Aggregated Counts and Lists of Native Species in Terrestrial Bioregions 1900-2023

Species occurrence data from the Atlas of Living Australia (ALA), between 1900 and 2023, were used to create data summaries of native species in terrestrial bioregions (IBRA7). This data collection comprises two datasets: counts of native species in each terrestrial bioregion, and lists of native species with taxonomic information and EPBC status in each terrestrial bioregion. \n\nThe counts of native species by bioregion informed an analysis of change in the proportion of species likely to persist over the very long term (S), using the species-area relationship (SAR) with a z-value of 0.25 (S = A^z), and average condition (A) within each bioregion over a time series from the Habitat Condition Assessment System (HCAS) version 3.0. A national-level indicator can then be derived as a species richness weighted average of the bioregional analysis. The counts of EPBC Act threatened species by bioregions is used to inform an interpretation of the condition status of each bioregion. The lists of native species by bioregion provide a basis for an updated analysis that takes into account the fact that species are shared between bioregions and this has an impact on the proportion of species likely to persist over the very long term, when summarised at a national level. These outputs support interpretation of the HCAS and National Connectivity Index (NCI) for the Australian Government’s environment corporate performance measure EN01 (2023-24 Annual Report of the Department of Climate Change, Energy, the Environment and Water). This data collection may also be relevant for other types of analysis at the bioregional level or with different data inputs for the SAR analysis.\n\nThe ALA aggregates data from hundreds of different data providers, using different methods, into a single database. Consequently, observations in the ALA display spatial, temporal, and taxonomic bias that ensure care must be taken in their interpretation in downstream analysis. When summarising to the bioregional scale, survey effort is broadly correlated with accessibility, meaning that bioregions near major cities may appear disproportionately biodiverse relative to more remote regions. \nLineage: All species occurrence data aggregated by the ALA as of 25 June 2024 were downloaded and filtered using the galah R package to include only records:\n\n• passing the ALA general data quality profile (https://support.ala.org.au/support/solutions/articles/6000240256-getting-started-with-the-data-quality-filters)\n• occurring in the years 1900-2023\n• where the taxon was identified to at least species level \n• identified within an IBRA terrestrial bioregion \n\nA secondary download without the ALA data quality profile was additionally carried out to retrieve records that would have been initially excluded on the grounds of coordinate uncertainty. Records with a high degree of coordinate uncertainty (e.g. in the case of some highly threatened species) were included if their location had been indexed against an IBRA7 bioregion. \n\nSpecies were considered native if they were not listed on the Global Register of Introduced and Invasive Species - Australia (version 1.10). Species on the GRIIS were mapped to ALA names, and this was then used as the basis for excluding introduced and invasive species from the downloaded records. \n\nTwo summary datasets were created based on these filtered records. \n\nCounts of native species:\nThis dataset comprises aggregated counts of records of native species within each terrestrial bioregion, and the total number of native species recorded in the dataset across bioregions. The summary dataset is published as native_spp_counts_bioregion.csv and contains the following elements:\n\n1. IBRA7 terrestrial bioregion\n2. Count of native species in the given bioregion\n3. Total number of native species across all bioregions\n\nList of taxa in bioregions:\nThis dataset comprises taxonomic information and EPBC status for native species in each bioregion, and is published as native_taxon_list_bioregions.csv. EPBC status of taxa was inferred by mapping names of taxa on the EPBC list to ALA names, and joining these to the downloaded records. The dataset contains the following elements:\n\n1. Kingdom\n2. Phylum\n3. Class\n4. Order\n5. Family\n6. Genus\n7. Species\n8. Scientific name\n9. Taxon rank\n10. IBRA7 terrestrial bioregion\n11. EPBC status \n\nThe data_sources.csv file includes information on the source datasets within the Atlas of Living Australia that contributed to this collection.\n

本数据集采用1900年至2023年间的澳大利亚生物多样性图谱（Atlas of Living Australia, ALA）物种出现数据，用于生成陆地生物区（IBRA7）内本土物种的数据汇总。本数据集包含两类子数据集：一是各陆地生物区的本土物种数量统计，二是各陆地生物区包含分类学信息与《环境保护与生物多样性保护法案》（Environment Protection and Biodiversity Conservation Act, EPBC）保护等级的本土物种名录。

基于生物区的本土物种数量统计，结合物种-面积关系（species-area relationship, SAR）（z值为0.25，公式为S = A^z）与栖息地状况评估系统（Habitat Condition Assessment System, HCAS）3.0版时间序列中各生物区的平均栖息地状况（A），可分析极长期内物种存续可能性占比（S）的变化。随后可通过物种丰富度加权平均各生物区的分析结果，生成国家级指标。利用各生物区的EPBC法案受威胁物种数量统计，可辅助解读各生物区的栖息地状况等级。各生物区的本土物种名录为更新分析提供了基础——该分析需考虑物种在生物区间的共享特性，该特性会影响国家级汇总下极长期物种存续可能性占比。本数据集产出成果可支撑澳大利亚政府环境企业绩效指标EN01（2023-24年气候变化、能源、环境与水资源部年度报告）中HCAS与国家连通性指数（National Connectivity Index, NCI）的解读。本数据集也可用于其他生物区尺度的分析，或采用不同输入数据的物种-面积关系分析。

ALA将数百个不同数据提供者以不同方法采集的数据整合至单一数据库，因此ALA中的观测数据存在空间、时间与分类学偏差，后续分析时需谨慎解读。在汇总至生物区尺度时，调查采样强度与可达性大致相关，因此靠近大城市的生物区相较于偏远区域，其生物多样性评估结果可能偏高。

数据溯源：本研究下载并筛选了截至2024年6月25日由ALA整合的全部物种出现数据，筛选过程通过galah R包完成，仅保留符合以下条件的记录：
• 通过ALA通用数据质量过滤（https://support.ala.org.au/support/solutions/articles/6000240256-getting-started-with-the-data-quality-filters）
• 采集时间介于1900-2023年
• 分类单元鉴定至少至物种级
• 坐标已匹配至IBRA7陆地生物区

此外，本研究额外开展了一次未应用ALA数据质量过滤的下载，以获取因坐标不确定性被初始排除的记录。对于坐标不确定性较高的记录（如部分极危物种），若其位置已索引至IBRA7生物区，则予以保留。

本土物种判定规则：物种若未被列入《全球引入与入侵物种名录-澳大利亚版》（Global Register of Introduced and Invasive Species - Australia, GRIIS）1.10版，则视为本土物种。首先将GRIIS中的物种名称映射至ALA的物种名称，以此为依据从下载的记录中排除引入与入侵物种。

基于上述筛选后的记录，共生成两类汇总数据集：

1. 本土物种数量统计
本数据集包含各陆地生物区的本土物种记录汇总计数，以及数据集内所有生物区的本土物种总数量。汇总数据集以native_spp_counts_bioregion.csv为名发布，包含以下字段：
① IBRA7陆地生物区
② 对应生物区的本土物种数量
③ 所有生物区的本土物种总数量

2. 生物区物种名录
本数据集包含各生物区本土物种的分类学信息与EPBC保护等级，以native_taxon_list_bioregions.csv为名发布。物种的EPBC保护等级通过将EPBC名录中的物种名称映射至ALA物种名称，并与下载的记录关联后推断得到。数据集包含以下字段：
① 界（Kingdom）
② 门（Phylum）
③ 纲（Class）
④ 目（Order）
⑤ 科（Family）
⑥ 属（Genus）
⑦ 种（Species）
⑧ 学名
⑨ 分类单元等级
⑩ IBRA7陆地生物区
⑪ EPBC保护等级

此外，data_sources.csv文件包含了本数据集所引用的ALA内部源数据集的相关信息。