Figure 5
Patterns of extended haplotype homozygosity in Ethiopia. Panels (a) and (b) present Manhattan plots of the Rsb-based cross-population extended haplotype homozygosity (EHH) illustrating regions of divergent selection between Ethiopia and Thailand and Indonesia. Putative signals are numbered. Briefly, putative drivers include; chloroquine resistance transporter (pvcrt, PvP01_0109300) and prodrug activation and resistance esterase (PvP01_011010) at signal 1, lysine specific histone demethylase (PVP01_0118300) at signal 2, peptide chain release factor 2 (PvP01_0309000) at signal 3, phosphoinositide-binding protein PX1 (PvP01_0316400) at signal 4, acyl-CoA-synthetase (PvP01_0409900) at signal 5, merozoite surface protein (MSP) 4 and 5 (PVP01_0418300, PVP01_0418400) at signal 6, zinc finger protein (PvP01_0517200) at signal 7, serine/threonine protein phosphatase (PvP01_0603400) at signal 8, pvkelch protein K10 (PvP01_0607800) at signal 9, a tRNA (PVP01_0711200) at signal 10, PvP01_0824800 and PvP01_1115800 (unknown functions) at signals 11 and 12, oligomeric golgi complex subunit 4 (PvP01_1133300) at signal 13, an MSP7-like gene cluster at signal 14, intergenic region at signal 15, actin related protein ARP4 (PvP01_1326200) at signal 16 and liver-specific protein (PvP01_1330800) at signal 17. Panel (c) illustrates the comparative decay in EHH in the pvcrt-o region of signal 1. The dashed vertical grey line indicates the position at which the peak Rsb score was observed. The pink shaded region denotes the pvcrt-o region. While the peak Rsb is not located within pvcrt-o, haplotype homozygosity appears to decay less rapidly upstream (i.e., in the direction of pvcrt-o) than downstream of the signal peak. Ethiopia retains moderate haplotype homozygosity (EHHS > 0.1) within the pvcrt-o region. Panel (d) presents a Manhattan plot of the integrated haplotype score (iHS) illustrating regions under recent directional selection in Ethiopia alone. Only a single peak was detected in an intergenic region at signal 18. The data was derived from analyses on independent samples from Ethiopia (n = 102), Indonesia (n = 110) and Thailand (n = 87).
