How the freshwater biodiversity information system (FBIS) is supporting national freshwater fish conservation decisions in South Africa

DATA AVAILABILITY STATEMENT : The datasets presented in this study can be found in online repositories. The names of the repository/repositories and accession number(s) can be found in the article/Supplementary Material. Alternatively, the dataset can be accessed via the Freshwater Biodiversity Information System (freshwaterbiodiversity.org).In South Africa, anthropogenic pressures such as water over-abstraction, invasive species impacts, land-use change, pollution, and climate change have caused widespread deterioration of the health of river ecosystems. This comes at great cost to both people and biodiversity, with freshwater fishes ranked as the country’s most threatened species group. Effective conservation and management of South Africa’s freshwater ecosystems requires access to reliable and comprehensive biodiversity data. Despite the existence of a wealth of freshwater biodiversity data, access to these data has been limited. The Freshwater Biodiversity Information System (FBIS) was built to address this knowledge gap by developing an intuitive, accessible and reliable platform for freshwater biodiversity data in South Africa. The FBIS hosts high quality, high accuracy biodiversity data that are freely available to a wide range of stakeholders, including researchers, conservation practitioners and policymakers. We describe how the system is being used to provide freshwater fish data to a national conservation decision-support tool—The Department of Forestry, Fisheries, and the Environment (DFFE) National Environmental Screening Tool (NEST). The NEST uses empirical and modelled biodiversity data to guide Environmental Impact Assessment Practitioners in conducting environmental assessments of proposed developments. Occurrence records for 34 threatened freshwater fishes occurring in South Africa were extracted from the FBIS and verified by taxon specialists, resulting in 6 660 records being used to generate modelled and empirical national distribution (or sensitivity) layers. This represents the first inclusion of freshwater biodiversity data in the NEST, and future iterations of the tool will incorporate additional freshwater taxa. This case study demonstrates how the FBIS fills a pivotal role in the data-to-decision pipeline through supporting data-driven conservation and management decisions at a national level.Funding for the development of the Freshwater Biodiversity Information System (FBIS) was provided by the JRS Biodiversity Foundation Funding for the development of the Freshwater Biodiversity Information System (FBIS) was provided by the JRS Biodiversity Foundation. This work is based on the research supported in part by the National Research Foundation (NRF) of South Africa and the NRF-SAIAB DSI/ NRF Research Chair in Inland Fisheries and Freshwater Ecology.http://www.frontiersin.org/Environmental_Scienceam2024Zoology and EntomologySDG-14:Life below wate

Effect of storage regime on the stability of DNA used as a calibration standard for real-time polymerase chain reaction

This article looks at storage factors influencing the stability of potential DNA calibration standards for use in quantitative polymerase chain reaction (PCR). Target sequences from the bacteria Campylobacter jejuni were cloned into a plasmid vector. Samples of these potential calibration standards were stored at +4, −20, and −80 °C as aqueous and lyophilized samples and were prepared as both single-use aliquots and multiple-use preparations. Results showed that the samples stored as single-use aqueous solutions at +4 °C and lyophilized samples stored at +4 and −20 °C were the most stable. Samples stored as frozen aqueous solutions at −20 °C were the least stable

Conservation Assessments: Lycaenidae: Erikssonia - Lepidochrysops

Issue consists of one article divided into downloadable PDFs. This section contains the conservation assessments and Red Listings (all global) of the taxa assessed during the Southern African Lepidoptera Conservation Assessment (SALCA) project, ordered alphabetically by family and then by genus, species and subspecies. Details of the methods used can be found in the main article, with each assessment set out as follows: Taxon scientific name followed by the describer of the taxon and the date. English and Afrikaans common names. Name of the assessor/ taxon author. Red Listing with relevant categories and criteria, as per the IUCN Red Listing protocol (IUCN, 2017). For those Least Concern taxa which are rare, their rarity category is also given. Also indicated are those taxa endemic to the South Africa. Taxon images are arranged with males above and females below (upper side and underside). Specimen label data and photo credits are tabulated on pages 155–160. Seasonality table: This table shows the months of occurrence of the taxon, starting August and ending July. Each month is divided into quarters. Quarters for which there are Accepted records are highlighted in grey. Distribution map: The map’s extent is for South Africa. Data points are displayed for Accepted and Locally Extinct records. The following key is used for each data point: Red List category Symbol EX (also if a taxon is locally extinct) Black CR‒PE Dark purple CR Red EN Orange VU Yellow NT Mustard DD Lilac LC (rare categories) Blue LC Green Type locality: As originally stated by the describer. Taxonomy: Highlighting any relevant taxonomic issues. Distribution: A description of the taxon’s distribution. Habitat: A description of the taxon’s habitat. Vegetation types: The vegetation types where the taxon is found, based on the 2018 vegetation map (SANBI, 2018), for records flagged as both Accepted and Locally Extinct. For those sites where the taxon is locally extinct, the vegetation types are given in parentheses. Assessment rationale: The assessment rationale provides information which justifies the Red Listing and related categories and criteria. Change in status from the Southern African Butterfly Conservation Assessment (SABCA): For those taxa where the Red Listing changed from the previous SABCA assessment of 2012 (Mecenero et al., 2013), an evaluation is given of whether or not the change in status is genuine or non-genuine. Threats: A description of any threats relevant to the taxon. Conservation measures and research required: Any conservation measures or research required are mentioned here, where relevant. Relevant literature: Taxon-specific references published since SABCA are listed in this field, where applicable. The key references listed below were perused for all assessments. An example of citing a specific conservation assessment: “Woodhall, S.E. 2020. Abantis bicolor. pp. 34–35 In: Mecenero et al. 2020. Outcomes of the Southern African Lepidoptera Conservation Assessment (SALCA). Metamorphosis 31(4): 1–160”. Abbreviations: AOO:       Area of occupancy CR:           Critically Endangered CR–PE:    Critically Endangered – Possibly Extinct DD:          Data Deficient EN:           Endangered EOO:        Extent of occurrence EX:           Extinct LC:           Least Concern NT:           Near Threatened VU:          Vulnerable RELEVANT LITERATURE The relevant literature listed below applies to all the conservation assessments. Literature applying only to specific taxa is given after each conservation assessment. HENNING, G.A., TERBLANCHE, R.F. & BALL, J.B. (eds) 2009. South African Red Data Book: butterflies. SANBI Biodiversity Series Pretoria, South African National Biodiversity Institute. 13: 1–158. IUCN. 2017. Guidelines for Using the IUCN Red List Categories and Criteria. Version 13. Prepared by the Standards and Petitions Subcommittee. Download from: http://www.iucnredlist.org/documents/RedListGuidelines.pdf MECENERO, S., BALL, J.B., EDGE, D.A., HAMER, M.L., HENNING, G.A., KRÜGER, M., PRINGLE, E.L., TERBLANCHE, R.F. & WILLIAMS, M.C. 2013. Conservation Assessment of Butterflies of South Africa, Lesotho and Swaziland: Red List and Atlas. Saftronics (Pty) Ltd., Johannesburg & Animal Demography Unit, Cape Town. PRINGLE, E.L., HENNING, G.A. & BALL, J.B. (eds) 1994. Pennington's Butterflies of southern Africa. 2nd Edition. Cape Town, Struik-Winchester. 1–800, 210 pls. SANBI. 2018 Beta Vegetation Map of South Africa, Lesotho and Swaziland (Shapefile) [vector geospatial dataset] 2018. https://bgis.sanbi.org/SpatialDataset/Detail/669 (Accessed on 28 June 2020). WILLIAMS, M.C. 2019. Afrotropical Butterflies Encyclopaedia. http://www.metamorphosis.org.za/?p=articles&s=atb WOODHALL, S.E. 2020. Field guide to butterflies of South Africa (2nd Edn). Penguin Books South Africa

Conservation Assessments: Hesperiidae; Lycaenidae: Alaena - Capys

Issue consists of one article divided into downloadable PDFs. This section contains the conservation assessments and Red Listings (all global) of the taxa assessed during the Southern African Lepidoptera Conservation Assessment (SALCA) project, ordered alphabetically by family and then by genus, species and subspecies. Details of the methods used can be found in the main article, with each assessment set out as follows: Taxon scientific name followed by the describer of the taxon and the date. English and Afrikaans common names. Name of the assessor/ taxon author. Red Listing with relevant categories and criteria, as per the IUCN Red Listing protocol (IUCN, 2017). For those Least Concern taxa which are rare, their rarity category is also given. Also indicated are those taxa endemic to the South Africa. Taxon images are arranged with males above and females below (upper side and underside). Specimen label data and photo credits are tabulated on pages 155–160. Seasonality table: This table shows the months of occurrence of the taxon, starting August and ending July. Each month is divided into quarters. Quarters for which there are Accepted records are highlighted in grey. Distribution map: The map’s extent is for South Africa. Data points are displayed for Accepted and Locally Extinct records. The following key is used for each data point: Red List category Symbol EX (also if a taxon is locally extinct) Black CR‒PE Dark purple CR Red EN Orange VU Yellow NT Mustard DD Lilac LC (rare categories) Blue LC Green Type locality: As originally stated by the describer. Taxonomy: Highlighting any relevant taxonomic issues. Distribution: A description of the taxon’s distribution. Habitat: A description of the taxon’s habitat. Vegetation types: The vegetation types where the taxon is found, based on the 2018 vegetation map (SANBI, 2018), for records flagged as both Accepted and Locally Extinct. For those sites where the taxon is locally extinct, the vegetation types are given in parentheses. Assessment rationale: The assessment rationale provides information which justifies the Red Listing and related categories and criteria. Change in status from the Southern African Butterfly Conservation Assessment (SABCA): For those taxa where the Red Listing changed from the previous SABCA assessment of 2012 (Mecenero et al., 2013), an evaluation is given of whether or not the change in status is genuine or non-genuine. Threats: A description of any threats relevant to the taxon. Conservation measures and research required: Any conservation measures or research required are mentioned here, where relevant. Relevant literature: Taxon-specific references published since SABCA are listed in this field, where applicable. The key references listed below were perused for all assessments. An example of citing a specific conservation assessment: “Woodhall, S.E. 2020. Abantis bicolor. pp. 34–35 In: Mecenero et al. 2020. Outcomes of the Southern African Lepidoptera Conservation Assessment (SALCA). Metamorphosis 31(4): 1–160”. Abbreviations: AOO:       Area of occupancy CR:           Critically Endangered CR–PE:    Critically Endangered – Possibly Extinct DD:          Data Deficient EN:           Endangered EOO:        Extent of occurrence EX:           Extinct LC:           Least Concern NT:           Near Threatened VU:          Vulnerable RELEVANT LITERATURE The relevant literature listed below applies to all the conservation assessments. Literature applying only to specific taxa is given after each conservation assessment. HENNING, G.A., TERBLANCHE, R.F. & BALL, J.B. (eds) 2009. South African Red Data Book: butterflies. SANBI Biodiversity Series Pretoria, South African National Biodiversity Institute. 13: 1–158. IUCN. 2017. Guidelines for Using the IUCN Red List Categories and Criteria. Version 13. Prepared by the Standards and Petitions Subcommittee. Download from: http://www.iucnredlist.org/documents/RedListGuidelines.pdf MECENERO, S., BALL, J.B., EDGE, D.A., HAMER, M.L., HENNING, G.A., KRÜGER, M., PRINGLE, E.L., TERBLANCHE, R.F. & WILLIAMS, M.C. 2013. Conservation Assessment of Butterflies of South Africa, Lesotho and Swaziland: Red List and Atlas. Saftronics (Pty) Ltd., Johannesburg & Animal Demography Unit, Cape Town. PRINGLE, E.L., HENNING, G.A. & BALL, J.B. (eds) 1994. Pennington's Butterflies of southern Africa. 2nd Edition. Cape Town, Struik-Winchester. 1–800, 210 pls. SANBI. 2018 Beta Vegetation Map of South Africa, Lesotho and Swaziland (Shapefile) [vector geospatial dataset] 2018. https://bgis.sanbi.org/SpatialDataset/Detail/669 (Accessed on 28 June 2020). WILLIAMS, M.C. 2019. Afrotropical Butterflies Encyclopaedia. http://www.metamorphosis.org.za/?p=articles&s=atb WOODHALL, S.E. 2020. Field guide to butterflies of South Africa (2nd Edn). Penguin Books South Africa

Outcomes of the Southern African Lepidoptera Conservation Assessment (SALCA)

The Southern African Lepidoptera Conservation Assessment (SALCA) was a collaborative venture between the Lepidopterists’ Society of Africa (LepSoc Africa), the Brenton Blue Trust (BBT) and the South African National Biodiversity Institute (SANBI), and formed part of the National Biodiversity Assessment (NBA). SALCA was founded on the importance of Lepidoptera both ecologically and as biodiversity indicators and the proven expertise of the participants during the Southern African Butterfly Conservation Assessment (SABCA). The main outcomes of the SALCA project are presented and discussed here.The SALCA tool, a custom-designed interactive distribution database, enabled high quality data to be derived so that accurate conservation assessments could be produced in accordance with IUCN methodology. The Red Lists of SALCA and SABCA facilitated the first opportunity to calculate the Red List Index (RLI) for South African butterflies during the period from 2012–2018. Other metrics required for the NBA included protection level and threats analyses. A further outcome was the critical habitat mapping for butterflies, which formed part of a screening tool implemented by SANBI, to ensure that land use changes did not cause any further loss of butterfly biodiversity.A comprehensive distribution database was developed for South African moths, enabling data to be analysed so that moth species potentially threatened could be short-listed for further investigation.Geographical hotspots and ecosystems (vegetation types) containing butterflies of conservation concern are highlighted. The societal, economic and human wellbeing benefits of conserving Lepidoptera are identified. Responses by LepSoc Africa to the increasing pressures on South African Lepidoptera biodiversity, are also reported on and discussed. The significant outcomes of SABCA and SALCA are benchmarked against a well-known European butterfly atlasing and conservation assessment project.The 165 SALCA Red Lists and conservation assessments are presented at the end of this publication

Conservation Assessments: Nymphalidae; Papilionidae; Pieridae

Issue consists of one article divided into downloadable PDFs. This section contains the conservation assessments and Red Listings (all global) of the taxa assessed during the Southern African Lepidoptera Conservation Assessment (SALCA) project, ordered alphabetically by family and then by genus, species and subspecies. Details of the methods used can be found in the main article, with each assessment set out as follows: Taxon scientific name followed by the describer of the taxon and the date. English and Afrikaans common names. Name of the assessor/ taxon author. Red Listing with relevant categories and criteria, as per the IUCN Red Listing protocol (IUCN, 2017). For those Least Concern taxa which are rare, their rarity category is also given. Also indicated are those taxa endemic to the South Africa. Taxon images are arranged with males above and females below (upper side and underside). Specimen label data and photo credits are tabulated on pages 155–160. Seasonality table: This table shows the months of occurrence of the taxon, starting August and ending July. Each month is divided into quarters. Quarters for which there are Accepted records are highlighted in grey. Distribution map: The map’s extent is for South Africa. Data points are displayed for Accepted and Locally Extinct records. The following key is used for each data point: Red List category Symbol EX (also if a taxon is locally extinct) Black CR‒PE Dark purple CR Red EN Orange VU Yellow NT Mustard DD Lilac LC (rare categories) Blue LC Green Type locality: As originally stated by the describer. Taxonomy: Highlighting any relevant taxonomic issues. Distribution: A description of the taxon’s distribution. Habitat: A description of the taxon’s habitat. Vegetation types: The vegetation types where the taxon is found, based on the 2018 vegetation map (SANBI, 2018), for records flagged as both Accepted and Locally Extinct. For those sites where the taxon is locally extinct, the vegetation types are given in parentheses. Assessment rationale: The assessment rationale provides information which justifies the Red Listing and related categories and criteria. Change in status from the Southern African Butterfly Conservation Assessment (SABCA): For those taxa where the Red Listing changed from the previous SABCA assessment of 2012 (Mecenero et al., 2013), an evaluation is given of whether or not the change in status is genuine or non-genuine. Threats: A description of any threats relevant to the taxon. Conservation measures and research required: Any conservation measures or research required are mentioned here, where relevant. Relevant literature: Taxon-specific references published since SABCA are listed in this field, where applicable. The key references listed below were perused for all assessments. An example of citing a specific conservation assessment: “Woodhall, S.E. 2020. Abantis bicolor. pp. 34–35 In: Mecenero et al. 2020. Outcomes of the Southern African Lepidoptera Conservation Assessment (SALCA). Metamorphosis 31(4): 1–160”. Abbreviations: AOO:       Area of occupancy CR:           Critically Endangered CR–PE:    Critically Endangered – Possibly Extinct DD:          Data Deficient EN:           Endangered EOO:        Extent of occurrence EX:           Extinct LC:           Least Concern NT:           Near Threatened VU:          Vulnerable RELEVANT LITERATURE The relevant literature listed below applies to all the conservation assessments. Literature applying only to specific taxa is given after each conservation assessment. HENNING, G.A., TERBLANCHE, R.F. & BALL, J.B. (eds) 2009. South African Red Data Book: butterflies. SANBI Biodiversity Series Pretoria, South African National Biodiversity Institute. 13: 1–158. IUCN. 2017. Guidelines for Using the IUCN Red List Categories and Criteria. Version 13. Prepared by the Standards and Petitions Subcommittee. Download from: http://www.iucnredlist.org/documents/RedListGuidelines.pdf MECENERO, S., BALL, J.B., EDGE, D.A., HAMER, M.L., HENNING, G.A., KRÜGER, M., PRINGLE, E.L., TERBLANCHE, R.F. & WILLIAMS, M.C. 2013. Conservation Assessment of Butterflies of South Africa, Lesotho and Swaziland: Red List and Atlas. Saftronics (Pty) Ltd., Johannesburg & Animal Demography Unit, Cape Town. PRINGLE, E.L., HENNING, G.A. & BALL, J.B. (eds) 1994. Pennington's Butterflies of southern Africa. 2nd Edition. Cape Town, Struik-Winchester. 1–800, 210 pls. SANBI. 2018 Beta Vegetation Map of South Africa, Lesotho and Swaziland (Shapefile) [vector geospatial dataset] 2018. https://bgis.sanbi.org/SpatialDataset/Detail/669 (Accessed on 28 June 2020). WILLIAMS, M.C. 2019. Afrotropical Butterflies Encyclopaedia. http://www.metamorphosis.org.za/?p=articles&s=atb WOODHALL, S.E. 2020. Field guide to butterflies of South Africa (2nd Edn). Penguin Books South Africa

Conservation Assessments: Lycaenidae: Chrysoritis - Durbaniella

Issue consists of one article divided into downloadable PDFs. This section contains the conservation assessments and Red Listings (all global) of the taxa assessed during the Southern African Lepidoptera Conservation Assessment (SALCA) project, ordered alphabetically by family and then by genus, species and subspecies. Details of the methods used can be found in the main article, with each assessment set out as follows: Taxon scientific name followed by the describer of the taxon and the date. English and Afrikaans common names. Name of the assessor/ taxon author. Red Listing with relevant categories and criteria, as per the IUCN Red Listing protocol (IUCN, 2017). For those Least Concern taxa which are rare, their rarity category is also given. Also indicated are those taxa endemic to the South Africa. Taxon images are arranged with males above and females below (upper side and underside). Specimen label data and photo credits are tabulated on pages 155–160. Seasonality table: This table shows the months of occurrence of the taxon, starting August and ending July. Each month is divided into quarters. Quarters for which there are Accepted records are highlighted in grey. Distribution map: The map’s extent is for South Africa. Data points are displayed for Accepted and Locally Extinct records. The following key is used for each data point: Red List category Symbol EX (also if a taxon is locally extinct) Black CR‒PE Dark purple CR Red EN Orange VU Yellow NT Mustard DD Lilac LC (rare categories) Blue LC Green Type locality: As originally stated by the describer. Taxonomy: Highlighting any relevant taxonomic issues. Distribution: A description of the taxon’s distribution. Habitat: A description of the taxon’s habitat. Vegetation types: The vegetation types where the taxon is found, based on the 2018 vegetation map (SANBI, 2018), for records flagged as both Accepted and Locally Extinct. For those sites where the taxon is locally extinct, the vegetation types are given in parentheses. Assessment rationale: The assessment rationale provides information which justifies the Red Listing and related categories and criteria. Change in status from the Southern African Butterfly Conservation Assessment (SABCA): For those taxa where the Red Listing changed from the previous SABCA assessment of 2012 (Mecenero et al., 2013), an evaluation is given of whether or not the change in status is genuine or non-genuine. Threats: A description of any threats relevant to the taxon. Conservation measures and research required: Any conservation measures or research required are mentioned here, where relevant. Relevant literature: Taxon-specific references published since SABCA are listed in this field, where applicable. The key references listed below were perused for all assessments. An example of citing a specific conservation assessment: “Woodhall, S.E. 2020. Abantis bicolor. pp. 34–35 In: Mecenero et al. 2020. Outcomes of the Southern African Lepidoptera Conservation Assessment (SALCA). Metamorphosis 31(4): 1–160”. Abbreviations: AOO:       Area of occupancy CR:           Critically Endangered CR–PE:    Critically Endangered – Possibly Extinct DD:          Data Deficient EN:           Endangered EOO:        Extent of occurrence EX:           Extinct LC:           Least Concern NT:           Near Threatened VU:          Vulnerable RELEVANT LITERATURE The relevant literature listed below applies to all the conservation assessments. Literature applying only to specific taxa is given after each conservation assessment. HENNING, G.A., TERBLANCHE, R.F. & BALL, J.B. (eds) 2009. South African Red Data Book: butterflies. SANBI Biodiversity Series Pretoria, South African National Biodiversity Institute. 13: 1–158. IUCN. 2017. Guidelines for Using the IUCN Red List Categories and Criteria. Version 13. Prepared by the Standards and Petitions Subcommittee. Download from: http://www.iucnredlist.org/documents/RedListGuidelines.pdf MECENERO, S., BALL, J.B., EDGE, D.A., HAMER, M.L., HENNING, G.A., KRÜGER, M., PRINGLE, E.L., TERBLANCHE, R.F. & WILLIAMS, M.C. 2013. Conservation Assessment of Butterflies of South Africa, Lesotho and Swaziland: Red List and Atlas. Saftronics (Pty) Ltd., Johannesburg & Animal Demography Unit, Cape Town. PRINGLE, E.L., HENNING, G.A. & BALL, J.B. (eds) 1994. Pennington's Butterflies of southern Africa. 2nd Edition. Cape Town, Struik-Winchester. 1–800, 210 pls. SANBI. 2018 Beta Vegetation Map of South Africa, Lesotho and Swaziland (Shapefile) [vector geospatial dataset] 2018. https://bgis.sanbi.org/SpatialDataset/Detail/669 (Accessed on 28 June 2020). WILLIAMS, M.C. 2019. Afrotropical Butterflies Encyclopaedia. http://www.metamorphosis.org.za/?p=articles&s=atb WOODHALL, S.E. 2020. Field guide to butterflies of South Africa (2nd Edn). Penguin Books South Africa