A global carbon and nitrogen isotope perspective on modern and ancient human diet

Stable carbon and nitrogen isotope analyses are widely used to infer diet and mobility in ancient and modern human populations, potentially providing a means to situate humans in global food webs. We collated 13,666 globally distributed analyses of ancient and modern human collagen and keratin samples. We converted all data to a common “Modern Diet Equivalent” reference frame to enable direct comparison among modern human diets, human diets prior to the advent of industrial agriculture, and the natural environment. This approach reveals a broad diet prior to industrialized agriculture and continued in modern subsistence populations, consistent with the human ability to consume opportunistically as extreme omnivores within complex natural food webs and across multiple trophic levels in every terrestrial and many marine ecosystems on the planet. In stark contrast, isotope dietary breadth across modern nonsubsistence populations has compressed by two-thirds as a result of the rise of industrialized agriculture and animal husbandry practices and the globalization of food distribution networks

The genetic architecture of the human cerebral cortex

The cerebral cortex underlies our complex cognitive capabilities, yet little is known about the specific genetic loci that influence human cortical structure. To identify genetic variants that affect cortical structure, we conducted a genome-wide association meta-analysis of brain magnetic resonance imaging data from 51,665 individuals. We analyzed the surface area and average thickness of the whole cortex and 34 regions with known functional specializations. We identified 199 significant loci and found significant enrichment for loci influencing total surface area within regulatory elements that are active during prenatal cortical development, supporting the radial unit hypothesis. Loci that affect regional surface area cluster near genes in Wnt signaling pathways, which influence progenitor expansion and areal identity. Variation in cortical structure is genetically correlated with cognitive function, Parkinson's disease, insomnia, depression, neuroticism, and attention deficit hyperactivity disorder

Biological function in the twilight zone of sequence conservation

Abstract Strong DNA conservation among divergent species is an indicator of enduring functionality. With weaker sequence conservation we enter a vast ‘twilight zone’ in which sequence subject to transient or lower constraint cannot be distinguished easily from neutrally evolving, non-functional sequence. Twilight zone functional sequence is illuminated instead by principles of selective constraint and positive selection using genomic data acquired from within a species’ population. Application of these principles reveals that despite being biochemically active, most twilight zone sequence is not functional

Discovery and functional prioritization of Parkinson's disease candidate genes from large-scale whole exome sequencing.

BACKGROUND: Whole-exome sequencing (WES) has been successful in identifying genes that cause familial Parkinson's disease (PD). However, until now this approach has not been deployed to study large cohorts of unrelated participants. To discover rare PD susceptibility variants, we performed WES in 1148 unrelated cases and 503 control participants. Candidate genes were subsequently validated for functions relevant to PD based on parallel RNA-interference (RNAi) screens in human cell culture and Drosophila and C. elegans models. RESULTS: Assuming autosomal recessive inheritance, we identify 27 genes that have homozygous or compound heterozygous loss-of-function variants in PD cases. Definitive replication and confirmation of these findings were hindered by potential heterogeneity and by the rarity of the implicated alleles. We therefore looked for potential genetic interactions with established PD mechanisms. Following RNAi-mediated knockdown, 15 of the genes modulated mitochondrial dynamics in human neuronal cultures and four candidates enhanced α-synuclein-induced neurodegeneration in Drosophila. Based on complementary analyses in independent human datasets, five functionally validated genes-GPATCH2L, UHRF1BP1L, PTPRH, ARSB, and VPS13C-also showed evidence consistent with genetic replication. CONCLUSIONS: By integrating human genetic and functional evidence, we identify several PD susceptibility gene candidates for further investigation. Our approach highlights a powerful experimental strategy with broad applicability for future studies of disorders with complex genetic etiologies

Continuous analysis of δ18O and δD values of water by diffusion sampling cavity ring-down spectrometry: a novel sampling device for unattended field monitoring of precipitation, ground and surface waters

A novel sampling device suitable for continuous, unattended field monitoring of rapid isotopic changes in environmental waters is described. The device utilises diffusion through porous PTFE tubing to deliver water vapour continuously from a liquid water source for analysis of δ18O and δD values by Cavity Ring-Down Spectrometry (CRDS). Separation of the analysed water vapour from non-volatile dissolved and particulate contaminants in the liquid sample minimises spectral interferences associated with CRDS analyses of many aqueous samples. Comparison of isotopic data for a range of water samples analysed by Diffusion Sampling-CRDS (DS-CRDS) and Isotope Ratio Mass Spectrometry (IRMS) shows significant linear correlations between the two methods allowing for accurate standardisation of DS-CRDS data. The internal precision for an integration period of 3 min (standard deviation (SD) = 0.1 ‰ and 0.3 ‰ for δ18O and δD values, respectively) is similar to analysis of water by CRDS using an autosampler to inject and evaporate discrete water samples. The isotopic effects of variable air temperature, water vapour concentration, water pumping rate and dissolved organic content were found to be either negligible or correctable by analysis of water standards. The DS-CRDS system was used to analyse the O and H isotope composition in short-lived rain events. Other applications where finely time resolved water isotope data may be of benefit include recharge/discharge in groundwater/river systems and infiltration-related changes in cave drip water

Field-based cavity ring-down spectrometry of δ13C in soil-respired CO2

Measurement of soil-respired CO2 at high temporal resolution and sample density is necessary to accurately identify sources and quantify effluxes of soil-respired CO2. A portable sampling device for the analysis of δ13C values in the field is described herein.\ud \ud CO2 accumulated in a soil chamber was batch sampled sequentially in four gas bags and analysed by Wavelength-Scanned Cavity Ring-down Spectrometry (WS-CRDS). A Keeling plot (1/[CO2] versus δ13C) was used to derive δ13C values of soil-respired CO2. Calibration to the δ13C Vienna Peedee Belemnite scale was by analysis of cylinder CO2 and CO2 derived from dissolved carbonate standards. The performance of gas-bag analysis was compared to continuous analysis where the WS-CRDS analyser was connected directly to the soil chamber.\ud \ud Although there are inherent difficulties in obtaining absolute accuracy data for δ13C values in soil-respired CO2, the similarity of δ13C values obtained for the same test soil with different analytical configurations indicated that an acceptable accuracy of the δ13C data were obtained by the WS-CRDS techniques presented here. Field testing of a variety of tropical soil/vegetation types, using the batch sampling technique yielded δ13C values for soil-respired CO2 related to the dominance of either C3 (tree, δ13C=−27.8 to−31.9 ‰) or C4 (tropical grass, δ13C=−9.8 to−13.6 ‰) photosynthetic pathways in vegetation at the sampling sites. Standard errors of the Keeling plot intercept δ13C values of soil-respired CO2 were typically<0.4 ‰ for analysis of soils with high CO2 efflux (>7–9 μmol m−2 s−1)

Paleoclimate and paleoenvironment reconstruction of paleosols spanning the Lower to Upper Cretaceous from the Rukwa Rift Basin, Tanzania

The Cretaceous Period is considered the archetypical greenhouse interval, yet there is mounting evidence for intermittent cooler climatic phases throughout this geologic span. Few continental climate histories exist for the Cretaceous south of the paleoequator, and fewer still for Africa during this time. The Cretaceous Galula Formation is one of the few exposed fossiliferous continental sedimentary successions from what is now subequatorial Africa that also contains paleosols and spans both the Early and Late Cretaceous series. Bulk sediment and pedogenic carbonate nodules were sampled from paleosols located throughout ~500 m of the Galula Formation stratotype section, including four from the lower Mtuka Member (Aptian-Cenomanian) and four from the upper Namba Member (Cenomanian-Campanian), to reconstruct the paleoclimate and paleoenvironment of the Rukwa Rift Basin. The Mtuka paleosols developed on channel fill deposits in a semi-arid climate amidst well-defined wet and dry seasons that predominantly generated vertic Calcisols. Geochemical and morphological climofunctions determined that mean annual precipitation (MAP) increased up-section from 454 to 860 mm/yr, whereas the δ18O values of pedogenic carbonates and Bt horizon major-element paleothermometry estimated mean annual temperature (MAT) remained relatively steady, ranging between 12.9 and 13.9 °C throughout the Mtuka Member. The paleosols of the overlying Namba Member formed on channel fill and overbank deposits proximal to the main channels, in a semi-arid to sub-humid climate with little seasonality, forming mostly calcic Argillisols. The Namba paleosols formed under slightly wetter and cooler conditions, recording MAP values between 602 and 987 mm/yr, and MAT estimates between 10.3 and 12.5 °C. These data are consistent with the Mtuka paleosols corresponding to the cool greenhouse period that spanned the Aptian-Albian, with the Namba paleosols corresponding to Late Cretaceous cooling following the Cretaceous Thermal Maximum. This work demonstrates that temperate conditions prevailed in the Rukwa Rift Basin during the mid-Late Cretaceous

Microwave extraction–isotope ratio infrared spectroscopy (ME-IRIS): a novel technique for rapid extraction and in-line analysis of δ18O and δ2H values of water in plants, soils and insects

RATIONALE: Traditionally, stable isotope analysis of plant and soil water has been a technically challenging, labour-intensive and time-consuming process. Here we describe a rapid single-step technique which combines Microwave Extraction with Isotope Ratio Infrared Spectroscopy (ME-IRIS).\ud \ud METHODS: Plant, soil and insect water is extracted into a dry air stream by microwave irradiation within a sealed vessel. The water vapor thus produced is carried to a cooled condensation chamber, which controls the water vapor concentration and flow rate to the spectrometer. Integration of the isotope signals over the whole analytical cycle provides quantitative δ18O and δ2H values for the initial liquid water contained in the sample. Calibration is carried out by the analysis of water standards using the same apparatus. Analysis of leaf and soil water by cryogenic vacuum distillation and IRMS was used to validate the ME-IRIS data.\ud \ud RESULTS: Comparison with data obtained by cryogenic distillation and IRMS shows that the new technique provides accurate water isotope data for leaves from a range of field-grown tropical plant species. However, two exotic nursery plants were found to suffer from spectral interferences from co-extracted organic compounds. The precision for extracted leaf, stem, soil and insect water was typically better than ±0.3 ‰ for δ18O and ±2 ‰ for δ2H values, and better than ±0.1 ‰ for δ18O and ±1 ‰ for δ2H values when analyzing water standards. The effects of sample size, microwave power and duration and sample-to-sample memory on isotope values were assessed.\ud \ud CONCLUSIONS: ME-IRIS provides rapid and low-cost extraction and analysis of δ18O and δ2H values in plant, soil and insect water (≈10–15 min for samples yielding ≈ 0.3 mL of water). The technique can accommodate whole leaves of many plant species

Punctuated eustatic sea-level rise in the early mid-Holocene

Whether eustatic sea-level rise through the Holocene has been punctuated or continuous has remained controversial for almost two decades. Resolving this debate has implications for predicting future responses of remaining ice sheets to climate change an

Punctuated eustatic sea-level rise in the early mid-Holocene

Whether eustatic sea-level rise through the Holocene has been punctuated or continuous has remained controversial for almost two decades. Resolving this debate has implications for predicting future responses of remaining ice sheets to climate change and also for understanding the drivers of human settlement and dispersal patterns through prehistory. Here we present a sea-level curve for the past 8900 yr from Singapore, a tectonically stable location remote from ice-loading effects. We also present critical and unique sedimentation rate, organic delta C-13, and foraminiferal delta C-13 proxy records of sea-level change derived from a shallow-marine sediment core from the same area over the same time interval. The sea-level curve, corroborated by the independent proxy records, suggests rapid rise at a rate of 1.8 m/100 yr until 8100 cal (calibrated) yr B.P., a near cessation in the rate of sea-level rise between 7800 and 7400 cal yr B.P., followed by a renewed rise of 4-5 m that was complete by 6500 cal yr B.P. We suggest that this period of relatively stable sea level during the early to mid-Holocene enabled modern deltas to advance, providing a highly productive environment for the establishment of coastal sedentary agriculture. Periods of rapid sea-level rise before and after may have catalyzed significant postglacial episodes of human dispersal in coastal regions.</p