Table 1.

Some complex features whose evolution is potentially explained by CNE

Complex feature	Phylogenetic breadth (age)	Excess capacity (realizes suppressive epistasis)	Biased variation (fixed through random genetic drift)	(Inter-) dependency	References for CNE view	References for alternative selective view
Gene duplication	All taxa	Redundant second copy of a gene	Loss-of-function mutations are more probable than gain-of-function mutations	Reciprocal loss-of-function mutations render each duplicate essential to maintain function	Lynch et al. (1999) and Stoltzfus (1999)	Kondrashov and Kondrashov (2006) and Kondrashov and Koonin (2004)
Scrambled genes	Ciliates	Sites that flank transposon-like insertions and unscrambling machinery that recognizes those sites	Further scrambling of gene pieces is more probable than mutational unscrambling	Proliferation of transposon-like insertions make the unscrambling machinery essential	Katz and Kovner (2010), Prescott and Greslin (1992) and Stoltzfus (1999)	Katz and Kovner (2010) and Maurer-Alcalá and Nowacki (2019)
gRNA-mediated pan-editing	Kinetoplastids	gRNA and pre-existing precursor editisome	Small deletions are more probable than small insertions	Accumulations of deletions in primordial cryptogenes make the precursor editisome essential	Covello and Gray (1993) and Stoltzfus (1999)	Speijer (2006), Landweber and Gilbert (1993) and Stuart (1993)
Spliceosome	Eukaryotes	Modular function of group II intron ribozymes, trans-acting snRNAs, and RNA-stabilizing proteins	RNA structure-disrupting or loss-of-function mutations are more probable	Structural defects in group II introns make trans-acting snRNAs and proteins essential	Stoltzfus (1999)	Bandea (2009) and Nilsen (2003)
Spliceosomal intron spread in eukaryotic genomes	Eukaryotes	A nuclear envelope that de-coupled transcription from translation, and the spliceosome	Further spliceosomal intron insertion into genes is more probable than their precise mutational removal	Proliferation of spliceosomal introns in nuclear genomes makes the spliceosome essential for their splicing from pre-mRNAs	Cavalier-Smith (1991)	Bandea (2009)

Note that excess capacities allow for effectively neutral biased variation to accumulate through random genetic drift, thereby creating (inter-)dependencies