DOI: 10.5061/dryad.2ngf1vhwv
title: Ant handling changes myrmecochore seed coat microbiomes and alters diversity of seed-borne plant pathogenic fungi

description: The putative benefits to seeds in myrmecochory (ant-mediated seed
 dispersal) are often cast in a reward context. However, microbes have been
 mostly overlooked as seed mortality agents in myrmecochory, as have
 potential treatments provided by ant-handling. We investigated the effects
 of ant handling on the diversity of seed coat fungal communities of three
 myrmecochorous plant species. Ant-handling altered measures of both alpha
 and beta diversity of fungal communities. Ant-handled seeds harbored
 different overall fungal communities and plant pathogen communities than
 non-ant-handled seeds. The myrmecochore pathogenic fungal community showed
 high dissimilarity (high pairwise community turnover) between ant-handled
 and control seeds, while beta diversity measures for ant-handled seeds and
 seeds with manually-removed elaiosomes were less dissimilar. Ant handling
 may offer an additional benefit to myrmecochorous seeds via the reduction
 of the seed coat pathogenic community, which may be driven by elaiosome
 removal or as a byproduct of ant cleaning behaviors and chemical
 secretions. 
description: # Ant handling changes myrmecochore seed coat microbiomes and alters
 diversity of seed-borne plant pathogenic fungi
 The following are
 associated with this manuscript: **Alpha Diversity R Scripts (for all
 fungi, animal pathogens, plant pathogens, and myrmecochore pathogens)**
 AlphaDiveristy_All_Fungi.R * This is the R script for analyzing the Alpha
 Diversity (using Hill numbers via HillR) for all fungal taxa associated
 with seed washes AlphaDiveristy_Myrmecochore_Paths.R * This is the R
 script for analyzing the Alpha Diversity (using Hill numbers via HillR)
 for all fungal taxa identified as pathogenic to myrmecochores associated
 with seed washes AlphaDiveristy_Plant_Paths.R * This is the R script for
 analyzing the Alpha Diversity (using Hill numbers via HillR) for all
 fungal taxa identified as pathogenic to plants associated with seed washes
 AlphaDiversity_Animal_Paths.R * This is the R script for analyzing the
 Alpha Diversity (using Hill numbers via HillR) for all fungal taxa
 identified as pathogenic to animals associated with seed washes **Beta
 Diversity R Scripts (for all fungi, animal pathogens, plant pathogens, and
 myrmecochore pathogens)** BetaDiveristy_AnimalPaths.R * This is the R
 script for analyzing the Beta Diversity (calculated as community turnover
 using Hill numbers via HillR) for all fungal taxa identified as pathogenic
 to animals associated with seed washes BetaDiversity_AllFungi.R * This is
 the R script for analyzing the Beta Diversity (calculated as community
 turnover using Hill numbers via HillR) for all fungal taxa associated with
 seed washes BetaDiversity_MyrmecochorePaths.R * This is the R script for
 analyzing the Beta Diversity (calculated as community turnover using Hill
 numbers via HillR) for all fungal taxa identified as pathogenic to
 myrmecochores associated with seed washes BetaDiversity_PlantPaths.R *
 This is the R script for analyzing the Beta Diversity (calculated as
 community turnover using Hill numbers via HillR) for all fungal taxa
 identified as pathogenic to plants associated with seed washes **RDA R
 Scripts (for all fungi, animal pathogens, plant pathogens, and
 myrmecochore pathogens)** RDA_AllFungi.R * This is the R script for
 analyzing the Beta Diversity (as a distance-based redundancy analysis
 using vegan) for all fungal taxa associated with seed washes while
 controlling for seed type RDA_AnimalPathogens.R * This is the R script for
 analyzing the Beta Diversity (as a distance-based redundancy analysis
 using vegan) for all fungal taxa identified as pathogenic to animals
 associated with seed washes while controlling for seed type
 RDA_MyrmeochorePathogens.R * This is the R script for analyzing the Beta
 Diversity (as a distance-based redundancy analysis using vegan) for all
 fungal taxa identified as pathogenic to myrmecochores associated with seed
 washes while controlling for seed type RDA_PlantPathogens.R * This is the
 R script for analyzing the Beta Diversity (as a distance-based redundancy
 analysis using vegan) for all fungal taxa identified as pathogenic to
 plants associated with seed washes while controlling for seed type
 **Qiime2 Pipeline for sequence processing and rarefaction**
 Qiime2_ITS_To_Taxonomy_Pipeline * This is the Qiime2 Pipeline from real
 sequence reads through the processing of those reads
 Qiime2_RarefiedTable_Pipeline_toFunGuild * This is the Qiime2 Pipeline
 from processed and trimmed reads to rarefied samples to taxonomic
 assignment of ASVs though FunGuild **Associated Excel datafiles for above
 scripts** For all excel files, the following abbreviations are true: * For
 Samples- BR indicates a bloodroot seed wash; WG indicates a wild ginger
 seed wash; JD indicates a twinleaf seed wash; A indicates an ant-handled
 seed wash; C indicates a control seed wash; CE indicates a no elaiosome
 seed wash (in which the elaiosome was sterilely, manually removed; numbers
 indicate replicates (1-16) * For Seed_Type- Bloodroot indicates a
 bloodroot seed wash (*Sanguinaria canadensis)*; WildGinger indicates a
 wild ginger seed wash (*Asarum canadense)*; Twinleaf indicates a twinleaf
 seed wash (*Jeffersonia diphylla) * * Treatment- Ant indicates an
 ant-handled seed wash; Control indicates a control seed wash;
 ControlNoElaiosome indicates a no elaiosome seed wash (in which the
 elaiosome was sterilely, manually removed) * For Ant samples only:
 ColonyCode indicates the individual colony that handled the seeds;
 ColonySize indicates the number of worker ants in that colony;
 ColonyLocation indicates where that colony was collected from;
 HandlingScore is a numerical scale from 1 (no ant handling of seeds) to 5
 (all seeds were handled by ants and all elaiosomes were removed by ants).
 * All other columns without clear names (i.e., random letters and numbers)
 indicate Amplicon Sequence Variants (ASVs) and thus are a unique fungal
 species KingFungiTablewithTax * See above for column descriptors. Numbers
 in each row under each ASVs indicate the abundance of that ASV in that
 sample. Rows indicate a sample. This is the complete fungal data
 KingFungiTablewithTax_AnimalPathogens_DummyCode * See above for column
 descriptors. Numbers in each row under each ASVs indicate the abundance of
 that ASV in that sample. Rows indicate a sample. This is only the fungi
 ASVs that were identified as Animal Pathogens. There is an additional
 column (Dummy_OTU) with an abundance of 1 for all samples to deal with
 zero data (no animal pathogens in some samples) in dbRDA analyses.
 KingFungiTablewithTax_AnimalPathogens_Remove0s * See above for column
 descriptors. Numbers in each row under each ASVs indicate the abundance of
 that ASV in that sample. Rows indicate a sample. This is only the fungi
 ASVs that were identified as Animal Pathogens. In this dataset used for
 beta diversity, samples with no animal pathogens were removed for analysis
 KingFungiTablewithTax_PlantPathogens_DummyCode * See above for column
 descriptors. Numbers in each row under each ASVs indicate the abundance of
 that ASV in that sample. Rows indicate a sample. This is only the fungi
 ASVs that were identified as Plant Pathogens. There is an additional
 column (Dummy_OTU) with an abundance of 1 for all samples to deal with
 zero data (no plant pathogens in some samples) in dbRDA analyses.
 KingFungiTablewithTax_PlantPathogens_Remove0s * See above for column
 descriptors. Numbers in each row under each ASVs indicate the abundance of
 that ASV in that sample. Rows indicate a sample. This is only the fungi
 ASVs that were identified as Plant Pathogens. In this dataset used for
 beta diversity, samples with no plant pathogens were removed for analysis
 mpbg.qs_Hardcode0s * See above for some column descriptors. q0, q1, q2,
 q3, q4, q5, q6 columns are all Hill number calculations (order q) for that
 sample. This is only the fungi ASVs that were identified as Myrmecochore
 Pathogens. In this dataset used for alpha diversity, samples with no
 myrmecochore pathogens were hardcoded to 0 (i.e., having no myrmecochore
 pathogens) Myr_Paths_by_Genus_DummyCode * See above for column
 descriptors. Numbers in each row under each ASVs indicate the abundance of
 that ASV in that sample. Rows indicate a sample. This is only the fungi
 ASVs that were identified as Myrmecochore Pathogens. There is an
 additional column (Dummy_OTU) with an abundance of 1 for all samples to
 deal with zero data (no myrmecochore pathogens in some samples) in dbRDA
 analyses. Myr_Paths_by_Genus_Remove0s * See above for column descriptors.
 Numbers in each row under each ASVs indicate the abundance of that ASV in
 that sample. Rows indicate a sample. This is only the fungi ASVs that were
 identified as Myremecochore Pathogens. In this dataset used for beta
 diversity, samples with no mrymecochore pathogens were removed for
 analysis pp.qs_Hardcode0s * See above for some column descriptors. q0, q1,
 q2, q3, q4, q5, q6 columns are all Hill number calculations (order q) for
 that sample. This is only the fungi ASVs that were identified as Plant
 Pathogens. In this dataset used for alpha diversity, samples with no plant
 pathogens were hardcoded to 0 (i.e., having no plant pathogens)
 ap.qs_Hardcode0s * See above for some column descriptors. q0, q1, q2, q3,
 q4, q5, q6 columns are all Hill number calculations (order q) for that
 sample. This is only the fungi ASVs that were identified as Animal
 Pathogens. In this dataset used for alpha diversity, samples with no
 animal pathogens were hardcoded to 0 (i.e., having no animal pathogens) ##
 Sharing/Access information N/A ## Code/Software All statistics were run in
 R version 3.6.0 All sequence processing was done in Qiime2