Field sampling and DNA-barcoding of fig pollinator wasps across host species and host developmental phase and on non-Ficus controls
Data files
Oct 04, 2023 version files 598.13 KB
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databar.csv
79.08 KB
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datac.csv
124.93 KB
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pollinator_arrivals_w_nonFicus.csv
80.69 KB
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README.md
10.14 KB
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SuppMaterial_R_script_barcoding.rtf
54.36 KB
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SuppMaterial_R_script_bootstrapping.rtf
134.74 KB
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SuppMaterial_R_script_trapping_data.rtf
114.18 KB
Abstract
To better understand factors that might contribute to this observed range of specificity, we used sticky traps to capture fig-pollinating wasp individuals at 13 Ficus species, sampling at different stages of the reproductive cycle of the host figs (e.g. trees with receptive inflorescences, or vegetative trees, bearing only leaves). We also sampled at other tree species, using them as non-Ficus controls. DNA barcoding allowed us to identify the wasps to species, and therefore assign their presence and abundance to host fig species and the developmental stage of that individual tree. Here we upload the data and the R scripts used to analyze these data.
README: Field sampling and DNA-barcoding of fig pollinator wasps across host species and host developmental phase and on non-Ficus controls
https://doi.org/10.5061/dryad.6m905qg5j
GENERAL INFORMATION
1. Title of the dataset; Field sampling and DNA-barcoding of fig pollinator wasps across host species and host developmental phase and on non-Ficus controls
2. Author information;
Name: Aafke Oldenbeuving
Institution: Naturalis Biodiversity Center
Address: P.O. box 9517, 2333 CC Leiden
Email: aafke.oldenbeuving@naturalis.nl
3. Date of data collection: years 2016-2019
4. Geographic location of data collection: Barro Colorado
5. Information about funding sources that supported the collection of the data: KNAW Fonds Ecologie\, NWO Doctoral Grant for Teachers\, grant number 023.003.072
SHARING/ACCESS INFORMATION
1. Licenses/restrictions placed on the data: CC0 1.0 Universal (CC0 1.0) Public Domain
2. Links to publications that cite or use the data:
https://onlinelibrary.wiley.com/doi/epdf/10.1002/ece3.10501
3. Links to other publicly accessible locations of the data: None
4. Links/relationships to ancillary data sets: None
5. Was data derived from another source? No
A. If yes, list source(s): NA
6. Recommended citation for this dataset:
10.5061/dryad.6m905qg5j
DATA & FILE OVERVIEW
1. File list:
A) databar.csv
B) datac.csv
C) pollinator_arrivals_w_nonFicus.csv
D) SuppMaterial R script barcoding.rtf
E) SuppMaterial R script bootstrapping.rtf
F) SuppMaterial R script trapping data.rtf
2. Relationship between files; yes
dataset A) can be run in script D)
dataset B) can be run in script F)
dataset C) can be run in script E)
3. Additional related data collected that was not included in the current data package: None
4. Are there multiple versions of the dataset? No
A. If yes, name of file(s) that was updated: NA
i. Why was the file updated? NA
ii. When was the file updated? NA
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DATA-SPECIFIC INFORMATION FOR: databar.csv
1. Number of variables: 16
2. Number of cases / rows: 532
3. Variable list:
- CODE = code for individual pollinator used during DNA-barcoding
- HOST_SP = Ficus species to which the tree belongs on which this pollinator was caught
- graph = additional column to assign individuals to different graphs
- PHASE = developmental phase of the tree when the pollinator was caught
- HOST-TREE = code for the individual host tree on which the pollinator was caught
- DATE = date on which the pollinator was caught
- ID_Carlos … = the species identity as determined by phylogenic analyses of the DNA barcoees
- pollID = code for the species identity
- TYPhost = code for the Ficus this pollinator is usually emerging from
- correct = if pollinator was or was not found on the host it typically emerges from (1/0), ? as value means we did not know if this species typically emerged from this host
- for_gemA = indicating for Pegoscapus gemellus A what host type the Ficus tree in this row belongs to; vegetative non-host (veg_nonhost) / vegetative host (veg_host) / receptive non-host (fl_nonhost) / receptive host(fl_host)
- for_gemB = indicating for Pegoscapus gemellus B what host type the Ficus tree in this row belongs to; vegetative non-host (veg_nonhost) / vegetative host (veg_host) / receptive non-host (fl_nonhost) / receptive host(fl_host)
- for_gemC = indicating for Pegoscapus gemellus A what host type the Ficus tree in this row belongs to; vegetative non-host (veg_nonhost) / vegetative host (veg_host) / receptive non-host (fl_nonhost) / receptive host(fl_host)
- for_tond = indicating for Pegoscapus gemellus A what host type the Ficus tree in this row belongs to; vegetative non-host (veg_nonhost) / vegetative host (veg_host) / receptive non-host (fl_nonhost) / receptive host(fl_host)
- for_hoffA = indicating for Pegoscapus gemellus A what host type the Ficus tree in this row belongs to; vegetative non-host (veg_nonhost) / vegetative host (veg_host) / receptive non-host (fl_nonhost) / receptive host(fl_host)
- for_hoffB = indicating for Pegoscapus gemellus A what host type the Ficus tree in this row belongs to; vegetative non-host (veg_nonhost) / vegetative host (veg_host) / receptive non-host (fl_nonhost) / receptive host(fl_host)
4. Missing data codes:
last column “value” was not used
5. Specialized formats or other abbreviations used: none
###############################################################################
DATA-SPECIFIC INFORMATION FOR: B) datac.csv
1. Number of variables: 17
2. Number of cases / rows: 729
3. Variable list:
- species = code for the Ficus species where this datapoint was collected
- Ficus_species = species name on which this datapoint was collected
- treeID = code for the individual host tree on which this datapoint was collected
- type = developmental phase the tree was in when this datapoint was collected
- date = the date on which the sticky trap was put up in the field
- year = the year in which the datapoint was collected
- Ndays = number of days the sticky trap remained in the tree
- Nwasps = numer op Pegoscapus spp. pollinators counted on the trap
- wpd = Nwasps divided by Ndays to get the number of pollinators per 24h
- for_gemA = indicating for Pegoscapus gemellus A what host type the Ficus tree in this row belongs to; vegetative non-host (veg_nonhost) / vegetative host (veg_host) / receptive non-host (fl_nonhost) / receptive host(fl_host)
- for_gemB = indicating for Pegoscapus gemellus B what host type the Ficus tree in this row belongs to; vegetative non-host (veg_nonhost) / vegetative host (veg_host) / receptive non-host (fl_nonhost) / receptive host(fl_host)
- for_gemC = indicating for Pegoscapus gemellus A what host type the Ficus tree in this row belongs to; vegetative non-host (veg_nonhost) / vegetative host (veg_host) / receptive non-host (fl_nonhost) / receptive host(fl_host)
- for_tond = indicating for Pegoscapus gemellus A what host type the Ficus tree in this row belongs to; vegetative non-host (veg_nonhost) / vegetative host (veg_host) / receptive non-host (fl_nonhost) / receptive host(fl_host)
- for_hoffA = indicating for Pegoscapus gemellus A what host type the Ficus tree in this row belongs to; vegetative non-host (veg_nonhost) / vegetative host (veg_host) / receptive non-host (fl_nonhost) / receptive host(fl_host)
- for_hoffB = indicating for Pegoscapus gemellus A what host type the Ficus tree in this row belongs to; vegetative non-host (veg_nonhost) / vegetative host (veg_host) / receptive non-host (fl_nonhost) / receptive host(fl_host)
- data_origin = Excel files where author keeps additional data (including these counts)
- remarks = occasional remarks from the field work
4. Missing data codes: none
5. Specialized formats or other abbreviations used: none
###############################################################################
DATA-SPECIFIC INFORMATION FOR: C) pollinator_arrivals_w_nonFicus.csv
1. Number of variables: 11
2. Number of cases / rows: 789
3. Variable list:
- species = code for the Ficus species where this datapoint was collected
- Ficus_species = species name on which this datapoint was collected
- treeID = code for the individual host tree on which this datapoint was collected
- type = developmental phase the tree was in when this datapoint was collected
- date = the date on which the sticky trap was put up in the field
- year = the year in which the datapoint was collected
- Ndays = number of days the sticky trap remained in the tree
- Nwasps = numer op Pegoscapus spp. pollinators counted on the trap
- wpd = Nwasps divided by Ndays to get the number of pollinators per 24h
- data_origin = Excel files where author keeps additional data (including these counts)
- remarks = occasional remarks from the field work
4. Missing data codes: none
5. Specialized formats or other abbreviations used: none
<br>
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<br>
SCRIPT-SPECIFIC INFORMATION FOR: SuppMaterial R script barcoding.rtf
<br>
R version 4.1.3 (2022-03-10) -- "One Push-Up"
Copyright (C) 2022 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin17.0 (64-bit)
This script was used to compare the host-specificity of Pegoscapus pollinators trapped at receptive host trees with those trapped at vegetative host trees. The script also creates graphs on these data.
version of the used packages
MASS = 7.3-57
lme4 = 1.1-29
###############################################################################
SCRIPT-SPECIFIC INFORMATION FOR: SuppMaterial R script bootstrapping.rtf
R version 4.1.3 (2022-03-10) -- "One Push-Up"
Copyright (C) 2022 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin17.0 (64-bit)
This script was used to make estimates for 6 species of Pegoscapus pollinators of the number of individuals present at 4 types of Ficus trees; receptive or vegetative, and of each either their typical host or hosts belonging to another species. The script also creates graphs on these data.
version of the used packages
ggplot2 = 3.3.6
plyr = 1.8.7
ggsinif = 0.6.3
###############################################################################
SCRIPT-SPECIFIC INFORMATION FOR: SuppMaterial R script trapping data.rtf
R version 4.1.3 (2022-03-10) -- "One Push-Up"
Copyright (C) 2022 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin17.0 (64-bit)
This script was used to compare the number of Pegoscapus pollinators trapped in Ficus trees that were either receptive or vegetative. And to the number of Pegoscapus pollinators trapped non-Ficus control trees. The script also creates graphs on these data. We make a comparison in which all 13 sampled Ficus species are lumped, and we make comparisons for individual Ficus species.
version of used packages
library(pscl) = 1.5.5
library(glmmTMB) = 1.1.2
library(multcomp) = 1.4-19
Methods
The datasets were collected in the landscape surrounding the Barro Colorado Island field station of the Smithsonian Tropical Research Institute in Panama and DNA-bardcoding preparations were done in the NAOS laboratories of the Smithsonian Tropical Research Institute in Panama. Purification and sequencing were done in Korea (Macrogen). Data was collected from 2016–2019.