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Table 1 A few representative studies on overlapping genes, organized alphabetically with summary of principle conclusions and data type

From: A statistical analysis of the three-fold evolution of genomic compression through frame overlaps in prokaryotes

Authors Year Genomes IE VE SM Genes & Homology Evolutionary Process
Lillo & Krakauer 2007 58 Prokaryote RC & TC MA & MB NS Study of E. coli genome Neutrality & Selection
Boi et al [2] 2004 ? Eukaryote GR NS NS NS Selection on regulation
Das & Yanofsky [3] 1989 1 Prokaryote TC NS NS Study of 2 genes Selection on expression
Fukuda et al. [6] 1999 2 Prokaryote NS NS NE Study of 480 & 677 genes Neutral mutation to stop codon
Fukuda et al [7] 2003 3 Prokaryote NS NS NS NS Neutral mutation to stop and start
Johnson & Chisholm [13] 2004 198 Prokaryote TC NS NS Study of 2 genomes Selection on expression
Krakauer [15] 2000 NS RC & TC MA NS NS Selection on replication and expression
Krakauer [16] 2002 NS RC & TC MA & MB NS NS Selection on replication and expression
Makalowska et al. [22] 2005 7 Eukaryote GR NS NS NS Neutrality
Merino et al. [25] 1994 28 Prok & 8 Euk GR NS NS Study of E. coli genome Selection on regulation
Miyata & Yasunaga [24] 1978 1 Prokaryote NS MA NS Study of -x174 Selection on replication
Normark et al. [26] 1983 ? Prokaryote TC NS NS NS Selection on expression
Oppenheim & Yanofsky [28] 1980 1 Prokaryote TC NS NS E. coli Trp operon Selection on expression
Pavesi et al. [29] 1997 ? Viral NS MB IC NS Selection on coding
Rogozin et al. [30] 2002 ? Prokaryotes NS MB NS NS Selection on coding
Sakharkar et al [31] 2005 9 Prokaryotes RC NS NS Study of 2 genomes Selection on replication
Sander & Schulz [32] 1979 2 Prokaryote NS MB NS Study of SV40 & -x174 genes Selection on coding
Welch et al. [39] 2000 1 Prokaryote TC NS NS Study of V anguillarum Selection for iron biosynthesis
  1. Key: IE – Immediate Effect, VE – variational effect, SM – Statistical Model NS – Not in Study, TC – translational coupling, RC – replicative compression, GR antisense gene regulation MB – mutational buffering, MA – mutational amplification, NE – Neutral expectation under statistical model, IC – Shannon information content of overlap. The ? symbols records an unknown number lineages. The column labeled "Genes and detailed homology" captures the pattern of many studies to couple the statistics of large databases with the detailed analysis of a small number of overlapping genes from well studied genomes. The difference between selection on expression versus selection on regulation seeks to discriminate between co-expression (as in a codon) and active inhibition or activation (such as through anti-sense), The difference between selection on replication and selection on coding reflects a difference only in emphasis as both imply a greater number of genes in a shorter sequence.
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