Tree composition mitigates the negative effects of urbanization on specialist and generalist forest moth communities
Data files
Apr 16, 2025 version files 1.35 MB
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allmoths_traits_12feb2024_format.csv
681.34 KB
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final_foodplant_analysis.Rmd
2.98 KB
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JAGS_moth_analysis.txt
2.98 KB
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JAGS_moth_richness_rarefied.txt
2.93 KB
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JAGS_moth_specializationDistance_analysis.txt
2.90 KB
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leps_withplants.csv
199.29 KB
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moth_bayesian_analysis.Rmd
15.10 KB
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moth_data.csv
15.61 KB
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moth_rareifiedRichness_generalists.csv
9.06 KB
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moth_rareifiedRichness_specialists.csv
8.73 KB
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README.md
9.64 KB
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rlq_data_justHerbivores.RDS
160.10 KB
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rlq_data.RDS
224.08 KB
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site_summary.csv
14.38 KB
Abstract
Changes at local and landscape scales impact forests embedded in urban and urbanizing landscapes. In the Northeast USA, urban forest fragments are characterized by smaller sizes, low connectivity, and novel plant assemblages relative to intact natural areas. Disruptions of connectivity from landscape-scale development can negatively impact habitat suitability and colonization by terrestrial insects, but managing local tree compositions may offset negative impacts, especially for phytophagous taxa specialized to host plants.
Here, we surveyed nocturnal moth community diversity using light traps deployed within forest fragments that varied in surrounding urban development, tree floristics, and tree structure.
We found that local and landscape-scale factors interact to affect temperate forest moth communities. In most cases, impervious surface (as a proxy for urbanization) negatively impacted moth communities, whereas the basal area of Lepidoptera-rich host plants positively affected moth communities. However, the magnitude of benefits of Lepidoptera-rich host trees were most apparent at low levels of urbanization and most substantial for specialists over generalists.
Practical Implication: These results provide evidence that forest management approaches prioritizing tree species that support a high richness of species interactions can offset the adverse effects of fragmentation on vital insect taxa at different levels of urban development. However, at high levels of urban development, other urban-associated mechanisms, such as artificial light, pesticides, and reduced dispersal, may inhibit sustainable populations of sensitive moth species.
R script, JAGS model, and data used to test relationships between moth community metrics, urbanization and forest characteristics in Delaware and Pennsylvania, USA.
Missing data is indicated by NA.
Description of the data and file structure
File 1: JAGS_moth_analysis.txt-
- JAGS model used to test relationships between moth community metrics, urbanization, and forest characteristics.
File 2: JAGS_moth_specializationDistance_analysis.txt
- JAGS model used to test relationships between moth specialization distance, urbanization, and forest characteristics.
File 3: JAGS_moth_richness_rarefied.txt
- JAGS model used to test relationships between moth rarefied richness, urbanization, and forest characteristics.
File 4: moth_bayesian_analysis.Rmd
- R script that loads datasets and formats data for the JAGS model. Has code for summarizing and visualizing posterior distributions.
File 5: site_summary.csv - site-level summaries of moth abundance, moth biomass, impervious surface, basal area, genus richness and Lepidoptera-rich tree basal area.
site_format: character string, site name
plot: numeric, plot ID
year: numeric, year
specialist_abundance: numeric, abundance of genus-specialist moths
generalist_abundance: numeric, abundance of genus-generalist moths
other_abundance:numeric, abundance of other moths
total_abundance:numeric, total abundance of moths
specialist_biomass: numeric, biomass (in mg) of genus-specialist moths
generalist_biomass: numeric, biomass (in mg) of genus-generalist moths
other_biomass: numeric, biomass (in mg) of other moths
total_biomass:: numeric, biomass (in mg) of all moths
specialist_family_abundance: numeric, abundance of family-specialist moths
generalist_family_abundance: numeric, abundance of family-generalist moths
other_family_abundance: numeric, abundance of other moths
total_family_abundance: numeric, abundance of all moths
specialist_family_biomass: numeric, biomass (in mg) of family-specialist moths
generalist_family_biomass: numeric, biomass (in mg) of family-generalist moths
other_family_biomass: numeric, biomass (in mg) of other moths
total_family_biomass: numeric, biomass (in mg) of all moths
total_basal: numeric, total basal area of trees
genera_richness:numeric, total genera richness of trees
keystone_basal:numeric,total basal area of keystone trees
productivity_index: numeric, productivity value (basal area * lepidoptera richness supported)
productivity: numeric, productivity value (basal area * lepidoptera richness supported)
lat_fixed: latitude
long_fixed: longitude
imperv_1km_mean: numeric, mean proportion of impervious surface within 1km
imperv_500m_mean: numeric, mean proportion of impervious surface within 500m
prop_keystone: numeric, proportion of keystone tree biomass
year_factor: numeric, year as a factor
rep: unique ID
scaled_imperv: numeric, scaled value of impervious surface
scaled_basal: numeric, scaled value of basal area
scaled_genera: numeric, scaled value of genera richness
scaled_keystone: numeric, scaled value of keystone basal area
year_binary: binary, 2018=1
File 6: allmoths_traits_12feb2024_format.csv - Individual species and counts for each sampling event with associated traits.
Site: Character string, site name
plot: numeric, plot ID
date: Date, date of sampling
count: numeric, total number of moth individuals
species: character string, moth scientific name
species_good: character string, moth scientific name
foodtype_broad: category, food type
foodtype_specific: category, food type
hostplants_genera: numeric, number of host plant genera
hostplants_family:numeric, number of host plant families
wing_low: numeric, minimum wing measurement
wing_high: numeric, maximum wing measurement
exotic: binary, exotic to the United States, yes=1
specialization_distance: phylogenetic distance among host plant genera
specialization_notes: character string, notes about specialization
gbif_totalCount: Number of gbif observations
sampleSize: Number of gbif observations
area_km2: numeric, area in km2 of all gbif observations (minimum convex polygon)
minFlight: numeric, earliest month observed in gbif records
maxFlight: numeric, latest month observed in gbif records
lengthFlight: numeric, range of flight from min to max
gbif_notes: notes
date_format: date, formatted date
year: numeric,year of sampling
month: numeric, month of sampling
specialist: category, specialist or generalist at the genus level
specialist_family: category, specialist or generalist at the family level
File 7: moth_rareifiedRichness_specialists.csv - Rarefied richness of genus specialist moths
Assemblage: character string, unique assemblage (plot + year)
Diversity: category string, estimate type
Observed: numeric: observed number of species
Estimator: numeric: estimated number of species
s.e.: numeric, standard error
LCL: numeric, lower confidence limit
UCL: numeric, upper confidence limit
variance: numeric, variance estimate
ID: numeric, plot ID
site_format: character string, site name
plotID: numeric, plot ID
year: numeric,year
scaled_imperv: scaled variable, impervious surface
scaled_basal:scaled variable, basal area all trees
scaled_genera: scaled variable, number of plant genera
scaled_keystone:scaled variable,basal area of keystone trees
Site: character string, site name
year_factor: numeric, year as a factor
rep: numeric, unique ID
year_binary: binary, year where 2018 = 1
File 8: moth_rareifiedRichness_generalists.csv - Rarefied richness of genus generalist moths (output from iNext)
Assemblage: character string, unique assemblage (plot + year)
Diversity: category string, estimate type
Observed: numeric: observed number of species
Estimator: numeric: estimated number of species
s.e.: numeric, standard error
LCL: numeric, lower confidence limit
UCL: numeric, upper confidence limit
variance: numeric, variance estimate
ID: numeric, plot ID
site_format: character string, site name
plotID: numeric, plot ID
year: numeric,year
scaled_imperv: scaled variable, impervious surface
scaled_basal:scaled variable, basal area all trees
scaled_genera: scaled variable, number of plant genera
scaled_keystone:scaled variable,basal area of keystone trees
Site: character string, site name
year_factor: numeric, year as a factor
rep: numeric, unique ID
year_binary: binary, year where 2018 = 1
File 9. leps_withplants.csv moth species, counts, and basal area of host trees at each plot
plot: numeric, plot ID
mothID: character string, moth scientific name
mothID_format:character string, moth scientific name
count: numeric, count of moth individuals
total_basal_all: numeric, basal area of all known host plants
planttype: category, plant type woody (wood)
num_hostplants: numeric, number of known host genera
category: specialism category (generalist or specialist)
File 10. final_foodplant_analysis.Rmd
- Rscript to run GLMM of Host plant relationships with the abundance of individual species.
File 11. rlq_data.RDS
- Data file of matrices for RLQ and Fourth Corner Analysis.
File 12. rlq_data_justHerbivores.RDS
- Data file of matrices for RLQ and Fourth Corner Analysis for just herbivores.
File 13. moth_data.csv
ID: numeric, unique ID
plot: numeric, plot number
year: numeric, year
specialist_abundance: numeric, abundance of genus-specialist moths
generalist_abundance: numeric, abundance of genus-generalist moths
other_abundance:numeric, abundance of other moths
total_abundance:numeric, total abundance of moths
specialist_richness: numeric, richness of genus-specialist moths
generalist_richness: numeric, richness of genus-generalist moths
other_richness: numeric, richness of other moths
total_richness: numeric, total richness of moths
specialist_biomass: numeric, biomass (in mg) of genus-specialist moths
generalist_biomass: numeric, biomass (in mg) of genus-generalist moths
other_biomass: numeric, biomass (in mg) of other moths
total_biomass:: numeric, biomass (in mg) of all moths
specialist_family_richness
generalist_family_richness
other_family_richness
total_family_richness
specialist_family_abundance: numeric, abundance of family-specialist moths
generalist_family_abundance: numeric, abundance of family-generalist moths
other_family_abundance: numeric, abundance of other moths
total_family_abundance: numeric, abundance of all moths
specialist_family_biomass: numeric, biomass (in mg) of family-specialist moths
generalist_family_biomass: numeric, biomass (in mg) of family-generalist moths
other_family_biomass: numeric, biomass (in mg) of other moths
total_family_biomass: numeric, biomass (in mg) of all moths
plotID: numeric, plot number
site: character, site name
siteID.x: numeric, plot number
total_basal: numeric, total basal area of trees
genera_richness:numeric, total genera richness of trees
keystone_basal:numeric,total basal area of keystone trees
productivity_index: numeric, productivity value (basal area * lepidoptera richness supported)
productivity: numeric, productivity value (basal area * lepidoptera richness supported)
siteID.y: character, site and plot name
site_name: character: site name
lat_fixed: latitude
long_fixed: longitude
imperv_1km_mean: numeric, mean proportion of impervious surface within 1km
imperv_500m_mean: numeric, mean proportion of impervious surface within 500m
imperv_100m_mean: numeric, mean proportion of impervious surface within 100m
imperv_50m_mean: numeric, mean proportion of impervious surface within 50m
prop_keystone: numeric, proportion of keystone plants
site_format: character, formatted site name