There are three important considerations when pooling specimens for hybridization during HybSeq:
- DNA library concentration
- Source material (fresh vs. herbarium tissue)
- Phylogenetic clustering
For this exercise, use the table below to design a pooling strategy for 53 Artocarpus specimens. For reference, use the previous phylogenetic treatment of Artocarpus from Zerega et al., 2010 (click here for the paper).
| Sample no. | genus | subgenus | species | library ng/uL | Sample type |
|---|---|---|---|---|---|
| 1 | Antiaropsis | descipiens | 0.887 | silica-dried | |
| 2 | Maclura | pomifera | 4.78 | silica-dried | |
| 3 | Hullettia | griffithiana | 5.12 | silica-dried | |
| 4 | Artocarpus | Artocarpus | chama | 8.6 | silica-dried |
| 5 | Artocarpus | Artocarpus | hispidus | 0.887 | silica-dried |
| 6 | Artocarpus | Artocarpus | maingayi | 1.21 | silica-dried |
| 7 | Artocarpus | Artocarpus | obtusus | 9.8 | silica-dried |
| 8 | Artocarpus | Pseudojaca | altissimus | 2.57 | silica-dried |
| 9 | Artocarpus | Artocarpus | scortechinii | 10.3 | silica-dried |
| 10 | Artocarpus | Artocarpus | treculianus | 1.57 | silica-dried |
| 11 | Artocarpus | Pseudojaca | hypargyraeus | silica-dried | |
| 12 | Artocarpus | Pseudojaca | dadah | 0.853 | silica-dried |
| 13 | Artocarpus | Pseudojaca | fulvicortex | 4.97 | silica-dried |
| 14 | Artocarpus | Pseudojaca | glaucus | 4.07 | silica-dried |
| 15 | Artocarpus | Pseudojaca | gomezianus | 5.3 | silica-dried |
| 16 | Artocarpus | Pseudojaca | nitidus | 5.43 | silica-dried |
| 17 | Artocarpus | Pseudojaca | cf lacucha | 1.89 | silica-dried |
| 18 | Artocarpus | Pseudojaca | nitidus | 2.73 | silica-dried |
| 19 | Artocarpus | Pseudojaca | ovatus | 0.867 | silica-dried |
| 20 | Artocarpus | Pseudojaca | pithecogallus | 10.7 | silica-dried |
| 21 | Artocarpus | Pseudojaca | tomentosulus | 14.1 | silica-dried |
| 22 | Artocarpus | Pseudojaca | tonkinensis | 6.23 | silica-dried |
| 23 | Artocarpus | Pseudojaca | vriesianus | 2 | silica-dried |
| 24 | Artocarpus | Prainea | papuana | 1.94 | silica-dried |
| 25 | Artocarpus | Pseudojaca | cf. dadah | 0.88 | silica-dried |
| 26 | Artocarpus | Pseudojaca | nitidus | 2.25 | silica-dried |
| 27 | Artocarpus | Pseudojaca | cf lacucha | 2.85 | silica-dried |
| 28 | Streblus | glaber | 2.01 | silica-dried | |
| 29 | Ficus | macrophylla | 4.94 | silica-dried | |
| 30 | Artocarpus | Artocarpus | mariannensis | 18.5 | silica-dried |
| 31 | Artocarpus | Artocarpus | melinoxylus | 11.3 | silica-dried |
| 32 | Artocarpus | Pseudojaca | hypargyraeus | 4.27 | herbarium |
| 33 | Artocarpus | Artocarpus | blancoi | 2.96 | herbarium |
| 34 | Artocarpus | Artocarpus | nobilis | 7.83 | herbarium |
| 35 | Artocarpus | Artocarpus | pinnatisectus MAYBE | 1.59 | herbarium |
| 36 | Artocarpus | Cauliflori | annulatus | 1.29 | herbarium |
| 37 | Artocarpus | Pseudojaca | nitidus ssp. nitidus | 0.549 | herbarium |
| 38 | Artocarpus | Artocarpus | sp. nov. | 1.74 | herbarium |
| 39 | Artocarpus | Probably Artocarpus | sp. nov. | 2.89 | herbarium |
| 40 | Artocarpus | Artocarpus | jarrettiae | 0.999 | herbarium |
| 41 | Artocarpus | Artocarpus | cf. lowii | 31 | herbarium |
| 42 | Artocarpus | Artocarpus | melinoxylus ssp melinoxylus | 11.2 | herbarium |
| 43 | Artocarpus | Artocarpus | multifidus | 8.44 | herbarium |
| 44 | Artocarpus | Artocarpus | sarawakensis | 2.61 | herbarium |
| 45 | Artocarpus | Pseudojaca | albobrunneus | 32.1 | herbarium |
| 46 | Artocarpus | Probably Pseudojaca | altissimus | 1.46 | herbarium |
| 47 | Artocarpus | Pseudojaca | longifolius | 8.22 | herbarium |
| 48 | Artocarpus | Pseudojaca | petelotii | 11.2 | herbarium |
| 49 | Artocarpus | Pseudojaca | rubrovenius | 12 | herbarium |
| 50 | Artocarpus | Pseudojaca | subrotundifolius | 3.53 | herbarium |
| 51 | Artocarpus | Pseudojaca | xanthocarpus | 1.23 | herbarium |
| 52 | Artocarpus | Pseudojaca | styracifolius | 1.59 | herbarium |
| 53 | Artocarpus | Artocarpus | horridus | 0.387 | herbarium |