Figure Legends
Figure 1. Map of the study areas and infection prevalence from 2005-2016. (A) Map of East Sepik and Madang study area villages and locations on the north coast of Papua New Guinea (inset) The graphs show the pre-LLIN (2005/6) and post-LLIN (2010-2014) molecular prevalence for (B) East Sepik and (C) Madang for both P. falciparum (light grey) and P. vivax (dark grey) and proportion of multiclonal infections (black line) (Arnott et al., 2013; Barry et al., 2013; Kattenberg et al., 2020; Koepfli et al., 2017; Koepfli et al., 2015; Mueller et al., 2009; Senn et al., 2012).
Figure 2. Changing diversity of P. falciparum andP. vivax populations over an intensifying period of malaria control (2005-2014). Allelic Richness (Rs ) in P. falciparum (A) (n= 860) and P. vivax (B) (n=755) populations pre- (≤2006) and post-LLIN (≥2010) mass-distributions. Error bars indicate standard deviations.
Figure 3. Genetic differentiation estimates among P. falciparum and P. vivax populations pre- and post-LLIN mass-distributions. Pairwise Jost’s D values for (A) P. falciparum and (B) P. vivax. Pairwise Jost’s D values and 95% confidence intervals were estimated with 1000 bootstraps using the diveRsity package in R. Pairwise FST values (Weir and Cockerham) are shown in figure S1.
Figure 4. Bayesian cluster analysis of P. falciparum (A) and P. vivax (B) of pre- (2005/6) and post-LLIN studies (2010-2014). Individual samples are sorted by province and year (solid lines), catchment area (dashed line) and cluster membership (colour). Madang catchments are organised as Malala, Mugil, Utu and ESP2 and 2012-13 as Brukham, Burui, Ilahita, Ulupu, and Wombisa (no infections in 2012). As identified in the genetic differentiation analysis (Jost’s D, Figure 3), there was moderate differentiation for P. falciparumbetween the ESP1 (Wosera area) 2005 and Madang 2006 versus the other studies (only one province included pre-LLIN), which is believed to be for a large part caused by experimental- and data analysis differences. Therefore, these P. falciparum studies were grouped separately for the population structure analysis, in order to avoid artificial changes in ancestry over time.
Figure 5. Unrooted neighbour-joining tree of P. vivax isolates in East Sepik province in 2012-13. Relatedness among haplotypes was defined by calculating the pairwise distance and neighbour-joining tree using the APE package in R and the tree was visualized using Phylocanvas through microreact.org (Argimon et al., 2016; ”Microreact,”). Colours and shapes indicate the village where the isolates were collected. Very closely related isolates are observed in the village of Sunuhu (dark grey circles).