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Open Access Highly Accessed Research article

Molecular evolution and phylogenetics of rodent malaria parasites

Ricardo S Ramiro1*, Sarah E Reece123 and Darren J Obbard13

Author Affiliations

1 Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, United Kingdom

2 Institute of Immunology and Infection Research, University of Edinburgh, Edinburgh, United Kingdom

3 Centre for Immunity, Infection and Evolution, University of Edinburgh, Edinburgh, United Kingdom

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BMC Evolutionary Biology 2012, 12:219  doi:10.1186/1471-2148-12-219

Published: 14 November 2012

Additional files

Additional file 1:

Summary of the rodent malaria parasite genotypes used. Lines in bold represent clones. Location: CAM - Cameroon; CAR - Central African Republic; CON - Congo; DRC - Democratic Republic of the Congo; NIG - Nigeria. Mixed infection: nk - not known; Pcc - P. c. chabaudi; Pv - P. vinckei; Pvp - P. v. petteri; Pyk - P. y. killicki; Pysp - P. y. subsp.; Pyy - P. y. yoelii. ? - information is uncertain. Note that where isolate and arrival dates are equal is because infected T. rutilans were shipped to Edinburgh.

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Additional file 2:

Posterior probabilities for the speciation models sampled by BPP, using the different algorithms and fine-tune parameters (ε,a and m). Priors were kept constant: θ~G(1.5,300) and τ0~G(1.5,30). Each speciation model is represented using 0–1 flags for the interior nodes, with 0 indicating a collapsed node and 1 a resolved node. Nodes are ordered as in Figure 1, with the first flag corresponding to node a, the second to node b, and so on up to node l. Each cell has the posterior probability for two replicate runs of BPP, which started with different speciation models. NS: model not sampled.

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Additional file 3:

Posterior probabilities for the speciation models sampled by BPP, using different values for theθ prior. We used algorithm 0 with fine-tune ε = 5 for this analysis. Speciation model and cell content are as described for Additional file 2.

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Additional file 4:

Ensemble genealogical sorting index (gsiT) for the independently evolving lineages identified by BPP.

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Additional file 5:

Population sizes for the rodent malaria subspecies as inferred by *BEAST. Point estimates (and 95% HPDs) are shown for each calibration. Pb - P. berghei; Pca - P. c. adami; Pcc - P. c. chabaudi; Pcsp - P. c. subsp.; Pvb - P. v. brucechwatti; Pvl - P. v. lentum; Pvp - P. v. petteri; Pvsp - P. v. subsp.; Pvv - P. v. vinckei; Pyk - P. y. killicki; Pyn - P. y. nigeriensis; Pysp - P. y. subsp.; Pyy - P. y. yoelii.

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Additional file 6:

Pairwise comparisons ofπA,πSandπASacross taxa.p-values for pairwise Wilcoxon tests with Bonferroni corrections are shown. p < 0.05 are highlighted in bold. b - P. berghei, c - P. chabaudi, cc - P. c. chabaudi, v - P. vinckei, vp - P. v. petteri, y - P. yoelii, yy - P. y. yoelii.

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Additional file 7:

Summary of the analysis of polymorphism and divergence in the four species of rodent malaria across the 11 loci. n - number of genotypes analysed; MK - McDonald-Kreitman test; * represents statistically significant MK tests or Tajima's D; estimates in bold are outliers in Figure 2. Variation in the number of sequenced genotypes (Table 2) and an absence of polymorphism and/or divergence in some taxa meant we could not obtain these statistics for every gene in all lineages.

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Additional file 8:

Best likelihood models and estimates of the proportion of adaptive substitutions across loci (α¯). Divergence was measured to the inferred ancestral sequence of the P. chabaudi-P. vinckei clade (P. c. chabaudi and P. v. subsp.) or the P. berghei-P. yoelii clade (P. y. yoelii). The best (highest Akaike weight) and secondary models are shown, with Akaike weights in brackets. Estimates of α¯ (and 95% CI) across loci were obtained from 1000 bootstraps on the results of model ii. Likelihood models: i) α is constrained to zero at all loci, i.e. no adaptive evolution; ii) α is a free-parameter common to all loci; and iii) α can take a different value at each locus.

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Additional file 9:

Species tree inferred by *BEAST under the Pacheco2011-A calibration. Node labels are posterior probabilities and node bars represent 95% Highest Posterior Densities on the height of each node. Axis is in million years ago (Mya).

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Additional file 10:

Summary of the analysis of polymorphism and divergence for the subspecies of rodent malaria across the 11 loci. Legend as for Additional file 7.

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Additional file 11:

Primer sequences (5’-3’) used in PCR for the selected loci. PCR cycling conditions: 95°C for 3 min.; 10 cycles of: 94°C for 30s, 57°C for 30s (−1°C per cycle), 72°C for 1.5 min.; 35 cycles of: 94°C for 30s, 47°C for 30s, 72°C for 1.5 min.; 72°C for 3 min.

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Additional file 12:

Gene tree inferred by BEAST fordhfr. Node labels are posterior probabilities. We chose to present the dhfr gene tree, as this is one of the locus for which we obtained sequence data for more isolates (56, as for rnabind) and for which node support was stronger. This is an example of the gene trees we obtained and we note that the branch lengths and their order may not be the same as for the multi-locus analysis or other gene trees. Therefore, the gene tree does not necessarily reflect relatedness between genotypes within each subspecies.

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