Fig. 3: Hidden Markov model SNP categories of Daphnia magna temporal subpopulations separated by time in OHZ pond in Belgium. | Nature Communications

Fig. 3: Hidden Markov model SNP categories of Daphnia magna temporal subpopulations separated by time in OHZ pond in Belgium.

From: Extensive standing genetic variation from a small number of founders enables rapid adaptation in Daphnia

Fig. 3

a Genomic differentiation (FST) along scaffold 00512, the longest scaffold in the reassembled D. magna genome, between the pre-fish and the high-fish subpopulation. b Genomic differentiation (FST) along scaffold 00512 between the high-fish and the reduced-fish subpopulation. Patterns in other scaffolds are similar. c Box-plots showing the significant reduction (Mann–Whitney U test, upper tailed, statistic = 173,517.5, P value = 9.78E-20) in average length of HMM-detected islands of divergence between the pre-fish to high-fish (n = 6111;minima: 0.70, maxima: 4.80, center: 2.95, Q1: 2.50, Q3: 3.41; lower fence: 1.15, upper fence: 4.73) and high-fish to reduced-fish (n = 2879; minima: 0.60, maxima: 4.81, center: 2.83; Q1: 2.36, Q3: 3.26; lower fence: 1.04, upper fence: 4.58), outliers are defined as the data points more than three times of the interquartile range above Q3 or below Q1 transitions. d Histogram representing the overlap coefficient for all the overlapping HMM-detected islands of high divergence. The high values for the overlap coefficient suggest a high overlap between the islands of divergence between the two transitions. e An example illustrating the reduction in length of a HMM-detected island of divergence from the larger island of divergence in the pre-fish to high-fish transition (top) to a substantially smaller island in the high-fish to reduced-fish transition (bottom). f Example of reshuffling of a HMM-detected island of divergence in the pre-fish to high-fish transition (top) to the high-fish to reduced-fish transition (bottom). The stars in plots a, b and e, f indicate outlier SNPs. Red regions in plots a, b indicate overlapping islands of high divergence, whereas yellow regions indicate nonoverlapping (i.e., transition-specific) islands of high divergence. The pink boxes in plot e, f demarcate the HMM-detected island of divergence. The blue and orange boxes in plots e, f demarcate regions that harbor SNPs that are likely targeted by selection, or that are likely impacted by hitchhiking, respectively.

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