A paleoecological context to assess the development of oak forest in Colombia: A comment on Zorilla-Azcué, S., Gonzalez-Rodríguez, A., Oyama, K., González, M.A., & Rodríguez-Correa, H., The DNA history of a lonely oak: Quercus humboldtii phylogeography in the Colombian Andes. Ecology and Evolution 2021, doi: 10.100-2/ ece3.7529

The present “comment” on Zorilla-Azcué et al.’s paper “The DNA history of a lonely oak: Quercus humboldtii phylogeography in the Colombian Andes. Ecology and Evolution 2021, doi:10.100-2/ece3.7529” provides the paleoecological understanding of oak forest since Quercus became apparent in the Northern Andes three glacial–interglacial cycles ago. The interpretation of phylogeographical data is placed in an up-to-date paleoecological context. We arrived at sharper conclusions how genetic diversity between Q. humboldtii populations might have been driven by the dynamic environmental theatre of the recent Pleistocene. This paleoecological context also serves the potential future analyses of other arboreal taxa from the Andean montane forest belt. We show that hypotheses to be tested should grow out of phylogenetic analysis and paleoecological understanding together.publishedVersio

Geochronological database and classification system for age uncertainties in Neotropical pollen records.

The newly updated inventory of palaeoecological research in Latin America offers an important overview of sites available for multi-proxy and multi-site purposes. From the collected literature supporting this inventory, we collected all available age model metadata to create a chronological database of 5116 control points (e.g. 14C, tephra, fission track, OSL, 210Pb) from 1097 pollen records. Based on this literature review, we present a summary of chronological dating and reporting in the Neotropics. Difficulties and recommendations for chronology reporting are discussed. Furthermore, for 234 pollen records in northwest South America, a classification system for age uncertainties is implemented based on chronologies generated with updated calibration curves. With these outcomes age models are produced for those sites without an existing chronology, alternative age models are provided for researchers interested in comparing the effects of different calibration curves and age-depth modelling software, and the importance of uncertainty assessments of chronologies is highlighted. Sample resolution and temporal uncertainty of ages are discussed for different time windows, focusing on events relevant for research on centennial- to millennial-scale climate variability. All age models and developed R scripts are publicly available through figshare, including a manual to use the scripts

60 years of scientific deep drilling in Colombia: The north Andean guide to the Quaternary

We sketch the initial history of collecting deep cores in terrestrial and marine sedimentary basins and ice cores to study environmental and climate change. Subsequently, we focus on the development of long records from the Northern Andes. The 586 m long pollen record from ancient Lake Bogotá reflects the last 2.25 × 106 years with ∼ 1.2 kyr resolution, whereas the sediment core reflects almost the complete Quaternary. The 58 m long composite core from Lake Fúquene covers the last 284 ka with ∼ 60 years resolution. We address the various challenges and limitations of working with deep continental cores. For the tropics, the presence of these deep cores has made the Northern Andes a key area in developing and testing hypotheses in the fields of ecology, paleobiogeography, and climate change. We summarize the results in the figures, and for details on the paleoenvironmental reconstructions, we refer to the corresponding literature. We provide an overview of the literature on long continental records from all continents (see the Supplement). Based on our 50 years of experience in continental core drilling, developing a research capacity to analyze the large amounts of samples, and keeping a team together to publish the results, we listed suggestions in support of deep continental records aimed at studying environmental and climate change over long intervals of time.publishedVersio

Long-Term Vegetation Dynamics in a Megadiverse Hotspot: The Ice-Age Record of a Pre-montane Forest of Central Ecuador.

Tropical ecosystems play a key role in many aspects of Earth system dynamics currently of global concern, including carbon sequestration and biodiversity. To accurately understand complex tropical systems it is necessary to parameterise key ecological aspects, such as rates of change (RoC), species turnover, dynamism, resilience, or stability. To obtain a long-term (>50 years) perspective on these ecological aspects we must turn to the fossil record. However, compared to temperate zones, collecting continuous sedimentary archives in the lowland tropics is often difficult due to the active landscape processes, with potentially frequent volcanic, tectonic, and/or fluvial events confounding sediment deposition, preservation, and recovery. Consequently, the nature, and drivers, of vegetation dynamics during the last glacial are barely known from many non-montane tropical landscapes. One of the first lowland Amazonian locations from which palaeoecological data were obtained was an outcrop near Mera (Ecuador). Mera was discovered, and analysed, by Paul Colinvaux in the 1980s, but his interpretation of the data as indicative of a forested glacial period were criticised based on the ecology and age control. Here we present new palaeoecological data from a lake located less than 10 km away from Mera. Sediment cores raised from Laguna Pindo (1250 masl; 1°27'S, 78°05'W) have been shown to span the late last glacial period [50-13 cal kyr BP (calibrated kiloyears before present)]. The palaeoecological information obtained from Laguna Pindo indicate that the region was characterised by a relatively stable plant community, formed by taxa nowadays common at both mid and high elevations. was the dominant taxon until around 30 cal kyr BP, when it was replaced by , Asteraceae and among other taxa. Heat intolerant taxa including , , and peaked around the onset of the Last Glacial Maximum (c. 21 cal kyr BP). The results obtained from Laguna Pindo support Colinvaux's hypothesis that glacial cooling resulted in a reshuffling of taxa in the region but did not lead to a loss of the forest structure. Wide tolerances of the plant species occurring to glacial temperature range and cloud formation have been suggested to explain Pindo forest stability. This scenario is radically different than the present situation, so vulnerability of the tropical pre-montane forest is highlighted to be increased in the next decades

Ecosystem services show variable responses to future climate conditions in the Colombian páramos

Background: The páramos, the high-elevation ecosystems of the northern Andes, are well-known for their high species richness and provide a variety of ecosystem services to local subsistence-based communities and regional urbanizations. Climate change is expected to negatively affect the provision of these services, but the level of this impact is still unclear. Here we assess future climate change impact on the ecosystem services provided by the critically important páramos of the department of Boyacá in Colombia, of which over 25% of its territory is páramo. Methods: We first performed an extensive literature review to identify useful species of Boyacá, and selected 103 key plant species that, based on their uses, support the provision of ecosystem services in the páramos. We collated occurrence information for each key species and using a Mahalanobis distance approach we applied climate niche modelling for current and future conditions. Results: We show an overall tendency of reduction in area for all ecosystem services under future climate conditions (mostly a loss of 10% but reaching up to a loss of 40%), but we observe also increases, and responses differ in intensity loss. Services such as Food for animals, Material and Medicinal, show a high range of changes that includes both positive and negative outcomes, while for Food for humans the responses are mostly substantially negative. Responses are less extreme than those projected for individual species but are often complex because a given ecosystem service is provided by several species. As the level of functional or ecological redundancy between species is not yet known, there is an urgency to expand our knowledge on páramos ecosystem services for more species. Our results are crucial for decision-makers, social and conservation organizations to support sustainable strategies to monitor and mitigate the potential consequences of climate change for human livelihoods in mountainous settings.publishedVersio

Rate-of-change analysis in palaeoecology revisited: a new approach

Dynamics in the rate of compositional change (rate-of-change; RoC), preserved in paleoecological sequences, are thought to reflect changes due to exogenous (climate and human forcing) or endogenous (local dynamics and biotic interactions) drivers. However, changes in sedimentation rates and sampling strategies can result in an uneven distribution of time intervals and are known to affect RoC estimates. Furthermore, there has been relatively little exploration of the implications of these challenges in quantifying RoC in paleoecology. Here, we introduce R-Ratepol – an easy-to-use R package – that provides a robust numerical technique for detecting and summarizing RoC patterns in complex multivariate time-ordered stratigraphical sequences. First, we compare the performance of common methods of estimating RoC and detecting periods of high RoC (peak-point) using simulated pollen-stratigraphical data with known patterns of compositional change and temporal resolution. In addition, we propose a new method of binning with a moving window, which shows a more than 5-fold increase in the correct detection of peak-points compared to the more traditional way of using individual levels. Next, we apply our new methodology to four representative European pollen sequences and show that our approach also performs well in detecting periods of significant compositional change during known onsets of human activity, early land-use transformation, and changes in fire frequency. Expanding the approach using R-Ratepol to open-access paleoecological datasets in global databases, such as Neotoma, will allow future paleoecological and macroecological studies to quantify major changes in biotic composition or in sets of abiotic variables across broad spatiotemporal scales.publishedVersio

A guide to the processing and standardization of global palaeoecological data for large-scale syntheses using fossil pollen

Aim: Palaeoecological data are crucial for comprehending large-scale biodiversity patterns and the natural and anthropogenic drivers that influence them over time. Over the last decade, the availability of open-access research databases of palaeoecological proxies has substantially increased. These databases open the door to research questions needing advanced numerical analyses and modelling based on big-data compilations. However, compiling and analysing palaeoecological data pose unique challenges that require a guide for producing standardized and reproducible compilations. Innovation: We present a step-by-step guide of how to process fossil pollen data into a standardized dataset compilation ready for macroecological and palaeoecological analyses. We describe successive criteria that will enhance the quality of the compilations. Though these criteria are project and research question-dependent, we discuss the most important assumptions that should be considered and adjusted accordingly. Our guide is accompanied by an R-workflow—called FOSSILPOL—and corresponding R-package—called R-Fossilpol—that provide a detailed protocol ready for interdisciplinary users. We illustrate the workflow by sourcing and processing Scandinavian fossil pollen datasets and show the reproducibility of continental-scale data processing. Main Conclusions: The study of biodiversity and macroecological patterns through time and space requires large-scale syntheses of palaeoecological datasets. The data preparation for such syntheses must be transparent and reproducible. With our FOSSILPOL workflow and R-package, we provide a protocol for optimal handling of large compilations of fossil pollen datasets and workflow reproducibility. Our workflow is also relevant for the compilation and synthesis of other palaeoecological proxies and as such offers a guide for synthetic and cross-disciplinary analyses with macroecological, biogeographical and palaeoecological perspectives. However, we emphasize that expertise and informed decisions based on palaeoecological knowledge remain crucial for high-quality data syntheses and should be strongly embedded in studies that rely on the increasing amount of open-access palaeoecological data.publishedVersio