The dynamic relationship between temperate and tropical circulation systems across South Africa since the Last Glacial Maximum

A fundamental and long-standing question of southern African palaeoclimatology is the way tropical and temperate climate system dynamics have influenced rainfall regimes across the subcontinent since the Last glacial maximum. In this paper, we analyse a selection of recently published palaeoclimate reconstructions along a southwest-northeast transect across South Africa. These records span the last 22,000 years, and encompass the transition between the region's winter and summer rainfall zones. In synthesis, these records confirm broad elements of the dominant paradigm, which proposes an inverse coeval relationship between temperate and tropical systems, with increased precipitation in the winter (summer) rainfall zone during glacial (interglacial) periods. Revealed, however, is a substantially more complex dynamic, with millennial-scale climate change events being strongly – even predominantly – influenced by the interaction and combination of temperate and tropical systems. This synoptic forcing can create same sign anomalies across the South African rainfall zones, contrary to expectations based on the classic model of phase opposition. These findings suggest a new paradigm for the interpretation of southern African palaeoenvironmental records that moves beyond simple binary or additive influences of these systems

Linking upwelling intensity and orbital-scale climate variability in South Africa's winter rainfall zone: Insights from a ~70,000-year hyrax midden record

The climate of Africa's southwestern Cape is characterised by a strongly seasonal winter precipitation regime, with late Quaternary climate variability generally considered to have been driven by the position of the southern westerlies. This paper presents a unique ∼70,000 year-long palaeoclimatic record from a rock hyrax midden from South Africa's winter rainfall zone, enabling the analysis of regional climate systems since the beginning of marine isotope stage 4. The data suggest that the last glacial period was relatively humid compared to the Holocene, likely due to cooler temperatures, more extensive Antarctic sea-ice extent and an equatorward displacement of the westerly storm track. However, orbital-scale climate variability associated with the 23 kyr precessional cycle primarily correlates with changes in upwelling intensity in the Benguela system, implying an important role for the blocking of tropical easterly flow in driving long-term climatic variability. These factors combined during glacial periods to significantly amplify rainfall seasonality in the southwestern Cape, bringing more winter rainfall via mid-latitude frontal systems, while reducing the proportion of summer rainfall, particularly during the glacial periods of the late Quaternary. The results therefore highlight the need to consider a complex suite of circulation systems and dynamics when inferring drivers of long-term environmental change in the region

The chemistry of American and African amber, copal, and resin from the genus Hymenaea

The comparison of the chemical composition of fossilized amber, copal, and resin is important for determining the botanic origin and original chemical composition of fossilized amber and copal, and for understanding the ecologic role of resin. Here we use solid phase microextraction–gas chromatography–mass spectrometry (SPME–GC–MS) to investigate the volatile and semi-volatile composition of amber, copal and resin from Africa and the Americas, produced by trees from the genus Hymenaea. We found there are four subgroups of Hymenaea resin, copal, and amber, based upon age and chemical similarity: African amber, American amber, African resin/copal (which also includes Colombian copal), and American resin/copal. This analysis allows us to narrow down the potential botanic origin of amber and copal samples, and also indicates that within this genus, resin similarity does not correspond closely with phylogenetic relationships. Therefore, resin chemistry may have been controlled by ecologic pressures, such as defence against herbivores, wood borers, humidity, and diseases and the original chemical composition of amber and copal could potentially be used to understand the role of resin in plant–insect interactions through time

Variability in soil and foliar stable carbon and nitrogen isotope compositions in the winter rainfall biomes of South Africa

We present the stable carbon and nitrogen isotope compositions of 204 plants and 99 soils from South Africa's Fynbos and Succulent Karoo biomes, from which we assess variability in δ13C and δ15N within and between the biomes. Higher foliar δ13C in the Succulent Karoo (−22.4 ± 4.7‰) primarily reflects a greater abundance of CAM photosynthesis relative to Fynbos (−25.7 ± 3.5‰). For C3 plants within the Fynbos Biome, there is no statistically significant relationship between δ13C and climate, suggesting that within the present sampling framework, local-scale variability masks expected climatic controls on C3 plant δ13C. Soil and foliar δ15N are highly variable, but foliar δ15N is significantly higher in the Succulent Karoo (7.7 ± 3.9‰) compared to the Fynbos (4.4 ± 3.3‰). Soil and foliar δ15N correlate, with soils 3 ± 1‰ more enriched in 15N. Both soil and foliar δ15N show stronger correlations with climate than δ13C, and they accord with the previously observed tendency for higher δ15N with greater aridity. The relationship between δ15N and mean annual rainfall is, however, relatively steep (2.4 ± 0.6‰ per 100 mm rainfall), potentially implying additional controls on δ15N variability. These data provide a benchmarking of contemporary isotopic variability, anticipated to support future archaeological, palaeoenvironmental and C and N cycling research.<br

Investigation of organic matter and biomarkers from Diepkloof Rock Shelter, South Africa: insights into Middle Stone Age site usage and palaeoclimate

Diepkloof Rock Shelter (DRS) represents a site of major interest for reconstructing early human behaviours during the Middle Stone Age (MSA). Rock shelters such as DRS also potentially preserve information concerning the environmental context for such behaviours. In this respect the organic matter composition of rock shelter sediments has rarely been investigated in detail, particularly at the molecular level. Here, we used pyrolysis-gas chromatography/mass spectrometry (py-GC/MS) to systematically assess the organic matter composition of bulk sediments within the MSA and Later Stone Age (LSA) sequence at DRS. From this we sought to gain insights into site usage, taphonomy and burning practices. Additionally, we analysed the chain length distribution of leaf-wax n-alkanes as well as their hydrogen and carbon isotopic compositions (δDwax and δ13Cwax) to investigate their potential as hydroclimate and vegetation indicators. This constitutes the first leaf-wax isotopic data in a terrestrial context of this antiquity in South Africa. Py-GC/MS shows a dichotomy between stratigraphic units (SUs) of high organic matter content, producing a range of pyrolysis products, including homologous series of long chain n-alkene/n-alkane doublets and alkyl-nitriles, and SUs of low organic matter content, dominated by aromatic, heterocyclic N and polycyclic aromatic hydrocarbon (PAH) pyrolysis products; typical molecular burning products. Several SUs of the Intermediate Howiesons Poort interval exhibit the latter composition, consistent with micromorphological evidence. δ13Cwax remains stable throughout the MSA, but leaf-wax n-alkane chain length and δDwax increase during the Late Howiesons Poort interval. Comparison with such patterns in modern plants in the region suggests this represents a shift towards the input of more arid-adapted vegetation into the shelter, driven either by aridification at the site locale or a change in selection practices. Our results suggest that these techniques have further potential in southern Africa and globally at sites where organic matter preservation is high

Holocene sea level and environmental change on the west coast of South Africa: evidence from plant biomarkers, stable isotopes and pollen

We present an 8,000-year biomarker and stable carbon isotope record from the Verlorenvlei Estuary, South Africa. We assessed how leaf wax lipids, insoluble macromolecular organic matter, bulk C/N data and compound-specific stable carbon isotopes were linked to the site’s palynological record and to evidence for regional sea level and environmental change. Down-core trends in bulk δ13C are closely coupled to trends in pollen types from saline-tolerant taxa. These trends are mirrored by variations in the incorporation of reduced sulphur into macromolecular organic matter. This process, quantified with the thiophene ratio, is closely associated with periods of higher sea level 8,000-4,300 cal yr BP. We propose the thiophene ratio is a proxy for relative marine influence within (peri) estuarine sediments. All measured variables indicate differences between early-middle Holocene (8,000-4,300 cal BP) and late Holocene conditions at Verlorenvlei. The former period was more saline and preserves more labile macromolecular organic matter. Marine influence declined after 4,300 cal yr BP, and although the abundance of short-chain-length n-alkanes suggests continued presence of wetland flora until 2,500 cal yr BP, organic matter preservation became poorer and a drying trend was inferred, most notably for the interval 2,500-900 cal BP. Increasing freshwater inundation is apparent during the last 700 cal years, consistent with several records from this region. Leaf wax n-alkane distributions are largely uncorrelated with bulk organic matter variables, with the exception of the abundance of C31 and C33 n-alkanes, which are negatively correlated with δ13CTOC. Furthermore, C31-C33 n-alkane δ13C values are uncorrelated with C23-C29 δ13C and δ13CTOC. They are also higher than our newly measured terrestrial (C3) vegetation C29 and C31 end-member values of -35 ± 2 and -34 ± 1‰, respectively. These patterns are best explained by a dominant contribution of local riparian vegetation to the C23-C29 n-alkanes, but time-varying contributions of non-local leaf waxes to the C31-C33 signals. This renders inferences concerning regional environmental change from long-chain leaf waxes potentially challenging in this setting

Seasonal variability in methane and nitrous oxide fluxes from tropical peatlands in the western Amazon basin

The Amazon plays a critical role in global atmospheric budgets of methane (CH4) and nitrous oxide (N2O). However, while we have a relatively good understanding of the continental-scale flux of these greenhouse gases (GHGs), one of the key gaps in knowledge is the specific contribution of peatland ecosystems to the regional budgets of these GHGs. Here we report CH4 and N2O fluxes from lowland tropical peatlands in the Pastaza–Marañón foreland basin (PMFB) in Peru, one of the largest peatland complexes in the Amazon basin. The goal of this research was to quantify the range and magnitude of CH4 and N2O fluxes from this region, assess seasonal trends in trace gas exchange, and determine the role of different environmental variables in driving GHG flux. Trace gas fluxes were determined from the most numerically dominant peatland vegetation types in the region: forested vegetation, forested (short pole) vegetation, Mauritia flexuosa-dominated palm swamp, and mixed palm swamp. Data were collected in both wet and dry seasons over the course of four field campaigns from 2012 to 2014. Diffusive CH4 emissions averaged 36.05 ± 3.09 mg CH4–C m−2 day−1 across the entire dataset, with diffusive CH4 flux varying significantly among vegetation types and between seasons. Net ebullition of CH4 averaged 973.3 ± 161.4 mg CH4–C m−2 day−1 and did not vary significantly among vegetation types or between seasons. Diffusive CH4 flux was greatest for mixed palm swamp (52.0 ± 16.0 mg CH4–C m−2 day−1), followed by M. flexuosa palm swamp (36.7 ± 3.9 mg CH4–C m−2 day−1), forested (short pole) vegetation (31.6 ± 6.6 mg CH4–C m−2 day−1), and forested vegetation (29.8 ± 10.0 mg CH4–C m−2 day−1). Diffusive CH4 flux also showed marked seasonality, with divergent seasonal patterns among ecosystems. Forested vegetation and mixed palm swamp showed significantly higher dry season (47.2 ± 5.4 mg CH4–C m−2 day−1 and 85.5 ± 26.4 mg CH4–C m−2 day−1, respectively) compared to wet season emissions (6.8 ± 1.0 mg CH4–C m−2 day−1 and 5.2 ± 2.7 mg CH4–C m−2 day−1, respectively). In contrast, forested (short pole) vegetation and M. flexuosa palm swamp showed the opposite trend, with dry season flux of 9.6 ± 2.6 and 25.5 ± 2.9 mg CH4–C m−2 day−1, respectively, versus wet season flux of 103.4 ± 13.6 and 53.4 ± 9.8 mg CH4–C m−2 day−1, respectively. These divergent seasonal trends may be linked to very high water tables (> 1 m) in forested vegetation and mixed palm swamp during the wet season, which may have constrained CH4 transport across the soil–atmosphere interface. Diffusive N2O flux was very low (0.70 ± 0.34 µg N2O–N m−2 day−1) and did not vary significantly among ecosystems or between seasons. We conclude that peatlands in the PMFB are large and regionally significant sources of atmospheric CH4 that need to be better accounted for in regional emissions inventories. In contrast, N2O flux was negligible, suggesting that this region does not make a significant contribution to regional atmospheric budgets of N2O. The divergent seasonal pattern in CH4 flux among vegetation types challenges our underlying assumptions of the controls on CH4 flux in tropical peatlands and emphasizes the need for more process-based measurements during periods of high water table

Molecular fingerprinting of wetland organic matter using pyrolysis-GC/MS: an example from the southern Cape coastline of South Africa

Pyrolysis–gas chromatography mass spectrometry (py-GC/MS) allows the characterisation of complex macromolecular organic matter. In lakes and wetlands this can potentially be used to assess the preservation/diagenesis and provenance of sediment organic matter. It can complement palaeoenvironmental investigations utilising ‘bulk’ sediment variables such as total organic carbon (TOC) and TOC/total nitrogen ratios. We applied py-GC/MS analyses to a ~32,000-year sediment record from the southern Cape coastline of South Africa. We used the results to evaluate the sources and extent of degradation of organic matter in this semi-arid environment. Marked down-core changes in the relative abundance of multiple pyrolysis products were observed. Correspondence analysis revealed that the major driver of this down-core variability in OM composition was selective preservation/degradation. Samples comprising highly degraded OM are primarily confined to the lower half of the core, older than ~12,000 years, and are characterised by suites of low-molecular-weight aromatic pyrolysis products. Samples rich in organic matter, e.g. surface sediments, are characterised by products derived from fresh emergent or terrestrial vegetation, which include lignin monomers, plantderived fatty acids and long-chain n-alkanes. Pyrolysates from the late glacial-early Holocene period, approximately mid-way down the core are characterised by distinct suites of long-chain n-alkene/n-alkane doublets, which may reflect the selective preservation of recalcitrant aliphatic macromolecules and/or enhanced inputs of the algal macromolecule algaenan/polymerised algal lipids. Increased TOC, lower δ[superscript 13]C and increased abundance of more labile lignin and fatty acid products at the same depths suggest this period was associated with increased lake primary productivity and enhanced inputs of terrestrial OM. TOC is the only ‘bulk’ parameter correlated with the correspondence analysis axes extracted from the py-GC/MS data. Distinct fluctuations in TOC/total nitrogen ratio are not explained by variation in organo-nitrogen pyrolysis products. Notwithstanding, the study suggests that py-GC/MS has potential to complement palaeolimnological investigations, particularly in regions such as southern Africa, where other paleoenvironmental proxy variables in sediments may be lacking or equivocal

Synchrotron scans for gut microbiota and dehydration experiments.

<p>Synchrotron tomographic images (A,B,E,F,I,J) and drawings (C,D,G,H,K,L) of: (a,c) an antibiotic treated fly and (B,D) an untreated, wildtype fly, both fresh when entombed; (e,g) an antibiotic treated fly and (F,H) an untreated wildtype fly, both dried on the surface of the resin before complete entombment; and (I,K) an antibiotic treated fly, and (J,L) an untreated, wildtype fly, both dried isolated from the resin prior to complete entombment. Colours identical to <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0195482#pone.0195482.g002" target="_blank">Fig 2</a>. White arrows indicate ruptured abdomens, and black arrows indicate bubbles. Scale bars = 1 mm.</p

Synchrotron scans for resin chemistry experiments.

<p>Synchrotron tomographic images (A,B) and drawings (C,D) of flies in resin showing state of decay after 18 months entombment in (A) <i>W</i>. <i>nobilis</i> resin, and in (B) <i>P</i>. <i>sylvestris</i> resin. (A,C) The fly retains most of the cuticle, some of the internal soft tissues (black arrows) and bubbles within the body margin are small. (B,D) The fly retains some cuticle; there is a gap between resin and cuticle (white arrows) and extensive, and large bubbles. Internal soft tissue is absent. Instead the body margins are filled with a medium of the same density as the resin (compare the areas indicated by black circles) and which connects to the resin (black arrow), indicating that this is resin, not soft tissues. In the drawings (C,D), orange represents resin, white represents cuticle, grey represents internal soft tissue, and red represents bubbles. Scale bars = 1 mm.</p