Table 1.
Summary statistics of laboratory populations.
Table 2.
Summary of variants used for comparison of laboratory and field collected schistosomes.
Fig 1.
Population structure in S. mansoni laboratory populations.
(A) PCA plot showing clustering of sequenced S. mansoni laboratory populations. (B) Admixture analysis with k = 5 populations.
Fig 2.
Comparable nucleotide diversity in field and laboratory populations.
(A) Average nucleotide diversity (π) across the whole genome for each laboratory population calculated in 25 kb windows and plotted for each autosome. The line indicates a LOESS smoothed curve. (B) Box and whisker plot showing nucleotide diversity (π) in 25 kb windows across the CDS in laboratory and field populations. Outliers are not shown. Wilcoxon tests compares π from laboratory and field populations (C) Histogram showing numbers of derived fixed alleles in each of the laboratory and field populations. Wilcoxon tests compares numbers of derived fixed alleles from laboratory and field populations.
Fig 3.
Indicators of recent bottlenecks in laboratory populations.
(A) Bar plots showing mean and standard error of Tajima’s D in each population. We used a Wilcoxon test to compare means of Tajima’s D in field and laboratory populations. (B) Line plot showing the empirical cumulative distribution function (ECDF) of allele frequencies in each population. A permutation-based Kolmogorov-Smirnov test was used to compare field vs laboratory distributions (see S4 Fig).
Fig 4.
Slower LD decay in laboratory populations.
(A) r2 showing LD decay with physical distance between all autosomal SNPs in laboratory populations and exonic SNPs in field populations along the chromosomes. The points show mean values calculated over 1 kb windows while the fitted lines show relationship between distance and LD decay in each population. The plots are on a log scale. (B) Bar plot showing position when r2 = 0.5 (LD0.5) for field and laboratory populations. A Wilcoxon test was used to compare LD0.5 in field and laboratory populations. S5 Fig shows LD calculated using exonic SNPs, while S6 Fig shows LD between unlinked markers on different chromosomes.
Fig 5.
Reduced effective population size in laboratory populations.
Bar plots showing effective population size Ne calculated with (A) NeEstimator and (B) COLONY. The y-axis is split to show both high and low Ne values clearly. The error bars represent a 95% confidence interval. We used Wilcoxon tests to compare Ne in laboratory and field populations. Infinite values were set to 100,000 for this purpose.
Table 3.
Nc, Ne estimates and ratios.
Fig 6.
Bottleneck simulation over 400 generations.
Line plot showing simulated reduction in genetic diversity of schistosome populations of different sizes over 400 generations. We used constant N ranging from 5 – 400. H0 indicates heterozygosity at time 0. The horizontal dashed line (38%) shows of the % reduction in diversity observed in our laboratory populations when compared to field populations.
Table 4.
Nucleotide diversity in Brugia malayi and B. pahangi.