Sharing pollinators and pollen-associated viruses: understanding the diversity of the pollen virome within a co-flowering community
Data files
Jun 25, 2025 version files 35.82 KB
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PollenVirome_Correlations.csv
715 B
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PollenVirome_CorrelationsNoOutliers.csv
580 B
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PollenVirome_HostPlants.tre
732 B
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PollenVirome_ModelSelectionPagelsInput.csv
1.49 KB
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PollenVirome_ModelSelectionPagelsRCode.R
11.63 KB
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PollenVirome_Nodes.csv
324 B
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PollenVirome_PlantPhylogeny.csv
806 B
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PollenVirome_PlantPhylogenyRCode.R
1.54 KB
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PollenVirome_PlantPlantNetworkInput.csv
322 B
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PollenVirome_PlantPlantNetworkRCode.R
1.40 KB
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PollenVirome_PlantTraitPCAInput.csv
985 B
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PollenVirome_PlantTraitPCARCode.R
1.60 KB
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PollenVirome_PlotLifeHistory.csv
918 B
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PollenVirome_SamplingCorrelationRCode.R
2.20 KB
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README.md
10.57 KB
Abstract
Co-flowering plant species frequently share pollinators, flower-inhabiting bacteria, and fungi, but whether pollen-associated viruses are shared is unknown. Given that pollen-associated viruses are sexually transmitted diseases, their diversity is expected to increase with pollinator sharing. We conducted a metagenomic study to identify pollen-associated viruses from 18 co-flowering plant species to determine whether 1) life history, floral traits, or pollination generalism were associated with viral richness, and 2) plants shared pollen-associated viruses. We demonstrated that pollination generalism influences pollen-associated virus richness and the extent of pollen virus sharing between plant species. We also revealed that perenniality, multiple flowers, and bilateral floral symmetry were associated with high pollen viral richness locally, confirming and extending patterns observed previously at a continental scale. Our results highlight the importance of plant-pollinator interactions as drivers of plant-viral interaction diversity.
November 26, 2024; updated May 30, 2025 and June 2, 2025
This Dryad repository contains all data and R code for “Sharing Pollinators and Viruses: Virus Diversity of Pollen in a Co-Flowering Community” by Fetters et al.
Plant trait input data and PCA R code
PollenVirome_PlantTraitPCAInput.csv contains floral and pollen grain trait data that was measured on 10 flowers per plant species by Wei et al. (2021) and used to conduct the principal component analysis (PCA) described in the manuscript.
List of variables:
Plant_species: the names of the 18 focal plant species
Flower_shape: general morphology of the flowers of a plant species; open (aster-like, coded as 0) vs. closed (labiate or salverform, coded as 1)
Flower_symmetry: symmetry of the flowers of a plant species; radial (coded as 0) vs. bilateral (coded as 1)
Flower_restrictiveness: whether the flower shape of a plant species restricts access to its floral rewards; unrestrictive (coded as 0) vs. restrictive (coded as 1)
Inflorescence_type: type of floral display presented by a plant species; single flower or flowers spaced far apart on a stem (coded as 0) vs. multiple flowers (coded as 1)
Flower_tube_length: distance from the ovaries to the beginning of the flower tube (petal separation) of the flowers of a plant species; 0 for plant species whose flowers do
not have tubes; units = mm
Flower_size: diameter of the flowers of a plant species, measured across their longest length; units = mm
Pollen_grain_texture: texture of the pollen grain exines of a plant species; smooth (psilate or granulate, coded as 0) vs. spiky (echinate, coded as 1)
Pollen_grain_length: diameter of the pollen grains of a plant species, measured across their longest length; units = mm
PollenVirome_PlantTraitPCARCode contains the code necessary to conduct the principal component analysis (PCA) described in the manuscript, view the output, and create biplots.
Plant phylogeny input data and R code
PollenVirome_PlantPhylogeny.csv contains the species names, as well as the plant genus and family to which they belong
List of variables:
species: the names of the 18 focal plant species
genus: the plant genus to which a plant species belongs
family: the plant family to which a plant species belongs
PollenVirome_PlantPhylogenyRCode contains the code necessary to build and visualize the plant phylogeny included in the model building, selection, and averaging processes described in the manuscript.
Sampling correlation input data and R code
PollenVirome_Correlations.csv contains the conservative and relaxed estimate of pollen-associated virus richness, the number of individuals from which pollen was collected, the number of flowers from which pollen was collected, and the number of genomes in the subtraction libraries published in Fetters (2021) for each focal plant species.
PollenVirome_CorrelationsNoOutliers.csv contains the same information as PollenVirome_Correlations.csv; however, plant species for which >100 individuals or flowers were sampled were removed.
List of variables:
Plant_species: the names of the 18 focal plant species
Conservative_estimate: the number of known viruses, coding-complete novel viral genomes, and coding-complete novel viral variants published in Fetters (2021)
Relaxed_estimate: the conservative number of viruses, plus those identified by their RNA-dependent RNA polymerase (RdRp) conserved domains (CDs) from both partial viral genomes and variants published in Fetters (2021)
Number_individuals: the number of individual plants from which pollen was collected in May 2018 in McLaughlin Natural Reserve, Lower Lake, CA, USA
Number_flowers: the number of flowers from which pollen was collected in May 2018 in McLaughlin Natural Reserve, Lower Lake, CA, USA
Subtraction_library_size: the number of genomes from the National Center for Biotechnology Information (NCBI) database included in the subtraction libraries for each focal plant species published in Fetters (2021)
PollenVirome_SamplingCorrelationRCode contains the code for correlating (with and without outliers) the conservative and relaxed estimates of pollen-associated virus richness with: subtraction library size, each other, number of individuals from which pollen was collected, and the number of flowers from which pollen was collected.
Model selection, model averaging, and Pagel’s lambda input data and R code
PollenVirome_ModelSelectionPagelsInput.csv contains, for each focal plant species, the plant family to which a focal plant species belongs, the dependent variables (conservative and relaxed estimates of pollen-associated virus richness) for the model selection and average process described in the manuscript, the possible independent variables (PC1, PC2 [generated by the PCA above], pollinator partner diversity [published in Wei et al. [2021]], and life history [coded as 0 = annual [one reproductive episode] or 1 = perennial [multiple reproductive episodes]]), and the number of flowers from which pollen was collected as a co-variate.
List of variables:
Plant_species: the names of the 18 focal plant species
Family: the plant family to which a plant species belongs
Conservative_estimate_richness: the number of known viruses, coding-complete novel viral genomes, and coding-complete novel viral variants published in Fetters (2021)
Relaxed_estimate_richness: the conservative number of viruses, plus those identified by their RNA-dependent RNA polymerase conserved domains from both partial viral genomes and variants published in Fetters (2021)
Number_flowers: the number of flowers from which pollen was collected in May 2018 in McLaughlin Natural Reserve, Lower Lake, CA, USA
PC1: floral and pollen grain trait PC values for each plant species, generated by the PCA above
PC2: floral and pollen grain trait PC values for each plant species, generated by the PCA above
Partner_diversity: derived from multiple pollinator observations per week from April to June of 2016 and 2017 published in Wei et al. (2021)
Life_history: whether a plant species is an annual (one reproductive episode during its lifetime, coded as 0) or a perennial (multiple reproductive episodes over its lifetime, coded as 1)
Similarly, PollenVirome_PlotLifeHistory.csv contains the information necessary to plot the relationship between the categorical variable “life history” (whether a plant species is an annual or perennial) and the number of pollen-associated viruses it has.
List of variables:
Conservative_estimate_richness: the number of known viruses, coding-complete novel viral genomes, and coding-complete novel viral variants published in Fetters (2021)\
Relaxed_estimate_richness: the conservative number of viruses, plus those identified by their RNA-dependent RNA polymerase conserved domains from both partial viral genomes and variants published in Fetters (2021)
Life_history: whether a plant species is an annual (one reproductive episode during its lifetime) or a perennial (multiple reproductive episodes over its lifetime)
Plant_species: the names of the 18 focal plant species\
Family: the plant family to which a plant species belongs
PollenVirome_HostPlants.tre is the tree file for the plant phylogeny generated above used for the phylogenetically controlled model selection and averaging processes described in the manuscript.
PollenVirome_ModelSelectionPagelsRCode contains the code necessary to define all possible models explaining the conservative and relaxed estimates of pollen-associated virus richness, selecting the best models, averaging the best models that differ by two or less in their Akaike Information Criterion corrected for small sample sizes (AICc), and plot the results. It also contains the code to calculate Pagel’s lambda for both estimates of pollen-associated virus richness, the two PCs, pollinator partner diversity, and the number of flowers.
Pollen-associated virus sharing plant-plant network input data and R code
PollenVirome_PlantPlantNetworkInput.csv contains the number of pollen-associated viruses that each pair of plants shares. This file helps to create the plant-plant network topology.
List of variables:
plant1: one part of a pair of plants that shares a number of pollen-associated viruses
plant2: the other part of a pair of plants that shares a number of pollen-associated viruses
viruses: the number of pollen-associated viruses that a pair of plants shares
PollenVirome_Nodes.csv contains the number of viruses that a plant species shares with other plants, as well as a plant species’ pollinator Shannon diversity and number of viruses in the relaxed estimate of pollen-associated viruses that a plant has. This file helps to scale and label the nodes and color the edges of the network.
List of variables:
Plant: the four-letter species code for a focal plant species; created by combining the first two letters of the genus name with the first two letters of the species name
Viruses: the number of viruses that a focal plant species shares with other plant species in the network
Pollinator_Shannon_diversity: derived from multiple pollinator observations per week from April to June of 2016 and 2017 published in Wei et al. (2021)
Conservative: the number of known viruses, coding-complete novel viral genomes, and coding-complete novel viral variants published in Fetters (2021)
Relaxed: the conservative number of viruses, plus those identified by their RNA-dependent RNA polymerase conserved domains from both partial viral genomes and variants published in Fetters (2021)
PollenVirome_PlantPlantNetworkRCode contains the code necessary to create the plant-plant pollen-associated virus sharing network described in the manuscript. It also contains code for correlating the number of shared pollen-associated viruses with pollinator partner diversity and the conservative and relaxed estimates of pollen-associated virus richness.
Literature cited
Fetters, A. M. 2021. Exploring the ecological drivers of the pollen virome. University of Pittsburgh ProQuest Dissertations and Theses 30841941.
Wei, N., R. L. Kaczorowski, G. Arceo-Gómez, E. M. O’Neill, R. A. Hayes, and T.-L. Ashman. 2021. Pollinators contribute to the maintenance of flowering plant diversity. Nature 597: 688 – 692.