Risks to carbon storage from land-use change revealed by peat thickness maps of Peru

This work was funded by NERC (grant ref. NE/R000751/1) to I.T.L., A.H., K.H.R., E.T.A.M., C.M.A., T.R.B., G.D. and E.C.D.G.; Leverhulme Trust (grant ref. RPG-2018-306) to K.H.R., L.E.S.C. and C.E.W.; Gordon and Betty Moore Foundation (grant no. 5439, MonANPeru network) to T.R.B., E.N.H.C. and G.F.; Wildlife Conservation Society to E.N.H.C.; Concytec/British Council/Embajada Británica Lima/Newton Fund (grant ref. 220–2018) to E.N.H.C. and J.D.; Concytec/NERC/Embajada Británica Lima/Newton Fund (grant ref. 001–2019) to E.N.H.C. and N.D.; the governments of the United States (grant no. MTO-069018) and Norway (grant agreement no. QZA-12/0882) to K.H.; and NERC Knowledge Exchange Fellowship (grant ref no. NE/V018760/1) to E.N.H.C.Tropical peatlands are among the most carbon-dense ecosystems but land-use change has led to the loss of large peatland areas, associated with substantial greenhouse gas emissions. To design effective conservation and restoration policies, maps of the location and carbon storage of tropical peatlands are vital. This is especially so in countries such as Peru where the distribution of its large, hydrologically intact peatlands is poorly known. Here field and remote sensing data support the model development of peatland extent and thickness for lowland Peruvian Amazonia. We estimate a peatland area of 62,714 km2 (5th and 95th confidence interval percentiles of 58,325 and 67,102 km2, respectively) and carbon stock of 5.4 (2.6–10.6) PgC, a value approaching the entire above-ground carbon stock of Peru but contained within just 5% of its land area. Combining the map of peatland extent with national land-cover data we reveal small but growing areas of deforestation and associated CO2 emissions from peat decomposition due to conversion to mining, urban areas and agriculture. The emissions from peatland areas classified as forest in 2000 represent 1–4% of Peruvian CO2 forest emissions between 2000 and 2016. We suggest that bespoke monitoring, protection and sustainable management of tropical peatlands are required to avoid further degradation and CO2 emissions.PostprintPeer reviewe

Understanding different dominance patterns in western Amazonian forests

Dominance of neotropical tree communities by a few species is widely documented, but dominant trees show a variety of distributional patterns still poorly understood. Here, we used 503 forest inventory plots (93,719 individuals ≥2.5 cm diameter, 2609 species) to explore the relationships between local abundance, regional frequency and spatial aggregation of dominant species in four main habitat types in western Amazonia. Although the abundance-occupancy relationship is positive for the full dataset, we found that among dominant Amazonian tree species, there is a strong negative relationship between local abundance and regional frequency and/or spatial aggregation across habitat types. Our findings suggest an ecological trade-off whereby dominant species can be locally abundant (local dominants) or regionally widespread (widespread dominants), but rarely both (oligarchs). Given the importance of dominant species as drivers of diversity and ecosystem functioning, unravelling different dominance patterns is a research priority to direct conservation efforts in Amazonian forests.Publisher PDFPeer reviewe

The distribution and amount of carbon in the largest peatland complex in Amazonia

Peatlands in Amazonian Peru are known to store large quantities of carbon, but there is high uncertainty in the spatial extent and total carbon stocks of these ecosystems. Here, we use a multi-sensor (Landsat, ALOS PALSAR and SRTM) remote sensing approach, together with field data including 24 forest census plots and 218 peat thickness measurements, to map the distribution of peatland vegetation types and calculate the combined above- and below-ground carbon stock of peatland ecosystems in the Pastaza-Marañon foreland basin in Peru. We find that peatlands cover 35 600 ± 2133 km2 and contain 3.14 (0.44–8.15) Pg C. Variation in peat thickness and bulk density are the most important sources of uncertainty in these values. One particular ecosystem type, peatland pole forest, is found to be the most carbon-dense ecosystem yet identified in Amazonia (1391 ± 710 Mg C ha−1). The novel approach of combining optical and radar remote sensing with above- and below-ground carbon inventories is recommended for developing regional carbon estimates for tropical peatlands globally. Finally, we suggest that Amazonian peatlands should be a priority for research and conservation before the developing regional infrastructure causes an acceleration in the exploitation and degradation of these ecosystems

Finishing the euchromatic sequence of the human genome

The sequence of the human genome encodes the genetic instructions for human physiology, as well as rich information about human evolution. In 2001, the International Human Genome Sequencing Consortium reported a draft sequence of the euchromatic portion of the human genome. Since then, the international collaboration has worked to convert this draft into a genome sequence with high accuracy and nearly complete coverage. Here, we report the result of this finishing process. The current genome sequence (Build 35) contains 2.85 billion nucleotides interrupted by only 341 gaps. It covers ∼99% of the euchromatic genome and is accurate to an error rate of ∼1 event per 100,000 bases. Many of the remaining euchromatic gaps are associated with segmental duplications and will require focused work with new methods. The near-complete sequence, the first for a vertebrate, greatly improves the precision of biological analyses of the human genome including studies of gene number, birth and death. Notably, the human enome seems to encode only 20,000-25,000 protein-coding genes. The genome sequence reported here should serve as a firm foundation for biomedical research in the decades ahead

Rethinking the fall of the planter class

This issue of Atlantic Studies began life as a one-day conference held at Chawton House Library in Hampshire, UK, and funded by the University of Southampton. The conference aimed, like this issue, to bring together scholars currently working on the history of the British West Indian planter class in the eighteenth and nineteenth centuries and to discuss how, when, and why the fortunes of the planters went into decline. As this introduction notes, the difficulties faced by the planter class in the British West Indies from the 1780s onwards were an early episode in a wider drama of decline for New World plantation economies. The American historian Lowell Ragatz published the first detailed historical account of their fall. His work helped to inform the influential arguments of Eric Williams, which were later challenged by Seymour Drescher. Recent research has begun to offer fresh perspectives on the debate about the decline of the planters, and this collection brings together articles taking a variety of new approaches to the topic, encompassing economic, political, cultural, and social histor

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

San Andreas Fault Zone Mineralogy, Geochemistry, and Physical Properties from SAFOD Cuttings and Core

The San Andreas Fault Observatory at Depth (SAFOD), drilled near the town of Parkfield, California (Fig. 1) (Hickmen et al., 2004) as part of the U.S. National Science Foundation\u27s EarthScope Project (see http://www.earthscope.org), provieds a continuous set of samples through the active San Andreas Fault (SAF) zone. These samples can help address decades-old questions such as apparent weakness of the SAF (Zoback, 2000) providing the unparalleled opportunity to contrain the parameters that control the behavior of plate counding faults like the San Andreas. Samples collected form SAFOD also complement studies of exhumed fault zones. While studies of exhumed fault zones have benefit from regionally extensive exposures that allow for detailed mapping and analyses (Chester and Chester, 1998; Evans and Chester, 1995), such studies also have inherent limitations including uncertainty about stress states and styles of deformation (i.e., seisomgenic vs. creeping). Moreover, mineral assemblages in exhumed fault zones can be altered during exhumation, obscuring fault-related mineral assemblages and textures (Solum et al., 2003; Solum and can der Pluijm, 2004). The SAFOD target zone contains two parallel strands that generate repeating M2 earthquakes in addition to having a component of creep (Nadeau et al., 2004). Therefore, SAFOD also offeres the opportunity to obtain samples from seismogenic and aseismic faults and to constrain the rheology of the active SAF system