Bimodality and alternative equilibria do not help explain long-term patterns in shallow lake chlorophyll-a

Since its inception, the theory of alternative equilibria in shallow lakes has evolved and been applied to an ever wider range of ecological and socioecological systems. The theory posits the existence of two alternative stable states or equilibria, which in shallow lakes are characterised by either clear water with abundant plants or turbid water where phytoplankton dominate. Here, we used data simulations and real-world data sets from Denmark and north-eastern USA (902 lakes in total) to examine the relationship between shallow lake phytoplankton biomass (chlorophyll-a) and nutrient concentrations across a range of timescales. The data simulations demonstrated that three diagnostic tests could reliably identify the presence or absence of alternative equilibria. The real-world data accorded with data simulations where alternative equilibria were absent. Crucially, it was only as the temporal scale of observation increased (>3 years) that a predictable linear relationship between nutrient concentration and chlorophyll-a was evident. Thus, when a longer term perspective is taken, the notion of alternative equilibria is not required to explain the response of chlorophyll-a to nutrient enrichment which questions the utility of the theory for explaining shallow lake response to, and recovery from, eutrophication.C.D.S. and T.A.D. would like to thank June and Derek Sayer for extraordinary support over many years. The authors of this work have been supported by a number of projects over the elephantine gestation period of this manuscript. These include support from the Poul Due Jensen Fonden, Danmarks Frie Forskningsfond Natur og Univers project GREENLAKES (No. 9040-00195B) and the UFM-funded project LTER_DK for Long Term Ecosystem Research in Denmark. In addition, support was provided by The European Union’s Horizon 2020 research and innovation programmes under grant agreement No 869296—The PONDERFUL Project”, TREICLAKE under grant agreement No 951963, and the AQUACOSM project and by the European Commission EU H2020- INFRAIA-project (No. 731065) and AQUACOSMplus (No. 871081). E.J. was also supported by the TÜBITAK outstanding researcher programme2232 (project 118C250) and AnaEE, Denmark. The work of D.G. was funded by the Fourth Period of Programme-oriented Funding, Helmholtz Association of German ResearchCentres, Research Field Earth and Environment.C.D.S. and T.A.D. would like to thank June and Derek Sayer for extraordinary support over many years. The authors of this work have been supported by a number of projects over the elephantine gestation period of this manuscript. These include support from the Poul Due Jensen Fonden, Danmarks Frie Forskningsfond Natur og Univers project GREENLAKES (No. 9040-00195B) and the UFM-funded project LTER_DK for Long Term Ecosystem Research in Denmark. In addition, support was provided by The European Union’s Horizon 2020 research and innovation programmes under grant agreement No 869296—The PONDERFUL Project”, TREICLAKE under grant agreement No 951963, and the AQUACOSM project and by the European Commission EU H2020- INFRAIA-project (No. 731065) and AQUACOSMplus (No. 871081). E.J. was also supported by the TÜBITAK outstanding researcher programme2232 (project 118C250) and AnaEE, Denmark. The work of D.G. was funded by the Fourth Period of Programme-oriented Funding, Helmholtz Association of German ResearchCentres, Research Field Earth and Environment

Will they be back? A framework to guide rare macrophyte conservation decisions in lakes

Shallow lake restoration typically focusses on the re-establishment of macrophytes. The likelihood of a species returning to a site is contingent on dispersal, proximity to propagule sources, and the on-site propagule-bank viability. We explore the potential of palaeoecological records in combination with botanical surveys and distribution maps, to ascertain the loss of three submerged macrophytes (Littorella uniflora, Najas flexilis, and Elatine hydropiper) from, respectively, two lakes (Barton Broad, Norfolk and Esthwaite Water, Cumbria) and one lake landscape (Greater Glasgow, Scotland). We discuss re-establishment likelihood when accounting for species' autoecology and current water-chemistry conditions. L. uniflora is widespread in the United Kingdom but absent locally in Norfolk without known seed bank, hence is unlikely to naturally recolonise Barton Broad. Furthermore, current conditions are unsuitable for this species suggesting that nutrient reduction is required prior to translocation. N. flexilis is extinct in Cumbria and the long distances involved (>100 km) for recolonisation of Esthwaite Water suggest that spatial dispersal is unlikely, rendering the seed bank the last chance of natural recovery. Alternatively, translocation may be feasible. E. hydropiper is a nationally scarce species in the United Kingdom yet would have only a short dispersal distance (~10 km) to recolonise Loch Libo, hence there being no requirement for translocation. In exploring the recovery possibilities for the three focal plant species, we develop a time–space integrated framework that can be employed to guide conservation decisions for other species, enabling a more rational use of translocations in the future, in line with international guidelines

Agricultural origins on the Anatolian plateau

This paper explores the explanations for, and consequences of, the early appearance of food production outside the Fertile Crescent of Southwest Asia, where it originated in the 10th/9th millennia cal BC. We present evidence that cultivation appeared in Central Anatolia through adoption by indigenous foragers in the mid ninth millennium cal BC, but also demonstrate that uptake was not uniform, and that some communities chose to actively disregard cultivation. Adoption of cultivation was accompanied by experimentation with sheep/goat herding in a system of low-level food production that was integrated into foraging practices rather than used to replace them. Furthermore, rather than being a short-lived transitional state, low-level food production formed part of a subsistence strategy that lasted for several centuries, although its adoption had significant long-term social consequences for the adopting community at Boncuklu. Material continuities suggest that Boncuklu’s community was ancestral to that seen at the much larger settlement of Çatalhöyük East from 7100 cal BC, by which time a modest involvement with food production had been transformed into a major commitment to mixed farming, allowing the sustenance of a very large sedentary community. This evidence from Central Anatolia illustrates that polarized positions explaining the early spread of farming, opposing indigenous adoption to farmer colonization, are unsuited to understanding local sequences of subsistence and related social change. We go beyond identifying the mechanisms for the spread of farming by investigating the shorter- and longer-term implications of rejecting or adopting farming practices.</p

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