PMC

Maximum parsimony analysis of the gene Glucosamine-6-phosphate (nagB, COG0363). The tree depicts the strict consensus of 6 most parsimonious reconstructions. Bootstrap values above 75 are shown on nodes. Rooting was done with the paralog gene Phosphogluconate. E stands for Eukarya, B for Bacteria, and A for Archaea. The number 1 refers to sequences of the gene under analysis, and the number 2 to sequences of the paralog used for rooting.

The node height test. (a) If an Euk-Bac distribution was caused by gene loss, than the E1-B1 (Eukarya to Bacteria) average distance is expected to be higher than the average B1-B1 (Bacteria to Bacteria) distance. (b) However, if eukaryotic genes (E1) were gained by transfer from a particular group of bacteria (B1), than the average E1-B1 distance should not be higher than the average B1-B1 distance. These predictions were done based on the assumption that substitution rates are homogeneous across taxa.

Distributional profile method. A first screening for genes involved in ancient IHGT was done using the distributional profile method. Based on the most accepted hypothesis of phylogenetic relationships between the three domains of life, genes that occur in Eukarya and Bacteria, but not in Archaea, or genes that occur in Archaea and Bacteria, but not in Eukarya were potential candidates to have been horizontally transferred between domains. Genes found in one of those two phyletic distributional categories were further tested for HGT (see text).