3.1. Subsurface morphology of the study site, sediment coring, and radiocarbon dating
The Zahájí site was surveyed in 1999, 2004, 2021, and 2022. The position of the boreholes is shown in Fig. 5 and a description of the relevant analyses is provided in Table 1. In 2022, the valley floor was surveyed using electrical resistivity tomography (ERT) (for more detail on this method, see Supplementary material, S1.) and hand-operated corers (coring chamber diameter of 2.5cm) in a transect across the valley. A total of 21 boreholes were documented, and lithologically significant horizons were sampled for environmental analyses.
Based on drilling and ERT profiling, the valley floor has an irregular surface; it slopes gently towards the NW. The organic deposits reach a maximum thickness of 8.6m in the central difference in elevation between the bottom at the SE and NW edges is approx. 4.5m. The organic deposits reach a maximum thickness of 8.6m in the central part of the valley, where a channel-like structure parallel to the valley axis was identified. This represents the former stream channel, which folded towards the NW wall of the canyon during the Holocene.
Table 1. Zahájí. Overview of documentation points (cores) from Fig. 5.
AMS radiocarbon dating of 37 organic samples was performed in laboratories in Poznań (Poz), Erlangen (Erl), and Prague (CRL) (Table 2, Table 3). The OxCal 4.4 calibration programme was used to determine sample ages along with the IntCal20 calibration curve for Northern Hemisphere terrestrial samples (Bronk Ramsey, 2009; Reimer et al., 2020).
Table 2. Zahájí. Radiocarbon dates from multiple cores. Calibrated in OxCal 4.4 software using IntCal20 (Bronk Ramsey, 2009; Reimer et al., 2020).
Fig. 5. Plan of the Zahájí site. Left: position of the lithostratigraphical cross-section (black crosses) and the ERT profile (red line; see Fig. 6). Right: detail of the Podbradecký potok valley floor showing coring and sampling sites. Red cross – position of the fingernail finding; black crosses – cores ZA 2–17 for lithostratigraphical and morphological analyses and for survey on millet macroremains (see Table 1); yellow square – original pit from 1999; purple ellipse – assumed area of millet spread; ZAH – position of the profiles ZAH 2004, ZAH 2015, ZAH A–C (see Table 1); A – organic-rich surface sediment sample; B – sample for water chemistry; C – Fe-rich surface sediment sample.
Table 3. Zahájí. Radiocarbon dates from millet grains and the human nail (ZAH A–C and ZA1 cores). Calibrated in OxCal 4.4 software using IntCal20 (Bronk Ramsey, 2009; Reimer et al., 2020). R_combine = combination of all measurements of millet.
lab code
|
material
|
BP
|
±
|
BC from
|
BC to
|
%
|
CRL 20_215
|
millet grain
|
3136
|
18
|
1491
|
1316
|
95.4
|
CRL 20_216
|
millet grain
|
3096
|
18
|
1423
|
1295
|
95.4
|
CRL 20_309
|
millet grain
|
3098
|
23
|
1426
|
1291
|
95.4
|
ETH-107373
|
millet grain
|
3103
|
23
|
1430
|
1292
|
95.4
|
UA3216
|
millet grain
|
3122
|
30
|
1493
|
1293
|
95.4
|
Poz-29572
|
millet grain
|
3140
|
40
|
1502
|
1296
|
95.4
|
R_combine
|
millet grains
|
3113
|
10
|
1428
|
1311
|
95.4
|
CRL 20_308A
|
nail
|
3045
|
44
|
1419
|
1197
|
95.4
|
CRL 20_308B
|
nail
|
3096
|
24
|
1425
|
1287
|
95.4
|
3.2. Sediment lithostratigraphy, geochemistry, and micromorphology
Three major lithological horizons (LH_1, LH_2, LH_3) can be distinguished in the laterally heterogeneous sedimentary record of the swamp (Fig. 6). LH_1 (ca. 1100BC–recent) is composed of brown to black woody peat with variable admixtures of clay and sand which form irregular layers up to several centimetres thick. Sediments are dominated by silicates (SiO2, TiO2, Na2O, K2O), which make up about 80% of dry sediment content. The organic carbon content is relatively low and falls with the range 7–23%. The maximum sulphur content measured is around 10%. LH_2 (ca. 1600–1100BC) consists of a light grey clay and locally fine-grained sandy clays alternating with mossy layers. Fe2O3 and Al2O3 contents reach extremely high values of 40–60% and are accompanied by enormously increased sulphur concentrations (up to 14%). This horizon contains very abundant iron and alum (potassium-aluminium sulphate) concretions several centimetres across, which formed here as a result of the geochemistry of the environment. According to the results of an XRD analysis, the concretions are formed of goethite (α-Fe3+O(OH)) and basaluminite (=felsőbányaite;Al4(SO4) (OH)10·4H2O). At the base of sequence LH_2, the alum coupled with the high iron concentrations form a mechanically resistant encrustation(for a more detailed description of the base of LH_2, where the millet layer and the fingernail were discovered, see Fig. 6). The sequence LH_3 (ca. 7300–1600BC) is characterized by a dark brown to black mushy peat with frequent deposits of red to yellow-red clay 5–25cm thick, alternating with layers of sand and gravel and abundant Fe/Al concretions. The number of mineral clasts increases towards the base to form more substantial accumulations at the bottom. Like LH_2, Fe2O3 and Al2O3 contents are high (up to 72% and 21% respectively), but the sulphur content is low (3–4%) and the organic carbon content is relatively high (~15–20%).
The basal part of LH_2, represented by the cores ZAH B and ZAH C, was analysed for chemical composition and micromorphology, which confirmed the unusual sediment chemistry, including the presence of goethite and basaluminite. These two minerals precipitate under oxic, low-pH conditions (for more detail, see Supplementary material, S1).
Fig. 6. Zahájí. (A) Results of electrical resistivity tomography; (B) Stratigraphical cross-section of the valley of the Podbradecký Brook.
3.3. Paleobotanical record and reconstruction of the vegetation cover
The preservation of organic remains is excellent across the entire swamp as a result of the acidic conditions and the high content of basaluminite, a compound that prevents the biological degradation of organic materials (Pokorný et al., 2010). The unusual chemical composition also accounts for the fact that the deposit is exceptionally thick and demonstrably without any stratigraphic hiatuses, providing a fossil record that is unique for the otherwise dry lowlands of central Europe.
The first fieldwork at the Zahájí site started 25 years ago with a pollen profile from 1999 (here, ZAH 2004). In 2008, a second profile (here, ZAH2015) was drilled from the bottom of a pit originally hand dug in 1999 and which reached a depth of 2.0m. Reference cores ZAH A–C and ZH 1–17 from 2021 were drilled to a depth of 5.0m by a piston corer (coring chamber diameter of 5.0cm and length of 1.0m). ZAH A–C were drilled immediately adjacent to the two original profiles, also from the bottom of the hand-dug pit. An additional drilling was carried out in the immediate vicinity of ZAH A–C to recover enough millet for the analysis (Fig. 5). To provide enough material, two parallel cores, ZAH B and ZAH C, were wet-sieved and analysed for plant macrofossils. Both cores were correlated visually according to prominent lithological horizons. A description of the laboratory work and the data are appended in Supplementary material, S2.
The plant macrofossil diagram (Fig. 7) clearly shows the position of millet (Panicum miliaceum) grains, rachis, stems and roots within the investigated core section. They occur in association with local vegetation: the remains of birches (Betula sect. albae), sedges (Carex), and, importantly, Potamogeton, all of which provide evidence of a local aquatic environment, most likely, given the combination of taxa detected, a very small pool of shallow water.
The pollen diagram (Fig. 8) is in full agreement with these findings (see Potamogeton, Cyperaceae, and Hordeum-type – the pollen taxon that includes pollen grains of both Hordeum and Panicum). In the vegetation signal captured by pollen analysis, evidence of cereal cultivation is exceptionally strong across the whole section. Even Secale cereale (rye), then presumably only a cereal weed rather than an intentionally cultivated crop (Behre, 1992), is present in large quantities. Grazing was also important in the same period, as evidenced by the persistent presence of Plantago lanceolata and Rumex acetosa-type pollen. The composition of forest stands is not subject to significant change in this short time period.
Fig. 7. Zahájí site. Diagram showing plant macrofossil stratigraphy obtained for the ZAH B and ZAH C cores. The X-axes scales show absolute numbers of finds in 25cm3 of sediment.
3.4. Analysis of past and modern aquatic fauna
Some 26 sediment samples from the ZAH B core were taken in 2.0cm steps from the depth interval 419–471cm for analysis of the subfossil remains of aquatic invertebrates (insects, cladocerans, and bryozoans). For more detail regarding the extraction, quantification, and identification of the remains, see the Supplementary material, S3.
Two modern sediment samples for zoological analysis and two water samples (one for analysis of planktonic fauna and one for pH and conductivity) were collected from the current wetland as reference samples up to 10.0m from the ZAH coring site, i.e., outside the channel of the current brook (Fig. 4; Table 1). The waterlogged surface with very slow running water in the middle of the brook valley is patchy, with two distinct sediment types: one with a striking red colour (assumed to reflect high iron content), and the other with a dark colour and a high organic content. The iron concentration in the first sample was measured by an XRF device (Vanta, Olympus). In addition, a reference surface (0.0–1.0cm) sediment sample and water samples for pH, conductivity, and planktonic fauna were taken in 2022 from Kamencové jezero (Kamencové Lake, 50.472° N, 13.425° E), a strongly acidic post-mining lake with uniquely high concentrations of dissociated potassium alum (Hrdinka, 2012). Live aquatic invertebrates were extracted from all sediment samples using 500µm, 100µm and 40µm sieves and later manually picked and identified under a dissecting optical microscope. For characterization of the water samples, we used a laboratory pH-meter (SevenCompact pH meter, Mettler–Toledo) and a conductometer (Seven2Go Cond meter, Mettler–Toledo).
A section of the ZAH B core (52cm long) around the millet layer revealed two distinct faunal biozones (Fig. 9). The older biozone (471–451cm) is characterized by rare findings of aquatic invertebrate remains. Within this biozone, chironomid head capsule (HC) concentrations are lower than 6 HCs per 1cm3, concentrations of other insect groups are lower than 3 individuals per 1cm3, and concentrations cladoceran remains are lower than 10 per sample. The taxonomic composition indicates the presence of a very shallow and likely ephemeral shallow pond (or several small ponds) at the bottom of the Podbradecký Brook valley. Specifically, the environment of the very shallow lentic water body is indicated by the presence of inhabitants of lentic waters such as chironomids of the genus Chironomus and the cladoceran species Chydorus sphaericus. Other taxa, namely of the chironomid genera Gymnometriocmemus – Bryophaenocladius, Limnophyes, and Pseudorthocladius are known from spring-fed streams, wet soil and shallow ponds (or the splash zones of bigger lakes) and are often associated with mosses (see high concentrations of moss in this biozone (Fig. 7). The presence of ceratopogonid HCs (Diptera: Ceratopogonidae) and Sialis mandibles (order Megaloptera) is common in both lentic and lotic waters. An isolated finding of a sciarid HC (Diptera: Sciaridae) indicates a wet soil environment.
The younger biozone (451–419cm) was distinguished according to the abundant subfossil remains of lake taxa, indicating an increase in water level and the existence of a perennial shallow lake. The biozone was not, however, rich in (morpho)species: a total of just 6 chironomid taxa, 4 non-chironomid insect taxa, 3 cladoceran taxa, and 1 bryozoan taxa. The most numerous remains belong to the cladoceran Chydorus sphaericus and reach high abundances up to thousands of individuals per 3cm3. Other cladocerans (genera Ceriodaphnia and Daphnia) are represented only by single findings of resting eggs (ephippia).
Fig. 8. Zahájí site. Diagram showing pollen percentages for the ZAH B core.
Fig. 9. Zahájí site. Diagram showing aquatic invertebrate stratigraphy for the ZAH B core. Two types of wetland environment (on the left) were distinguished based on the ecology of the fossil assemblages. Chydorus sphaericus concentrations are shown using a semiquantitative scale (0 = absence; 1 = from 1 to 9 individuals per sample; 2 = from 10 to 100 individuals per sample; 3 = from 100 to 999 per sample; 4 = ≥ 1,000 per sample). HC – head capsule; MNI – minimum number of individuals.
The most numerous chironomid HCs (abundances up to 27 HC per 1cm3 of sediment) represent the genus Chironomus, a taxon usually associated with soft sediments from various types of lake. Other chironomids, namely Ablabesmyia, Limnophyes, Paratendipes nudisquama-type, Psectrocladius, Pseudorthocladius, and Thienemannimyia-type, were found in low abundances (< 1 HC per 1cm3) and represent the fauna of small streams and/or the littoral zone of lakes. Of the non-chironomid finds, larval remains of diving beetles (family Dytiscidae) are worth mentioning as most species are lentic. Overall, the invertebrate assemblages with low species richness and the dominance of Chydorus sphaericus and Chironomus are unusual and clearly indicate extreme conditions.
Zoological analysis of the two modern sediment samples from the waterlogged surface of the current bog revealed the absence of invertebrate fauna in the Fe-rich sample (38.5% of Fe in dry sample according to the XRF analysis) and the presence of invertebrate fauna of running waters and wet soils (mainly chironomids of the subfamily Orthocladiinae) without any lake taxa in the organically rich sample. The sediment samples from Kamencové jezero were dominated by chironomids of the genus Chironomus. The pH and conductivity (K25) values for the Zahájí site (the hand-dug pit) and Kamencové jezero water samples were 5.97 and 865µS/cm and 3.4 and 1016µS/cm respectively. No cladoceran species, including C. sphaericus, were observed in the modern plankton samples from the two sites.
3.5. Analysis of the human nail
A human nail was discovered with the millet remains in the ZA1 core. It was difficult to measure the dimensions of the nail because immediately after picking it out of the swamp it started to shrink. The maximum measured width was 12.0mm (at the fracture point), the maximum length was 8.2mm, and it was ca. 0.5–1.0mm thick at the edge. Parts of the nail (one side and the underside) were damaged by the corer (Fig. 10).
Judging by its morphological features, the nail is likely to be from the thumb or big toe. On the inner side of the nail plate, fine longitudinal grooves are evident as a remnant of attachment to the nail bed, and it also appears that three layers of the human nail plate can be distinguished (namely the dorsal, intermediate, and ventral nail plate; Kobayashi et al., 1999). Slight vertical grooves are evident on the outer surface. Mild vertical grooves often appear on the nails of older adults, probably due to a slowing of cell turnover. The translucent texture of the plate is probably suppressed by the tanning process, although its colour falls far short of the colouring seen on the nails of Old Croghan Man (Giles, 2020, p. 258).
Fig. 10. A – Photo of the human nail shortly after it shrank as a result of drying out; B – A044_report, SciLifeLab Ancient DNA, Evolutionary Biology Centre, Norbyvägen 18C, Uppsala 752 36, Sweden.
The nail seems to be manicured on the distal edge, just as it is, for example, in the case of St. Bees Man and Lindow Man (Brothwell, 1986, p. 39). Its surface was smooth and bore only small scratches that were hardly visible and might have been made after it was deposited in the wetland; there are also no signs of the damage from manual work that can be found, for example, in the nails of the Greenland mummies (Hart Hansen et al. (eds.), 1991, p. 80, fig. 64). Here, numerous transverse cuts in the thumbnails were probably made by a knife.
Ancient DNA (aDNA) was extracted from a 20mg sample of the fingernail, from which two DNA sequencing libraries were prepared. The aDNA processing and the data analysis were performed at the SciLifeLab Ancient DNA facility. Sequencing was performed by the SNP&SEQ Technology Platform in Uppsala, part of the National Genomics Infrastructure, Sweden, hosted by the Science for Life Laboratory (for more information, see Supplementary material, S4). Unfortunately, although DNA data was generated from the sample, the amount that matched human DNA was extremely low, like the blank controls. The interpretation is that no human aDNA was preserved in the specimen (Magnus Lundgren, Ancient DNA project A0 44). This is no surprise given the high acidity of the water in the bog (Fischer, 2012, p. 111). Until now, DNA has only been recovered from preserved teeth and bones, as in the case of Vittrup Man, deposited in a Danish bog between 3300 and 3100BC (Fischer et al., 2024).
3.6. Analysis of organic residues
Part of the ZAH A sediment core was scanned for organic residues to provide information regarding whether any other part of the human body might be still preserved in the swamp. A total of 4 samples (2–8g of dried, grounded and sieved sediment) were Soxhlet extracted using a chloroform/methanol mixture (v/v, 2:1), saponified, fractionated to neutral and acidic fractions, and run by GC/TOF-MS (Agilent 8890 coupled to a TOF-MS analyser Pegasus BT from Leco).
All extracts of the analysed sediment samples were examined for various lipid groups to explore whether there are any specific biomarkers indicating the presence of decomposing human adipose tissue, such as free fatty acids and their oxidative products or steroids (Bull et al., 2009; Lerchi et al., 2022; Queirós et al., 2023). Neither the total lipid extracts (TLEs) nor the neutral and acidic fractions of the TLEs revealed any signs of biomarkers which could be directly related either to adipocere formation or decomposing adipose tissue. The total lipid extracts and acidic fractions contained mainly free fatty acids, dominated by long even fatty acids C18:0–C28:0, together with ω-hydroxyfatty acids (e.g. 16-hydroxypalmitic acid). Neutral fractions dominated with free fatty alcohols (C18–C28), long odd linear n-alkanes (C27, C31), long dicarboxylic acids, phytol and plant derived steroids – stigmasterol, β-sitosterol, campesterol, and 5β-stigmastanol, a degradative product of stigmasterol and sitosterol (Evershed and Connolly, 1994) (Fig. S1).
3.7. Millet layer
A layer of uncharred millet grains, rachis, stalks and roots (Fig. 11) was detected at a depth of 4.35m to 4.50m in ZAH2004, ZAH2009, ZAH A–C, ZA1, ZA7, and ZA16. This implies that the millet was dispersed over an area of at least 6 m2 (Fig. 4). The original thickness of the millet layer is difficult to determine because of the action of taphonomic processes, but the plants appear to have been thrown/deposited/spread into the lake as a single event and formed a layer a few centimetres thick at most.
Radiocarbon dating of the millet remains (ca. 1428–1311BC) places the site in a group of the four oldest dates from Bohemia and among the oldest dates from central Europe (Fig. S2; in reference to Filipović et al., 2020). At Bohemian sites, most millet finds come from contexts that differ from the broader archaeology of central Europe: one from a wetland (this study), two from abris in a remote sandstone rocky area, and one from the heavily fortified Velim site, which is known for the large number of human sacrifices in ditches and is usually classified as a cult site (Harding et al., 2007). Only one find comes from an ordinary settlement pit. This assessment may, however, be swayed by the fact that macroremains from settlements of archaeologically known age are not commonly radiocarbon-dated in Czechia.
Fig. 11. Collection of plant macroremains from depth 444cm, ZAH B and ZAH C cores. The sample is clearly dominated by Panicum miliaceum, including complete fruits and one stem. Photo: P. Pokorný.
We attempted to recover preserved DNA from two millet grain samples (Z1 and Z2) recovered at a depth of 444cm from the ZAH B and ZAH C cores. DNA extractions were performed in a dedicated clean room facility at the Department of Archaeology, University of Cambridge, UK, following the protocol in Wales and Kistler (2019). Two extraction blanks were carried out to assess laboratory contamination. Libraries for shotgun sequencing were constructed following Meyer and Kircher (2010) and sequenced on an Illumina MiSeq instrument.
Raw sequence data were trimmed of adapter sequence using Paleomix v.1.3.8 (Schubert et al., 2014) and checked for quality using FastQC v. 0.11.9 (Andrews, 2010). Trimmed sequence data were aligned against the reference genome of broomcorn millet (Zou et al., 2019) in Paleomix. Assessment of ancient DNA authenticity was performed using mapDamage v. 2.0 (Jonsson et al., 2013).
Some 1,468,577 sequence reads were retained from sample Z1 following adapter trimming, and 2,121,763 from sample Z2. Only 0.09 % of trimmed reads from Z1 aligned to the broomcorn millet genome, and 0.12 % from Z2. This is comparable with the overall alignment rate from the sequenced extraction blanks. mapDamage plots for sample Z1 showed profiles consistent with damaged modern DNA rather than authentic ancient DNA. Sample Z2 showed nucleotide misincorporation patterns consistent with some authentic ancient DNA of low quality, as well as damaged modern DNA.
These results indicated that, as with the human fingernail, very little endogenous DNA was preserved in the Zahájí millet. Although some studies have reported successful extraction and sequencing of endogenous DNA from waterlogged plant material, the majority of these have been from lignified tissues such as grape pips and subfossil wood remains (Schworer et al., 2022).