Table 1.
Mitochondrial and microsatellite diversity statistics for parasites within chad (subdivided by host species) and among all four endemic countries.
Fig 1.
Distribution of mitochondrial haplotypes across Chad and among host species.
Distribution of mitochondrial haplotypes across the geographic range and host species sampled in Chad. Host species are indicated by point shape and mitochondrial haplotype by color. The map was generated with QGIS v2.18.13 [46]. River paths and national park boundaries were extracted from Landsat 8 imagery provided courtesy of the U.S. Geological Survey (http://glovis.usgs.gov/).
Table 2.
Mean pairwise divergence (p-distance) of mitochondrial lineages within and between dracunculid parasites.
Fig 2.
Phylogenetic relationship of African and North American Dracunculus spp. cox1 haplotypes.
Genealogical relationship among unique partial cox1 haplotypes found in a subset of African D. medinensis and North American D. insignis and D. lutrae (North American species sequences from [10]). Country of origin (for African samples) and parasite species are defined beside each branch. Definitive host species from which all or some of the parasite haplotypes were recovered are indicated by icons to the right of the tree. Trees were inferred in MrBayes v3.2.6 [36] with two independent MCMC analyses of 1 million generations each. Posterior probabilities indicated at branch nodes.
Fig 3.
Phylogenies of mitochondrial lineages illustrate that African D. medinensis are a single species.
(A) Genealogical relationship among unique D. medinensis haplotypes (concatenated cytB-cox3-nd3-nd5) from the four remaining endemic countries in Africa. Color and shape of tips indicate country of origin. Haplotypes where at least one parasite was collected from a non-human host are denoted with asterisks (*). (B) Relationship among unique D. medinensis haplotypes from Chad only. Circle size reflects prevalence of each haplotype in the Chadian population (smallest circles = 1) and color indicates the definitive host from which parasites were collected. Trees were inferred in MrBayes v3.2.6 [36] with two independent MCMC analyses of 1 million generations each. Posterior probabilities are indicated at branch nodes.
Fig 4.
PCoA and sPCA suggest geographic differentiation of Chadian D. medinensis but no differentiation by host species.
(A) PCoA of derived maternal genotypes for Chadian parasites. Point shape and color denote host species, and fill transparency indicates broad geographic origin of the parasite (northern or southern region). (B) Interpolation of lagged principal scores of the first component from the sPCA, plotted over the sampling area in Chad. Sampling locations of each parasite specimen are indicated by open circles, and genetic similarity is represented by color contours. The arrow in the lower left inset illustrates the clinal gradient in the context of the dominant geographic features of the sampling area. A barplot of the eigenvalues produced by the sPCA is shown in the upper right insert, illustrating the dominance of the first component within the sPCA.
Fig 5.
Inference of D. medinensis population subdivision among the four endemic countries.
(A) Posterior assignment of individual D. medinensis worms collected from the four endemic countries into K = 6 clusters of shared ancestry. (B) Assignment of worms from only Ethiopia and South Sudan into K = 4 clusters of shared ancestry. In both analyses, each bar represents an individual worm and color indicates proportional assignment to one or more clusters. Bar colors are only informative within each assignment analysis, not between the two. Most likely K was inferred using the TI method in MavericK v1.0 [26].
Fig 6.
Inference of D. medinensis subdivision among host species and geographic regions within Chad.
(A) Posterior assignment of all D. medinensis worms collected from within Chad into K = 2 clusters of shared ancestry, as inferred using the TI method in MavericK v1.0 to determine most likely K [26]. Each bar represents an individual worm and color indicates proportional assignment to one or more clusters. Individuals have been sorted by geographic region (i.e., north or south of Manda National Park) and definitive host species. (B) Assignment of worms when analysis is restricted by broad geographic region (i.e., north or south of Manda National Park) in MavericK v1.0. Northern worms were assigned into K = 2 clusters and worms from southern villages into K = 8 clusters. Within each geographic region, worms are sorted by village and definitive host species. Bar colors are only informative within each assignment analysis and should not be used for comparison among them. (C) Spatial clustering of individuals in BAPS v6.0 for most likely K = 16. Individual parasites plotted onto the map of the sampling area is depicted on the left, and Voronoi tessellation of clusters is illustrated on the right. Mapped point shape indicates host species and color indicates the cluster to which an individual was assigned. The map was generated with QGIS v2.18.13 [46]. River paths and national park boundaries were extracted from Landsat 8 imagery provided courtesy of the U.S. Geological Survey (http://glovis.usgs.gov/). Note that the cluster coloring scheme is not uniform between the mapped points and tessellation.
Table 3.
Analysis of molecular variance (AMOVA) of Chadian D. medinensis among host species and broad geographic origin.
Table 4.
Pairwise FST among mitochondrial haplotypes and pseudo-dominant microsatellite phenotypes in Chadian D. medinensis.
Table 5.
Pairwise FST Among derived maternal microsatellite genotypes in Chadian D. medinensis.
Fig 7.
Bayesian skyline plot of the Chadian D. medinensis population over time.
Derived from Chadian D. medinensis mitochondrial sequences (concatenated cytB-cox3-nd3-nd5, sampled from 2014ā2016). The x-axis is in years (0 to 2016 CE) and the y-axis is NeĻ (the product of the effective population size of female parasites and the generation time). Assuming a generation time of 1 year, this is equivalent to the effective population size of female parasites Nef. Analysis assumed a strict molecular clock and mutation rate of 1.57 x 10ā7 mutations per site per generation.