DOI: 10.5061/dryad.fxpnvx0sq
title: Emergence and radiation of distemper viruses in terrestrial and marine mammals - Input files, bash and R codes for analysing PDV and CDV sequence data

description: Canine distemper virus (CDV) and phocine distemper virus (PDV) are major
 pathogens to terrestrial and marine mammals. Yet little is known about the
 timing and geographical origin of distemper viruses and to what extent it
 was influenced by environmental change and human activities. To address
 this, we i) performed the first comprehensive time-calibrated phylogenetic
 analysis of the two distemper viruses; ii) mapped distemper antibody and
 virus detection data from marine mammals collected between 1972-2018; iii)
 and compiled historical reports on distemper dating back to the 18th
 century. We find that CDV and PDV diverged in the early 17th century.
 Modern CDV strains last shared a common ancestor in the 19th century with
 a marked radiation during the 1930s-50s. Modern PDV strains are of more
 recent origin, diverging in the 1970s-80s. Based on the compiled
 information on distemper distribution, the diverse host range of CDV and
 basal phylogenetic placement of terrestrial morbilliviruses, we
 hypothesize a terrestrial CDV-like ancestor giving rise to PDV in the
 North Atlantic. Moreover, given the estimated timing of distemper origin
 and radiation, we hypothesize a prominent role of environmental change
 such as the Little Ice Age, and human activities like globalisation and
 war in distemper virus evolution.
description: The data sets were created by compiling recently
 published H gene PDV sequences and CDV sequence data obtained from NCBI.
 The first data (Alignment 1)
 set consists of 446 near-complete H gene sequences (25 PDV + 421 CDV
 sequences; 1,668 bp; position 7,199-8,866 in NC_001921) comprising the
 majority of distemper H gene sequences available in GenBank at the time of
 analysis (July 2020). The
 second data set (Alignment 2) represents the full sequences
 used in the Bayesian phylogenetic analyses. The alignment
 consists of 125 full-length H gene sequences (25 PDV and 100 CDV; 1,812
 bp; position 7,079-8,890 in NC_001921), representing major PDV and CDV
 clades in terrestrial and marine mammals detected between 1982-2018.
 Both data sets were imported
 and edited in Geneious version 9.1.8, the alignments were generated using
 MUSCLE and sequences were edited to the same reading frame and length
 excluding stop codons. Sequences obtained through the studies
 Stokholm et al, 2019 and Puryear et al, in review, have not been made
 publicly available yet but sequences have been submitted to genbank and
 will be released under the accession numbers OK104948-91 and
 MW581015-26. The third data set (Alignment 3) was used
 for the final Bayesian phylogenetic analyses. It consists of 125
 Hemagglutinin gene sequences (25 PDV sequences and 100 CDV sequences)
 without the 3rd codon positions (1,208 bp). The 3rd codon positions were
 removed due to the detection of substitution saturation.
 The bash codes included here were used for the following
 tasks:<br>  - Edit the input sequence names in the fasta
 file.<br>  - Edit the fasta files for excluding the third codon
 positions.<br>  - Submit many slurm jobs in parallel on a remote
 server, that can run BEAST v.2.6.3 in parallel for multiple xml files at
 once.<br> - Edit many xml files created in 'BEAuti' in
 order to be able to perform stepping stone (or pathsampling) analysis in
 order to obtain marginal likelihood values for each analysis of each xml
 file.<br>  - Collect the marginal likelihood values generated from
 each individual analysis.<br>  - Start multiple slurm jobs in
 'treeanotator' in parallel to get consensus tress.<br>  -
 Collect all consensus trees.<br>  <br> The R code included
 here was used to generate Supplementary Figure 3 
 "Rcode_for_making_Supplementary Figure_3_2021mar.R" based on
 "marginal_lkhoods_tmp08.txt". The code can be run in R v.4.0.2.
 It is used to plot a diagram that shows a summary of the tree age
 estimates and HPD 95 % intervals of CDV, PDV and CDV/PDV sequences of
 BEAST analyses using different setups. The tree ages are obtained from the
 consensus trees generated through the BEAST analysis of each xml
 file. Please note that all these pieces of code have
 been setup to run on a specific remote server. They will need to be
 adjusted in order to be able to run elsewhere.