A checklist of European butterfly larval foodplants
Data files
Jan 18, 2024 version files 105.45 MB
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apg4.csv
36.13 KB
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butterfly_red_list_2010.csv
26.47 KB
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butterfly_synonym.csv
807.48 KB
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larval_host_plant_status.csv
679 B
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larval_host_plant.csv
688.78 KB
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larval_plants.csv
2.38 MB
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mnemosyne.csv
2.43 MB
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plant_geography_level1.zip
2.40 MB
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plant_geography_level2.zip
2.73 MB
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plant_geography_level3.zip
3.72 MB
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plant_geography_level4.zip
3.87 MB
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README.md
18.76 KB
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reference.csv
274.06 KB
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region.csv
3.10 KB
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result-data-figures.xlsx
19.51 KB
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wcvp_extendedb.csv
211.75 KB
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wcvp-v11.zip
85.43 MB
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wiemers_distribution.csv
390.36 KB
Abstract
Butterflies are charismatic insects, and have been well studied, particularly in Europe. They are disproportionately used in generating and testing hypotheses; on everything from general evolutionary processes, such as speciation, or host association dynamics; to conservation-related studies, such as climate change or habitat loss.
Accurate lists of the larval foodplants for European butterflies are not readily available. Mistakes are propagated and information can’t be checked for accuracy. The level of evidence is unknown, and how usage varies between countries poorly understood.
The study consulted 1,119 references to produce 19,488 records of larval foodplants for European butterflies. This resulted in 5,589 larval host plant records for 464 European butterfly species, with multiple references, enabling information to be checked. Information was unavailable for 59 species. The level of evidence for each relationship show the current state of knowledge.
Significant issue were identified for 3.9% of records extracted from references due to mistakes, ambiguous or unknown plant names, distribution issues, resulting in information being lost. Plants with a questionable distributions suggest either misidentification, or species that have been split.
Little is known about plant usage in eastern Europe. The larval foodplants of many monophagous and Satyrinae butterflies are poorly studied. Only 64% of threatened 2010 Red Listed butterflies have reliable host plant records.
The study has provided ecologists with a valuable resource, of a more accurate checklist of the larval foodplants for each European country. Why plant usage varies over a butterfly’s distribution, opens up some interesting research questions.
Title: A checklist of European butterfly larval foodplants
Author: Harry E. Clarke
Address: 70 Norwood Road, Effingham, Leatherhead, Surrey KT24 5NX, United Kingdom
e-mail: Harry@HarryClarke.me.uk
Date of collection: 11 December 2023
Georgraphy: Europe
Keywords: Hostplants, habitat, conservation, Lepidoptera, Papilionoidea
INTRODUCTION
These are the files and data that was used to produce the paper “A checklist of European butterfly larval foodplants”
The database used in the study was PostgreSQL version 12 and later version 14
The R scripts used to load data, and to produce Figures 2 to 5 was version 4.2.2. The R scripts reqire the following packages to be installed
install.packages(“RODBC”)
install.packages(“odbc”)
install.packages(“RPostgres”)
install.packages(ggplot2)
install.packages(dplyr)
install.packages(extrafont) # fonts
install.packages(stringr) # For string wrap
install.packages(patchwork) # for combining plots together
QGIS version 3.32 was used in the production of the maps.
NOTE the order of creating the database tables, and loading the data into the tables has not been tested, although they are believed to be correct.
CONTENTS
A - SQL scripts to create the database tables - 2 files
B - Open source data files downloaded from external sources - 9 files
C - Data files created as part of the study - 9 files
D - SQL scripts used to enter the raw data - 7 files
E - SQL scripts used to undertake checks and to create the larval_host_plant table - 12 files
F - SQL scripts used to undertake analysis and outputs - 17 files
G - Files used to produce maps and figures for the paper - 4 files
TOTAL number of files = 60 + 1 = 61 including this file (README.txt)
The SQL scripts wwere used on a PostgreSQL database version 12 and 14. As PostgreSQL complies very closely with SQL Standards, the scripts should work on any relational database with little or no modification.
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create_tables.sql
text file containing a SQL script to create the database tables. It assumes the database contains two schemas “world” and “europe”. -
create_views.sql
text file containing a SQL script to create views of the database tables
B - Open source data files downloaded from external sources
Dryad for files 1, 3, 4, 6-9
Zenodo for file 5
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apg4.csv - data downloaded from APG IV (2016) An update of the Angiosperm Phylogeny Group classification for the orders and families of flowering plants: APG IV. Botanical Journal of the Linnean Society 181(1): 1–20. https://doi.org/10.1111/boj.12385
id integer, unique
scientific_name text
taxon_rank text
authors text
parent_name text
accepted_name text
nomenclatural_status text -
No file provided.
The data for the table wiemers_2018 is available at https://doi.org/10.3897/zookeys.811.28712.suppl1 -
butterfly_red_list_2010.csv - data extracted from van Swaay C, Cuttelod A, Collins S, Maes D, Munguira ML, S̆as̆ić M, Settele J, Verovnik R, Verstrael T, Warren M, Wiemers M, Wynhoff I (2010) European Red List of Butterflies. Publications Office of the European Union, Luxembourg, 47 pp. And linked to the butterfly_synonym table
NOTE This file must be loaded AFTER the table europe.butterfly_synonym has been loaded.butterfly text
authors text
europe_red text
eu27_red text
butterfly_id integer links to field id in table buttefly_synonym
Legend for fields europe_red and eu27_red are as per IUCN definitions
EX = Extinct
EW = Extinct in the wild
CR = Critically Endangered
EN = Endangered
VU = Vulnerable
NT = Near Threatened
LC = Least Concern
DD = Data Deficient
NE = Not Evaluated -
wcvp-v11.zip - version 11 of the World Checklist of Vascular Plants (WCVP) downloaded from https://powo.science.kew.org/
This zip file contains three files
README_WCVP.xlsx
wcvp_distribution.csv
wcvp_names.csv
These three files will need to be extracted from the ZIP file.
4a) README_WCVP.xlsx - key to to wcvp distribution and names files4b) wcvp_distribution.csv
plant_locality_id integer, unique
plant_name_id integer, links to plant_name_id field in table wcvp_names
continent_code_l1 integer - Level 1
continent text,
region_code_l2 integer, - Level 2
region text,
area_code_l3 text, Level 3
area text,
introduced integer,
extinct integer,
location_doubtful integer
For defintions of Level 1, Level 2 and Level 3 see files 6-9 below.4c) wcvp_names.csv
plant_name_id integer, unique
ipni_id character, id for the taxon published in https://www.ipni.org/
taxon_rank text,
taxon_status text,
family text,
genus_hybrid text,
genus text,
species_hybrid text,
species text,
infraspecific_rank text,
infraspecies text,
parenthetical_author text,
primary_author text,
publication_author text,
place_of_publication text,
volume_and_page text,
first_published text,
nomenclatural_remarks text,
geographic_area text,
lifeform_description text,
climate_description text,
taxon_name text,
taxon_authors text
accepted_plant_name_id integer,
basionym_plant_name_id text,
replaced_synonym_author text,
homotypic_synonym boolean,
parent_plant_name_id text,
powo_id text, the same as field ipni_id, plus unpublished ids.
hybrid_formula text,
reviewed text -
read_wcvp.R - text file containing an R script to load the WCVP data into the database tables, as they cannot be imported directly. The file will need to be edited to provide the connection and password to the database, and the location of two files extracted from the file wcvp-v11.zip
6-9) Four files of the World Geographical Scheme for Recording Plant Distributions (WGSRPD) was downloaded from https://github.com/tdwg/wgsrpd
These files are only required for the generation of the map for Figure 6
a) plant_geography_level1.zip
b) plant_geography_level2.zip
c) plant_geography_level3.zip
d) plant_geography_level4.zip
Each ZIP file contains a GIS Shapefile (consisting of several files). The Shapefiles were loaded into QGIS, which was then used to populate the four database tables:
world.plant_geography_level1
world.plant_geography_level2
world.plant_geography_level3
world.plant_geography_level4
C - Data files created as part of the study (Dryad)
There are 7 CSV files with UTF8 encoding.
The fields, plant_name_id, powo_id and ipni_id are as defined in version 11 of the World Checklist of Vascular Plants (WCVP), which is available from the Plants Of the World Online website https://powo.science.kew.org/
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butterfly_synonym.csv - accepted and synonym scientific names of European butterflies
id integer, unique
family text
subfamily text
genus text
species text
subspecies text
taxon_name text
authors text
rank text
taxonomic_status text
accepted_id integer, is NULL if taxonomic_status is “Accepted”, otherwise id of taxon that is accepted.
parent_id integer
species_order integer, number to order species in taxonmic order
tribe text
subtribe text -
reference.csv - References used for larval foodplants of European butterflies
id integer, unique
short_ref text
full_reference text
ref_type character(1) - not used. -
region.csv - Countries
id integer, unique
region_name text
iso3166_2_code text
vehicle_code text
area_code_l3 text
region_code_l2 integer
continent_code_l1 integer -
wiemers_distribution.csv
the data was downloaded from Wiemers M, Balletto E, Dincă V, Faltynek Fric Z, Lamas G, Lukhtanov V, Munguira ML, van Swaay CAM, Vila R, Vliegenthart A, Wahlberg N, Verovnik R (2018) An updated checklist of the European Butterflies (Lepidoptera, Papilionoidea). ZooKeys 811: 9–45. https://doi.org/10.3897/zookeys.811.28712
and re-arrangedid integer, unique
wiemers_id integer linked to the field id in the table wiemers_2018
regions_id integer linked to the field id in the table region
status text
Legend for the status field is:
A = Absent
P = Present
P? = Possibly present
M = Regular migrant
I = Irregular migrant
Ex = Regionally extinct -
wcvp_extendedb.csv - plant names and status
id integer, unique
plant_id text
plant_name_id text - defined in wcvp11_names
ipni_id text - as in table wcvp11_names
taxon_name text
taxon_authors text
name_status text
notes text -
larval_plants.csv - data extracted from references for larval foodplants of European butterflies
id integer, unique
butterfly text
plant text
habitat text
usage text
region text
country_id integer - see region table
ref_id integer - see reference table
source_ref_id integer
stage text
butterfly_id integer - see butterfly_synonym tables
plant_id text - see wcvp_extendedb table
notes text
questionable integer -
larval_host_plant_status.csv - status of larval foodplants of European butterflies
id integer, unique
description text
evidence text -
larval_host_plant.csv - larval foodplants of European butterflies (accepted names)
id integer, unqiue
butterfly_id integer
powo_id text - defined in wcvp11_names
status integer - links to id in table larval_host_plant_status
references text - list of short references, full reference is given in table reference
countries text - list of countries
questionable_countries text - list of countries -
mnemosyne.csv
The data for this table was created from the data in the table “europe.larval_plants”, and the geometry from the table “world.plant_geography_level3”. It was used to produce the map in Figure 6.
It provides the larval plants of the butterfly Parnassius mnemosyneid integer, unique
area_code_text - links to field area_code in table regions
blanda integer = 1 when Corydalis blanda present
pumila integer = 1 when Corydalis pumila present
solida integer = 1 when Corydalis solida present
b_larvae integer = 1 when Corydalis blanda used by larvae
p_larvae integer = 1 when Corydalis pumila used by larvae
s_larvae integer = 1 when Corydalis solida used by larvae
geom geometry(MultiPolygon,4326)
cava integer = 1 when Corydalis cava present
intermedia integer = 1 when Corydalis intermedia present
c_larvae integer = 1 when Corydalis cava used by larvae
i_larvae integer = 1 when Corydalis intermedia used by larvae
distribution integer - not used
D - SQL scripts used to enter the raw data (Zenodo)
data was entered manually into the table “region”
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insert_butterfly_synomyn.sql
text file containing a SQL script to select and insert a new butterfly synomym -
insert_reference.sql
text file containing a SQL script to insert a new reference -
insert_published_plant.sql
text file containing a SQL script to insert a published plant into table wcvp_extendedb -
insert_ambig_plant.sql
text file containing a SQL script to insert an ambiguous plant into table wcvp_extendedb -
insert_agg_plant.sql
text file containing a SQL script to insert an aggregate plant species into table wcvp_extendedb -
insert_larval_plant.sql
text file containing a SQL script to insert a larval foodplant, extracted from a reference, into the larval_plants table -
select_plant.sql
text file containing a SQL script to list all plants for a given taxon_name, and their accepted name if it exists
E - SQL scripts used to undertake checks and to create the larval_host_plant table (Zenodo)
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check_butterfly_distribution.sql
text file containing a SQL script to manually check the distribution of a butterfly -
select_reference.sql
text file containing a SQL script to manually check the references for a butterfly -
seclect_accepted_plant.sql
text file containing a SQL script to manually check entered, assumed and accepted plant and butterfly names are reasonablee for a butterfly -
insert_accepted_butterfly_plants.sql
text file containing a SQL script to insert records into the larval_host_plant table for a butterfly - stage 1 -
select_evidence.sql
text file containing a SQL script to manually check the evidence for each larval host plant for a butterfly -
edit_larval_host_plant.sql
text file containing a SQL script to manually the larval_host_plant table to enter the evidence -
select_larval_host_plant.sql
text file containing a SQL script to manually check the larval host plants evidence for a butterfly (readable format) -
check_plant_orders.sql
text file containing a SQL script to manually check the plant orders for a particular subfamily/tribe/subtribe -
edit_butterfly_synonym.sql
text file containing a SQL script to check the ordering and details of the accepted butterfly species -
select_butterfly_country.sql
text file containing a SQL script to list the countries/regions with host plant records -
select_larval_plants.sql
text file containing a SQL script to list the larval plant usage. Edit script for different conditions. -
update_accepted_butterfly_plants.sql
text file containing a SQL script to update the larval_host_plant table following some edits to the larval_plants table.
F - SQL scripts used to undertake analysis and outputs (Zenodo)
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output_plant_taxon_rank.sql
text file containing a SQL script to output data for Table 2 in the Article -
output_plant_taxon_status.sql
text file containing a SQL script to output data for Table 3 in the Article -
count_records_evidence.sql
text file containing a SQL script to count the number of records, used to create Figure 2 in the Manuscript. The script must be edited (see comments) to produce output for the various columns of the table. -
count_butterfly_evidence.sql
text file containing a SQL script to count the number of butterfly species for each level of evidence, used to create Figure 2 in the Manuscript. The script must be edited (see comments) to produce output for the various columns of the table. -
count_red_list_evidence.sql
text file containing a SQL script to count the number of butterfly species for each level of Red List vulnerability, used to create Figure 3 in the Manuscript. The file is edited to produce the output for all and reliable records. -
count_red_list_butterflies.sql
text file containing a SQL script to count the number of butterfly species for each level of Red List vulnerability, used to create Figure 3 in the Manuscript. -
count_monophageous_evidence.sql
text file containing a SQL script to count the number of butterfly species, used to create Figure 4 in the manuscript in the Results Table. The script must be edited (see comments) to produce output for the various columns of the table. -
count_monophageous_butterflies.sql
text file containing a SQL script to count the number of butterfly species, used to create Figure 5 in the manuscript in the Results Table. The script must be edited (see comments) to produce output for the various columns of the table. -
count_butterfly_subfamilies.sql
text file containing a SQL script to count the number of accepted butterflies in each subfamily. Used to create the totals in Figure 5 in the manuscript. -
count_num_plant_taxons.sql
text file containing a SQL script to count the number of entries for each unique plant taxon name used in larval_plants table. Used to find some examples for the manuscript. -
count_num_plant_usage.sql
text file containing a SQL script to count the number of different plants with the same taxon name, but different taxon authors extracted from the references. Used to find some examples for the manuscript. -
select_parnassius_mnemosyne_larval_plants.sql
text file containing a SQL script used to generate the larval foodplants in each country for the butterfly Parnassius mnemosyne. Used as an intrim script to create the table europe.mnemosyne -
output_larval_host_plant.sql
text file containing a SQL script to output content for Supplementart file S1 -
output_reference.sql
text file containing a SQL script to output content for Supplementary file S2 -
count_monophageous.sql
text file containing a SQL script to manually count the number of plant orders, families, genera and species for each butterfly where the evidence is at levels 1, 2, 3 and plant distribution is reasonable (reliable records) output content for Supplementary file S4 -
select_plant_families_for_butterfly_subtribes.sql
text file containing a SQL script to output content for Supplementary file S5 -
select_red_list.sql
text file containing a SQL script to output content for Supplementary file S6
G - Outputs
This section contains 4 files. There usage is described below:
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num_plant_records.qml (Zenodo)
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result-data-figures.xlsx (Dryad)
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Plot figures for Larval foodplant.R (Zenodo)
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europe_mnemosyne.qml (Zenodo)
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To recreate Figure 1 using QGIS
a) connect to the database table world.plant_geography_level3
This table is used to provide the background outlines for the TDWG Level 3 regions
b) connect to the database view europe.num_plant_records
This view provides the number of records per country/region
c) Load the qgis style file num_plant_records.qml -
result-data-figures.xlsx
Microsoft Excel file containg the data for Figures 2 to 5. For the source of this data, see the comments in the file plot_figures_for_larval_foodplant.R -
plot_figures_for_larval_foodplant.R
text file containing an R script to generate figures 2 to 5. The data was manually entered from the the file “result-data-figures.xlsx”. Comments identify the SQL scipts that were run to produce the data, which was entered into the Excel File, and then copied into the data frames to produce the plots.
Running the script will generate the figures. The script will need modifying to the folder to store the figures in. -
To recreate Figure 6 using QGIS
a) connect to the database table world.plant_geography_level3
This table is used to provide the background outlines for the TDWG Level 3 regions
b) connect to the database table europe.mnemosyne and rename layer to “Corydalis distribution”
This table contains the distribution of larval plants for the butterfly Parnassius mnemosyne
c) Load the qgis style from file europe_mnemosyne.qml for the “Corydalis distribution” layer
Two strategies were deployed to obtain information on larval foodplants. Firstly books providing lists of larval foodplant usage for each country. And, secondly, publications providing primary evidence (oviposition, eggs or larvae found in the wild) for larval foodplant usage. Breeding records were included to support usage in the wild records, or where there was limited information on a particular butterfly species.