Table 2.

Parameters and Output Summary of BAYESCAN Sensitivity Test

Species	BAYESCAN Model Parameters	Total No. Dominant DArT Markers	No. Markers Included in BS Analysis	F IS Prior (Uniform between… )	Prior Odds	No. Outliers Detected by BS Analysis	Max Outlier Q Value a	% of Input	Outlier FST Mean	Nonoutlier FST Mean	Stringency
E. tricarpa	Default	6,544	3,684	0–1	10	131	0.049	3.50	0.3312	0.1368	Low
E. tricarpa	BS-recommended PO + generic eucalypt FIS ( Byrne 2008 )	6,544	3,684	0.01–0.3 b	100	94	0.050	2.60	0.3210	0.1200	Medium
E. tricarpa	Relatively high BS-recommended PO + generic eucalypt F IS (Byrne 2008)	6,544	3,684	0.01–0.3 b	200	80	0.0571	2.22	0.3305	0.1206	Medium
E. tricarpa	High PO (Lotterhos and Whitlock 2014) + generic eucalypt F IS (Byrne 2008)	6,544	3,684	0.01–0.3 b	3,685	41	0.044	1.10	0.3210	0.1238	High
E. loxophleba	Default	4,851	3,530	0–1	10	62	0.047	1.80	0.2456	0.0663	Low
E. loxophleba	BS-recommended PO + species-specific F IS (Byrne 2008)	4,851	3,530	0.01–0.08 c	100	50	0.047	1.40	0.2159	0.0443	Medium
E. loxophleba	Relatively high BS-recommended + species-specific F IS (Byrne 2008)	4,851	3,530	0.01–0.08 c	200	45	0.044	1.28	0.2236	0.0444	Medium
E. loxophleba	High PO (Lotterhos and Whitlock 2014) + species-specific FIS	4,851	3,530	0.01–0.08 c	3,531	50	0.050	1.40	0.2160	0.0440	Medium–high
E. loxophleba	BS-recommended PO + generic eucalypt F IS (Byrne 2008)	4,851	3,530	0.01–0.3	100	49	0.047	1.39	0.2286	0.0480	Medium–high
E. loxophleba	Relatively high BS-recommended + species-specific F IS (Byrne 2008)	4,851	3,530	0.01–0.3	200	44	0.043	1.25	0.2365	0.0482	Medium–high
E. loxophleba	High PO (Lotterhos and Whitlock 2014) + generic eucalypt F IS (Byrne 2008)	4,851	3,530	0.01–0.3	3,531	32	0.034	0.90	0.2616	0.0487	High
E. salubris lineage 1	Default	16,122	14,949	0–1	10	43	0.048	0.20	0.2141	0.0517	Low
E. salubris lineage 1	Low PO + generic eucalypt F IS (Byrne 2008)	16,122	14,949	0.01–0.3 b	100	22	0.046	0.15	0.1933	0.0341	Medium
E. salubris lineage 1	BS-recommended PO + generic eucalypt FIS ( Byrne 2008 )	16,122	14,949	0.01–0.3 b	200	18	0.043	0.12	0.2164	0.0371	Medium
E. salubris lineage 1	High PO (Lotterhos and Whitlock 2014) + generic eucalypt F IS (Byrne 2008)	16,122	14,949	0.01–0.3 b	14,950	7	0.007	0.04	0.2730	0.0370	High
E. salubris lineage 2	Default	16,122	8,089	0–1	10	33	0.049	0.40	0.3196	0.0874	Low
E. salubris lineage 2	BS-recommended PO + generic eucalypt FIS ( Byrne 2008 )	16,122	8,089	0.01–0.3 b	100	17	0.047	0.20	0.3284	0.0672	Medium
E. salubris lineage 2	Relatively high BS-recommended PO + generic eucalypt F IS (Byrne 2008)	16,122	8,089	0.01–0.3 b	200	13	0.0517	0.16	0.3507	0.0673	Medium–high
E. salubris lineage 2	High PO (Lotterhos and Whitlock 2014) + generic eucalypt F IS (Byrne 2008)	16,122	8,089	0.01–0.3 b	8,090	8	0.015	0.10	0.3997	0.0677	High

Note.—Bold rows represent the sets of outlier markers that were used in the mapping and colocation analyses.

^aThe Q value is the false discovery rate (FDR) analog of a P-value; it is the minimum FDR at which a locus may become significant. A Q value of 0.05 means that 5% of outliers (i.e., those having a Q value ≤0.05) are expected to be falsely positive. A 5% threshold for Q values is much more stringent than a 5% threshold for P values in classical statistics (Foll 2012).

^bNo species-specific information available—F _IS prior based on estimated average value for eucalypts (Byrne 2008).

^cF _IS for E. loxophleba ca. 0.046 (Byrne 2008).