Detection of DNA in lake sediments holds promise as a tool to study processes like extinction, colonization, adaptation and evolutionary divergence. However, low concentrations make sediment DNA difficult to detect, leading to high false negative rates. Additionally, contamination could potentially lead to high false positive rates. Careful laboratory procedures can reduce false positive and negative rates, but should not be assumed to completely eliminate them. Therefore, methods are needed that identify potential false positive and negative results, and use this information to judge the plausibility of different interpretations of DNA data from natural archives. We developed a Bayesian algorithm to infer the colonization history of a species using records of DNA from lake‐sediment cores, explicitly labelling some observations as false positive or false negative. We illustrate the method by analysing DNA of whitefish (Coregonus lavaretus L.) from sediment cores covering the past 10,000 years from two central Swedish lakes. We provide the algorithm as an R‐script, and the data from this study as example input files. In one lake, Stora Lögdasjön, where connectivity with the proto‐Baltic Sea and the degree of whitefish ecotype differentiation suggested colonization immediately after deglaciation, DNA was indeed successfully recovered and amplified throughout the post‐glacial sediment. For this lake, we found no loss of detection probability over time, but a high false negative rate. In the other lake, Hotagen, where connectivity and ecotype differentiation suggested colonization long after deglaciation, DNA was amplified only in the upper part of the sediment, and colonization was estimated at 2,200 bp based on the assumption that successful amplicons represent whitefish presence. Here the earliest amplification represents a false positive with a posterior probability of 41%, which increases the uncertainty in the estimated time of colonization. Complementing careful laboratory procedures aimed at preventing contamination, our method estimates contamination rates from the data. By combining these results with estimates of false negative rates, our models facilitate unbiased interpretation of data from natural DNA archives.

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Monitoring of surface waters in the boreal region over the last decades shows that waters are becoming browner. This timeframe may not, however, be sufficient to capture underlying trajectories and driving mechanisms of lake-water quality, important for prediction of future trajectories. Here we synthesize data from seven lakes in the Swedish boreal landscape, with contemporary lake-water total organic carbon (TOC) concentrations of 1.4-14.4 mg L −1 , to conceptualize how natural and particularly human-driven processes at the landscape scale have regulated lake-water TOC levels over the Holocene. Sediment-inferred trends in TOC are supported by several proxies, including diatom-inferred pH. Before $ 700 CE, all lakes were naturally acidic (pH 4.7-5.4) and the concentrations of inferred lake-water TOC were high (10-23 mg L −1 ). The introduction of traditional human land use from $ 700 CE led to a decrease in lake-water TOC in all lakes (to 5-14 mg L −1 ), and in four poorly buffered lakes, also to an increase in pH by > 1 unit. During the 20 th century, industrial acid deposition was superimposed on centuries of land use, which resulted in unprecedentedly low lake-water TOC in all lakes (3-11 mg L −1 ) and severely reduced pH in the four poorly buffered lakes. The other lakes resisted pH changes, likely due to close connections to peatlands. Our results indicate that an important part of the recent browning of boreal lakes is a recovery from human impacts. Furthermore, on a conceptual level we stress that contemporary environmental changes occur within the context of past, long-term disturbances.

The history of mining and smelting and the associated pollution have been documented using lake sediments for decades, but the broader ecological implications are not well studied. We analyzed sediment profiles covering the past ~10,000 years from three lakes associated with an iron blast furnace in central Sweden, as an example of the many small-scale furnaces with historical roots in the medieval period. With a focus on long-term lake-water quality, we analyzed multiple proxies including geochemistry, pollen and charcoal, diatom composition and inferred pH, biogenic silica (bSi), visible near-infrared spectroscopy (VNIRS)-inferred lake-water total organic carbon (LW-TOC), and VNIRS-inferred sediment chlorophyll (sed-Chl). All three lakes had stable conditions during the middle Holocene (~5000 BCE to 1110 CE) typical of oligo-dystrophic lakes: pH 5.4–5.6, LW-TOC 15–18 mg L−1. The most important diatom taxa include, for example, Aulacoseira scalaris, Brachysira neoexilis, and Frustulia saxonica. From ~1150 CE, decreases in LW-TOC, bSi, and sed-Chl in all three lakes coincide with a suite of proxies indicating disturbance associated with local, small-scale agriculture, and the more widespread use of the landscape in the past (e.g. forest grazing, charcoal production). Most important was a decline in LW-TOC by 30–50% in the three lakes prior to the 20th century. In addition, the one lake (Fickeln) downstream of the smelter and main areas of cultivation experienced a shift in diatom composition (mainly increasing Asterionella formosa) and a 0.6 pH increase coinciding with increasing cereal pollen and signs of blast furnace activity. The pH did not change in the other two lakes in response to disturbance; however, these lakes show a slight increase (0.3–0.5 pH units) because of modern liming. LW-TOC has returned to background levels in the downstream lake and remains lower in the other two.