DOI: 10.5061/dryad.7wm37pw3k
title: Sharing pollinators and pollen-associated viruses: understanding the diversity of the pollen virome within a co-flowering community

description: 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.
description: # Sharing pollinators and pollen-associated viruses: understanding the
 diversity of the pollen virome within a co-flowering community #####
 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 &gt;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.