Reflections on the Use of Ecological Attributes and Traits in Quaternary Botany

There has been an upsurge of interest and research activity in trait-based approaches in ecology, biogeography, and macroecology. I discuss if this upsurge has impacted Quaternary botany (the study of plant remains preserved in sediments). I show that ecological attributes (including traits) have played and continue to play an integral part in the interpretation of Quaternary botanical data in terms of reconstructing past environments and interpreting long-term changes in plant assemblages. This use started over 120 years ago and continues to the present. It is unclear if a “new” Quaternary botany based on traits will develop because of the taxonomic limitations of much Quaternary botanical data.publishedVersio

High-elevation limits and the ecology of high-elevation vascular plants: legacies from Alexander von Humboldt

Alexander von Humboldt and Aimé Bonpland in their Essay on the Geography of Plants discuss what was known in 1807 about the elevational limits of vascular plants in the Andes, North America, and the European Alps and suggest what factors might influence these upper elevational limits. Here, in light of current knowledge and techniques, I consider which species are thought to be the highest vascular plants in twenty mountain areas and two polar regions on Earth. I review how one can try to compare elevational limits in different parts of Earth. I discuss recent advances in high-elevation plant ecology that would surely have fascinated von Humboldt such as the special snow-roots in some snow-bed plants and the coldest place on Earth where a vascular plant is growing. I briefly outline an ignored von Humboldt legacy, Mendelssohn’s Humboldt Cantata. In conclusion I summarise the foundations and legacies that von Humboldt created for global high-elevation ecology and biogeography.publishedVersio

What is natural? The importance of a long-term perspective in biodiversity conservation and management

Ecosystems change in response to factors such as climate variability, invasions, and wildfires. Most records used to assess such change are based on short-term ecological data or satellite imagery spanning only a few decades. In many instances it is impossible to disentangle natural variability from other, potentially significant trends in these records, partly because of their short time scale. We summarize recent studies that show how paleoecological records can be used to provide a longer temporal perspective to address specific conservation issues relating to biological invasions, wildfires, climate change, and determination of natural variability. The use of such records can reduce much of the uncertainty surrounding the question of what is ‘natural’ and thereby start to provide important guidance for long-term management and conservation

distantia: an open-source toolset to quantify dissimilarity between multivariate ecological time-series

There is a large array of methods to extract knowledge and perform ecological forecasting from ecological time‐series. However, in spite of its importance for data‐mining, pattern‐matching and ecological synthesis, methods to assess their similarity are scarce. We introduce distantia (v1.0.1), an R package providing general toolset to quantify dissimilarity between ecological time‐series, independently of their regularity and number of samples. The functions in distantia provide the means to compute dissimilarity scores by time and by shape and assess their significance, evaluate the partial contribution of each variable to dissimilarity, and align or combine sequences by similarity. We evaluate the sensitivity of the dissimilarity metrics implemented in distantia, describe its structure and functionality, and showcase its applications with two examples. Particularly, we evaluate how geographic factors drive the dissimilarity between nine pollen sequences dated to the Last Interglacial, and compare the temporal dynamics of climate and enhanced vegetation index of three stands across the range of the European beech. We expect this package may enhance the capabilities of researchers from different fields to explore dissimilarity patterns between multivariate ecological time‐series, and aid in generating and testing new hypotheses on why the temporal dynamics of complex‐systems changes over space and time.publishedVersio

High resolution Late-glacial and early-Holocene summer air temperature records from Scotland inferred from Chironomid assemblages

Lateglacial and early-Holocene mean July air temperatures have been reconstructed, using a chironomid-based inference model, from lake-sediment sequences from Abernethy Forest, in the eastern Highlands of Scotland, and Loch Ashik, on the Isle of Skye in north-west Scotland. Chronology for Abernethy Forest was derived from radiocarbon dates of terrestrial plant macrofossils deposited in the lake sediments. Chronology for Loch Ashik was derived from tephra layers of known ages, the first age-depth model of this kind. Chironomid-inferred temperatures peak early in the Lateglacial Interstadial and then gradually decline by about 1 °C to the beginning of the Younger Dryas (YD). At Abernethy Forest, the Lateglacial Interstadial is punctuated by three centennial-scale cold oscillations which appear to be synchronous with the Greenland Interstadial events GI-1d, when temperatures at Abernethy fell by 5.9 °C, GI-1c, when temperatures fell by 2.3 °C, and GI-1b, when temperatures fell by 2.8 °C. At Loch Ashik only the oscillation correlated with GI-1d is clearly defined, when temperatures fell by 3.8 °C. The start of the YD is clearly marked at both sites when temperatures fell by 5.5 °C at Abernethy Forest and 2.8 °C at Loch Ashik. A warming trend is apparent during the late-YD at Abernethy Forest but at Loch Ashik late-YD temperatures became very cold, possibly influenced by its close proximity to the Skye ice-field. The rapidly rising temperatures at the YD – Holocene transition occur about 300 years earlier at both sites than changes in sediment lithology and loss-on-ignition. The temperature trends at both sites are broadly similar, although between-site differences may result from the influence of local factors. Similar climate trends are found at other sites in the northern British Isles. However, the British summer temperature records differ in detail from trends in the oxygen-isotope records from the Greenland ice-cores and from other chironomid-inferred temperature records available from Scandinavia, north-west Europe and central Europe, which suggest important differences in the influence of climatic forcing at regional scales.publishedVersio

An expanded calibration model for inferring lakewater and air temperatures from fossil chironomid assemblages in northern Fennoscandia

Chironomid-temperature inference models based on an expanded data set of surface-sediment and limnological data from 53 Subarctic lakes in northern Fennoscandia have been developed using eight different numerical techniques, each based on slightly different underlying statistical models or ecological assumptions. The study sites are mostly small, shallow, bathymetrically simple, oligotrophic lakes, with a pH range from 5.0 to 7.8, a total organic carbon range from 2.5 to 12.6 mg l- 1, a mean July lakewater temperature ranging from 6.1 to 15.4°C, and a mean July air temperature ranging from 8.5 to 14.9°C. A series of redundancy analyses (RDA) identified sediment organic content, maximum lake depth, and lakewater temperature as being the most important explanatory variables. Variance partitioning by partial RDAs further suggested that each of these variables accounted for a significant fraction of variance independent from each other. Different cali bration models were assessed on the basis of their statistical performance, with particular reference to prediction errors and the amount of bias along the temperature gradient. Of the eight calibration models, modern analogue techniques, weighted averaging partial least squares, simple weighted averaging with an‘inverse’ deshrinking regression, and linear partial least squares consistently performed best. These methods can all be used to develop transfer functions for surface-water and air July temperatures with a root mean squared error of predic tion (RMSEP) of about 1.5–1.6°C (water temperature) and 0.8–1.1°C (air temperature), as assessed by leave-one-out cross-validation. The resulting models do, however, have relatively high maximum biases (up to 3.9°C) in the lowest segments of the air and water temperature gradients, highlighting the need for enlarging and expanding the calibration data set to include lower temperatures

Weighted average regression and environmental calibration as a tool for quantifying climate-driven changes in vegetation

Aims: Studies of the climatic responses of plant assemblages via vegetation-based environmental reconstructions by weighted averaging (WA) regression and calibration are a recent development in modern vegetation ecology. However, the performance of this technique for plot-based vegetation datasets has not been rigorously tested. We assess the estimation accuracy of the WA approach by comparing results, mainly the root mean square error of prediction (RMSEP) of WA regressions for six different vegetation datasets (total species, high-frequency species and low-frequency species as both abundance and incidence) each from two sites. Methods: Vegetation-inferred environment (plot elevation) calibrated over time is used to quantify the elevational shift in species assemblages. Accuracy of the calibrations is assessed by comparing the linear regression models developed for estimating elevational shifts. The datasets were also used for the backward predictions to check the robustness of the forward predictions. Important Findings: WA regression has a fairly high estimation accuracy, especially with species incidence datasets. However, estimation bias at the extremes of the environmental gradient is evident with all datasets. Out of eight sets (each set with a model for total species, low-frequency species and high-frequency species) of WA regression models, the lowest RMSEPs are produced in the four models based on the total species datasets and in three models based on the high-frequency species only. The inferred environment mirrored the estimation precision of the WA regressions, i.e. precise WA regression models produced more accurate calibrated environmental estimates, which, in turn, resulted in regression models with a higher adjusted r2 for estimating the elevational shift in the species assemblages. Reliable environmental estimates for plot-based datasets can be achieved by WA regression and calibration, although the edge effect may be evident if species turnover is high along an extensive environmental gradient. Species incidence (0/1) data may improve the estimation accuracy by minimizing any potential census and field estimation errors that are more likely to occur in species abundance datasets. Species data processing cannot guarantee the most reliable WA regression models. Instead, generally optimal estimations can be achieved by using all the species with a consistent taxonomy in the training and reconstruction datasets.acceptedVersio

Holocene changes in atmospheric circulation recorded in the oxygen-isotope stratigraphy of lacustrine carbonates from northern Sweden

The oxygen-isotope composition of local precipitation (d18OP) is reconstructed from carbonate lake-sediment components in a sediment core covering the last 10000 calendar years from Lake Tibetanus, a small, hydrologically open, groundwater-fed lake in the Abisko area, northern Sweden. Comparison of the d18OP history with a pollen-based palaeotemperature record from the same core clearly reveals pronounced deviations from the normally expected temporal d18OP-temperature relation (so-called ‘Dansgaard relation’) that may be a function of changing oceanicity. The transition from relatively moist, maritime conditions in the early Holo cene to a much drier climate after 6500 cal. BP is re‘ ected by major changes in forest extent and composition as recorded by pollen and plant macrofossil data. At the time of maximum in‘ uence of westerly air-mass circulation (high zonal index) c. 9500 cal. BP, brought about by high summer insolation and enhanced meridi onal pressure gradients, d18OP at Lake Tibetanus was about 2 higher than would be predicted by the modern isotope-temperature relation. The occurrence of long-term changes in d18OP-temperature relations, which are more sensitive measures of palaeoclimate than either d18OP or temperature alone, needs to be taken into account when extracting palaeoclimatic information from continental oxygen-isotope records

Chemical variations in Quercus pollen as a tool for taxonomic identification: Implications for long-term ecological and biogeographical research

Aim Fossil pollen is an important tool for understanding biogeographical patterns in the past, but the taxonomic resolution of the fossil‐pollen record may be limited to genus or even family level. Chemical analysis of pollen grains has the potential to increase the taxonomic resolution of pollen analysis, but present‐day chemical variability is poorly understood. This study aims to investigate whether a phylogenetic signal is present in the chemical variations of Quercus L. pollen and to assess the prospects of chemical techniques for identification in biogeographical research. Location Portugal. Taxon Six taxa (five species, one subspecies) of Quercus L., Q. faginea, Q. robur, Q. robur ssp. estremadurensis, Q. coccifera, Q. rotundifolia and Q. suber belonging to three sections: Cerris, Ilex and Quercus (Denk, Grimm, Manos, Deng, & Hipp, 2017). Methods We collected pollen samples from 297 individual Quercus trees across a 4° (~450 km) latitudinal gradient and determined chemical differences using Fourier‐transform infrared spectroscopy (FTIR). We used canonical powered partial least squares regression (CPPLS) and discriminant analysis to describe within‐ and between‐species chemical variability. Results We find clear differences in the FTIR spectra from Quercus pollen at the section level (Cerris: ~98%; Ilex: ~100%; Quercus: ~97%). Successful discrimination is based on spectral signals related to lipids and sporopollenins. However, discrimination of species within individual Quercus sections is more challenging: overall, species recall is ~76% and species misidentifications within sections lie between 18% and 31% of the test set. Main Conclusions Our results demonstrate that subgenus level differentiation of Quercus pollen is possible using FTIR methods, with successful classification at the section level. This indicates that operator‐independent FTIR approaches can surpass traditional morphological techniques using light microscopy. Our results have implications both for providing new insights into past colonization pathways of Quercus, and likewise for forecasting future responses to climate change. However, before FTIR techniques can be applied more broadly across palaeoecology and biogeography, our results also highlight a number of research challenges that still need to be addressed, including developing sporopollenin‐specific taxonomic discriminators and determining a more complete understanding of the effects of environmental variation on pollen‐chemical signatures in Quercus.publishedVersio

Does pollen-assemblage richness reflect floristic richness? A review of recent developments and future challenges

Current interest and debate on pollen-assemblage richness as a proxy for past plant richness have prompted us to review recent developments in assessing whether modern pollen-assemblage richness reflects contemporary floristic richness. We present basic definitions and outline key terminology. We summarise four basic needs in assessing pollen–plant richness relationships — modern pollen data, modern vegetation data, pollen–plant translation tables, and quantification of the co-variation between modern pollen and vegetation compositional data. We discuss three key estimates and one numerical tool — richness estimation, evenness estimation, diversity estimation, and statistical modelling. We consider the inherent problems and biases in assessing pollen–plant richness relationships — taxonomic precision, pollen-sample:pollen-population ratios, pollen-representation bias, and underlying concepts of evenness and diversity. We summarise alternative approaches to studying pollen–plant richness relationships. We show that almost all studies which have compared modern pollen richness with contemporary site-specific plant richness reveal good relationships between palynological richness and plant richness. We outline future challenges and research opportunities — interpreting past pollen-richness patterns, estimating richness from macrofossils, studying pollen richness at different scales, partitioning diversity and estimating beta diversity, estimating false, hidden, and dark richness, and considering past functional and phylogenetic diversity from pollen data. We conclude with an assessment of the current state-of-knowledge about whether pollen richness reflects floristic richness and explore what is known and unknown in our understanding of pollen–plant richness relationships.acceptedVersio