The construction and interpretation of gene trees is fundamental in molecular systematics. If the gene is defined in a historical (coalescent) sense, there can be multiple gene trees within the single contiguous set of nucleotides, and attempts to construct a single tree for such a sequence must deal with homoplasy created by conflict among divergent histories. On a larger scale, incongruence is expected among gene tree topologies at different loci of individuals within sexually reproducing species, and it has been suggested that this discordance can be used to delimit species. A practical concern for such topological methods is that polymorphisms may be maintained through numerous cladogenic events; this polymorphism problem is less of a concern for nontopological approaches to species delimitation using molecular data. Although a central theoretical concern in molecular systematics is discordance between a given gene tree and the true "species tree," the primary empirical problem faced in reconstructing taxic phylogeny is incongruence among the trees inferred from different sequences. Linkage relationships limit character independence and thus have important implications for handling multiple data sets in phylogenetic analysis, particularly at the species level, where incongruence among different historically associated loci is expected. Gene trees can also be reconstructed for loci that influence phenotypic characters, but there is at best a tenuous relationship between phenotypic homoplasy and homoplasy in such gene trees. Nevertheless, expression patterns and orthology relationships of genes involved in the expression of phenotypes can in theory provide criteria for homology assessment of morphological characters.