Data from: Temporal biotic homogenisation patterns due to urbanisation are taxon-dependent

Iwachido, Yuki 1 ; Yamamoto, Sumire1; Sun, Xi1; Sasaki, Takehiro1

Published Mar 25, 2025 on Dryad. https://doi.org/10.5061/dryad.hqbzkh1tn

Data files

Mar 25, 2025 version files 1.77 MB

Abstract

Aim: Accelerated urbanisation poses a major threat to global biodiversity. However, few studies have explored patterns of temporal biotic homogenisation due to urbanisation across multiple taxa.

Location: Tokyo, Japan

Methods: We examined the temporal changes in species richness and composition in 15 remnant green spaces across the Tokyo metropolitan area, Japan, focusing on native species of three taxa (plants: 15 sites, birds: 7 sites, and butterflies: 7 sites). First, we compared gamma diversity and species composition (dispersion and itself) between two surveys at a regional scale included all study sites. Furthermore, we assessed temporal change in alpha diversity (species richness over time) and temporal beta diversity (changes in species composition over time) at each green space. We also clarified the relationships between those indices and environmental variables. To determine the species more impacted by urbanisation, we examined the relationship between the rate of species loss and their traits related to dispersal and adaptation.

Results: Gamma diversity decreased from the first to the second survey regardless of taxa. However, the pattern of temporal diversity changes due to urbanisation varied among taxa. For plants, temporal changes in alpha diversity decreased with the number of years between surveys. For birds, temporal beta diversity increased with the number of years between surveys. For butterflies, the dispersion of species composition at the regional scale decreased slightly from the first and the second survey. Annual herb and water-dispersal plant species, as well as bird species with higher diet specialization, were more prone to lose due to urbanisation. Main conclusions: Our findings demonstrate that patterns of temporal biotic homogenisation due to urbanisation vary among taxa. Therefore, enhancing species diversity within each green space and promoting species composition differences among green spaces is necessary to maximise multi-taxa diversity in urban areas.

https://doi.org/10.5061/dryad.hqbzkh1tn

Description of the data and file structure

This data contains the raw data for plant (df_plant_output.csv), bird (df_bird_output.csv), and butterfly (df_butterfly_output.csv) communities of past and present at each green space, and environments for each green space (df_env_output.csv), and script for analysis (analysis.html). Those not found in the database are indicated as NA in the trait values for each taxon.

Discriptions:

raw data for plant commuties (df_plant_output.csv)

site: study site name
time: survey time (past or present)
value: Whether it was discovered at the time of the survey (all value are 1)
exotic: Native species or Exotic species
sciname: scientific species name
growth: growth form at each species (tree, perennial, annual, NA)
disper: dispersal mode (grabity, wind, animal, water, NA)

raw data for bird commuties (df_bird_output.csv)

site: study site name
time: survey time (past or present)
sciname: scientific species name
value: Whether it was discovered at the time of the survey (all value are 1)
exotic: Native species or Exotic species
Beak: beak lenght for each bird species (centimeter)
HWI: hand-wing index for each bird species (ratio)
Mass: body mass for each bird species (gram)
spec_diet: specilization of diet for bird species (bigger values indicate a smaller feeding range) (unit less)
spec_nest: specilization of nest place for bird species (bigger values indicate a limited nest place) (unit less)

raw data for butterfly commuties (df_butterfly_output.csv)

site: study site name
time: survey time (past or present)
sciname: scientific species name
value: Whether it was discovered at the time of the survey (all value are 1)
exotic: Native species or Exotic species
FlightDuration: number of months per year that can be inhabited (month)
WS: wing span for each butterfly species (cm)
hostplant: number of host plant species richness

raw data for environmental variables (df_env_output.csv)

site: study site name
year: number of years between surveys (past and present)
area: size of green space (m2)
green_rate: green cover around study site within 1km (ratio)

Code/software

All statistical analysis code in R (analysis.html)

This is code for all analysis (Fig. 1-5)