DOI: 10.5281/zenodo.15142190
title: Systematic conservation planning for mammals in the Australian Monsoonal Tropics: data files

description: 1. Prepared data for phylogenetic least squares (PGLS) models of extinction risk for AMT mammals (01_amt_pgls_input_data.csv): 

This dataset contains the final, transformed, and standardised variables used as input to phylogenetic least squares (PGLS) models examining the ecological and environmental correlates of extinction risk in terrestrial mammal species. The data include the ordinal response variable representing species’ current IUCN Red List category, alongside a range of predictor variables such as life history traits, bioclimatic conditions, range overlap with invasive species, and mean fire frequency (total and late dry season fire) within each species' range. All species included in the dataset occur are native to the Australian Monsoonal Tropics, and species scientific names are provided to enable matching with external phylogenetic trees or trait databases.







scientificName: species' binomial name

ordinalThreat: ordinal response variable from 1-10 combining species' IUCN Red List category and population trend

centroid_lat: centroid latitude for each species' IUCN distribution area

centroid_long: centroid longitude for each species' IUCN distribution area

area_total: total area (m^2) of species' IUCN distribution area

area_amt: area (m^2) of species' IUCN distribution area overlapping with AMT

percent_overlap: (area_amt / area_total) * 100

percentOverlap_st: above variable, standardised

adult_mass_g_tr_st: adult mass (g) for each species; transformed and standardised

age_first_reproduction_d_tr_st: age of first reproduction (days) for each species; transformed and standardised 

litter_size_n_tr_st: litter size (n) for each species; transformed and standardised

litters_per_year_n_tr_st: litters per year (n) for each species; transformed and standardised

rangeArea_km2_tr_st: geographic range area (km^2) transformed and standardised

foxAreaProp_tr_st: proportion of each species' range overlapping with distribution of red foxes in AMT; transformed and standardised

toadAreaProp_tr_st: proportion of each species' range overlapping with distribution of cane toads in AMT; transformed and standardised

mean_firefreq_st: mean total fire frequency in each species' range; standardised

mean_latefire_st: mean late dry season fire frequency in each species' range; standardised

mean_bio8_st: mean temperature of wettest quarter for each species' range; standardised

mean_hii_tr_st: mean human influence index (HII) for each species range; transformed and standardised




 

2. Model outputs from phylogenetic least squares (PGLS) analyses of extinction risk in AMT mammals (02_amt_pgls_output_data.csv): 

This dataset includes the mean fitted extinction risk values from phylogenetic least squares (PGLS) models assessing associations between species traits, environmental variables, and extinction risk for terrestrial mammals in the Australian Monsoonal Tropics. Mean fitted values were obtained by averaging fitted values from 100 models run using 100 random mammal phylogenies. The dataset also includes species' latent extinction risk values, calculated by subtracting the ordinal response variable (combining IUCN Red List category and trend) from the mean fitted value. 







scientificName: species' binomial name

redlistCategory: category on IUCN Red List

populationTrend: population trend (declining, increasing, stable) as per IUCN Red List

ordinalThreat: ordinal response variable from 1-10 combining species' IUCN Red List category and population trend

mean_fitted_risk: fitted risk values from PGLS models averaged over 100 models

latent_risk: species' latent extinction risk values




 

3. Species feature data used in systematic conservation planning for AMT mammals (03_amt_scp_feature_data.csv):

This dataset contains the feature data used as input to the prioritizr algorithm for systematic conservation planning. It includes species distribution data (range size and proportion of range in AMT) and protection targets for current risk and latent risk native terrestrial mammal species occurring in the Australian Monsoonal Tropics.







scientificName: species' binomial name

id: numeric ID assigned to each species

prop: proportion of species' range in AMT

ordinalThreat: ordinal response variable from 1-10 combining species' IUCN Red List category and population trend

mean_fitted_risk: fitted risk values from PGLS models averaged over 100 models

latent_risk: species' latent extinction risk values

area_total: total area (m^2) of species' IUCN distribution area

area_amt: area (m^2) of species' IUCN distribution area overlapping with AMT

percent_overlap: (area_amt / area_total) * 100

threatenedSpecies: ordinalThreat for species listed as Endangered or Critically Endangered (other species NA)

threatenedSpecies_scaled: above threat values scaled

target_1: protection targets (% of AMT range to secure) assigned to each species under the first target of protecting currently threatened species

positiveLatentRisk: latent risk values for high latent risk species (other species NA)

latentRisk_scaled: above values scaled

target_2: protection targets (% of AMT range to secure) assigned to each species under the second target of protecting potentially threatened (high latent risk) species




 

4. Planning unit data used in systematic conservation planning for AMT mammals (04_amt_scp_pu_data.csv): 

This dataset includes spatial and cost-related attributes of planning units (PUs) used in the prioritizr analyses to identify priority conservation areas. Each PU record includes land tenure, area-weighted cost proxies, and whether a given PU is locked in or out (logical) in the scenario modelling exercises.







id: planning unit ID number

area: PU area (m^2)

capad: CAPAD protected area category (if protected area is dominant land tenure in PU)

nt: binary variable for whether PU is Native Title land (1) or not (0)

ilua: binary variable for whether PU is under an Indigenous Land Use Agreement (1) or not (0)

pastoral: binary variable for whether PU is under pastoral tenure (1) or not (0)

status: binary variable for whether PU is currently protected in the National Reserve System (1) or not (0)

locked_in: logical variable indicating whether PUs should be locked into prioritizr algorithm selection

locked_out_obj1: logical variable indicating whether PUs should be locked out from prioritizr algorithm selection under Objective 1

locked_out_obj2: logical variable indicating whether PUs should be locked out from prioritizr algorithm selection under Objective 2

cost: proxy cost computed from medium employee income (MEI) and human influence index (HII) values for each PU

cost_adjusted_pu: above cost values weighted by PU area

main_id: numeric ID indicating dominant PU land tenure classification

main_type: broad type of dominant PU land tenure classification

category: description of dominant PU land tenure classification

median_income: median employee income (MEI) value for PU local government area

hii_oceania: mean human influence index value for PU

normal_hii: above HII value standardised

normal_mei: above HII value standardised

area_prop: area of PU as a proportion of maximum PU area




 

The R code used to prepare and derive these data files can be accessed via GitHub and Zenodo emmelinenorris/amt-scp: amt-scp v1.0.