Taxonomy, distribution and classification of ecosystem-types, integrating the recent IUCN function-based typology and local conceptualizations

1. Introduction: This dataset is a work in progress. It compiles data gathered on ecosystem-types and their distribution based on a series of field studies led by the author, in Seychelles and West and Central Africa (Senterre 2014, Senterre & Wagner 2014, Senterre 2016, Senterre et al. 2017, 2019, 2020, 2021a, 2022). The aims of this dataset are: a. To share in an explicit and transparent way data on proposed taxonomies of ecosystems, i.e. conceptualizations of ecosystem-types, including explicit ecosystem names and management of synonymies. b. To develop ecosystem red listing based on transparent and falsifiable distribution raw data, combining distribution modeling (maps) and in situ observation of individual stand occurrences. c. To illustrate in detail how to deal with ecosystem data following the approach described in Senterre et al. (2021b) (i.e. "ecosystemology" approach). d. To integrate the above approach with the newly developed function-based typology of ecosystems (Keith et al. 2022), therefore contributing to bridging the persistent gap between the global and the local scales in ecosystem descriptions and classifications. 2. Context and versions: This dataset was initially planned for publication on GBIF (Global Biodiversity Information Facility), as part of a project developed for the review of Key Biodiversity Areas in Seychelles: "Mainstreaming recent species and ecosystem distribution data into Key Biodiversity Areas assessments in Seychelles" (https://www.gbif.org/dataset/f513fe98-b1c3-45ee-8e14-7f2a5b7890bf). In the first version of the GBIF dataset (https://www.gbif.org/dataset/f513fe98-b1c3-45ee-8e14-7f2a5b7890bf), we proposed an analysis of the potential 'core' and 'extension' files available in GBIF for a publication of ecosystem-type names (and synonymies) and their corresponding occurrences recorded from field observations. This is an original analysis of taxonomic principles managed entirely at the scale of local observable objects, and their history of identifications or interpretations. Toward the end of the above-mentioned GBIF project, considering the limitations and gaps currently present in GBIF, it was decided to restrict the GBIF dataset to a simple 'metadata' entry and to publish the complete version of this dataset in Zenodo. This allows to include all tables needed, as well as all required fields without having to accommodate them within the limited GBIF structure (see metadata description on GBIF for more details). The fields of the tables published here are described in the GBIF metadata entry and in the ecosystemology paper (Senterre et al. 2021b). 3. New development on typology aspects: In addition, considering that the new IUCN global typology of ecosystems is now published (Keith et al. 2022), we have reviewed in detail the possibility of integration of ecosystems conceptualized using our ecosystemology approach within the new IUCN typology. The result of this analysis is being considered for a publication, and this Zenodo dataset would then be published in full (i.e. including all typology aspects) as supplementary materials. In the meantime, I would be happy to discuss any of these aspects with whoever is interested. 4. Access to ecosystem data for conservation actors: Finally, the actual data (published here) on ecosystem-types, their names, synonymies, classification, distribution, and red list status are compiled into a format that we designed to be useful to conservation actors in the form of interactive webpages (produced with R as shiny apps). This development is based on very limited resources, and the author is still quite new to R, so any help or feedback on ways to improve the scripts would be very much welcomed. The interactive page is available here (currently filtered to Seychelles' data only, although the dataset contains data beyond the Seychelles): https://shiny.bio.gov.sc/bioeco/ The R scripts are available on Github: https://github.com/bsenterre/ecosystemology 5. Tables contained in this dataset: a. Ecosystem taxonomy tables: ecoSpecies: Contains the list of all ecosystem-type names with their unique identifier. ecoOccurrences: Contains the list of individual stand occurrences, including ecosystem characters as standardized in Senterre et al. (2021b; i.e. virtual ecosystem specimen). ecoSpeciesProfiles: Contains basic metadata on ecosystem-types, such as their Red List evaluations. ecoIdentifications: Contains all the different interpretations/identifications (referring to the table ecoSpecies or to higher levels of classification, see below) made on the stands observed in the ecoOccurrences table. b. Ecosystem typology tables (TO BE ADDED LATER): IUCNL3: This is just a transcription, as is, of the IUCN global typology version 2.1. IUCNL3BIOCrossover: This table defines and comments correspondences between BIOL2 (the level 2 of the typology used by us) and the IUCN typology L3 (level 3). BIOL2: This is a variation based on the IUCN typology, here our level 2. BIOL3: This is a variation based on the IUCN typology, here our level 3. BIOL4: This is a variation based on the IUCN typology, here our level 4. ecoGenus: This is a general type of stand (thus excluding any regional ecosystem connotation), defined at a local scale and never combined with any geographic connotation (see ecosystemology paper: Senterre et al. 2021b). ecoFamily: This is a generalized version of the ecoGenus (i.e. still excluding any regional, sub-regional or geographic aspect). ecoOrder: This is a further generalized version of the ecoGenus (see also Senterre et al. 2020). lifeZone: This is a basic and incomplete list of life zones as defined following the Holdridge (1967) approach, with some additional elements proposed in Senterre et al. (2021b). 6. Literature cited: Holdridge, L. R. 1967. Life zone ecology. Tropical Science Center, San Jose, Costa Rica. Keith, D. A., J. R. Ferrer-Paris, E. Nicholson, M. J. Bishop, B. A. Polidoro, E. Ramirez-Llodra, M. G. Tozer, J. L. Nel, R. Mac Nally, E. J. Gregr, K. E. Watermeyer, F. Essl, D. Faber-Langendoen, J. Franklin, C. E. R. Lehmann, A. Etter, D. J. Roux, J. S. Stark, J. A. Rowland, N. A. Brummitt, U. C. Fernandez-Arcaya, I. M. Suthers, S. K. Wiser, I. Donohue, L. J. Jackson, R. T. Pennington, T. M. Iliffe, V. Gerovasileiou, P. Giller, B. J. Robson, N. Pettorelli, A. Andrade, A. Lindgaard, T. Tahvanainen, A. Terauds, M. A. Chadwick, N. J. Murray, J. Moat, P. Pliscoff, I. Zager, and R. T. Kingsford. 2022. A function-based typology for Earth’s ecosystems. . Nature 610:513–518. doi:10.1038/s41586-022-05318-4. Senterre, B. 2014. Mapping habitat-types within the Hummingbird site at Dugbe (Liberia, West Africa). Consultancy Report, Missouri Botanical Garden. P. 56. https://doi.org/10.13140/RG.2.2.32628.48003. Senterre, B. 2016. Habitat-type ground-truthing and assessment of ecosystem conservation value in the Bel Air Alufer mining site (Guinea, West Africa), with recommendations for improving the draft map of land cover types. Consultancy Report, Missouri Botanical Garden, A study conducted for Alufer Mining Limited. P. 54. Senterre, B., E. Bidault, and T. Stévart. 2019. Identification et évaluation des écosystèmes menacés du Mont Nimba. Rapport de consultance, Missouri Botanical Garden (MBG), Africa and Madagascar Department. P. 106. https://doi.org/10.13140/RG.2.2.13242.93129. Senterre, B., E. Bidault, T. Stévart, and P. P. Lowry II. 2020. Assessment of Key Biodiversity Areas in the Lofa-Gola-Mano & Nimba complexes (West Africa) using ecosystem criteria. Final Report, Missouri Botanical Garden. P. 146. 10.13140/RG.2.2.17934.89924. Senterre, B., E. Bidault, T. Stévart, M. Wagner, and P. Lowry. 2017. Mapping habitat-types in south-east Kouilou (Republic of Congo). Consultancy Report, Missouri Botanical Garden (MBG), Africa and Madagascar Department, St. Louis, Missouri, USA. P. 163. Senterre, B., R. M. Bristol, G. Gendron, and E. Henriette. 2021a. Fine-tuning conservation priorities in Seychelles at the landscape scale, using global KBA guidelines with both species and ecosystem criteria. Consultancy Report, United Nations Development Programme, GOS/UNDP/GEF Programme Coordination Unit, Victoria, Seychelles. Senterre, B., P. P. Lowry II, E. Bidault, and T. Stévart. 2021b. Ecosystemology: a new approach toward a taxonomy of ecosystems. . Ecological Complexity 47:100945. doi:https://doi.org/10.1016/j.ecocom.2021.100945. Senterre, B., A.-H. Paradis, E. Bidault, T. Stévart, and P. P. Lowry II. 2022. Qualité et distribution des savanes montagnardes du Nimba. Rapport de consultance, Missouri Botanical Garden (MBG), Africa and Madagascar Department. P. 73. http://dx.doi.org/10.13140/RG.2.2.13433.34401. Senterre, B., and M. Wagner. 2014. Mapping Seychelles habitat-types on Mahé, Praslin, Silhouette, La Digue and Curieuse. Consultancy Report, Government of Seychelles, United Nations Development Programme, Victoria, Seychelles. P. 119. https://doi.org/10.13140/RG.2.1.4558.6009.1. 引言：本数据集尚处于开发阶段。本数据集整合了作者在塞舌尔以及西非和中非开展的一系列野外调查所收集的生态系统类型及其分布数据（Senterre 2014, Senterre & Wagner 2014, Senterre 2016, Senterre et al. 2017, 2019, 2020, 2021a, 2022）。本数据集的目标如下： a. 以明确透明的方式共享生态系统类型分类体系的相关数据，即生态系统类型的概念框架，包括标准化的生态系统名称及同物异名处理规则。 b. 基于透明且可证伪的原始分布数据，结合分布模型（地图）与单个样地的原位观测结果，开展生态系统红色名录评估。 c. 详细演示如何遵循Senterre等人（2021b）提出的方法（即“生态系统学（ecosystemology）”方法）处理生态系统数据。 d. 将上述方法与最新提出的基于功能的生态系统分类体系（Keith et al. 2022）相结合，以期弥补生态系统描述与分类中全球尺度与局部尺度之间长期存在的鸿沟。 2. 背景与版本：本数据集最初计划作为塞舌尔关键生物多样性区域（Key Biodiversity Areas, KBA）评估项目的一部分，在全球生物多样性信息设施（Global Biodiversity Information Facility, GBIF）上发布，该项目题为“将最新物种与生态系统分布数据纳入塞舌尔关键生物多样性区域评估”（https://www.gbif.org/dataset/f513fe98-b1c3-45ee-8e14-7f2a5b7890bf）。在该GBIF数据集的首个版本（https://www.gbif.org/dataset/f513fe98-b1c3-45ee-8e14-7f2a5b7890bf）中，我们针对在GBIF中可用的潜在“核心”与“扩展”文件开展了分析，旨在发布生态系统类型名称（及同物异名）及其对应野外观测记录的分布数据。这是一项原创性分析，其分类学原则完全基于局部可观测对象及其鉴定或解释历史进行管理。在上述GBIF项目接近尾声时，考虑到当前GBIF存在的局限性与数据缺口，我们决定将GBIF上的数据集仅保留为简单的“元数据”条目，并将本数据集的完整版本发布至泽诺多（Zenodo）。此举可容纳所有所需表格及字段，无需受限于GBIF有限的结构（详细信息请参见GBIF上的元数据描述）。本数据集所发布表格的字段已在GBIF元数据条目及生态系统学论文（Senterre et al. 2021b）中进行了说明。 3. 分类体系相关的新进展：此外，鉴于国际自然保护联盟（International Union for Conservation of Nature, IUCN）最新的全球生态系统分类体系已发布（Keith et al. 2022），我们已详细评估了将采用生态系统学方法构建的生态系统概念纳入该新版IUCN分类体系的可行性。该分析的结果正待发表，届时本泽诺多数据集将作为补充材料完整发布（涵盖所有分类体系相关内容）。在此期间，欢迎任何感兴趣的人士与我就上述任一内容展开讨论。 4. 面向保护工作者的生态系统数据获取途径：最后，本数据集所发布的实际数据（包括生态系统类型、名称、同物异名、分类体系、分布数据及红色名录评估状态）已被整理为便于保护工作者使用的格式，即基于R语言Shiny应用开发的交互式网页。该开发工作受限于有限的资源，且作者本人对R语言尚不够熟练，因此任何针对脚本改进的建议或反馈都将不胜感激。交互式网页目前仅筛选了塞舌尔地区的数据（尽管本数据集包含塞舌尔以外的区域数据），访问地址为：https://shiny.bio.gov.sc/bioeco/。R语言脚本可在GitHub上获取：https://github.com/bsenterre/ecosystemology。 5. 本数据集包含的表格： a. 生态系统分类学表格： - ecoSpecies：包含所有生态系统类型名称及其唯一标识符的列表。 - ecoOccurrences：包含单个样地的观测记录列表，其中的生态系统特征已按照Senterre等人（2021b）的标准进行了统一（即虚拟生态系统标本）。 - ecoSpeciesProfiles：包含生态系统类型的基础元数据，例如其红色名录评估结果。 - ecoIdentifications：包含针对ecoOccurrences表格中观测样地所开展的所有不同解释/鉴定结果（可指向ecoSpecies表格或更高级别的分类体系，详见下文）。 b. 生态系统分类体系表格（待后续添加）： - IUCNL3：原样转录的IUCN全球生态系统分类体系版本2.1。 - IUCNL3BIOCrossover：该表格定义并注释了BIOL2（本研究使用的分类体系第2级）与IUCN分类体系L3（第3级）之间的对应关系。 - BIOL2：基于IUCN分类体系构建的变体，为本研究的分类体系第2级。 - BIOL3：基于IUCN分类体系构建的变体，为本研究的分类体系第3级。 - BIOL4：基于IUCN分类体系构建的变体，为本研究的分类体系第4级。 - ecoGenus：一类通用的样地类型（因此不包含任何区域生态系统内涵），定义于局部尺度，且未与任何地理内涵相结合（详见生态系统学论文：Senterre et al. 2021b）。 - ecoFamily：ecoGenus的广义版本（同样不包含任何区域、亚区域或地理维度）。 - ecoOrder：ecoGenus的进一步广义版本（另参见Senterre et al. 2020）。 - lifeZone：基于霍尔德里奇（Holdridge 1967）方法定义的基础且不完整的生命带列表，另加入了Senterre等人（2021b）提出的部分新增条目。 6. 引用文献： Holdridge, L. R. 1967. 生命带生态学（Life zone ecology）. Tropical Science Center, San Jose, Costa Rica. Keith, D. A., J. R. Ferrer-Paris, E. Nicholson, M. J. Bishop, B. A. Polidoro, E. Ramirez-Llodra, M. G. Tozer, J. L. Nel, R. Mac Nally, E. J. Gregr, K. E. Watermeyer, F. Essl, D. Faber-Langendoen, J. Franklin, C. E. R. Lehmann, A. Etter, D. J. Roux, J. S. Stark, J. A. Rowland, N. A. Brummitt, U. C. Fernandez-Arcaya, I. M. Suthers, S. K. Wiser, I. Donohue, L. J. Jackson, R. T. Pennington, T. M. Iliffe, V. Gerovasileiou, P. Giller, B. J. Robson, N. Pettorelli, A. Andrade, A. Lindgaard, T. Tahvanainen, A. Terauds, M. A. Chadwick, N. J. Murray, J. Moat, P. Pliscoff, I. Zager, and R. T. Kingsford. 2022. 地球生态系统的功能型分类体系（A function-based typology for Earth’s ecosystems）. 自然（Nature）610:513–518. doi:10.1038/s41586-022-05318-4. Senterre, B. 2014. 利比里亚Dugbe蜂鸟栖息地的生境类型制图（Mapping habitat-types within the Hummingbird site at Dugbe (Liberia, West Africa)）. 咨询报告（Consultancy Report）, Missouri Botanical Garden. P. 56. https://doi.org/10.13140/RG.2.2.32628.48003. Senterre, B. 2016. 几内亚Bel Air Alufer矿区的生境类型实地验证与生态系统保护价值评估（Habitat-type ground-truthing and assessment of ecosystem conservation value in the Bel Air Alufer mining site (Guinea, West Africa), with recommendations for improving the draft map of land cover types）. 咨询报告（Consultancy Report）, Missouri Botanical Garden, 为Alufer Mining Limited开展的研究. P. 54. Senterre, B., E. Bidault, T. Stévart. 2019. 宁巴山濒危生态系统的鉴定与评估（Identification et évaluation des écosystèmes menacés du Mont Nimba）. 咨询报告（Rapport de consultance）, Missouri Botanical Garden (MBG), Africa and Madagascar Department. P. 106. https://doi.org/10.13140/RG.2.2.13242.93129. Senterre, B., E. Bidault, T. Stévart, P. P. Lowry II. 2020. 基于生态系统标准的洛法-戈拉-马诺与宁巴综合体（西非）关键生物多样性区域评估（Assessment of Key Biodiversity Areas in the Lofa-Gola-Mano & Nimba complexes (West Africa) using ecosystem criteria）. 最终报告（Final Report）, Missouri Botanical Garden. P. 146. 10.13140/RG.2.2.17934.89924. Senterre, B., E. Bidault, T. Stévart, M. Wagner, P. Lowry. 2017. 刚果东南部奎卢地区的生境类型制图（Mapping habitat-types in south-east Kouilou (Republic of Congo)）. 咨询报告（Consultancy Report）, Missouri Botanical Garden (MBG), Africa and Madagascar Department, St. Louis, Missouri, USA. P. 163. Senterre, B., R. M. Bristol, G. Gendron, E. Henriette. 2021a. 结合物种与生态系统标准的全球KBA指南在塞舌尔景观尺度保护优先级优化中的应用（Fine-tuning conservation priorities in Seychelles at the landscape scale, using global KBA guidelines with both species and ecosystem criteria）. 咨询报告（Consultancy Report）, United Nations Development Programme, GOS/UNDP/GEF Programme Coordination Unit, Victoria, Seychelles. Senterre, B., P. P. Lowry II, E. Bidault, T. Stévart. 2021b. 生态系统学：生态系统分类的新途径（Ecosystemology: a new approach toward a taxonomy of ecosystems）. 生态复杂性（Ecological Complexity）47:100945. doi:https://doi.org/10.1016/j.ecocom.2021.100945. Senterre, B., A.-H. Paradis, E. Bidault, T. Stévart, P. P. Lowry II. 2022. 宁巴山山地草原的质量与分布（Qualité et distribution des savanes montagnardes du Nimba）. 咨询报告（Rapport de consultance）, Missouri Botanical Garden (MBG), Africa and Madagascar Department. P. 73. http://dx.doi.org/10.13140/RG.2.2.13433.34401. Senterre, B., M. Wagner. 2014. 塞舌尔马埃岛、普拉兰岛、锡卢埃特岛、拉迪格岛及居里岛的生境类型制图（Mapping Seychelles habitat-types on Mahé, Praslin, Silhouette, La Digue and Curieuse）. 咨询报告（Consultancy Report）, Government of Seychelles, United Nations Development Programme, Victoria, Seychelles. P. 119. https://doi.org/10.13140/RG.2.1.4558.6009.