The Freshwater Biodiversity Information System (FBIS) Fish Data
Citation
Kajee M, Dallas H, Shelton J, Swannepoel A, Griffiths C (2023). The Freshwater Biodiversity Information System (FBIS) Fish Data. Version 1.6. Freshwater Research Centre. Occurrence dataset https://doi.org/10.15468/gmk6hg accessed via GBIF.org on 2024-08-25.Description
Freshwater fishes are regarded as South Africa’s most threatened species group. Long-term distributional data for freshwater fish species can be vital for detecting critical ecosystem changes, such as species range shifts, new records of non-native invasions and loss of ecosystem services or unique biodiversity. Understanding exactly how the abundance and distribution of freshwater fishes (both native and non-native) are changing is pivotal to effectively manage and conserve unique and threatened freshwater biodiversity and ecosystems. In light of this, a comprehensive freshwater fish dataset (freshwaterbiodiversity.org) was built, comprising all available records of formally described freshwater fish species occurring in South Africa. The comprehensive search for data resulted in the accrual of a total of 60 837 records of freshwater fish from South Africa, which includes 35 955 records new records to the Global Biodiversity Information Facility (GBIF). Of the 101 native species occurring in the country, almost half of all assessed species were found to be threatened, with the number of occurrences decreasing in recent years. Conversely, the number of occurrences and distribution ranges of many non-native species were found to be increasing, especially within the past three decades. These data have provided a much-needed update to the known status and distribution of freshwater fishes in the country.Purpose
Despite a rich history and well-established freshwater fish research infrastructure in South Africa, to date there has been limited sharing of this knowledge or data on a national scale. For example, experts within the country have yet to compile and agree upon a comprehensive list of all freshwater fish species known to occur in South Africa (Bills, personal communication, 2018 October 23; Skelton, personal communication, 2018 October 23). Furthermore, the country still does not possess a comprehensive centralised database to store, share and visualise freshwater fish distributional data. Having these data easily accessible to all freshwater stakeholders is critical for biodiversity planning, conservation, management and decision/policy making. Long-term distributional data for freshwater fish species can be vital for detecting critical ecosystem changes, such as past disturbances resulting in species range shifts, evaluating species resilience to anthropogenic impacts, identifying new records of non-native species invasions and loss of ecosystem services or unique biodiversity (Dudgeon et al., 2006; Chakona et al., 2020). Understanding exactly how the abundance and distribution of freshwater fishes (both native and non-native) are changing is pivotal to effectively manage and conserve South Africa’s unique and threatened freshwater biodiversity and ecosystems. In short, not being able to effectively observe, record and track trends in freshwater fish populations can have serious implications for our ability to sustainably manage freshwater ecosystems and the services they provide. In response to these knowledge gaps, this chapter primarily aims to: i) Create a comprehensive, up-to-date list of freshwater fish taxa occurring in South Africa (hereafter referred to as the Master Species List); ii) ii) Collect, collate and consolidate historic and current species occurrence data for these freshwater fishes; and iii) iii) Examine and visualise spatio-temporal patterns in the data to provide an updated, comprehensive review of the status and distribution of these species. Specifically, the aim is to interrogate the dataset to evaluate how key species attributes (such as taxon origin, endemism and conservation status) vary in time and space. Finally, this chapter will be used to formulate key questions and hypotheses for investigation in following chapters of this thesis.Sampling Description
Study Extent
The geographic scope of this project was restricted to the boundaries of the Republic of South Africa, but also included the Kingdom of Eswatini (formerly Swaziland) and the Kingdom of Lesotho (for convenience purposes, this study area is hereafter referred to as ‘South Africa’). Data collection was limited to rivers, dams and freshwater lakes within South Africa. Importantly, estuarine and marine systems were excluded.Sampling
Using a Master Species List of freshwater fishes (see below for details on how this list was developed), a comprehensive freshwater fish data set was built, using data from multiple sources, in order to compile all known, accessible records of freshwater fish occurrences in South Africa. Specific details pertaining to the scope of the data set, as well as the collection and analyses of the data, are provided in the sections below. All data were uploaded onto the Freshwater Biodiversity Information System (FBIS) database (Dallas et al., 2021; freshwaterbiodiversity.org). The FBIS database is an online, open-access biodiversity database developed by the Freshwater Research Centre (FRC) in collaboration with the Kartoza and the South African National Biodiversity Institute (SANBI) and funded by the JRS Biodiversity Foundation. The FBIS database will serve as the long-term storage facility for the data collated during this study. Coverage includes all freshwater fish species known to occur in the wild (species held in captivity were excluded) within South Africa. For the purpose of this chapter, only formally described species recognised using the GBIF taxonomic backbone were included. All formally described sub-species were also included, listed under their parent taxa. Species in the process of being described, or that belong to groups that are currently under taxonomic review (such as those belonging to the genera Enteromius, Galaxias and Sandelia) were omitted completely from the data collection and analyses of this chapter, pending resolution of their taxonomic status. Freshwater fish species are defined as species that spend all, or a critical part, of their lives in either freshwater or brackish environments (IUCN Freshwater Fish Specialist Group, 2015; Arthington et al., 2016). For the purpose of this study, only primary freshwater fish (fishes living in inland waters, with little or no tolerance of saltwater), secondary freshwater fish (fishes relatively tolerant of salt water, but normally living in inland waters) and diadromous/catadromous fish (fishes that, in the course of their life cycle, regularly migrate between inland waters and the sea, or vice versa) species were included. Importantly, both marine peripheral and sporadic marine species were omitted entirely from both the data collection and analysis (see Skelton (2001) for ecological-tolerance category definitions). Based on these criteria, a preliminary freshwater fish species list was compiled using the South African Institute of Aquatic Biodiversity’s (SAIAB) database and the RHP (River Health Programme) (2015) Rivers Database (Dallas et al., 2007). This preliminary list of taxa was then updated using the freshwater fish field guide by Skelton (2001), as well as subsequent scientific papers, including Skelton (2002), Skelton (2016), Ellender and Weyl (2014) and Weyl et al. (2020). From these sources, a preliminary Master Species List for freshwater fishes was compiled (See Table S. 2). This contained 297 fish species (comprising both native and non-native fishes) known to occur in the whole of southern Africa (defined by Skelton (2001) as the region “south of the northernmost watershed of the Cunene, Okavango and Zambezi rivers, but excluding Lake Malawi and the Shire River above the Kapachira Falls”; Skelton, 2001). All 297 fish species were included in this preliminary Master Species List to ensure that any recently translocated or introduced species from one of South Africa’s neighbouring countries were not mistakenly omitted from the data search. 2.2.3. Data Collection Occurrence Data Published Data A thorough literature search was undertaken for each species included on the preliminary Master Species List, starting in November 2018 and culminating in January 2020. The literature search was conducted using Google Scholar. To ensure that relevant papers were identified, the following search term combination was used for all native freshwater fishes: “Genus species” and “South Africa” (where “Genus species” represents the scientific name of each taxon). A different search term was used for non-native species, to further refine the search. The following search term was used: "Genus species" and "South Africa" and "study" OR "survey" OR "sample" OR "site" and "map" OR "coordinate" OR "coordinates" OR "latitude" OR "longitude" OR "GPS"” (where “Genus species” represents the scientific name of each taxon). Relevant articles were identified based on their titles, abstracts, methods and results sections. Only the first 500 search results returned by Google Scholar were assessed for relevancy, due to time constraints. This number was selected based on an initial trial phase, which determined that after 500 search results, Google Scholar mostly outputted irrelevant, obscure articles. Articles (including peer-reviewed publications, theses and published reports) were deemed to be relevant if information from the title, abstract or methods section indicated that the article contained occurrence data for the specific freshwater fish taxon in South Africa. If an article was deemed to be relevant, the article was catalogued in a Microsoft Excel (365 ProPlus) spreadsheet and the PDF version of the article was downloaded. Data from each relevant article were extracted once all species searches were complete. Detailed explanation of the data extraction process is provided below. If an article was not deemed to be relevant, this was also catalogued in Microsoft Excel and a reason for disregarding the article was logged. Databases Occurrence data for freshwater fishes in South Africa were also collected from 15 national databases curated within FBIS, and from one international database, the Global Biodiversity Information Facility (GBIF), which included the South African Institute for Aquatic Biodiversity (SAIAB) database. (Table 2. 1). Table 2. 1. List of databases accessed to search for freshwater fish occurrence records in South Africa. # Name of Database 1 Global Biodiversity Information Facility (GBIF)* 2 South African National Parks Fish Database 3 Limpopo Department of Environmental Affairs Fish Database 4 Rivers Database 2015 5 Mpumalanga Tourism and Parks Agency Fish Database 6 Cape Nature State of Biodiversity Database 7 Clean Stream Biological Services Fish Database 8 Inkomati-Usuthu Catchment Management Agency Database 9 Nepid Fish Database 10 Ecotone Freshwater Consultants Database 11 Ecosun Database 12 Department of Water and Sanitation Regional Fish Database 13 Gauteng Department of Agriculture and Rural Development Database 14 Freshwater Research Centre Monitoring Database 15 The Biodiversity Company SASS and Fish Database * The Global Biodiversity Information Facility’s (GBIF) database. These data included all data uploaded to GBIF by South African and International research institutions like SAIAB, as well as citizen science data from iNaturalist that were classified by GBIF as “Research Grade” data. Unpublished Data Several freshwater fish experts and conservation organisations from across the country were identified and contacted to request any additional unpublished data that may exist in analog form, or on private hardware (See Table S. 3). Additionally, several presentations were delivered at conferences, workshops and meetings to appeal for data. In October 2019, the FBIS database was launched online and opened for the upload of additional data by approved, registered users. These data were validated by experts and downloaded on 22 September 2022, and also incorporated into this study. 2.2.4. Data Extraction Each article that was deemed to be relevant during the literature search was inspected for GPS coordinates. In cases where GPS coordinates were not provided, the paper was temporarily archived and catalogued, and an email was sent to the listed corresponding author asking whether these were available and if so, requesting a copy. Where site-specific coordinates were provided, these were converted to decimal degrees and entered into the dataset. Available metadata, including collector details, physico-chemical data, sampling method and abundance measures were also documented for each record. See Table S. 4 for details of the full list of parameters included during data extraction. All data were then uploaded into the FBIS. 2.2.5. Biological Information Species Diversity and Origin Once data collection was complete, species with no known occurrence records in South Africa were removed from the preliminary Master Species List. This list was then sent via email to various freshwater fish experts (See Table S. 3) in South Africa for comment. After several iterations, a subset of 134 species were included in the first Master Species List for freshwater fishes in South Africa (See Table S. 5). The GBIF database (GBIF.org, 2018) was used to ensure that the most recent, accepted scientific name of each species was recorded. All previous scientific names and subspecies names were also included as attributes in the Master Species List. In addition, the taxonomic classification (Kingdom, Phylum, Class, Order, Family, Genus and Species) was downloaded for each species using the GBIF database (GBIF.org, 2018) and cross-referenced with current information available on the International Union for the Conservation of Nature (IUCN) Red List of Threatened Species website (IUCN Red List, 2020). Common names for each species were sourced using the SAIAB database, the freshwater field guide of Skelton (2001), or the IUCN Red List of Threatened Species website (IUCN Red List, 2020). Information pertaining to species origin was determined using historic distribution records from the IUCN Red List of Threatened Species website (IUCN Red List, 2020), the GBIF database (GBIF.org, 2018), Skelton (2001) and Ellender and Weyl (2014). Each species was classified as being either ‘native’ (taxon occurring within its natural range – past or present – and dispersal potential) or ‘non-native’ (alien or extralimital taxa) (Dallas et al., 2021). Ecological Tolerance Category Information pertaining to the ecological tolerance of each species was determined using Skelton (2001). Each species was classified as being either ‘primary freshwater’; ‘secondary freshwater’; or ‘diadromous’. This classification was confirmed with relevant fish experts in the country (Skelton, personal communication, 01 April 2020; Chakona et al., personal communication, 14 September 2020). Endemism The endemism category of each species was determined using definitions provided on the FBIS (Dallas et al., 2021). Species were classified based on the following definitions: Widespread – occurring in more than one Freshwater Ecoregion and not restricted to southern Africa; Subregional endemic – endemic to southern Africa; National endemic – occurring in more than one Freshwater Ecoregion, but restricted to South Africa; Regional endemic level 1 – endemic to South Africa, but occurs in more than one primary catchment within a single Freshwater Ecoregion; Regional endemic level 2 – endemic to one primary catchment in South Africa; Micro-endemic 1 – endemic to less than five rivers, within one primary catchment in South Africa; Micro-endemic 2 – endemic to one river in South Africa. Conservation Status The IUCN Red List of Threatened Species website (IUCN Red List, 2020) classifies species into six main categories based on their extinction risk. Each species was classified as either ‘Not Evaluated’, ‘Data Deficient’, ‘Least Concern’, ‘Near Threatened’, ‘Vulnerable’, ‘Endangered’ or ‘Critically Endangered’.Quality Control
The collected data were standardised and uploaded onto the FBIS platform. Distribution and abundance patterns were assessed and visualised in R Software (Version 3.5.0; R Core Team, Vienna, Austria). The total number of records were calculated for: each data source; each year; each species; each origin category; each ecological tolerance category; each endemism category; and each IUCN conservation category. In addition, the total number of species occurring in each category was also calculated for: each species; each origin category; each ecological tolerance category; each endemism category; and each IUCN conservation category. These calculations were then repeated for each of South Africa’s nine provinces.Method steps
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Taxonomic Coverages
Coverage includes all freshwater fish species known to occur in the wild (species held in captivity were excluded) within South Africa. For the purpose of this chapter, only formally described species recognised using the GBIF taxonomic backbone were included. All formally described sub-species were also included, listed under their parent taxa. Species in the process of being described, or that belong to groups that are currently under taxonomic review (such as those belonging to the genera Enteromius, Galaxias and Sandelia) were omitted completely from the data collection and analyses of this chapter, pending resolution of their taxonomic status. Freshwater fish species are defined as species that spend all, or a critical part, of their lives in either freshwater or brackish environments (IUCN Freshwater Fish Specialist Group, 2015; Arthington et al., 2016). For the purpose of this study, only primary freshwater fish (fishes living in inland waters, with little or no tolerance of saltwater), secondary freshwater fish (fishes relatively tolerant of salt water, but normally living in inland waters) and diadromous/catadromous fish (fishes that, in the course of their life cycle, regularly migrate between inland waters and the sea, or vice versa) species were included. Importantly, both marine peripheral and sporadic marine species were omitted entirely from both the data collection and analysis (see Skelton (2001) for ecological-tolerance category definitions).
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Geographic Coverages
The geographic scope of this project was restricted to the boundaries of the Republic of South Africa, but also included the Kingdom of Eswatini (formerly Swaziland) and the Kingdom of Lesotho (for convenience purposes, this study area is hereafter referred to as ‘South Africa’). Data collection was limited to rivers, dams and freshwater lakes within South Africa. Importantly, estuarine and marine systems were excluded.
Bibliographic Citations
- Dallas, H., Shelton, J., Sutton, T., Tri Cuptura, D., Kajee, M. & Job, N. 2021. The Freshwater Biodiversity Information System (FBIS)–mobilising data for evaluating long-term change in South African rivers. African Journal of Aquatic Science. DOI: 10.2989/16085914.2021.1982672. - DOI: 10.2989/16085914.2021.1982672.
- Freshwater Biodiversity Information System (FBIS). 2022. Downloaded from https://freshwaterbiodiversity.org on <current date> - https://freshwaterbiodiversity.org
Contacts
Mohammed Kajeeoriginator
position: PhD Student
University of Cape Town
17 Albion Road, Rondebosch
Cape Town
7700
Western Cape
ZA
Telephone: 0790567990
email: kjxmoh007@myuct.ac.za
homepage: http://www.frcsa.org.za
userId: http://scholar.google.com/citations?user=YtAgS7gAAAAJ&hl=en
Helen Dallas
originator
position: Executive Director
Freshwater Research Centre
Imhoff's Gift
Cape Town
7975
Western Cape
ZA
email: helen@frcsa.org.za
homepage: http://www.frcsa.org.za
userId: http://scholar.google.com/citations?user=8LxReLkAAAAJ&hl=en&oi=ao
Mohammed Kajee
metadata author
position: PhD Student
Freshwater Research Centre
Imhoff's Gift
Cape Town
7975
Western Cape
ZA
Telephone: 0790567990
email: kjxmoh007@myuct.ac.za
homepage: http://www.frcsa.org.za
userId: http://scholar.google.com/citations?user=YtAgS7gAAAAJ&hl=en
Helen Dallas
metadata author
position: Executive Director
Freshwater Research Centre
Imhoff's Gift
Cape Town
7975
Western Cape
ZA
Telephone: 0790567990
email: helen@frcsa.org.za
homepage: http://www.frcsa.org.za
userId: http://scholar.google.com/citations?user=8LxReLkAAAAJ&hl=en&oi=ao
Jeremy Shelton
metadata author
position: Researcher
Freshwater Research Centre
Imhoff's Gift
Cape Town
7975
Western Cape
ZA
Telephone: 0790567990
email: jeremy@frcsa.org.za
homepage: http://www.frcsa.org.za
userId: http://scholar.google.com/citations?user=YtAgS7gAAAAJ&hl=en
Aneri Swannepoel
metadata author
position: Researcher
Freshwater Research Centre
Imhoff's Gift
Cape Town
7700
Western Cape
ZA
homepage: http://www.frcsa.org.za
userId: https://www.linkedin.com/profile/view?id=aneri-swanepoel-b48605170/?originalSubdomain=za
Charles Griffiths
metadata author
position: Professor
University of Cape Town
21 Chemistry Road
Cape Town
7700
Western Cape
ZA
email: charles.griffiths@uct.ac.za
userId: http://scholar.google.com/citations?user=CrccRZcAAAAJ
Mohammed Kajee
user
position: PhD Student
Freshwater Research Centre
Imhoff's Gift
Cape Town
7975
Western Cape
ZA
Telephone: 0790567990
email: kjxmoh007@myuct.ac.za
homepage: http://www.frcsa.org.za
userId: http://scholar.google.com/citations?user=YtAgS7gAAAAJ&hl=en
Helen Dallas
principal investigator
position: Executive Directors
Freshwater Research Centre
Imhoff's Gift
Cape Town
7975
Western Cape
ZA
email: helen@frcsa.org.za
homepage: http://www.frcsa.org.za
userId: http://scholar.google.com/citations?user=YtAgS7gAAAAJ&hl=en
Mohammed Kajee
administrative point of contact
position: PhD Student
Freshwater Research Centre
Imhoff's Gift
Cape Town
7975
Western Cape
ZA
Telephone: 0790567990
email: kjxmoh007@myuct.ac.za
homepage: http://www.frcsa.org.za
userId: http://scholar.google.com/citations?user=YtAgS7gAAAAJ&hl=en
Helen Dallas
administrative point of contact
position: Executive Director
Freshwater Research Centre
Imhoff's Gift
Cape Town
7700
Western Cape
ZA
email: helen@frcsa.org.za
homepage: http://www.frcsa.org.za
userId: http://scholar.google.com/citations?user=8LxReLkAAAAJ&hl=en&oi=ao