Phylogenomics of a rapid radiation: is chromosomal evolution linked to increased diversification in north american spiny lizards (Genus Sceloporus)?

Leaché, Adam D.; Banbury, Barbara L.; Linkem, Charles W.; de Oca, Adrián Nieto-Montes

doi:10.1186/s12862-016-0628-x

Table 1 Specimens included in the study

From: Phylogenomics of a rapid radiation: is chromosomal evolution linked to increased diversification in north american spiny lizards (Genus Sceloporus)?

Species	Voucher	RAW reads	Clean pairs	idba contig	idba loci
angustus group (2/2)
Sceloporus angustus	LACM 134741	3,788,618	3,457,044	1205	579
Sceloporus grandaevus	ROM 26215	1,342,322	1,134,076	700	521
clarkii group (2/2)
Sceloporus clarkii	MVZ 245876	2,844,162	2,543,574	1223	579
Sceloporus melanorhinus	MZFC 7454	3,384,030	2,971,666	1298	580
formosus group (11/15)
Sceloporus acanthinus	ANMO1932	3,734,696	3,350,382	1971	575
Sceloporus adleri	UWBM 6608	8,137,738	7,364,486	4460	576
Sceloporus cryptus	MZFC 7438	2,350,112	2,133,386	1036	577
Sceloporus druckercolini	JAC 25172	2,760,330	2,463,818	1357	559
Sceloporus formosus	RVT 76	3,354,056	2,960,696	1550	569
Sceloporus formosus	ANMO 1248	2,192,170	1,693,102	948	541
Sceloporus formosus scitulus	UWBM 6623	5,476,146	4,950,836	2243	577
Sceloporus internasalis	JAC 22552	4,393,164	3,792,716	2119	573
Sceloporus lunaei	not sampled	–	–	–	–
Sceloporus lundelli	not sampled	–	–	–	–
Sceloporus malachiticus	MVZ 263420	5,373,316	4,945,178	2673	578
Sceloporus salvini	not sampled	–	–	–	–
Sceloporus smaragdinus	unknown	1,891,310	1,461,336	938	546
Sceloporus stejnegeri	MZFC 7452	3,981,586	3,470,518	3492	383
Sceloporus subpictus	MZFC 8028	6,456,814	5,737,156	5349	572
Sceloporus taeniocnemis	MVZ 264322	1,892,698	1,423,322	771	247
Sceloporus tanneri	not sampled	–	–	–	–
gadoviae group (2/2)
Sceloporus gadoviae	UWBM 7309	6,519,836	5,991,130	1835	577
Sceloporus maculosus	JAM 650	3,140,176	2,691,774	2339	339
graciosus group (3/3)
Sceloporus arenicolus	ADL 047	2,637,380	2,266,994	946	579
Sceloporus graciosus	MVZ 240898	6,241,172	5,631,350	3413	576
Sceloporus vandenburgianus	TWR 430	4,961,440	4,386,238	1435	581
grammicus group (6/6)
Sceloporus anahuacus	AMH684	3,986,550	3,219,532	1512	573
Sceloporus asper	JAC23686	7,225,354	4,490,778	2723	573
Sceloporus grammicus	UWBM 6585	4,406,008	3,910,096	2054	576
Sceloporus grammicus microlepidotus	UOGV2525	1,315,156	1,051,322	702	518
Sceloporus heterolepis	MZFC 8017	4,824,734	3,952,154	4777	344
Sceloporus palaciosi	UWBM 7313	10,419,276	9,501,996	2546	578
Sceloporus shannonorum	JADE 220	5,377,848	5,003,792	4205	563
jalapae group (2/2)
Sceloporus jalapae	UWBM 7318	4,557,808	4,128,130	1228	575
Sceloporus ochoterenae	UWBM 6641	3,716,194	3,242,038	1449	579
magister group (6/6)
Sceloporus hunsakeri	ADG 98	2,336,356	1,724,688	1168	580
Sceloporus licki	ADG 73	5,951,168	5,355,664	4806	554
Sceloporus lineatulus	unknown	8,289,082	7,293,688	7954	567
Sceloporus magister cephaloflavus	UWBM 7395	4,391,974	3,903,318	1457	578
Sceloporus magister bimaculosus	DGM 924	1,818,256	1,472,176	1015	549
Sceloporus magister magister	ROM 14488	8,938,692	8,446,102	5308	561
Sceloporus magister uniformis	DGM 474	11,528,354	10,328,510	8009	574
Sceloporus magister uniformis	MVZ 162077	4,856,264	3,818,418	2286	562
Sceloporus orcutti	UWBM 7654	5,061,334	4,346,088	1695	579
Sceloporus orcutti	RWM 798	3,769,420	2,886,214	1486	564
Sceloporus zosteromus	ADG 49	3,256,502	2,843,448	1274	577
Sceloporus zosteromus	ADG 74	14,267,908	12,650,332	5117	579
megalepidurus group (2/3)
Sceloporus halli	not sampled	–	–	–	–
Sceloporus megalepidurus	MZFC 8026	4,443,820	3,916,852	3922	546
Sceloporus pictus	LCM 1149	3,581,154	3,310,488	2674	576
merriami group (1/1)
Sceloporus merriami	LSUMZ 48844	3,786,064	3,181,240	1134	578
poinsettii group (10/12)
Sceloporus aureolus	RVT 54	5,861,080	5,350,974	2627	566
Sceloporus aureolus	JAC 22409	5,310,894	4,798,000	2361	568
Sceloporus cyanogenys	FMQ 3250	3,588,644	3,028,816	3126	378
Sceloporus cyanostictus	unknown	2,276,708	1,830,554	1122	549
Sceloporus dugesii	UTAR 23955	3,147,022	2,445,678	1887	236
Sceloporus macdougalli	MZFC 7017	5,546,916	4,884,484	3456	559
Sceloporus minor	UOGV 1369	6,196,168	5,486,782	3883	564
Sceloporus mucronatus	UWBM 6636	4,831,958	4,464,672	2783	578
Sceloporus oberon	not sampled	–	–	–	–
Sceloporus ornatus	JAM 652	3,298,578	2,602,280	2533	311
Sceloporus poinsettii	LSUMZ 48847	3,518,050	3,088,022	3029	309
Sceloporus serrifer	UTAR 39870	3,255,154	2,896,292	2649	579
Sceloporus sugillatus	not sampled	–	–	–	–
pyrocephalus group (2/2)
Sceloporus nelsoni	ANMO 3749	1,786,424	1,489,126	1380	578
Sceloporus pyrocephalus	unknown	2,960,302	1,701,102	723	567
Sceloporus pyrocephalus	UTAR 53473	2,510,072	1,987,732	1711	576
scalaris group (10/11)
Sceloporus aeneus	RWB 769	3,950,636	3,201,546	1868	541
Sceloporus aurantius	RWB 1024	5,101,362	4,469,276	2943	544
Sceloporus bicanthalis	UWBM 7307	[45]	[45]	[45]	583
Sceloporus brownorum	RWB 6136	4,763,078	3,880,564	2676	559
Sceloporus chaneyi	RWB 6199	5,669,414	4,989,592	3018	543
Sceloporus goldmani	not sampled	–	–	–	–
Sceloporus samcolemani	JJW 698	7,011,786	6,414,192	6966	511
Sceloporus samcolemani	RWB 6263	1,252,600	1,174,070	865	509
Sceloporus scalaris	UWBM 6589	6,473,054	5,873,872	3253	575
Sceloporus scalaris	RWB 6247	3,654,246	3,176,608	2603	536
Sceloporus slevini	RWB 741	4,044,246	3,096,622	1329	526
Sceloporus subniger	RWB 686	2,348,238	2,073,796	3028	517
Sceloporus subniger "West"	RWB 645	7,806,116	7,173,556	1532	577
Sceloporus unicanthalis	JJ UANL 2/11	3,823,644	3,613,842	1651	558
siniferus group (3/4)
Sceloporus carinatus	UWBM 6614	5,530,392	5,075,056	3202	577
Sceloporus cupreus	not sampled	–	–	–	–
Sceloporus siniferus	UWBM 6653	2,520,248	2,276,060	971	560
Sceloporus siniferus	MVZ 236299	4,928,056	4,507,972	1750	569
Sceloporus squamosus	UTAR 39846	2,220,578	1,990,330	1855	579
spinosus group (3/3)
Sceloporus edwardtaylori	UWBM 6588	3,662,374	3,288,800	1769	578
Sceloporus horridus	MZFC 7458	2,687,744	2,205,246	2100	241
Sceloporus spinosus	UWBM 6672	3,349,020	3,069,336	1682	571
torquatus group (5/5)
Sceloporus bulleri	FMQ 2815	4,561,554	4,287,202	2990	554
Sceloporus insignis	ANMO 1130	2,778,082	2,445,878	1275	554
Sceloporus insignis	unknown	8,364,794	7,792,166	6936	571
Sceloporus jarrovii	LSUMZ 48786	3,875,608	3,536,668	3359	535
Sceloporus lineolateralis	MZFC 6650	4,062,766	3,406,354	3365	264
Sceloporus torquatus	UWMB 6600	8,116,338	7,474,646	4694	576
Sceloporus torquatus	UOGV 2526	3,381,124	3,072,114	2917	578
undulatus group (10/10)
Sceloporus cautus	MZFC 7414	8,275,890	7,070,754	1828	581
Sceloporus consobrinus	ADL105	1,417,172	1,185,840	773	534
Sceloporus cowlesi	AMNH 154059	4,275,658	3,889,018	2001	575
Sceloporus exsul	UWBM 6590	6,472,236	5,934,742	3189	574
Sceloporus occidentalis	UWBM 6281	[13]	[13]	[13]	540
Sceloporus occidentalis	MVZ 245697	2,319,900	2,137,418	1469	564
Sceloporus olivaceus	UWBM 7968	2,263,854	1,994,096	1088	580
Sceloporus tristichus	ADL189	5,483,728	5,010,016	2721	572
Sceloporus undulatus	ADL182	742,440	661,418	743	577
Sceloporus virgatus	MVZ 150112	2,818,968	2,451,942	905	575
Sceloporus woodi	MVZ 10643	1,430,400	1,277,004	870	574
utiformis group (0/1)
Sceloporus utiformis	not sampled	–	–	–	–
variabilis group (6/7)
Sceloporus chrysostictus	UTAR 53535	3,682,608	3,321,192	1536	572
Sceloporus cozumelae	not sampled	–	–	–	–
Sceloporus couchii	MZFC 6676	4,611,012	3,855,118	2613	394
Sceloporus parvus	MZFC 6664	4,973,960	4,489,574	5075	561
Sceloporus smithi	UWBM 6662	2,046,916	1,901,554	998	575
Sceloporus teapensis	UTAR 52778	4,352,968	3,926,160	3545	565
Sceloporus variabilis	UWBM 6678	6,819,682	6,201,808	2537	577
Sceloporinae outgroups
Petrosaurus thalassinus	MVZ 161183	[13]	[13]	[13]	523
Urosaurus ornatus	UWBM 7587	[13]	[13]	[13]	577
Uta stansburiana	UWBM 7605	[13]	[13]	[13]	538
Callisaurini outgroups
Callisaurus draconoides	MVZ 265543	[13]	[13]	[13]	575
Callisaurus draconoides	MVZ unknown	10,414,104	9,871,780	44,419	574
Cophosaurus texanus	UWBM 7347	[13]	[13]	[13]	573
Holbrookia maculata	UWBM 7362	[13]	[13]	[13]	573
Uma notata	SDSNH 76166	[13]	[13]	[13]	577
Phrynosomatini outgroups
Phrynosoma asio	UWBM 7281	[45]	[45]	[45]	565
Phrynosoma blainvillii	CAS 200652	[45]	[45]	[45]	565
Phrynosoma braconnieri	UWBM7282	[45]	[45]	[45]	561
Phrynosoma cerroense	MVZ 161206	[45]	[45]	[45]	579
Phrynosoma cornutum	MVZ 238582	[45]	[45]	[45]	575
Phrynosoma coronatum	UABC 1007	[45]	[45]	[45]	364
Phrynosoma ditmarsi	RRM 2459	[45]	[45]	[45]	576
Phrynosoma douglasii	UWBM 7227	[45]	[45]	[45]	515
Phrynosoma goodei	CAS 229922	[45]	[45]	[45]	574
Phrynosoma hernandesi	MVZ 245875	[45]	[45]	[45]	573
Phrynosoma mcallii	CAS 229923	[45]	[45]	[45]	538
Phrynosoma modestum	MVZ 238583	[45]	[45]	[45]	545
Phrynosoma orbiculare	UWBM 7285	[45]	[45]	[45]	508
Phrynosoma platyrhinos	MVZ 161495	[45]	[45]	[45]	563
Phrynosoma sherbrookei	MZFC 28101	[13]	[13]	[13]	579
Phrynosoma solare	MVZ 241510	[45]	[45]	[45]	410
Phrynosoma taurus	UWBM 7296	[45]	[45]	[45]	559
Iguanidae outgroups
Gambelia wislizenii	UWBM 7353	[13]	[13]	[13]	549
Liolaemus darwinii	LJAMM-CNP 14634	[13]	[13]	[13]	581

Data on species diversity was taken from the Reptile Database [85]
Targeted sequence capture data for species used in previous studies [13, 45] are listed with their voucher information and the number of loci

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ISSN: 2730-7182

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