Optimising sampling and analysis protocols in environmental DNA studies

Ecological surveys risk incurring false negative and false positive detections of the target species. With indirect survey methods, such as environmental DNA, such error can occur at two stages: sample collection and laboratory analysis. Here we analyse a large qPCR based eDNA data set using two occupancy models, one of which accounts for false positive error by Griffin et al. (2020), and a second that assumes no false positive error by Stratton et al. (2020). Additionally, we apply the Griffin et al. (2020) model to simulated data to determine optimal levels of replication at both sampling stages. The Stratton et al. (2020) model, which assumes no false positive results, consistently overestimated both overall and individual site occupancy compared to both the Griffin et al. (2020) model and to previous estimates of pond occupancy for the target species. The inclusion of replication at both stages of eDNA analysis (sample collection and in the laboratory) reduces both bias and credible interval width in estimates of both occupancy and detectability. Even the collection of >1 sample from a site can improve parameter estimates more than having a high number of replicates only within the laboratory analysis

The topographic evolution of the Tibetan Region as revealed by palaeontology

The Tibetan Plateau was built through a succession of Gondwanan terranes colliding with Asia during the Mesozoic. These accretions produced a complex Paleogene topography of several predominantly east–west trending mountain ranges separated by deep valleys. Despite this piecemeal assembly and resultant complex relief, Tibet has traditionally been thought of as a coherent entity rising as one unit. This has led to the widely used phrase ‘the uplift of the Tibetan Plateau’, which is a false concept borne of simplistic modelling and confounds understanding the complex interactions between topography climate and biodiversity. Here, using the rich palaeontological record of the Tibetan region, we review what is known about the past topography of the Tibetan region using a combination of quantitative isotope and fossil palaeoaltimetric proxies, and present a new synthesis of the orography of Tibet throughout the Paleogene. We show why ‘the uplift of the Tibetan Plateau’ never occurred, and quantify a new pattern of topographic and landscape evolution that contributed to the development of today’s extraordinary Asian biodiversity

A vector of high-temperature paleo-fluid flow deduced from\ud mass transfer across permeability barriers (quartz veins)

Quartz veins acted as impermeable barriers to regional fluid flow and not as fluid-flow conduits in Mesoproterozoic rocks of the Mt Painter Block, South Australia. Systematically distributed asymmetric alteration selvedges consisting of a muscovite-rich zone paired with a biotite-rich zone are centered on quartz veins in quartz–muscovite–biotite schist. Geometric analysis of the orientation and facing of 126 veins at Nooldoonooldoona Waterhole reveals a single direction along which a maximum of all veins have a muscovite-rich side, irrespective of their specific individual orientation. This direction represents a Mesoproterozoic fluid-flow vector and the veins represent permeability barriers to the flow. The pale muscovite-rich zones formed on the downstream side of the vein and the dark biotite-rich zones mark the upstream side. The alteration couplets formed from mica schist at constant Zr, Ga, Sc, and involved increases in Si, Na, Al and decreases in K, Fe, Mg for pale alteration zones, and inverse alteration within dark zones. The asymmetry of the alteration couplets is best explained by the pressure dependence of mineral–fluid equilibria. These equilibria, in combination with a Darcian flow model for coupled advection and diffusion, and with permeability barriers imposed by the quartz veins, simulate the pattern of both fluid flow and differential, asymmetric metasomatism. The determined vector of fluid flow lies along the regional foliation and is consistent with the known distribution of regional alteration products. The presence of asymmetric alteration zones in rock containing abundant pre-alteration veins suggests that vein-rich material may have generally retarded regional fluid flow

Methane clumped isotopes: Progress and potential for a new isotopic tracer

The isotopic composition of methane is of longstanding geochemical interest, with important implications for understanding petroleum systems, atmospheric greenhouse gas concentrations, the global carbon cycle, and life in extreme environments. Recent analytical developments focusing on multiply substituted isotopologues (‘clumped isotopes’) are opening a valuable new window into methane geochemistry. When methane forms in internal isotopic equilibrium, clumped isotopes can provide a direct record of formation temperature, making this property particularly valuable for identifying different methane origins. However, it has also become clear that in certain settings methane clumped isotope measurements record kinetic rather than equilibrium isotope effects. Here we present a substantially expanded dataset of methane clumped isotope analyses, and provide a synthesis of the current interpretive framework for this parameter. In general, clumped isotope measurements indicate plausible formation temperatures for abiotic, thermogenic, and microbial methane in many geological environments, which is encouraging for the further development of this measurement as a geothermometer, and as a tracer for the source of natural gas reservoirs and emissions. We also highlight, however, instances where clumped isotope derived temperatures are higher than expected, and discuss possible factors that could distort equilibrium formation temperature signals. In microbial methane from freshwater ecosystems, in particular, clumped isotope values appear to be controlled by kinetic effects, and may ultimately be useful to study methanogen metabolism

Recent advances in isotopes as palaeolimnological proxies

Isotope geochemistry is an essential part of environmental and climate change research and over the last few decades has contributed significantly to our understanding of a huge array of environmental problems, not least in palaeolimnology and limnogeology. Here we describe some of the recent developments in the use of stable isotopes in palaeo-lake research. These are: better preparation, analysis, and interpretation of biogenic silica oxygen and silicon isotopes; extraction and characterisation of specific compounds such as leaf waxes and algal lipids for isotope analysis; determining the excess of 13C–18O bonds in clumped isotopes; and the measurement of multiple isotope ratios in chironomid chitin. These advances have exciting prospects and it will be interesting to see how these techniques develop further and consequently offer a real advancement in our science over the next decade

Implications of streamlining theory for microbial ecology

Whether a small cell, a small genome or a minimal set of chemical reactions with self-replicating properties, simplicity is beguiling. As Leonardo da Vinci reportedly said, 'simplicity is the ultimate sophistication'. Two diverging views of simplicity have emerged in accounts of symbiotic and commensal bacteria and cosmopolitan free-living bacteria with small genomes. The small genomes of obligate insect endosymbionts have been attributed to genetic drift caused by small effective population sizes (Ne). In contrast, streamlining theory attributes small cells and genomes to selection for efficient use of nutrients in populations where Ne is large and nutrients limit growth. Regardless of the cause of genome reduction, lost coding potential eventually dictates loss of function. Consequences of reductive evolution in streamlined organisms include atypical patterns of prototrophy and the absence of common regulatory systems, which have been linked to difficulty in culturing these cells. Recent evidence from metagenomics suggests that streamlining is commonplace, may broadly explain the phenomenon of the uncultured microbial majority, and might also explain the highly interdependent (connected) behavior of many microbial ecosystems. Streamlining theory is belied by the observation that many successful bacteria are large cells with complex genomes. To fully appreciate streamlining, we must look to the life histories and adaptive strategies of cells, which impose minimum requirements for complexity that vary with niche