Systematic conservation planning for mammals in the Australian Monsoonal Tropics: data files

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 v1.0.1. 澳大利亚季风热带区（Australian Monsoonal Tropics, AMT）哺乳动物灭绝风险系统发育最小二乘（phylogenetic least squares, PGLS）模型的预处理数据（01_amt_pgls_input_data.csv）： 本数据集包含经转换与标准化后的最终变量，作为系统发育最小二乘（phylogenetic least squares, PGLS）模型的输入数据，用于探究陆地哺乳动物物种灭绝风险与生态、环境关联分析。数据集包含代表物种当前IUCN红色名录（IUCN Red List）等级的有序响应变量，同时涵盖一系列预测变量，包括生活史特征、生物气候条件、与入侵物种的分布重叠范围，以及各物种分布区内的平均火灾频率（总火灾频率与旱季晚期火灾频率）。本数据集收录的所有物种均为澳大利亚季风热带区的本土物种，同时提供物种二项式学名，以方便匹配外部系统发育树或特征数据库进行后续分析。 以下为各变量说明： scientificName：物种二项式学名 ordinalThreat：结合物种IUCN红色名录等级与种群趋势得到的1~10的有序响应变量 centroid_lat：物种IUCN分布区的质心纬度 centroid_long：物种IUCN分布区的质心经度 area_total：物种IUCN分布区的总面积（单位：平方米） area_amt：物种IUCN分布区与AMT重叠的面积（单位：平方米） percent_overlap：(area_amt / area_total) * 100 percentOverlap_st：经标准化处理的上述百分比重叠变量 adult_mass_g_tr_st：经转换与标准化处理的物种成年体重（单位：克） age_first_reproduction_d_tr_st：经转换与标准化处理的物种首次繁殖年龄（单位：天） litter_size_n_tr_st：经转换与标准化处理的物种每胎幼崽数 litters_per_year_n_tr_st：经转换与标准化处理的物种每年产仔次数 rangeArea_km2_tr_st：经转换与标准化处理的物种地理分布区面积（单位：平方千米） foxAreaProp_tr_st：经转换与标准化处理的物种分布区与AMT内赤狐（red fox）分布区重叠比例 toadAreaProp_tr_st：经转换与标准化处理的物种分布区与AMT内蔗蟾（cane toads）分布区重叠比例 mean_firefreq_st：经标准化处理的物种分布区内平均总火灾频率 mean_latefire_st：经标准化处理的物种分布区内平均旱季晚期火灾频率 mean_bio8_st：经标准化处理的物种分布区内最湿季度平均气温 mean_hii_tr_st：经转换与标准化处理的物种分布区内平均人类影响指数（human influence index, HII） 2. 澳大利亚季风热带区（Australian Monsoonal Tropics, AMT）哺乳动物灭绝风险系统发育最小二乘（phylogenetic least squares, PGLS）模型输出数据（02_amt_pgls_output_data.csv）： 本数据集包含从系统发育最小二乘（PGLS）模型得到的平均拟合灭绝风险值，用于评估澳大利亚季风热带区陆地哺乳动物的物种特征、环境变量与灭绝风险之间的关联。平均拟合值通过对100次基于随机哺乳动物系统发育树运行得到的100个模型的拟合值取平均获得。数据集还包含物种的潜在灭绝风险值，该值通过用平均拟合值减去结合IUCN红色名录等级与种群趋势的有序响应变量计算得到。 以下为各变量说明： scientificName：物种二项式学名 redlistCategory：IUCN红色名录等级 populationTrend：IUCN红色名录所记录的种群趋势（下降、增长、稳定） ordinalThreat：结合物种IUCN红色名录等级与种群趋势得到的1~10的有序响应变量 mean_fitted_risk：经100个PGLS模型平均后的拟合风险值 latent_risk：物种潜在灭绝风险值 3. 澳大利亚季风热带区（Australian Monsoonal Tropics, AMT）哺乳动物系统保护规划所用的物种特征数据（03_amt_scp_feature_data.csv）： 本数据集包含用于优先区规划算法（prioritizr）系统保护规划的特征数据，涵盖物种分布数据（分布区面积与在AMT内的分布占比）以及针对澳大利亚季风热带区本土陆地哺乳动物的当前风险与潜在风险保护目标。 以下为各变量说明： scientificName：物种二项式学名 id：为每个物种分配的数字ID prop：物种分布区在AMT内的占比 ordinalThreat：结合物种IUCN红色名录等级与种群趋势得到的1~10的有序响应变量 mean_fitted_risk：经100个PGLS模型平均后的拟合风险值 latent_risk：物种潜在灭绝风险值 area_total：物种IUCN分布区的总面积（单位：平方米） area_amt：物种IUCN分布区与AMT重叠的面积（单位：平方米） percent_overlap：(area_amt / area_total) * 100 threatenedSpecies：被列为濒危（Endangered）或极危（Critically Endangered）的物种的ordinalThreat值（其余物种为NA threatenedSpecies_scaled：上述威胁值的标准化处理结果 target_1：在第一个保护目标（保护当前受威胁物种）下为每个物种分配的AMT分布区保护百分比目标 positiveLatentRisk：高潜在风险物种的潜在风险值（其余物种为NA） latentRisk_scaled：上述值的标准化处理结果 target_2：在第二个保护目标（保护潜在受威胁（高潜在风险）物种）下为每个物种分配的AMT分布区保护百分比目标 4. 澳大利亚季风热带区哺乳动物系统保护规划所用的规划单元数据（04_amt_scp_pu_data.csv）： 本数据集包含用于优先区规划算法（prioritizr）分析中用于识别优先保护区域的规划单元（planning units, PUs）的空间与成本相关属性。每个规划单元记录包含土地权属、面积加权成本代理变量，以及在情景建模练习中该规划单元是否被锁定纳入或排除出模型选择的逻辑变量。 以下为各变量说明： id：规划单元编号 area：规划单元面积（单位：平方米） capad：规划单元内占主导地位的土地权属的CAPAD保护地类别（CAPAD） nt：表示规划单元是否为原住民土地权（Native Title）土地的二元变量（1表示是，0表示否） ilua：表示规划单元是否受原住民土地使用协议（Indigenous Land Use Agreement, ILUA）约束的二元变量（1表示是，0表示否） pastoral：表示规划单元是否为放牧权属的二元变量（1表示是，0表示否） status：表示规划单元是否已纳入国家保护地系统的二元变量（1表示是，0表示否） locked_in：表示规划单元应被锁定纳入优先区规划算法选择的逻辑变量 locked_out_obj1：表示在目标1下规划单元应被锁定排除出优先区规划算法选择的逻辑变量 locked_out_obj2：表示在目标2下规划单元应被锁定排除出优先区规划算法选择的逻辑变量 cost：基于每个规划单元的中等雇员收入（medium employee income, MEI）与人类影响指数（HII）计算得到的成本代理值 cost_adjusted_pu：上述成本值经规划单元面积加权后的结果 main_id：表示规划单元主导土地权属类别的数字ID main_type：规划单元主导土地权属类别的宽泛类型 category：规划单元主导土地权属类别的描述 median_income：规划单元所在地方政府区域的中等雇员收入值 hii_oceania：规划单元的平均人类影响指数值 normal_hii：上述HII值的标准化处理结果 normal_mei：上述MEI值的标准化处理结果 area_prop：规划单元面积占最大规划单元面积的比例 用于制备和导出上述数据文件的R代码可通过GitHub与Zenodo平台的emmelinenorris/amt-scp: amt-scp v1.0获取。