The cryptic case of Otomys sloggetti (Sloggett’s vlei rat): Interpreting murid molar morphology in the fossil record

Vlei rats (Family: Muridae; Subfamily: Otomyinae) have a widespread distribution in southern Africa. They are favoured prey of barn and spotted eagle owls, and frequently become associated with archaeological deposits when the owls roost in cave sites. The phylogeny of several Otomyinae species is enigmatic, and Otomys sloggetti (Sloggett’s vlei rat) is no exception. This species has been referred to as the ‘ice rat’ and present distribution ranges are seemingly limited to mountainous areas, at high altitude, in Lesotho Drakensberg and the Karoo. It was thus surprising and unexpected when specimens closely resembling Otomys sloggetti (identification was based on molar morphology) were found in several archaeological sites on the south and west coasts of South Africa, and also in modern owl pellet assemblages – all extralimital to the current reported distribution. However, further examination of and comparison between these specimens, as well as extensive differences observed between comparative Otomys sloggetti specimens from museum collections, highlighted potential problems associated with the common practice of using tooth morphology to identify fossil murid species. We identified six molar morphotypes from the fossil and modern material, all of which bore a morphological resemblance to O. sloggetti. The material discussed in this paper suggests that cryptic, undescribed vlei rat species, or subspecies, have been in the past, and may yet be, co-occurring with modern populations of O. karoensis and O. irroratus. Phylogenetic studies need to be done in conjunction with morphological studies, as, currently, the relationship between the huge variation seen in interspecific morphology with genetics is little understood, different Otomys species are not always distinguishable morphologically, and considerable chromosomal polytypes have been found. Our findings highlight the need for extensive cladistic and genetic research on the Otomyinae. Significance: Mice and shrews from fossil sites are frequently used by archaeologists as indicators of past climatic and environmental conditions. Research into the species present in fossil assemblages is usually done on a single site basis and intersite comparisons are rare. The taxonomic conundrums presented by a vlei rat found in several South African archaeological sites indicates that such comparisons could result in the re-evaluation of identifications, and/or indicate the presence of cryptic species/subspecies. Phylogenetic studies are needed in conjunction with morphological studies, as the relationship between variations in interspecific tooth morphology (used to identify taxa) with genetics is little understood. This in turn will help to elucidate the relationship between morphology, biogeography and local adaptations.publishedVersio

The 100,000–77,000‑Year Old Middle Stone Age Micromammal Sequence from Blombos Cave, South Africa: Local Climatic Stability or a Tale of Predator Bias?

In this paper, we present a case study of the micromammal sequence from Marine Isotope Stage 5 (130,000–71,000 YBP) at Blombos Cave on the southern Cape coast of South Africa. Our analyses of the micromammal assemblage from 100,000 to 76,000 YBP shed light on micromammal taxonomic distributions, local palaeoenvironments, and site formation processes at this renowned Middle Stone Age site. Taphonomic analyses indicate that spotted eagle owls (Bubo africanus) were the main predator species responsible for accumulating the micromammals, but with contributions from barn owls (Tyto alba). In addition, the micromammal bones have been subjected to a range of post-depositional processes, some of which are associated with microbial actions likely resulting from human or animal activities in the cave. We have recorded three species in the archaeological assemblage that do not occur in the Blombos area today. These are the Hottentot golden mole (Amblysomus hottentotus), Duthie’s golden mole (Chlorotalpa duthieae), and Laminate vlei rat (Otomys laminatus). The biodiversity indices based on micromammal species suggest that local vegetation consisted of different habitats that could sustain a diverse small mammal population. During MIS 5c/5b, the diversity of species declined, but there was still a mosaic of vegetation habitats present in the local area. On a larger temporal scale, climate conditions were slightly more humid than at present, and winter rainfall was seemingly greater. The amount of winter rainfall would have been similar to locations currently c. 50–150 km further west of Blombos Cave. However, based on micromammal proxies, there were seemingly no major fluctuations visible in climate or vegetation composition during the entire 24,000-year period. We suggest that the explanation could be multifaceted, two potential factors being predator bias derived from the owls’ preference for generalist micromammal species or an actual reflection of local stable climatic and environmental conditions in the Blombos area.publishedVersio

Pilot fires: Preliminary Report from Interdisciplinary Actualistic Fire Experiments

Hearth formation processes are complex. They involve multiple actions, reactions, and activities before, during, and after an active fire and can also impact a wide range of materials and sediments at an archaeological site. Archaeologists approach combustion features and formation processes from multiple analytical perspectives. However, many experimental studies are limited to a strict analytical focus on a single or very few fire-related aspects to allow for careful control of specific variables. Six researchers report here on a multi-focus experimental approach in order to understand complex fire practices and heat-induced alteration of micromammals, ostrich eggshell fragments, mineral pigments, shellfish, and sediments. We designed and conducted five experiments with a state-of-the-art 3D documentation setup, active fires, and excavation through photogrammetry and spatial recording. We provide a brief general account of the experiments and an overview of the experimental design before comparing single-focus and multifaceted experiments and pointing to some of the benefits of our approach and potential areas for improvement. Multifaceted experiments are complex and resource-demanding, and proto-experiments should ideally be part of the experimental design. Our 3D recording and collaboration on documentation strategies provided a wide range of data that can further our understanding of prehistoric combustion features.publishedVersio

The Small Mammal Sequence from the c. 76 – 72 ka Still Bay Levels at Blombos Cave, South Africa – Taphonomic and Palaeoecological Implications for Human Behaviour

The Still Bay, c. 76–72 ka, a prominent techno-tradition during the Middle Stone Age of southern Africa, has yielded innovative technologies, symbolic material culture, and shows evidence of expansion of hunting techniques and subsistence strategies. In this paper we present the results of the first systematic, taphonomic and palaeoenvironmental study of micromammals from the Still Bay levels at Blombos Cave. Our taphonomic analysis indicates that the micromammals were accumulated by avian predators occupying the cave. Post-depositional processes affecting the micromammal assemblage include organic waste decomposition and conditions associated with a limestone cave environment. The palaeoenvironmental reconstruction shows that Marine Isotope Stage (MIS) 5a at Blombos Cave had diverse micromammal communities occupying a variety of habitats and with rainfall pattern equal to present. The transition from MIS 5a to 4 is indicated by less diverse micromammal assemblages, increase in grassland and scrub vegetation, shifts in seasonal precipitation, and a decline in shrubs associated with fynbos. The onset of the glacial conditions associated with MIS 4 is visible in the micromammal assemblage. However humans occupying Blombos Cave during this c. 5 ka period showed an ability to cope with changing environmental conditions and were able to adapt and utilise a variety of available resources

The cryptic case of Otomys sloggetti (Sloggett’s vlei rat): Interpreting murid molar morphology in the fossil record

Vlei rats (Family: Muridae; Subfamily: Otomyinae) have a widespread distribution in southern Africa. They are favoured prey of barn and spotted eagle owls, and frequently become associated with archaeological deposits when the owls roost in cave sites. The phylogeny of several Otomyinae species is enigmatic, and Otomys sloggetti (Sloggett’s vlei rat) is no exception. This species has been referred to as the ‘ice rat’ and present distribution ranges are seemingly limited to mountainous areas, at high altitude, in Lesotho Drakensberg and the Karoo. It was thus surprising and unexpected when specimens closely resembling Otomys sloggetti (identification was based on molar morphology) were found in several archaeological sites on the south and west coasts of South Africa, and also in modern owl pellet assemblages – all extralimital to the current reported distribution. However, further examination of and comparison between these specimens, as well as extensive differences observed between comparative Otomys sloggetti specimens from museum collections, highlighted potential problems associated with the common practice of using tooth morphology to identify fossil murid species. We identified six molar morphotypes from the fossil and modern material, all of which bore a morphological resemblance to O. sloggetti. The material discussed in this paper suggests that cryptic, undescribed vlei rat species, or subspecies, have been in the past, and may yet be, co-occurring with modern populations of O. karoensis and O. irroratus. Phylogenetic studies need to be done in conjunction with morphological studies, as, currently, the relationship between the huge variation seen in interspecific morphology with genetics is little understood, different Otomys species are not always distinguishable morphologically, and considerable chromosomal polytypes have been found. Our findings highlight the need for extensive cladistic and genetic research on the Otomyinae. Significance: Mice and shrews from fossil sites are frequently used by archaeologists as indicators of past climatic and environmental conditions. Research into the species present in fossil assemblages is usually done on a single site basis and intersite comparisons are rare. The taxonomic conundrums presented by a vlei rat found in several South African archaeological sites indicates that such comparisons could result in the re-evaluation of identifications, and/or indicate the presence of cryptic species/subspecies. Phylogenetic studies are needed in conjunction with morphological studies, as the relationship between variations in interspecific tooth morphology (used to identify taxa) with genetics is little understood. This in turn will help to elucidate the relationship between morphology, biogeography and local adaptations

Taxonomic habitat index for the micromammal species present in the M1 and M2 Upper phases at BBC.

<p>Taxonomic habitat index for the micromammal species present in the M1 and M2 Upper phases at BBC.</p

Location of BBC and other sites mentioned in the text.

<p>The blue and red lines indicate the approximate positions of the winter rainfall (WRZ) and summer rainfall zones (SRZ) respectively. The area between the contour lines is the intermediate gradient rainfall zone (YRZ), characterised by all year rainfall at transient intervals moving from west to east. The map includes a topography transect of the offshore platform marked in orange and based on data from Fischer et al. [<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0159817#pone.0159817.ref032" target="_blank">32</a>] (the topography transect of the offshore platform is similar but not identical to the original image from Bar-Matthews <i>et al</i>. [<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0159817#pone.0159817.ref033" target="_blank">33</a>] and is for illustrative purposes only). Satellite maps: A: <a href="http://Maplibrary.org" target="_blank">Maplibrary.org</a> (public domain): <a href="http://www.maplibrary.org/index.php" target="_blank">http://www.maplibrary.org/index.php</a>. B: NASA Earth Observatory (public domain): <a href="http://earthobservatory.nasa.gov/" target="_blank">http://earthobservatory.nasa.gov/</a>.</p

Reconstructed microhabitat at BBC during the SB based on the taxonomic habitat index.

<p>Results are given as stacked percentage distribution of the various vegetation and substrate types.</p

Dating of the overlying hiatus level and the M1 and M2 Upper phases comprising the Still Bay sequence at BBC.

<p>Dating of the overlying hiatus level and the M1 and M2 Upper phases comprising the Still Bay sequence at BBC.</p

Recorded breakage of humeri in the M1 and M2 Upper phase.

<p>Recorded breakage of humeri in the M1 and M2 Upper phase.</p