Functional structure of ant and termite assemblages in old growth forest, logged forest and oil palm plantation in Malaysian Borneo

Forested tropical landscapes around the world are being extensively logged and converted to agriculture, with serious consequences for biodiversity and potentially ecosystem functioning. Here we investigate associations between habitat disturbance and functional diversity of ants and termites—two numerically dominant and functionally important taxa in tropical rain forests that perform key roles in predation, decomposition, nutrient cycling and seed dispersal. We compared ant and termite occurrence and composition within standardised volumes of soil and dead wood in old growth forest, logged forest and oil palm plantation in Sabah, Malaysian Borneo. Termites occurred substantially less frequently in converted habitats than in old growth forest, whereas ant occurrences were highest in logged forest and lowest in old growth forest. All termite feeding groups had low occurrence in disturbed habitats, with soil feeders occurring even less frequently than wood feeders. Ant functional groups showed more variable associations, with some opportunist and behaviourally dominant groups being more abundant in degraded habitats. The importance of ants and termites in tropical ecosystems and such differing patterns of assemblage variation suggest that ecosystem functioning may be significantly altered in converted habitats.During this project SHL was funded by the Sime Darby Foundation (through SAFE), the UK Natural Environment Research Council (NERC), The University of East Anglia and The Sir Philip Reckitt Educational Trust. TMF was funded by a NERC small project grant (NE/H011307/1), the project Biodiversity of Forest Ecosystems CZ.1.07/2.3.00/20.0064 co-financed by the European Social Fund and the state budget of the Czech Republic, an Australian Research Council Discovery Grant (DP140101541), and a Czech Science Foundation standard grant (14-32302S).This is the author accepted manuscript. The final version has been published by Springer in Biodiversity and Conservation. It can be found here: http://link.springer.com/article/10.1007%2Fs10531-014-0750-2

The impacts of habitat disturbance on adult and larval dragonflies (Odonata) in rainforest streams in Sabah, Malaysian Borneo

$\textbf{1.}$ Dragonfly assemblages (Odonata: comprising damselflies, Zygoptera; and dragonflies, Anisoptera) in Southeast Asian rainforests are extremely diverse but increasingly threatened by habitat disturbance, including logging and conversion of forest to oil palm plantations. $\textbf{2.}$ Land-use change can affect dragonfly larval stages by altering within-stream environmental conditions, and adults by loss of perches, shade and hunting habitat. However, the extent to which dragonflies are affected by land-use change is not well known, and strategies for conservation are poorly developed. $\textbf{3.}$ We surveyed dragonfly adults and larvae, forest quality and stream environmental conditions across 16 streams in Sabah, Malaysia. Habitat surrounding the streams included pristine forest, selectively logged forest, oil palm with forested riparian buffer strips and oil palm without buffers. $\textbf{4.}$ Overall abundance and species richness of adult dragonflies stayed constant with habitat disturbance, but larval abundance and richness decreased with higher habitat disturbance, and larvae were largely absent from oil palm streams. There was also a clear shift in community composition of both adult and larval dragonflies. Anisoptera adults were more species rich and abundant, but Zygoptera adults were less species rich in more disturbed sites. $\textbf{5.}$ The presence of riparian buffers in oil palm plantations offered some protection for forest-associated dragonfly species, and streams with wider riparian buffers supported adult assemblages more similar to those found in logged forest. However, oil palm streams with riparian buffers still contained a depauperate larval assemblage compared to logged forest areas, and dragonfly assemblages in narrow riparian buffer streams were similar to those found in streams surrounded by continuous oil palm. $\textbf{6.}$ Our results provide clear evidence of the effect of land-use change on dragonflies. Conservation efforts to conserve forest communities should target the preservation of existing forest areas, but management within oil palm plantation landscapes to preserve riparian buffers can still have a marked beneficial effect on dragonfly communities.SHL was funded by a Natural Environment Research Council (NERC) studentship (1122589), Proforest, the Varley Gradwell Travelling Fellowship, Tim Whitmore Fund, Panton Trust and the Cambridge University Commonwealth Fund during this work. We have no conflicts of interest to declare

Retrovirus Integration Database (RID): A public database for retroviral insertion sites into host genomes

The NCI Retrovirus Integration Database is a MySql-based relational database created for storing and retrieving comprehensive information about retroviral integration sites, primarily, but not exclusively, HIV-1. The database is accessible to the public for submission or extraction of data originating from experiments aimed at collecting information related to retroviral integration sites including: the site of integration into the host genome, the virus family and subtype, the origin of the sample, gene exons/introns associated with integration, and proviral orientation. Information about the references from which the data were collected is also stored in the database. Tools are built into the website that can be used to map the integration sites to UCSC genome browser, to plot the integration site patterns on a chromosome, and to display provirus LTRs in their inserted genome sequence. The website is robust, user friendly, and allows users to query the database and analyze the data dynamically. Availability: https://rid.ncifcrf.gov; or http://home.ncifcrf.gov/hivdrp/resources.htm

Systematic mapping shows the need for increased socio-ecological research on oil palm

Abstract In the past century, oil palm has developed from a sustenance crop in West Africa to a major global agricultural commodity, with substantial impacts on biodiversity, the environment, society, and livelihoods. Although the oil palm industry contributes to local and national economies across the tropics, there are significant concerns about the negative effects of oil palm cultivation on biodiversity and ecosystem functioning, as well on local communities and farmers. There is a growing awareness of the need for managing agricultural landscapes more sustainably, and the importance of ecological, social, and also interdisciplinary research to inform this. To understand the current status of research across these areas for oil palm, we carried out a systematic mapping exercise to quantify social, ecological, and interdisciplinary socio-ecological research on oil palm cultivation, assess trends in the research, and to identify priority knowledge gaps in the literature. Literature was searched using adapted preferred reporting items for systematic reviews and meta-analyses and Collaboration for Environmental Evidence protocols. We reviewed 4959 publications on the ecological, social, and socioecological effects of oil palm cultivation. Each publication was classified according to study context (the study site location and type), comparators (the type of comparison the study makes), intervention (the potential action or decision being studied), and outcome (the effects of the intervention on the population). This resulted in 443 classified papers, which we then analyzed in more detail, to identify co-occurrence of different research foci between the disciplines and in socio-ecological research. We found a global increase in oil palm research over the past three decades, with a clear bias to Malaysia and Indonesia, mirroring global production trends. Over 70% of the research was focused on ecological outcomes, 19% on social, and less than 10% interdisciplinary. The majority of studies were conducted within industrial plantations, with comparisons to non-modified habitats, such as forests. Research has focused most on the effects of cultivation on yield, invertebrate biodiversity, and livelihood. To place our findings in context of production of palm oil and sustainability priorities, we used information on regional oil palm production in Tonnes, priorities of sustainable certification bodies, and recognized causes of yield gaps. The most pressing knowledge gaps included a lack of studies on the effects of plantation inputs on pollination and herbivory, the relationship between ecological factors and human health and wellbeing, and comparisons of different management practices within oil palm plantations. We advocate that these gaps become the focus of future research attention, as they lie in identified priority research areas and outcomes are likely to be critical to informing the development of more sustainable palm oil production.Gates Cambridge Trus

Systematic mapping shows the need for increased socio-ecological research on oil palm

Abstract In the past century, oil palm has developed from a sustenance crop in West Africa to a major global agricultural commodity, with substantial impacts on biodiversity, the environment, society, and livelihoods. Although the oil palm industry contributes to local and national economies across the tropics, there are significant concerns about the negative effects of oil palm cultivation on biodiversity and ecosystem functioning, as well on local communities and farmers. There is a growing awareness of the need for managing agricultural landscapes more sustainably, and the importance of ecological, social, and also interdisciplinary research to inform this. To understand the current status of research across these areas for oil palm, we carried out a systematic mapping exercise to quantify social, ecological, and interdisciplinary socio-ecological research on oil palm cultivation, assess trends in the research, and to identify priority knowledge gaps in the literature. Literature was searched using adapted preferred reporting items for systematic reviews and meta-analyses and Collaboration for Environmental Evidence protocols. We reviewed 4959 publications on the ecological, social, and socioecological effects of oil palm cultivation. Each publication was classified according to study context (the study site location and type), comparators (the type of comparison the study makes), intervention (the potential action or decision being studied), and outcome (the effects of the intervention on the population). This resulted in 443 classified papers, which we then analyzed in more detail, to identify co-occurrence of different research foci between the disciplines and in socio-ecological research. We found a global increase in oil palm research over the past three decades, with a clear bias to Malaysia and Indonesia, mirroring global production trends. Over 70% of the research was focused on ecological outcomes, 19% on social, and less than 10% interdisciplinary. The majority of studies were conducted within industrial plantations, with comparisons to non-modified habitats, such as forests. Research has focused most on the effects of cultivation on yield, invertebrate biodiversity, and livelihood. To place our findings in context of production of palm oil and sustainability priorities, we used information on regional oil palm production in Tonnes, priorities of sustainable certification bodies, and recognized causes of yield gaps. The most pressing knowledge gaps included a lack of studies on the effects of plantation inputs on pollination and herbivory, the relationship between ecological factors and human health and wellbeing, and comparisons of different management practices within oil palm plantations. We advocate that these gaps become the focus of future research attention, as they lie in identified priority research areas and outcomes are likely to be critical to informing the development of more sustainable palm oil production.Gates Cambridge Trus

Effects of Understory Vegetation Management on Plant Communities in Oil Palm Plantations in Sumatra, Indonesia

Oil palm plantations have expanded rapidly in recent decades, and are causing substantial impacts on tropical habitats and biodiversity. However, owing to its long lifespan (25-30 years), oil palm forms a much more varied and structurally-complex habitat than many other crops. This can include abundant understory vegetation and also epiphytes on palm trunks. However, the diversity of this plantation vegetation has been poorly studied, and there has been little consideration of the impacts of common plantation vegetation management practices on plant communities. We conducted a long-term vegetation management experiment that forms part of the Biodiversity and Ecosystem Function in Tropical Agriculture (BEFTA) Programme in Riau, Indonesia. We manipulated herbicide and manual cutting regimes within mature oil palm plantations to create three different understory complexity treatments (Reduced, Normal, and Enhanced vegetation) across replicated sets of plots. Plant communities were surveyed before and after experimental understory vegetation treatments began in three different microhabitats: within the middle of the plantation block (core), on the road edge (edge) and on oil palm trunks (trunk). Part of the sampling was also conducted during a drought event. We recorded 120 plant species, which comprised a mixture of native, non-native, ‘beneficial’, and ‘problem’ species. We found substantial variation in plant communities between edge, core, and trunk microhabitats, indicating high levels of heterogeneity within the plantation. There were significant effects of varying understory treatment within both core and edge microhabitats, but no spillover of impacts into the trunk microhabitat. We also observed substantial impacts of drought on plant communities, with declines in either biomass, percentage cover, or richness seen across core, edge, and trunk microhabitats during low-rainfall periods. Our findings highlight the diversity of plant communities that can be supported within oil palm plantations, and the substantial impacts that management decisions, and also drought, can have on them. Given the role that diverse plant communities can have in supporting species in other groups, this is likely to have a significant impact on the wider plantation biodiversity. We suggest that plantation management strategies give greater consideration to within-plantation understory plant communities and choose more wildlife-friendly options where possible.This work was funded by The Isaac Newton Trust Cambridge, Golden Agri Resources, and the Natural Environment Research Council [grant number NE/P00458X/1]

The effects of catchment and riparian forest quality on stream environmental conditions across a tropical rainforest and oil palm landscape in Malaysian Borneo

Freshwaters provide valuable habitat and important ecosystem services, but are threatened worldwide by habitat loss and degradation. In Southeast Asia, rainforest streams are particularly threatened by logging and conversion to oil palm, but we lack information on the impacts of this on freshwater environmental conditions, and the relative importance of catchment versus riparian-scale disturbance. We studied sixteen streams in Sabah, Borneo, including old growth forest, logged forest, and oil palm sites. We assessed forest quality in riparian zones and across the whole catchment, and compared it with stream environmental conditions including water quality, structural complexity and organic inputs. We found that streams with the highest riparian forest quality were nearly 4 °C cooler, over 20 cm deeper, had over 40% less sand, greater canopy cover, more stored leaf litter and wider channels than oil palm streams with the lowest riparian forest quality. Other variables were significantly related to catchment-scale forest quality, with streams in the highest quality forest catchments having 40% more bedrock and 20 times more dead wood, along with higher phosphorus, and lower nitrate-N levels compared to streams with the lowest catchment-scale forest quality. Although riparian buffer strips went some way to protecting waterways, they did not maintain fully forest-like stream conditions. In addition, logged forest streams still showed signs of disturbance 10-15 years after selective logging. Our results suggest that maintenance and restoration of buffer strips can help to protect healthy freshwater ecosystems, but logging practices and catchment-scale forest management also need to be considered.During this work SHL was funded by a Natural Environment Research Council (NERC) studentship (number 1122589), Proforest, the Varley Gradwell Travelling Fellowship, Tim Whitmore Fund, Panton Trust and the Cambridge University Commonwealth Fund. MP and RME were supported by European Research Council Project number 281986. HB was funded by the S.T. Lee Fund

Electron transport through 8-oxoG: NEGF/DFT study

We present a first-principles study of the conductance of Guanine and 8-Oxoguanine (8-oxoG) attached to Au(111) electrodes. Cellular levels of 8-oxoG have been found in larger concentrations in cancer patients. The current through the structure was calculated using a DFT–NEGF formalism. We have compared flat and pyramidal electrode geometries and show that there is a measurable difference between the I–V characteristics of the pristine molecule and the 8-oxoG. For a flat electrode geometry, 8-oxoG produces a 2.57 (18.3) times increase in current than the corresponding counterpart at 3 V with a bond separation of 1.2 Å (2.4 Å). This can be attributed to molecular orbital energies shifting at the junction. Overall the flat geometry produces larger currents. We have also investigated the sensitivity of the current to the electrode molecule separation. For the flat geometry, the current dropped approximately 80% (97%) for 8-oxoG (pristine Guanine) with the doubling of the electrode separation

Phase separation and suppression of critical dynamics at quantum transitions of itinerant magnets: MnSi and (Sr1−x_{1-x}Cax_{x})RuO3_{3}

Quantum phase transitions (QPTs) have been studied extensively in correlated electron systems. Characterization of magnetism at QPTs has, however, been limited by the volume-integrated feature of neutron and magnetization measurements and by pressure uncertainties in NMR studies using powderized specimens. Overcoming these limitations, we performed muon spin relaxation ($\mu$SR) measurements which have a unique sensitivity to volume fractions of magnetically ordered and paramagnetic regions, and studied QPTs from itinerant heli/ferro magnet to paramagnet in MnSi (single-crystal; varying pressure) and (Sr$_{1-x}$Ca$_{x}$)RuO$_{3}$ (ceramic specimens; varying $x$). Our results provide the first clear evidence that both cases are associated with spontaneous phase separation and suppression of dynamic critical behavior, revealed a slow but dynamic character of the ``partial order'' diffuse spin correlations in MnSi above the critical pressure, and, combined with other known results in heavy-fermion and cuprate systems, suggest a possibility that a majority of QPTs involve first-order transitions and/or phase separation.Comment: 11 pages, 4 figures, 21 authors, to appear in Nature Physic