Computational protocol: Molecular Surveillance for Lymphoproliferative Disease Virus in Wild Turkeys (Meleagris gallopavo) from the Eastern USA

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Protocol publication

[…] We performed a phylogenetic analysis on 184 partial p31/capsid (CA) sequences of all LPDV strains recovered from wild turkeys in the USA during the period 2009–2013 (58 previously published sequences and 126 newly obtained here), combined with the prototype Israeli strain recovered in 1978. These sequences were aligned in MUSCLE [] which resulted in a final data set of 185 sequences, 413 nt in length. A maximum likelihood (ML) phylogeny was then estimated using PhyML 3.0 [] and employing the GTR+Gamma+Proportion Invariant (GTR+G+I) model of nucleotide substitution, with all parameter values estimated from the data in hand, and utilizing a combination of nearest neighbor interchange (NNI) and subtree pruning and regrafting (SPR) branch-swapping. To infer support for individual nodes, a bootstrap analysis was conducted using 1000 replicate ML trees, using the nucleotide substitution model specified above and NNI branch-swapping.To determine the extent of phylogeographic structure in the data—that is, whether there is more phylogenetic clustering by US state of sampling than expected by chance alone—we employed two phylogeny-trait association tests: the Association Index (AI) and Parsimony Score (PS), both of which are available in the BaTS package []. In addition, we used the Maximum Clade (MC) statistic to determine which individual US states showed the strongest spatial clustering. Phylogenetic uncertainty in the data was incorporated through the use of the posterior distribution of trees determined from a Bayesian Markov chain Monte Carlo analysis undertaken using the BEAST package []. For this analysis we employed the GTR+G+I substitution model as above, a constant population size prior, and a relaxed uncorrelated lognormal molecular clock, which was run for 100 million generations. Finally, we performed 1000 random permutations of sampling locations to create a null distribution for each BaTS statistic. […]

Pipeline specifications

Software tools MUSCLE, PhyML, BEAST
Applications Phylogenetics, Nucleotide sequence alignment
Organisms Meleagris gallopavo
Diseases Lymphoproliferative Disorders, HIV Infections