Persistence across Pleistocene ice ages in Mediterranean and extra-Mediterranean refugia: phylogeographic insights from the common wall lizard

Salvi, Daniele; Harris, D James; Kaliontzopoulou, Antigoni; Carretero, Miguel A; Pinho, Catarina

doi:10.1186/1471-2148-13-147

Table 2 Summary statistics of genetic diversity for each gene, clade, and region

From: Persistence across Pleistocene ice ages in Mediterranean and extra-Mediterranean refugia: phylogeographic insights from the common wall lizard

		nd4						cytb						mc1r						acm4						pdc
Clades	Localities	N	ns	S	h	Hd	π (*10³)	N	ns	S	h	Hd	π (*10³)	N	ns	S	h	Hd	π (*10³)	N	ns	S	h	Hd	π (*10³)	N	ns	S	h	Hd	π (*10³)
1	1, 16, 18	7	873	8	5	0.91	4.67	8	411	5	3	0.61	5.20	14	683	3	3	0.28	0.74	14	423	1	2	0.26	0.82	12	342	2	2	0.30	2.45
			754	3.55	1.93	0.93	4.71		391	2.07	1.63	0.63	5.48		576	0.41	1.25	0.25	0.71		323	0.3	1.3	0.30	0.93		248	1.24	1.62	0.33	2.69
2	3-9, 11, 12	13	873	9	13	1.00	3.98	13	411	2	3	0.30	1.15	28	683	4	3	0.14	0.50	26	423	0	1	0.00	0.00	26	342	3	3	0.66	5.49
			754	3.05	2	1.00	4.05		391	0.47	1.33	0.33	1.24		576	0.54	1.24	0.24	0.94		323	0	1	0.00	0.00		248	2.41	2.41	0.68	5.56
3	13- 15	6	873	5	5	0.93	3.36	6	411	4	4	0.87	5.47	12	683	1	2	0.17	0.29	10	423	1	2	0.20	0.62	12	342	2	2	0.49	3.93
			754	2.41	1.92	0.92	3.20		391	2.09	1.9	0.90	5.53		576	0.15	1.15	0.15	0.26		323	0.2	1.2	0.20	0.62		248	1.66	1.83	0.47	3.82
4	37-39	7	873	7	6	0.95	4.93	7	411	7	4	0.81	9.07	14	683	3	3	0.39	1.16	14	423	2	3	0.56	2.35	14	342	4	3	0.48	6.41
			754	3.49	1.92	0.92	4.63		391	2.94	1.75	0.75	7.78		576	0.7	1.42	0.42	1.22		323	0.81	1.6	0.60	2.51		248	2.72	1.94	0.45	6.01
5	23, 25, 26	6	873	10	6	1	5.31	8	411	8	3	0.61	10.14	12	683	4	4	0.64	1.71	14	423	3	4	0.75	3.61	12	342	3	4	0.77	4.77
			754	3.81	2	1	5.05		391	3.70	1.53	0.53	9.46		576	0.96	1.61	0.61	1.67		323	1.29	1.77	0.77	3.99		248	2.18	2.79	0.77	4.89
6	20-22	3	873	1	2	0.67	0.88	3	411	2	3	1.00	3.53	6	683	0	1	0.00	0.00	6	423	1	2	0.60	1.86	6	342	0	1	0.00	0.00
			754	0.65	1.65	0.65	0.86		391	1.3	2	1.00	3.44		576	0	1	0.00	0.00		323	0.51	1.51	0.51	1.58		248	0	1	0.00	0.00
7	32, 33	3	873	3	3	1.00	3.10	3	411	1	2	0.67	1.76	6	683	1	2	0.33	0.58	6	423	3	5	0.93	4.33	6	342	3	3	0.60	4.05
			754	2.29	2	1.00	3.04		391	0.62	1.62	0.62	1.64		576	0.29	1.29	0.29	0.50		323	1.44	1.97	0.97	4.46		248	1.92	2.29	0.58	3.89
8	34	3	873	11	3	1.00	9.73	3	411	10	2	0.67	17.64	6	683	1	2	0.33	0.58	6	423	2	3	0.80	3.30	6	342	1	2	0.33	1.35
			754	7.54	2	1.00	10.00		391	7.5	1.75	0.75	19.84		576	0.29	1.29	0.29	0.50		323	1.05	1.78	0.78	3.25		248	0.62	1.62	0.31	1.25
9	27, 28, 30, 31	6	873	18	6	1.00	10.52	6	411	9	3	0.73	12.17	12	683	4	5	0.58	1.16	12	423	1	2	0.17	0.52	12	342	2	3	0.67	3.44
			754	8.3	2	1.00	11.01		391	4.94	1.78	0.78	13.07		576	0.63	1.54	0.54	1.09		323	0.21	1.21	0.21	0.65		248	1.45	2.33	0.62	3.25
10	29	2	873	2	2	1.00	2.65	3	411	1	2	0.67	1.76	4	683	2	2	0.50	1.74	4	423	1	2	0.50	1.55	6	342	1	2	0.53	2.16
			754	-	-	-	-		391	0.67	1.67	0.67	1.77		576	1	1.5	0.50	1.74		323	0.49	1.49	0.49	1.52		248	0.91	1.91	0.52	2.11
11	35, 36	4	873	6	4	1.00	4.42	4	411	1	2	0.50	1.32	8	683	2	3	0.71	1.49	8	423	0	1	0.00	0.00	8	342	1	2	0.43	1.74
			754	3.28	2	1.00	4.35		391	0.52	1.52	0.52	1.38		576	0.85	1.71	0.71	1.48		323	0	1	0.00	0.00		248	0.76	1.76	0.41	1.67
12	46	1	873	-	-	-	-	1	411	-	-	-	-	0	-	-	-	-	-	0	-	-	-	-	-	0	-	-	-	-	-
			754						391	-	-	-	-		-	-	-	-	-		-	-	-	-	-		-	-	-	-	-
13	40, 41	2	873	3	2	1.00	3.98	2	411	2	2	1.00	5.29	4	683	1	2	0.50	0.87	4	423	2	3	0.83	3.10	4	342	0	1	0.00	0.00
			754	-	-	-	-		391	-	-	-	-		576	0.52	1.52	0.52	0.90		323	1.05	1.88	0.88	3.25		248	-	-	-	-
14	42-45	3	873	16	3	1.00	14.15	4	411	10	4	1.00	14.11	4	683	1	2	0.50	0.87	6	423	0	1	0.00	0.00	6	342	0	1	0.00	0.00
			754	10.17	2	1.00	13.49		391	5.26	2	1.00	13.92		576	0.51	1.51	0.51	0.89		323	0	1	0.00	0.00		248	0	1	0.00	0.00
15	48-52	9	873	11	9	1.00	4.86	7	411	0	1	0.00	0.00	18	683	0	1	0.00	0.00	18	423	2	3	0.45	2.45	18	342	0	1	0.00	0.00
			754	3.85	2	1.00	5.11		391	0	1	0.00	0.00		576	0	1	0.00	0.00		323	0.8	1.45	0.45	2.48		248	0	1	0.00	0.00
16	47	1	873	-	-	-	-	1	411	-	-	-	-	2	683	0	1	0.00	0.00	2	423	0	1	0.00	0.00	0	-	-	-	-	-
			754						391	-	-	-	-		576	-	-	-	-		323	-	-	-	-		-	-	-	-	-
17	53	3	873	2	3	1.00	1.77	2	411	0	1	0.00	0.00	6	683	0	1	0.00	0.00	4	423	2	2	0.67	4.13	6	342	0	1	0.00	0.00
			754	1.26	2	1.00	1.67		391	-	-	-	-		576	0	1	0.00	0.00		323	1.34	1.67	0.67	4.15		248	0	1	0.00	0.00
		79	873	142	74	1.00	28.21	81	411	83	42	0.97	40.05	156	688	24	21	0.37	0.92	154	423	11	13	0.57	2.40	154	342	13	12	0.73	6.67
Region	Clades
Balkans	12, 13, 14	7	873	53	7	1	27.92	8	411	38	8	1	36.66	10	683	2	3	0.38	0.69	12	423	3	4	0.56	1.97	10	342	0	1	0	0.00
			754	-	-	-	-		391	-	-	-	-		576	-	-	-	-		323	-	-	-	-		248	-	-	-	-
Italy	7, 8, 9, 10	14	873	60	14	1	27.49	16	411	43	10	0.94	35.45	28	683	8	8	0.44	0.99	28	423	3	5	0.57	2.19	30	342	6	6	0.62	3.24
			754	47.88	7	1	27.25		391	34.87	6.48	9.42	35.35		576	2.6	3.31	0.41	0.90		323	2.58	3.85	0.56	2.17		248	2.76	3.47	0.62	3.20
Iberia	1*, 2, 3	24	873	32	22	0.99	15.29	25	411	21	9	9.78	18.94	50	683	8	6	0.19	0.56	46	423	2	3	0.13	0.40	46	342	3	3	0.58	4.56
			754	24.84	6.89	0.99	14.75		391	17.66	4.7	0.79	19.25		576	1.61	2.06	0.20	0.56		323	0.77	1.77	0.14	0.45		248	2.68	2.69	0.58	4.62

N, sample size (in number of gene copies), ns number of sites, S, number of segregating sites, h number of haplotypes, Hd haplotype diversity, π nucleotide diversity. For the diversity measures S, h, Hd, and π values calculated under a resampling approach are also reported below values calculated on the original datasets. For the number of sites, for each case the first row represents the size of the alignment while the second row represents the number of sites after discarding Ns or unphased positions; “-“ means that no resampling was conducted for that set. *excluding locality 1.

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