On the phylogeny of Mustelidae subfamilies: analysis of seventeen nuclear non-coding loci and mitochondrial complete genomes

Yu, Li; Peng, Dan; Liu, Jiang; Luan, Pengtao; Liang, Lu; Lee, Hang; Lee, Muyeong; Ryder, Oliver A; Zhang, Yaping

doi:10.1186/1471-2148-11-92

Table 1 Characterization of Nuclear introns and mt genes examined in the present study

From: On the phylogeny of Mustelidae subfamilies: analysis of seventeen nuclear non-coding loci and mitochondrial complete genomes

Sequence type	Fragments name	TEs	Aligned^a	Final data^b	Parsimony-informative sites	Nucleotide Composition				Ti/Tv	Best fit model	Among-site Rate Variation		Pairwise Distance (%)
						A	T	G	C			I	α
Nucear introns	Cidea-1	YES	1590	1134	343	0.308	0.240	0.230	0.222	1.5	TrN+G	0	0.9770	7.5
	Coro1c-4	YES	1435	1332	339	0.242	0.280	0.234	0.243	2.4	K81uf+G	0	0.9379	6.3
	Coro1c-5	YES	1380	1099	140	0.309	0.321	0.210	0.160	2.2	TVM+G	0	0.9084	4.7
	Guca1b-3	YES	711	711	149	0.230	0.186	0.289	0.295	1.6	HKY+G	0	0.7174	6.1
	Ociad1-4	YES	1576	1014	200	0.328	0.393	0.145	0.134	1.9	TVM+G	0	1.3754	4.1
	Plod2-13	NO	1317	1230	236	0.293	0.325	0.229	0.153	2.0	GTR+G	0	1.555	3.3
	Plod2-14	YES	1685	1068	263	0.342	0.327	0.180	0.151	1.4	TVM+G	0	1.4866	3.7
	Ssr1-5	YES	1180	783	131	0.324	0.382	0.160	0.134	2.2	GTR+G	0	1.4043	3.6
	Tbc1d7-6	YES	1153	1095	326	0.247	0.293	0.261	0.199	1.5	TIM+G	0	0.7365	8.2
	Tinagl1-1	YES	1263	1260	250	0.208	0.208	0.295	0.290	2.4	HKY+G	0	0.7637	3.2
	Tinagl1-3	YES	1115	1014	193	0.179	0.238	0.281	0.301	1.9	K81uf+G	0	0.7201	3.7
	Wasf1-3	YES	1195	1021	161	0.314	0.345	0.170	0.171	1.8	GTR+G	0	1.6253	3.9
	Wasf1-6	YES	1276	1077	207	0.308	0.354	0.191	0.147	2.2	TVM+G	0	1.7531	4.1
	Wasf1-7	NO	1380	1147	223	0.314	0.355	0.165	0.166	2.0	GTR+G	0	0.6571	3
	Ttr-1	YES	1130	895	159	0.263	0.279	0.227	0.231	2.4	TVM+G	0	1.3403	4.6
	Fgb-4	YES	847	523	71	0.307	0.307	0.215	0.171	2.0	HKY	0	equal	4.5
	Fgb-7	YES	642	611	102	0.292	0.327	0.186	0.195	1.4	GTR	0	equal	5.1
	Com1^c		15893	12570	1735	0.279	0.301	0.219	0.201	2.0	TVM+I+G	0.17	0.9090	4.4
	Com2^c		15893	15038	2137	0.279	0.302	0.218	0.201	1.9	GTR+I+G	0.18	0.9078	4.6
	Com3^c		15893	15688	2170	0.279	0.303	0.218	0.200	1.8	GTR+I+G	0.18	0.9052	4.6
Mt genes	ND1		957		357	0.309	0.274	0.122	0.295	2.6	GTR+I+G	0.53	0.7988	17.3
	ND2		1044		483	0.363	0.263	0.098	0.275	2.1	GTR+I+G	0.35	0.859	23
	COX1		1545		556	0.282	0.302	0.175	0.241	3.1	GTR+I+G	0.58	1.1772	19.1
	COX2		684		252	0.323	0.276	0.142	0.260	3.3	K81uf+I+G	0.56	1.0711	19.6
	ATP8		204		92	0.388	0.291	0.077	0.243	2.2	GTR+I+G	0.42	1.3437	22.8
	ATP6		681		290	0.306	0.291	0.116	0.287	3.3	GTR+I+G	0.46	0.7582	21.6
	COX3		784		303	0.273	0.286	0.154	0.286	2.6	TrN+I+G	0.53	0.8079	20.2
	ND3		348		160	0.320	0.279	0.130	0.272	2.5	TrN+I+G	0.38	0.956	22.3
	ND4L		297		127	0.287	0.324	0.124	0.265	2.9	TVM+I+G	0.43	0.7530	22.5
	ND4		1378		609	0.323	0.278	0.115	0.284	2.8	GTR+I+G	0.42	0.835	22.1
	ND5		1830		739	0.331	0.274	0.115	0.280	2.6	TIM+I+G	0.42	0.8367	19.6
	ND6		534		192	0.417	0.203	0.101	0.278	2.7	K81uf+I+G	0.46	0.656	16.3
	CYTB		1140		446	0.295	0.278	0.134	0.293	2.8	TVM+I+G	0.5	1.1027	18.7
	12SrRNA		988		236	0.371	0.229	0.178	0.223	2.8	GTR+I+G	0.37	0.3532	9.2
	16SrRNA		1626		403	0.369	0.243	0.174	0.213	2.1	GTR+I+G	0.47	0.5765	10.5
	tRNA		1558		301	0.353	0.281	0.157	0.209	4.0	GTR+I+G	0.48	0.4371	7.3
	D-loop		941		315	0.308	0.277	0.166	0.249	1.9	HKY+I+G	0.3	0.4867	11.4
	Combined		16537		5855	0.329	0.272	0.140	0.259	2.7	GTR+I+G	0.5	0.9372	16.9

Note: Ti = Transition; Tv = Transversion; I = Proportion of invariable sites; α = Gamma distribution shape parameter; TEs = Transposible Elements. If TEs were detected in introns, it indicated YES, otherwise it indicated NO.
a The length of sequences which were aligned using the CLUSTAL software with default settings.
b The length of analyzed data, after the ambiguous areas of the alignment were removed by Gblocks 0.91b.
c The length of all introns concatenated, after the ambiguous areas of the alignment were removed by Gblocks 0.91b with no gap (Com1), half gap (Com2), and all gap (Com3) parameters.

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