Supplemental nesting habitat increases bee abundance in apple orchards
Creators: name: Hyjazie, Batoule F.
name: Forrest, Jessica R. K.
Publisher: name: Zenodo
Year: 2023
Subjects: Agriculture
Cavity-nesting bees
Fruit set
Pollinators
Pollination
Resource limitation
Solitary bees
Trap-nest

description: Hyjazie and Forrest, 2023

Code repository for Hyjazie and Forrest, 2023: "Supplemental nesting habitat increases bee abundance in apple orchards"

This Rmarkdown file is divided into two sections: main manuscript and supporting information. The main manuscript is further divided into two sections: Year 1 and Year 2 (which includes a subsection of Year 1 + Year 2 (i.e., All Years)). Each of these sections has two sub-sections: abundance and apple quality. Supporting information includes all information relating to trap nests.

Each of these subsections will report a code for some general summary statistics, models, and/or figures. All files are excel files. Missing values are depicted as N/A.

Main Manuscript

Variables Common in All Spreadsheets





Orchard: Unique two-letter identifier for each orchard, reflecting site pairings used for treatment assignment. For example, Orchard IDs “HM” (with one treatment plot) and “IC” (with one control plot) are paired as Orchard “HC”. N = 16 levels.




Orchard ID: Unique two-letter identifier for each orchard, reflecting orchard ownership. Some orchards had only a single plot (either control or treatment) and needed to be paired with a plot in another (nearby) orchard; these pairings are reflected in the “Orchard” variable. N=16 levels.




Site: Numerical identifier since each orchard either had 1, 2 or 3 sites.




Site ID: Numerical identifier since each orchard either had 1, 2 or 3 sites and accounts for orchards that only have plot (either control or treatment) and needed to be paired with another (n=16).




Plot: Control (without trap nests) or Treatment (with trap nests).




Shaded TºC: Measured temperature in the shade.




Unshaded TºC: Measured temperature out of the shade.




% Cloud Cover: Estimated percent of cloud cover (0% = no cloud in sight).




Wind (m/s): Measured wind speed.



Abundance





"Osmia_Abundance_1.xlsx": Excel file with Osmia abundance data (Year 1)




"Bee_Abundance_1.xlsx": Excel file with total bee abundance data (Year 1)




"Total_Abundance_1.xlsx": Excel file with total pollinator abundance data (all flower visitors including non-bees) (Year 1)




"Total_Abundance_Year_2.xlsx": Excel file with total abundance data (Year 2)



Variables





Round: Sampling period (either during apple bloom, pre-thinning (Round 2), or post-thinning (Round 3)).




Transect: 3 transect walks were conducted per sampling period per orchard per site (either 1, 2, or 3).




Date: Date of transect walk.




Start Time: Start time of transect walk.




End Time: End time of transect walk.




Taxa: Taxon of floral visitor to nearest genus whenever possible.




Count: Count of floral visitor observed during particular transect walk.




Bee: Binary column to indicate if the taxon in question is a bee or non-bee flower visitor.




Sex: Male or Female or Unknown (N/A).



Apple





"Apple_1.xsls": Excel file with all apple data (Year 1)




"Apple_Year_2.xslx": Excel file with all apple data (Year 2)



Variables





Tree #: Numerical identifier (1, 2, or 3) for the tree measured in each plot (each plot had 3 trees).




Age: Age of tree (either adult or dwarf)




Tree Height (cm)




N Bud #: Number of apple flower buds on the North-facing branch.




N Pre-Thinning Fruit #: Number of apples growing on the North-facing branch pre-thinning.




N Post-Thinning Fruit #: Number of apples growing on the North-facing branch post-thinning.




S Bud #: Number of apple flower buds on the South-facing branch.




S Pre-Thinning Fruit #: Number of apples growing on the South-facing branch pre-thinning.




S Post-Thinning Fruit #: Number of apples growing on the South-facing branch post-thinning.




N Apple 1 Circumference (cm): Circumference (measure of apple quality) of 1st apple (tip) on the North-facing branch.




N Apple 2 Circumference (cm): Circumference (measure of apple quality) of 2nd apple (mid-section) on the North-facing branch.




N Apple 3 Circumference (cm): Circumference (measure of apple quality) of 3rd apple (nearest to trunk) on the North-facing branch.




S Apple 1 Circumference (cm): Circumference (measure of apple quality) of 1st apple (tip) on the South-facing branch.




S Apple 2 Circumference (cm): Circumference (measure of apple quality) of 2nd apple (mid-section) on the South-facing branch.




S Apple 3 Circumference (cm): Circumference (measure of apple quality) of 3rd apple (nearest to trunk) on the South-facing branch.




Fruits Measured: Count of number of fruits with a circumference value




Mean Non-Zero Circumference (cm): Mean of circumference of fruits with a circumference value.



Supporting Information

Trap Nests





"Trap_Nest_Edge_Effects.xlsx": Excel file with distance from orchard edge for each trap nest (Year 1)




"Trap_Nest_Final_Count.xlsx": Excel file with final tally trap nest occupants for each trap nest (Year 1). Some values differ from those obtained from summing values in "Trap_Nest_Total.xlsx" because values in this file were adjusted following x-ray examination of nest contents (so, values in this file for cell numbers per nest are more accurate).




"Trap_Nest_Total.xlsx": Excel file with running tally (taken for every sampling period) of trap nest occupants for each trap nest (Year 1)




"Pollen.xlsx": Excel file with pollen data extracted from trap nests (Year 1)



Variables





Trap Nest ID: Unique alphanumerical identifier for each of the 10 trap nests present within every orchard and site.




Trap Nest Hole # (or Hole #): Numerical identifier indicating the designated location of the hole within a particular trap-nest.




Trap Nest Edge Distance (m): Distance of a particular trap-nest from orchard edge.




Trap Nest Edge: The type of edge (forest, road, or field)




Round: Sampling period of trap nest monitoring (either during apple bloom, pre-thinning (Round 2), or post-thinning (Round 3), Round 4, or Final Count (at thend of summer of Year 1)).




Date: Date of trap-nest monitoring.




Total Hole #: Total number of possible holes within a particular trap-nest (varies from 10-14).




Size: Size of nest (small=S, medium=M, large=L).




"# New Cells": Number of new cells produced since the last visit (if no new cells=0).




"# Total Cells": Number of total cells including those of the new cells that were produced (if no new cells, this number remains unchanged since the last visit).




"# Surviving Osmia": Number of surviving Osmia per nest as determined by X-ray.




"# Surviving Osmia": Number of surviving female Osmia per nest as determined by X-ray.




Seal: Type of nest seal (material) that was used for nest construction (mud, leaf, or resin). This helps to identify taxa.




Taxa: Type of insect that constructed the nest. "Chelostomoides" = resin bees (Megachile: Chelostomoides) and wasps (Passaloecus). "Wasp" = potter wasps (eumenine Vespidae) and Trypoxylon. "Megachile" = leaf-cutting Megachile.




Sealed: Binary (yes or no) to indicate if the nest was sealed.