Recent community warming of moths in Finland is driven by extinction in the north and colonisation in the south
Data files
Jun 30, 2025 version files 1.11 MB
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Ellis_et_al_full_analysis.zip
1.10 MB
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README.md
4.61 KB
Abstract
As the climate warms, species are shifting their ranges to match their climatic niches, leading to "thermophilisation" of ecological communities. We currently have little understanding of the population-level processes driving this community-level warming, particularly at rapidly warming high latitudes. Using 30 years of high-resolution moth monitoring data across a 1,200 km latitudinal gradient in Finland, we found that higher latitude communities are experiencing more rapid thermophilisation. We attribute this spatial variation to community-wide colonisation-extinction dynamics, both for the full community and for different thermal affinity groups. Our findings reveal that latitudinal variation in the pathways underpinning thermophilisation is the net outcome of opposite forces: In the north, community warming is driven by the extinction of cold-affiliated species, while in the south, it is driven by high colonisation rates of warm-affiliated species. Thus, we show how species' thermal affinities influence community reorganisation and highlight the elevated extinction risk among cold-affiliated species.
Author: Emilie E. Ellis
Contact: emilie.ellis95@gmail.com
Date: June 2025
Summary:
Here we have the core analysis for the manuscript ‘Recent community warming of moths in Finland is driven by extinction in the north and colonisation in the south’. There are 2 scripts included, script 1 (‘1_overall_script_final.R) is the core script that runs through every step of the analysis. A separate script, 2_MLE_thermal_groups.R is the core analysis of the manuscript but it takes about 3 days to run.
The following folder structure should be be followed:
Ellis_et_al_full_analysis should contain two folders: dataframes and scripts.
1. Data frames:
‘Ellis_et_al_full_analysis/data_frames_organised/‘ will contains the following files:
1) Ellis_et_al_full_analysis/data_frames_organised/1_STI_data_cleaned.csv
Description: The mean species temperature index per species. This also contains the correct synonyms for each moth species to match the moth data (see 2 below).
Data structure:
- new_REC_names: Species synonym to match the names in our clean moth data
- Species: Species name (original)
- manntmp.mean: the mean temperature of a species’ European distribution (species temperature index STI)
2) Ellis_et_al_full_analysis/data_frames_organised/2_cleaned_moth_data.csv
Description: cleaned raw data that was used for analysis: i) we confined our data to sites for which temporal change can be reliably established, we chose sites with at least 10 years of data; and ii) to derive a comparable baseline between sites, we excluded any sites that started data collection later than 2005. These filtering processes resulted in 728 species in 62 sites (see script 2 ‘2_cleaning_raw_data.R’.
Data structure:
- SiteID: the individual site identifiers.
- Species: Moth species name
- Year: The year the sample was collected (aggregated of weekly samples during the summer of each year)
- Obs: species specific abundance in each site and year.
3) Ellis_et_al_full_analysis/data_frames_organised/3_abiotic_meta_data.csv
*Description: * abiotic data for each site.
Data structure
- SiteID: the individual site identifiers.
- BZ: bioclimate zone (three levels: SB south boreal, MB middle boreal and NB north boreal, see Figure S1 in the MS).
- latitude_wgs_84: latitude (EPSG:3067) projected coordinate system in Finland.
- longitude_wgs_84 : longitude (EPSG:3067) projected coordinate system in Finland.
- lat: latitude converted from Finnish projects to geographic coordinates in decimal degrees WGS84
- long: longitude converted from Finnish projects to geographic coordinates in decimal degrees WGS84
4) Ellis_et_al_full_analysis/data_frames_organised/4_BioclimaticZonesFinland
*Description: * this is a folder containing the files needed to read a shape file in R to create a map of Finland (see script Ellis_et_al_full_analysis/scripts/4_generate_Finland_outline_map.R)
5) Ellis_et_al_full_analysis/data_frames_organised/5_MLE_thermal_group_outputs
*Description: * this is a folder containing the 12 outputs from script 2_MLE_thermal_groups.R which are the model summaries for each group vs latitude, abundance and species pools (e.g. each thermal group: cold adapted (cold), cold tolerant (coldish) , warm tolerant (warm) and warm adapted (hot) each tested separately against explanatory variables.
e.g. cold_abundance is the MLE output (model summary) testing how colonisation and extinction rtes of cold adapted species are explained by abundance of insects.
2. Scripts:
‘Ellis_et_al_full_analysis/scripts/‘ will contains the following files:
1) 1_overall_script.R:
Description: This script is the main script that runs all analysis of the manuscript (except final maximum likelihood estimates (in the other script).
Output: Full analysis and figures contained in this manuscript .
8) 8_MLE_thermal_groups.R:
Description: Second part of the main analysis. Using maximum likelihood approaches to estimate the effects latitude, site abundance and available species pools drive extinction-colonisation dynamics (one value per site). This script takes a long time to run (72 hours).
Outputs: a new folder called data_frames_organised/10_MLE_thermal_group_outputs/ with the following outputs:
- cold_latitude.RDS
- coldish_latitude.RDS
- warm_latitude.RDS
- hot_latitude.RDS
- cold_abundance.RDS
- coldish_abundance.RDS
- warm_abundance.RDS
- hot_abundance.RDS
- cold_pool.RDS
- coldish_pool.RDS
- warm_pool.RDS
- hot_pool.RDS
