Table 1.

Genome assemblies used in this study

	Species	Genome assembly
Rodent + Rabbit	Mus musculus (Mouse)	Jul. 2007 (mm9)
	Rattus norvegicus (Rat)	Nov. 2004 (rn4)
	Cavia porcellus (Guinea pig)	Feb. 2008 (cavPor3)
	Oryctolagus cuniculus (Rabbit)	Apr. 2009 (oryCun2)
Bird	Gallus gallus (Chicken)	May 2006 (galGal3)
	Taeniopygia guttata (Zebra finch)	Jul. 2008 (taeGut1)
	Meleagris gallopavo (Turkey)	Dec. 2009 (melGal1)
Fish	Danio rerio (Zebrafish)	Jul. 2010 (danRer7)
	Takifugu rubripes (Fugu)	Oct. 2004 (fr2)
	Tetraodon nigroviridis (Tetraodon)	Mar. 2010 (tetNig2)
	Gasterosteus aculeatus (Stickleback)	Feb. 2006 (gasAcu1)
	Oryzias latipes (Medaka)	Oct. 2005 (oryLat2)

Reference genomes for each of the four groups are listed first