Parallel divergent adaptation along replicated altitudinal gradients in Alpine trout

Keller, Irene; Schuler, Jolanda; Bezault, Etienne; Seehausen, Ole

doi:10.1186/1471-2148-12-210

BMC Ecology and Evolution

Table 1 List of putatively adaptive loci detected within drainages or individual rivers in Alpine trout populations

From: Parallel divergent adaptation along replicated altitudinal gradients in Alpine trout

	Outlier scan							Genotype-altitude association
Drainage	Rhi				Rho	T	P	all	Rhi
River within drainage		Reuss	Thur	A-Rhi
# polymorphic markers	148	120	129	143	169	152	209	229	148
# pops	7	2	3	2	2	3	3	16	7
# ind	175	36	83	55	53	63	78	369	175
Loc1	2.92	NA	1.76	NA	NA	NA	0.01	0.38	0.00
Loc2	0.99	NA	0.18	NA	NA	NA	0.01	0.32	0.39
Loc3	0.96	NA	0.33	NA	−0.08	NA	−0.03	0.60	0.15
Loc4	0.73	NA	0.08	0.13	0.01	0.00	NA	0.25	0.07
Loc5	0.71	0.02	0.09	0.02	−0.06	−0.03	0.05	0.14	0.07
Loc6	0.65	0.11	0.10	0.14	0.02	−0.02	−0.02	0.04	0.01
Loc7	0.58	−0.01	0.67	NA	0.00	−0.02	−0.03	0.60	0.01
Loc8	0.55	0.01	0.06	−0.01	0.06	0.06	−0.04	0.39	0.00
Loc9	0.46	−0.01	0.08	−0.01	0.03	−0.06	−0.01	0.41	0.80
Loc10	0.44	0.03	0.06	0.06	0.06	NA	−0.03	0.24	0.28
Loc11	0.42	0.43	0.00	0.04	−0.09	−0.01	0.02	0.03	0.27
Loc12	0.41	NA	0.17	NA	NA	NA	−0.03	0.56	0.00
Loc13	0.33	−0.01	0.02	0.03	0.03	0.06	−0.01	0.41	0.36
Loc14	0.18	0.00	0.73	−0.03	−0.04	0.02	−0.03	0.00	0.07
Loc15	−0.04	NA	0.43	0.01	0.00	NA	0.04	0.61	0.90
Loc16	0.06	−0.03	0.38	NA	NA	0.01	−0.03	0.10	0.07
Loc17	0.33	−0.02	−0.10	0.77	−0.04	0.11	−0.01	0.12	0.00
Loc18	−0.10	0.01	NA	0.04	−0.05	0.71	−0.01	0.41	0.00
Loc19	−0.11	−0.03	0.06	0.01	−0.07	−0.07	0.02	0.00	0.01
Loc20	−0.08	0.01	0.07	−0.03	−0.02	0.03	−0.01	0.00	0.51
Loc21	NA	NA	NA	NA	−0.03	−0.04	−0.02	0.01	NA
Loc22	−0.21	−0.05	0.05	−0.01	−0.01	−0.06	0.02	0.02	0.04
Loc23	−0.13	NA	−0.07	0.03	−0.05	NA	−0.03	0.02	0.10
Loc24	−0.10	−0.02	−0.03	−0.05	−0.02	0.11	−0.02	0.02	0.01
Loc25	−0.05	0.00	−0.10	0.04	−0.05	0.24	−0.04	0.03	0.87
Loc26	−0.16	NA	NA	NA	NA	NA	NA	0.03	0.00
Loc27	NA	NA	−0.01	NA	0.00	NA	−0.02	0.03	NA
Loc28	−0.13	0.00	0.04	−0.03	−0.02	0.10	−0.02	0.03	0.01
Loc29	0.15	0.01	0.03	−0.01	0.01	−0.05	−0.01	0.03	0.06
Loc30	0.05	NA	NA	−0.01	NA	−0.06	−0.03	0.04	0.04
Loc31	−0.05	−0.03	0.01	NA	0.03	NA	0.00	0.04	0.78
Loc32	−0.07	NA	NA	0.00	0.01	NA	0.00	0.04	0.08
Loc33	−0.12	NA	NA	0.18	NA	NA	0.00	0.06	0.00
Loc34	0.00	−0.02	0.06	0.08	−0.04	−0.03	−0.02	0.13	0.00
Loc35	−0.11	NA	−0.03	−0.06	0.02	NA	−0.04	0.12	0.00
Loc36	−0.03	0.03	−0.03	−0.01	−0.04	−0.10	−0.02	0.65	0.00

a) Signature of selection (Outlier scan): Logarithm of the posterior odds for AFLP markers detected as significant outliers in at least one drainage- or river-specific analysis. Bold underlined font indicates tests significant at a threshold consistent with a false discovery rate of 20%.
b) Genotype-altitude association: All: Results of a permutation test assessing the association between AFLP band frequency and altitude accounting for drainage structure. Listed are all markers with a one-sided P-value ≤0.05 (bold and underlined). Rhi: P-values from a logistic regression testing for an association between AFLP band frequency and altitude within the Rhine. Listed are all markers significant after Bonferroni correction (bold and underlined). Bold type only indicates P-values ≤0.05 but not significant after multiple test correction.
To investigate the possibility of repeated but weak patterns, all results are shown for the listed markers. Rhi Rhine, Rho Rhone, T Ticino, P Poschiavino, A-Rhi Alpine Rhine. NA marker monomorphic or containing too much missing data.

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ISSN: 2730-7182

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