Fire and human management of late Holocene ecosystems in southern Africa

Globally, fire is a primary agent for modifying environments through the long-term coupling of human and natural systems. In southern Africa, control of fire by humans has been documented since the late Middle Pleistocene, though it is unclear when or if anthropogenic burning led to fundamental shifts in the region\u27s fire regimes. To identify potential periods of broad-scale anthropogenic burning, we analyze aggregated Holocene charcoal sequences across southern Africa, which we compare to paleoclimate records and archaeological data. We show climate-concordant variability in mid-Holocene fire across much of the subcontinent. However, increased regional fire activity during the late Holocene (~2000 BP) coincides with archaeological change, especially the introduction and intensification of food production across the region. This increase in fire is not readily explained by climate changes, but rather reflects a novel way of using fire as a tool to manage past landscapes, with outcomes conditioned by regional ecosystem characteristics

SARS-CoV-2 Omicron is an immune escape variant with an altered cell entry pathway

Vaccines based on the spike protein of SARS-CoV-2 are a cornerstone of the public health response to COVID-19. The emergence of hypermutated, increasingly transmissible variants of concern (VOCs) threaten this strategy. Omicron (B.1.1.529), the fifth VOC to be described, harbours multiple amino acid mutations in spike, half of which lie within the receptor-binding domain. Here we demonstrate substantial evasion of neutralization by Omicron BA.1 and BA.2 variants in vitro using sera from individuals vaccinated with ChAdOx1, BNT162b2 and mRNA-1273. These data were mirrored by a substantial reduction in real-world vaccine effectiveness that was partially restored by booster vaccination. The Omicron variants BA.1 and BA.2 did not induce cell syncytia in vitro and favoured a TMPRSS2-independent endosomal entry pathway, these phenotypes mapping to distinct regions of the spike protein. Impaired cell fusion was determined by the receptor-binding domain, while endosomal entry mapped to the S2 domain. Such marked changes in antigenicity and replicative biology may underlie the rapid global spread and altered pathogenicity of the Omicron variant

Investigation of hospital discharge cases and SARS-CoV-2 introduction into Lothian care homes

Background The first epidemic wave of severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) in Scotland resulted in high case numbers and mortality in care homes. In Lothian, over one-third of care homes reported an outbreak, while there was limited testing of hospital patients discharged to care homes. Aim To investigate patients discharged from hospitals as a source of SARS-CoV-2 introduction into care homes during the first epidemic wave. Methods A clinical review was performed for all patients discharges from hospitals to care homes from 1st March 2020 to 31st May 2020. Episodes were ruled out based on coronavirus disease 2019 (COVID-19) test history, clinical assessment at discharge, whole-genome sequencing (WGS) data and an infectious period of 14 days. Clinical samples were processed for WGS, and consensus genomes generated were used for analysis using Cluster Investigation and Virus Epidemiological Tool software. Patient timelines were obtained using electronic hospital records. Findings In total, 787 patients discharged from hospitals to care homes were identified. Of these, 776 (99%) were ruled out for subsequent introduction of SARS-CoV-2 into care homes. However, for 10 episodes, the results were inconclusive as there was low genomic diversity in consensus genomes or no sequencing data were available. Only one discharge episode had a genomic, time and location link to positive cases during hospital admission, leading to 10 positive cases in their care home. Conclusion The majority of patients discharged from hospitals were ruled out for introduction of SARS-CoV-2 into care homes, highlighting the importance of screening all new admissions when faced with a novel emerging virus and no available vaccine

Examining the effects of climate change and human impacts on a high-resolution, late Holocene paleofire record from South Africa’s winter rainfall zone

Fire is central to the Cape Floristic Region’s highly biodiverse and disturbance-adapted Fynbos Biome. However, prehistoric fire regimes, their ecological consequences, and their relationships with large-scale climate drivers and human activities remain poorly understood. Here, we use a high-resolution sedimentary charcoal record from Verlorenvlei, a coastal lake situated on the west coast, to interrogate links between fire, climate, and pastoralism in the Fynbos Biome. Our record has a robust chronology supported by 24 radiocarbon dates and provides a continuous sedimentary sequence spanning the last 4200 years, documenting fire activity before and after the local arrival of pastoralists in the Verlorenvlei area ∼1500 cal years BP. Fire at Verlorenvlei over the last 4200 years is variable, with relatively low activity until ∼2000 cal years BP, after which variable but generally higher fire activity occurs until the highest period of fire activity from ∼1450 – 1800 CE (∼500 – 150 cal years BP). The increase in fire activity ∼2000 years ago corresponds with a shift in the diatom assemblage at Verlorenvlei from marine towards brackish and freshwater species, reflecting increased precipitation derived from a strengthening of the southern westerly winds. The peak in fire activity beginning ∼1450 CE (∼500 cal years BP), near the onset of the Little Ice Age, tracks a second diatom-inferred strengthening of the westerly winds. Other southern hemisphere and Antarctic records further corroborate this increased westerly influence after ∼2000 years. Linear regression modeling on the fire record indicates that moisture availability is the primary driver of fire at Verlorenvlei, with little evidence that human populations influenced fire. Our reconstruction suggests that fire activity at Verlorenvlei is limited by moisture availability and that wetter conditions facilitate increased vegetation (i.e., fuel) and intensified fire at this otherwise fuel-limited site. This work has implications for management and conservation decisions in response to future predictions of a warmer and drier climate along South Africa’s west coast

High-resolution record of Holocene climate change dynamics from southern Africa’s temperate-tropical boundary, Baviaanskloof, South Africa

International audienceSouth Africa's southern Cape is a highly dynamic climatic region that is influenced by changes in both temperate and tropical atmospheric and oceanic circulation dynamics. Recent research initiatives suggest that the major elements of the regional climate system have acted both independently and in combination to establish a mosaic of distinct climate regions and potentially steep climate response gradients across the southern Cape. To consider this further, we present new high resolution δ 13 C and δ 15 N data from a rock hyrax (Procavia capensis) midden from Baviaanskloof, in the Cape Fold Mountains of South Africa's Eastern Cape Province. Spanning the last 7200 years, these data provide detailed information regarding environmental changes in the mid-and late Holocene, allowing us to assess the spatio-temporal nature of climate change anomalies across the wider region. Throughout the full duration of the record, a negative correlation between humidity and palaeotemperature reconstructions from nearby Cango Cave is observed. In conjunction with correlations with Southern Ocean sea-surface temperatures and sea-ice presence, we infer a dominant influence of the southern westerlies in determining multi-millennial scale hydroclimate variability. At shorter, multi-centennial to millennial timescales, the Baviaanskloof data indicate a clearer expression of tropical influences, highlighting a delicate balance between the mechanisms driving regional climate dynamics across timescales, and the sensitivity of the region to changes in global boundary conditions

Temperature change in subtropical southeastern Africa during the past 790,000 yr

Across the glacial-interglacial cycles of the late Pleistocene (~700 k.y.), temperature variability at low latitudes is often considered to have been negligible compared to changes in precipitation. However, a paucity of quantified temperature records makes this difficult to reliably assess. In this study, we used the Bayesian method CREST (Climate REconstruction SofTware) to produce a 790,000 yr quantified temperature reconstruction from a marine pollen record from southeast Africa. The results reveal a strong similarity between temperature variability in subtropical Africa and global ice volume and CO2 concentrations, indicating that temperature in the region was not controlled by local insolation, but followed global trends at these time scales, with an amplitude of ~4 °C between glacial minima and interglacial maxima. The data also enabled us to make an assessment of the impact of temperature change on pollen diversity, with results showing there is no link between glacial-age temperatures/CO2 and a loss of diversity in this record

Mean Annual Temperature changes reconstructions from marine core MD96-2048

This dataset contains the best estimates for Mean Annual Temperature Reconstructions from marine core MD96-2048. Under Other version, the xlsx file contains the 1) best estimates for Mean Annual Temperature Reconstructions, 2) posterior distribution of probabilities for each sample, 3) conversion table of plant species to pollen taxa, 4) percentage data used in the reconstruction, 5) list of selected and excluded pollen taxa

Vegetation and climate dynamics during the last glacial period in the fynbos-afrotemperate forest ecotone, southern Cape, South Africa

International audienceDespite the southern Cape's great climatic and botanical significance (occupying the transition between the temperate and subtropical circulation systems and forming part of a global biodiversity hotspot), palaeoenvironmental data for this region of southern Africa is limited. This study presents pollen, charcoal and sedimentological data preserved in the Vankervelsvlei wetland, situated in the modern year-round rainfall zone at the ecotone between the Fynbos and Afrotemperate Forest biomes. Combining optically stimulated luminescence and radiocarbon dating techniques, it was possible to establish a chronology for a sediment sequence spanning the last 140,000 years, the longest record yet produced in the region. The data suggest that MIS 5d was relatively warmer (low fynbos pollen percentages and Pentzia-type pollen) than later MIS 5, MIS 4 and most of MIS 3 (~96e37 ka), which were characterised by decreased temperatures (dominance of ericaceous fynbos). The pollen data indicate a complex response to the change from interglacial to glacial conditions, and suggest an important threshold is crossed in regional ecological dynamics. We postulate that during MIS 5d increased summer rainfall under warmer conditions may have offset increased potential evapotranspiration, allowing for the development of more extensive forests. During its early stages of development Vankervelsvlei was more open (increased aquatics and coarse sediment), trapping more longer-distance pollen (Podocarpus). As the mire became more closed, local elements dominated; a succession that is reflected in significant changes in the pollen assemblage, as Podocarpus remains only in trace percentages, but pollen of Can-thium and Morella, which occupy nearly identical climatic niches as Podocarpus, increase in abundance. It is suggested that drought stress remains limited during the last glacial period as a result of reduced temperatures, compensating for what may have been a more seasonal winter-dominated rainfall regime, and that changes in the pollen record relate to vegetation succession and the development of the wetland rather than to major changes in moisture availability. Due to the virtual absence of palaeodata from the southern Cape covering MIS 5 to MIS 3, the establishment of this record provides an important contribution to the overall palaeoenvironmental history of the region

A high resolution 15,600-year pollen and microcharcoal record from the Cederberg Mountains, South Africa

International audienceThe Cederberg Mountains (Western Cape Province, South Africa) are located within the Fynbos Biome, which exhibits some of the highest levels of species richness and endemism in the world. The region's post-glacial vegetation history, however, remains largely unknown. Presented here are high resolution pollen and microcharcoal records spanning the last 15,600 years obtained from the De Rif rock hyrax midden from the Driehoek Valley of the central Cederberg. In this region, previous pollen studies have shown muted variability in vegetation community composition during periods of globally marked climatic variability (e.g. the last glacial–interglacial transition). In our record, however, significant changes in vegetation composition are apparent. Most notably, they indicate a shift from ericaceous/restioid fynbos (present from 15,600 to 13,300 cal yr BP) to a brief, but prominent, development of proteoid fynbos at the beginning of the Holocene around 11,200 cal yr BP. This vegetation shift is associated with increased moisture at the site, and coincides with reduced fire frequency as indicated by the microcharcoal record. At 10,400 cal yr BP, there is a marked reduction in Protea-type pollen, which is replaced by thicket, characterised by Dodonaea, which became the dominant arboreal pollen type. This shift was likely the result of a long relatively fire-free period coupled with warmer and wetter climates spanning much of the early Holocene. A brief but marked decrease in water availability around 8500–8000 cal yr BP resulted in the strong decrease of Dodonaea pollen. The vegetation of the mid-to late Holocene is characterised by the increased occurrence of Asteraceae and succulent taxa, suggesting substantially drier conditions. These data give unprecedented insight into the vegetation dynamics across a period of substantial, rapid climate change, and while they confirm the presence of fynbos elements throughout the last 15,600 years, the results highlight significant fluctuations in the vegetation that were triggered by changes in both climate and fire regimes