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Journal of Archaeological Science 83 (2017) 1e11

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Journal of Archaeological Science

journal homepage: http : / /www.elsevier .com/locate/ jas

Visualising scales of process: Multi-scalar geoarchaeologicalinvestigations of microstratigraphy and diagenesis at hominin bearingsites in South African karst

Tara Edwards a, Elle Grono b, Andy I.R. Herries a, c, Frank J. Brink d, Ulrike Troitzsch e,Tim Senden f, Michael Turner f, Aleese Barron b, Lauren Prossor b, Tim Denham b, *

a The Australian Archaeomagnetism Laboratory, Department of Archaeology and History, La Trobe University, Bundoora, Melbourne, VIC, 3086, Australiab School of Archaeology and Anthropology, Australian National University, Canberra, ACT 2601, Australiac Centre for Anthropological Research, University of Johannesburg, Gauteng, South Africad Centre for Advanced Microscopy, Australian National University, Canberra, ACT, 2601, Australiae Research School of Earth Sciences, Australian National University, Canberra, ACT, 2601, Australiaf Research School of Physics and Engineering, Australian National University, Canberra, ACT 2601, Australia

a r t i c l e i n f o

Article history:Received 7 August 2016Received in revised form2 May 2017Accepted 10 May 2017Available online 24 May 2017

Keywords:KarstMicromorphologyHomininPalaeokarstQEM-EDSCT

* Corresponding author.E-mail address: Tim.Denham@anu.edu.au (T. Denh

http://dx.doi.org/10.1016/j.jas.2017.05.0070305-4403/© 2017 Elsevier Ltd. All rights reserved.

a b s t r a c t

Multi-scalar geoarchaeological investigations were conducted on several samples of sediment (dolomitecave sediments, ferricrete ridge, speleothem, tufa and tufa cave sediments) from four early homininfossil-bearing sites (Taung Type Site, Haasgat, Drimolen Main Quarry, Elandsfontein) in different SouthAfrican karst environments. The study was designed to test the value of geoarchaeological techniques foridentifying and characterising environments of deposition and diagenetic processes involved in siteformation within different mediums and different karst environments. The traditional petrographicmethod is weighed against two relatively new methodological contributions to site formation anddiagenesis: Computed Tomography (CT) and automated Quantitative Evaluation of Minerals using EnergyDispersive Spectroscopy (QEM-EDS), employing QEMSCAN® technology. An integrated micro-samplingapproach is outlined for successful cross-correlation between techniques. The study demonstrates thatdifferent analyses vary in their ability to visualise different types of process e primary and secondary.Thin section petrography remains the ‘gold standard’ for analyses conducted at the micro-scale, whileQEM-EDS and CT offer exciting potential to perform meso-scale analyses and are best utilised as com-plementary rather than alternative techniques to petrography.

© 2017 Elsevier Ltd. All rights reserved.

1. Introduction

Scalar issues are fundamental to the discipline of geo-archaeology, which encompasses a range of analytical and inter-pretive scales from the landscape to the archaeological deposit(Stein, 1993; Butzer, 2008; Denham, 2008; Jones, 2010; Batemanet al., 2010; Fouache, 2013; McNamee et al., 2013). This studypresents a mixed-method multi-scalar approach to geo-archaeological investigation, defined here as the use of compli-mentary investigative methods at varying scales of resolution toincrease the interpretative potential for studying human-environmental relations. A multi-scalar approach provides links

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between macro-scale (landscape) studies and micro-scale (sitestratigraphy and deposit) characterisation (Butzer, 2008). Thisprocess, referred to by Butzer (2008:403) as ‘scale-switching, fromthe large to the small and back’ is at the core of geoarchaeology.

Multi-technique geoarchaeological investigations greatlyenhance the interpretative potential for identifying environmentalprocesses which act across varying scales between the archaeo-logical deposit and the landscape. Moreover, using amixed-methodframework of analysis, integration of different techniques canovercome limitations associated with each respective techniqueand provide comparative and complimentary datasets for crosscorrelation and multi-proxy validation (Canti, 1995; Denham,2008; Shillito et al., 2011; Milek and Roberts, 2013; Canti andHuisman, 2015:104e105). The multi-scalar mixed-method geo-archaeological investigation presented here combined thin section

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petrography (micro-scale) with automated QEM-EDS (QEMSCAN)and selective Computed Tomography (CT) (meso-scale).

1.1. Sites and samples

The results of five rock samples are drawn from a broader studyinvestigating environments of deposition and diagenetic processesat four hominin fossil-bearing karstic sites in South Africa: TaungType Site, Haasgat, Drimolen Main Quarry and Elandsfontein(Fig. 1). The presentation is selective and focuses on the respectiveability of each technique to visualise primary and secondary pro-cesses for different sediment types (dolomite cave sediments, fer-ricrete ridge, speleothem, tufa and tufa cave sediments) acrossmultiple analytical scales.

Haasgat and Drimolen are early Pleistocene (between 2.3 and1.4 Ma) hominin-bearing palaeocave deposits (Keyser et al., 2000;Adams, 2012; Herries et al., 2014; Adams et al., 2016; Leece et al.,2016a,b). Both sites formed within ~2.6 Ga Malmani dolomite andare now palaeokarst remnants of heavily eroded ancient caves.Drimolen contains Paranthropus robustus and early Homo, whereasHaasgat has only recently yielded a hominin tooth (Moggi et al.,2010; Leece et al., 2016a,b). The sample from the Drimolen MainQuarry (DRM09) is a speleothem that appears to cap the strati-graphic sequence within the palaeocave. The speleothem formedwithin a more recent cave that formed at the interface between thedolomite and palaeocave sediments. The sample was taken toestablish stratigraphic relationships for dating purposes. TheHaasgat sample (HGTFH24) was used in a palaeomagnetic study ofthe site and yielded inconclusive results (Herries et al., 2014) thatare thought to represent alteration of the sample by later karsticprocesses; the current investigations are designed to clarify the

Fig. 1. Site location map and

sample's diagenetic history.Samples TH41 and TH33 are from the Buxton-Norlim Lime-

works, which is located 15 km northwest of the town of Taung,some 300 kmwest of Drimolen and Haasgat (Kuhn et al., 2016). Thelimeworks is famous for the discovery in 1924 of the first earlyhominin from Africa and the type specimen of Australopithecusafricanus, the Taung Child (Dart,1925). The skull originates from theType Site that consists of two remnant pinnacles of tufa (thewestern Dart Pinnacle and eastern Hrdli�cka Pinnacle), the rest hasbeen mined away. Associated with these pinnacles are twodifferent clastic sedimentary units that contain fossils and havepreviously been interpreted as cave fills (McKee, 1993). The older ofthese units is a ~3.0e2.6 Ma (Herries et al., 2013) pink micrite,which is the source of the Taung Child Skull, and thought to haveformed simultaneously as an open air deposit (Hopley et al., 2013;Herries et al., 2013). Sample TH33 was recovered from this depositat the base of the Hrdli�cka Pinnacle. Sample TH41 is a quartz rich,calcite cemented sample that was recovered from a younger(2.6e2.0 Ma) red sandstone at the base of the Hrdli�cka Pinnacle,which potentially represents the infill of more recent caves thatformed within the tufa and pink micrite, and contains extensiveprimate fossils. Sampling was designed to further clarify thedepositional environment of fossil-bearing deposits at Taung.

Sample EFT9427 comes from the hominin and Acheulian-bearing fossil deposits of Elandsfontein. The site consists of a largecalcrete ridge onto which an extensive dune field has beendeposited (Braun et al., 2013). Within the dunes are abundantfossils and Acheulian artefacts, including a skull cap of Homo hei-delbergensis dated to c1.1 and 0.6 Ma (Klein et al., 2007; Braun et al.,2013). Criss-crossing the dune field are a series of raised ferricreteridges, whichmay be the core of more ancient eroded dunes (Braun

photographs of each site.

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et al., 2013). Sample EFT9427 is a ferruginous quartz arenite derivedfrom one of these ridges.

2. Methods

2.1. Field sampling

In the field, selective sampling targeted specific stratigraphicunits and boundaries that presented opportunities to investigatedepositional history, diagenesis, and the reliability of samples fordating. Semi-consolidated rock samples were removed with achisel, wrapped securely with packaging material and clearlylabelled with orientation and sample number (see Goldberg andMacphail, 2003 for field sampling protocols). The rock sampleswere transported to The Australian Archaeomagnetism Laboratoryat La Trobe University for palaeomagnetic analysis. Subsamples ofthe blocks were then shipped to the Geoarchaeology ResearchGroup Laboratory at the Australian National University for com-plementary geoarchaeological analyses.

2.2. Micro-sampling

Mixed-method investigations are facilitated by resin impreg-nation of samples for thin section petrography that produce‘mirror-image’ sediment blocks of the prepared thin section as by-products (Fig. S1). These impregnated blocks are available forcomplementary analyses, thereby enabling precise cross-correlation of resultant datasets (e.g. Goldberg et al., 2009;Mentzer and Quade, 2013). This micro-sampling technique facili-tates a mixed-method approach that bridges scales of analysislinking micro-scalar investigations (petrography) with meso-scaleanalyses (CT and QEM-EDS) and macro-level (field-based)observations.

2.3. Thin section analysis

Petrography is a long-established technique for obtainingmineralogical and textural information regarding the origin, for-mation and diagenesis of rock samples. Reliable mineral identifi-cation is achieved through observation of a suite of opticalproperties in both plane and cross polarised light (Adams et al.,1984; Gribble and Hall, 1999; Nesse, 2004; MacKenzie andGuilford, 2013). A number of qualitative and quantitative parame-ters are recorded including microstructure and porosity, size andangularity of grains, and extent of diagenesis (Harwood, 1988; Belland Lindsay, 1999). Whilst most observations are recorded asqualitative data, abundance and size of mineral grains and porosityare often semi-quantified by visual estimation using area-percentage charts (Folk et al., 1970; Bullock et al., 1985).

Thin sections approximately 30 mm thick were prepared andmounted to glass slides at Adelaide Petrographic Laboratories. Thinsections were cut to a larger size (75 � 50 mm) than standardpetrographic thin sections (50 � 25 mm) to more effectively cap-ture heterogeneity and potential diagenesis within samples(Bullock et al., 1985; Macphail and Goldberg, 1995). Unlike auto-mated methods that produce quantitative data, such as CT andQEM-EDS, thin section analysis primarily produces qualitative,descriptive data. In order to increase the reliability, thin sectionswere examined in isolation by two different analysts and resultscompared.

Thin sections were first scanned with a high-resolution Epsonperfection V700 photo flatbed colour image scanner at a resolutionof 1200 dpi. The scans permitted meso-scale observation of theentirety of the thin section, including detection of bedding andsedimentary structures, boundaries, colour variation and porosity

(Arpin et al., 2002). Thin sections were observed at magnificationsof 20x-400x under plane polarised light (PPL), cross polarised light(XPL) and oblique incident light (OIL) using an Olympus CX31polarising microscope. Photomicrographs were imaged with anOlympus CS30 3 MP colour camera and processed using OlympusStream V1.9.1 imaging software.

2.4. QEM-EDS (QEMSCAN®)

QEM-EDS (Quantitative Evaluation of Minerals using EnergyDispersive Spectroscopy) was originally developed in the late 1970sby CSIRO in Australia for rapid, quantitative and operator-independent acquisition of X-ray spectra for mineralogical analysis(Butcher et al., 2000; Pirrie et al., 2004). The method utilises anautomated scanning electron microscope which has been equippedwith multiple energy-dispersive X-ray spectrometers to optimise X-raycount rate. QEM-EDSdata outputs typically includemineralmapsandmodal mineralogy percentages. Each pixel is assigned a mineralspecies from the Species Identification Library, or SIP (Haberlah et al.,2011a,b) represented by a different colour (see note to Table S1).

QEM-EDS analyses can be conducted on polished thin sections(30 mm) prepared without a cover slip or on thick sediment slices(typically 3e5 mm). In this study ‘mirror-image’ sub-samplesapproximately 1e2 mm thick were prepared (Fig. S1). The sedi-ment slices were ground to a constant thickness, mounted ontoglass slides, finished using a <1 mm diamond-based polishing me-dium, and submersed in an ultrasonic bath with deionised waterfor 30 s to remove any remaining dirt or debris. After cleaning, thesamples were coated with a 20 nm layer of carbon using a DynavacCS300 coating unit in order to prevent build-up of static chargeduring exposure to the electron beam.

QEM-EDS analysis was performed using an FEI Quanta QEMS-CAN® system at the Centre for Advanced Microscopy (CAM) at theAustralian National University. Data were collected in field imagescan mode, 15 kV accelerating voltage, 10 nA probe current and astep size of 15 mm (Table S1). FEI iMeasure software was used fordata acquisition and FEI iDiscover software was used for raw dataprocessing, noise reduction, frame stitching, refinement of mineralidentification and modal analysis.

Previous studies have shown that QEM-EDS mineral identifica-tion is comparable to other well-established microanalyticalmethods (Goodall et al., 2005). However, QEM-EDS does notperform well in the discrimination of clay minerals or of mineralswith similar or identical chemical compositions (Pirrie et al., 2004;Knappett et al., 2011; Ayling et al., 2012). When employing iDis-cover, a potential source of error in QEM-EDS mineralogical iden-tifications is the assignment of minerals on a ‘first match basis’according to a ranked mineral database in which the hierarchy ofthe available mineral list (SIP) can influence the assigned mineralidentification (Haberlah et al., 2011b:5). To alleviate such problems,Quantitative Powder X-ray Diffraction (QXRD) was used to confirmor adjust the mineral identification criteria by rearranging themineral list hierarchy, editing fitting parameters for existing min-eral entries, or adding missing minerals to the SIP list.

2.5. QXRD

Quantitative Powder XRD obtained bulk mineralogical infor-mation to calibrate the QEM-EDS mineralogical identifications andrankings (Table S2). QXRD was conducted on bulk sub-samples atthe XRD laboratory in the Research School of Earth Sciences,Australian National University. For each sample, a sediment slicewas cut directly from the ‘mirror-image’ face of the rock sampleusing a diamond saw (Fig. S1). Two grams of sediment were milledfor 8min in ethanol with aMcCroneMicronizingMill, dried at 40 �C

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and powdered using an agate mortar and pestle. Amorphous con-tent was quantified by the addition of 20% (wt.) corundum, acrystalline aluminium oxide (1 mm Al2O3, Baikowski). Powder XRDwas performed on a SIEMENS D501 Bragg-Brentano diffractometerequipped with a graphite monochromator and scintillation detec-tor, using CuKa radiation. Samples were suspended on a side-packed sample holder, and analysed from 2 to 70� 2q, at a stepwidth of 0.02�, and a scan speed of 1� per minute. The results wereinterpreted using the Bruker AXS software package Diffracplus Eva10 (2003) with PDF2 database for phase identification, and thenquantified using Siroquant V3 software.

2.6. CT

Originally designed for medical purposes in the 1970s(Hounsfield, 1972, 1973) X-ray computed tomography has beenapplied to soils and sediments to obtain three dimensional struc-tural information relating to size and spatial distribution of pores(Kilfeather and van der Meer, 2008) and contextual spatial relationsof heterogeneous inclusions within archaeological deposits(Huisman et al., 2014). Early application of CT to soils and sedimentstypically produced low resolution output due to limitations ofcomputer processing, (e.g., Perret et al., 1997). Advances in designand computing have allowed for improvements in resolution, withCT systems today potentially providing sub-micron resolution(Varslot et al., 2011).

CT equipment used here was designed and built within theResearch School of Physics and Engineering, ANU (Varslot et al.,2011). The system uses a transmission-style continuously-pum-ped X-ray tube, operated in this case at 80 kV with a 1 mmaluminium filter to yield images at 46 mm (voxel size) resolution.Each samplewasmounted on a stage thatmoves in a helical motionto recover uniformly precise geometric radiographic information.Images were rendered using the open-source program, Drishti v2.6.2 (Limaye, 2012).

Although multiple samples have been subject to CT analysis aspart of the broader study, only the results for one sample are pre-sented here. Samples EFT9427 from Elandsfontein presents asextremely well-homogenised in both thin section and QEM-EDSanalyses, whereas CT enables the processes not identified byother methods to be readily visualised and interpreted.

3. Results

The major primary and secondary processes of formationidentified in each of the five samples are summarised below. Re-sults are presented from youngest to oldest, which accords withchanges in depositional environment from tufa, tufa cave infill,palaeocave sediment, palaeocave speleothem and ferricrete ridge.A series of images depict the petrographic and QEM-EDS datasetsalongside each other to enable visual comparison and cross-correlation, including between the meso-scale scanned thin sec-tions and QEM-EDS mineral maps. As the images only represent aminor sub-set of the features observed in the samples, they wereselected based on the extent to which they permit visualisation offormation processes and cross-correlation between petrographicand QEM-EDS data outputs. For QEM-EDS mineral maps, note thatpercentage areas of minerals are given relative to 100%, after thepercentage assigned ‘background’ is removed.

3.1. Taung, sample TH33 (tufa)

Sample TH33 is primarily composed of calcite formed as a tufawith a predominantly spongy microstructure. Occasional detritalquartz grains had clay coatings (Fig. 2b) and secondary calcite spar

was precipitated in void spaces (Fig. 2e). The top of the samplecontained a ‘sand pocket’, an accumulation of quartz grains encasedby multiple phases of concentric calcite growth (Fig. 2aec).

Petrography identified several units of tufa growth from thebasal layer upwards and two typical ‘growth hiatuses’ (Fig. 2a,c-d).The first hiatus displayed evidence of diagenesis, including elon-gate feathery calcite crystals extending through and beyond thehiatus (Fig. 2c). The second hiatus exhibits columnar calciteprecipitated perpendicular to the substrate (Fig. 2d). Calcite pre-cipitation in void space indicates recrystallisation occurred after theformation of the hiatus (Fig. 2e).

QEM-EDS analysis of TH33 permitted visualisation of primaryprocesses of deposition showing alternating microstratigraphiclayers of the quartz sand fraction within the predominant calcitegrowth (Fig. 2feg). Visualisation of these textural attributes isvaluable for gaining insight into the fluctuating energy conditionspresent within the depositional environment over time.

3.2. Taung, sample TH41 (tufa cave infill)

The petrographic analysis revealed TH41 to be a relatively ho-mogenous sample comprised of detrital quartz in a post-depositional calcite cement (Fig. 3a). While the fine fraction isdominated by secondary calcite, fine reddish-orange clay and silt-sized material form coatings around detrital quartz grains andmicro-aggregates within interstitial spaces (Fig. 3aeb). Secondarycalcite precipitation within voids is predominantly drusy mosaicspar (Fig. 3aeb).

The QEM-EDS analysis of TH41 revealed a complex relationshipbetween quartz grains and the calcite cement (Fig. 3ced). Thepresence of montmorillonite, illite and kaolinite confirms thecoatings on quartz grains to be clay. There are several calcite veinsand ‘donuts’ visible in the computed image, representing concen-trated areas of precipitation.

3.3. Haasgat, sample HGTFH24 (palaeocave sediment)

HGTFH24 represents an intermediate category in which bothprimary depositional components (micritic mud and inclusions ofdetrital quartz with rare bone) and secondary reworking (calcitespar precipitation and dissolution microstructures) contribute tothe heterogeneous character of the sample (Fig. 4). Quartz grainsrange from several microns up to 3 mm in diameter (Fig. 4a and d).Several clays (confirmed by QXRD) form coatings to thick crustsaround coarse detrital material (Fig. 4aeb). The high, variableporosity throughout the sample is likely to result from dissolutionprocesses (Fig. 4c) which were probably responsible for alterationof the original sedimentary structures and thereby affected thepalaeomagnetic signal in the sample.

The QEM-EDS mineral map displays possible primary beddingstructures, such as the four large quartz grains distributed on onelateral plane (Fig. 4ced). QEM-EDS identified the majority of thesample to be calcite (confirmed by QXRD), with additional quartzand amorphous material represented.

3.4. Drimolen, sample DRM09 (speleothem and associatedsediment)

DRM09 is a stratified sample comprising a calcite flowstoneabove reworked, quartz rich sediment, separated by a sharp,distinct boundary (Fig. 5a). The nature of the contact between thetwo units, specifically the calcite crystal growth patterns, indicatesthe flowstone did not form onto the underlying sediment, but thatthe sediment was deposited beneath it at a later time. The pseudo-basal unit is comprised of detrital, reworked quartz grains with rare

Fig. 2. Stratigraphic summary for TH33. Scan of thin section showing locations of photomicrographs (top left) and impregnated billet showing area sampled for QEM-EDS (bottomleft). Photomicrographs of: (a) ‘sand pocket’ comprising quartz grains within secondary sparry calcite matrix encased in crystal calcite (XPL); (b) magnification of quartz grainsshowing deformations and coatings; (c) magnification of encasing calcite growth characterised by multiple concentric growth hiatuses, with diagenised calcite crystals extendingthrough the growth hiatus (XPL); (d) alternating microstratification of quartz sand and calcite crystals (PPL, left and XPL, right); and, (e) micritic texture of basal unit with secondarycalcite spar precipitate in voids (PPL, left and XPL, right). QEM-EDS mineral maps of: (f) sampled area, including modal percentages (for minerals >0.01% of total area); and, (g)magnification of alternating microstratification of detrital quartz sand and calcite crystals comparable to photomicrograph (d).

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bone fragments (Fig. 5a). A secondary drusy mosaic calcite sparcements the basal section. The top unit is entirely composed offlowstone exhibiting a variety of textures (Fig. 5bed) and diage-netic alteration (Fig. 5d). Microscopic investigation revealed at leastsix phases of speleothem growth within the upper portion of thesample, determined through changes in calcite fabric. Precipitationof the flowstone is punctuatedwith hiatuses throughout, indicatingmultiple growth periods under a variety of cave conditions (Fig. 5e).Calcite pseudomorphs indicate replacement of aragonite by themore stable calcium carbonate polymorph calcite (the absence ofaragonite was confirmed by QXRD). Porosity was low throughoutthe sample and most voids were infilled with secondary drusymosaic spar indicating re-precipitation within the basal unit andflowstone. Deformation of the calcite crystals is evident in the formof striations, linear alteration and sutured contacts (Fig. 5d).

Application of QEM-EDS revealed the homogenous mineralog-ical nature expected of a speleothem sample, with the top unitentirely composed of calcite (Fig. 5feg). The QEM-EDS mineral mapshowsmicroporosity of the sample (Fig. 5g), the boundary betweensandstone and flowstone (Fig. 5feg) and presence of apatite (bone)in the basal unit. Quartz is identified in the basal unit, howeverQEM-EDS imaging did not reveal weathering of quartz grains orclay coatings. Similarly, calcite/aragonite is identified by QEM-EDSbut the method cannot differentiate these polymorphic mineralsnor differentiate phases of calcite crystal growth formation andhiatuses within the flowstone (Fig. 5f).

3.5. Elandsfontein, sample EFT9427 (‘ferricrete ridge’)

Petrographic investigations characterised EFT9427 as a

homogenous, clast-supported sample of ferruginous quartz arenite(Fig. 6). Optical investigation identified no discernible units of for-mation. The sub-angular to sub-rounded quartz grains are moder-ately sorted and cemented by the iron-bearing mineral goethite(confirmed byQXRD). Goethite forms thick crusts around the grainsand in some cases has degraded and extended across the grainsurfaces (Fig. 6a).

QEM-EDS investigation of this sample confirmed a clast-supported microstructure, consisting of quartz (Fig. 6bec).Further, it confirmed the ferrous cement as goethite, and revealedthe presence of siderite, which was not identified through petro-graphic investigation. The density of goethite cementationthroughout the sample varies, but in two dimensions did notindicate any regular structure (Fig. 6bec).

Building upon identified concentrations visible in thin sectionpetrography and QEM-EDS, the three dimensional CT scan clearlyshows increased concentrations of goethite as external hypo-coatings around infilled voids, predominantly meso-scale chan-nels (Fig. 7; also see Animation S1). The channels are of uniformthickness, suggesting meso-faunal bioturbation rather than rootaction. Thus, CT imagery sheds light on three dimensional ho-mogenisation processes that are not fully characterised using twodimensional techniques.

Supplementary video related to this article can be found athttp://dx.doi.org/10.1016/j.jas.2017.05.007.

4. Discussion

The results of the study demonstrate that different techniquesvary in their ability to visualise the primary and secondary

Fig. 3. Stratigraphic summary for TH41. Scan of thin section showing locations of photomicrographs (top left) and impregnated billet showing area sampled for QEM-EDS (bottomleft, note cracking is a result of post-collection drying of sample). Photomicrographs of: (a) quartz grains in red-orange clay and silt matrix cemented with fine-grained calcite spar,the central void is infilled with drusy calcite spar (PPL, top and XPL, bottom); (b) clay coatings and fine calcite spar surrounding a quartz grain (PPL, left and XPL, right). QEM-EDSmineral maps of: (c) sampled area, including modal percentages (for minerals >0.15% of total area); and, (d) magnification of void filled with secondary calcite precipitate com-parable to photomicrograph (a). (For interpretation of the references to colour in this figure legend, the reader is referred to the web version of this article.)

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processes involved in site formation (Table 1). The following dis-cussion evaluates the contributions of petrography, QEM-EDS and,in a more limited way, CT in characterising the depositional andpost-depositional histories, environments of deposition and taph-onomic integrity of the five samples investigated. The samples havebeen arbitrarily divided into three groups to represent the range ofsite formation processes. The groupings convey the extent to whichthe samples show primary processes and/or inherited stratificationcompared to those which show extensive homogenisation oforiginal stratigraphy by secondary processes.

4.1. Group 1

In the highly stratified speleothem (DRM09) and tufa (TH33)samples, primary deposition is largely preserved and therebysamples have great potential for reconstructing environments ofdeposition.

Petrography was of most value for sample DRM09, enablingestablishment of a hierarchy of primary deposition and subsequentin situ mineral formation and diagenesis. Petrographic analysisdemonstrated that the quartzose basal unit comprised detritalquartz grains and preserved bone fragments reworked within amicritic matrix. Petrographic observation of the boundary betweenthe basal quartzose unit and the overlying calcite flowstonerevealed the complexity of the stratigraphic association betweenthese two units. Based on petrographic observations, the flowstonedid not form on top of the quartzose unit it currently overlays,rather, the flowstone likely formed a false floor, under whichsediment was later deposited. Thus there is an inverted strati-graphic relationship between the lower sediments and upperflowstone. The bulk of sediments in this area of the Drimolen Cavehave a reversed magnetic polarity, whereas this quartzose unit

underlying the DRM09 flowstone has a normal magnetic polarity.Thus the flowstone initially formed over older reversed polaritydeposits; a small cavity formed at the interface between theflowstone and the reversed polarity sediments, which infilled withthe younger normal polarity sediments (Herries et al., 2014).Petrography established that the flowstone comprised multiplephases of crystal growth and hiatuses, as well as subsequentdeformation of the calcite crystals. Such a hierarchy of depositionand diagenesis cannot be established by QEM-EDS. QEM-EDS canonly detect the distribution of CaCO3, represented by a uniformcolour in the mineralogical maps, but does not differentiate phasesand types of calcite crystal formation. QEM-EDS visually representsporosity, which assists with the identification of samples foruranium-lead analysis and of potential contamination by secondarysediments that could affect palaeomagnetic analysis.

Similar to DRM09, optical microscopy contributed the majorityof information relating to formation processes within tufa sampleTH33. Optical microscopy differentiated micrite from secondarycalcite spar and established multiple phases and rates of calcitegrowth. These can assist with environmental reconstruction; forexample, cycles of crystal growth and hiatuses may suggest alter-nating wetting and drying conditions over time. Such inferencesaccord with recent reinterpretations of this being an open air de-posit that formed during drier phases within the formation of theThabaseek tufa, rather than the infilling of a cave formedwithin thetufa (Hopley et al., 2013; Kuhn et al., 2016). Clear indicators ofdiagenetic processes, including crystal deformation andmineral re-precipitation, were established using petrography and providefurther insight into changing environmental conditions throughtime. While optical microscopy enables a hierarchy of depositionaland diagenetic processes to be reconstructed, QEM-EDS contributessignificant visual information regarding the meso-scale

Fig. 4. Stratigraphic summary for HGTFH24. Scan of thin section showing locations of photomicrographs (top left) and impregnated billet showing area sampled for QEM-EDS(bottom left). Photomicrographs of: (a) coarse polycrystalline quartz clast with micrite coating, within a micritic groundmass containing quartz grains and secondary calcitespar (PPL, top and XPL, bottom); (b) bone fragment at higher magnification (PPL, left and XPL, right). QEM-EDS mineral maps of: (c) sampled area, including modal percentages (forminerals >0.10% of total area); and, (d) magnification of coarse quartz grains (yellow) and apatite (pink, most likely bone) comparable to photomicrographs (a) and (b). Note primarybedding structures are visible in QEM-EDS scan (c), including layer of coarse quartz grains comparable to photomicrograph (a). (For interpretation of the references to colour in thisfigure legend, the reader is referred to the web version of this article.)

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distribution and patterning of quartz grains, specifically alternatingquartz sand deposition and calcite growth.

4.2. Group 2

The sample HGTFH24 exhibits significant heterogeneity and acomplex depositional and diagenetic history. The co-presence ofprimary and secondary characteristics in HGTFH24 make it an idealsample to assess the relative strengths of petrography and QEM-EDS in characterising and differentiating processes.

Petrographic analysis of HGTFH24 revealed the sample to be areworked combination of micrite, calcite spar and detrital quartz,which site stratigraphy suggests represents the accumulation ofwinnowed sediment derived from a breccia at the cave entrance(Herries et al., 2014). Fragments of isolated bone were potentiallyincorporated into the sample through in-wash and subsequentadmixture through homogenising processes. While there is occa-sional calcite spar, micrite is the dominant form of calcitethroughout the sample. Discrimination of calcite spar from micriteis not possible using QEM-EDS as they share the same chemicalcomposition (CaCO3). Despite this limitation, HCTFH24 exemplifiesthe added value of utilising QEM-EDS technology. The QEM-EDSmineral map of HCTFH24 offers clear visualisation of meso-scaleprocesses, permitting identification of possible primary deposi-tional events and subsequent secondary processes of cementationand homogenisation. Four large quartz grains aligned on a lateralplane provide evidence of a primary event which deposited rela-tively coarse detrital sediment into an otherwise low energyenvironment. QEM-EDS imaging reveals an irregular density ofcementation throughout the sample, with the possibility of soft

sediment deformation at the bottom left of the sample. These ob-servations went largely unnoticed by petrographic analysis. In thiscase, petrographic observations of the sample at the micro-scaleprevented ready characterisation of heterogeneity at the meso-scale. Such identifications of post-depositional alteration whenthe sediment was soft are critical for understanding the timing andnature of acquisition and lock-in of a detrital remanent magnet-isation in cave sediments and the effects of these processes on therecording of the magnetic field. Secondary alteration likely explainswhy this sample recorded inconsistent directions of magnetisation,whereas other blocks from the same layer recorded stable reversedpolarity directions (Herries et al., 2014).

4.3. Group 3

The highly homogeneous samples TH41 and EFT9427 revealsignificant reworking of the original microstratigraphy. Combineduse of petrography, CT and QEM-EDS was effective in characterisingsecondary processes and evaluating taphonomic disturbance inthese samples.

Both petrography and QEM-EDS identified sample EFT9427 as aferruginous quartz arenite with no discernible microstratigraphy.QEM-EDS analysis rapidly and visually established the homoge-neity of the sample, whilst illuminating some minor mineralcomponents such as orthoclase, which were not detected bypetrography. The mineral maps provide a visual representation ofporosity and variation in the distribution of goethite cementation.Due to the extremely homogenous nature of EFT9427, QEM-EDSand petrography provided similar types of information. Petrog-raphy revealed differing degrees of angularity and degradation of

Fig. 5. Stratigraphic summary for DRM09. Scan of thin section showing locations of photomicrographs (top left) and impregnated billet showing area sampled for QEM-EDS (bottomleft). Photomicrographs of: (a) boundary between upper calcite flowstone and reworked sandstone with embedded bone fragment (PPL, left and XPL, right); (bec) calcite crystalformation in flowstone (XPL); (d) deformation of calcite crystals, exhibiting sutured contacts and alteration lines (XPL); and, (e) several phases of crystal growth punctuated byhiatuses (PPL, left and XPL, right). QEM-EDS mineral maps of: (f) sampled area, including modal percentages (for minerals >0.05% of total area); and, (g) magnification of contactbetween flowstone and sandstone. The presence of apatite (pink) confirms the identification of bone in (a). (For interpretation of the references to colour in this figure legend, thereader is referred to the web version of this article.)

T. Edwards et al. / Journal of Archaeological Science 83 (2017) 1e118

quartz grains. The absence of calcite spar cement andmarine fossilssuggests a terrestrial environment of deposition, with uniformgrain size distribution possibly indicative of an aeolian, palaeo-dune environment. Computed tomography sheds light on exten-sive bioturbation within the sample, visible as infilled channelswith external goethite hypocoatings.

In TH41, both petrographic and QEM-EDS analyses establishedthe alteration of primary stratification through homogenisingprocesses. Microscopic investigation of TH41 identified completereworking of primary sedimentary structures and extensive pre-cipitation and cementation of secondary calcite within voids.Diagenetic markers such as crystal surface alteration and shapedeformation were commonly observed. Whilst mineral diagenesiswas not detected using QEM-EDS, the technique was particularlyuseful for visualising the spatial distribution of mineral inclusions,secondary cementation and microporosity. Overall, petrographicdata provided specific contextual information with which toreconstruct a hierarchy of site formation processes, whereas QEM-EDS provided rapid, quantitative and visual compositional andspatial data to add further value to the petrographic work. The dataconfirm this deposit as reworked aeolian sand that infilled fissurecaves formed within the tufa. TH41 contrasts with TH33, whichlikely represents tufa formation rather than deposition within acave.

4.4. Advantages and limitations of QEM-EDS and CT

The mineral map outputs of QEM-EDS illustrate the technique'svalue as an intermediate scale of analysis to visually assesscompositional and contextual information simultaneously.

Although meso-scale interpretation is possible from scans of entirethin sections, such interpretations are based on optical propertiesonly, including: stratification versus homogenisation; colour dif-ferences between minerals, particles and inclusions; and, variousstructural elements. By contrast, QEM-EDS generally providesclearer visualisations of these same properties together with in situmineral analyses that preserve the original context, structure andmineral associations. QEM-EDS images reveal precise locations ofminerals in relation to primary sedimentary structures and diage-netic redistribution of material and recrystallisation. In comparisonto petrography, QEM-EDS detects rare inclusions of minerals as wellas providing useful quantitative modal mineral percentages.Furthermore QEM-EDS performs well on heterogeneous deposits,providing a bridging level of analysis to micro-scalar techniqueswhich are sometimes unable to characterise meso-scale processes.Other advantages of QEM-EDS technology is fast data acquisitionspeed and operator independence leading to data output that isstatistically reliable and reproducible.

While providing powerful imagery, QEM-EDS has limitations.The technique is able to identify a mineral and visually display itsdistribution and associations, however it cannot unequivocallydetermine whether it is a primary or secondary constituent, forexample whether calcium carbonate is calcite, aragonite or micrite.Using QEM-EDS only, primary constituents such as marine fossilsand micritic mud cannot be differentiated from calcite that haseither precipitated as spar cement in void spaces or as part ofspeleothem growth. It is necessary to validate identification ofpolymorphic minerals, such as calcite and aragonite, using ancillarytechniques such as QXRD. Another limitation relevant for archae-ologists is the mineral apatite, which petrographic observation

Fig. 6. Stratigraphic summary for EFT9427. Scan of thin section showing location of photomicrographs (top left) and impregnated billet showing area sampled for QEM-EDS (bottomleft). Photomicrographs of: (a) clast-supported homogenous microstructure comprising quartz grains with iron-rich coatings in (PPL, top; XPL, middle and OIL, bottom). QEM-EDSmineral maps of: (b) sampled area, including modal percentages (for minerals >0.03% of total area); and, (c) magnification of goethite coatings on quartz grains.

Fig. 7. X-ray computed tomography slice through volumetric data for EFT9427. Thetwo-dimensional slice shows circular and curvilinear concentrations of goethite (yel-low) as hypo-coatings around infilled voids. See Animation S1 for three dimensionalvisualisation of sample. (For interpretation of the references to colour in this figurelegend, the reader is referred to the web version of this article.)

T. Edwards et al. / Journal of Archaeological Science 83 (2017) 1e11 9

confirmed to be bone on the basis of microstructure.Computer tomography provides three dimensional spatial data

and detects heterogeneity in seemingly homogeneous samples. Theresults of the CT analysis unequivocally confirm deep-seated con-cerns of thin section analysts that the sample size of a thin section(30 mm thickness with a viewing surface of typically no larger than7.5 cm length by 5 cmwidth) in relation to the object of study (e.g. astratigraphic column) is not a true representation of the relativeheterogeneity in a sample (for example, Bullock et al., 1985;

Adderley et al., 2001; Stoops, 2003). The sedimentary matrix isfundamentally a three dimensional system of which petrographycan only study a two dimensional representation. CT provides rapidvisual data that recreates this three dimensional matrix and canhighlight specific locations for thin section analysis. As Huismanet al. (2014:594) recommended, CT can be used effectively as apreliminary non-destructive technique to ‘guide micro-sampling’for further analysis. The combination of compositional andcontextual data presents CT as an attractive meso-scalar techniqueto bridge macro-scale and micro-scale investigations.

5. Conclusions and recommendations

There is no single approach to best analyse and interpret stra-tigraphy, regardless of whether the research questions arearchaeological, pedological or geological in nature and scope. Thisgeoarchaeological multi-method investigation of samples fromearly hominid sites in South Africa compared and cross-correlatedthe results of traditional thin section petrography with two auto-mated, quantitative scientific techniques, QEM-EDS and CT. Thisstudy has shown that distinct scientific methods vary in their ca-pacity to visualise the primary and secondary processes involved insite formation.

The application of QEM-EDS and CT can provide invaluable datafor meso-scale analysis, helping to visualise primary processespreserved within microstratigraphy and secondary processes thatcontribute to the relative heterogeneity or homogeneity of a sedi-mentary matrix (as in samples HGHTF and EFT9427, respectively).This information acts as a fundamental framework upon which tohang the highly detailed results of the petrographic analysis whileproviding a readily interpretable level of analysis for the non-specialist to visualise the processes that formed, preserved and

Table 1Advantages and limitations of geoarchaeological techniques utilised in this study.

Technique Uses and advantages Limitations

Thin Section Description(transmitted/cross-polarised/reflected light)

�Identification of major minerals�Observation of microstructure, porosity andmicrostratigraphy�Preserves depositional and post-depositional contextand mineral associations�Ability to differentiate primary and secondaryprocesses and reconstruct hierarchies of deposition, in-situ mineral formation, crystal growth phases anddiagenetic alterations

�Specialist knowledge and training necessary. Technicaldata is often not accessible to non-specialists.�Limited acquisition of quantitative, statistically reliabledata�Two dimensional observation of a three dimensionalsystem�Limited observation of meso-scale processes�Opaque minerals and clay minerals not observable.Some minerals require staining techniques for positiveidentification

QEM-EDS �Mineral identification includes some amorphous andopaque minerals�Mineral abundances (modal percentages by area)�Visual output shows mineral spatial distribution andassociations�Observation of microstructure, porosity andmicrostratigraphy�Visualises meso-scale processes and detectsheterogeneity�Fast, automated, operator-independent dataacquisition�Quantitative, statistically reliable data

�Mineral identification not reliable for minerals withsimilar or identical chemical composition (e.g. calciteand aragonite)�Clay minerals not reliably identified�Resins and organics not reliably distinguished from‘background’ (porosity)�Limited differentiation of primary and secondaryprocesses (e.g. primary and secondarymineral phases ofcalcite crystallisation)�Two dimensional observation of a three dimensionalsystem

Computed Tomography �Three dimensional, quantitative spatial data�Visualises meso-scale processes and detectsheterogeneity�Fast, automated and operator-independent dataacquisition

�High analytical costs�Limited accessibility of technique�Technical knowledge of data processing softwarerequired

X-ray Powder Diffraction �Mineral identification and abundances�Clay identification�Quantitative, statistically reliable data

�Amorphous mineral phases not identified�Spatial distribution and associations not preserved�Textural characteristics not measured�Produces combined averages of heterogeneous andmicrostratigraphic deposits

T. Edwards et al. / Journal of Archaeological Science 83 (2017) 1e1110

modified the stratigraphy over time. Neither QEM-EDS nor CT canreplace the petrographic method, as such it is recommended thatthey are used to compliment and cross-correlate the results ob-tained by petrography. By using a complimentary suite of tech-niques, primary environments of deposition and secondarydiagenetic processes can be more confidently elucidated. Theseresults are significant in their own right, yet they also assist withdetermining the reliability and comparability of different datingtechniques, such as uranium-lead dating and paleomagnetism.

This study contributes towards an assessment of the future ofthin section analysis in view of the availability of more advancedtechniques in the twenty-first century (see Stoops, 2014). Thetechnique has always been plagued by its intrinsic subjectivity andits requisite dependence on technical knowledge and expertise(Griffiths, 1967:204; Catt and Weir, 1976:86; Kooistra, 1990), oftento the detriment of communicating results to other researchers.Thin section analysts, particularly those working within larger,interdisciplinary earth science and archaeological research frame-works, are constantly facing the challenge of disseminating tech-nical data on a level that most researchers can understandregardless of their specialisation. Weighing the value of petrog-raphy against automated petrographic analytical techniques mir-rors an earlier concern ‘not to lose sight of [thin section analysis] infavor of the latest instrumentation’ (Gunter, 2004:43). Despitequalifications, this study has found that thin section analysis re-mains the ‘gold standard’ in characterising site formation processesand diagenesis.

Acknowledgments

TD devised and directed the multi-scalar geoarchaeological in-vestigations, in conjunction with TE, EG and AIRH. TE and EG un-dertook double-blind thin section petrography; FB, EG and LP the

QEM-EDS (using QEMSCAN®); UT the QXRD; and TS and MT theCT analysis and AB the CT image processing. The authors thank:Shane Paxton and John Vickers (RSES, ANU) for preparing QEM-EDSsamples, Adelaide Petrographics Laboratory for the production ofpetrographic thin sections. The work was funded by an ARC FutureFellowship (FT120100399) to AIRH. Sampling at Elandsfontein wassupported by an NSF grant (1219494) to Dr David Braun and DrNaomi Levin and at Haasgat by a Leakey Foundation Grant to DrJustin Adams and AIRH.We also thank Dr Colin Menter for access toDrimolen and the South African Heritage Resource Agency andHeritage Western Cape for providing permits for sampling andexport. Additional thanks to Alex F Blackwood for figure editing.Funding for UTwas obtained by Dr Penelope L King (DP150104604).

Appendix A. Supplementary data

Supplementary data related to this article can be found at http://dx.doi.org/10.1016/j.jas.2017.05.007.

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