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 geoarchaeological

investigations of microstratigraphy and diagenesis at hominin bearing
sites 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, Australia
b
School of Archaeology and Anthropology, Australian National University, Canberra, ACT 2601, Australia
c
Centre for Anthropological Research, University of Johannesburg, Gauteng, South Africa
d
Centre for Advanced Microscopy, Australian National University, Canberra, ACT, 2601, Australia
e
Research School of Earth Sciences, Australian National University, Canberra, ACT, 2601, Australia
f
Research School of Physics and Engineering, Australian National University, Canberra, ACT 2601, Australia

a r t i c l e i n f o a b s t r a c t

Article history: Multi-scalar geoarchaeological investigations were conducted on several samples of sediment (dolomite
Received 7 August 2016 cave sediments, ferricrete ridge, speleothem, tufa and tufa cave sediments) from four early hominin
Received in revised form fossil-bearing sites (Taung Type Site, Haasgat, Drimolen Main Quarry, Elandsfontein) in different South
2 May 2017
African karst environments. The study was designed to test the value of geoarchaeological techniques for
Accepted 10 May 2017
Available online 24 May 2017
identifying and characterising environments of deposition and diagenetic processes involved in site
formation within different mediums and different karst environments. The traditional petrographic
method is weighed against two relatively new methodological contributions to site formation and
Keywords:
Karst
diagenesis: Computed Tomography (CT) and automated Quantitative Evaluation of Minerals using Energy
Micromorphology Dispersive Spectroscopy (QEM-EDS), employing QEMSCAN® technology. An integrated micro-sampling
Hominin approach is outlined for successful cross-correlation between techniques. The study demonstrates that
Palaeokarst different analyses vary in their ability to visualise different types of process e primary and secondary.
QEM-EDS Thin section petrography remains the ‘gold standard’ for analyses conducted at the micro-scale, while
CT QEM-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 between macro-scale (landscape) studies and micro-scale (site

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; Bateman
et al., 2010; Fouache, 2013; McNamee et al., 2013). This study
presents 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 to
increase the interpretative potential for studying human-
environmental relations. A multi-scalar approach provides links
* Corresponding author.
E-mail address: Tim.Denham@anu.edu.au (T. Denham).
stratigraphy and deposit) characterisation (Butzer, 2008). This
process, referred to by Butzer (2008:403) as ‘scale-switching, from
the large to the small and back’ is at the core of geoarchaeology.
Multi-technique geoarchaeological investigations greatly
enhance the interpretative potential for identifying environmental
processes which act across varying scales between the archaeo-
logical deposit and the landscape. Moreover, using a mixed-method
framework of analysis, integration of different techniques can
overcome limitations associated with each respective technique
and provide comparative and complimentary datasets for cross
correlation and multi-proxy validation (Canti, 1995; Denham,
2008; Shillito et al., 2011; Milek and Roberts, 2013; Canti and
Huisman, 2015:104e105). The multi-scalar mixed-method geo-
archaeological investigation presented here combined thin section

http://dx.doi.org/10.1016/j.jas.2017.05.007
0305-4403/© 2017 Elsevier Ltd. All rights reserved.
2 T. Edwards et al. / Journal of Archaeological Science 83 (2017) 1e11
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 study
investigating environments of deposition and diagenetic processes
at four hominin fossil-bearing karstic sites in South Africa: Taung
Type Site, Haasgat, Drimolen Main Quarry and Elandsfontein
(Fig. 1). The presentation is selective and focuses on the respective
ability 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) across
multiple analytical scales.
Haasgat and Drimolen are early Pleistocene (between 2.3 and
1.4 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 and
are now palaeokarst remnants of heavily eroded ancient caves.
Drimolen contains Paranthropus robustus and early Homo, whereas
Haasgat has only recently yielded a hominin tooth (Moggi et al.,
2010; Leece et al., 2016a,b). The sample from the Drimolen Main
Quarry (DRM09) is a speleothem that appears to cap the strati-
graphic sequence within the palaeocave. The speleothem formed
within a more recent cave that formed at the interface between the
dolomite and palaeocave sediments. The sample was taken to
establish stratigraphic relationships for dating purposes. The
Haasgat sample (HGTFH24) was used in a palaeomagnetic study of
the site and yielded inconclusive results (Herries et al., 2014) that
are thought to represent alteration of the sample by later karstic
processes; the current investigations are designed to clarify the
Fig. 1. Site location map and photographs of each site.
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 km west of Drimolen and Haasgat (Kuhn et al., 2016). The
limeworks is famous for the discovery in 1924 of the first early
hominin from Africa and the type specimen of Australopithecus
africanus, the Taung Child (Dart, 1925). The skull originates from the
Type Site that consists of two remnant pinnacles of tufa (the
western Dart Pinnacle and eastern Hrdli
cka Pinnacle), the rest has
been mined away. Associated with these pinnacles are two
different clastic sedimentary units that contain fossils and have
previously been interpreted as cave fills (McKee, 1993). The older of
these 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 have
formed simultaneously as an open air deposit (Hopley et al., 2013;
Herries et al., 2013). Sample TH33 was recovered from this deposit
at 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 that
formed within the tufa and pink micrite, and contains extensive
primate fossils. Sampling was designed to further clarify the
depositional 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 large
calcrete ridge onto which an extensive dune field has been
deposited (Braun et al., 2013). Within the dunes are abundant
fossils 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 ferricrete
ridges, which may be the core of more ancient eroded dunes (Braun
 T. Edwards et al. / Journal of Archaeological Science 83 (2017) 1e11
et al., 2013). Sample EFT9427 is a ferruginous quartz arenite derived
from one of these ridges.
2. Methods
2.1. Field sampling
In the field, selective sampling targeted specific stratigraphic
units and boundaries that presented opportunities to investigate
depositional history, diagenesis, and the reliability of samples for
dating. Semi-consolidated rock samples were removed with a
chisel, wrapped securely with packaging material and clearly
labelled with orientation and sample number (see Goldberg and
Macphail, 2003 for field sampling protocols). The rock samples
were transported to The Australian Archaeomagnetism Laboratory
at La Trobe University for palaeomagnetic analysis. Subsamples of
the blocks were then shipped to the Geoarchaeology Research
Group 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 for
complementary 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 analysis
linking micro-scalar investigations (petrography) with meso-scale
analyses (CT and QEM-EDS) and macro-level (field-based)
observations.
2.3. Thin section analysis
Petrography is a long-established technique for obtaining
mineralogical 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 optical
properties in both plane and cross polarised light (Adams et al.,
1984; Gribble and Hall, 1999; Nesse, 2004; MacKenzie and
Guilford, 2013). A number of qualitative and quantitative parame-
ters are recorded including microstructure and porosity, size and
angularity of grains, and extent of diagenesis (Harwood, 1988; Bell
and Lindsay, 1999). Whilst most observations are recorded as
qualitative data, abundance and size of mineral grains and porosity
are 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 and
mounted to glass slides at Adelaide Petrographic Laboratories. Thin
sections were cut to a larger size (75  50 mm) than standard
petrographic 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 and
QEM-EDS, thin section analysis primarily produces qualitative,
descriptive data. In order to increase the reliability, thin sections
were examined in isolation by two different analysts and results
compared.
Thin sections were first scanned with a high-resolution Epson
perfection V700 photo flatbed colour image scanner at a resolution
of 1200 dpi. The scans permitted meso-scale observation of the
entirety of the thin section, including detection of bedding and
sedimentary structures, boundaries, colour variation and porosity
3
(Arpin et al., 2002). Thin sections were observed at magnifications
of 20x-400x under plane polarised light (PPL), cross polarised light
(XPL) and oblique incident light (OIL) using an Olympus CX31
polarising microscope. Photomicrographs were imaged with an
Olympus CS30 3 MP colour camera and processed using Olympus
Stream V1.9.1 imaging software.
2.4. QEM-EDS (QEMSCAN®)
QEM-EDS (Quantitative Evaluation of Minerals using Energy
Dispersive Spectroscopy) was originally developed in the late 1970s
by 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 an
automated scanning electron microscope which has been equipped
with multiple energy-dispersive X-ray spectrometers to optimise X-
ray count rate. QEM-EDS data outputs typically include mineral maps
and modal mineralogy percentages. Each pixel is assigned a mineral
species 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-samples
approximately 1e2 mm thick were prepared (Fig. S1). The sedi-
ment slices were ground to a constant thickness, mounted onto
glass slides, finished using a <1 mm diamond-based polishing me-
dium, and submersed in an ultrasonic bath with deionised water
for 30 s to remove any remaining dirt or debris. After cleaning, the
samples were coated with a 20 nm layer of carbon using a Dynavac
CS300 coating unit in order to prevent build-up of static charge
during 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 the
Australian National University. Data were collected in field image
scan mode, 15 kV accelerating voltage, 10 nA probe current and a
step size of 15 mm (Table S1). FEI iMeasure software was used for
data acquisition and FEI iDiscover software was used for raw data
processing, noise reduction, frame stitching, refinement of mineral
identification and modal analysis.
Previous studies have shown that QEM-EDS mineral identifica-
tion is comparable to other well-established microanalytical
methods (Goodall et al., 2005). However, QEM-EDS does not
perform well in the discrimination of clay minerals or of minerals
with 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 of
the available mineral list (SIP) can influence the assigned mineral
identification (Haberlah et al., 2011b:5). To alleviate such problems,
Quantitative Powder X-ray Diffraction (QXRD) was used to confirm
or adjust the mineral identification criteria by rearranging the
mineral 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 and
rankings (Table S2). QXRD was conducted on bulk sub-samples at
the XRD laboratory in the Research School of Earth Sciences,
Australian National University. For each sample, a sediment slice
was cut directly from the ‘mirror-image’ face of the rock sample
using a diamond saw (Fig. S1). Two grams of sediment were milled
for 8 min in ethanol with a McCrone Micronizing Mill, dried at 40  C
4 T. Edwards et al. / Journal of Archaeological Science 83 (2017) 1e11
and powdered using an agate mortar and pestle. Amorphous con-
tent was quantified by the addition of 20% (wt.) corundum, a
crystalline aluminium oxide (1 mm Al2O3, Baikowski). Powder XRD
was performed on a SIEMENS D501 Bragg-Brentano diffractometer
equipped 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 step
width of 0.02 , and a scan speed of 1 per minute. The results were
interpreted using the Bruker AXS software package Diffracplus Eva
10 (2003) with PDF2 database for phase identification, and then
quantified using Siroquant V3 software.
2.6. CT
Originally designed for medical purposes in the 1970s
(Hounsfield, 1972, 1973) X-ray computed tomography has been
applied 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 relations
of heterogeneous inclusions within archaeological deposits
(Huisman et al., 2014). Early application of CT to soils and sediments
typically produced low resolution output due to limitations of
computer processing, (e.g., Perret et al., 1997). Advances in design
and computing have allowed for improvements in resolution, with
CT systems today potentially providing sub-micron resolution
(Varslot et al., 2011).
CT equipment used here was designed and built within the
Research 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 mm
aluminium filter to yield images at 46 mm (voxel size) resolution.
Each sample was mounted on a stage that moves in a helical motion
to recover uniformly precise geometric radiographic information.
Images were rendered using the open-source program, Drishti v
2.6.2 (Limaye, 2012).
Although multiple samples have been subject to CT analysis as
part of the broader study, only the results for one sample are pre-
sented here. Samples EFT9427 from Elandsfontein presents as
extremely well-homogenised in both thin section and QEM-EDS
analyses, whereas CT enables the processes not identified by
other methods to be readily visualised and interpreted.
3. Results
The major primary and secondary processes of formation
identified in each of the five samples are summarised below. Re-
sults are presented from youngest to oldest, which accords with
changes 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 datasets
alongside 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 a
minor sub-set of the features observed in the samples, they were
selected based on the extent to which they permit visualisation of
formation processes and cross-correlation between petrographic
and QEM-EDS data outputs. For QEM-EDS mineral maps, note that
percentage areas of minerals are given relative to 100%, after the
percentage assigned ‘background’ is removed.
3.1. Taung, sample TH33 (tufa)
Sample TH33 is primarily composed of calcite formed as a tufa
with a predominantly spongy microstructure. Occasional detrital
quartz grains had clay coatings (Fig. 2b) and secondary calcite spar
was precipitated in void spaces (Fig. 2e). The top of the sample
contained a ‘sand pocket’, an accumulation of quartz grains encased
by multiple phases of concentric calcite growth (Fig. 2aec).
Petrography identified several units of tufa growth from the
basal 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 the
hiatus (Fig. 2c). The second hiatus exhibits columnar calcite
precipitated perpendicular to the substrate (Fig. 2d). Calcite pre-
cipitation in void space indicates recrystallisation occurred after the
formation of the hiatus (Fig. 2e).
QEM-EDS analysis of TH33 permitted visualisation of primary
processes of deposition showing alternating microstratigraphic
layers of the quartz sand fraction within the predominant calcite
growth (Fig. 2feg). Visualisation of these textural attributes is
valuable for gaining insight into the fluctuating energy conditions
present 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 is
dominated by secondary calcite, fine reddish-orange clay and silt-
sized material form coatings around detrital quartz grains and
micro-aggregates within interstitial spaces (Fig. 3aeb). Secondary
calcite precipitation within voids is predominantly drusy mosaic
spar (Fig. 3aeb).
The QEM-EDS analysis of TH41 revealed a complex relationship
between quartz grains and the calcite cement (Fig. 3ced). The
presence of montmorillonite, illite and kaolinite confirms the
coatings on quartz grains to be clay. There are several calcite veins
and ‘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 both
primary depositional components (micritic mud and inclusions of
detrital quartz with rare bone) and secondary reworking (calcite
spar precipitation and dissolution microstructures) contribute to
the heterogeneous character of the sample (Fig. 4). Quartz grains
range from several microns up to 3 mm in diameter (Fig. 4a and d).
Several clays (confirmed by QXRD) form coatings to thick crusts
around coarse detrital material (Fig. 4aeb). The high, variable
porosity throughout the sample is likely to result from dissolution
processes (Fig. 4c) which were probably responsible for alteration
of the original sedimentary structures and thereby affected the
palaeomagnetic signal in the sample.
The QEM-EDS mineral map displays possible primary bedding
structures, such as the four large quartz grains distributed on one
lateral plane (Fig. 4ced). QEM-EDS identified the majority of the
sample to be calcite (confirmed by QXRD), with additional quartz
and amorphous material represented.
3.4. Drimolen, sample DRM09 (speleothem and associated
sediment)
DRM09 is a stratified sample comprising a calcite flowstone
above reworked, quartz rich sediment, separated by a sharp,
distinct boundary (Fig. 5a). The nature of the contact between the
two units, specifically the calcite crystal growth patterns, indicates
the flowstone did not form onto the underlying sediment, but that
the sediment was deposited beneath it at a later time. The pseudo-
basal unit is comprised of detrital, reworked quartz grains with rare
 T. Edwards et al. / Journal of Archaeological Science 83 (2017) 1e11 5

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 (bottom
left). Photomicrographs of: (a) ‘sand pocket’ comprising quartz grains within secondary sparry calcite matrix encased in crystal calcite (XPL); (b) magnification of quartz grains
showing deformations and coatings; (c) magnification of encasing calcite growth characterised by multiple concentric growth hiatuses, with diagenised calcite crystals extending
through 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 secondary
calcite 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).

bone fragments (Fig. 5a). A secondary drusy mosaic calcite spar
cements the basal section. The top unit is entirely composed of
flowstone exhibiting a variety of textures (Fig. 5bed) and diage-
netic alteration (Fig. 5d). Microscopic investigation revealed at least
six phases of speleothem growth within the upper portion of the
sample, determined through changes in calcite fabric. Precipitation
of the flowstone is punctuated with hiatuses throughout, indicating
multiple growth periods under a variety of cave conditions (Fig. 5e).
Calcite pseudomorphs indicate replacement of aragonite by the
more stable calcium carbonate polymorph calcite (the absence of
aragonite was confirmed by QXRD). Porosity was low throughout
the sample and most voids were infilled with secondary drusy
mosaic spar indicating re-precipitation within the basal unit and
flowstone. Deformation of the calcite crystals is evident in the form
of 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 unit
entirely composed of calcite (Fig. 5feg). The QEM-EDS mineral map
shows microporosity of the sample (Fig. 5g), the boundary between
sandstone and flowstone (Fig. 5feg) and presence of apatite (bone)
in the basal unit. Quartz is identified in the basal unit, however
QEM-EDS imaging did not reveal weathering of quartz grains or
clay coatings. Similarly, calcite/aragonite is identified by QEM-EDS
but the method cannot differentiate these polymorphic minerals
nor differentiate phases of calcite crystal growth formation and
hiatuses within the flowstone (Fig. 5f).
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 by QXRD). Goethite forms thick crusts around the grains
and in some cases has degraded and extended across the grain
surfaces (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 revealed
the presence of siderite, which was not identified through petro-
graphic investigation. The density of goethite cementation
throughout the sample varies, but in two dimensions did not
indicate any regular structure (Fig. 6bec).
Building upon identified concentrations visible in thin section
petrography and QEM-EDS, the three dimensional CT scan clearly
shows 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 uniform
thickness, suggesting meso-faunal bioturbation rather than root
action. Thus, CT imagery sheds light on three dimensional ho-
mogenisation processes that are not fully characterised using two
dimensional techniques.
Supplementary video related to this article can be found at
http://dx.doi.org/10.1016/j.jas.2017.05.007.

4. Discussion
3.5. Elandsfontein, sample EFT9427 (‘ferricrete ridge’)
The results of the study demonstrate that different techniques
Petrographic investigations characterised EFT9427 as a vary in their ability to visualise the primary and secondary
6 T. Edwards et al. / Journal of Archaeological Science 83 (2017) 1e11

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 (bottom
left, 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-EDS
mineral 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.)

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 and
post-depositional histories, environments of deposition and taph-
onomic integrity of the five samples investigated. The samples have
been arbitrarily divided into three groups to represent the range of
site formation processes. The groupings convey the extent to which
the samples show primary processes and/or inherited stratification
compared to those which show extensive homogenisation of
original stratigraphy by secondary processes.
4.1. Group 1
In the highly stratified speleothem (DRM09) and tufa (TH33)
samples, primary deposition is largely preserved and thereby
samples have great potential for reconstructing environments of
deposition.
Petrography was of most value for sample DRM09, enabling
establishment of a hierarchy of primary deposition and subsequent
in situ mineral formation and diagenesis. Petrographic analysis
demonstrated that the quartzose basal unit comprised detrital
quartz grains and preserved bone fragments reworked within a
micritic matrix. Petrographic observation of the boundary between
the basal quartzose unit and the overlying calcite flowstone
revealed the complexity of the stratigraphic association between
these two units. Based on petrographic observations, the flowstone
did not form on top of the quartzose unit it currently overlays,
rather, the flowstone likely formed a false floor, under which
sediment was later deposited. Thus there is an inverted strati-
graphic relationship between the lower sediments and upper
flowstone. The bulk of sediments in this area of the Drimolen Cave
have 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 polarity
deposits; a small cavity formed at the interface between the
flowstone and the reversed polarity sediments, which infilled with
the younger normal polarity sediments (Herries et al., 2014).
Petrography established that the flowstone comprised multiple
phases of crystal growth and hiatuses, as well as subsequent
deformation of the calcite crystals. Such a hierarchy of deposition
and diagenesis cannot be established by QEM-EDS. QEM-EDS can
only detect the distribution of CaCO3, represented by a uniform
colour in the mineralogical maps, but does not differentiate phases
and types of calcite crystal formation. QEM-EDS visually represents
porosity, which assists with the identification of samples for
uranium-lead analysis and of potential contamination by secondary
sediments that could affect palaeomagnetic analysis.
Similar to DRM09, optical microscopy contributed the majority
of information relating to formation processes within tufa sample
TH33. Optical microscopy differentiated micrite from secondary
calcite spar and established multiple phases and rates of calcite
growth. These can assist with environmental reconstruction; for
example, cycles of crystal growth and hiatuses may suggest alter-
nating wetting and drying conditions over time. Such inferences
accord with recent reinterpretations of this being an open air de-
posit that formed during drier phases within the formation of the
Thabaseek tufa, rather than the infilling of a cave formed within the
tufa (Hopley et al., 2013; Kuhn et al., 2016). Clear indicators of
diagenetic processes, including crystal deformation and mineral re-
precipitation, were established using petrography and provide
further insight into changing environmental conditions through
time. While optical microscopy enables a hierarchy of depositional
and diagenetic processes to be reconstructed, QEM-EDS contributes
significant visual information regarding the meso-scale
 T. Edwards et al. / Journal of Archaeological Science 83 (2017) 1e11 7

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 calcite
spar (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 (for
minerals >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 primary
bedding 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 this
figure legend, the reader is referred to the web version of this article.)

distribution and patterning of quartz grains, specifically alternating
quartz sand deposition and calcite growth.
4.2. Group 2
The sample HGTFH24 exhibits significant heterogeneity and a
complex depositional and diagenetic history. The co-presence of
primary and secondary characteristics in HGTFH24 make it an ideal
sample to assess the relative strengths of petrography and QEM-
EDS in characterising and differentiating processes.
Petrographic analysis of HGTFH24 revealed the sample to be a
reworked combination of micrite, calcite spar and detrital quartz,
which site stratigraphy suggests represents the accumulation of
winnowed sediment derived from a breccia at the cave entrance
(Herries et al., 2014). Fragments of isolated bone were potentially
incorporated into the sample through in-wash and subsequent
admixture through homogenising processes. While there is occa-
sional calcite spar, micrite is the dominant form of calcite
throughout the sample. Discrimination of calcite spar from micrite
is not possible using QEM-EDS as they share the same chemical
composition (CaCO3). Despite this limitation, HCTFH24 exemplifies
the added value of utilising QEM-EDS technology. The QEM-EDS
mineral map of HCTFH24 offers clear visualisation of meso-scale
processes, permitting identification of possible primary deposi-
tional events and subsequent secondary processes of cementation
and homogenisation. Four large quartz grains aligned on a lateral
plane provide evidence of a primary event which deposited rela-
tively coarse detrital sediment into an otherwise low energy
environment. QEM-EDS imaging reveals an irregular density of
cementation 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 this
case, petrographic observations of the sample at the micro-scale
prevented ready characterisation of heterogeneity at the meso-
scale. Such identifications of post-depositional alteration when
the sediment was soft are critical for understanding the timing and
nature of acquisition and lock-in of a detrital remanent magnet-
isation in cave sediments and the effects of these processes on the
recording of the magnetic field. Secondary alteration likely explains
why this sample recorded inconsistent directions of magnetisation,
whereas other blocks from the same layer recorded stable reversed
polarity directions (Herries et al., 2014).
4.3. Group 3
The highly homogeneous samples TH41 and EFT9427 reveal
significant reworking of the original microstratigraphy. Combined
use of petrography, CT and QEM-EDS was effective in characterising
secondary processes and evaluating taphonomic disturbance in
these samples.
Both petrography and QEM-EDS identified sample EFT9427 as a
ferruginous quartz arenite with no discernible microstratigraphy.
QEM-EDS analysis rapidly and visually established the homoge-
neity of the sample, whilst illuminating some minor mineral
components such as orthoclase, which were not detected by
petrography. The mineral maps provide a visual representation of
porosity and variation in the distribution of goethite cementation.
Due to the extremely homogenous nature of EFT9427, QEM-EDS
and petrography provided similar types of information. Petrog-
raphy revealed differing degrees of angularity and degradation of
8 T. Edwards et al. / Journal of Archaeological Science 83 (2017) 1e11

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 (bottom
left). Photomicrographs of: (a) boundary between upper calcite flowstone and reworked sandstone with embedded bone fragment (PPL, left and XPL, right); (bec) calcite crystal
formation in flowstone (XPL); (d) deformation of calcite crystals, exhibiting sutured contacts and alteration lines (XPL); and, (e) several phases of crystal growth punctuated by
hiatuses (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 contact
between 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, the
reader is referred to the web version of this article.)

quartz grains. The absence of calcite spar cement and marine fossils
suggests a terrestrial environment of deposition, with uniform
grain size distribution possibly indicative of an aeolian, palaeo-
dune environment. Computed tomography sheds light on exten-
sive bioturbation within the sample, visible as infilled channels
with external goethite hypocoatings.
In TH41, both petrographic and QEM-EDS analyses established
the alteration of primary stratification through homogenising
processes. Microscopic investigation of TH41 identified complete
reworking of primary sedimentary structures and extensive pre-
cipitation and cementation of secondary calcite within voids.
Diagenetic markers such as crystal surface alteration and shape
deformation were commonly observed. Whilst mineral diagenesis
was not detected using QEM-EDS, the technique was particularly
useful for visualising the spatial distribution of mineral inclusions,
secondary cementation and microporosity. Overall, petrographic
data provided specific contextual information with which to
reconstruct a hierarchy of site formation processes, whereas QEM-
EDS provided rapid, quantitative and visual compositional and
spatial data to add further value to the petrographic work. The data
confirm this deposit as reworked aeolian sand that infilled fissure
caves formed within the tufa. TH41 contrasts with TH33, which
likely represents tufa formation rather than deposition within a
cave.
4.4. Advantages and limitations of QEM-EDS and CT
The mineral map outputs of QEM-EDS illustrate the technique's
value as an intermediate scale of analysis to visually assess
compositional and contextual information simultaneously.
Although meso-scale interpretation is possible from scans of entire
thin sections, such interpretations are based on optical properties
only, including: stratification versus homogenisation; colour dif-
ferences between minerals, particles and inclusions; and, various
structural elements. By contrast, QEM-EDS generally provides
clearer visualisations of these same properties together with in situ
mineral analyses that preserve the original context, structure and
mineral associations. QEM-EDS images reveal precise locations of
minerals in relation to primary sedimentary structures and diage-
netic redistribution of material and recrystallisation. In comparison
to petrography, QEM-EDS detects rare inclusions of minerals as well
as providing useful quantitative modal mineral percentages.
Furthermore QEM-EDS performs well on heterogeneous deposits,
providing a bridging level of analysis to micro-scalar techniques
which are sometimes unable to characterise meso-scale processes.
Other advantages of QEM-EDS technology is fast data acquisition
speed and operator independence leading to data output that is
statistically reliable and reproducible.
While providing powerful imagery, QEM-EDS has limitations.
The technique is able to identify a mineral and visually display its
distribution and associations, however it cannot unequivocally
determine whether it is a primary or secondary constituent, for
example whether calcium carbonate is calcite, aragonite or micrite.
Using QEM-EDS only, primary constituents such as marine fossils
and micritic mud cannot be differentiated from calcite that has
either precipitated as spar cement in void spaces or as part of
speleothem growth. It is necessary to validate identification of
polymorphic minerals, such as calcite and aragonite, using ancillary
techniques such as QXRD. Another limitation relevant for archae-
ologists is the mineral apatite, which petrographic observation
 T. Edwards et al. / Journal of Archaeological Science 83 (2017) 1e11 9

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 (bottom
left). Photomicrographs of: (a) clast-supported homogenous microstructure comprising quartz grains with iron-rich coatings in (PPL, top; XPL, middle and OIL, bottom). QEM-EDS
mineral maps of: (b) sampled area, including modal percentages (for minerals >0.03% of total area); and, (c) magnification of goethite coatings on quartz grains.

Adderley et al., 2001; Stoops, 2003). The sedimentary matrix is

fundamentally a three dimensional system of which petrography
can only study a two dimensional representation. CT provides rapid
visual data that recreates this three dimensional matrix and can
highlight specific locations for thin section analysis. As Huisman
et al. (2014:594) recommended, CT can be used effectively as a
preliminary non-destructive technique to ‘guide micro-sampling’
for further analysis. The combination of compositional and
contextual data presents CT as an attractive meso-scalar technique
to bridge macro-scale and micro-scale investigations.

5. Conclusions and recommendations

There is no single approach to best analyse and interpret stra-

Fig. 7. X-ray computed tomography slice through volumetric data for EFT9427. The
two-dimensional slice shows circular and curvilinear concentrations of goethite (yel-
low) as hypo-coatings around infilled voids. See Animation S1 for three dimensional
visualisation of sample. (For interpretation of the references to colour in this figure
legend, the reader is referred to the web version of this article.)
confirmed to be bone on the basis of microstructure.
Computer tomography provides three dimensional spatial data
and detects heterogeneity in seemingly homogeneous samples. The
results 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 than
7.5 cm length by 5 cm width) in relation to the object of study (e.g. a
stratigraphic column) is not a true representation of the relative
heterogeneity in a sample (for example, Bullock et al., 1985;
tigraphy, regardless of whether the research questions are
archaeological, pedological or geological in nature and scope. This
geoarchaeological multi-method investigation of samples from
early hominid sites in South Africa compared and cross-correlated
the results of traditional thin section petrography with two auto-
mated, quantitative scientific techniques, QEM-EDS and CT. This
study has shown that distinct scientific methods vary in their ca-
pacity to visualise the primary and secondary processes involved in
site formation.
The application of QEM-EDS and CT can provide invaluable data
for meso-scale analysis, helping to visualise primary processes
preserved within microstratigraphy and secondary processes that
contribute 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 to
hang the highly detailed results of the petrographic analysis while
providing a readily interpretable level of analysis for the non-
specialist to visualise the processes that formed, preserved and
10 T. Edwards et al. / Journal of Archaeological Science 83 (2017) 1e11

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

Technique Uses and advantages Limitations

Thin Section Description Identification of major minerals
(transmitted/cross-polarised/reflected light) Observation of microstructure, porosity and
microstratigraphy
Preserves depositional and post-depositional context
and mineral associations
Ability to differentiate primary and secondary
processes and reconstruct hierarchies of deposition, in-
situ mineral formation, crystal growth phases and
diagenetic alterations
QEM-EDS Mineral identification includes some amorphous and
opaque minerals
Mineral abundances (modal percentages by area)
Visual output shows mineral spatial distribution and
associations
Observation of microstructure, porosity and
microstratigraphy
Visualises meso-scale processes and detects
heterogeneity
Fast, automated, operator-independent data
acquisition
Quantitative, statistically reliable data
Computed Tomography Three dimensional, quantitative spatial data
Visualises meso-scale processes and detects
heterogeneity
Fast, automated and operator-independent data
acquisition
X-ray Powder Diffraction Mineral identification and abundances
Clay identification
Quantitative, statistically reliable data
Specialist knowledge and training necessary. Technical
data is often not accessible to non-specialists.
Limited acquisition of quantitative, statistically reliable
data
Two dimensional observation of a three dimensional
system
Limited observation of meso-scale processes
Opaque minerals and clay minerals not observable.
Some minerals require staining techniques for positive
identification
Mineral identification not reliable for minerals with
similar or identical chemical composition (e.g. calcite
and aragonite)
Clay minerals not reliably identified
Resins and organics not reliably distinguished from
‘background’ (porosity)
Limited differentiation of primary and secondary
processes (e.g. primary and secondary mineral phases of
calcite crystallisation)
Two dimensional observation of a three dimensional
system
High analytical costs
Limited accessibility of technique
Technical knowledge of data processing software
required
Amorphous mineral phases not identified
Spatial distribution and associations not preserved
Textural characteristics not measured
Produces combined averages of heterogeneous and
microstratigraphic deposits

modified the stratigraphy over time. Neither QEM-EDS nor CT can
replace the petrographic method, as such it is recommended that
they 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 secondary
diagenetic processes can be more confidently elucidated. These
results are significant in their own right, yet they also assist with
determining the reliability and comparability of different dating
techniques, such as uranium-lead dating and paleomagnetism.
This study contributes towards an assessment of the future of
thin section analysis in view of the availability of more advanced
techniques in the twenty-first century (see Stoops, 2014). The
technique has always been plagued by its intrinsic subjectivity and
its requisite dependence on technical knowledge and expertise
(Griffiths, 1967:204; Catt and Weir, 1976:86; Kooistra, 1990), often
to 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 understand
regardless 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] in
favor of the latest instrumentation’ (Gunter, 2004:43). Despite
qualifications, this study has found that thin section analysis re-
mains the ‘gold standard’ in characterising site formation processes
and 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 the
CT analysis and AB the CT image processing. The authors thank:
Shane Paxton and John Vickers (RSES, ANU) for preparing QEM-EDS
samples, Adelaide Petrographics Laboratory for the production of
petrographic thin sections. The work was funded by an ARC Future
Fellowship (FT120100399) to AIRH. Sampling at Elandsfontein was
supported by an NSF grant (1219494) to Dr David Braun and Dr
Naomi Levin and at Haasgat by a Leakey Foundation Grant to Dr
Justin Adams and AIRH. We also thank Dr Colin Menter for access to
Drimolen and the South African Heritage Resource Agency and
Heritage Western Cape for providing permits for sampling and
export. Additional thanks to Alex F Blackwood for figure editing.
Funding for UT was 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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