Data from: Untangling colour diversity: Ecogeographic patterns in two Scolopendra species revealed by citizen science
Data files
Jul 08, 2026 version files 200.44 KB
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Biogeography.zip
188.18 KB
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README.md
12.26 KB
Abstract
We compiled georeferenced photographic occurrence records of Scolopendra mutilans and S. japonica from citizen-science platforms and online sources. Each record was classified by species and leg colour morph (red or yellow). We mapped species and morph distributions. Then, we analysed their predators and prey based on photographs and occurrence records using spatial point pattern models and realised climatic niche analysis. The two species showed broadly overlapping ranges, predators, prey, and climatic niches. In contrast, patterns of morph co-occurrence differed markedly: in S. mutilans, morphs were sympatric nationwide, whereas in S. japonica they co-occurred only in restricted Pacific coastal areas. Within S. mutilans, morphs differed in their associated predator species, and their realised climatic niches showed significant but relatively small differences. Within S. japonica, the red morph’s realised niche was fully nested within that of the yellow, with neither prey nor predator differences detected. These occurrence records reveal species-specific spatial patterns in the distribution and co-occurrence of colour morphs in Japanese Scolopendra. The dataset provides a geographic baseline for future studies on the ecological and evolutionary processes underlying colour polymorphism, and offers a reproducible resource for spatial and climatic analyses.
README information
- File name: README.md
- Authors: Ryosuke Uno and Shouta Iyoda
- Corresponding author: Ryosuke Uno
- Email address: uno.ryosuke.33w@st.kyoto-u.ac.jp
- Date created: 2026-02-03
- Date revised: 2026-07-01
Description of the data and file structure
This dataset contains occurrence data together with R Markdown scripts used for analyses in this study.
The focal taxa are Scolopendra mutilans and Scolopendra japonica.
External environmental raster files and vector files are not redistributed.
Instead, users should download the external data directly from their original providers and place the files in the directories described below before running the analysis scripts.
Dataset information
- File count: 7 files in total
- .xlsx 1
- .csv 3
- .Rmd 3
Data structure and explanation
Biogeography/
├── Analysis_Sj.Rmd
├── Analysis_Sm.Rmd
├── Analysis_Species.Rmd
└── data/
├── 04_Mukade_csv/
│ ├── 00_RY_Sp0122.csv
│ ├── 01_RY_mutilans0120.csv
│ └── 02_RY_japonica_0120.csv
└── Rawdata.xlsx
| File | Description |
|---|---|
| Analysis_Sj.Rmd | R Markdown script for analyses of Scolopendra japonica. |
| Analysis_Sm.Rmd | R Markdown script for analyses of Scolopendra mutilans. |
| Analysis_Species.Rmd | R Markdown script for interspecific analyses comparing S. japonica and S. mutilans. |
| data/04_Mukade_csv/00_RY_Sp0122.csv | Occurrence dataset used for interspecific analyses. Each row represents one occurrence record. |
| data/04_Mukade_csv/01_RY_mutilans0120.csv | Occurrence dataset used for analyses of S. mutilans. Each row represents one occurrence record. |
| data/04_Mukade_csv/02_RY_japonica_0120.csv | Occurrence dataset used for analyses of S. japonica. Each row represents one occurrence record. |
| data/Rawdata.xlsx | Raw occurrence and colour-pattern data. Geographic information for some records from Biome Inc. is withheld to protect observer privacy. |
Data Description and column definitions
data/
This folder contains the raw occurrence and colour-pattern data, as well as a subfolder containing the subset datasets used in the analyses.
Rawdata.xlsx:
Raw occurrence and colour-pattern data. Media platform names, URLs, and usernames have been removed to protect copyright, licensing, and observer privacy. Geographic information for some records provided by Biome Inc. has also been withheld to protect observer privacy.
Column definitions
-centipede species: Scientific name of the species recorded.
-latitude: Latitude of the record location. Values are given in decimal degrees
-longitude: Longitude of the record location. Values are given in decimal degrees
-leg_colour: Leg colour category (Red or Yellow) for the observed individual.
-elevation: Elevation of the recorded location. Values are given in meters above sea level.
-data_type: Type of information of the record. This column identifies whether each row was used as a distribution record, a predator record, a prey-item record, or a combined record.
These categories are defined as follows:
├── Distribution | Occurrence record for spatial analysis.
├── Predator | Record used for predator analysis. This record does not have geolocation information.
├── Prey item | Record used for prey item analysis. This record does not have geolocation information.
├── Distribution/Predator | Record used for both spatial analysis and predator analysis.
├── Distribution/Prey item | Record used for both spatial analysis and prey item analysis.
-prey/predator_Order: Taxonomic order of the prey or predator associated with the record. For predator records, this column indicates the order of the predator. For prey-item records, this column indicates the order of the prey item. A dash (-) indicates that no prey or predator information applies to that record.
-prey/predator_species: Scientific name or lowest available taxonomic identification of the prey or predator associated with the record. For predator records, this column indicates the predator taxon. For prey-item records, this column indicates the prey-item taxon. A dash (-) indicates that no prey or predator information applies to that record.
Missing and unavailable information
The string WITHHELD indicates that the information has been withheld to protect privacy. Values marked as WITHHELD should be treated as unavailable information, not as zero values or evidence of absence.
A dash (-) indicates that the corresponding field is not applicable to that record. For example, prey/predator columns contain - when the record does not include prey or predator information.
04_Mukade_csv/
This folder contains subset datasets derived from the raw occurrence data.
These files were used for each spatial analysis.
00_RY_Sp0122.csv
01_RY_mutilans0120.csv
02_RY_japonica_0120.csv
All three subset datasets have the same structure, as described below.
Column definitions
-Number: Anonymized record identifier. In the publicly shared dataset, original record identifiers are not provided and are replaced with the placeholder value 999 to protect observer privacy and confidential information associated with Biome Inc. records.
This column has no analytical meaning in the public dataset and should not be interpreted as a unique record number.
Access to the original identifiers may be considered upon reasonable request to the corresponding author (uno.ryosuke.33w[at]st.kyoto-u.ac.jp, please replace [at] with @), subject to permission from the data provider and applicable privacy and confidentiality restrictions.
-leg_colour: Leg colour category (Red or Yellow) for the observed individual.
-latitude: Latitude of the record location. Values are given in decimal degrees.
-longitude: Longitude of the record location. Values are given in decimal degrees.
Please note that the WITHHELDindicates that geolocation information from Biome Inc. is withheld in the shared dataset to protect observer privacy.
External environmental and GIS data not included in this Dryad submission
No GeoTIFF (.tif) files are included in this Dryad submission. The environmental raster files used by the analysis scripts were derived from external datasets and should be downloaded directly by users from the original providers. The derived stacked raster files are also not included; they can be reproduced locally by running the R Markdown scripts after placing the external data in the required folders.
Note: If you have any questions or need any assistance with this dataset, please feel free to reach out to the corresponding author.
Required external raster files: ENVIREM
Create the following directory:
Biogeography/gisData/envirem/
Download the current 30 arc-second ENVIREM rasters from the ENVIREM website (https://envirem.github.io/), and place the following files in the directory above:
current_30arcsec_aridityIndexThornthwaite.tif
current_30arcsec_climaticMoistureIndex.tif
current_30arcsec_continentality.tif
current_30arcsec_PETDriestQuarter.tif
Relevant ENVIREM variables used here:
| Raster variable | Meaning | Units |
|---|---|---|
| aridityIndexThornthwaite | Thornthwaite aridity index: Index of the degree of water deficit below water need. | Unitless index. |
| climaticMoistureIndex | Relative wetness and aridity metric. | Unitless index. |
| continentality | Average temperature difference between the warmest and coldest months. | Degrees Celsius. |
| PETDriestQuarter | Mean monthly potential evapotranspiration of the driest quarter. | mm/month. |
Required external raster files: WorldClim version 2.1
Create the following directory:
Biogeography/gisData/WorldClimV2/
Download the 30 arc-second WorldClim version 2.1 bioclimatic variables and place the following files from the WorldClim website (https://www.worldclim.org/data/bioclim.html) in the directory above:
wc2.1_30s_bio_2.tif
wc2.1_30s_bio_3.tif
wc2.1_30s_bio_4.tif
wc2.1_30s_bio_8.tif
wc2.1_30s_bio_9.tif
wc2.1_30s_bio_10.tif
wc2.1_30s_bio_11.tif
wc2.1_30s_bio_15.tif
wc2.1_30s_bio_18.tif
Relevant WorldClim variables used here:
| Raster variable | Meaning | Units |
|---|---|---|
| BIO2 | Mean diurnal range: mean of monthly maximum temperature minus minimum temperature. | Degrees Celsius |
| BIO3 | Isothermality: BIO2 / BIO7 × 100. | Unitless |
| BIO4 | Temperature seasonality. | Unitless |
| BIO8 | Mean temperature of the wettest quarter. | Degrees Celsius |
| BIO9 | Mean temperature of the driest quarter. | Degrees Celsius |
| BIO10 | Mean temperature of the warmest quarter. | Degrees Celsius |
| BIO11 | Mean temperature of the coldest quarter. | Degrees Celsius |
| BIO15 | Precipitation seasonality. | Unitless |
| BIO18 | Precipitation of the warmest quarter. | mm |
Required external vector file: Ecoregions 2017
The Ecoregions 2017 shapefile is not included in this Dryad package because it is an external dataset. To reproduce analyses requiring this layer, create the following directory:
Biogeography/input/ecoregions2017/
Download and extract Ecoregions2017.zip from the original provider, then place the following files in the directory above:
Ecoregions2017.dbf
Ecoregions2017.prj
Ecoregions2017.shp
Ecoregions2017.shx
R code for download:
dir.create("input", showWarnings = FALSE)
download.file(
"https://storage.googleapis.com/teow2016/Ecoregions2017.zip",
destfile = "input/Ecoregions2017.zip",
mode = "wb"
)
unzip("input/Ecoregions2017.zip", exdir = "input/ecoregions2017")
Derived raster files not included
The following derived GeoTIFF files are not included in this Dryad package:
input/environmentalData/env_S_japonica.tif
input/environmentalData/env_S_mutilans.tif
input/environmentalData/env_Sp.tif
These files are stacked environmental raster layers clipped to the analysis area.
They can be regenerated locally from the external ENVIREM, WorldClim, and Ecoregions files by running the R Markdown scripts.
Code and software
The analyses are provided as R Markdown (.Rmd) files.
All .Rmd files are located directly under Biogeography/ directory.
Users should open and run the R Markdown scripts from the top-level Biogeography/ directory so that the relative paths used in the scripts work correctly.
Recommended workflow:
- Unzip
Biogeography.zip. - Download the external ENVIREM, WorldClim, and Ecoregions files listed above.
- Place the downloaded files in the indicated directories without changing file names.
- Open the R Markdown files (
.Rmd) in RStudio. - Run the scripts from the project root directory.
Code/software
All analyses were done in R (R version 4.5.1).