1 Dimensions of the fossil specimen UW88-1100. http://sajs.co.za/index.php/SAJS/article/downloadSuppFile/583/2897
Six extant species of elephant shrew inhabit areas from the west to the east coast of southern Africa (Namibia, Botswana, South Africa and Mozambique). 10Each of these species also is known from Plio-Pleistocene fossil assemblages of South Africa. 12,13,14 Two additional extinct species, Elephantulus antiquus and Elephantulus broomi, are present in Plio-Pleistocene fossil assemblages of South Africa. 12,13 Two of the extant species found in Plio-Pleistocene South African cave sites (i.e. Elephantulus fuscus and Elephantulus brachyrhynchus) were ruled out for the Malapa specimen because they possess a third lower molar, whereas the specimen from Malapa lacks this tooth. Several dental features identify Elephantulus to species, notably the number of cusps on the incisors and on the upper premolars. 9,10 Although cuspal patterns can be adequately visualised on the rendering, the hemi-mandible from Malapa (UW88-1100) does not retain the more taxonomically diagnostic lower incisors, upper dentition and maxilla. It is therefore imprudent to rule out any of the four extant taxa (i.e. Elephantulus edwardii, Elephantulus myurus, Elephantulus rupestris and Elephantulus intufi; Figure 4), or the two South African extinct species (E. antiquus and E. broomi) on the basis of the hemi-mandible alone, leading us to provisionally assign this hemi-mandible to Elephantulus sp. DiscussionAdvantages of the new method Incorporation of microCT into fossil preparation techniques, together with the opportunity to acquire digital measurements using the in silico approach, provided several unique advantages over traditional techniques in this case. Firstly, continuing traditional preparation of the occlusal surfaces in the tiny fossil likely would have destroyed informative morphology because of the delicate condition of the specimen. Secondly, physical preparation, whether using an air drill or applying chemicals, can be quite time-consuming. MicroCT scanning of the fossil required only about an hour; acquiring a stack of .tif or DICOM images was accomplished in less time. Thirdly, once the fossil had been scanned, potentially risky handling of the damaged specimen was drastically reduced. Moreover, the importance of reduced handling was not fully appreciated until the condition of the specimen (i.e. the presence of abundant microcracks) was fully illuminated through microCT scanning. Macrocracks on the external surface (on the lingual side previously exposed) were visible with the naked eye, but only after virtual images were taken and the rendering was obtained, was it documented that microcracks were actually running throughout the whole hemi-mandible. From the 3D rendering, suitable images for conducting comparative studies were generated. These studies included examination of internal dimensions via virtual sectioning, as well as the ability to manipulate the rendering of the specimen freely in all three dimensions. It also was possible to take repeatable measurements on the rendering (to an accuracy of sub-100 micron), which could be used in comparisons with measurements on other free specimens. None of these data would have been obtainable on the actual specimen, unless destructive methods were employed (i.e. the continuation of physical preparation, sectioning, etc.). Lastly, commercial visualisation software (e.g. Avizo 6.2, VGStudio Max) provides the ability to zoom in, which in this case allowed observation of finer details on the specimen through magnification. Such software also permits the digital extraction of a specific structure (e.g. individual or multiple teeth; Figure 5) from which a 3D printout can be produced. The 3D printout can be transported and distributed for use, or can even serve as the basis for producing a mould of the fossil in order to distribute casts. Research perspectives Diagenesis in the caves of the Sterkfontein Valley often results in bone remains being preserved within dense matrix such as calcified clastic sediments. 3,8 Image data acquisition using microtomography, or even medical computed tomography, coupled with 3D reconstruction and extraction of specimens, facilitates exploration inside matrix blocks without requiring substantial manual preparation, which itself is associated with financial and time costs. In this particular case, the specimen was revealed on the surface of the block, after initial physical preparation. The in silico method allowed us to explore the extent of the fossil partially hidden inside the block. This method also permitted virtual identification, measurements and 3D extraction of the specimen whilst it was still inside the block, and without risking further damage to the specimen. As demonstrated in the case of the Malapa fossil (UW88-1100), this approach permits the prescreening of matrix blocks in order to apply cost–benefit analyses for deciding whether to pursue further physical preparation by taking into consideration the value of the informational content of fossils imprisoned within matrix blocks. Some microfauna species are excellent indicators of the localised environmental conditions such as climate and landscape. 14Therefore, identification of microfaunal remains is a useful tool during the assembly of palaeoclimatic and palaeoenvironmental reconstructions. 14The elephant shrew in southern Africa typically occupies an arid environment, from desert to dry savanna or dry shrubland, but resides in close proximity to a water source. 10Three species, E. rupestris, E. myurus and E. edwardii are associated with rocky ridges and outcrops, or koppies, whereas E. intufi occupies burrows under bushes and is indicative of regions characterised by scrub bush, thin grass cover and sandy substrate. 10Further additions to the Malapa micromammal assemblage will be informative to the nature of the Malapa palaeoenvironment, perhaps narrowing the present characterisation even more. Because of the geological context of cave sites in the Cradle of Humankind, it is a long and laborious process to identify the presence of small-bodied fauna, to extract them from the encasing matrix and to identify them to the level of species. The application of microCT scanning and in silico preparation techniques will more easily facilitate each of these steps, particularly for microfauna, by minimising (1) the amount of preparation damage to specimens and (2) the misallocation of valuable manual preparation time and effort on specimens yielding comparatively little new information. Conclusions Incorporating microCT scanning and segmentation of renderings into palaeontological preparation methods offers an alternative that can limit damage to valuable fossils and reduce time-consuming manual preparation and physical extraction of fossils from matrix. The use of 3D renderings of fossils enhances an opportunity to identify and describe fossil remains that otherwise would be limited when using traditional physical preparation techniques. This method can be particularly advantageous when studying small, damaged or delicate specimens. It also can be useful in other scenarios, including in the analysis of larger taxa from Plio-Pleistocene sites from the Cradle of Humankind where the majority of fossils are often encased within matrix. Acknowledgements We are very grateful to Teresa Kearney and the Ditsong National Museum for providing access to an invaluable reference collection and for valuable discussions over the identification of the specimen. We thank DebTech of De Beers Group Services for permission to use their imaging facilities. We are very grateful to Tea Jashashvili for sharing her comments and advice during the digital extraction and reconstruction of the specimen. We thank Roseberry Languza for his manual preparation work on the specimen. We wish to acknowledge the National Research Foundation and the Department of Science and Technology in South Africa, particularly the African Origins Platform programme, for funding the creation and the development of facilities that contributed to this research. Competing interests We declare that we have no financial or personal relationships which may have inappropriately influenced us in writing this article. Authors’ contributions Aurore Val performed the 3D rendering and palaeontological identification of the specimen, and wrote the article. Kristian Carlson assisted with the microCT scan of the specimen and assisted with the 3D rendering of the specimen and the writing of the article. Christine Steininger assisted in the palaeontological identification of the specimen, participated in discussions about the palaeoenvironmental implications and made very useful comments on the article. Job Kibii assisted in the palaeontological identification and provided field data as well as useful comments on the article. Cecil Churms allowed access to the microCT scanner and conducted the microCT scan of the specimen. Brian Kuhn photographed the specimen, assisted in the palaeontological identification and commented on the article. Lee Berger is a joint permit holder for the site of Malapa.1.http://dx.doi.org/10.1126/science.1184944 2.http://dx.doi.org/10.1126/science.11849503.BrainCKThe hunters or the hunted? An introduction to African cave taphonomy19814.BrainCKSwartkrans: A cave’s chronicle of early man19935.ClarkeRKumanKThe Sterkfontein caves palaeontological and archaeological site [pamphlet]20006.http://dx.doi.org/10.1016/j.quaint.2008.05.0177.http://dx.doi.org/10.1126/science.12036978.http://dx.doi.org/10.1016/0305-4403(83)90034-19.HillsonSTeeth. 2nd ed200510.The mammals of the southern Africa subregion. 3rd ed200511.Avizo®201012.Notes on the systematics of micromammals from Sterkfontein200036839013. http://dx.doi.org/10.1016/S0016-6995(98)80022-314.http://dx.doi.org/10.1006/jhev.2001.0483