Altered gene expression and ecological divergence in sibling allopolyploids of Dactylorhiza (Orchidaceae)

Table 3 Transcriptomic patterns under environmental selection.

cDNA fragment¹	Fragment present always and only in^2,3	Environmental factor⁴	G test		Spearman test
			P-value	Q-value	r _s	P-value
M41	Dm	BIO8	0.000099	0.0103	0.87	0.0005
		SunpVII	0.0022	0.027	0.64	0.03
M16	Dm from Alps and Scandinavia	BIO8	0.00015	0.0103	0.84	0.001
M59	Britain (Dt and De)	BIO8	0.00015	0.0103	-0.84	0.001
		SunpVII	0.00015	0.0103	-0.85	0.001
M38	Dm from Alps and	VapPres	0.00015	0.0103	-0.84	0.001
	Scandinavia	SunpIII	0.00015	0.0103	0.85	0.001
M12	-	BIO1	0.00033	0.0108	-0.78	0.005
M82	-	BIO8	0.00033	0.0108	-0.78	0.005
M4	Scandinavia (Dm and Dt)	BIO13, BIO16	0.00033	0.0108	-0.78	0.005
M37	-	SunpIII	0.00033	0.0108	0.79	0.004
M43	-	SunpVII	0.00033	0.0108	0.79	0.004
M58	Scotland (Dt and De)	SunpVII	0.00033	0.0108	-0.79	0.004
M18	-	BIO8	0.00043	0.013	0.84	0.001
M62	-	SunpVII	0.0011	0.017	-0.79	0.004
M1	Dt from Britain	SunpIII	0.0012	0.017	-0.68	0.02
M33	Pyrenees (Dm)	SunpIII, SunpVII, BIO1	0.0012	0.017	0.68	0.02
M65	All except Pyrenees	SunpIII, SunpVII, BIO1	0.0012	0.017	-0.68	0.02
M10	Alps (Dm)	BIO1, VapPres	0.0012	0.017	-0.68	0.02
M80	All except Alps	BIO1, VapPres	0.0012	0.017	0.68	0.02
M3	Dm from Scandinavia	BIO8	0.0012	0.017	0.68	0.02
M84	-	BIO13, BIO16	0.0012	0.017	-0.68	0.02
M44	All except De	VapPres	0.0012	0.017	-0.68	0.02
M57	De	VapPres	0.0012	0.017	0.68	0.02
M29	-	VapPres	0.0015	0.019	-0.75	0.008
M39	-	SunpVII	0.0015	0.019	0.76	0.007
		VapPres	0.0044	0.048	-0.79	0.004
M61	-	SunpVII	0.0015	0.019	-0.76	0.007
M36	-	SunpIII	0.0022	0.027	0.72	0.01
M20	-	BIO8	0.0041	0.045	0.79	0.004
M32	-	BIO8	0.0041	0.045	0.79	0.004

Details of the 27 cDNA-AFLP patterns most likely to drive adaptation to divergent environments, together with the corresponding environmental variables involved, as indicated by the likelihood ratio (G) test implemented in SAM [58]. Significance measurements for the regressions have been adjusted for multiple testing into Q-values according to Storey [70]. We report here only relationships with Q values < 0.05. As a way to report effect size for each significant regression we also report Spearman's r_s, following recommendations of Nakagawa [68]. Several environmental parameters show a degree of correlation, complicating attempts to identify the variable that may exert greatest selective pressure. The underlined markers are novel in allopolyploids (i.e. absent from the parents).
¹For details on cDNA-AFLP markers see http://dx.doi.org/10.5061/dryad.8795 or additional file 1.
²The patterns reported in this column refer only to polyploidy individuals.
³Dm - D. majalis; De - D. ebudensis; Dt - D. traunsteineri.
⁴BIO1 - annual mean temperature; BIO8 - mean temperature of wettest quarter; BIO13 - precipitation of wettest month; BIO16 - precipitation of wettest quarter; VapPres - yearly averages for vapour pressure (in hPa); SunpIII - % of maximum sunlight hours in March; SunpVII - % of maximum sunlight hours in July.

ISSN: 2730-7182