European Forest Cover During the Past 12,000 Years: A Palynological Reconstruction Based on Modern Analogs and Remote Sensing

Rolling down that mountain: microgeographical adaptive divergence during a fast population expansion along a steep environmental gradient in European beech

Forest tree populations harbour high genetic diversity thanks to large effective population sizes and strong gene flow, allowing them to diversify through adaptation to local environmental pressures within dispersal distance. Many tree populations also experienced historical demographic fluctuations, including spatial population contraction or expansions at various temporal scales, which may constrain their ability to adapt to environmental variations. Our aim is to investigate how recent contraction and expansion events interfere with local adaptation, by studying patterns of adaptive divergence between closely related stands undergoing environmentally contrasted conditions, and having or not recently expanded. To investigate genome-wide signatures of local adaptation while accounting for demography, we analysed divergence in a European beech population by testing pairwise differentiation among four tree stands at ~35k Single Nucleotide Polymorphisms from ~9k genomic regions. We applied three divergence outlier search methods resting on different assumptions and targeting either single SNPs or contiguous genomic regions, while accounting for the effect of population size variations on genetic divergence. We found 27 signals of selective signatures in 19 target regions. Putatively adaptive divergence involved all stand pairs. We retrieved signals both when comparing old-growth stands and recently colonised areas and when comparing stands within the old-growth area. Therefore, adaptive divergence processes have taken place both over short time spans, under strong environmental contrasts, and over short ecological gradients, in populations that have been stable in the long term. This suggests that standing genetic variation supports local, microgeographic divergence processes, which can maintain genetic diversity at the landscape level.

Floristic diversity and its relationships with human land use varied regionally during the Holocene

Humans have caused growing levels of ecosystem and diversity changes at a global scale in recent centuries but longer-term diversity trends and how they are affected by human impacts are less well understood. Analysing data from 64,305 pollen samples from 1,763 pollen records revealed substantial community changes (turnover) and reductions in diversity (richness and evenness) in the first ~1,500 to ~4,000 years of the Holocene epoch (starting 11,700 years ago). Turnover and diversity generally increased thereafter, starting ~6,000 to ~1,000 years ago, although the timings, magnitudes and even directions of these changes varied among continents, biomes and sites. Here, modelling these diversity changes, we find that most metrics of biodiversity change are associated with human impacts (anthropogenic land-cover change estimates for the last 8,000 years), often positively but the magnitudes, timings and sometimes directions of associations differed among continents and biomes and sites also varied. Once-forested parts of the world tended to exhibit biodiversity increases while open areas tended to decline. These regionally specific relationships between humans and floristic diversity highlight that human-biodiversity relationships have generated positive diversity responses in some locations and negative responses in others, for over 8,000 years.

Spatial ecology of moose in Sweden: Combined Sr-O-C isotope analyses of bone and antler

The study of spatial (paleo)ecology in mammals is critical to understand how animals adapt to and exploit their environment. In this work we analysed the 87Sr/86Sr, δ18O and δ13C isotope composition of 65 moose bone and antler samples from Sweden from wild-shot individuals dated between 1800 and 1994 to study moose mobility and feeding behaviour for (paleo)ecological applications. Sr data were compared with isoscapes of the Scandinavian region, built ad-hoc during this study, to understand how moose utilise the landscape in Northern Europe. The 87Sr/86Sr isoscape was developed using a machine-learning approach with external geo-environmental predictors and literature data. Similarly, a δ18O isoscape, obtained from average annual precipitation δ18O values, was employed to highlight differences in the isotope composition of the local environment vs. bone/antler. Overall, 82% of the moose samples were compatible with the likely local isotope composition (n = 53), suggesting that they were shot not far from their year-round dwelling area. 'Local' samples were used to calibrate the two isoscapes, to improve the prediction of provenance for the presumably 'non-local' individuals. For the latter (n = 12, of which two are antlers and ten are bones), the probability of geographic origin was estimated using a Bayesian approach by combining the two isoscapes. Interestingly, two of these samples (one antler and one bone) seem to come from areas more than 250 km away from the place where the animals were hunted, indicating a possible remarkable intra-annual mobility. Finally, the δ13C data were compared with the forest cover of Sweden and ultimately used to understand the dietary preference of moose. We interpreted a difference in δ13C values of antlers (13C-enriched) and bones (13C-depleted) as a joint effect of seasonal variations in moose diet and, possibly, physiological stresses during winter-time, i.e., increased consumption of endogenous 13C-depleted lipids.

Profile of tree-related microhabitats in the primeval Białowieża Forest: A benchmark for temperate woodlands

Tree-related Microhabitats (TreMs) are a key structural element having a significant impact on the biodiversity and functioning of forest ecosystems. Although forests enjoying long-term protection host richer and more abundant TreMs compared to managed stands, the quantity and quality of such microstructures in primeval temperate forests are unknown. This study investigates for the first time the assemblage of TreMs in the Białowieża Forest (BF), which is regarded as the last surviving fragment of pristine lowland forests in the temperate zone of Europe. Relatively undisturbed by human activity since the last glacial period, the BF ecosystem has remained remarkably intact, which may have given rise to its unique TreM assemblage. Here, we show that a primeval forest is characterized by an exceptionally high richness and density of TreMs compared to previously studied natural forests, and that the richness, density and diversity of TreMs are spatially heterogeneous at the micro-scale but homogeneous at the macro-scale. This indicates that adjacent small fragments of habitat (0.05 ha) may have different TreM profiles, but large patches of forest (several ha) host similar assemblages of TreMs. Our profile of TreMs depends on the basal area and density of living trees, the basal area of dead standing trees and the dominance of specific TreM-hosting tree species in a stand. Our study suggests that both the ecological continuity and complexity of a forest supporting many different tree species and the diversity of TreM-forming biota that typically occurs in primeval temperate forests are factors that appear to contribute to the observed profile of TreMs. The results of our study set a benchmark for the quantity and quality of TreMs in broadleaved temperate forests and indicate that the long-term spontaneous natural processes occurring in primeval forests lead to the emergence of ultra-rich, complex assemblages of TreMs.

Shedding light on the effects of climate and anthropogenic pressures on the disappearance of Fagus sylvatica in the Italian lowlands: evidence from archaeo-anthracology and spatial analyses

Fagus sylvatica is one of the most representative trees of the European deciduous broadleaved forests, yet the impact of changing climatic conditions and anthropogenic pressures (anthromes) on its presence and distribution in the coastal and lowland areas of the Mediterranean Basin has long been overlooked. Here, we first analysed the local forest composition in two different time intervals (350-300 Before Current Era, BCE and 150-100 BCE) using charred wood remains from the Etruscan site of Cetamura (Tuscany, central Italy). Additionally, we reviewed all the relevant publications and the wood/charcoal data obtained from anthracological analysis in F. sylvatica, focusing on samples that date back to 4000 years before present, to better understand the drivers of beech presence and distribution during the Late Holocene (LH) in the Italian Peninsula. Then, we combined charcoal and spatial analyses to test the distribution of beech woodland at low elevation during LH in Italy and to evaluate the effect of climate change and/or anthrome on the disappearance of F. sylvatica from the lowlands. We collected 1383 charcoal fragments in Cetamura belonging to 21 woody taxa, with F. sylvatica being the most abundant species (28 %), followed by other broadleaved trees. We identified 25 sites in the Italian Peninsula with beech charcoals in the last 4000 years. Our spatial analyses showed a marked decrease in habitat suitability of F. sylvatica from LH to the present (ca. 48 %), particularly in the lowlands (0-300 m above sea level, a.s.l.) and in areas included between 300-600 m a.s.l. with a subsequent shift upwards of the beech woodland of ca. 200 m from the past to the present. In the lowland areas, where F. sylvatica has disappeared, anthrome alone and climate + anthorme had a main effect on beech distribution whitin 0-50 m a.s.l., while the climate from 50 to 300 m a.s.l. Furthermore, climate affect also the beech distrinution in the areas >300 m a.s.l., while climate + anthrome and antrhome alone were mainly focused on the lowland areas. Our results highlight the advantage of combining different approaches, such as charcoal analysis and spatial analyses, to explore biogeographic questions about the past and current distribution of F. sylvatica, with important implications for today's forest management and conservation policies.

Population Genomics for Insect Conservation

Insects constitute vital components of ecosystems. There is alarming evidence for global declines in insect species diversity, abundance, and biomass caused by anthropogenic drivers such as habitat degradation or loss, agricultural practices, climate change, and environmental pollution. This raises important concerns about human food security and ecosystem functionality and calls for more research to assess insect population trends and identify threatened species and the causes of declines to inform conservation strategies. Analysis of genetic diversity is a powerful tool to address these goals, but so far animal conservation genetics research has focused strongly on endangered vertebrates, devoting less attention to invertebrates, such as insects, that constitute most biodiversity. Insects' shorter generation times and larger population sizes likely necessitate different analytical methods and management strategies. The availability of high-quality reference genome assemblies enables population genomics to address several key issues. These include precise inference of past demographic fluctuations and recent declines, measurement of genetic load levels, delineation of evolutionarily significant units and cryptic species, and analysis of genetic adaptation to stressors. This enables identification of populations that are particularly vulnerable to future threats, considering their potential to adapt and evolve. We review the application of population genomics to insect conservation and the outlook for averting insect declines.

The Quaternary lions of Ukraine and a trend of decreasing size in Panthera spelaea

The fossil record of the cave lion, Panthera spelaea, suggests a gradual decrease in body size, the process peaking just before the extinction of the species at the end of the Late Pleistocene. Such an evolutionary trend appears rather unusual for a large felid species and requires further investigation. This study reviews the cave lions of Ukraine, whose fossils are known from 46 localities dated from 800 kyr to 18–17 kyr ago, with a special emphasis on size changes through time. We describe several important finds including those of Panthera spelaea fossilis from Sambir, Panthera spelaea ssp. from Bilykh Stin Cave and Panthera spelaea spelaea from Kryshtaleva Cave. We make subspecific identifications of specimens from the region and focus on their size characteristics. Our analysis of Ukrainian cave lions agrees with the temporal trend of decreasing size, particularly accelerating during MIS 2, as exemplified by the extremely small female skull from Kryshtaleva Cave. We provide a direct AMS date for this specimen (22.0–21.5 cal kyr BP), which suggests that the Kryshtaleva lioness must have belonged to a Panthera spelaea spelaea population forced south by the spreading ice sheet. We discuss some palaeoecological aspects of the evolutionary history and eventual extinction of the cave lion. Finally, we review the subfossil records of the extant lion Panthera leo known from several Ukrainian sites archaeologically dated to 6.4–2.0 kyr BP. These finds most probably represent the Persian lion Panthera leo persica.

Demographic Expansions and the Emergence of Host Specialization in Genetically Distinct Ecotypes of the Tick-Transmitted Bacterium Anaplasma phagocytophilum

In Europe, genetically distinct ecotypes of the tick-vectored bacterium Anaplasma phagocytophilum circulate among mammals in three discrete enzootic cycles. To date, potential ecological factors that contributed to the emergence of these divergent ecotypes have been poorly studied. Here, we show that the ecotype that predominantly infects roe deer (Capreolus capreolus) is evolutionarily derived. Its divergence from a host generalist ancestor occurred after the last glacial maximum as mammal populations, including roe deer, recolonized the European mainland from southern refugia. We also provide evidence that this host specialist ecotype's effective population size (N_e) has tracked changes in the population of its roe deer host. Specifically, both host and bacterium have undergone substantial increases in N_e over the past 1,500 years. In contrast, we show that while it appears to have undergone a major population expansion starting ~3,500 years ago, in the past 500 years, the contemporary host generalist ecotype has experienced a substantial reduction in genetic diversity levels, possibly as a result of reduced opportunities for transmission between competent hosts. IMPORTANCE The findings of this study reveal specific events important for the evolution of host specialization in a naturally occurring, obligately intracellular bacterial pathogen. Specifically, they show that host range shifts and the emergence of host specialization may occur during periods of population growth in a generalist ancestor. Our results also demonstrate the close correlation between demographic patterns in host and pathogen for a specialist system. These findings have important relevance for understanding the evolution of host range diversity. They may inform future work on host range dynamics, and they provide insights for understanding the emergence of pathogens that have human and veterinary health implications.

rspatialdata: a collection of data sources and tutorials on downloading and visualising spatial data using R

Spatial and spatio-temporal data are used in a wide range of fields including environmental, health and social disciplines. Several packages in the statistical software R have been recently developed as clients for various databases to meet the growing demands for easily accessible and reliable spatial data. While documentation on how to use many of these packages exist, there is an increasing need for a one stop repository for tutorials on this information. In this paper, we present rspatialdata a website that provides a collection of data sources and tutorials on downloading and visualising spatial data using R. The website includes a wide range of datasets including administrative boundaries of countries, Open Street Map data, population, temperature, vegetation, air pollution, and malaria data. The goal of the website is to equip researchers and communities with the tools to engage in spatial data analysis and visualisation so that they can address important local issues, such as estimating air pollution, quantifying disease burdens, and evaluating and monitoring the United Nation’s sustainable development goals.

A new method based on surface-sample pollen data for reconstructing palaeovegetation patterns

AIM

Biomisation has been the most widely used technique to reconstruct past regional vegetation patterns because it does not require an extensive modern pollen dataset. However, it has well-known limitations including its dependence on expert judgement for the assignment of pollen taxa to plant functional types (PFTs) and PFTs to biomes. Here we present a new method that combines the strengths of biomisation with those of the alternative dissimilarity-based techniques.

LOCATION

The Eastern Mediterranean-Black Sea Caspian Corridor (EMBSeCBIO).

TAXON

Plants.

METHODS

Modern pollen samples, assigned to biomes based on potential natural vegetation data, are used to characterize the within-biome means and standard deviations of the abundances of each taxon. These values are used to calculate a dissimilarity index between any pollen sample and every biome, and thus assign the sample to the most likely biome. We calculate a threshold value for each modern biome; fossil samples with scores below the threshold for all modern biomes are thus identified as non-analogue vegetation. We applied the new method to the EMBSeCBIO region to compare its performance with existing reconstructions.

RESULTS

The method captured changes in the importance of individual taxa along environmental gradients. The balanced accuracy obtained for the EMBSeCBIO region using the new method was better than obtained using biomisation (77% vs. 65%). When the method was applied to high-resolution fossil records, 70% of the entities showed more temporally stable biome assignments than obtained using biomisation. The technique also identified likely non-analogue assemblages in a synthetic modern dataset and in fossil records.

MAIN CONCLUSIONS

The new method yields more accurate and stable reconstructions of vegetation than biomisation. It requires an extensive modern pollen dataset, but is conceptually simple, and avoids subjective choices about taxon allocations to PFTs and PFTs to biomes.

Pollen-Based Maps of Past Regional Vegetation Cover in Europe Over 12 Millennia—Evaluation and Potential

Realistic and accurate reconstructions of past vegetation cover are necessary to study past environmental changes. This is important since the effects of human land-use changes (e.g. agriculture, deforestation and afforestation/reforestation) on biodiversity and climate are still under debate. Over the last decade, development, validation, and application of pollen-vegetation relationship models have made it possible to estimate plant abundance from fossil pollen data at both local and regional scales. In particular, the REVEALS model has been applied to produce datasets of past regional plant cover at 1° spatial resolution at large subcontinental scales (North America, Europe, and China). However, such reconstructions are spatially discontinuous due to the discrete and irregular geographical distribution of sites (lakes and peat bogs) from which fossil pollen records have been produced. Therefore, spatial statistical models have been developed to create continuous maps of past plant cover using the REVEALS-based land cover estimates. In this paper, we present the first continuous time series of spatially complete maps of past plant cover across Europe during the Holocene (25 time windows covering the period from 11.7 k BP to present). We use a spatial-statistical model for compositional data to interpolate REVEALS-based estimates of three major land-cover types (LCTs), i.e., evergreen trees, summer-green trees and open land (grasses, herbs and low shrubs); producing spatially complete maps of the past coverage of these three LCTs. The spatial model uses four auxiliary data sets—latitude, longitude, elevation, and independent scenarios of past anthropogenic land-cover change based on per-capita land-use estimates (“standard” KK10 scenarios)—to improve model performance for areas with complex topography or few observations. We evaluate the resulting reconstructions for selected time windows using present day maps from the European Forest Institute, cross validate, and compare the results with earlier pollen-based spatially-continuous estimates for five selected time windows, i.e., 100 BP-present, 350–100 BP, 700–350 BP, 3.2–2.7 k BP, and 6.2–5.7 k BP. The evaluations suggest that the statistical model provides robust spatial reconstructions. From the maps we observe the broad change in the land-cover of Europe from dominance of naturally open land and persisting remnants of continental ice in the Early Holocene to a high fraction of forest cover in the Mid Holocene, and anthropogenic deforestation in the Late Holocene. The temporal and spatial continuity is relevant for land-use, land-cover, and climate research.

Reassessing the role of climate change in the Tupi expansion (South America, 5000-500 BP)

The expansion of forest farmers across tropical lowland South America during the Late Holocene has long been connected to climate change. The more humid conditions established during the Late Holocene are assumed to have driven the expansion of forests, which would have facilitated the dispersal of cultures that practised agroforestry. The Tupi, a language family of widespread distribution in South America, occupies a central place in the debate. Not only are they one of the largest families in the continent, but their expansion from an Amazonian homeland has long been hypothesized to have followed forested environments wherever they settled. Here, we assess that hypothesis using a simulation approach. We employ equation-based and cellular automaton models, simulating demic-diffusion processes under two different scenarios: a null model in which all land cells can be equally settled, and an alternative model in which non-forested cells cannot be settled or delay the expansion. We show that including land cover as a constraint to movement results in a better approximation of the Tupi expansion as reconstructed by archaeology and linguistics.

Spatially Continuous Land-Cover Reconstructions Through the Holocene in Southern Sweden

Climate change and human activities influence the development of ecosystems, with human demand of ecosystem services altering both land use and land cover. Fossil pollen records provide time series of vegetation characteristics, and the aim of this study was to create spatially continuous reconstructions of land cover through the Holocene in southern Sweden. The Landscape Reconstruction Algorithm (LRA) was applied to obtain quantitative reconstructions of pollen-based vegetation cover at local scales, accounting for pollen production, dispersal, and deposition mechanisms. Pollen-based local vegetation estimates were produced from 41 fossil pollen records available for the region. A comparison of 17 interpolation methods was made and evaluated by comparing with current land cover. Simple kriging with cokriging using elevation was selected to interpolate the local characteristics of past land cover, to generate more detailed reconstructions of trends and degree of variability in time and space than previous studies based on pollen data representing the regional scale. Since the Mesolithic, two main processes have acted to reshape the land cover of southern Sweden, originally mostly covered by broad-leaved forests. The natural distribution limit of coniferous forest has moved southward during periods with colder climate and retracted northward during warmer periods, and human expansion in the area and agrotechnological developments has led to a gradually more open landscape, reaching maximum openness at the beginning of the 20th century. The recent intensification of agriculture has led to abandonment of less fertile agricultural fields and afforestation with conifer forest.

Languedoc lagoon environments and man: Building a modern analogue botanical macroremain database for understanding the role of water and edaphology in sedimentation dynamics of archaeobotanical remains at the Roman port of Lattara (Lattes, France)

A new method to evaluate archaeological wetland sites in a more objective way was tested. Different wetland environments have been sampled in areas of a nature reserve and their macroremain content analysed to build a modern analogue dataset. This dataset was then used to characterise archaeological samples from a navigation channel from the Roman port city Lattara. In the modern analogue samples, the different wetland types (saline/brackish or fresh water) could be differentiated in the correspondence analysis. Within these groups, the sampled area of the littoral (submerged, shoreline, unsubmerged) could also be differentiated. This dataset can therefore provide a basis for the interpretation of the nature and degree of aquatic influence and layer formation processes in archaeobotanical records of coastal sites. In the tested archaeological samples from the navigation channel of Lattara, changes in space and time could be tracked using the modern analogue dataset and geoarchaeological information. The channel lost its fresh water supply and silted up over a short period of time (approx. 100 years).

Archaeological assessment reveals Earth’s early transformation through land use

Environmentally transformative human use of land accelerated with the emergence of agriculture, but the extent, trajectory, and implications of these early changes are not well understood. An empirical global assessment of land use from 10,000 years before the present (yr B.P.) to 1850 CE reveals a planet largely transformed by hunter-gatherers, farmers, and pastoralists by 3000 years ago, considerably earlier than the dates in the land-use reconstructions commonly used by Earth scientists. Synthesis of knowledge contributed by more than 250 archaeologists highlighted gaps in archaeological expertise and data quality, which peaked for 2000 yr B.P. and in traditionally studied and wealthier regions. Archaeological reconstruction of global land-use history illuminates the deep roots of Earth’s transformation and challenges the emerging Anthropocene paradigm that large-scale anthropogenic global environmental change is mostly a recent phenomenon.

Forest Landscape Change and Preliminary Study on Its Driving Forces in Ślęża Landscape Park (Southwestern Poland) in 1883–2013

Changes in forest landscapes have been connected with human activity for centuries and can be considered one of the main driving forces of change from a global perspective. The spatial distribution of forests changes along with the geopolitical situation, demographic changes, intensification of agriculture, urbanization, or changes in land use policy. However, due to the limited availability of historical data, the driving forces of changes in forest landscapes are most often considered in relation to recent decades, without taking long-term analyses into account. The aim of this paper is to determine the level and types of landscape changes and make preliminary study on natural and socio-economic factors on changes in forest landscapes within the protected area, Ślęża Landscape Park, and its buffer zone using long-term analyses covering a period of 140 years (1883–2013). A comparison of historical and current maps and demographic data related to three consecutive periods of time as well as natural and location factors by using the ArcGIS software allows the selected driving forces of forest landscape transformations to be analyzed. We took into account natural factors such as the elevation, slope, and exposure of the hillside and socio-economic drivers like population changes, distances to centers of municipalities, main roads, and built-up areas.

Highly diverse Bronze Age population dynamics in Central-Southern Europe and their response to regional climatic patterns

The reconstruction of past demographic patterns is a fundamental step towards a better understanding of human-environment relations, especially in terms of quantifiable anthropic impact and population susceptibility to environmental changes. The recently developed Summed Calibrated Probability Distributions (SCPD) approach, based on large collections of archaeological radiocarbon dates, provides a new tool to obtain continuous prehistoric population curves suitable for comparison with palaeoenvironmental time series. Despite a wide application in Mesolithic and Neolithic contexts worldwide, the use of the SCPD method remains rare for post-Neolithic societies. Our aim is to address this visible gap and apply the SCPD approach to South European archeological contexts between the Bronze Age and the transition into the Iron Age (1800-800 cal. BC), then evaluating these results against local archeological narratives and palaeoecological data. We first test the SCPD method at a supra regional scale, ranging from the Ebro to the Danube rivers, and subsequently in five selected regions within this area. We then compare the regional population curves to climate data reconstructed from local palynological records. Our results highlight the contrast between a stable supra regional demographic trend and more dynamic regional patterns. We do not observe any convincing long-term correlations between population and climate, but localized episodes of demographic stagnation or decline are present in conjunction with climatic shifts or extremes. Nevertheless, climate change as a triggering factor should be considered with caution, especially in peripheral areas where the archaeological data is faint, or where local evidence points to contemporaneous, ongoing landscape overexploitation.