As species and their genomes diverge during evolutionary history, the sets of genes and their sequences also diverge. Gene duplication has been proposed as a crucial source of evolutionary innovation in organisms, like Eukaryotes, with small effective population sizes (Ohno, 1970). With duplication, comes initial redundancy, followed by neofunctionalization, subfunctionalization, and most commonly pseudogenization (Lynch, 2001). This differential retention of duplicate genes can result in a different phylogenetic tree for individual gene families than for the species as a whole. When differential parsing of shared ancestral gene and nucleotide polymorphism is added to the picture as well as uncertainty in tree calculation methodologioes, the correlation between the evolutionary history of a gene and a species becomes murky.
In the development of a large scale database for understanding species evolution through the evolution of gene families (Liberles et al., 2001; Roth et al., 2005), it has been necessary to develop a soft parsimony based approach to map gene trees onto species trees.
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A. C. Berglund, P. J. Steffansson, M. J. Betts, and D. A. Liberles, Optimal gene trees from sequences and species trees using a soft interpretation of parsimony, Journal of Molecular Evolution (2006).
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