Table 1. Summary of ezRAD results from 2 lanes of Illumina GAIIx sequencing across a range of taxonomic diversity.

Organisms run with ezRAD include: the limpet Cellana talcosa; sea stars Cryptasterina hystera, C. pentagona & Patiria miniata; reef fish Paracirrhites arcatus; corals Porites lobata, P. compressa & Pocillopora damicornis; and the spinner dolphin Stenella longirostris. Lane use indicates the proportion of a single lane of PE100bp sequencing on the GAIIx flow cell. Library prep specifies what those libraries contained. Paired reads are the number of reads in each index parsed file returned after initial quality control (QC) filter from the sequencer. Reads and % Pass QC are the number of sequence reads remaining after excluding all sequences for which Phred scores were <20, contained adapter sequences, or were less than 20 bp long after adapters were cut. Mapped reads and High quality mapped reads are the number of reads overall and the number reads that passed quality control, respectively, that were assembled de novo into contigs. Contig statistics and polymorphic SNP counts reported here come from the bash script pipeline described in File S2.

Species	Lane use	Library prep	Paired reads	Reads passing QC	% Pass QC	No. contigs	Mapped reads	High quality mapped	Variable sites	Shared SNPs	>10X SNPs shared	>30X SNPs shared	SNPs Per contig
Cellana talcosa	1/3	2 pools of 24 individ	8,109,327	4,472,365	55.15	189,444	8,389,669	3,483,833	127,609	73,014	49,761	9,997	0.26
Cryptasterina hystera	1/12	1 pool of 10 individ	6,441,832	3,880,080	60.23	27,007	2,242,589	655,509	36,666	36,666	31,127	12,827	1.15
Cryptasterina pentagona	1/12	1 pool of 10 individ	1,804,165	325,137	18.02	4,354	1,452,171	148,580	9,501	9,501	8,058	3,538	1.85
Patiria miniata	3/4	4 pools of 20 individ	15,632,982	13,132,267	84.00	635,376	47,718,931	14,987,372	1,167,981	187,597	143,254	21,914	0.23
Paracirrhites arcatus	2/3	8 tagged individ	13,586,625	5,261,386	38.72	205,360	22,892,817	3,088,806	171,712	2,705	2,447	366	0.01
Paracirrhites arcatus	1/6	2 pools of 4 individ	2,733,965	995,543	36.41	13,340	2,980,976	324,331	20,512	10,221	7,249	2,082	0.54
Pocillopora damicornis	1/6	2 tagged individ	3,289,007	2,929,932	89.08	164,553	5,710,298	2,956,701	232,734	110,454	80,221	21,658	0.49
Porites compressa	1/4	3 tagged individ	5,512,212	3,852,694	69.89	123,874	7,011,801	2,338,160	297,648	77,346	60,149	13,040	0.49
Porites lobata	1/4	3 tagged individ	7,131,427	3,926,250	55.06	95,887	7,587,534	2,689,310	275,769	65,731	47,617	9,419	0.50
Stenella longirostris	1/3	4 pools of 2 individ	7,660,053	2,563,007	33.46	43,427	9,910,871	1,022,661	69,208	7,502	7,280	3,828	0.17