Genomic signatures of relaxed disruptive selection associated with speciation reversal in whitefish

Table 2 Number of selection candidate loci identified using Dfdist and BayeScan within individual lake flocks (global comparisons)

Species Flock	# Species	# Individuals	# Poly. Loci	# Candidate loci Dfdist		Total	# Candidate loci BayeScan		Total	Shared Loci	% Similarity
				≥ 0.95	≥ 0.99		≥ 0.5	≥ 1
Neuchâtel	2	14	241	5	0	5	2	0	2	2	40
Biel	2	13	262	1	1	2	0	0	0	0	0
Thun	5	35	306	18	4	22	3	1	4	4	18
Brienz	3	16	216	9	2	11	1	1	2	2	18
Lucerne	3	26	266	9	2	11	3	0	3	2	18
Constance	5	30	279	4	1	5	0	0	0	0	0
Walen	2	17	229	2	2	4	2	0	2	2	50
Zuerich	2	18	230	5	3	8	3	1	4	4	50
Maggiore	2	14	223	11	2	13	1	2	3	3	23
			Total	64	17	81	15	5	20

Presented are the numbers of species, individuals and polymorphic AFLP loci comprising each species flock data set. Identified Dfdist outlier loci are grouped according to how many fell between the 95% and 99% quantiles (≥ 0.95), and how many fell above the 99% quantile (≥ 0.99). BayeScan outlier loci are grouped by their Bayesian posterior probability of being under selection (Log₁₀ Bayes factor scores): “substantial” 0.5 to 1 (≥ 0.5), “strong” 1 to 1.5 (≥ 1). Also shown: the number of AFLP loci identified as selection candidates by both outlier detection methods and the overall similarity between sets of candidate loci recovered in Dfdist and in BayeScan, for each species flock.

ISSN: 2730-7182