Table 3.
CNVs showing evidence of population-specific adaptation. Only those CNVs that either had FST greater than 0.30 or which showed significant transmission intensity-related clines in population frequency are shown
| CNV name | CNV type | FSTa | Clineb | Annotationsc |
|---|---|---|---|---|
| cnv5_101 | Amplification | 0.64 | - *** | 6-cysteine protein (P38) SET domain protein, putative (SET9) |
| cnv12_413 | Amplification | 0.64 | -* | |
| cnv9_242 | Amplification | 0.44 | P1 nuclease, putative | |
| cnv13_478 | Deletion | 0.46 | - † | E1-E2 ATPase, putative |
| cnv9_254 | Deletion | 0.41 | protein phosphatase-beta thioredoxin-like protein 2 (TLP2) zinc binding protein (Yippee), putative histone deacetylase 1 (HDAC1) | |
| cnv3_051 | Amplification | 0.34 | circumsporozoite- and TRAP-related protein (CTRP) | |
| cnv3_036 | Amplification | 0.32 | -† | Plasmodium exported protein (hyp1), unknown function (GEXP21) |
| Plasmodium exported protein, unknown function | ||||
| Plasmodium exported protein, unknown function | ||||
| cnv6_129 | Deletion | 0.30 | ubiquitin-conjugating enzyme E2, putative polypyrimidine tract binding protein, putative | |
| cnv4_078 | Amplification | 0.30 | -† | |
| cnv11_354 | Deletion | 0.27 | Plasmodium exported protein (PHISTc), unknown function (GEXP12) | |
| Plasmodium exported protein (hyp11), unknown function | ||||
| Plasmodium exported protein, unknown function | ||||
| cnv11_355 | Deletion | 0.18 | -*** | antigen 332, DBL-like protein (Pf332) |
| cnv9_269 | Deletion | 0.27 | -*** | gametocyte development protein 1 (GDV1) |
| Plasmodium exported protein, unknown function (GEXP22) | ||||
| gametocytogenesis-implicated protein (GIG) | ||||
| Plasmodium exported protein, unknown function | ||||
| cytoadherence linked asexual protein 9 (CLAG9) | ||||
| ring-exported protein 1 (REX1) | ||||
| ring-exported protein 2 (REX2) | ||||
| early transcribed membrane protein (ETRAMP9) | ||||
| ring-exported protein 4 (REX4) | ||||
| virulence-associated protein 1 (VAP1) | ||||
| Plasmodium exported protein (PHISTc), unknown function | ||||
| (GEXP05) | ||||
| lysophospholipase, putative | ||||
| Plasmodium exported protein (PHISTc), unknown function | ||||
| Plasmodium exported protein (PHISTb), unknown function | ||||
| Plasmodium exported protein, unknown function | ||||
| lysophospholipase, putative | ||||
| cnv1_007 | Amplification | 0.26 | -** | tubulin-specific chaperone a, putative N-acetyltransferase, putative |
| cnv14_549 | Amplification | 0.21 | -*** | thioredoxin peroxidase 1 (Trx-Px1) copper transporter |
| cnv11_355 | Deletion | 0.18 | - *** | antigen 332-DBL-like protein (Pf332) |
| cnv2_023 | Deletion | 0.14 | -* | conserved Plasmodium membrane protein, unknown function |
| cnv12_368 | Deletion | 0.07 | -* | glycerol-3-phosphate dehydrogenase, putative |
aMaximum of pairwise population FST values
bSignificance of transmission intensity cline in CNV frequency after Benjamini-Hochberg correction for multiple testing. (†, P < 0.10;*, P < 0.05;**, P < 0.01;***, P < 0.001; +, positive association; −, negative association). Four further CNVs had clines with adjusted P < 0.10 but FST < 0.3 and so are not shown (three amplifications, cnv9_262, − †; cnv5_109, + †; cnv14_573, − †, and one deletion, cnv7_193, − †)
cExcluding genes with no known or putative function