Emergence and radiation of distemper viruses in terrestrial and marine mammals - Input files, bash and R codes for analysing PDV and CDV sequence data

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,...

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Bibliographic Details
Main Authors: Stokholm, Iben, Puryear, Wendy, Sawatzki, Kaitlin, Wilhelm Knudsen, Steen, Terkelsen, Thilde, Becher, Paul, Siebert, Ursula, Tange Olsen, Morten
Format: Other/Unknown Material
Language:unknown
Published: Zenodo 2021
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Online Access:https://doi.org/10.5281/zenodo.5539996
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Summary: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 18 th century. We find that CDV and PDV diverged in the early 17 th century. Modern CDV strains last shared a common ancestor in the 19 th 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. Funding provided by: Velux Fonden Crossref Funder Registry ID: http://dx.doi.org/10.13039/100008397 Award Number: 123012 Funding provided by: Innovationsfonden Crossref Funder Registry ID: http://dx.doi.org/10.13039/100012774 Award Number: 6180-00001B and 6180-00002B Funding provided by: Forschungszentrum Jülich GmbH, German Federal Ministry of Education and Research* Crossref Funder Registry ID: Award Number: FKZ 03F0767A Funding provided by: Academy of Finland Crossref Funder Registry ID: http://dx.doi.org/10.13039/501100002341 Award Number: 311966 Funding provided by: Stiftelsen för Miljöstrategisk Forskning Crossref Funder Registry ID: http://dx.doi.org/10.13039/100007633 Award Number: