Table 1 Incongruent groupings of the two haplotypes in individuals L4-L11.

Individual	Analyzed phased segments	Incongruent phased segments	Different patterns of incongruence	Observed patterns of incongruence
L4	303	9	7	L5-L9 (1), L5-L11 (1), L6-L7 (1), L6-L8 (1), L6-L11 (3), L7-L11 (1), L10-L11 (1)
L5	303	9	8	L4-L7 (1), L4-L9 (1), L4-L10 (2), L6-L9 (1), L6-L10 (1), L6-L11 (1), L7-L11 (1), L9-L10 (1)
L6	303	13	9	L4-L10 (1), L5-L8 (2), L5-L9 (1), L7-L10 (2), L7-L11 (1), L8-L9 (1), L8-L10 (1), L8-L11 (3), L9-L11 (1)
L7	303	4	2	L4-L8 (1), L5-L9 (3)
L8	303	11	8	L4-L5 (1), L4-L7 (1), L5-L7 (1), L5-L10 (1), L6-L7 (1), L6-L9 (2), L6-L11 (3), L9-L10 (1)
L9	303	5	5	L4-L8 (1), L5-L10 (1), L5-L11 (1), L6-L8 (1), L7-L8 (1)
L10	303	7	6	L4-L9 (1), L4-L11 (2), L5-L6 (1), L6-L7 (1), L7-L8 (1), L7-L11 (1)
L11	303	7	6	L4-L7 (1), L5-L6 (1), L5-L8 (2), L6-L10 (1), L7-L8 (1), L7-L9 (1)

For each individual, we computed the number of phased segments such that the reciprocal closest counterparts of the two haplotypes were found in two different individuals (see “Methods” section). Only incongruent groupings of the two haplotypes with strong bootstrap support (≥70%) were considered. The numbers of identified incongruent segments along with the numbers of different patterns of incongruence observed for each individual, L4-L11, are shown. For each individual, each unique pair of other individuals harboring reciprocal closest counterparts of its two haplotypes at least at one locus constitutes a separate pattern of incongruence. The patterns of incongruence observed for each individual are listed, with the number of segments for which each pattern was observed given in parentheses. For this analysis, we used the segments of the A. vaga genome harboring at least 15 non-singleton SNPs simultaneously phased in all individuals L4-L11. Segments with more than two highly similar hits (≥90% identity) in the L1 genome, as well as segments harboring multiple paralogous regions were removed from this analysis. In total, out of the 303 analyzed phased genomic segments, 52 exhibited incongruent groupings of the two haplotypes at least in one individual with strong bootstrap support. Overall numbers of occurrences for each pattern of incongruence listed in the rightmost column are shown in Supplementary Table 19.

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