Representative species sets for vascular plants generated for the Biodiversity Indicator Program, first assessment: expected survival and state of all known species - supplementary data package

This collection contains the data, processes and descriptions of workflows required to produce the representative species sets for vascular plants used in the NSW Biodiversity Indicator Program first assessment. The labels given to the datasets in this collection are defined in the workflow diagram and data links spreadsheet. This is a supplementary dataset that was used as an input to the three derived indicators for vascular plants: \n1.2a expected survival of all known species \n2.1a within-species genetic diversity (for all known species) \n2.1b extant area occupied (for all known species). \nDetails are given in the explanatory notes attached with this package and the method implementation report (Nipperess DA, Faith DP, Williams KJ, King D, Manion G, Ware C, Schmidt R, Love J, Drielsma M, Allen S & Ware C 2019, Expected survival and state of all known species: Data packages for the Biodiversity Indicator Program, first assessment.) accessed through the NSW Biodiversity Indicator Program website (see related links). \nLineage: Biological data used in this collection are a list of vascular plant species for NSW, generated from all NSW occurrence records (kingdom Plantae) downloaded from the Atlas of Living Australia (https://www.ala.org.au). Taxa were excluded from this list if they were not from a major subclass of vascular plants (Cycadidae, Pinidae, Magnoliidae, or a fern subclass); not a species-level or subspecific taxon; not listed as a valid name in both the Australian Plant Census (https://biodiversity.org.au/nsl/services/APC) and NSW PlantNet (http://plantnet.rbgsyd.nsw.gov.au/); or not listed as native in either the Australian Plant Census or NSW PlantNet. Data cleaning reduced the original list of 16,501 unique names to 5,528 species. All available occurrence records for this set of 5,528 species of vascular plants were downloaded from the Atlas of Living Australia. Records were then removed if they were not a preserved specimen; if spatial (latitude / longitude) or temporal (year of collection) data were incomplete; if they were a cultivated specimen; if they occurred more than 5 km outside the coastline of Australia; if they were collected prior to 1950; or their coordinate uncertainty (if known) was greater than or equal to 3000 meters. Cleaning reduced the initial dataset of 7,802,849 records for 5,528 species to 1,243,554 records for 5,506 species. These included occurrences anywhere in Australia, of which 4,859 species were represented by at least one occurrence within NSW (including ACT and commonwealth properties). A project-specific unique ID was assigned to each species to enable traceability in subsequent analyses. For other datasets within this repository, the process of how they were derived is described in the method implementation report. An existing GDM for vascular plants was used to represent the diversity of ecological environments occupied by vascular plants in New South Wales. This model is based on vascular plant survey data from across south-eastern continental Australia (‘NARCliM Domain’) and used 25 environmental predictors (19 climate, 6 substrate). \nRepresentative sets of species to be selected were developed using the .NET Survey Gap Analysis Tool. Diagnostic measures of environmental representation and range size were used to select an optimal number of demand points (1149) which were equated with the names of the species selected as representative. These species were then used as an input to the three derived indicators for vascular plants: \n1.2a expected survival of all known species \n2.1a within-species genetic diversity (for all known species) \n2.1b extant area occupied (for all known species). \nDetails are given in the explanatory notes attached with this package

本集合包含生成新南威尔士州生物多样性指标计划（NSW Biodiversity Indicator Program）首次评估所用维管植物（vascular plants）代表性物种集所需的数据、流程及工作流描述。本集合中数据集的标签定义于工作流图和数据链接表格中。本数据集为补充数据集，用作维管植物三个衍生指标的输入：
1.2a 所有已知物种的预期存活
2.1a 种内遗传多样性（针对所有已知物种）
2.1b 现存占据面积（针对所有已知物种）。
详情见本数据包附带的解释说明及方法实施报告（Nipperess DA, Faith DP, Williams KJ, King D, Manion G, Ware C, Schmidt R, Love J, Drielsma M, Allen S & Ware C 2019, 《所有已知物种的预期存活与状态：生物多样性指标计划首次评估数据包》），该报告可通过新南威尔士州生物多样性指标计划网站获取（见相关链接）。
谱系信息：本集合所用生物数据为新南威尔士州维管植物物种列表，该列表基于从澳大利亚生物地图集（Atlas of Living Australia，https://www.ala.org.au）下载的所有新南威尔士州植物界（Plantae）出现记录生成。若分类单元满足以下任一条件，则从列表中排除：不属于维管植物的主要亚纲（苏铁亚纲Cycadidae、松亚纲Pinidae、木兰亚纲Magnoliidae或蕨类亚纲）；非物种级或亚种级分类单元；未同时列入澳大利亚植物名录（Australian Plant Census，简称APC，https://biodiversity.org.au/nsl/services/APC）和新南威尔士植物网（NSW PlantNet，http://plantnet.rbgsyd.nsw.gov.au/）的有效名称；或未在澳大利亚植物名录或新南威尔士植物网中列为本地物种。数据清洗后，原始的16501个唯一名称列表缩减至5528个物种。
从澳大利亚生物地图集下载了该5528种维管植物的所有可用出现记录。若出现记录满足以下任一条件，则予以移除：非保存标本；空间（纬度/经度）或时间（采集年份）数据不全；为栽培标本；位于澳大利亚海岸线以外5公里以上；采集于1950年前；或坐标不确定性（若已知）大于等于3000米。清洗后，初始的5528种物种的7802849条记录缩减至5506种物种的1243554条记录。这些记录涵盖澳大利亚境内所有地区的出现情况，其中4859种物种在新南威尔士州（含澳大利亚首都领地ACT及联邦属地）至少有一次出现记录。为每个物种分配了项目专属唯一ID，以便后续分析中的可追溯性。
对于本知识库中的其他数据集，其衍生过程详见方法实施报告。使用现有的维管植物GDM模型（广义差异模型，Generalized Dissimilarity Modeling）来表征新南威尔士州维管植物所占据的生态环境多样性。该模型基于澳大利亚东南部大陆（"NARCliM Domain"）的维管植物调查数据，采用25个环境预测因子（19个气候因子，6个基质因子）。
代表性物种集通过.NET Survey Gap Analysis Tool工具筛选生成。利用环境代表性和分布范围大小的诊断指标，筛选出最优数量的需求点（1149个），这些需求点与选中的代表性物种名称一一对应。这些物种随后用作维管植物三个衍生指标的输入：
1.2a 所有已知物种的预期存活
2.1a 种内遗传多样性（针对所有已知物种）
2.1b 现存占据面积（针对所有已知物种）。
详情见本数据包附带的解释说明。