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Mediterranean forest communities are particularly diverse but at risk due to their sensitivity to global warming. Understanding the long-term vulnerability of Mediterranean vegetation to climate change is crucial for conservation and management purposes. Studies on past changes of forest communities in response to climate change at ecologically meaningful resolutions (i.e., decadal time scales) are therefore essential, but still very rare. The Holocene thermal maximum (HTM; ca. 10,000–5,000 ​cal ​years before the present (BP)) may be used to study species and community responses to warmer conditions than during recent decades. We performed high-resolution multiproxy palaeoecological analyses on sediments from crater Lake Mezzano in central Italy to reconstruct vegetation, diversity, and fire dynamics between 8,450 and 7,050 ​cal ​years BP. Ordination, cross-correlation, and species-response analyses were used to investigate the response of Mediterranean forest communities to HTM climate warming, human impact, and fire. Vegetational changes prior to 7,450 ​cal ​years BP were driven by climate. Fagus sylvatica spread into mixed deciduous oak forests during the Early Holocene in response to declining seasonality (cooler summers and warmer winters). Subsequently, Fagus sylvatica declined and evergreen Quercus ilex expanded after 8,200 ​cal ​years BP when the climate became warmer. Although reduced, Fagus sylvatica remained important together with deciduous oaks. The co-existence of Fagus sylvatica and evergreen Quercus forests is extremely rare today. Human impact significantly affected forest vegetation after 7,450 ​cal ​years BP, when Neolithic agricultural activities became important, ultimately extirpating these special communities but fostering the overall biodiversity. However, their past occurrence in several central Italian calderas during the HTM suggests that these environments provided habitats that permitted the thriving of cool-temperate forests of Fagus sylvatica under mesomediterranean conditions, with summers ca. 1–2 ​°C warmer than today. Cool and moist calderas may thus become increasingly important for maintaining Mediterranean mesophilous forest species under global warming conditions.

Pollen, spores, and microscopic charcoal from the sediments of Grosssee (1,619 m a.s.l.), a small lake in the lower subalpine vegetation zone of the Glarus Alps, Switzerland, were analysed to reconstruct vegetation patterns and land use over the past ca. 12,300 calibrated C-14 years bp (cal bp). Pollen data revealed an open landscape covered with grasses and herbs such as Artemisia during the Late Glacial Period. The catchment was likely initially afforested with Betula and Pinus cembra or Pinus sylvestris during the Early Holocene. Thermophilous taxa such as Ulmus, Tilia, and Alnus glutinosa-type expanded from ca. 11,000-9,200 cal bp, and mesophyllic Picea abies and Fagus sylvatica followed, and expanded beginning from ca. 8,000-7,600 cal bp. Interestingly, Alnus viridis (synonym: A. alnobetula) expanded about 2,000 years earlier than at comparable sites in the northern Swiss Alps. Its expansion was profound and persistent, and percentages > 15% were already achieved by ca. 7,000 cal bp. Local erosion events that followed are well explained by vegetation changes and inferred human land use activities at Grosssee. In particular, this led to a more open landscape, and land uses (e.g. grazing) intensified from the Mid- to Late Holocene. Indicators of environmental disturbance including persistently high levels of A. viridis, monolete fern spores, and microscopic charcoal were pronounced after ca. 4,000 cal bp. At that time, high influxes of spores from coprophilous fungi and the consistent presence of cultural indicators (Cerealia-type, Plantago lanceolata) indicate increased grazing and high levels of human impact. Land use and grazing activities seemed to have been particularly pronounced and to have promoted diversity in the vegetation over the past 1,000 years.

Analysis of environmental DNA (eDNA) through DNA metabarcoding has become an important technique for environmental science as it allows precise reconstructions of species communities in a fast, cheap and non-invasive way. In this study, we scrutinize how environmental reconstructions derived from metabarcoding data may be affected by a process in which sample specific labels (tags), added to sequences for identification of individual samples, are changed unintentionally during adapter ligation causing translocation of sequences between samples (‘tag jumping’). We compare animal and plant communities reconstructed using sedimentary eDNA records processed according two different protocols: (i) a twin-tagging approach (control) where all amplicons received the same tag on both sides (N = 102); and (ii) a combinatorial tagging protocol (affected by tag jumps) where each amplicon received a unique combination, but where some tags on each side were reused to form new combinations (N = 102). We analyzed six different sediment matrices and observed higher average number of taxa in the combinatorial tagging dataset in comparison to our twin-tagged dataset serving as a reference for results unaffected by tag jumps. In the control dataset with twin tagged amplicons, reconstructed animal communities were statistically different in 14 out of 15 pairwise comparisons, while only 8 out of 15 of the comparisons were different when samples were analyzed using the combinatorial tagging protocol. All of the inferred plant communities were statistically different when analyzed with a twin-tagging approach, while 20% of these plant communities were not different in our combinatorial tagged dataset. Our results clearly show that tag jumps added species to samples where they were not originally present and affects interpretations of species diversity and time-trends for whole communities. We conclude that tag jumping, being rarely discussed in metabarcoding studies, constitutes a concern in parity with direct sample contamination.

Although rare, temporally and taxonomically highly-resolved palaeoecological studies with high chronological precision are essential to perform detailed comparisons with precisely dated independent evidence such as archaeological findings, historical events, or palaeoclimatic data. Using a new highly-resolved and chronologically precise sedimentary record from Lago di Mezzano (central Italy), we reconstruct decadal-scale vegetation, species diversity, and fire dynamics, aiming to better understand the linkages between climate, land use, fire, and plant communities from the Neolithic to the Copper Age (c. 5100–3100 cal. BC). Closed, mixed beech-oak forests, including evergreen Quercus ilex, dominated the landscape around Lago di Mezzano during the Neolithic and were disturbed by repeated opening phases, with important implications for lake biogeochemistry and mixing regimes. This was in conjunction with increasing fire activity to promote agro-pastoral practices, as inferred from increasing charcoal, Cerealia type, Triticum type, Hordeum type, Plantago lanceolata type, and Urtica pollen. Fires, on their turn, augmented species diversity (richness and evenness). The comparison of the Mediterranean record from Lago di Mezzano with available continuous and high-precision submediterranean and cool-temperate palynological sequences suggests comparable land use pulses across Southern and Central European regions, most likely in connection with climate change. The outcomes of this study are not only of palaeoecological and archaeological interest; they may also help to improve projections of ecosystem dynamics under future global change.

Reconstructing hydrological variability is critical for understanding Lake Victoria's ecosystem history, the evolution of its diverse endemic fish community, the dynamics of vegetation in the catchment, and the dispersal of aquatic and terrestrial fauna in the East African Rift system during Latest Pleistocene and Holocene times. Whereas consensus exists on widespread desiccation of Lake Victoria ∼18 – 17 ka, the re-filling history (16 – 13 ka) has remained highly controversial. Here, we present data from four new sediment cores along a depth transect. We use lithostratigraphic core correlation, sediment facies, XRF data, wetland vegetation analysis (Typha pollen), and ¹⁴C chronologies of unprecedented precision to document Latest Pleistocene lake-level variability. At our coring site in the central basin, local Typha wetlands existed >16.7 ka, alternating with periods of desiccation. Moisture increased slightly between ca. 16.7 – 14.5 ka and wetlands with permanent, shallow ponds established simultaneously in the center and the marginal, more elevated parts of the flat lake basin. After ca. 14.0 ka, lake levels increased; wetlands in the central basin were submerged and replaced by lacustrine environments and a >50 m deep lake established ca. 13.5 ka, likely with intermittent overflow most of the time. The lake reached modern or even above-modern levels around 10.8 ka. This lake-level history is consistent with regional terrestrial paleoenvironmental reconstructions, notably the expansion of Afromontane and rainforest. Our data suggest a complex picture of paleoclimatic conditions in Eastern Africa and teleconnections to the North-Atlantic and Indian Ocean domains.

The Lake Victoria ecosystem is emblematic of the catastrophic effects that human activities, particularly cultural eutrophication, can have on freshwater biodiversity. However, little is known about the long-term spatial and temporal pattern of aquatic primary paleo-production (PPaq) and producer communities in Lake Victoria and how these patterns relate to past climate variability, landscape evolution, lake hydrology, mixing regimes, nutrient cycling, and biodiversity dynamics in the past 17 kyr. We use sediments from four well-dated cores along a transect from offshore to nearshore sites, and exploit XRF element scanning and hyperspectral imaging data, TC, TN, bSi, δ13C and δ15N, and sedimentary pigments to investigate paleolimnological variability and change. Our findings demonstrate that changes in PPaq and algal communities during the past 17 kyr were closely related to hydroclimatic changes, lake mixing, and nutrient availability. During the wetland phase (16.7–14.5 cal ka BP), PPaq levels remained generally low, while chromophytes and chlorophytes dominated the algal community. Following the rapid lake level rise (∼14.2 cal ka BP) during the early African Humid Period (AHP), PPaq levels steadily increased, accompanied by a shift towards cyanobacteria and chromophytes. During the Holocene, our results suggest repeated short-lived arid intervals (∼10.5, ∼9, 7.8–7.2, ∼4, and 3.2–3.0 cal ka BP) and two distinct periods of enhanced lake mixing associated with high PPaq and high diatom productivity: the first one between 11 and 9 cal ka BP, which coincided with the maximum of the AHP (high precipitation, high wind, enhanced mixing), and the second, less pronounced one, between 7 and 4 cal ka BP. Between these two periods (i.e. 9–7 cal ka BP) we observe reduced diatom productivity, relatively low PPaq, and high C/N ratios, suggesting conditions with more stable lake stratification, likely associated with reduced wind strength, and some nutrient limitation (N and P). Finally, the drier conditions around the end of the AHP (ca. 4 cal ka BP) and during the late Holocene were associated with decreasing lake mixing and increasing dominance of cyanobacteria. Given our reconstruction of PPaq over the past 17 kyr, we conclude that the levels in the 20th century are unprecedentedly high, consistent with the massive human-mediated impact on the Lake Victoria ecosystem including biodiversity loss.

Ferruginous conditions prevailed in the oceans through much of Earth's history. However, minerals recording these conditions remain difficult to interpret in terms of biogeochemical processes prior to lithification. In Lake Towuti, Indonesia, ferruginous sediments are deposited under anoxic sulfate-poor conditions similar to the Proterozoic oceans, allowing the study of mineralogical (trans)formations during microbial diagenesis.

Comprehensive pore water geochemistry, high resolution geochemical core profiles, and electron microscopy of authigenic minerals revealed in situ formation of magnetite, millerite, and abundant siderite and vivianite along a 100 m long sequence. Framboidal magnetites represent primary pelagic precipitates, whereas millerite, a sulfide mineral often overlooked under sulfate-poor conditions, shows acicular aggregates entangled with siderite and vivianite resulting from saturated pore waters and continuous growth during burial. These phases act as biosignatures of microbial iron and sulfate reduction, fermentation and methanogenesis, processes clearly traceable in pore water profiles.

Variability in metal and organic substrates attests to environment driven processes, differentially sustaining microbial processes along the stratigraphy. Geochemical profiles resulting from microbial activity over 200 kyr after deposition provide constraints on the depth and age of mineral formation within ferruginous records.

Analysis of environmental DNA detected in lake sediments shows promise to become a great paleoecological technique that can provide detailed information about organism communities living in past environments. However, when interpreting sedimentary environmental DNA records, it is of crucial importance to separate ecosystem responses to large-scale environmental change from “noise” caused by changes in sediment provenance or potential post-depositional DNA mobility. In this study, we show that plant and mammalian communities reconstructed from sediments are strongly affected by sediment provenance, but unaffected by vertical mobility of DNA after sediment deposition. We observe that DNA from aquatic plants was abundant in background sediment, while embedded detrital event layers (sediment deposited under erosion events) primarily contained terrestrial plants; hence, vertical mobility of aquatic plant DNA across sediment layers was negligible within our studied lakes. About 33% of the identified terrestrial plant genera were only found in detrital sediment, suggesting that sediment origin had a strong impact on the reconstructed plant community. Similarly, DNA of some mammalian taxa (Capra hircus, Ursus arctos, Lepus, and Felis) were only or preferentially found in detrital event layers. Temporal changes across the Holocene were the main drivers of change for reconstructed plant communities, but sediment type was the second most important factor of variance. Our results highlight that erosion and sediment provenance need to be considered when reconstructing past mammalian and plant communities using environmental DNA from lake sediments.

Metabarcoding of environmental DNA constitutes a state-of-the-art tool for environmental studies. One fundamental principle implicit in most metabarcoding studies is that individual sample amplicons can still be identified after being pooled with others—based on their unique combinations of tags—during the so-called demultiplexing step that follows sequencing. Nevertheless, it has been recognized that tags can sometimes be changed (i.e., tag jumping), which ultimately leads to sample crosstalk. Here, using four DNA metabarcoding data sets derived from the analysis of soils and sediments, we show that tag jumping follows very specific and systematic patterns. Specifically, we find a strong correlation between the number of reads in blank samples and their topological position in the tag matrix (described by vertical and horizontal vectors). This observed spatial pattern of artefactual sequences could be explained by polymerase activity, which leads to the exchange of the 3′ tag of single stranded tagged sequences through the formation of heteroduplexes with mixed barcodes. Importantly, tag jumping substantially distorted our data sets—despite our use of methods suggested to minimize this error. We developed a topological model to estimate the noise based on the counts in our blanks, which suggested that 40%–80% of the taxa in our soil and sedimentary samples were likely false positives introduced through tag jumping. We highlight that the amount of false positive detections caused by tag jumping strongly biased our community analyses.