Detecting Evolutionary Incompatibilities From Protein Sequences

Sneath, P. H. A., M. J. Sackin, and R. P. Ambler 1975. Detecting evolutionary incompatibilities from protein sequences. Syst. Zool. 24:311–332.—The study of evolutionary phenomena such as reticulate evolution, gene transfer, convergence and mosaic evolution, and their differentiation from mistaken evolutionary homology (i.e., orthology), requires methods for detecting cladistic incompatibilities. Protein sequences are potentially valuable for such investigations, and for these two main strategies are proposed. Strategy (a) is to look for unexpected similarities between segments of the sequences using cross-association or similar methods. Strategy (b) (which assumes satisfactory prior alignment of the sequences) is to compare the sites in the sequence and test whether the observed co-occurrences would readily fit a single cladogram; for this Le Quesne's method of testing for cladistic incompatibilities has been adapted to protein sequences. Studies have been made on a number of cytochromes. Strategy (a) reveals unexpected high similarity among the N-terminal portions of some eukaryote and prokaryote cytochromes, and there appear to be several short segments that differ in their patterns of similarity. It is not yet clear whether functional requirements or gene transfer is the explanation. Strategy (b) has been tested on sequences where the evolutionary history appears straightforward and also on simulated disturbances of cladogeny and homologization. It seems to be a sensitive technique for such studies. Strategy (b) has also the advantage that it should permit the partitioning of characters into sets that may reflect different evolutionary behavior even when such sets cannot be distinguished by inspection. Preliminary trials suggest that such sets could be recovered by cluster analysis of character compatibility matrices.