Many-core algorithms for statistical phylogenetics

Viruses in the Ebolavirus and Marburgvirus genera (family Filoviridae) have been associated with large outbreaks of hemorrhagic fever in human and nonhuman primates. The first documented cases occurred in primates over 45 years ago, but the amount of virus genetic diversity detected within bat populations, which have recently been identified as potential reservoir hosts, suggests that the filoviruses are much older. Here, detailed Bayesian coalescent phylogenetic analyses are performed on 97 whole-genome sequences, 55 of which are newly reported, to comprehensively examine molecular evolutionary rates and estimate dates of common ancestry for viruses within the family Filoviridae. Molecular evolutionary rates for viruses belonging to different species range from 0.46 ؋ 10 ؊4 nucleotide substitutions/site/year for Sudan ebolavirus to 8.21 ؋ 10 ؊4 nucleotide substitutions/site/year for Reston ebolavirus. Most recent common ancestry can be traced back only within the last 50 years for Reston ebolavirus and Zaire ebolavirus species and suggests that viruses within these species may have undergone recent genetic bottlenecks. Viruses within Marburg marburgvirus and Sudan ebolavirus species can be traced back further and share most recent common ancestors approximately 700 and 850 years before the present, respectively. Examination of the whole family suggests that members of the Filoviridae, including the recently described Lloviu virus, shared a most recent common ancestor approximately 10,000 years ago. These data will be valuable for understanding the evolution of filoviruses in the context of natural history as new reservoir hosts are identified and, further, for determining mechanisms of emergence, pathogenicity, and the ongoing threat to public health.

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“…This is especially true for more-variable genes, like the glycoprotein gene, that undergo strong purifying selection (26,51).…”

Section: Resultsmentioning

confidence: 99%

Molecular Evolution of Viruses of the Family Filoviridae Based on 97 Whole-Genome Sequences

Carroll

Towner

Sealy

et al. 2013

J Virol

153

129

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“…We used relaxed molecular clock and fossil calibrations to obtain time-calibrated phylogenies by: (i) running 50 independent RAXML searches with the best partition scheme to obtain a ML estimate of phylogeny; (ii) selecting the best tree model in many-core parallel BEAST v. 1.6.1 [39,40] with the ML phylogeny as the starting tree; and (iii) applying the best tree model in parameter and tree searches in BEAST. The best fit between the pure-speciation (Yule) and birth-death (speciationextinction) model was evaluated in BEAST by running 20 million generations in MCMCMC searches.…”

Section: Methodsmentioning

confidence: 99%

Morphological innovation, diversification and invasion of a new adaptive zone

et al. 2011

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How ecological opportunity relates to diversification is a central question in evolutionary biology. However, there are few empirical examples of how ecological opportunity and morphological innovation open new adaptive zones, and promote diversification. We analyse data on diet, skull morphology and bite performance, and relate these traits to diversification rates throughout the evolutionary history of an ecologically diverse family of mammals (Chiroptera: Phyllostomidae). We found a significant increase in diversification rate driven by increased speciation at the most recent common ancestor of the predominantly frugivorous subfamily Stenodermatinae. The evolution of diet was associated with skull morphology, and morphology was tightly coupled with biting performance, linking phenotype to new niches through performance. Following the increase in speciation rate, the rate of morphological evolution slowed, while the rate of evolution in diet increased. This pattern suggests that morphology stabilized, and niches within the new adaptive zone of frugivory were filled rapidly, after the evolution of a new cranial phenotype that resulted in a certain level of mechanical efficiency. The tree-wide speciation rate increased non linearly with a more frugivorous diet, and was highest at measures of skull morphology associated with morphological extremes, including the most derived Stenodermatines. These results show that a novel stenodermatine skull phenotype played a central role in the evolution of frugivory and increasing speciation within phyllostomids.

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“…Bayesian phylogenetic analyses were performed in BEAST v. 1.7.1 [6] using BEAGLE [13]. We used the HKY85 þ G substitution model, and the uncorrelated lognormal model of changes in substitution rate [6], and partitioned our alignment by codon position [14].…”

Section: Methodsmentioning

confidence: 99%

Molecular dating of human-to-bovid host jumps by Staphylococcus aureus reveals an association with the spread of domestication

et al. 2012

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).Host species switches by bacterial pathogens leading to new endemic infections are important evolutionary events that are difficult to reconstruct over the long term. We investigated the host switching of Staphylococcus aureus over a long evolutionary timeframe by developing Bayesian phylogenetic methods to account for uncertainty about past host associations and using estimates of evolutionary rates from serially sampled whole-genome data. Results suggest multiple jumps back and forth between human and bovids with the first switch from humans to bovids taking place around 5500 BP, coinciding with the expansion of cattle domestication throughout the Old World. The first switch to poultry is estimated at around 275 BP, long after domestication but still preceding large-scale commercial farming. These results are consistent with a central role for anthropogenic change in the emergence of new endemic diseases.

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Many-core algorithms for statistical phylogenetics

Cited by 390 publications

References 30 publications

Molecular Evolution of Viruses of the Family Filoviridae Based on 97 Whole-Genome Sequences

Molecular Evolution of Viruses of the Family Filoviridae Based on 97 Whole-Genome Sequences

Morphological innovation, diversification and invasion of a new adaptive zone

Molecular dating of human-to-bovid host jumps by Staphylococcus aureus reveals an association with the spread of domestication

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