Habitat heterogeneity enables spatial and temporal coexistence of native and invasive macrophytes in shallow lake landscapes

Macrophyte invasive alien species (IAS) fitness is often hypothesised to be associated with beneficial environmental conditions (environmental matching) or species-poor communities. However, positive correlations between macrophyte IAS abundance and native plant richness can also arise, due to habitat heterogeneity (defined here as variation in abiotic and native biotic conditions over space and time). We analysed survey and palaeoecological data for macrophytes in satellite lakes along the Upper Lough Erne (ULE) system (Northern Ireland, UK), covering a gradient of eutrophication and connectivity to partition how environmental conditions, macrophyte diversity and habitat heterogeneity explained the abundance of Elodea canadensis, a widely distributed non-native macrophyte in Europe. E. canadensis abundance positively correlated with macrophyte richness at both the within- and between-lake scales indicating coexistence of native and invasive species over time. E. canadensis was also more prolific in highly connected and macrophyte-rich lakes, but sparser in the more eutrophic-isolated ones. Partial boosted regression trees revealed that in eutrophic-isolated lakes, E. canadensis abundances correlated with water clarity (negatively), plant diversity (positively), and plant cover (negatively) whereas in diverse-connected lakes, beta diversity (both positively and negatively) related to most greatly E. canadensis abundance. Dense macrophyte cover and unfavourable environmental conditions thus appear to confer invasibility resistance and sufficient habitat heterogeneity to mask any single effect of native biodiversity or environmental matching in controlling E. canadensis abundance. Therefore, in shallow lake landscapes, habitat heterogeneity variously enables the coexistence of native macrophytes and E. canadensis, reducing the often-described homogenisation effects of invasive macrophytes.Output Status: Forthcoming/Available Onlin

The evolving SARS-CoV-2 epidemic in Africa: Insights from rapidly expanding genomic surveillance

INTRODUCTION Investment in Africa over the past year with regard to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) sequencing has led to a massive increase in the number of sequences, which, to date, exceeds 100,000 sequences generated to track the pandemic on the continent. These sequences have profoundly affected how public health officials in Africa have navigated the COVID-19 pandemic. RATIONALE We demonstrate how the first 100,000 SARS-CoV-2 sequences from Africa have helped monitor the epidemic on the continent, how genomic surveillance expanded over the course of the pandemic, and how we adapted our sequencing methods to deal with an evolving virus. Finally, we also examine how viral lineages have spread across the continent in a phylogeographic framework to gain insights into the underlying temporal and spatial transmission dynamics for several variants of concern (VOCs). RESULTS Our results indicate that the number of countries in Africa that can sequence the virus within their own borders is growing and that this is coupled with a shorter turnaround time from the time of sampling to sequence submission. Ongoing evolution necessitated the continual updating of primer sets, and, as a result, eight primer sets were designed in tandem with viral evolution and used to ensure effective sequencing of the virus. The pandemic unfolded through multiple waves of infection that were each driven by distinct genetic lineages, with B.1-like ancestral strains associated with the first pandemic wave of infections in 2020. Successive waves on the continent were fueled by different VOCs, with Alpha and Beta cocirculating in distinct spatial patterns during the second wave and Delta and Omicron affecting the whole continent during the third and fourth waves, respectively. Phylogeographic reconstruction points toward distinct differences in viral importation and exportation patterns associated with the Alpha, Beta, Delta, and Omicron variants and subvariants, when considering both Africa versus the rest of the world and viral dissemination within the continent. Our epidemiological and phylogenetic inferences therefore underscore the heterogeneous nature of the pandemic on the continent and highlight key insights and challenges, for instance, recognizing the limitations of low testing proportions. We also highlight the early warning capacity that genomic surveillance in Africa has had for the rest of the world with the detection of new lineages and variants, the most recent being the characterization of various Omicron subvariants. CONCLUSION Sustained investment for diagnostics and genomic surveillance in Africa is needed as the virus continues to evolve. This is important not only to help combat SARS-CoV-2 on the continent but also because it can be used as a platform to help address the many emerging and reemerging infectious disease threats in Africa. In particular, capacity building for local sequencing within countries or within the continent should be prioritized because this is generally associated with shorter turnaround times, providing the most benefit to local public health authorities tasked with pandemic response and mitigation and allowing for the fastest reaction to localized outbreaks. These investments are crucial for pandemic preparedness and response and will serve the health of the continent well into the 21st century

Tree cover in the early Holocene in temperate Europe and implications for the practice of re-wilding in nature conservation

This thesis addresses the methodological challenges of determining the variability of large herbivore populations through time and their impact on European vegetation. Large herbivores are at the heart of conservation policy. However, opinions widely diverge on whether we should aim for fewer herbivores and managed populations or, on the contrary as advocated by the rewilding movement, more herbivores and self-regulating populations acting as ecosystem engineers. This controversy has roots in a debate regarding the nature of ecosystems before the prevalence of human activities. Baseline ecosystems are either described as continuous forest cover with passive large herbivores, or, in contrast, as mosaics with patchy forest cover driven inter alia by bison, aurochs and horses, now rare or extinct in Europe. The main obstacle in moving this debate forward is a poor understanding of large-herbivore densities in the past. I analysed modern pollen and spore assemblages from known environmental settings to improve palaeoecological interpretation of fossil assemblages dating from the pre-human (baseline) period. The sites investigated are the rewilded grasslands of the Oostvaardersplassen (The Netherlands), the mosaic habitats of The New Forest (UK) and the old-growth closedcanopy forest of Białowieża (Poland). I demonstrate that the common practice of interpreting pollen percentages fails to estimate past forest cover in situations with natural grazing. As an explanation, I suggest that pollen productivity fluctuates with biotic factors such as herbivory and canopy shading. As a result, new insights into the baseline debate require additional lines of evidence. In this thesis, I develop an existing methodology to reconstruct past herbivore presence using fossil dung fungal spores. I synthesise current knowledge of this method with an emphasis on spore identification and, finally, I demonstrate that dung fungal spore abundance in lake sediments can be translated into large herbivore numbers. The evidence presented in this thesis contributes to the debate on re-wilding and addresses a fundamental challenge of nature conservation in the human-dominated landscapes of Europe.</p

Do dung fungal spores make a good proxy for past distribution of large herbivores?

The importance of herbivory as a long-term driver of ecosystem change is a topic that has been hotly debated over the past few years. An understanding of the interaction between herbivores and ecosystems is particularly important for conservation policies aimed at re-wilding. Dung fungal spores have been highlighted as an important potential proxy to reconstruct large herbivore densities across past landscapes. However, this proxy appears to have been used and interpreted in a variety of ways in addition to highly variable taxonomic identification of dung fungal spores. Here we review studies that have utilised fungal spore assemblages to assess past herbivore presence and test the validity of this method. We aim to determine whether there is a set of identifiable dung fungal spores that can unequivocally track variation of large herbivore activity through time and across regions. Our meta-analysis identifies: spore types that are commonly found to be indicative of large herbivores and their geographical ranges, linkages between these spores and their biological origin, and the most appropriate quantitative method to express their abundance for comparisons through time and across sites

Data from: Quantification of population sizes of large herbivores and their long-term functional role in ecosystems using dung fungal spores

The relationship between large herbivore numbers and landscape cover over time is poorly understood. There are two schools of thought: one views large herbivores as relatively passive elements upon the landscape and the other as ecosystem engineers driving vegetation succession. The latter relationship has been used as an argument to support reintroductions of large herbivores onto many landscapes in order to increase vegetation heterogeneity and biodiversity through local-scale disturbance regimes. Most of the research examining the relationship between large herbivores and their impact on landscapes has used extant studies. An alternative approach is to estimate the impact of variations in herbivore populations through time using fossil dung fungal spores and pollen in sedimentary sequences. However, to date, there has been little quantification of fossil dung fungal spore records and their relationship to herbivore numbers, leaving this method open to varied interpretations. In this study, we developed further the dung fungal spore method and determined the relationship between spore abundance in sediments (number cm−2 year−1) and herbivore biomass densities (kg ha−1). To establish this relationship, we used the following: (i) the abundance of Sporormiella spp., Sordaria spp. and Podospora spp. spores in modern sediments from ponds and (ii) weekly counts of contemporary wildlife over a period of 5 years from the rewilded site, Oostvaardersplassen, in the Netherlands. Results from this study demonstrate that there is a highly significant relationship between spore abundance and local biomass densities of herbivores that can be used in the calibration of fossil records. Mammal biomass density (comprising Konik horses, Heck cattle and red deer) predicts in a highly significant way the abundance of all dung fungal spores amalgamated together. This relationship is apparent at a very local scale (<10 m), when the characteristics of the sampled ponds are taken into account (surface area of pond, length of shoreline). In addition, we identify that dung fungal spores are principally transported into ponds by surface run-off from the shores. These results indicate that this method provides a robust quantitative measure of herbivore population size over time

Phytolith analysis reveals the intensity of past land use change in the Western Ghats biodiversity hotspot

This paper presents a study of phytoliths (opal silica bodies from plants) from sediment sequences obtained from two tropical forest patches in the Western Ghats of India: a sacred grove (sequence covers last 550 cal BP) and a forest patch in a plantation (sequence covers last 7500 cal BP). The sites are located at mid-elevation (c. 650–1400 m above sea level) in a mosaic landscape showing anthropogenic open habitats and plantations as well as some evergreen forests. The aim of this paper is to evaluate the landscape composition of grassland and forest over time in the region, grassland being invariably shaped by anthropogenic activities, particularly fire for cultivation. We identified and classified phytoliths into 34 morphotypes from five taxonomic groups: Poaceae (grasses), Cyperaceae (sedges), Arecaceae (palms), Pteridopsida (ferns) and woody dicotyledons (broad-leaved trees and shrubs). We also calculated the humidity–aridity index (Iph). First, our results show that grasses are the most represented phytolith types in both sites, followed by broad-leaved trees and shrubs, palms, sedges, and ferns. Second, the highly variable climatic index Iph over the last 1000 years suggest that changes in phytolith percentage (e.g. broad-leaved trees) might be caused by human agro-pastoral activities, such as clearing through fires and irrigation. Prior to these human activities, the phytolith signal for early Holocene climate is congruent with the existing literature. Finally, this study compares new phytolith results with previous pollen data from the same sites. We find good agreement between these two botanical proxies throughout, thus validating our findings. We provide important evidence regarding the history of environmental change due to anthropogenic activities in the Western Ghats. This has important implications because it provides insights into how tropical forest will respond to increased intensity of human activities

Data from: Quantification of population sizes of large herbivores and their long-term functional role in ecosystems using dung fungal spores

The relationship between large herbivore numbers and landscape cover over time is poorly understood. There are two schools of thought: one views large herbivores as relatively passive elements upon the landscape and the other as ecosystem engineers driving vegetation succession. The latter relationship has been used as an argument to support reintroductions of large herbivores onto many landscapes in order to increase vegetation heterogeneity and biodiversity through local-scale disturbance regimes. Most of the research examining the relationship between large herbivores and their impact on landscapes has used extant studies. An alternative approach is to estimate the impact of variations in herbivore populations through time using fossil dung fungal spores and pollen in sedimentary sequences. However, to date, there has been little quantification of fossil dung fungal spore records and their relationship to herbivore numbers, leaving this method open to varied interpretations. In this study, we developed further the dung fungal spore method and determined the relationship between spore abundance in sediments (number cm−2 year−1) and herbivore biomass densities (kg ha−1). To establish this relationship, we used the following: (i) the abundance of Sporormiella spp., Sordaria spp. and Podospora spp. spores in modern sediments from ponds and (ii) weekly counts of contemporary wildlife over a period of 5 years from the rewilded site, Oostvaardersplassen, in the Netherlands. Results from this study demonstrate that there is a highly significant relationship between spore abundance and local biomass densities of herbivores that can be used in the calibration of fossil records. Mammal biomass density (comprising Konik horses, Heck cattle and red deer) predicts in a highly significant way the abundance of all dung fungal spores amalgamated together. This relationship is apparent at a very local scale (<10 m), when the characteristics of the sampled ponds are taken into account (surface area of pond, length of shoreline). In addition, we identify that dung fungal spores are principally transported into ponds by surface run-off from the shores. These results indicate that this method provides a robust quantitative measure of herbivore population size over time. The data package contains one dataset: - Contains all the data used in Baker et al 2016 ME

Baker et al 2016 MEE

Contains all the data used in Baker et al 2016 ME