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Hyperspectral imaging (HSI) in situ core scanning has emerged as a valuable and novel tool for rapid and non-destructive biogeochemical analysis of lake sediment cores. Variations in sediment composition can be assessed directly from fresh sediment surfaces at ultra-high-resolution (40–300 μm measurement resolution) based on spectral profiles of light reflected from sediments in visible, near infrared, and short-wave infrared wavelengths (400–2500 nm). Here, we review recent methodological developments in this new and growing field of research, as well as applications of this technique for paleoclimate and paleoenvironmental studies. Hyperspectral imaging of sediment cores has been demonstrated to effectively track variations in sedimentary pigments, organic matter, grain size, minerogenic components, and other sedimentary features. These biogeochemical variables record information about past climatic conditions, paleoproductivity, past hypolimnetic anoxia, aeolian input, volcanic eruptions, earthquake and flood frequencies, and other variables of environmental relevance. HSI has been applied to study seasonal and inter-annual environmental variability as recorded in individual varves (annually laminated sediments) or to study sedimentary records covering long glacial–interglacial time-scales (>10,000 years).

Historical records of trace elements in lake sediments provide source-to-sink information about potentially toxic pollutants across space and time. We investigated two lakes located at different elevations in the Ecuadorian Andes to understand how trace element fluxes are related to (i) geology, (ii) erosion in the watersheds, and (iii) local point sources and atmospheric loads. In remote Lake Fondococha (4150 m a.s.l.), total Hg fluxes stay constant between ca. 1760 and 1950 and show an approximately 4.4-fold increase between pre-1950 and post-1950 values. The post-1950 increase in fluxes of other trace elements (V, Cr, Co, Ni, Cu, Zn, As, Cd, and Pb) is lower (2.1–3.0-fold) than for Hg. Mostly lithogenic sources and enhanced soil erosion contribute to their post-1950 increase (lithogenic contribution: > 85%, Hg: ~ 58%). Average post-1950 Hg fluxes are approximately 4.3 times higher in peri-urban Lake Llaviucu (3150 m a.s.l.) than in the remote Lake Fondococha. Post-1950 fluxes of the other trace elements showed larger differences between Lakes Fondococha and Llaviucu (5.2 < 25–29.5-fold increase; Ni < Pb–Cd). The comparison of the post-1950 average trace element fluxes that are derived from point and airborne sources revealed 5–687 (Hg–Pb) times higher values in Lake Llaviucu than in Lake Fondococha suggesting that Lake Llaviucu’s proximity to the city of Cuenca strongly influences its deposition record (industrial emissions, traffic, caged fishery). Both lakes responded with temporary drops in trace element accumulations to park regulations in the 1970s and 1990s, but show again increasing trends in recent times, most likely caused by increase in vehicular traffic and openings of copper and gold mines around Cajas National Park.

&lt;p&gt;Lake Victoria (LV), Africa&amp;#8217;s largest lake is situated in the African Great Rift Valley. Due to its shallowness (max.68 m; mean 40 m) and limited river inflow, LV is very sensitive to variations in climate and lake level fluctuations. As a result, LV has undergone repeated low stand periods, or even complete desiccation during the Late Pleistocene with profound effects on the aquatic ecosystem. One example is the emergence of a unique biodiversity of endemic cichlid species following the lake&amp;#8217;s last desiccation event during the last glacial and subsequent refilling commencing ~15,000 years ago.&lt;/p&gt;&lt;p&gt;In an interdisciplinary project we aim at reconstructing linkages between paleoenvironmental variability, disturbances and adaptive species radiation by combining approaches from paleogenomics, paleoecology and paleolimnology. For this purpose, four sediment cores along a depth-transect (near-shore to offshore), covering ca. the past 14,000 years, are analyzed.&lt;/p&gt;&lt;p&gt;We present first paleolimnological results of long-term changes of using (isotope-)geochemical indicators including: Sedimentary pigments and biogenic silica to infer aquatic productivity supported by micro X-ray Fluorescence (XRF) derived element geochemistry, &lt;sup&gt;13&lt;/sup&gt;C and &lt;sup&gt;15&lt;/sup&gt;N, and sedimentary phosphorus fraction analyses providing information on changes in sediment composition.&lt;/p&gt;&lt;p&gt;The results suggest that the infilling of the LV basin was a long-term step-wise process. This is shown by elevated and variable indicators for lithogenic input (e.g Ti, Zr and K) and interpreted as mobilization of substrate from the shorelines by a dynamic lake level prior to its stabilization in the Early and Mid-Holocene. &amp;#160;This process is mainly reflected in the core taken at the greatest water depth (65 m). Simultaneously, the aquatic productivity (BSi and chloropigments) increased rapidly after the refilling of the lake basin in the Late-Glacial. A gradual drying of the climate and a following shift to a more oxygenated water column is observed in the Mid-to Late Holocene indicated by a decline in chemically weathered material (e.g Rb/K &amp; K/Al ratios) and abundance of Mn.&lt;/p&gt;

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&lt;p&gt;Lake Victoria is the largest tropical lake on the planet. Located in East Africa at an altitude of 1135 m asl, it lies across the limits between two major climatic zones with a temperature and moisture gradient and associated tropical biomes, the rain forest, and the savanna. At higher altitudes &gt; 1200&amp;#8211;2500 m a.s.l. temperatures are significantly lower and vegetation forms an Afromontane belt. Primarily triggered by climate shifts, these three biomes and fire regimes have been dynamically interspersing over the last 17,000 years.&lt;/p&gt;&lt;p&gt;Here, we present a robust &lt;sup&gt;14&lt;/sup&gt;C chronology mainly based on macroscopic charcoal using the MICADAS system of LARA at the University of Bern, new palynological data used as biostratigraphic control, and the first continuous charcoal record in Lake Victoria to establish the fire history.&lt;/p&gt;&lt;p&gt;Our pollen and macro&amp;#8211;charcoal records, support the assumption that throughout time regional fire dynamics are controlled by biome&amp;#8217;s changes, and that climate was the main driver of these vegetation shifts at least until the Iron Age. Our results indicate that during the Last Glacial Maxima and Heinrich Stadial 1, under dry and colder climates the savanna was dominating, with low fire regimes before 15,000 cal yr BP and increased fire occurrence between 15,000 and 14,000 cal yr BP. After this period, the Afromontane forest started to expand, and warmer and humid climates promoted the growth of rain forests and reduced fire events, which is particularly observed in the African Humid Period (between ca. 11,500 and 5000 cal yr BP). Subsequently, our records indicate a global maximum of fire occurrence at 5000 cal yr BP, followed by unexpectedly low fire regimes during the Iron Age and the subsequent periods.&lt;/p&gt;&lt;p&gt;This work is part of a SINERGIA project funded by the Swiss National Foundation which seeks to unravel the long-term causes and consequences of Lake Victoria&amp;#8217;s ecosystem dynamics with a special focus on the evolution of fish species and other biotas from the late Pleistocene to the present.&lt;/p&gt;

&lt;p&gt;The East African (hydro-)climate response to perturbations during the deglacial transition (e.g. Older and Younger Dryas) is complex and expressed heterogeneously in different paleoclimatic records. Lake Victoria (LV), Africa&amp;#8217;s largest lake, desiccated entirely during the dry last glacial (&gt;16.3 kyr BP) and subsequently refilled as climate conditions got more humid, reaching a highstand during the Early Holocene. However, existing sediment records from LV do not have sufficient resolution to fully resolve short-term hydroclimate changes during the deglacial transition (especially between 14 and 11 kyr BP). There is little direct evidence of late-glacial lake level fluctuations in LV so far because intermediate water depth coring sites suitable to record intermittent lowstands are missing.&lt;/p&gt;&lt;p&gt;By analysing sediment cores along a near-shore/shallow water (current water depth 22 m) to offshore/deep water (current water depth 63 m) coring transect covering the past 16,000 years, we aim at a more accurate spatial and temporal reconstruction of LV&amp;#8217;s deglacial lake level history in response to regional hydroclimate changes.&lt;/p&gt;&lt;p&gt;Core stratigraphy and geochemical evidence, combined with a robust radiocarbon chronology, demonstrate a stepwise infilling of the Lake Victoria basin after its last complete desiccation (&lt; 16.3 kyr BP). Following the dry late glacial Heinrich 1 event, an intermediate water level prevailed between 16.3 and 14.4 kyr BP, with uninterrupted deposition of fine-grained, organic matter-rich pelagic muds at our deep-water site and coarser, sandy-clay deposits at the near shore site. A second dry episode during the Older Dryas (~14 kyr BP) is marked by an abrupt decline in lake level with deposition of coarse mollusc shell bearing sediments at the near shore site indicating a littoral depositional environment. This shift in hydroclimate in the Lake Victoria basin is congruent with a brief period of cooling and drying during the B&amp;#246;lling/Aller&amp;#246;d (Dansgard Oeschger Event 1), which is also recorded in other East African Lakes. Subsequently, Lake Victoria reached maximum water levels with the onset of the African Humid Period in the early Holocene at around 11 kyr BP, which is expressed by elevated input of chemically weathered material (e.g. Rb/K) and deposition of fine-grained muds at both the near shore and offshore sites.&lt;/p&gt;