein and nucleic acid sequences, due in part to the development of new sequencing techniques (1, 2), has led to a renewed interest in the evolution of these sequences and the organisms from which they came. We wish to discuss here some problems with the commonly used method (3, 4) (the matrix method) for calculating evolutionary trees from molecular sequence data and to present an alternative method that, in theory, eliminates these problems. Because the analytic proof of our method depends on a knowledge of existing methods, we will briefly review what is necessary from the existing literature, then discuss the problems with the matrix method in some detail.An evolutionary tree representation of nucleic acid or protein sequence differences among several organisms should give the following information: (I) the correct pattern of branching of the various present-day organisms from one another (that is, the correct tree "topology"); (ii) the correct position on the tree of the common ancestor to all the present-day organisms (that is, the correct tree "root"); and (iii) of secondary importance, a reasonable estimate of the number of mutations along each of the tree branches (branch mutations).One type of such a representation is presented in Fig. la for five hypothetical present-day organisms, A, B, C, D, and E, and their common ancestor X. In this representation, the topology is shown by the order in which the branches connect: C and D are most closely related in the sense that they connect first, then CD connects to E, and A connects to B. The root of the tree with the common ancestor X is shown to be between the groups AB and CDE. This pictorial representation may also be represented...

Pattern analysis of 5S rRNA.

“…The question could be decided by the reconstruction of early nodal sequences. Phylogenetic trees for various ensembles of 5S rRNA have been reported in the literature (6)(7)(8)(9). Dendrograms based on mutation distances, however, yield only relative branching orders, in which the earliest node remains uncertain.…”

“…These comprise 115 eukaryotic, 37 eubacterial, 9 chloroplastic, and 1 mitochondrial sequence. In addition, 17 archaebacterial sequences were kindly provided by G. E. Fox, C. R.…”

The alignment of sets of sequences and the construction of phyletic trees: An integrated method

“…The combination of the alignment algorithm and tree construction based on group averages generates trees that represent compromises between the advantages and disadvantages of these approaches: a limited amount of unequal mutation rate is allowed in a tree in which the overall similarity of evolutionary lines is optimised. (b) Present-day ancestor method (Klotz et al 1979(Klotz et al , 1981Blanken et al 1982): This method assumes that there is a tree topology in the data and, if this assumption is warranted, it finds the correct tree toplogy, notwithstanding variable mutation rates. To this end the pairwise distances are converted to correct for their shared distance from a hypothesised common ancestor.…”

The nucleotide sequence ofBeneckea harveyi 5S rRNA

“…These favorable considerations imply that 5S rRNA may afford unique opportunities for the study of molecular evolution. Currently this is manifested in comparisons of 5S rRNA primary structure (Klotz et al 1979;Hori and Osawa 1979) which allow determination of phylogenetic relationships. In the longer view, since structural variability is also known to occur in 5S rRNA Woese 1975, Bellemare et al 1973;Wrede and Erdmann 1973) it will be very important to conduct comparative studies of structural features in 5S rRNA.…”