Table 1.

Data Set Characteristics.

Data Set	Loci	Repeat Filtering	Total Positions	Parsimony Positions	% Loci				Species per Locus
					Exons	Introns	UTRs	Intergenic
All mapped loci	89,593	RepBase	7,884,184	401,097	25.41	39.97	3.83	30.79	2.96
Min. Taxa	30,801	RepBase	2,710,488	401,097	26.56	40.42	3.86	29.17	6.31
Dre Group	3,406	RepBase	299,728	62,805	39.12	31.53	4.84	24.52	13.77
All Danios	1,720	RepBase	151,360	27,799	38.38	30.89	3.99	26.73	15.25
pyRAD	60,216	None	5,296,122	258,690	NA	NA	NA	NA	3.47

Note.—NA, not available.