Data and code for "Leaf dry matter content is phylogenetically conserved and related to environmental conditions, especially wildfire activity"

Data and code for "Leaf dry matter content is phylogenetically conserved and related to environmental conditions, especially wildfire activity"<br>Files in the folder:<br>1 - LDMCdataset.csv<br>It contains:<br>species: species names checked according to the World Flora Online (https://www.worldfloraonline.org/)<br>phylogenetic_groups: classify according to APG III (2009)(http://www.mobot.org/MOBOT/research/APweb/).<br>growth_form: classify according to the descriptions of each species’ adult form in the Encyclopedia of Life (https://eol.org/)<br>postfire_regeneration: species that have or do not have traits associated with postfire regeneration<br>regeneration_strategies: seeders (facultative seeders and obligate seeders), non-seeders (obligate resprouters), and unknown (species were only reported to have seedling emergence in the first year after fire, but it is unclear how they specifically regenerated)<br>LDMC: leaf dry matter content (original unit: g g-1)<br>FA: defined as the logarithm of the average number of fire incidences in each region divided by the size of the region, as recorded by the Moderate Resolution Imaging Spectroradiometer (MODIS) sensor in the Terra satellite at 30 seconds resolution, no unit<br>TN: soil total nitrogen content (original unit: g kg-1)<br>MAT: mean annual temperature (original unit: ℃)<br>MAP: mean annual precipitation (original unit: mm)<br>AI: aridity index (the ratio of mean annual precipitation to mean annual reference evapotranspiration)<br>2 - LDMC.treeThe phylogenetic tree for the species list in LDMCdataset.csv.<br>3 - Main_Analysis_Code.RIt contains all the analytical steps to reproduce the results reported in the main text.<br>4 - Check_Species_Names.RCode for verifying and correcting species names. Species names are matched against the World Flora Online Taxonomic Backbone using the WorldFlora package.<br>5 - GBIF_Coordinate_Cleaning_and_Environmental_Data_Extraction.RCode for extracting species distribution data from GBIF, cleaning erroneous coordinates, and linking these coordinates to environmental variables such as fire activity, soil total nitrogen content, mean annual temperature, mean annual precipitation, and aridity index.<br>6 - Figure_Replication_Steps.txtProvides detailed instructions on replicating Figures 1–4 using Origin software.<br>7 - WFOTaxonomicBackbone_v.1.7_20220712.zipThe World Flora Online Taxonomic Backbone database used for species name verification (Source:https://www.worldfloraonline.org/downloadData).<br>8 - unchecked_species_name.csvA list of species names prior to review and correction.<br>9 - wc2.1_30s_bio_1.tifRaster file containing global data for mean annual temperature (MAT) at 30 seconds resolution from the WorldClim (https://www.worldclim.org/data/worldclim21.html).<br>10 - wc2.1_30s_bio_12.tifRaster file containing global data for mean annual precipitation (MAP) at 30 seconds resolution from the WorldClim (https://www.worldclim.org/data/worldclim21.html).<br>11 - fire activity.tifRaster file with fire activity index data prepared for spatial analysis in the study (source: https://doi.org/10.6084/m9.figshare.4579327.v2).<br>12 - nitrogen.tifRaster file for soil total nitrogen content sourced from SoilGrids (https://geodata.ucdavis.edu/geodata/soil/soilgrids/).<br>13 - ai_v3_yr.tifRaster file for aridity index sourced from the Global Aridity Index database (https://doi.org/10.6084/m9.figshare.7504448.v6).

本数据集与配套代码对应论文《叶片干物质含量具有系统发育保守性且与环境条件密切相关，尤以野火活动为甚》。
文件夹内包含的文件如下：
1. LDMCdataset.csv：该文件包含以下字段：
- species（物种名）：已根据世界植物在线（World Flora Online, WFO）（https://www.worldfloraonline.org/）完成校验的物种学名
- phylogenetic_groups（系统发育类群）：依据2009年被子植物系统发育组III（Angiosperm Phylogeny Group III, APG III, 2009）（http://www.mobot.org/MOBOT/research/APweb/）进行的分类
- growth_form（生长型）：依据生命百科全书（Encyclopedia of Life, EOL）（https://eol.org/）中各物种成年个体形态描述完成的分类
- postfire_regeneration（火后更新能力）：标注物种是否具有与火后更新相关的功能性状
- regeneration_strategies（更新策略）：分为播种者类群（facultative seeders兼性播种者与obligate seeders专性播种者）、非播种者类群（obligate resprouters专性萌蘖更新者）以及未知类群（仅报道火灾后第一年出现实生苗，但具体更新机制尚不明确的物种）
- LDMC（叶片干物质含量，Leaf Dry Matter Content）：原始单位为g·g⁻¹
- FA（火活动指数）：定义为各区域平均火灾发生次数的对数除以区域面积，数据来自Terra卫星搭载的中分辨率成像光谱仪（Moderate Resolution Imaging Spectroradiometer, MODIS）传感器记录，分辨率为30秒，无计量单位
- TN（土壤全氮含量）：原始单位为g·kg⁻¹
- MAT（年平均气温）：原始单位为℃
- MAP（年平均降水量）：原始单位为mm
- AI（干旱指数）：定义为年平均降水量与年平均参考蒸散量的比值
2. LDMC.tree：对应LDMCdataset.csv中物种列表的系统发育树文件
3. Main_Analysis_Code.R：包含复现论文正文报告结果所需的全部分析步骤代码
4. Check_Species_Names.R：用于校验与校正物种学名的代码，通过WorldFlora软件包将物种学名匹配至世界植物在线分类骨干数据库
5. GBIF_Coordinate_Cleaning_and_Environmental_Data_Extraction.R：用于从全球生物多样性信息设施（Global Biodiversity Information Facility, GBIF）提取物种分布数据、清理错误坐标，并将这些坐标与火灾活动、土壤全氮含量、年平均气温、年平均降水量及干旱指数等环境变量进行关联的代码
6. Figure_Replication_Steps.txt：提供使用Origin软件复现图1至图4的详细操作说明
7. WFOTaxonomicBackbone_v.1.7_20220712.zip：用于物种学名校验的世界植物在线分类骨干数据库（数据来源：https://www.worldfloraonline.org/downloadData）
8. unchecked_species_name.csv：待校验与校正的物种学名列表
9. wc2.1_30s_bio_1.tif：来自WorldClim数据库（https://www.worldclim.org/data/worldclim21.html）的30秒分辨率全球年平均气温（MAT）栅格数据文件
10. wc2.1_30s_bio_12.tif：来自WorldClim数据库的30秒分辨率全球年平均降水量（MAP）栅格数据文件
11. fire activity.tif：本研究空间分析所用的火活动指数栅格数据文件（数据来源：https://doi.org/10.6084/m9.figshare.4579327.v2）
12. nitrogen.tif：源自SoilGrids数据库的土壤全氮含量栅格数据文件（https://geodata.ucdavis.edu/geodata/soil/soilgrids/）
13. ai_v3_yr.tif：源自全球干旱指数数据库的干旱指数栅格数据文件（https://doi.org/10.6084/m9.figshare.7504448.v6）