Ferris, S. D. and G. S. Whitt (Department of Genetics and Development, University of Illinois, Urbana, Illinois 61801) 1978. Phylogeny of tetraploid catostomidfishes based on the of duplicate gene expression. Syst. Zool. 27:189-206.-A distinctive property of polyploids, the of duplicate gene expression over time, allows phylogenetic inferences to be drawn from multilocus isozyme data. Once the loss of a duplicate gene expression has begun, soon after polyploidization, primitive and derived character states are clearly defined, though not immune to errors in coding. Even with a relatively small number of characters, cladistic, and phenetic trees may be constructed which are similar to each other and to those based on morphology. The Wagner method is shown to be a particularly appropriate method of analysis for handling gene duplication data. Comparison of patristic and phenetic distances has revealed little homoplasy for species in closely related genera of catostomid fishes, but increasing homoplasy for comparisons between more divergent taxa. With increasing employment of isozyme technology, and the concomitant increase in the number of characters it should be possible to analyze many other polyploid taxa with this cladistic technique. [Duplicate gene expression; cladistic analysis; catostomid fishes.] A continuing challenge in the use of the cladistic method in systematics is the identification of primitive and derived character states (Mayr, 1976). This problem becomes particularly acute when allelic isozyme (allozyme) data are employed in the analysis. For example, Avise (1974) has suggested primarily phenetic means of analyzing such data, whereas Farris (1972) has derived several statistical approaches for determining ancestral positions in Wagner networks (Lundberg, 1972) so that phylogenies may be inferred. The present report describes the analysis of a biological system in which multilocus isozyme data may be readily coded into primitive and derived character states. This method of analysis should be useful for assessing the relationships of species whose ancestors have undergone substantial gene duplications. Specifically, we report the results of phenetic and cladistic analyses based on the of duplicate gene 1 Send reprint requests to G. S. Whitt. 2 Present address: Department of Biochemistry, University of California, Berkeley, California 94720. expression in tetraploid catostomid fishes (Teleostomi, Cypriniformes). The Catostomidae are a coherent family of predominantly North American freshwater fishes. Their coherence arises in part from their presumed descent from a single tetraploid ancestor 50 million years ago (Uyeno and Smith, 1972). Uyeno and Smith have demonstrated that species of catostomids have twice the number of chromosomes and cellular DNA content of related families of Cypriniformes, e.g., the diploid species of cyprinids. Ferris and Whitt (1977a) have investigated the expression of duplicate genes in representatives of most of the catostomid genera by employing starch gel electrophoresis of enzymes encoded in 20 loci (the diploid number). The average catostomid species expressed 47% of its genes in duplicate (range 35-65%), an observation consistent with tetraploidy followed by a partial functional diploidization. As a consequence of our observation of substantial differences in the extent of duplicate gene expression among species we decided to test the postulate that these differences in gene expression would reflect their evolution-