The first arriving virus shapes within-host viral diversity during natural epidemics
Data files
Sep 06, 2023 version files 5.68 KB
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allData.RData
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README.md
Abstract
Viral diversity has been discovered across scales from host individuals to populations. However, the drivers of viral community assembly are still largely unknown. Within-host viral communities are formed through coinfections, where the interval between the arrival times of viruses may vary. Priority effects describe the timing and order in which species arrive in an environment, and how early colonizers impact subsequent community assembly. To study the effect of the first-arriving virus on subsequent infection patterns of five focal viruses, we set up a field experiment using naïve Plantago lanceolata plants as sentinels during a seasonal virus epidemic. Using joint species distribution modelling, we find both positive and negative effects of early season viral infection on late season viral colonization patterns. The direction of the effect depends on both the host genotype and which virus colonized the host early in the season. It is well-established that co-occurring viruses may change the virulence and transmission of viral infections. However, our results show that priority effects may also play an important, previously unquantified role in viral community assembly. The assessment of these temporal dynamics within a community ecological framework will improve our ability to understand and predict viral diversity in natural systems.
README: ViralCommHmsc
This repository accompanies the manuscript "The first arriving virus shapes within-host viral community assembly during natural epidemics" by Maija Jokinen et al. and provides the R scripts and their initial input data that are required to reproduce the manuscript's Hmsc joint species distributional modelling results.
Variables:
- PLANT ID The plant individual that the community sample came from
- Timepoint Sampling timepoints 1 = early season timepoint T1, 2,3,4 = late season timeperiod, pooled for the analysis T2,T3,T4
- Plant ID The plant individual that the community sample came from
- CLOSTERO Presence/absence (1/0) of Closterovirus
- ENAMO Presence/absence (1/0) of Enamovirus
- BETAPARTITI Presence/absence (1/0) of Betapartitivirus
- PLV Presence/absence (1/0) of PLV
- CAULIMO Presence/absence (1/0) of Caulimovirus
- Transplant population Population the plant was kept for the experiment (1 = 877, 2 = 3302, 3 = 9031, 4 = 433)
- Host genotype Name of the maternal plant used for cloning (1 = 511_14, 2 = 609_19, 3 = 2818_6, 4 = 4_13)
- Number of leaves Number of leaves at the beginning of the experiment
- Lenght Length of the longest leaf
- Width Width of the longest leaf
- Leaf area A=pi* ab, where a and b are half axis of the ellipse (i.e, a= Lenght/2 and b=Width/2)
- Plant area Leaf area*Leaves
- Herbivory 1 if the plant had herbivory damage when sample was taken, 0 if not
Disclaimer: The code in this repository may still undergo revisions.
Authors: The scripts were adapted by Mirkka Jones from Hmsc course scripts 2020 written by Hmsc-developers Otso Ovaskainen, Jari Oksanen, and others, of which later versions are available at https://www.helsinki.fi/en/researchgroups/statistical-ecology/software/hmsc
Contacts:
Mirkka Jones at helsinki.fi.
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