Selected article for: "data set and prior rate"
Author: Mordecai, Gideon J; Wilfert, Lena; Martin, Stephen J; Jones, Ian M; Schroeder, Declan C
Title: Diversity in a honey bee pathogen: first report of a third master variant of the Deformed Wing Virus quasispecies
  • Document date: 2015_11_17
    • ID: k2n6ropo_30
    Snippet: In addition, a Bayesian analysis of the polyprotein encoding region of the sequences was carried out using an MCMC model, permitting a molecular clock model to be run within BEAST v1.8.1 (Figure 3 ) (Drummond et al., 2012) . Divergence times were calculated based on a tip-dated coalescent model, with an evolutionary rate prior based on three independent tip-dated fragments of DWV type A. The samples in the tree span 11 years (2000) (2001) (2002) .....
    Document: In addition, a Bayesian analysis of the polyprotein encoding region of the sequences was carried out using an MCMC model, permitting a molecular clock model to be run within BEAST v1.8.1 (Figure 3 ) (Drummond et al., 2012) . Divergence times were calculated based on a tip-dated coalescent model, with an evolutionary rate prior based on three independent tip-dated fragments of DWV type A. The samples in the tree span 11 years (2000) (2001) (2002) (2003) (2004) (2005) (2006) (2007) (2008) (2009) (2010) (2011) , and the samples used for estimating the evolutionary rate span 11, 13 and 22 years for the RdRp-, capsidand lp-fragments, respectively. The Bayesian tree of the nucleotide sequences had a similar structure to the amino acid tree, showing that the Type C viral variant is distinct from type A and B. The molecular clock estimation predicts that Type C diverged from the other DWV variants 319 years ago (57-1010 95% highest posterior density), and type A and B disassociated from each other 181 years ago (38-497 95% highest posterior density). This estimate is unlikely to be biased by substitution saturation, as there is no evidence for saturation in our data set (Xia et al., 2003) .

    Search related documents:
    Co phrase search for related documents
    • amino acid and bayesian tree: 1, 2, 3
    • amino acid and BEAST run: 1
    • amino acid and clock model: 1, 2
    • amino acid and coalescent model: 1, 2
    • amino acid and divergence time: 1, 2, 3, 4, 5, 6
    • amino acid tree and bayesian tree: 1
    • amino acid tree and BEAST run: 1
    • amino acid tree and clock model: 1
    • amino acid tree and coalescent model: 1
    • bayesian analysis and BEAST run: 1
    • bayesian analysis and clock model: 1, 2
    • bayesian analysis and coalescent model: 1, 2
    • bayesian analysis and divergence time: 1, 2
    • bayesian tree and BEAST run: 1
    • bayesian tree and clock estimation: 1, 2
    • bayesian tree and clock model: 1, 2, 3, 4
    • bayesian tree and coalescent model: 1
    • BEAST run and clock model: 1
    • clock model and coalescent model: 1, 2, 3, 4, 5