Table 3.
Results from the assignation of test samples using the genetic assignment software GeneClass2 (94)
| AMERICA | AFRICA | ||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| HB REFERENCE SET I | HB REFERENCE SET II | HB REFERENCE SET III | HB REFERENCE SET I | HB REFERENCE SET II | HB REFERENCE SET III | ||||||||||||
| Country | N | Sample ID | Country | N | Sample ID | Country | N | Sample ID | Country | N | Sample ID | Country | N | Sample ID | Country | N | Sample ID |
| Argentina | 47 | Argentina | 47 | Argentina | 47 | Kenya | 59 | Kenya | 59 | Kenya | 59 | ||||||
| 32 | AHB | 30 | AHB | 30 | A | 59 | SSA | 59 | SSA | 59 | A | ||||||
| 11 | EHB | 2 | EHB | 14 | C | Madagascar | 14 | Madagascar | 14 | Madagascar | 14 | ||||||
| 1 | PRHB | 0 | PRHB | 3 | O | 14 | SSA | 14 | SSA | 14 | A | ||||||
| 3 | SSA | 3 | SSA | Morocco | 25 | Morocco | 25 | Morocco | 25 | ||||||||
| 8 | EU DOM | 3 | AHB | 3 | AHB | 25 | A | ||||||||||
| 4 | US DOM | 22 | SSA | 22 | SSA | ||||||||||||
| Bolivia | 60 | Bolivia | 60 | Bolivia | 60 | Seychelles | 16 | Seychelles | 16 | Seychelles | 16 | ||||||
| 53 | AHB | 53 | AHB | 60 | A | 16 | AHB | 16 | AHB | 15 | A | ||||||
| 7 | SSA | 7 | SSA | 1 | O | ||||||||||||
| Costa Rica | 10 | Costa Rica | 10 | Costa Rica | 10 | South Africa | 52 | South Africa | 52 | South Africa | 52 | ||||||
| 10 | AHB | 10 | AHB | 10 | A | 52 | SSA | 52 | SSA | 52 | A | ||||||
| Mexico | 46 | Mexico | 46 | Mexico | 46 | Tunisia | 15 | Tunisia | 15 | Tunisia | 15 | ||||||
| 46 | AHB | 46 | AHB | 38 | A | 13 | AHB | 13 | AHB | 15 | A | ||||||
| 8 | O | 2 | SSA | 2 | SSA | ||||||||||||
| Panama | 36 | Panama | 36 | Panama | 36 | Zambia | 43 | Zambia | 43 | Zambia | 43 | ||||||
| 26 | AHB | 26 | AHB | 36 | A | 37 | SSA | 37 | SSA | 37 | A | ||||||
| 10 | SSA | 10 | SSA | 6 | EHB | 5 | EHB | 6 | O | ||||||||
| Puerto Rico, USA | 169 | Puerto Rico, USA | 169 | Puerto Rico, USA | 169 | 1 | carnica | ||||||||||
| 165 | PRHB | 164 | PRHB | 133 | O | ||||||||||||
| 4 | AHB | 4 | AHB | 32 | C | ||||||||||||
| 1 | US DOM | 4 | M | ||||||||||||||
| USA | 99 | USA | 99 | USA | 99 | ||||||||||||
| 4 | AHB | 2 | AHB | 82 | C | ||||||||||||
| 65 | EHB | 14 | EHB | 17 | O | ||||||||||||
| 30 | PRHB | 2 | PRHB | ||||||||||||||
| 11 | EU DOM | ||||||||||||||||
| 70 | US DOM | ||||||||||||||||
| EUROPE | ASIA | ||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| HB REFERENCE SET I | HB REFERENCE SET II | HB REFERENCE SET III | HB REFERENCE SET I | HB REFERENCE SET II | HB REFERENCE SET III | ||||||||||||
| Country | N | Sample ID | Country | N | Sample ID | Country | N | Sample ID | Country | N | Sample ID | Country | N | Sample ID | Country | N | Sample ID |
| Italy | 42 | Italy | 42 | Italy | 42 | Israel | 20 | Israel | 20 | Israel | 20 | ||||||
| 34 | EHB | 23 | EHB | 6 | A | 20 | EHB | 8 | EHB | 13 | C | ||||||
| 1 | PRHB | 0 | PRHB | 36 | C | 2 | EU DOM | 7 | O | ||||||||
| 1 | AHB | 0 | AHB | 10 | US DOM | ||||||||||||
| 6 | SSA | 6 | SSA | Rep. Georgia | 26 | Rep. Georgia | 26 | Rep. Georgia | 26 | ||||||||
| 1 | EU DOM | 26 | EHB | 26 | anatoliaca | 26 | O | ||||||||||
| 12 | US DOM | Turkey | 73 | Turkey | 73 | Turkey | 73 | ||||||||||
| Malta | 10 | Malta | 10 | Malta | 10 | 73 | EHB | 64 | anatoliaca | 68 | O | ||||||
| 7 | AHB | 4 | AHB | 8 | O | 8 | EHB | 5 | C | ||||||||
| 1 | EHB | 6 | US DOM | 2 | C | 1 | US DOM | ||||||||||
| 2 | PRHB | ||||||||||||||||
| Portugal | 8 | Portugal | 8 | Portugal | 8 | ||||||||||||
| 8 | AHB | 8 | iberiensis | 8 | M | ||||||||||||
| Spain | 4 | Spain | 4 | Spain | 4 | ||||||||||||
| 4 | AHB | 4 | iberiensis | 4 | M | ||||||||||||
Samples were genotyped with the 251 SNPs in common with the reference samples from a total 272 SNPs in the Fluidigm assay. Assignations of the unknown samples are to the closest available in the two reference sets of samples given as input to GeneClass2. Reference Set I. Avalos et al. [84] (30 PRHB from Puerto Rico; 28 AHB from Mexico and 30 EHB from Hawaii); Wallberg et al. [53] (10 AHB from Brazil and 10 each of three species from Africa (SSA, Sub Saharan Africa), A. m. adansonii, A. m. scutellata, and A. m. capensis). Reference Set II. The above data plus the remaining samples from Wallberg et al. [53]; A. m. anatoliaca (10); A. m. mellifera EU Domestic (20); A. m. mellifera US Domestic (10); A. m. carnica (10); A. m. iberiensis (10), A. m. ligustica (10); A. m. syriaca (10), A. m. mellifera, Sweden, Norway, Europe (20). Reference Set III. Collapsed populations of main groups from Wallberg et al. [53]; Group M: A. m. mellifera, Sweden (10), Norway, Europe (10), A. m. iberiensis (10); Group C: A. m. ligustica (10), A. m. carnica (10); Group O: A. m. anatoliaca (10), A. m. syriaca (10); Group A: A. m. adansonii (10), A. m. scutellata (10), and A. m. capensis (10). Genotype data from the three sets of reference samples were run separately along with the genotypes of the unknown worldwide collection of HB test samples as input for GeneClass2. Group categories follow Wallberg et al. [53]
AHB African honey bee, EHB European honey bee, PRHB Puerto Rico honey bee, SSA Sub-Saharan African honey bee, US DOM United States domestic honey bee, EU DOM European domestic honey bee