« The endosymbiont hypothesis has been refined in two major ways. First, as it became increasingly apparent (especially for mitochondria) that many organellar functions are encoded in the nucleus, it was assumed that these nuclear genes had been relocated to the nucleus by lateral transfer from the organellar genome (a reason why some genes have remained in the organelle is then needed). Second, 16S rRNA phylogenies also required that, at least for chloroplasts, existing organelles are descended not from one endosymbiont but from several which invaded different lineages at different times. A central unresolved problem concerns whether mitochondrial evolution is monophyletic or polyphyletic. Moreover, there is substantial evidence for secondary loss of the mitochondrion from various protists, in which several well identified mitochondrial genes are found in the nuclear chromosomes. Multiple independent losses and gains of genes (and of full mitochondria and chloroplasts) is probably the norm. »
« The dinucleotide relative abundance values of temperate double-stranded DNA phages are very close to their hosts, filamentous and single-stranded DNA phages are moderately to distantly related to their hosts, and lytic double-stranded DNA phages are generally distant from their hosts, with phage T7 being substantially farther than phage T4. This gradient in similarity to the host parallels the extent to which the phage uses the complete replication and repair machinery of the host and the duration of such use. »
~ “Compositional biases of bacterial genomes and evolutionary implications”. S. Karlin, J. Mrazek, A.M. Campbell. Journal of Bacteriology, Vol. 179, No. 12, 1997.