Fitting the Gene Lineage into its Species Lineage, a Parsimony Strategy Illustrated by Cladograms Constructed from Globin Sequences

Fitting the gene lineage into its species lineage, a parsimony strategy illustrated by cladograms constructed from globin sequences. Syst. Zool. 28:132–163.—The gene phylogeny for a set of contemporary species is defined as the ancestral order of branching of evolutionarily related gene lineages leading to the expressed genes in the contemporary species. The species phylogeny for this set of species is defined as the evolutionary branching of species lineages leading to the contemporary species. Since a given gene may duplicate within its species lineage, and distinct sister genes may be expressed by different species, the topologies of the gene and species lineages may not be the same for the same set of contemporary species. The present paper develops a parsimony strategy for scoring the gene duplications and gene expression events needed to fit gene lineages into their corresponding species lineages. In the usual parsimony reconstruction, an effort is made to minimize the number of nucleotide replacements throughout the tree. In the present study, the sum of nucleotide replacements, gene duplications, and gene expression events is the value to be minimized. Gene expression events are further subclassified as gene loss events, activating regulator mutations, and inactivating regulator mutations. Analysis of amino acid sequence data from the alpha and beta hemoglobins and myoglobins suggests that the gene lineages deviate relatively little from established species relationships, and that most contemporary gene pairs in this phylogenetic system may be regarded as orthologous (split at the time of speciation) rather than paralogous (split prior to speciation). It also appears that as the statistical sample of orthologous sequence sites becomes greatly enlarged by tandem alignment of enough different types of protein chains, the parsimony reconstruction based strictly on minimal nucleotide replacement length will itself reveal the correct cladogram for the set of contemporary species.