Determination of the number of zones in a biostratigraphical sequence

Pollen identification through convolutional neural networks: First application on a full fossil pollen sequence

The automation of pollen identification has seen vast improvements in the past years, with Convolutional Neural Networks coming out as the preferred tool to train models. Still, only a small portion of works published on the matter address the identification of fossil pollen. Fossil pollen is commonly extracted from organic sediment cores and are used by paleoecologists to reconstruct past environments, flora, vegetation, and their evolution through time. The automation of fossil pollen identification would allow paleoecologists to save both time and money while reducing bias and uncertainty. However, Convolutional Neural Networks require a large amount of data for training and databases of fossilized pollen are rare and often incomplete. Since machine learning models are usually trained using labelled fresh pollen associated with many different species, there exists a gap between the training data and target data. We propose a method for a large-scale fossil pollen identification workflow. Our proposed method employs an accelerated fossil pollen extraction protocol and Convolutional Neural Networks trained on the labelled fresh pollen of the species most commonly found in Northeastern American organic sediments. We first test our model on fresh pollen and then on a full fossil pollen sequence totalling 196,526 images. Our model achieved an average per class accuracy of 91.2% when tested against fresh pollen. However, we find that our model does not perform as well when tested on fossil data. While our model is overconfident in its predictions, the general abundance patterns remain consistent with the traditional palynologist IDs. Although not yet capable of accurately classifying a whole fossil pollen sequence, our model serves as a proof of concept towards creating a full large-scale identification workflow.

Impacts of climate warming and atmospheric deposition on recent shifts in chironomid communities in two alpine lakes, eastern China

Climate warming and atmospheric deposition are altering alpine lake ecosystems at unprecedented rates, whereas their direct and indirect effects on primary consumer communities are unclear. This study presents sedimentary multi-proxy records including chironomids, diatoms, elements and stable isotopes of carbon and nitrogen in 210Pb-dated cores from two alpine lakes located above the timberline in the Taibai Mountain, eastern China. Before ∼2000 CE, chironomid communities were co-dominated by Heterotrissocladius marcidus-type and Micropsectra atrofasciata-type in the two lakes. Thereafter, Tanytarsus glabrescens-type increased rapidly to be a dominant species. Redundancy analyses (RDAs) revealed that chironomid fauna shifts were significantly correlated with rising diatom concentrations in both lakes, declining Ti content in the upstream lake and δ13C depletion in the downstream lake. Although temperature, precipitation and δ15N were not significant explanatory variables in RDAs, climate warming and atmospheric deposition likely promoted terrestrial and aquatic primary production, indicated by synchronous increases in organic matter contents and diatom concentrations in the two sediment cores. Since diatoms contain essential polyunsaturated fatty acids that are essential for chironomids, rising diatom concentrations can promote food quantity and quality. In addition, increased primary production would create organic substrates for chironomid larvae. Recent shifts in chironomid fauna driven by indirect effects of global warming and atmospheric deposition might be a widespread phenomenon in alpine lakes, probably triggering regime shifts in headwater lake ecosystems.

Characterization of driving factors for the long-term succession of bloom-forming cyanobacterial genera in Lake Erhai, southwest China

Cyanobacterial blooms pose a global environmental concern, with various genera contributing to their formation. The harmfulness of cyanobacterial blooms varies depending on the specific genus, yet the factors triggering their formation remain incompletely understood. This study conducted qPCR of sediment DNA in Lake Erhai to reconstruct the historical succession of three common bloom-forming cyanobacterial genera (i.e., Microcystis, Dolichospermum, and Aphanizomenon). The driving factors and their corresponding thresholds were identified, and human activities related to driving factors were evaluated. The results revealed two successions in the past century. The first succession transitioned from Aphanizomenon (1902-1978) to Microcystis and Dolichospermum (1978-1999), driven by TN:TP and TP. The second succession shifted from Microcystis and Dolichospermum (1978-1999) to Microcystis (1999-2010), driven by TP, TN:TP, and temperature. The thresholds of TP and TN:TP for the Microcystis bloom were 0.023 mg/L and 17, respectively. TN:TP was significantly influenced by domestic pollution and crop farming in both successions, while TP was significantly impacted by domestic pollution in the first succession and by pollution from crop and dairy farming in the second succession. These results shed light on the underlying mechanism responsible for the blooms of various cyanobacterial genera and could serve as a valuable reference for effectively preventing and controlling nutrient input in the watershed.

Anthropogenic activities altering the ecosystem in Lake Yamzhog Yumco, southern Qinghai-Tibetan Plateau

Lakes on the Qinghai-Tibet Plateau (QTP) have been subject to multiple environmental pressures from rapid climate change and intensified human activity in recent decades. However, their ecological effects on the lake ecosystem remain largely unclear due to the lack of long-term monitoring data. This study presented the environmental and ecological changes of the lake Yamzhog Yumco (Southern QTP) over the past three decades based on multi-proxy analysis (geochemistry and sedaDNA) on a high-time resolution sediment core. The result showed that the lake exhibited a continuous eutrophication process from 2004 CE, which has accelerated since 2014 CE. The nutrient enrichment was mainly attributed to anthropogenic emissions from the catchment. The sedimentary ancient DNA (sedaDNA) metabarcoding data registered a sensitive response of aquatic communities to the additional nutrient supply. Eukaryotic algae and aquatic invertebrate communities exhibited similar temporal dynamics, characterized by the increase in eutrophic taxa and the decrease in oligotrophic taxa. Change points analysis suggested that lake ecosystems underwent a slight ecological shift in 2003 CE and an abrupt shift in 2012 CE driven by nutrient enrichment. Quantitative analysis revealed that nutrients and human activity accounted for 27.9 % and 21.7 % of the temporal variation in aquatic communities, whereas climate change only explained 6.9 % of the total variation. From a paleolimnological view, our study supported that regional human activity could distinctly alter the nutrient level and aquatic community structure of lake ecosystems in the QTP. Considering that anthropogenic disturbance will continuously increase, it is crucial to strengthen the field monitoring of the lakes on the plateau and make effective management measures to avoid irreversible ecological consequences.

Mercury deposition and redox transformation processes in peatland constrained by mercury stable isotopes

Peatland vegetation takes up mercury (Hg) from the atmosphere, typically contributing to net production and export of neurotoxic methyl-Hg to downstream ecosystems. Chemical reduction processes can slow down methyl-Hg production by releasing Hg from peat back to the atmosphere. The extent of these processes remains, however, unclear. Here we present results from a comprehensive study covering concentrations and isotopic signatures of Hg in an open boreal peatland system to identify post-depositional Hg redox transformation processes. Isotope mass balances suggest photoreduction of HgII is the predominant process by which 30% of annually deposited Hg is emitted back to the atmosphere. Isotopic analyses indicate that above the water table, dark abiotic oxidation decreases peat soil gaseous Hg0 concentrations. Below the water table, supersaturation of gaseous Hg is likely created more by direct photoreduction of rainfall rather than by reduction and release of Hg from the peat soil. Identification and quantification of these light-driven and dark redox processes advance our understanding of the fate of Hg in peatlands, including the potential for mobilization and methylation of HgII.

A Continuous Centennial Late Glacial-Early Holocene (15-10 cal kyr BP) Palynological Record from the Iberian Pyrenees and Regional Comparisons

This paper presents the first continuous (gap-free) Late Glacial-Early Holocene (LGEH) pollen record for the Iberian Pyrenees resolved at centennial resolution. The main aims are (i) to provide a standard chronostratigraphic correlation framework, (ii) to unravel the relationships between vegetation shifts, climatic changes and fire, and (iii) to obtain a regional picture of LGEH vegetation for the Pyrenees and the surrounding lowlands. Seven pollen assemblage zones were obtained and correlated with the stadial/interstadial phases of the Greenland ice cores that serve as a global reference. Several well-dated datums were also derived for keystone individual taxa that are useful for correlation purposes. Four vegetation types were identified, two of them corresponding to conifer and deciduous forests (Cf, Df) and two representing open vegetation types (O1, O2) with no modern analogs, dominated by Artemisia-Poaceae and Saxifraga-Cichorioideae, respectively. Forests dominated during interstadial phases (Bølling/Allerød and Early Holocene), whereas O1 dominated during stadials (Oldest Dryas and Younger Dryas), with O2 being important only in the first half of the Younger Dryas. The use of pollen-independent proxies for temperature and moisture allowed the reconstruction of paleoclimatic trends and the responses of the four vegetation types defined. The most relevant observation in this sense was the finding of wet climates during the Younger Dryas, which challenges the traditional view of arid conditions for this phase on the basis of former pollen records. Fire incidence was low until the Early Holocene, when regional fires were exacerbated, probably due to the combination of higher temperatures and forest biomass accumulation. These results are compared with the pollen records available for the whole Pyrenean range and the surrounding lowlands within the framework of elevational, climatic and biogeographical gradients. Some potential future developments are suggested on the basis of the obtained results, with an emphasis on the reconsideration of the LGEH spatiotemporal moisture patterns and the comparison of the Pyrenees with other European ranges from different climatic and biogeographical regions.

Diatom responses to warming, heavy rains and human impact in a Mediterranean lake since the preindustrial period

In the Mediterranean region, annual mean air temperature will continue to increase during the 21st century, while seasonal precipitation is expected to decrease and extreme events to be more frequent. Human-induced climate change will severely impact aquatic ecosystems. A subdecadal stratigraphic diatom record of Lake Montcortès (central Pyrenees) was investigated, focusing on the potential responses of diatoms to anthropogenic warming and catchment alteration. The study includes the end of the Little Ice Age (LIA), the transition to the industrial and postindustrial eras, and the recent global warming and its current acceleration. Sediment samples were treated and diatoms taxonomically identified. Relationships between diatom taxa abundances and climatic (temperature and precipitation) and environmental (land use, soil erosion, and eutrophication) variables were investigated using multivariate statistical methods. The results indicate that, from ca. 1716 to 1971 CE, the diatom community was dominated by Cyclotella cyclopuncta and showed small perturbations, despite the pressure of important stressors such as strong cooling episodes, droughts and an intense use of the lake for hemp retting during the 18th and 19th centuries. However, during the 20th century, other centric species gained relevance, and from the 1970s on, Cyclotella ocellata competed with C. cyclopuncta for dominance. These changes coincided with pulse-like disturbances in the form of extreme rainfall events along with the gradual 20th century increase in global temperature. These perturbations affected the planktonic diatom community and led to instability dynamics. The benthic diatom community did not reflect any comparable shifts under the effect of the same climatic and environmental variables. Because heavy rainfall episodes are likely to intensify with current climate change in the Mediterranean region, their importance as stressors of planktonic primary producers should be taken into account as potential disrupters of biogeochemical cycles and trophic networks of lakes and ponds.

High resolution ancient sedimentary DNA shows that alpine plant diversity is associated with human land use and climate change

The European Alps are highly rich in species, but their future may be threatened by ongoing changes in human land use and climate. Here, we reconstructed vegetation, temperature, human impact and livestock over the past ~12,000 years from Lake Sulsseewli, based on sedimentary ancient plant and mammal DNA, pollen, spores, chironomids, and microcharcoal. We assembled a highly-complete local DNA reference library (PhyloAlps, 3923 plant taxa), and used this to obtain an exceptionally rich sedaDNA record of 366 plant taxa. Vegetation mainly responded to climate during the early Holocene, while human activity had an additional influence on vegetation from 6 ka onwards. Land-use shifted from episodic grazing during the Neolithic and Bronze Age to agropastoralism in the Middle Ages. Associated human deforestation allowed the coexistence of plant species typically found at different elevational belts, leading to levels of plant richness that characterise the current high diversity of this region. Our findings indicate a positive association between low intensity agropastoral activities and precipitation with the maintenance of the unique subalpine and alpine plant diversity of the European Alps.

A paleolimnological context of ecological vulnerability for the freshwater ecosystems of Sable Island National Park Reserve, Canada

Protected areas require long-term monitoring to understand the influence and extent of ecosystem stress to inform management and conservation decisions. As long-term data are not always available, paleolimnological methods offer a way of extending our knowledge of past environmental conditions necessary to use as context for remediation. Here, we examine four sediment cores and additional surface sediments from 14 ponds located on Sable Island National Park Reserve Canada (SINPR), where long-term ecological changes and vulnerability to disturbance are not well defined. We develop a paleolimnological approach to assessing environmental vulnerability through the use of biological indicators (Diptera: Chironomidae), where shifts in the environment are inferred by shifts in chironomid assemblages over time. Analysis of surface sediments show four distinct assemblage types reflecting four different habitat conditions; primarily represented by the presence of Glyptotendipes, Chironomus, Microtendipes, and Dicrotendipes. Differences in habitat conditions through time based on these results are then compared to biostratigraphic analysis of sediment cores from four of the ponds. We found that two ponds had large shifts in chironomids assemblages that were associated with changes in habitat over time, while two others that were not as exposed to the influence of erosion and influx of sand dunes did not. Our findings established a baseline of historical change in SINPR, broadening the scope of long-term monitoring, which is essential for defining goals for management and conservation of the ecological integrity of Sable Island.

Vegetation responses to past volcanic disturbances at the Araucaria araucana forest‐steppe ecotone in northern Patagonia

Volcanic eruptions play an important role in vegetation dynamics and its historical range of variability. However, large events are infrequent and eruptions with a significant imprint in today's vegetation occurred far in the past, limiting our understanding of ecological processes. Volcanoes in southern Andes have been active during the last 10 ka and support unique ecosystems such as the Araucaria–Nothofagus forest. Araucaria is an endangered species, with a fragmented distribution and well‐adapted to fire and volcanic disturbances. Yet, it was suggested that volcanism might have increased the fragmentation. Through the use of pollen and tephra analysis from a sedimentary record, this paleoecological study aims to provide an insight into the vegetation responses to past volcanic disturbances, to assess the role of volcanic disturbance on the vegetation dynamics and to determine if the current fragmentation has been caused by volcanism. Results show that during the last 9 kyr, 39 tephra falls buried the vegetation around Lake Relem, more frequently between 4 and 2 ka. The pollen percentage indicates that the vegetation changed after small tephra fall but seldom caused significant changes. However, the large eruption of Sollipulli volcano (~3 ka) changed the environmental conditions affecting severely the vegetation. Ephedra dominated the early successional stage, perhaps facilitating Nothofagus recovering after ~500 years. Slight increase of Araucaria and Nothofagus obliqua‐type pollen percentages suggests that forest resisted without permanent changes and recovered relatively fast after the large eruption, perhaps because of sparse biological legacies distributed in the landscape. In the study area, the relative stability of Araucaria pollen after several tephra fall suggests no change in its past distribution at the current forest‐steppe ecotone, thus not affecting its current conservation status. Perhaps, random factors, the colonization patterns of the high elevations in the Andes after deglaciation and topography might play a more important role than previously thought.

Holocene wildfire and vegetation dynamics in Central Yakutia, Siberia, reconstructed from lake-sediment proxies

Wildfires play an essential role in the ecology of boreal forests. In eastern Siberia, fire activity has been increasing in recent years, challenging the livelihoods of local communities. Intensifying fire regimes also increase disturbance pressure on the boreal forests, which currently protect the permafrost beneath from accelerated degradation. However, long-term relationships between changes in fire regime and forest structure remain largely unknown. We assess past fire-vegetation feedbacks using sedimentary proxy records from Lake Satagay, Central Yakutia, Siberia, covering the past c. 10,800 years. Results from macroscopic and microscopic charcoal analyses indicate high amounts of burnt biomass during the Early Holocene, and that the present-day, low-severity surface fire regime has been in place since c. 4,500 years before present. A pollen-based quantitative reconstruction of vegetation cover and a terrestrial plant record based on sedimentary ancient DNA metabarcoding suggest a pronounced shift in forest structure toward the Late Holocene. Whereas the Early Holocene was characterized by postglacial open larch-birch woodlands, forest structure changed toward the modern, mixed larch-dominated closed-canopy forest during the Mid-Holocene. We propose a potential relationship between open woodlands and high amounts of burnt biomass, as well as a mediating effect of dense larch forest on the climate-driven intensification of fire regimes. Considering the anticipated increase in forest disturbances (droughts, insect invasions, and wildfires), higher tree mortality may force the modern state of the forest to shift toward an open woodland state comparable to the Early Holocene. Such a shift in forest structure may result in a positive feedback on currently intensifying wildfires. These new long-term data improve our understanding of millennial-scale fire regime changes and their relationships to changes of vegetation in Central Yakutia, where the local population is already being confronted with intensifying wildfire seasons.

The vanishing and the establishment of a new ecosystem on an oceanic island - Anthropogenic impacts with no return ticket

A multiproxy approach was applied to a sediment core retrieved from the deep crater Lake Funda, located in the middle of the North Atlantic Ocean on Flores Island, Azores archipelago (Portugal). The purpose of this study was to determine how this ecosystem responded to natural and anthropogenic forces over the last millennium. We distinguished three main phases in lake evolution using multiproxy reconstructions and documentary sources. (A) Climate and lake catchment processes, as well as internal ones, were the main drivers of ecosystem variability before 1335 CE, when human disturbances were absent in the Lake Funda catchment. (B) The second phase is marked by unprecedented changes in all studied proxies between 1335 and 1560 CE, including abrupt changes in the composition and diversity of diatom and chironomid assemblages. Synergistic effects from high climate variability and the onset of human disturbances in the catchment (e.g., introduction of livestock) during the Medieval Climate Anomaly-Little Ice Age transition, led to an increase in lake trophic state from mesotrophic to eutrophic conditions. (C) In the last phase (1560 CE to the present), the eutrophic conditions in Lake Funda were maintained through a positive feedback loop between lake productivity and in-lake phosphorous recycling. Variability within the lake ecosystem was mainly associated with climate variability and internal lake dynamics (e.g., phosphorus remobilization). Our results show that a paleoecological approach is crucial to understanding lake ecological states in the present-day in order to develop locally adapted management and restoration strategies. A long-term perspective enables us to understand the harmful consequences of ongoing climate change and human disturbances on lake ecosystems.

Temperature and precipitation dominates millennium changes of eukaryotic algal communities in Lake Yamzhog Yumco, Southern Tibetan Plateau

Despite significant climate change on the Tibetan Plateau, the historical succession trend and underlying driving mechanism of aquatic ecosystem in alpine lake remain unclear. In this study, palaeolimnological analysis and high-throughput sequencing of sedimentary DNA were used to investigate environmental changes, primary productivity, and eukaryotic algal community succession over the past millennium in Lake Yamzhog Yumco of the southern Tibetan Plateau. Lake primary productivity significantly increased after ~1850 CE and algal community succession occurred in three stages including the Medieval Warm Periods (approximately 1000-1250 CE), the Little Ice Age (1250-1850 CE), and the Current Warm Period (1850-2020 CE). Moreover, succession was synchronous with inferred climate changes. Partial least square path modeling indicated that climate factors affected primary productivity and eukaryotic algal community structure by affecting nutrient loading. The results suggest that glacier melting and permafrost degradation caused by climate warming, combined with increased precipitation, may be the major driving factors of nutrient concentration increases, phytoplankton biomass increases, and shifts in community composition. Considering the expected trends of future climate change and continuous warming, the restoration of vegetation cover and reduction of non-point source nutrient loading in the Tibetan Plateau is urgently needed to mitigate climate change impacts on alpine lake aquatic ecosystems.

Diatom assemblage responses to multiple environmental stressors in a deep brackish plateau lake, SW China

Eutrophication, climate change, water level fall, fish introduction, and salinity have been widely recorded to impact lake ecosystems around the world. However, the combined responding pattern in the lake ecosystem to the above multiple environmental stressors is not well understood. Here, we present diatom assemblage and geochemical indicators (total organic carbon (TOC), total nitrogen (TN), and total phosphorous (TP)) in lake sediment to investigate the long-term trends in the aquatic ecosystem in response to multiple environmental stressors in Lake Chenghai, a deep brackish lake located on Yunnan-Guizhou Plateau, SW China, during the past 80 years. We identified 8 genera and 15 species of diatom reaching a relative abundance of ≥ 2% in at least one sample, with the dominant taxa such as Cyclotella rhomboideo-elliptica and Aulacoseira alpigena through the sediment core. There was a clear shift in the diatom community from oligotrophic species of C. rhomboideo-elliptica to eutrophic species such as Cyclotella meneghiniana and Cyclostephanos dubius becoming dominant since ca. 1998 CE. In addition, the changes in the fish introduction, water level, temperature, and salinity also resulted in the variation in abundance of planktonic and benthic diatoms. The increase in the abundance of diatoms of C. rhomboideo-elliptica since ca. 1986 CE may be related to the decline in water level and increasing fish production. For one thing, the decline in water level reduces the concentrations of benthic diatoms but increases the relative biomass of planktonic diatoms. For another, the increasing fish production results in the decrease in the zooplankton biomass, thus reducing the predation pressure on planktonic algae. Besides, some specific species such as C. meneghiniana may respond to the increased nutrient release and increased salinity since ca. 1998 CE. Combined, our findings demonstrate that trophic level is the main driver of diatom assemblage changes, and other environmental variables including water level, fish introduction, and climate warming also contribute to diatom community variation in this brackish plateau lake during the last 80 years.

Climatic and Anthropogenic Drivers of Forest Succession in the Iberian Pyrenees during the Last 500 Years: A Statistical Approach

Anticipating future successional forest trends in the face of ongoing global change is an essential conservation target. Mountain forests are especially sensitive to environmental shifts, and their past responses to climatic and anthropogenic (external) drivers may provide a basis for improving predictions of future developments. This paper uses independent high-resolution palynological and paleoclimatic reconstructions to statistically analyze the long-term effects of external drivers on regional forest succession in the central Iberian Pyrenees during the last 500 years. The statistical methods used are Gaussian response analysis, cluster analysis, rate-of-change analysis, principal component analysis, and redundancy analysis. The dominant taxa of these forests (Quercus, Betula, Pinus) showed significant relationships with summer temperature, summer drought, and autumn precipitation. Immediate and delayed (by two or more decades) responses of these trees to climatic drivers were identified. Regional succession showed a closed path, starting at the end points around the attraction domain of pine-dominated forests. This trajectory was determined by a trend toward anthropogenic forest clearing (16th to 18th centuries) and a reverse trend of natural forest recovery (18th to 20th centuries). Forest clearing was due to burning, facilitated by drought, and was followed by the expansion of cropping and grazing lands. Forest recovery was fostered by reduced human pressure and rising temperatures. The statistical approach used in this work has unraveled ecological relationships that remained unnoticed in previous works and would be important for predicting future successional trends under changing climates. The reported response lags of individual taxa to climatic drivers may complicate the establishment of reliable ecological relationships and should be addressed in future studies.

Reconstruction of Ecological Transitions in a Temperate Shallow Lake of the Middle Yangtze River Basin in the Last Century

Exogenous drivers may cause a gradual and reversible change in a lake equilibrium, or they may force it over a threshold to a persistent alternative stable state, described as a regime shift in the ecosystem. In the mid-and-lower Yangtze River Basin (MLYB), major environmental problems in shallow lakes have been eutrophication and abrupt algal blooms under anthropogenic disturbances for the recent century. Much value is therefore placed on understanding the changes in shallow-lake ecosystems that characteristically precede changes in the state of the lake. Here, we describe a case study of the paleolimnological signature in diatom assemblages of various types of regime shifts caused by historically documented anthropogenic drivers in a temperate shallow lake: Taibai Lake. We evaluate the effectiveness of paleolimnological data as a surrogate for long-term monitoring. Algorithms using sequential t and F statistics detected breakpoints in the time series of diatom assemblages, in 1994–1996, 1974–1977, 1952–1956, and 1931–1934, respectively. The regression statistics suggest that the hydrodynamic–ecosystem and aquacultural–ecosystem relationships fit better in the breakpoint regression model, and the relationship between nutrient loading and ecosystem state suits the linear model. Feedback loops help reconstruct dynamic changes in Taibai influenced by major stressors. Our study exemplifies the value of system approaches to identifying regime shifts and their possible causes in shallow lakes from paleolimnological records. The case study of Taibai set an example of reconstructing the ecological regime shifts in shallow lakes in the MLYB and understanding the state changes in lake ecosystems, which will benefit effective lake management.

Metal contamination in alkaline Phantom Lake (Flin Flon, Manitoba, Canada) generates strong responses in multiple paleolimnological proxies

The copper-zinc smelter at Flin Flon (Manitoba) operated between 1930 and 2010 and emitted large amounts of metal(loid)s and sulphur dioxide into the atmosphere, damaging the surrounding terrestrial landscapes and depositing airborne industrial pollutants into aquatic ecosystems. However, the extent of biological impairment in regional lakes is largely unknown. Here, we analysed biological and geochemical proxies preserved in a dated sediment core from Phantom Lake, collected seven years after the smelter closed in 2010. Our objectives were to determine how smelting history affected long-term trends in (1) sedimentary elements, (2) biota across multiple trophic levels, and (3) spectrally-inferred chlorophyll a and lake-water total organic carbon. The effects of smelting activities were clearest in the diatom record, in concordance with modest responses in chironomid and cladoceran assemblages. Several metal(loid)s were naturally high and exceeded sediment quality guidelines during the pre-smelting era. With the opening of the smelter, metal(loid) concentrations in sediments increased through the 1930s, peaked in the 1960s, and declined thereafter with technological improvements but remained above background to this day. Although modest declines in inferred lake-water total organic carbon indicate reduced terrestrial carbon supply following sulphate deposition in the catchment, the diatom record showed no evidence of acidification as the lake was and remained well-buffered. Pre-smelting diatom and invertebrate assemblages were diverse and indicated oligo-mesotrophic conditions. Smelting was associated with the loss of metal-sensitive biological indicators and the emergence of assemblages dominated by metal-tolerant, generalist taxa. Diatoms tracked substantial reductions in aerial emissions since the 1990s, particularly after the smelter closed, but also indicated that the biological effects of metal pollution persist in Phantom Lake. Examining the effects of a base metal smelter on a well-buffered lake offered insights into multi-trophic level responses to severe metal contamination and potential recovery without the confounding effects of concurrent changes in lake acidity.

Climate and Species Traits Drive Changes in Holocene Forest Composition Along an Elevation Gradient in Pacific Canada

Projected changes in climate are expected to shift the ranges of many tree species poleward and to higher elevations. Here, we examine past changes in forest composition in Pacific Canada using a paleoecological approach and investigate the role of past changes in climate and differences in species traits in changing forest compositions. We present a new pollen record from a mid-elevation fen on central Vancouver Island, British Columbia that shows (1) Pinus contorta-dominated communities starting 14,000 cal yr BP, (2) an abrupt transition to Pseudotsuga menziesii and Tsuga heterophylla forests by 10,600 cal yr BP, and (3) a gradual transition to Tsuga heterophylla-dominated forests in the mid-Holocene. We combine this mid-elevation record with nearby pollen records along a 1,400-m elevation gradient to assess sorting of dominant woody plant taxa and their life history and stress tolerance traits over the last 14,000 years. Multivariate time series confirm elevational sorting of woody plant taxa through time with the modern elevational zonation of tree taxa established by 6,000 cal yr BP. Some taxa have consistently occupied low and middle elevations (P. menziesii, Alnus rubra) or high elevations (Tsuga mertensiana), whereas other taxa (P. contorta, T. heterophylla) have occurred at a wider range of elevations. Three-table statistical techniques reveal significant relationships among forest composition, independent paleoclimate records, and species traits. Tree species with similar traits tend to be most abundant at similar times and those that are functionally dissimilar are separated in time. For example, species with “fast” life history strategies (e.g., P. contorta, Alnus viridis) are most abundant in late-glacial plant communities, while those with “slow” life history strategies (e.g., T. heterophylla, T. mertensiana) are most abundant in mid-late Holocene forests. This research highlights that woody plant taxa and their functional traits are sorted on long timescales in association with environmental change. Turnover in forest composition is driven primarily by changes in climate, which acts as a filter on species traits to direct changes in forest dynamics.

Three Millennia of Vegetation, Land-Use, and Climate Change in SE Sicily

This study presents the first Late Holocene marine pollen record (core ND2) from SE Sicily. It encompasses the last 3000 years and is one of the most detailed records of the south-central Mediterranean region in terms of time resolution. The combined approach of marine palynology and historical ecology, supported by independent palaeoclimate proxies, provides an integrated regional reconstruction of past vegetational dynamics in relation to rapid climatic fluctuations, historical socio-economic processes, and past land-use practices, offering new insights into the vegetation history of SE Sicily. Short-term variations of sparse tree cover in persistently open landscapes reflect rapid hydroclimatic changes and historical land-use practices. Four main phases of forest reduction are found in relation to the 2.8 ka BP event, including the Late Antique Little Ice Age, the Medieval Climate Anomaly, and the Little Ice Age, respectively. Forest recovery is recorded during the Hellenistic and Roman Republican Periods, the Early Middle Ages, and the last century. Agricultural and silvicultural practices, as well as stock-breeding activities, had a primary role in shaping the current vegetational landscape of SE Sicily.

Key periods of peatland development and environmental changes in the middle taiga zone of Western Siberia during the Holocene

The response of peatlands to climate change can be highly variable. Through understanding past changes we can better predict the response of peatlands to future climate change. We use a multi-proxy approach to reconstruct the surface wetness and carbon accumulation of the Mukhrino mire (Western Siberia), describing the development of the mire since peat formation in the early Holocene, around 9360 cal. year BP. The mire started as a rich fen which initiated after paludification of a spruce forest (probably in response to a wetter climate), while the Mukhrino mire progressed to ombrotrophic bog conditions (8760 cal. year BP). This transition coincided with the intensive development of mires in Western Siberia and was associated with active carbon accumulation (31 g m-2 year-1). The ecosystem underwent a change to a tree-covered state around 5860 cal. year BP, likely in response to warming and possible droughts and this accompanied low carbon accumulation (12 g m2 year-1). If the future climate will be warmer and wetter, then regional mires are likely to remain a carbon sink, alternatively, a reversion to the wooded state with reduced carbon sink strength is possible.

First modern human settlement recorded in the Iberian hinterland occurred during Heinrich Stadial 2 within harsh environmental conditions

As the south-westernmost region of Europe, the Iberian Peninsula stands as a key area for understanding the process of modern human dispersal into Eurasia. However, the precise timing, ecological setting and cultural context of this process remains controversial concerning its spatiotemporal distribution within the different regions of the peninsula. While traditional models assumed that the whole Iberian hinterland was avoided by modern humans due to ecological factors until the retreat of the Last Glacial Maximum, recent research has demonstrated that hunter-gatherers entered the Iberian interior at least during Solutrean times. We provide a multi-proxy geoarchaeological, chronometric and paleoecological study on human–environment interactions based on the key site of Peña Capón (Guadalajara, Spain). Results show (1) that this site hosts the oldest modern human presence recorded to date in central Iberia, associated to pre-Solutrean cultural traditions around 26,000 years ago, and (2) that this presence occurred during Heinrich Stadial 2 within harsh environmental conditions. These findings demonstrate that this area of the Iberian hinterland was recurrently occupied regardless of climate and environmental variability, thus challenging the widely accepted hypothesis that ecological risk hampered the human settlement of the Iberian interior highlands since the first arrival of modern humans to Southwest Europe.

Holocene vegetation, fire and land use dynamics at Lake Svityaz, an agriculturally marginal site in northwestern Ukraine

Observing natural vegetation dynamics over the entire Holocene is difficult in Central Europe, due to pervasive and increasing human disturbance since the Neolithic. One strategy to minimize this limitation is to select a study site in an area that is marginal for agricultural activity. Here, we present a new sediment record from Lake Svityaz in northwestern Ukraine. We have reconstructed regional and local vegetation and fire dynamics since the Late Glacial using pollen, spores, macrofossils and charcoal. Boreal forest composed of Pinus sylvestris and Betula with continental Larix decidua and Pinus cembra established in the region around 13,450 cal bp, replacing an open, steppic landscape. The first temperate tree to expand was Ulmus at 11,800 cal bp, followed by Quercus, Fraxinus excelsior, Tilia and Corylus ca. 1,000 years later. Fire activity was highest during the Early Holocene, when summer solar insolation reached its maximum. Carpinus betulus and Fagus sylvatica established at ca. 6,000 cal bp, coinciding with the first indicators of agricultural activity in the region and a transient climatic shift to cooler and moister conditions. Human impact on the vegetation remained initially very low, only increasing during the Bronze Age, at ca. 3,400 cal bp. Large-scale forest openings and the establishment of the present-day cultural landscape occurred only during the past 500 years. The persistence of highly diverse mixed forest under absent or low anthropogenic disturbance until the Early Middle Ages corroborates the role of human impact in the impoverishment of temperate forests elsewhere in Central Europe. The preservation or reestablishment of such diverse forests may mitigate future climate change impacts, specifically by lowering fire risk under warmer and drier conditions.

SUPPLEMENTARY INFORMATION

The online version contains supplementary material available at 10.1007/s00334-021-00844-z.

Middle Holocene Climate Oscillations Recorded in the Western Dvina Lakeland

Although extensive archeological research works have been conducted in the Serteya region in recent years, the Holocene climate history in the Western Dvina Lakeland in Western Russia is still poorly understood. The Neolithic human occupation of the Serteyka lake–river system responded to climate oscillations, resulting in the development of a pile-dwelling settlement between 5.9 and 4.2 ka cal BP. In this paper, we present the quantitative paleoclimatic reconstructions of the Northgrippian stage (8.2–4.2 ka cal BP) from the Great Serteya Palaeolake Basin. The reconstructions were created based on a multiproxy (Chironomidae, pollen and Cladocera) approach. The mean July air temperature remained at 17–20 °C, which is similar to the present temperature in the Smolensk Upland. The summer temperature revealed only weak oscillations during 5.9 and 4.2 ka cal BP. A more remarkable feature during those events was an increase in continentality, manifested by a lower winter temperature and lower annual precipitation. During the third, intermediate oscillation in 5.0–4.7 ka cal BP, a rise in summer temperature and stronger shifts in continental air masses were recorded. It is still unclear if the above-described climate fluctuations are linked to the North Atlantic Oscillation and can be interpreted as an indication of Bond events because only a few high-resolution paleoclimatic reconstructions from the region have been presented and these reconstructions do not demonstrate explicit oscillations in the period of 5.9 and 4.2 ka cal BP.

Vegetation Changes in Southeastern Siberia During the Late Pleistocene and the Holocene

Relationships between climate, species composition, and species richness are of particular importance for understanding how boreal ecosystems will respond to ongoing climate change. This study aims to reconstruct changes in terrestrial vegetation composition and taxa richness during the glacial Late Pleistocene and the interglacial Holocene in the sparsely studied southeastern Yakutia (Siberia) by using pollen and sedimentary ancient DNA (sedaDNA) records. Pollen and sedaDNA metabarcoding data using the trnL g and h markers were obtained from a sediment core from Lake Bolshoe Toko. Both proxies were used to reconstruct the vegetation composition, while metabarcoding data were also used to investigate changes in plant taxa richness. The combination of pollen and sedaDNA approaches allows a robust estimation of regional and local past terrestrial vegetation composition around Bolshoe Toko during the last ∼35,000 years. Both proxies suggest that during the Late Pleistocene, southeastern Siberia was covered by open steppe-tundra dominated by graminoids and forbs with patches of shrubs, confirming that steppe-tundra extended far south in Siberia. Both proxies show disturbance at the transition between the Late Pleistocene and the Holocene suggesting a period with scarce vegetation, changes in the hydrochemical conditions in the lake, and in sedimentation rates. Both proxies document drastic changes in vegetation composition in the early Holocene with an increased number of trees and shrubs and the appearance of new tree taxa in the lake’s vicinity. The sedaDNA method suggests that the Late Pleistocene steppe-tundra vegetation supported a higher number of terrestrial plant taxa than the forested Holocene. This could be explained, for example, by the “keystone herbivore” hypothesis, which suggests that Late Pleistocene megaherbivores were able to maintain a high plant diversity. This is discussed in the light of the data with the broadly accepted species-area hypothesis as steppe-tundra covered such an extensive area during the Late Pleistocene.

8,000 years of climate, vegetation, fire and land-use dynamics in the thermo-mediterranean vegetation belt of northern Sardinia (Italy)

Knowledge about the vegetation history of Sardinia, the second largest island of the Mediterranean, is scanty. Here, we present a new sedimentary record covering the past ~ 8,000 years from Lago di Baratz, north-west Sardinia. Vegetation and fire history are reconstructed by pollen, spores, macrofossils and charcoal analyses and environmental dynamics by high-resolution element geochemistry together with pigment analyses. During the period 8,100-7,500 cal bp, when seasonality was high and fire and erosion were frequent, Erica arborea and E. scoparia woodlands dominated the coastal landscape. Subsequently, between 7,500 and 5,500 cal bp, seasonality gradually declined and thermo-mediterranean woodlands with Pistacia and Quercus ilex partially replaced Erica communities under diminished incidence of fire. After 5,500 cal bp, evergreen oak forests expanded markedly, erosion declined and lake levels increased, likely in response to increasing (summer) moisture availability. Increased anthropogenic fire disturbance triggered shrubland expansions (e.g. Tamarix and Pistacia) around 5,000-4,500 cal bp. Subsequently around 4,000-3,500 cal bp evergreen oak-olive forests expanded massively when fire activity declined and lake productivity and anoxia reached Holocene maxima. Land-use activities during the past 4,000 years (since the Bronze Age) gradually disrupted coastal forests, but relict stands persisted under rather stable environmental conditions until ca. 200 cal bp, when agricultural activities intensified and Pinus and Eucalyptus were planted to stabilize the sand dunes. Pervasive prehistoric land-use activities since at least the Bronze Age Nuraghi period included the cultivation of Prunus, Olea europaea and Juglans regia after 3,500-3,300 cal bp, and Quercus suber after 2,500 cal bp. We conclude that restoring less flammable native Q. ilex and O. europaea forest communities would markedly reduce fire risk and erodibility compared to recent forest plantations with flammable non-native trees (e.g. Pinus, Eucalyptus) and xerophytic shrubland (e.g. Cistus, Erica).

Ancient plant DNA reveals High Arctic greening during the Last Interglacial

Summer warming is driving a greening trend across the Arctic, with the potential for large-scale amplification of climate change due to vegetation-related feedbacks [Pearson et al., Nat. Clim. Chang. (3), 673-677 (2013)]. Because observational records are sparse and temporally limited, past episodes of Arctic warming can help elucidate the magnitude of vegetation response to temperature change. The Last Interglacial ([LIG], 129,000 to 116,000 y ago) was the most recent episode of Arctic warming on par with predicted 21st century temperature change [Otto-Bliesner et al., Philos. Trans. A Math. Phys. Eng. Sci. (371), 20130097 (2013) and Post et al., SciAdv (5), eaaw9883 (2019)]. However, high-latitude terrestrial records from this period are rare, so LIG vegetation distributions are incompletely known. Pollen-based vegetation reconstructions can be biased by long-distance pollen transport, further obscuring the paleoenvironmental record. Here, we present a LIG vegetation record based on ancient DNA in lake sediment and compare it with fossil pollen. Comprehensive plant community reconstructions through the last and current interglacial (the Holocene) on Baffin Island, Arctic Canada, reveal coherent climate-driven community shifts across both interglacials. Peak LIG warmth featured a ∼400-km northward range shift of dwarf birch, a key woody shrub that is again expanding northward. Greening of the High Arctic-documented here by multiple proxies-likely represented a strong positive feedback on high-latitude LIG warming. Authenticated ancient DNA from this lake sediment also extends the useful preservation window for the technique and highlights the utility of combining traditional and molecular approaches for gleaning paleoenvironmental insights to better anticipate a warmer future.

A high-resolution record of Holocene primary productivity and water-column mixing from the varved sediments of Lake Żabińskie, Poland

Eutrophication and anoxia are increasing in lakes worldwide. However, our understanding of variations of primary productivity and anoxia in lakes over thousands of years is limited. Long-term records are needed to understand the natural variability of lake ecosystems and to improve our understanding of drivers of productivity and anoxia. In this study, we used the varved sediment record of Lake Żabińskie, Poland to answer the following research questions: 1) How have primary production and water column oxygen concentrations varied during the past 10,800 years?; 2) what role did natural and anthropogenic forces have in driving changes in primary production or lake mixing regime? Recently developed hyperspectral imaging (HSI) techniques were used to quantify sedimentary chloropigments-a and bacteriopheopigments-a (Bphe-a) at sub-annual resolution. These data, combined with elemental data from micro X-ray fluorescence (μ-XRF) and pigment assemblage data from high-performance liquid chromatography (HPLC) measurements, were used to reconstruct paleolimnological conditions. Bphe-a was used as an indicator of anoxia, and its presence suggests that an extensive anoxic zone was present nearly continuously from 10.8 to 2.8 ka BP. Anoxic conditions, driven by thermal stratification, were promoted by closed forest cover during that time, which limited wind-driven mixing of the water column. After 2.8 ka BP, water column oxygenation occurred more frequently, particularly during periods of increased human agricultural activity and forest opening. Pronounced anoxia was again present continuously from ~610 to 1470 CE, concurrent with a period of reforestation. After ~1610 CE, deforestation caused increases in erosion rates, algal production, and water column oxygenation. Pigment assemblages indicate that the algal community during the past 150 years was different from any other time during the Holocene. This study demonstrates a clear link between lake biogeochemical processes and forest cover and shows the potential of HSI to produce extremely high-resolution records of past productivity and redox conditions from varved lake sediments.

Long-term dynamics of a cladoceran community from an early stage of lake formation in Lake Fukami-ike, Japan

An increase in nutrient levels due to eutrophication has considerable effects on lake ecosystems. Cladocerans are intermediate consumers in lake ecosystems; thus, they are influenced by both the bottom-up and top-down effects that occur as eutrophication progresses. The long-term community succession of cladocerans and the effects cladocerans experience through the various eutrophication stages have rarely been investigated from the perspective of the early-stage cladoceran community assemblage during lake formation. In our research, long-term cladoceran community succession was examined via paleolimnological analysis in the currently eutrophic Lake Fukami-ike, Japan. We measured the concentration of total phosphorus and phytoplankton pigments and counted cladoceran and other invertebrate subfossils in all layers of collected sediment cores, and then assessed changes in the factors controlling the cladoceran community over a 354-year period from lake formation to the present. The cladoceran community consisted only of benthic taxa at the time of lake formation. When rapid eutrophication occurred and phytoplankton increased, the benthic community was replaced by a pelagic community. After further eutrophication, large Daphnia and high-order consumers became established. The statistical analysis suggested that bottom-up effects mainly controlled the cladoceran community in the lake's early stages, and the importance of top-down effects increased after eutrophication occurred. Total phosphorus and phytoplankton pigments had positive effects on pelagic Bosmina, leading to the replacement of the benthic cladoceran community by the pelagic one. In contrast, the taxa established posteutrophication were affected more by predators than by nutrient levels. A decrease in planktivorous fish possibly allowed large Daphnia to establish, and the subsequent increase in planktivorous fish reduced the body size of the cladoceran community.

Responses of ichthyoplankton assemblages to the recent marine heatwave and previous climate fluctuations in several Northeast Pacific marine ecosystems

The effects of climate warming on ecosystem dynamics are widespread throughout the world's oceans. In the Northeast Pacific, large-scale climate patterns such as the El Niño/Southern Oscillation and Pacific Decadal Oscillation, and recently unprecedented warm ocean conditions from 2014 to 2016, referred to as a marine heatwave (MHW), resulted in large-scale ecosystem changes. Larval fishes quickly respond to environmental variability and are sensitive indicators of ecosystem change. Categorizing ichthyoplankton dynamics across marine ecosystem in the Northeast Pacific can help elucidate the magnitude of assemblage shifts, and whether responses are synchronous or alternatively governed by local responses to regional oceanographic conditions. We analyzed time-series data of ichthyoplankton abundances from four ecoregions in the Northeast Pacific ranging from subarctic to subtropical: the Gulf of Alaska (1981-2017), British Columbia (2001-2017), Oregon (1998-2017), and the southern California Current (1981-2017). We assessed the impact of the recent (2014-2016) MHW and how ichthyoplankton assemblages responded to past major climate perturbations since 1981 in these ecosystems. Our results indicate that the MHW caused widespread changes in the ichthyoplankton fauna along the coast of the Northeast Pacific Ocean, but impacts differed between marine ecosystems. For example, abundances for most dominant taxa were at all-time lows since the beginning of sampling in the Gulf of Alaska and British Columbia, while in Oregon and the southern California Current species richness increased as did abundances of species associated with warmer waters. Lastly, species associated with cold waters also increased in abundances close to shore in southern California during the MHW, a pattern that was distinctly different from previous El Niño events. We also found several large-scale, synchronized ichthyoplankton assemblage composition shifts during past major climate events. Current climate projections suggest that MHWs will become more intense and thus our findings can help project future changes in larval dynamics, allowing for improved ecosystem management decisions.

Zooplankton variability in the Strait of Georgia, Canada, and relationships with the marine survivals of Chinook and Coho salmon

The Strait of Georgia, Canada, has complex interactions among natural and human pressures that confound understanding of changes in this system. We report on the interannual variability in biomass of 12 zooplankton taxonomic groups in the deep (bottom depths greater than 50 m) central and northern Strait of Georgia from 1996 to 2018, and their relationships with 10 physical variables. Total zooplankton biomass was dominated (76%) by large-sized crustaceans (euphausiids, large and medium size calanoid copepods, amphipods). The annual anomaly of total zooplankton biomass was highest in the late 1990s, lowest in the mid-2000s, and generally above its climatological (1996-2010) average after 2011, although many individual groups had different patterns. Two latent trends (derived from dynamic factor analyses) described the variability of annual biomass anomalies underlying all zooplankton groups: a U-shaped trend with its minimum in the mid-2000s, and a declining trend from 2001 to 2011. Two latent trends also described the physical variables. The variability represented by these four latent trends clustered into two periods: 1996-2006, with generally declining zooplankton biomass and increasing salinities, and 2007-2018, with increasing zooplankton biomass and decreasing salinities. ARIMA modelling showed sea surface salinity at Entrance Island in the middle Strait of Georgia, the Pacific Decadal Oscillation, and the peak date of the spring phytoplankton bloom were significantly related to the two latent zooplankton trends. ARIMA models comparing zooplankton and physical variables with the marine survivals of four salmon populations which enter the Strait as juveniles (Chinook: Cowichan River, Puntledge River, Harrison River; Coho: Big Qualicum River) all included zooplankton groups consistent with known salmon prey; prominent among the physical variables were sea surface salinity and variables representing the flow from the Fraser River. These regressions explained (adjR2) 38 to 85% of the annual variability in marine survival rates of these salmon populations over the study time period. Although sea temperature was important in some relationships between zooplankton biomass and salmon marine survival, salinity was a more frequent and more important variable, consistent with its influence on the hydrodynamics of the Strait of Georgia system.

Land-use and climate controls on aquatic carbon cycling and phototrophs in karst lakes of southwest China

Land-use and climate changes have been repeatedly identified as important factors affecting terrestrial carbon budgets, however little is known about how deforestation and catchment development affect aquatic systems in carbonate-rich regions. Multi-proxy analyses of ²¹⁰Pb-dated sediment cores from two hard-water lakes with different land-use histories were applied for assessing carbon cycling and limnological changes in response to land-use changes over the past century in southwest China. Logging of primary forests in the catchment of Lugu Lake, starting in the 1950s, led to a significant increase of catchment erosion, as well as a consistent decline in inferred lake-water total organic carbon (TOC) levels and sediment carbonate accumulation. This process of recent deforestation may significantly reduce the role of lake systems to act as carbon sinks through hampering of both the soil organic carbon flux and the dissolution of catchment carbonate. The decline in lake-water TOC in Lugu Lake further increased algal production (i.e. tracked through sediment trends in chlorophyll a and its main diagenetic products) and changes in diatom composition. In comparison, there was little variation of sediment carbonate content in Chenghai Lake, which has a long history of catchment deforestation, while both primary production and lake-water TOC increased following cultural eutrophication during the last three decades. Furthermore, regional warming was associated with an increase in small-sized diatoms in both deep lakes, likely due to enhanced thermal stability. This study highlights the significant role of vegetation cover and land use in driving aquatic carbon cycling and phototrophs, revealing that deforestation can strongly reduce both inorganic and organic carbon export to lakes and thus aquatic carbon storage in karst landscapes.

Long-Term Responses of Mediterranean Mountain Forests to Climate Change, Fire and Human Activities in the Northern Apennines (Italy)

Fagus sylvatica (beech) dominates the montane forests of the Apennines and builds old-growth high-conservation value stands. However, recent severe drought-induced diebacks raise concern on the future persistence of these forests and of Southern European mesophilous woodlands overall, growing at their dry edge. To explore the history of Apennine beech-dominated forests, we draw on the multiproxy paleoecological record from Lago Verdarolo, which includes a robust vegetation-independent temperature reconstruction. Numerical techniques are used to investigate the drivers of long-term Mediterranean mountain forest dynamics. Specifically, we focus on disentangling the ecological factors that caused the shift from high-diversity mixed forests to beech-dominated stands and on assessing the occurrence of legacy effects on present-day forests. Abrupt climate change largely drove vegetation dynamics during the Late Glacial and Early Holocene. Species-rich mixed Abies alba (silver fir) forests dominated about 10,500—5500 years ago, under rather dry and warmer-than-today conditions (+ 1—2 °C) and limited fire occurrence. Cooler and moister summers and increasing fire activity caused declines in several fire-sensitive temperate deciduous trees (for example, Ulmus, Tilia, Fraxinus) and favored the establishment of fir-beech forests around 5500 years ago. Further enhancement of fire activity and farming around 2000 years ago led to local Abies alba extinction and forest impoverishment. We conclude that the currently widespread monospecific Apennine beech forests are the result of multi-millennial land-use intensification superimposed on Late Holocene cooling and moistening. Given their higher drought-tolerance compared to beech stands, reviving ancient species-rich mixed fir forests represents a feasible and ‘tested’ possibility to adapt forests to climate change.

Ecosystem shift of a mountain lake under climate and human pressure: A move out from the safe operating space

A multiproxy approach including chironomid, diatom, pollen and geochemical analyses was applied on short gravitational cores retrieved from an alpine lake (Lacul Bâlea) in the Southern Carpathians (Romania) to unveil how this lake responded to natural and anthropogenic forcing over the past 500 years. On the basis of chironomid and diatom assemblage changes, and supported by sediment chemical data and historical information, we distinguished two main phases in lake evolution. Before 1926 the lake was dominated by chironomids belonging to Micropsectra insignilobus-type and benthic diatoms suggesting well-oxygenated oligotrophic environment with only small-scale disturbance. We considered this state as the lake's safe operational space. After 1926 significant changes occurred: Tanytarsus lugens-type and T. mendax-type chironomids took over dominance and collector filterers increased until 1970 pointing to an increase in available nutrients. The diatom community showed the most pronounced change between 1950 and 1992 when planktonic diatoms increased. The highest trophic level was reconstructed between 1970 and 1992, while the indicator species of increasing nutrient availability, Asterionella formosa spread from 1982 and decreased rapidly at 1992. Statistical analyses evidenced that the main driver of the diatom community change was atmospheric reactive nitrogen (Nr) fertilization that drastically moved the community towards planktonic diatom dominance from 1950. The transformation of the chironomid community was primarily driven by summer mean temperature increase that also changed the dominant feeding guild from collector gatherers to collector filterers. Our results overall suggest that the speed of ecosystem reorganisation showed an unprecedented increase over the last 100 years; biological systems in many cases underwent threshold type changes, while several system components displayed non-hysteretic change between alternating community composition. We conclude that Lake Bâlea is outside of its safe operating space today. The main trigger of changes since 1926 was climate change and human impact acting synergically.

Long-term ecological changes in Mediterranean mountain lakes linked to recent climate change and Saharan dust deposition revealed by diatom analyses

Anthropogenic climate change and the recent increase of Saharan dust deposition has had substantial effects on Mediterranean alpine regions. We examined changes in diatom assemblage composition over the past ~180 years from high-resolution, dated sediment cores retrieved from six remote lakes in the Sierra Nevada Mountains of Southern Spain. In all lakes, changes in diatom composition began over a century ago, but were more pronounced after ~1970 CE, concurrent with trends in rising regional air temperature, declining precipitation, and increased Saharan dust deposition. Temperature was identified as the main predictor of diatom assemblage changes, whereas both Saharan dust deposition drivers, the Sahel precipitation index and the winter North Atlantic Oscillation, were secondary explanatory variables. Diatom compositional shifts are indicative of lake alkalinization (linked to heightened evapoconcentration and an increase in calcium-rich Saharan dust input) and reduced lake water turbulence (linked to lower water levels and reduced inflows to the lakes). Moreover, decreases in epiphytic diatom species were indicative of increasing aridity and the drying of catchment meadows. Our results support the conclusions of previous chlorophyll-a and cladoceran-based paleolimnological analyses of these same dated sedimentary records which show a regional-scale response to climate change and Saharan dust deposition in Sierra Nevada lakes and their catchments during the 20th century. However, diatom assemblages seem to respond to different atmospheric and climate-related effects than cladoceran assemblages and chlorophyll-a concentrations. The recent impact of climate change and atmospheric Saharan deposition on lake biota assemblages and water chemistry, as well as catchment water availability, will have important implications for the valuable ecosystem services that the Sierra Nevada provides.

Effects of climate warming and nitrogen deposition on subtropical montane ponds (central China) over the last two centuries: Evidence from subfossil chironomids

Many remote montane ecosystems are experiencing biogeochemical changes driven by warming climate and atmospheric pollution. Compared with circumpolar and temperate lakes, the responses of subtropical montane lakes to these external stressors have been less investigated. Here we present sedimentary multi-proxies records (i.e. chironomids, elements and stable isotope of carbon and nitrogen) in ²¹⁰Pb-dated cores from two montane ponds (central China). Before the 1900s, low biomass and the dominance of opportunistic species (e.g. Chironomus anthracinus-type) in both ponds might be in response to cold and harsh condition. Thereafter, chironomid communities in both ponds experienced pronounced shifts. Nutrient-tolerant/warm-adapted species (e.g. Chironomus sp., Polypedilum nubeculosum-type and Endochironomus impar-type) proliferated and biomass increased synchronously after the 1900s, suggestive of favorable condition for chironomid growth. Redundancy analyses revealed that changes in chironomid communities in both ponds were significantly correlated with rising temperature and δ¹⁵N depletion. Prolonged growing season and nitrogen subsidy would increase primary productivity, and hence enhancing food availability for chironomids. Catchment-mediated indirect effects of warming and nitrogen deposition, such as hydrological changes and terrestrial organic matter inputs, would impose further influences on chironomid communities. Taken together, the combined effects of climate warming and nitrogen deposition have caused significant shifts in primary consumers of these montane ponds, and imposed cascading effects on structure and function of subtropical montane aquatic ecosystems.

Aquatic community structure as sentinel of recent environmental changes unraveled from lake sedimentary records from the Atacama Desert, Chile

The Atacama Desert (21-26°S) is currently one of the driest places on Earth and metal(loid)s are of special concern for this region, which hosts the largest-known porphyry copper deposits produced in Chile. Evidence of past environmental conditions is commonly preserved in natural archives, such as lacustrine sediments. Sediment records obtained from Inca Coya Lake (22°20'S-68°35'W, 2534 m.a.s.l.), a small lake located in the Atacama Desert, reflected the evolution of regional mining activity during the 20th century and sedimentation associated with decadal climate variability. We studied the aquatic community structure changes recorded in sediment records from Inca Coya Lake. By analysis of magnetic properties (susceptibility, hysteresis curves and Curie temperatures), grain size and geochemical composition of the sediments, we identified environmental periods and changes in the community of benthic and planktonic organisms (diatoms and diapausing egg bank). We identified three detrital episodes that we interpret as dry/wet phases during the last 90 years associated with the increase of flash flood events promoting hypoxia oscillations; anthropogenic (mining activity) signals were also identified. Invertebrate community structure (primary consumers) reflected the metal exposure, measured as changes in assemblage composition through species turnover. Diatom community composition was best associated with variables related to wetter/drier alternation and consequent changes in oxygen availability. Bioindicators analyzed (diatoms, diapausing egg bank and invertebrate community) demonstrated to be excellent indicators of the bioavailability of compounds in the aquatic ecosystem of Inca Coya Lake, allowing the environmental impact assessment of the water resources due to flash floods and mining activity in the driest desert of the world.

Climate-induced changes in carbon flows across the plant-consumer interface in a small subarctic lake

Reconstructions of past food web dynamics are necessary for better understanding long-term impacts of climate change on subarctic lakes. We studied elemental and stable isotopic composition of sedimentary organic matter, photosynthetic pigments and carbon stable isotopic composition of Daphnia (Cladocera; Crustacea) resting eggs (δ13CClado) in a sediment record from a small subarctic lake. We examined how regional climate and landscape changes over the last 5800 years affected the relative importance of allochthonous and autochthonous carbon transfer to zooplankton. Overall, δ13CClado values were well in line with the range of theoretical values of aquatic primary producers, confirming that zooplankton consumers in subarctic lakes, even in the long-term perspective, are mainly fuelled by autochthonous primary production. Results also revealed greater incorporations of benthic algae into zooplankton biomass in periods that had a warmer and drier climate and clearer water, whereas a colder and wetter climate and lower water transparency induced higher contributions of planktonic algae to Daphnia biomass. This study thus emphasizes long-term influence of terrestrial-aquatic linkages and in-lake processes on the functioning of subarctic lake food webs.

Adjacency-constrained hierarchical clustering of a band similarity matrix with application to genomics

BACKGROUND

Genomic data analyses such as Genome-Wide Association Studies (GWAS) or Hi-C studies are often faced with the problem of partitioning chromosomes into successive regions based on a similarity matrix of high-resolution, locus-level measurements. An intuitive way of doing this is to perform a modified Hierarchical Agglomerative Clustering (HAC), where only adjacent clusters (according to the ordering of positions within a chromosome) are allowed to be merged. But a major practical drawback of this method is its quadratic time and space complexity in the number of loci, which is typically of the order of 10 4 to 10 5 for each chromosome.

RESULTS

By assuming that the similarity between physically distant objects is negligible, we are able to propose an implementation of adjacency-constrained HAC with quasi-linear complexity. This is achieved by pre-calculating specific sums of similarities, and storing candidate fusions in a min-heap. Our illustrations on GWAS and Hi-C datasets demonstrate the relevance of this assumption, and show that this method highlights biologically meaningful signals. Thanks to its small time and memory footprint, the method can be run on a standard laptop in minutes or even seconds.

AVAILABILITY AND IMPLEMENTATION

Software and sample data are available as an R package, adjclust, that can be downloaded from the Comprehensive R Archive Network (CRAN).

The Toledo Mountains: A Resilient Landscape and a Landscape for Resilience? Hazards and Strategies in a Mid-Elevation Mountain Region in Central Spain

The Toledo Mountains are a mid-elevation mountain range that separates the Tagus and Guadiana basins in the central area of the Iberian Peninsula. The location of these mountains allows the development of typical Mediterranean vegetation with some Atlantic influence. Consequently, typical broadleaved evergreen Mediterranean vegetation currently dominates the regional landscape, with the remarkable presence of more mesophilous species in sheltered and more humid microsites such as gorges (e.g., Prunus lusitanica, Taxus baccata, Ilex aquifolium) and mires/bogs (e.g., Betula pendula susbp. fontqueri, Erica tetralix, Myrica gale). Palaeoecological studies in these mountains are essential to understand the long-term ecology and original distribution of these valuable communities and are key to assess their resilience. Understanding the hazards and opportunities faced in the past by the plant communities of the Toledo Mountains is necessary to enhance the management and protection of those species currently threatened. This study focuses on El Perro mire, a peatland on the southern Toledo Mountains (central Spain) where climatic variability has played a major role in landscape dynamics at multi-decadal to millennial timescales. Climatic events such as the 4.2 ka cal. Before Present (BP) or the Little Ice Age triggered relevant landscape changes such as the spread and latter decline of birch and hazel forests. Human communities also seemed to be affected by these events, as their resilience was apparently jeopardized by the new climatic conditions and they were forced to find new strategies to cope with the new scenarios.

Unprecedented herbivory threatens rear-edge populations of Betula in southwestern Eurasia

Mediterranean rear-edge populations of Betula, located at the southwestern Eurasian margin of the distribution range, represent unique reservoirs of genetic diversity. However, increasing densities of wild ungulates, enhanced dryness, and wildfires threaten their future persistence. A historical perspective on the past responses of these relict populations to changing herbivory, fire occurrence and climatic conditions may contribute to assessing their future responses under comparable scenarios. We have reconstructed vegetation and disturbance (grazing, fire) history in the Cabañeros National Park (central-southern Spain) using the paleoecological records of two small mires. We particularly focused on the historical range of variation in disturbance regimes, and the dynamics of rear-edge Betula populations and herbivore densities. Changes in water availability, probably related to the North Atlantic Oscillation (NAO) index, and land-use history have played a crucial role in vegetation shifts. Our data suggest that heathlands (mainly Erica arborea and E. scoparia) and Quercus woodlands dominated during dry phases while Sphagnum bogs and Betula stands expanded during wet periods. Betula populations survived past moderately dry periods but were unable to cope with enhanced land use, particularly increasing livestock raising since ~1,100-900 cal. yr BP (850-1,050 CE), and eventually underwent local extinction. High herbivore densities not only contributed to the Betula demise but also caused the retreat of Sphagnum bogs. Ungulate densities further rose at ~200-100 cal. yr BP (1750-1850 CE) associated with the historically documented intensification of land use around the Ecclesiastical Confiscation. However, herbivory reached truly unprecedented values only during the last decades, following rural depopulation and subsequent promotion of big game hunting. For the first time in temperate and Mediterranean Europe, we have used the abundances of fossil dung fungal spores to assess quantitatively that current high herbivore densities exceed the historical range of variation. In contrast, present fire activity lies within the range of variation of the last millennia, with fires (mainly human-set) mostly occurring during dry periods. Our paleodata highlight the need of controlling the densities of wild ungulates to preserve ecosystem composition and functioning. We also urge to restore Betula populations in suitable habitats where they mostly disappeared because of excessive human activities.

The Apparent Resilience of the Dry Tropical Forests of the Nicaraguan Region of the Central American Dry Corridor to Variations in Climate Over the Last C. 1200 Years

The Central American Dry Corridor (CADC) is the most densely populated area of the Central American Isthmus and is subject to the greatest variability in precipitation between seasons. The vegetation of this region is composed of Dry Tropical Forests (DTF), which are suggested to be highly susceptible to variations in climate and anthropogenic development. This study examines the vulnerability of past DTF surrounding the Asese peninsula, Nicaragua to climatic and anthropogenic disturbances over the past c. 1200 years. Past vegetation, climate, burning, and animal abundance were reconstructed using proxy analysis of fossil pollen, diatoms, macroscopic charcoal, and Sporormiella. Results from this research suggest that DTF have been highly resilient to past climatic and anthropogenic perturbations. Changes in DTF structure and composition appear to be linked to the abundance and intensity of fire. Pre-Columbian anthropogenic impacts on DTF are not detected in the record; however, DTF taxa decline slightly after European contact (1522 C.E.). Overall the DTF for the Nicaraguan region of the CADC were found to be highly resilient to both climatic and anthropogenic disturbances, suggesting that this region will continue to be resilient in the face of future population expansion and climatic variation.

A Continuous Palynological Record of Forest Clearing at Rano Kao (Easter Island, SE Pacific) During the Last Millennium: Preliminary Report

Easter Island (Rapa Nui) deforestation has traditionally been viewed as a single event, synchronous in time and space across the island and caused by Polynesian settlers. However, recent studies have challenged this idea, introducing the concept of spatiotemporal heterogeneity and suggesting a role for climate change. This paper presents a continuous paleovegetation record of the last millennium (~960 to ~1710 CE), based on palynological analysis of a core from Lake Kao. During this time interval, deforestation was gradual, with three main pulses at ~1070 CE, ~1410 CE, and ~1600 CE, likely driven by drought, anthropogenic practices (mostly fire), or the coupling of both. Some forest regeneration trends have been documented after the first and the second deforestation pulses. Forests were totally removed by 1600 CE, coinciding with the full permanent human settlement of the Kao area. Comparison with other continuous palynological records available for the last millennium (Aroi marsh and Lake Raraku) confirms that forest clearing was heterogeneous in time and space, rather than synchronous island-wide.

Benthic studies in LTER sites: the use of taxonomy surrogates in the detection of long-term changes in lagoonal benthic assemblages

In benthic studies, the identification of organisms at the species level is known to be the best source for ecological and biological information even if time-consuming and expensive. However, taxonomic sufficiency (TS) has been proposed as a short-cut method for quantifying changes in biological assemblages in environmental monitoring. In this paper, we set out to determine whether and how the taxonomic complexity of a benthic assemblage influences the results of TS at two different long-term ecological research (LTER) sites in the Po delta region (north-eastern Italy). Specifically, we investigated whether TS can be used to detect natural and human-driven patterns of variation in benthic assemblages from lagoonal soft bottoms. The first benthic dataset was collected from 1996 to 2015 in a “choked” lagoon, the Valli di Comacchio, a lagoon characterised by long water residence times and heavy eutrophication, while the second was collected from 2004 to 2010 in a “leaky” lagoon, the Sacca di Goro, a coastal area with human pressure limited to aquaculture. Univariate and multivariate statistical analyses were used to assess differences in the taxonomic structure of benthic assemblages and to test TS on the two different datasets. TS seemed to work from species to family level at both sites, despite a higher natural variability of environmental conditions combined with multiple anthropogenic stressors. Therefore, TS at the family level may represent effective taxonomic surrogates across a range of environmental contexts in lagoon environments. Since the structure of the community and the magnitude of changes could influence the efficiency of taxonomic surrogates and data transformations in long-term monitoring, we also suggest periodic analyses at finer taxonomic levels in order to check the efficiency of the application of taxonomic substitutes in routine monitoring programmes in lagoon systems.

Tracing lake mixing and oxygenation regime using the Fe/Mn ratio in varved sediments: 2000 year-long record of human-induced changes from Lake Żabińskie (NE Poland)

This study explores the long-term drivers of changes in lake mixing regime and the causes of lacustrine anoxia in the 2000 year-long, varved sediment record from Lake Żabińskie in northeastern Poland. Annually resolved geochemical data (μXRF and CNS) and pollen data were used to find links between changes in catchment land use and lake mixing regime. Furthermore, we tested the applicability of the Fe/Mn ratio for the reconstruction of past water ventilation. Multivariate statistical analyses show that Fe and Mn were mostly independent of terrestrial inputs and lake trophy, meaning that the Fe/Mn ratio mainly responded to changes in redox potential in hypolimnetic waters. Characteristic changes of the Fe/Mn ratio corresponded to transformations of woodland cover in the catchment as registered by changes of the arboreal/non-arboreal pollen ratio. Six main phases of different lake mixing intensity were distinguished. The local landscape was more open during phases of intensified human impact and catchment deforestation, leading to the intensification of lake mixing. At times of negligible human impact, the catchment was mostly wooded, and thus the lake was well sheltered from intense wind-driven mixing. This led to periods of prolonged anoxia. The Fe/Mn record accurately traced past changes in lake mixing intensity and related shifts in water column oxygenation. During the last two millennia, the mixing regime of Lake Żabińskie mostly depended on human activity in the catchment and landscape openness, while long periods of anoxia were not exclusive to only the most recent sediments.

Geoarchaeological evidence from Angkor, Cambodia, reveals a gradual decline rather than a catastrophic 15th-century collapse

Alternative models exist for the movement of large urban populations following the 15th-century CE abandonment of Angkor, Cambodia. One model emphasizes an urban diaspora following the implosion of state control in the capital related, in part, to hydroclimatic variability. An alternative model suggests a more complex picture and a gradual rather than catastrophic demographic movement. No decisive empirical data exist to distinguish between these two competing models. Here we show that the intensity of land use within the economic and administrative core of the city began to decline more than one century before the Ayutthayan invasion that conventionally marks the end of the Angkor Period. Using paleobotanical and stratigraphic data derived from radiometrically dated sediment cores extracted from the 12th-century walled city of Angkor Thom, we show that indicia for burning, forest disturbance, and soil erosion all decline as early as the first decades of the 14th century CE, and that the moat of Angkor Thom was no longer being maintained by the end of the 14th century. These data indicate a protracted decline in occupation within the economic and administrative core of the city, rather than an abrupt demographic collapse, suggesting the focus of power began to shift to urban centers outside of the capital during the 14th century.

Assessing the impact of long-term changes in climate and atmospheric deposition on a shallow alpine lake from southeast Tibet

Regional warming and atmospheric nitrogen deposition have been widely recorded to impact remote catchments and alpine lakes; however, their independent roles and interactions have rarely been identified. Here, we combined down-core analyses of sedimentary mercury (Hg) and aluminum (Al) with multiple proxies (i.e. nitrogen stable isotope, chlorophyll a pigments, diatoms) for a radiometrically-dated sediment core of an alpine lake in southeast Tibet to track the atmospheric deposition of pollutants, and to examine possible effects of climate and catchment forcing over the past three centuries. The sediment data revealed that airborne deposition of Hg was recorded from the ~1860s, with an accelerating increase in anthropogenic Hg flux since the ~1960s. A synchronous decrease in reconstructed lake-water TOC indicated that acid deposition may have affected lake-water carbon concentrations and impaired catchment export of decomposed organic matter (OM). A moderate depletion of bulk sediment δ¹⁵N started from the ~1820s, but was followed by an enriching trend after the ~1970s. This positive shift of δ¹⁵N was associated with elevated sediment OM and decreased catchment runoff of clastic materials (as inferred by Al). Sediment OM content displayed an accelerating increase from the ~1960s, with an increased input of autochthonous sources (i.e. lower bulk sediment C:N ratios), such as algae (as inferred by sedimentary chlorophyll a pigments). Meanwhile, climate warming and decreased lake-water TOC enhanced the production of algae, which was characterized by a more enriched δ¹⁵N signal than that of allochthonous OM. Furthermore, atmospheric acid deposition was significantly related to diatom assemblage changes, with an increase in acidophilous taxa. Our sediment evidence revealed the dominating impact of climate and catchment processes on lake-water chemistry and algal shifts in the context of atmospheric nitrogen deposition, and highlighted an increasing link of external forcing with in-lake processes in enriching sediment δ¹⁵N signal over the last few decades.