| Initial definition of the 53 (35%) putative hybrids |
A1 |
‘High’ genome-wide heterozygosity (>=0.004) |
initial indicator for putative hybrids |
46 |
30% |
BPK157A1, BUMM3, CH32, CH34, CUK10, CUK11, CUK12, CUK2, CUK3, CUK4, CUK5, CUK6, CUK7, CUK8, CUK9, EP, GE, GEBRE1, GILANI, Inf055, Inf152, ISS174, ISS2426, ISS2429, LdonLV9, LEM3472, LRC-L53, LRC-L61, LRC-L740, Malta33, MAM, SUDAN1, SUKKAR2, 1026–8, 1S, 356WTV, 363SKWTI, 364SPWTII, 38-UMK, 383WTI, 45-UMK, 452BM, 597–2, 597LN, 762L, 855–9 |
| A2 |
‘Admixed’ between groups (admixture analysis) |
initial indicator for putative hybrids |
15 |
10% |
BPK512A1, CH32, CH34, CL-SL, EP, GE, Inf152, L60b, LEM3472, LRC-L1311, LRC-L1312, LRC-L1313, LRC-L740, MAM, OVN3 |
| Detailed investigation of the 53 (35%) putative hybrids |
B1 |
Heterozygous sites distributed relatively evenly across the genome and allele frequency profiles match coverage based somy estimates |
putative patterns of sexual crossing (F1/F2+), however, cannot be verified without identified putative parents; alternative explanation could be new mutations that are dominating the sample population through a recent bottleneck (e.g. cloning) |
18 |
12% |
Inf055, GEBRE1, LdonLV9, LRC.L61, SUDAN1, 1026–8, 1S, 356WTV, 363SKWTI, 364SPWTII, 38-UMK, 383WTI, 45-UMK, 452BM, 597–2, 597LN, 762L, 855–9 |
| B2 |
Evidence for parents between different groups (or between two distinct strains as previously shown for the CUK samples) alternating in the genome in a block like pattern |
putative patterns of sexual crossing (F2+), that is ‘hybrids’ |
16 (+1) |
10% (11%) |
CH32, CH34, CUK10, CUK11, CUK12, CUK2, CUK3, CUK4, CUK5, CUK6, CUK7, CUK8, CUK9, EP, GE, LEM3472, (LRC-L740) |
| B3 |
Extreme allele frequency variants only |
mixture of two different high versus low frequency clones or low frequency new mutations distributed across haplotypes in the sample |
7 |
5% |
BPK157A1, Inf152, ISS174, ISS2426, ISS2429, LRC-L53, MAM |
| B4 |
Intermediate peak allele frequency distributions including extreme frequency peaks |
mixture of scenarios B1 and B3, that is as B3 but high frequency clone has heterozygous sites itself |
4 |
3% |
BUMM3, LRC-L740, Malta33, SUKKAR2 |
| B5 |
no clear peak pattern of allele frequencies (several peaks at atypical frequencies) |
mixture of several clones |
1 |
0.01% |
GILANI |
| B6 |
to few heterozygous sites present to draw further conclusions beyond admixture results |
signatures are shadowed by too little segregating variation |
7 |
5% |
BPK512A1, CL-SL, L60b, LRC-L1311, LRC-L1312, LRC-L1313, OVN3 |
