Nuclear gene phylogeography using PHASE: dealing with unresolved genotypes, lost alleles, and systematic bias in parameter estimation

Garrick, Ryan C; Sunnucks, Paul; Dyer, Rodney J

doi:10.1186/1471-2148-10-118

Table 2 Characteristics of five empirical and 35 simulated datasets used in the present study.

From: Nuclear gene phylogeography using PHASE: dealing with unresolved genotypes, lost alleles, and systematic bias in parameter estimation

Empirical		Ambiguous	Polymorphism measure				Simulated		Ambiguous	Polymorphism measure
datasets	N	genotypes	S	A _N	G _N	H _O	datasets	N	genotypes	S	A _N	G _N	H _O
Pseudachorutinae sp.							Sim01	50	5	5	6	6	0.26
Sm2 Pop1	80	0	2	3	4	0.03	Sim02	50	14	5	6	11	0.58
Sm2 Pop2	61	0	2	3	3	0.02	Sim03	50	2	5	6	9	0.66
Sm2 Pop3	118	2	9	5	7	0.14	Sim04	50	9	5	6	9	0.50
Sm2 Pop4	62	0	2	4	4	0.03	Sim05	50	6	5	6	8	0.50
Average	80	1	4	4	5	0.06	Sim06	50	25	10	8	12	0.76
SmEF1α Pop1	81	2	9	6	9	0.10	Sim07	50	34	10	9	17	0.90
SmEF1α Pop2	60	8	6	3	4	0.13	Sim08	50	25	10	10	22	0.76
SmEF1α Pop3	105	40	11	9	12	0.39	Sim09	50	38	10	9	15	0.80
SmEF1α Pop4	54	9	6	6	8	0.22	Sim10	50	31	10	9	23	0.80
Average	75	15	8	6	8	0.21	Sim11	50	36	15	11	17	0.82
Acanthanura sp.							Sim12	50	38	15	12	30	0.86
Uc3 Pop1	26	0	2	3	4	0.08	Sim13	50	31	15	10	20	0.78
Uc3 Pop2	19	0	0	1	1	0.00	Sim14	50	32	15	11	19	0.76
Uc3 Pop3	67	3	8	8	9	0.24	Sim15	50	36	15	12	23	0.80
Uc3 Pop4	78	6	7	7	12	0.14	Sim16	50	39	20	13	31	0.90
Uc3 Pop5	15	8	17	9	11	0.67	Sim17	50	30	20	16	33	0.72
Average	41	3	7	6	7	0.23	Sim18	50	24	20	13	22	0.62
Uc180 Pop1	24	5	7	5	8	0.54	Sim19	50	27	20	12	21	0.62
Uc180 Pop2	19	1	2	2	2	0.05	Sim20	50	41	20	15	30	0.86
Uc180 Pop3	67	0	2	3	3	0.03	Sim21	50	40	25	19	37	0.90
Uc180 Pop4	78	0	1	2	2	0.01	Sim22	50	32	25	15	22	0.70
Uc180 Pop5	15	0	0	1	1	0.00	Sim23	50	30	25	17	32	0.72
Average	41	1	2	3	3	0.13	Sim24	50	20	25	13	21	0.70
UcEF1α Pop1	26	6	6	6	8	0.23	Sim25	50	35	25	18	29	0.84
UcEF1α Pop2	19	1	7	4	4	0.16	Sim26	50	40	30	20	39	0.84
UcEF1α Pop3	67	21	15	10	11	0.36	Sim27	50	41	30	17	36	0.90
UcEF1α Pop4	78	12	14	10	11	0.26	Sim28	50	32	30	19	29	0.82
UcEF1α Pop5	15	0	0	1	1	0.00	Sim29	50	40	30	21	38	0.90
Average	41	8	8	6	7	0.20	Sim30	50	41	30	22	42	0.92
Sm2	321	2	13	11	14	0.07	Sim31	50	37	35	17	35	0.88
SmEF1α	300	59	17	17	27	0.24	Sim32	50	41	35	17	36	0.94
Uc3	205	17	26	17	30	0.19	Sim33	50	41	35	16	32	0.88
Uc180	203	6	12	9	13	0.08	Sim34	50	46	35	20	38	0.92
UcEF1α	205	40	27	21	32	0.26	Sim35	50	38	35	15	28	0.80
Average	247	25	19	15	23	0.17	Average	50	31	20	13	25	0.77

Genetically distinct populations of two Collembola species identified previously [5, 40] were pooled prior to reanalysis using PHASE, but are separated here for comparison with the single-population simulated datasets. N is the number of diploid individuals, and 'ambiguous genotypes' are those containing at least two heterozygous sites. Polymorphism measures are: S, number of segregating sites; A_N, number of different alleles; G_N, number of different genotypes; H_O, observed heterozygosity.

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