Changes in Diversification Patterns and Signatures of Selection during the Evolution of Murinae-Associated Hantaviruses
Abstract
:1. Introduction
2. Results
2.1. Phylogenetic Analyses
2.2. Molecular Signatures of Selection
Methods | S segment (small dataset) | S segment (large dataset) | M segment | |||
---|---|---|---|---|---|---|
positively selected aa sites | percentage of negatively selected aa sites | positively selected aa sites | percentage of negatively selected aa sites | positively selected aa sites | percentage of negatively selected aa sites | |
SLAC | 43 * | 85% | 43 * | 90% | no site | 86% |
FEL | 43 * | 89% | no site | 92% | no site | 90% |
iFEL | 43 * | 88% | no site | 91% | no site | 90% |
FUBAR | 43 * | 98% | 43 * | 98% | no site | 97% |
MEME | 3, 4, 23, 39, 43 *, 69, 70, 71, 129, 183, 190, 209, 221, 233, 265, 313, 332, 334, 336, 357, 365, 369 | not tested | 2, 3, 4, 7, 23, 27, 39, 43 *, 69, 70, 75, 181, 209, 214, 221, 265, 310, 311, 312, 313, 326, 334, 336, 343, 365, 369, 396, 397, 398, 403, 405, 408 | not tested | 22, 29, 99, 189, 212, 208, 318, 340, 345, 377, 420, 461, 462, 540, 544, 635, 642, 643, 725, 766, 780, 810, 817, 821, 877, 942, 969, 995, 1003, 1048 | not tested |
2.3. Shifts in Diversification Rates and Patterns
2.4. Geographic Structuration Analyses
3. Discussion
3.1. Molecular Signatures of Selection
3.2. Co-Divergence between S and M Segments
3.3. Shifts in Diversification Rates
3.4. Ecological Drivers of the Diversification Rate Variability
3.5. Sampling Effects
4. Experimental
4.1. Sequences Acquisition
4.2. Molecular Signature of Selection
4.3. Phylogeny and Congruence between M and S Segment Trees
4.4. Phylogenetic Analyses
Model | Segment S | Segment M | ||
---|---|---|---|---|
LH | AIC | LH | AIC | |
Pure birth (Yule) | 537.98 | −1073.96 | 674.65 | −1347.31 |
Birth death (BD) | 540.18 | −1076.36 | 755.33 | −1506.7 |
4.5. Shifts in Diversification Rates and Patterns
4.6. Geographic Structuration Analyses
5.Conclusions
Supplementary Files
Acknowledgments
Author Contributions
Conflicts of Interest
References and Notes
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Castel, G.; Razzauti, M.; Jousselin, E.; Kergoat, G.J.; Cosson, J.-F. Changes in Diversification Patterns and Signatures of Selection during the Evolution of Murinae-Associated Hantaviruses. Viruses 2014, 6, 1112-1134. https://doi.org/10.3390/v6031112
Castel G, Razzauti M, Jousselin E, Kergoat GJ, Cosson J-F. Changes in Diversification Patterns and Signatures of Selection during the Evolution of Murinae-Associated Hantaviruses. Viruses. 2014; 6(3):1112-1134. https://doi.org/10.3390/v6031112
Chicago/Turabian StyleCastel, Guillaume, Maria Razzauti, Emmanuelle Jousselin, Gael J. Kergoat, and Jean-François Cosson. 2014. "Changes in Diversification Patterns and Signatures of Selection during the Evolution of Murinae-Associated Hantaviruses" Viruses 6, no. 3: 1112-1134. https://doi.org/10.3390/v6031112