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This paper evaluates risk-oriented frameworks for explaining environmental, social, and economic changes faced by fishing and herding communities in the Turkana Basin during and after the African Humid Period (AHP, 15–5 ka). The orbitally-forced AHP created moist conditions, high lake levels, and unusual hydrological connections across much of northern and eastern Africa. As arid conditions set in and rainfall decreased between 5.3 and 3.9 ka in eastern Africa, Lake Turkana (NW Kenya) shrank dramatically. Shoreline retreat coincided with an expansion of open plains, creating new ecological conditions and potential opportunities for early herders in the basin. In this changing landscape, economies shifted from food procurement (fishing/hunting aquatic resources) to food production (herding), likely through both in-migration by pastoralists and adoption of herding by local fishers. Early pastoralists also built at least seven megalithic pillar sites that served as communal cemeteries during this time. Recent research has shown that local environmental dynamics – both during and after the AHP – were complex, demanding a more careful interrogation of the notion that post-AHP life entailed new and/or heightened risks. Risk-buffering strategies might include mobility, diversification, physical storage, and exchange. Archaeologists working around Lake Turkana have proposed that economic shifts from fishing to pastoralism entailed increased mobility as a risk-buffering strategy to deal with aridity and resource unpredictability, and that pillar sites – as fixed landmarks in an unstable landscape – provided settings for congregation and exchange amongst increasingly mobile herding communities. However, recent research has shown that local environmental dynamics in the Lake Turkana basin – both during and after the AHP – were more complex than previously thought, necessitating re-evaluation of the notion that post-AHP life entailed new and/or heightened risks. Here, we explore risk buffering strategies (e.g. mobility, diversification, physical storage and/or exchange) as only one category of potential explanation for the new social practices observed in the region at this time. Gauging their applicability requires us to (a) assess the spatial mobility of communities and individuals interred at pillar sites; (b) evaluate whether and how mobility strategies may have changed as pastoralism supplanted fishing; and (c) examine alternative explanations for social and economic changes. [ABSTRACT FROM AUTHOR]

This paper explores the Holocene climatic dynamics of South Africa's southern Cape, a region that supports a large proportion of the Greater Cape Floristic Region and contains an array of important archaeological sites. While South African climates are generally characterised by marked rainfall seasonality, the southern Cape is currently situated at the interface between tropical and temperate climate systems, resulting in a largely aseasonal rainfall regime. This regime, however, is thought to have been particularly sensitive to past changes in late Quaternary boundary conditions, meaning that variability in either tropical or temperate systems could have significant environmental impacts. Evidence of past climate change, however, remains limited. We present a 9000-year record of hydroclimatic variability obtained from rock hyrax midden stable nitrogen records, from Papkuilsfontein, on the southern slope of the Anysberg Mountains. Resolved to an average 6-year resolution and spanning the period c. 9050 cal yr BP to 1990 CE, this is the highest resolution Holocene record from southern Africa and presents a unique opportunity for the detailed study of the primary drivers and spatial gradients of Holocene climate change in the southern Cape. The data indicate a long-term decrease in aridity across the Holocene and a pattern of variability that reveals remarkable similarities with records from the South African tropics and El Niño–Southern Oscillation proxies, highlighting the significance of tropical systems as drivers of Holocene climate change in the region. This substantially expands what has been previously considered to be the zone of tropical influence, extending from a coastal phenomenon associated with heat transport via the Agulhas Current to encompass much, if not all, of the Agulhas Plain south of the Cape Fold Mountains. These findings provide a valuable new climatic framework for contextualizing changes in ecological and archaeological records in the southern Cape, and contribute to a more comprehensive understanding of the spatio-temporal dynamics of climate systems in southern Africa. • Sub-decadal 9000-year record of aridity from South Africa's southern Cape. • Reveals dominance of tropical forcing across the southern Cape and Agulhas Plain. • ENSO variability indicated to be important driver of regional climate change. • Presents high-resolution framework for study of human-environment interactions. [ABSTRACT FROM AUTHOR]

Fossil pollen assemblages can assist in understanding biome responses to global climate change if there is reasonable probability that they represent specific biomes or bioregions. In this paper, we introduce a novel probabilistic presentation of pollen data and biome assignment. We apply a recently developed pollen-based vegetation classification method utilizing supervised machine learning to Southern Africa modern pollen assemblages. We present an updated modern pollen dataset from Southern Africa, linking the sites to previously defined vegetation units and, ultimately, we generate probabilistic classification for fossil assemblages to reconstruct past vegetation. The modern pollen dataset (N = 211 sites) represents a long vegetation gradient, from desert to forest biomes, capturing broad climate gradients ranging from arid to subtropical. We validate two models using Random Forest algorithm to classify modern vegetation at different spatial resolutions: subcontinental (biomes) and regional (bioregions). When the modern pollen assemblages (N = 164 sites) are used to predict the vegetation types, the classification models are correct in a number of cases. In our dataset of 164 sites, the classification model correctly classifies pollen assemblages from savanna (91% correct), grassland (87%), and coastal forest (82%) vegetation types, while the best results for classification of regional vegetation are achieved for sub-humid savanna (95%), dry savanna (95%), coastal forest (91%), and wet grassland (90%). We apply the models to a fossil pollen sequence at Wonderkrater in the South African savanna, to reconstruct subcontinental and regional changes in past vegetation states over the last 60 000 years. The most probable vegetation state dominating the region since the Late Pleistocene is sub-humid savanna yet grassland occurred at times associated with high vegetation variability. Within the record, the most frequent and amplified variability in the inferred vegetation states occurred during the transitional phase between the Late Pleistocene and the Holocene. The machine learning approach for reconstructing past vegetation, offers a more complex and nuanced view of past vegetation dynamics and has the potential to support quantitative proxy-based techniques for palaeoclimatic reconstructions. • Expanded modern pollen dataset for Southern Africa. • Probabilistic classification for fossil assemblages to reconstruct past vegetation. • Savanna-grassland dynamics reconstructed over the last 60 000 years at Wonderkrater. • Increased oscillations in probabilities of predicted biomes during Younger Dryas. [ABSTRACT FROM AUTHOR]

Abstract The spread of early herders across Africa is a pivotal event in prehistory, but the context of this event remains poorly understood due to a lack of paleoenvironmental data. We present new radiocarbon dates and multi-proxy Holocene paleoecological records for two distinct settings on the pathways through which livestock herding spread across eastern Africa: the Lake Turkana Basin, which has the earliest record of livestock in eastern Africa, and the Lake Victoria Basin, located farther south. Herbivore diet as inferred from tooth enamel carbon isotopes (n = 368), and pollen and leaf wax biomarker data, do not support a uniform ecological response to increased aridity at the end of the African Humid Period ∼5 kya, as had been previously thought. Rather, climate change had basin-specific ecological effects, and these in turn met differing human responses. Rather than extrapolating local ecological effects from regional climate records, archaeologists require basin-specific paleoecological data, deeply integrated with archaeological findings. This paper provides such integration for the first time in eastern Africa. Our results highlight the climatologically and ecologically distinctive areas around lake margins, necessitating future paleoenvironmental and archaeological research in inland areas. Highlights • Holocene climatic and environmental variability played a role in the southward spread of herders across Kenya and Africa. • Holocene climate change is well known, but ecological shifts associated with climatic changes are not. • We present a comprehensive paleoecological reconstruction of two lake basins that document herdering in eastern Africa. • We demonstrate that local rather than regional ecological mechanisms influenced early herder migrations in Africa. [ABSTRACT FROM AUTHOR]

The diverse lagoons and coastal lakes along the east coast of South Africa occupy incised valleys that were flooded during the rise and subsequent stabilisation of relative sea-level during the Holocene. Sedimentary deposits contained within these waterbodies provide an opportunity to investigate complex hydrological and sedimentological processes, and examine sea-level controls governing system geomorphic evolution. In this paper, we combine diatom and sulfur isotope analyses from two sediment cores extracted from the northern sub-basins of Lake St Lucia, a large shallow estuarine lake that is today largely isolated from direct ocean influence behind a Holocene-Pleistocene barrier complex. Analyses allow the reconstruction of hydrological changes associated with the geomorphic development of the system over the mid-to late Holocene. The sedimentary sequences indicate that St Lucia was a shallow, partially enclosed estuary/embayment dominated by strong tidal flows prior to ∼6200 cal. BP. Infilling was initiated when sea-level rise slowed and stabilised around present day levels, resulting in the accumulation of fine-grained sediment behind an emergent proto-barrier. Diatom assemblages, dominated by marine benthic and epiphytic species, reveal a system structured by marine water influx and characterised by marsh and tidal flat habitats until ∼4550 cal. BP. A shift in the biological community at ∼4550 cal. BP is linked to the development of a back-barrier water body that supported a brackish community. Marine planktonics and enrichments in δ 34 S suggest recurrent, large-scale barrier inundation events during this time, coincident with a mid-Holocene sea-level highstand. Periodic marine incursions associated with episodes of enhanced storminess and overwash remained prevalent until ∼1200 cal. BP, when further barrier construction ultimately isolated the northern basins from the ocean. This study provides the first reconstruction of the palaeohydrological environment at Lake St Lucia and highlights the long-term geomorphic controls that have shaped the recent evolution and natural dynamics of the system. Unlike most coastal lake systems, this system is particularly effective as an archive of geomorphological change. Systems driven by back-barrier modifications, such as Lake St Lucia, highlight how geomorphological changes driven by sediment-supply, climate and sea level can be distributed unevenly over several isolated back-barrier basins. [ABSTRACT FROM AUTHOR]

• Study at Luxmanda, Tanzania identified anthropogenic sediments dating to 3000 BP. • Anthropogenic sediment and ashy dung have ≥4-fold more nutrients than offsite samples. • Enriched sediments may have contributed to a more biodiverse and resilient ecosystem. In eastern Africa, ecologists have found that when mobile pastoralists abandon their temporary encampments, the accumulation of burned animal dung, wood, and other organic waste enriches the concentration of nutrients (e.g., calcium, phosphorous, magnesium) essential to soil health, in comparison to other soils without prior human habitation. These nutrient-enriched soils promote glade development and greater biodiversity. Geoarchaeological research on the time depth of this anthropogenic "nutrient hotspot" phenomenon has demonstrated that soils at several archaeological sites in southern Kenya still remain enriched in these soil macro- and micro- nutrients after several thousand years. However, soil scientists and geoarchaeologists do not yet understand how these anthropogenic soils vary over the extensive geographic conditions of eastern Africa. The discovery of a Pastoral Neolithic site (ca. 3000 BP) at Luxmanda on the Mbulu Plateau, Tanzania, provides an opportunity to examine if similar patterns of nutrient enrichment can be detected in a different geological and climatic zone. In this paper, we use geochemical and sedimentary analyses to determine how archaeological soils at Luxmanda differ from adjacent off-site soils and known archaeological soils in Kenya, as well as from computationally derived soil nutrient models for eastern Africa. Our results indicate that soils derived from anthropogenic sediments and ashy dung are 4 to 16-fold more abundant in soil macro nutrients relative to off-site or modeled values. This pattern fits previous studies' observations that elevated macro- and micro-nutrients in soils are strongly correlated with ancient pastoralist habitation sites. We conclude that anthropogenic soils found at Pastoral Neolithic archaeological sites may be a valuable, but unappreciated, soil resource in eastern Africa. [ABSTRACT FROM AUTHOR]

Dating population divergence within species from molecular data and relating such dating to climatic and biogeographic changes is not trivial. Yet it can help formulating evolutionary hypotheses regarding local adaptation and future responses to changing environments. Key issues include statistical selection of a demographic and historical scenario among a set of possible scenarios, and estimation of the parameter(s) of interest under the chosen scenario. Such inferences greatly benefit from (a) independent information on evolutionary rate and pattern at genetic markers; and (b) new statistical approaches, such as approximate Bayesian computation‐random forest (ABC‐RF), which provides reliable inference at a low computational cost and the possibility to measure prediction quality at the exact position of the observed data set. Here, we show full potential of the ABC‐RF approach including prior knowledge on microsatellite genetic markers to decipher the evolutionary history of the African arid‐adapted pest locust, Schistocerca gregaria, with support for a southern colonization of Africa, from a low number of founders of northern origin, dating back 2.6 Ky (90% CI: 0.9–6.6 Ky). We verify that this divergence time estimate accurately reflected true divergence time values by computing accuracy at a local posterior scale from simulated pseudo‐observed data sets. The inferred divergence history is better explained by the peculiar biology of S. gregaria, which involves a density‐dependent swarming phase with some exceptional spectacular migrations, rather than a continuous colonization resulting from the continental expansion of open vegetation habitats during more ancient Quaternary glacial climatic episodes. [ABSTRACT FROM AUTHOR]

Aim: Domestic animals first appeared in the archaeological record in northern Africa c. 9000 years before present and subsequently spread southwards throughout the continent. This geographic expansion is well studied and can broadly be explained in terms of the movement of pastoralist populations due to climate change. However, no studies have explicitly evaluated changes in the climatic niche of these domesticates. A priori, one cannot assume a relationship between the geographic spread of animal production and changes in climatic niche breadth because their relationship is highly variable. Therefore, we investigated Holocene changes in the climatic niche of domestic animals (animal production) and compared these to changes in the climatic niche of hunted terrestrial ungulates. Location: The African continent. Time period: 9000–500 BP. Major taxa studied: Domestic animals, hunted (wild) terrestrial ungulates. Methods: For the first time, we applied methods from environmental niche dynamics to archaeological data to reconstruct and quantify changes in the climatic niche breadth of animal production during the African Holocene. We used faunal remains from archaeological assemblages and associated radiocarbon dates to estimate the proportion of the African climate space used for animal production and hunting at 500‐year intervals. Results: We found that the climatic niche of domestic species broadened significantly with the geographic spread, most notably during the termination of the African Humid Period, whilst no such broadening occurred for the climatic niche of hunted species. Main conclusions: Our results provide a quantitative measure of the extent to which humans have constructed and adapted the climatic niche of animal production to manage their domestic animals across increasingly diverse ecological conditions. By incorporating ecological analysis into estimations of past land use, our methods have the potential to improve reconstructions of land use change, and to provide a foundation on which further niche construction hypotheses may be tested. [ABSTRACT FROM AUTHOR]

The Chew Bahir Drilling Project (CBDP) aims to test possible linkages between climate and evolution in Africa through the analysis of sediment cores that have recorded environmental changes in the Chew Bahir basin. In this statistical project we consider the Chew Bahir palaeolake to be a dynamical system consisting of interactions between its different components, such as the waterbody, the sediment beneath lake, and the organisms living within and around the lake. Recurrence is a common feature of such dynamical systems, with recurring patterns in the state of the system reflecting typical influences. Identifying and defining these influences contributes significantly to our understanding of the dynamics of the system. Different recurring changes in precipitation, evaporation, and wind speed in the Chew Bahir basin could result in similar (but not identical) conditions in the lake (e.g., depth and area of the lake, alkalinity and salinity of the lake water, species assemblages in the water body, and diagenesis in the sediments). Recurrence plots (RPs) are graphic displays of such recurring states within a system. Measures of complexity were subsequently introduced to complement the visual inspection of recurrence plots, and provide quantitative descriptions for use in recurrence quantification analysis (RQA). We present and discuss herein results from an RQA on the environmental record from six short (< 17 m) sediment cores collected during the CBDP, spanning the last 45 kyrs. The different types of variability and transitions in these records were classified to improve our understanding of the response of the biosphere to climate change, and especially the response of humans in the area. [ABSTRACT FROM AUTHOR]

Abstract: Recent integration of ecological niche models in phylogeographic studies is improving our understanding of the processes structuring genetic variation across landscapes. Previous studies on the amphibian Bufotes boulengeri boulengeri uncovered a surprisingly weak intraspecific differentiation across the Maghreb region. We widely sampled this species from Morocco to Egypt and sequenced one nuclear and three mitochondrial (mtDNA) genes to determine the level of genetic variability across its geographic range. We evaluated these data with ecological niche modeling to reveal its evolutionary history in response to climate change during the Quaternary. Our results highlight some mtDNA phylogeographic structure within this species, with one haplogroup endemic to coastal Morocco, and one haplogroup widely distributed throughout North Africa. No or little genetic differentiation is observed between isolated populations from the Hoggar Mountains, the Sabha district and the islands of Kerkennah and Lampedusa, compared to others populations. This can be explained by the expansion of the distribution range of B. b. boulengeri during glacial periods. This might have facilitated the species’ dispersal and subsequent gene flow between most North African localities. [ABSTRACT FROM AUTHOR]

Aim The aim of this study was to understand the origin of the forest flora currently found in the Dahomey Gap ( DG), a 200-km-wide forest-savanna mosaic separating the West African and Central African rain forest blocks. More specifically, using a widespread rain forest tree species, Distemonanthus benthamianus (Fabaceae), we will test the hypothesis that the DG populations are remnants of a population dating back from the African Humid Period of the Holocene, when West African and Central African rain forests were supposedly connected. Location Tropical forests of Upper Guinea (West Africa) and Lower Guinea (Atlantic Central Africa) and the forest-savanna mosaic of the DG extending from eastern Ghana to Benin. Methods Four hundred and twenty-nine D. benthamianus samples from West to Central Africa were genotyped with 11 nuclear microsatellite markers. After detecting geographically coherent gene pools, their genetic diversity and differentiation were estimated and their demographic histories were inferred using coalescent simulations and approximate Bayesian computation ( ABC) tests. Results Five parapatric gene pools were identified: three in Lower Guinea, one in Upper Guinea and one in the DG. ABC tests indicate that the DG gene pool probably originates from the admixture of adjacent Upper and Lower Guinean gene pools, with a higher contribution from Upper Guinea, at a timeframe consistent with the early Holocene (around 13-7 ka). The lower genetic diversity documented in the DG could result from a founder effect and/or from a demographic decline consistent with the Holocene climatic pejoration documented around 3 ka. Main conclusions This phylogeographical study inferring the history of the DG populations of D. benthamianus is consistent with palaeovegetation data that suggest that the forest flora of the DG might be essentially relicts of the early Holocene period when the Guineo-Congolian forest reached its maximum geographical distribution. [ABSTRACT FROM AUTHOR]