Description
Fossil remains of several Bovidae species were collected from three museums in South Africa for ancient DNA analysis. A total of 324 unique specimens were collected, of which 323 are georeferenced. The majority (320) were collected from the Iziko Museums of South Africa's Archaeology Collection in Cape Town, while three were collected from the National Museum Bloemfontein's Florisbad Quaternary Research Collection, and one was collected from the Ditsong National Museum of Natural History's Archaeozoology Collection in Pretoria. As the collections had not yet been digitized by the museums, permission was obtained by Deon de Jager to publish the occurences on GBIF on behalf of the museums.
Data Records
The data in this occurrence resource has been published as a Darwin Core Archive (DwC-A), which is a standardized format for sharing biodiversity data as a set of one or more data tables. The core data table contains 324 records.
This IPT archives the data and thus serves as the data repository. The data and resource metadata are available for download in the downloads section. The versions table lists other versions of the resource that have been made publicly available and allows tracking changes made to the resource over time.
Versions
The table below shows only published versions of the resource that are publicly accessible.
How to cite
Researchers should cite this work as follows:
de Jager D, Faith J T, O'Brien K, Lorenzen E (2024). Bovid fossils sampled for the project Palaeogenomes of a lost world: Ancient bovids of the submerged Palaeo-Agulhas Plain of southern Africa (PalaeoBovids). Version 1.1. South African National Biodiversity Institute. Occurrence dataset. https://ipt.sanbi.org.za/resource?r=palaeobovids_bovid-fossils-south-africa&v=1.1
Rights
Researchers should respect the following rights statement:
The publisher and rights holder of this work is South African National Biodiversity Institute. This work is licensed under a Creative Commons Attribution Non Commercial (CC-BY-NC 4.0) License.
GBIF Registration
This resource has been registered with GBIF, and assigned the following GBIF UUID: 0fab0ca0-5423-418f-b876-81b240418a9f. South African National Biodiversity Institute publishes this resource, and is itself registered in GBIF as a data publisher endorsed by South African Biodiversity Information Facility.
Keywords
Occurrence; Specimen; Bovidae; fossils; ancient DNA
Contacts
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https://orcid.org/https://orcid.org/0000-0003-4388-2624
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Geographic Coverage
All known localities are in South Africa, mainly the Western and Eastern Cape provinces, with at least two from the Free State (potentially a third, but the location is near the border of the Eastern Cape and Free State, with the uncertainty covering parts of both provinces). One record has an unknown locality, but is suspected to be from Namibia.
| Bounding Coordinates | South West [-34.886, 11.47], North East [-16.889, 28.169] |
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Taxonomic Coverage
Seven bovid species are represented in this dataset: Syncerus caffer caffer (Cape buffalo), Syncerus antiquus (giant long-horned buffalo, extinct), Tragelaphus oryx (common eland), Redunca arundinum (southern reedbuck), Redunca fulvorufula (mountain reedbuck), Pelea capreolus (grey rhebok), and Raphicerus melanotis (Cape grysbok).
| Kingdom | Animalia |
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| Phylum | Chordata |
| Class | Mammalia |
| Order | Artiodactyla |
| Family | Bovidae |
Temporal Coverage
| Living Time Period | Pleistocene to Holocene (approximately 130,000 to 1,500 years ago) |
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Project Data
The recent palaeoecological characterisation of the drowned Palaeo-Agulhas Plain (PAP, South Africa) placed the subfossil collections of African bovids into significant environmental and temporal context. However, it lacks a genetic characterisation of mammals. The EU-funded PalaeoBovids project will use palaeogenomic techniques to generate ancient mitochondrial genomic data of six African bovid species connecting five time periods over the last 100 000 years. The project, hosted at the GLOBE Institute (University of Copenhagen), will use the data to investigate drivers of temporal changes in genetic diversity – the emergence of pastoralism, over-hunting by colonial settlers, recent population fragmentation, and the impacts on various feeding groups. PalaeoBovids will deepen our understanding of the impact of climate, disease and humans on species extinction.
| Title | Palaeogenomes of a lost world: Ancient bovids of the submerged Palaeo-Agulhas Plain of southern Africa |
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| Identifier | https://cordis.europa.eu/project/id/101026951 |
| Funding | This project has received funding from the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie grant agreement No. 101026951. |
| Study Area Description | South African archaeological sites. Those bordering the Palaeo-Agulhas Plain were targeted and thus sites are mainly located in the Western and Eastern Cape provinces. Note that the sites themselves were not visited. Specimens were previously excavated (mainly in the 1960s and 1970s) and are curated in various museums in South Africa, which is where the specimens were collected from for this project. |
| Design Description | The aim of the project was to track changes in genetic diversity of bovids through time on the Palaeo-Agulhas Plain in relation to changes in climate and habitat availability, as well as increasing human pressures. Three ancient time periods were targeted for sampling, defined by marine isotope stages (MIS): MIS3 (57,000-29,000 years ago), MIS2 (29,000-11,700 years ago), and MIS1 (11,700-approximately 1,500 years ago). Samples representing modern populations of the same species were also collected, though these are not included in this occurrence dataset. Since the present-day habitat of the Cape Floristic Region is better suited to browsers and mixed feeders than to grazers, the target species were distributed across these categories to be able to detect differential changes in genetic diversity between these broader groups. The initial grazer target species were Syncerus caffer caffer (Cape buffalo), Syncerus antiquus (giant long-horned buffalo, extinct at transition between MIS2 and MIS1), and Redunca arundinum (southern reedbuck). The brower target species were Pelea capreolus (grey rhebok) and Raphicerus melanotis (Cape grysbok). The mixed feeder target species was Tragelaphus oryx (common eland). The sampling was distributed over several archaeological sites, to reduce the pressure on each site. |
Sampling Methods
The aim of the project was to track changes in genetic diversity of bovids through time on the Palaeo-Agulhas Plain in relation to changes in climate and habitat availability, as well as increasing human pressures. Three ancient time periods were targeted for sampling, defined by marine isotope stages (MIS): MIS3 (57,000-29,000 years ago), MIS2 (29,000-11,700 years ago), and MIS1 (11,700-approximately 1,500 years ago). Samples representing modern populations of the same species were also collected, though these are not included in this occurrence dataset. Since the present-day habitat of the Cape Floristic Region is better suited to browsers and mixed feeders than to grazers, the target species were distributed across these categories to be able to detect differential changes in genetic diversity between these broader groups. The initial grazer target species were Syncerus caffer caffer (Cape buffalo), Syncerus antiquus (giant long-horned buffalo, extinct at transition between MIS2 and MIS1), and Redunca arundinum (southern reedbuck). The brower target species were Pelea capreolus (grey rhebok) and Raphicerus melanotis (Cape grysbok). The mixed feeder target species was Tragelaphus oryx (common eland). The sampling was distributed over several archaeological sites, to reduce the pressure on each site. An ideal sample size of 20 specimens per species per time bin was initially proposed and adhered to as far as possible, but was not always reached due to specimen availability in reality, and in the case of Redunca arundinum in MIS1 the number was reduced to 10 specimens by the Heritage Western Cape committee that approved the project in that region due to the limited number of specimens of this species in that time bin. The occurences in this dataset thus represents the closest that we could come to reaching the target of 20 specimens per species per ancient time bin given the contraints described above.
| Study Extent | The archaelogical sites associated with the Palaeo-Agulhas Plain from which fossil specimens originated are: Boomplaas Cave, Byneskranskop 1, Die Kelders Cave 1, Elands Bay Cave, Klasies River Mouth, and Nelson Bay Cave, all of which are curated at the Iziko Museums of South Africa Archaeology Collection. Additionally, to increase the sample size of the extinct giant long-horned buffalo (Syncerus antiquus), other museums were approached and thus specimens originating from sites not associated with the Palaeo-Agulhas Plain were also obtained. These sites were: Rouxville and Parkeren-A Spitskop, which are curated at the National Museum Bloemfontein Florisbad Quaternary Research Collection. Finally, a giant long-horned buffalo specimen of unknown origin (although suspected to be Namibia) was obtained from the Ditsong National Museum of Natural History Archaeozoology Collection. |
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Method step description:
- During sampling in the museums, species identifications made by the excavating archaeologists/palaeontologists, or those that have subsequently studied the collections, were used to identify appropriate specimens of the target species. These identifications were based on morphology and thus mainly teeth were selected (n = 308), as these can be more reliably assigned to species level than bones (n = 16). In two cases, bones that were morphologically identified as Redunca sp. (can be either R. arundinum or R. fulvorufula) were genetically shown to be Pelea capreolus, as species of the same subfamily as Redunca. In one case, the genetic data refined a Redunca sp. classification to R. fulvorufula, and in three other cases R. fulvorufula were sampled inadvertently in place of R. arundinum. Hence the presence of R. fulvorufula in the dataset despite not being part of the initial project design. Note, genetic data are not available and will not be available for all specimens, due to the poor preservation of DNA. To reduce the risk of resampling individuals, specimens of the same species were not sampled from the same storage bag where possible, with the assumption that remains considered by the excavating archaeologists/palaeontologists to be from the same individual would have been kept together.
Collection Data
| Collection Name | Iziko Museums of South Africa Archaeology Unit |
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| Collection Identifier | https://www.iziko.org.za/collection/archaeology/ |
| Collection Name | National Museum Bloemfontein Florisbad Quaternary Research |
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| Collection Identifier | https://nationalmuseum.co.za/florisbad-quaternary-research/ |
| Collection Name | Ditsong National Museum of Natural History Archaeozoolgy Collection |
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| Collection Identifier | https://scientific-collections.gbif.org/collection/ddab00b0-21e0-4a91-abfc-081657d12d25 |
| Specimen preservation methods | No treatment |
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Additional Metadata
3D models of these specimens will be uploaded to MorphoSource (link to be added). Such models were generated for all but one specimen before destructive sampling for DNA analysis, as required by the South African Heritage Resources Agency for this project. The one specimen for which a 3D model is not available is SAMC:Archaeology:O14-4.4543 (Tragelaphus oryx) as the tooth was too fragment and the fragments too small to scan with the 3D scanner.
| Purpose | See Project Data. |
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| Maintenance Description | The database will be updated with sequences associated with the specimens once that data are published and stored in an International Nucleotide Sequence Database Collaboration (INSDC) repository. Scientific names and taxon classifications will be updated accordingly, should any DNA-based identifications differ from the original classification based on morphology. |
| Alternative Identifiers | https://ipt.sanbi.org.za/resource?r=palaeobovids_bovid-fossils-south-africa |