Extended Data Table 2. MQM model of only main effects of 14 candidate morphological QTL on niche score.

The table summarises a main effects-only MQM model enforced to contain all the selected candidate morphological QTL for niche score (run in R/qtl: niche score as response variable, Haley-Knott regression, with F2 family covariate). Model terms (at left) are named according to LG locations of the candidate QTL, which were limited to the one best candidate per LG prior to modelling (see Methods). For each QTL (model term), the table also gives: map position in centimorgans (cM); nearest SNP marker; percentage of total variance explained (PVE) for niche score; F-test statistic; corresponding degrees of freedom (d.f.); and P-value. Significant model terms indicated as follows: * 0.01 ≤ P < 0.05; † 0.001 ≤ P < 0.01; and ‡ P < 0.001. Overall model results (abbreviations: SS, sum of squares; LOD, logarithm₁₀ of odds score): SS_model = 169.34; d.f._model = 56; SS_error = 464.09; d.f._error = 473; LOD_model = 35.80; PVE_model = 26.73%; P-value (F) = 2.91×10^-11.

Model term	Map location (cM)	Nearest SNP	PVE	F	d.f.	P-value (F)
LG1	36.00	chrI:25560380	0.52 %	1.688	2	0.185991
LG2†	12.00	chrII:10092618	1.69 %	5.470	2	0.004480†
LG4‡	28.76	ChrIV:10997988	2.34 %	7.542	2	0.000596‡
LG7‡	26.99	chrVII:19857837	3.28 %	10.58	2	3.21×10.05‡
LG8‡	18.00	chrVIII:16299555	3.74 %	12.08	2	7.63×10.06‡
LG9	28.38	chrIX:6126845	0.84 %	2.719	2	0.066968
LG10	4.00	chrX:1275840	0.66 %	2.121	2	0.121029
LG12	38.00	chrXII:15046849	0.57 %	1.846	2	0.159010
LG13*	20.00	chrXIII:17392141	1.16%	3.733	2	0.024619*
LG14	39.55	chrXIV:4632223	0.24 %	0.776	2	0.460631
LG16†	13.52	chrXVI:9981125	2.16%	6.989	2	0.001020†
LG17	12.00	chrXVII:2232080	0.03 %	0.109	2	0.896894
LG20*	14.62	ChrXX:9279241	1.43 %	4.630	2	0.010198*
LG21	18.00	chrXXI:11060209	0.33 %	1.080	2	0.340247