Table 1.

Species Included in the Analysis and an Overview of the Sequence Capture Data

Species	Voucher	Raw Reads	Clean Reads	Nuclear Loci Captureda	Nuclear Loci k-mer Depthb	mtDNA (bp)c	mtDNA k-mer Depthd
Phrynosomatidae
Callisaurus draconoides	MVZ 265543	9,622,116	9,035,068	575	23,280	13,106	1,502,772
Cophosaurus texanus	UWBM 7347	9,176,180	8,625,204	573	24,401	15,609	2,482,706
Holbrookia maculata	UWBM 7362	12,314,136	11,604,340	573	31,000	12,865	1,307,531
Petrosaurus thalassinus	MVZ 161183	4,500,868	3,959,796	523	8,281	7,898	248,342
Phrynosoma sherbrookei	MZFC 28101	7,634,142	6,971,920	579	14,107	12,967	47,287
Sceloporus occidentalis	UWBM 6281	13,531,214	12,733,646	540	30,235	7,422	113,757
Uma notata	SDSNH 76166	2,332,400	2,099,068	577	4,232	7,296	20,763
Urosaurus ornatus	UWBM 7587	3,427,288	3,042,766	577	6,673	6,286	28,028
Uta stansburiana	UWBM 7605	12,927,696	12,085,734	538	25,034	16,703	1,144,368
Outgroups
Gambelia wislizenii	UWBM 7353	9,874,902	7,824,714	549	5,180	15,790	581,925
Liolaemus darwinii	LJAMM-CNP 14634	3,253,800	2,935,874	581	8,715	11,751	41,572

^aTotal loci targeted = 585.

^bAverage number of 90-bp k-mers across all captured loci.

^cTotal base pairs; aligned length = 17,187 bp.

^dNumber of 90-bp k-mers.