ALBERT

Description: Although luminescence sensitivity of quartz grains of desert sands has been used in discriminating provenance, it still remains unclear about its spatiotemporal variations and climatic implications. In this paper, the luminescence sensitivity of quartz grains from the northern margin of the Chinese Loess Plateau (CLP) was studied using single-aliquot optically stimulated luminescence (OSL) and “pseudo” single-grain OSL measurements. Our results indicate that the OSL sensitivities have lower values in sand/loess beds and higher values in paleosols. We suggest that the variations in OSL sensitivity of quartz grains with depth on the CLP are mainly influenced by the origin of the quartz grains as they are related to the loess-sized material production processes and the migration of desert regions. More quartz grains of glacial origin with lower luminescence sensitivity, together with the reduced durations of irradiation and exposure cycles induced by shorter transport distance due to desert expansion, account for the lower luminescence sensitivity of glacial periods. Moreover, both the mountain processes and the retreat–advance of deserts are ultimately related to climatic changes, therefore, the orbital scale variations of luminescence sensitivity are controlled by glacial–interglacial oscillations on the CLP.

Description: Ancient cities are excellent spatiotemporal indicators for the study of historical human activities and environmental change. The ancient city of Sanchahe is located at the southern margin of the Mu Us Desert, China. It is an ideal location for studying the complex relationships between historical desertification and human activities. Field observations of the ancient city walls, a well, and a spring, as well as 14C dating, grain size, spatial analysis of archaeological sites, and analyses of historical seismicity, indicated that neotectonics may have contributed to crustal uplift and accelerated fluvial incision of the Wuding River. This rapid incision caused a decline in groundwater levels, which is an important reason for the irreversible environmental degradation around Sanchahe city over the past 800 yr. This study provides new evidence for such environmental degradation and may contribute to a better understanding of historical desertification in the Mu Us Desert.

Description: About 5400 cal yr BP, a large landslide formed a 〉 400-m-tall dam in the upper Marsyandi River, central Nepal. The resulting lacustrine and deltaic deposits stretched 〉 7 km upstream, reaching a thickness of 120 m.14C dating of 7 wood fragments reveals that the aggradation and subsequent incision occurred remarkably quickly (∼ 500 yr). Reconstructed volumes of lacustrine (∼ 0.16 km3) and deltaic (∼ 0.09 km3) deposits indicate a bedload-to-suspended load ratio of 1:2, considerably higher than the ≤ 1:10 that is commonly assumed. At the downstream end of the landslide dam, the river incised a new channel through ≥ 70 m of Greater Himalayan gneiss, requiring a minimum bedrock incision rate of 13 mm/yr over last 5400 yr. The majority of incision presumably occurred over a fraction of this time, suggesting much higher rates. The high bedload ratio from such an energetic mountain river is a particularly significant addition to our knowledge of sediment flux in orogenic environments.

Description: Publication date: Available online 8 August 2015 Source: Quaternary Research Author(s): Socorro Lozano-García, Beatriz Ortega, Priyadarsi D. Roy, Laura Beramendi-Orosco, Margarita Caballero We inferred millennial-scale climate variations and paleohydrological conditions in the northern sector of the American tropics for 30.3–5.5 cal ka BP using geochemical characteristics of sediments from Lake Chalco in central Mexico. The sediment sequence is chronologically constrained with three tephra and nine radiocarbon dates. Temporal variations in titanium, total inorganic carbon, total organic carbon/titanium ratio, carbon/nitrogen ratio, and silica/titanium ratio indicate changes in runoff, salinity, productivity, and sources. Higher concentrations of Ti indicate more runoff during latest Marine Isotope Stage (MIS) 3 (30.3–28.6 cal ka BP). Runoff was lower during the last glacial maximum (LGM; 23–19 cal ka BP) than during the Heinrich 2 event (26–24 cal ka BP). The interval of reduced runoff continued up to 17.5 cal ka BP but increased during the Bølling/Allerød. Trends of decreasing runoff and increasing salinity are observed throughout MIS 1. Lake Chalco received less runoff during the LGM compared to deglaciation, opposite the trend of other North American tropical records. Different amounts of rainfall at different sites are possibly due to shifts in the position of the Intertropical Convergence Zone, changes in the size of the Altlantic warm pool, and varying sea-surface temperatures of the Atlantic and Pacific oceans.

Description: Publication date: Available online 31 July 2015 Source: Quaternary Research Author(s): Linda M. Reinink-Smith In northeastern Kuwait, ancient beach ridges and associated berms are separated from the present shoreline by a 4–6 km-wide sabkha. A diverse mollusk fauna in the beach ridges attests to a former open marine environment. A total of 21 AMS dates were obtained in this study. Thirteen mollusk samples from beach ridges yielded AMS dates ranging from ~ 6990 cal yr BP in the southeast to ~ 3370 cal yr BP in the northwest, suggesting a southeast to northwest age progression during the Holocene transgression. In contrast, four samples from berms throughout the study area yielded AMS dates of 5195–3350 cal yr BP showing no age progression; these berms consist largely of Conomurex persicus gastropods that aggregated by storms during a highstand at ~ 5000–3500 cal yr BP. The berms are presently at ~ + 6 m above sea level, 2–3 m above the beach ridges. Human settlements were common on the ridge crests before and after the highstand. Regression to present-day sea level commenced after the highstand, which is when the sabkha began forming. A landward, marine-built terrace, which yielded AMS dates > 43,500 14 C yr BP, probably formed during Marine Oxygen Isotope Stage 5e and hence is not genetically related to the beach ridges.

Description: Publication date: Available online 8 August 2015 Source: Quaternary Research Author(s): Matthew E. Kirby, Edward J. Knell, William T. Anderson, Matthew S. lachniet, Jennifer Palermo, Holly Eeg, Ricardo Lucero, Rosa Murrieta, Andrea Arevalo, Emily Silveira, Christine A. Hiner Silver Lake is the modern terminal playa of the Mojave River in southern California (USA). As a result, it is well located to record both influences from the winter precipitation dominated San Bernardino Mountains – the source of the Mojave River – and from the late summer to early fall North American monsoon at Silver Lake. Here, we present various physical, chemical and biological data from a new radiocarbon-dated, 8.2 m sediment core taken from Silver Lake that spans modern through 14.8 cal ka BP. Texturally, the core varies between sandy clay, clayey sand, and sand-silt-clay, often with abrupt sedimentological transitions. These grain-size changes are used to divide the core into six lake status intervals over the past 14.8 cal ka BP. Notable intervals include a dry Younger Dryas chronozone, a wet early Holocene terminating 7.8 – 7.4 cal ka BP, a distinct mid-Holocene arid interval, and a late Holocene return to ephemeral lake conditions. A comparison to potential climatic forcings implicates a combination of changing summer – winter insolation and tropical and N Pacific sea-surface temperature dynamics as the primary drivers of Holocene climate in the central Mojave Desert.

Description: For cancer and many other complex diseases, a large number of gene signatures have been generated. In this study, we use cancer as an example and note that other diseases can be analyzed in a similar manner. For signatures generated in multiple independent studies on the same cancer type and outcome, and for signatures on different cancer types, it is of interest to evaluate their degree of overlap. Many of the existing studies simply count the number (or percentage) of overlapped genes shared by two signatures. Such an approach has serious limitations. In this study, as a demonstrating example, we consider cancer prognosis data under the Cox model. Lasso, which is representative of a large number of regularization methods, is adopted for generating gene signatures. We examine two families of measures for quantifying the degree of overlap. The first family is based on the Cox-Lasso estimates at the optimal tunings, and the second family is based on estimates across the whole solution paths. Within each family, multiple measures, which describe the overlap from different perspectives, are introduced. The analysis of TCGA (The Cancer Genome Atlas) data on five cancer types shows that the degree of overlap varies across measures, cancer types and types of (epi)genetic measurements. More investigations are needed to better describe and understand the overlaps among gene signatures.

Description: The past two decades of microRNA (miRNA) research has solidified the role of these small non-coding RNAs as key regulators of many biological processes and promising biomarkers for disease. The concurrent development in high-throughput profiling technology has further advanced our understanding of the impact of their dysregulation on a global scale. Currently, next-generation sequencing is the platform of choice for the discovery and quantification of miRNAs. Despite this, there is no clear consensus on how the data should be preprocessed before conducting downstream analyses. Often overlooked, data preprocessing is an essential step in data analysis: the presence of unreliable features and noise can affect the conclusions drawn from downstream analyses. Using a spike-in dilution study, we evaluated the effects of several general-purpose aligners (BWA, Bowtie, Bowtie 2 and Novoalign), and normalization methods (counts-per-million, total count scaling, upper quartile scaling, Trimmed Mean of M, DESeq, linear regression, cyclic loess and quantile) with respect to the final miRNA count data distribution, variance, bias and accuracy of differential expression analysis. We make practical recommendations on the optimal preprocessing methods for the extraction and interpretation of miRNA count data from small RNA-sequencing experiments.

Description: Parameter estimation is a challenging computational problem in the reverse engineering of biological systems. Because advances in biotechnology have facilitated wide availability of time-series gene expression data, systematic parameter estimation of gene circuit models from such time-series mRNA data has become an important method for quantitatively dissecting the regulation of gene expression. By focusing on the modeling of gene circuits, we examine here the performance of three types of state-of-the-art parameter estimation methods: population-based methods, online methods and model-decomposition-based methods. Our results show that certain population-based methods are able to generate high-quality parameter solutions. The performance of these methods, however, is heavily dependent on the size of the parameter search space, and their computational requirements substantially increase as the size of the search space increases. In comparison, online methods and model decomposition-based methods are computationally faster alternatives and are less dependent on the size of the search space. Among other things, our results show that a hybrid approach that augments computationally fast methods with local search as a subsequent refinement procedure can substantially increase the quality of their parameter estimates to the level on par with the best solution obtained from the population-based methods while maintaining high computational speed. These suggest that such hybrid methods can be a promising alternative to the more commonly used population-based methods for parameter estimation of gene circuit models when limited prior knowledge about the underlying regulatory mechanisms makes the size of the parameter search space vastly large.

Description: Human housekeeping genes are often confused with essential human genes, and several studies regard both types of genes as having the same level of evolutionary conservation. However, this is not necessarily the case. To clarify this, we compared the differences between human housekeeping genes and essential human genes with respect to four aspects: the evolutionary rate (dN/dS), protein sequence identity, single-nucleotide polymorphism (SNP) density and level of linkage disequilibrium (LD). The results showed that housekeeping genes had lower evolutionary rates, higher sequence identities, lower SNP densities and higher levels of LD compared with essential genes. Together, these findings indicate that housekeeping and essential genes are two distinct types of genes, and that housekeeping genes have a higher level of evolutionary conservation. Therefore, we suggest that researchers should pay careful attention to the distinctions between housekeeping genes and essential genes. Moreover, it is still controversial whether we should substitute human orthologs of mouse essential genes for human essential genes. Therefore, we compared the evolutionary features between human orthologs of mouse essential genes and human housekeeping genes and we got inconsistent results in long-term and short-term evolutionary characteristics implying the irrationality of simply replacing human essential genes with human orthologs of mouse essential genes.

Description: Whole-genome search of genes is an essential approach to dissecting complex traits, but a marginal one-single-nucleotide polymorphism (SNP)/one-phenotype regression analysis widely used in current genome-wide association studies fails to estimate the net and cumulative effects of SNPs and reveal the developmental pattern of interplay between genes and traits. Here we describe a computational framework, which we refer to as two-side high-dimensional genome-wide association studies (2HiGWAS), to associate an ultrahigh dimension of SNPs with a high dimension of developmental trajectories measured across time and space. The model is implemented with a dual dimension-reduction procedure for both predictors and responses to select a sparse but full set of significant loci from an extremely large pool of SNPs and estimate their net time-varying effects on trait development. The model can not only help geneticists to precisely identify an entire set of genes underlying complex traits but also allow them to elucidate a global picture of how genes control developmental and dynamic processes of trait formation. We investigated the statistical properties of the model via extensive simulation studies. With the increasing availability of GWAS in various organisms, 2HiGWAS will have important implications for genetic studies of developmental compelx traits.

Description: Three principal approaches have been proposed for inferring the set of transcripts expressed in RNA samples using RNA-seq. The simplest approach uses curated annotations, which assumes the transcripts in a sample are a subset of the transcripts listed in a curated database. A more ambitious method involves aligning reads to a reference genome and using the alignments to infer the transcript structures, possibly with the aid of a curated transcript database. The most challenging approach is to assemble reads into putative transcripts de novo without the aid of reference data. We have systematically assessed the properties of these three approaches through a simulation study. We have found that the sensitivity of computational transcript set estimation is severely limited. Computational approaches (both genome-guided and de novo assembly) produce a large number of artefacts, which are assigned large expression estimates and absorb a substantial proportion of the signal when performing expression analysis. The approach using curated annotations shows good expression correlation even when the annotations are incomplete. Furthermore, any incorrect transcripts present in a curated set do not absorb much signal, so it is preferable to have a curation set with high sensitivity than high precision. Software to simulate transcript sets, expression values and sequence reads under a wider range of parameter values and to compare sensitivity, precision and signal-to-noise ratios of different methods is freely available online ( https://github.com/boboppie/RSSS ) and can be expanded by interested parties to include methods other than the exemplars presented in this article.

Description: Significant efforts have been made recently to improve data throughput and data quality in screening technologies related to drug design. The modern pharmaceutical industry relies heavily on high-throughput screening (HTS) and high-content screening (HCS) technologies, which include small molecule, complementary DNA (cDNA) and RNA interference (RNAi) types of screening. Data generated by these screening technologies are subject to several environmental and procedural systematic biases, which introduce errors into the hit identification process. We first review systematic biases typical of HTS and HCS screens. We highlight that study design issues and the way in which data are generated are crucial for providing unbiased screening results. Considering various data sets, including the publicly available ChemBank data, we assess the rates of systematic bias in experimental HTS by using plate-specific and assay-specific error detection tests. We describe main data normalization and correction techniques and introduce a general data preprocessing protocol. This protocol can be recommended for academic and industrial researchers involved in the analysis of current or next-generation HTS data.

Description: De novo motif discovery is a difficult computational task. Historically, dedicated algorithms always reported a high percentage of false positives. Their performance did not improve considerably even after they adapted to handle large amounts of chromatin immunoprecipitation sequencing (ChIP-Seq) data. Several studies have advocated aggregating complementary algorithms, combining their predictions to increase the accuracy of the results. This led to the development of ensemble methods. To form a better view on modern ensembles, we review all compound tools designed for ChIP-Seq. After a brief introduction to basic algorithms and early ensembles, we describe the most recent tools. We highlight their limitations and strengths by presenting their architecture, the input options and their output. To provide guidance for next-generation sequencing practitioners, we observe the differences and similarities between them. Last but not least, we identify and recommend several features to be implemented by any novel ensemble algorithm.

Description: Publication date: Available online 29 May 2015 Source: Quaternary Research Author(s): Taylor Louise Doran , Andy I.R. Herries , Philip J. Hopley , Hank Sombroek , John Hellstrom , Ed Hodge , Brian F. Kuhn The tufa deposits of the Ghaap Plateau escarpment provide a rich, yet minimally explored, geological archive of climate and environmental history coincident with hominin evolution in South Africa. This study examines the sedimentary and geochemical records of ancient and modern tufas from Buxton-Norlim Limeworks, Groot Kloof, and Gorrokop, to assess the potential of these sediments for providing reliable chronologies of high-resolution, paleoenvironmental information. Chronometric dating demonstrates that tufa formation has occurred from at least the terminal Pliocene through to the modern day. The stable isotope records show a trend toward higher, more variable δ 18 O and δ 13 C values with decreasing age from the end of the Pliocene onwards. The long-term increase in δ 18 O values corresponds to increasingly arid conditions, while increasing δ 13 C values reflect the changing proportion of C 3 /C 4 vegetation in the local environment. Analysis of the Thabaseek Tufa, in particular, provides valuable evidence for reconstructing the depositional and chronological context of the enigmatic Taung Child ( Australopithecus africanus ). Collectively, the results of the present study demonstrate the potential of these deposits for developing high-precision records of climate change and, ultimately, for understanding the causal processes relating climate and hominin evolution.

Description: Publication date: Available online 27 May 2015 Source: Quaternary Research Author(s): Nathan S. Schachtman , Kelly R. MacGregor , Amy Myrbo , Nora Rose Hencir , Catherine A. Riihimaki , Jeffrey T. Thole , Louisa I. Bradtmiller Few records in the alpine landscape of western North America document the geomorphic and glaciologic response to climate change during the Pleistocene–Holocene transition. While moraines can provide snapshots of glacier extent, high-resolution records of environmental response to the end of the Last Glacial Maximum, Younger Dryas cooling, and subsequent warming into the stable Holocene are rare. We describe the transition from the late Pleistocene to the Holocene using a ~ 17,000-yr sediment record from Swiftcurrent Lake in eastern Glacier National Park, MT, with a focus on the period from ~ 17 to 11 ka. Total organic and inorganic carbon, grain size, and carbon/nitrogen data provide evidence for glacial retreat from the late Pleistocene into the Holocene, with the exception of a well-constrained advance during the Younger Dryas from 12.75 to 11.5 ka. Increased detrital carbonate concentration in Swiftcurrent Lake sediment reflects enhanced glacial erosion and sediment transport, likely a result of a more proximal ice terminus position and a reduction in the number of alpine lakes acting as sediment sinks in the valley.

Description: Publication date: Available online 27 May 2015 Source: Quaternary Research Author(s): Charles G. Oviatt , David B. Madsen , David M. Miller , Robert S. Thompson , John P. McGeehin Shorelines and surficial deposits (including buried forest-floor mats and organic-rich wetland sediments) show that Great Salt Lake did not rise higher than modern lake levels during the earliest Holocene (11.5–10.2 cal ka BP; 10–9 14 C ka BP). During that period, finely laminated, organic-rich muds (sapropel) containing brine-shrimp cysts and pellets and interbedded sodium-sulfate salts were deposited on the lake floor. Sapropel deposition was probably caused by stratification of the water column — a freshwater cap possibly was formed by groundwater, which had been stored in upland aquifers during the immediately preceding late-Pleistocene deep-lake cycle (Lake Bonneville), and was actively discharging on the basin floor. A climate characterized by low precipitation and runoff, combined with local areas of groundwater discharge in piedmont settings, could explain the apparent conflict between evidence for a shallow lake (a dry climate) and previously published interpretations for a moist climate in the Great Salt Lake basin of the eastern Great Basin.

Description: The combination of DNA bisulfite treatment with high-throughput sequencing technologies has enabled investigation of genome-wide DNA methylation beyond CpG sites and CpG islands. These technologies have opened new avenues to understand the interplay between epigenetic events, chromatin plasticity and gene regulation. However, the processing, managing and mining of this huge volume of data require specialized computational tools and statistical methods that are yet to be standardized. Here, we describe a complete bisulfite sequencing analysis workflow, including recently developed programs, highlighting each of the crucial analysis steps required, i.e. sequencing quality control, reads alignment, methylation scoring, methylation heterogeneity assessment, genomic features annotation, data visualization and determination of differentially methylated cytosines. Moreover, we discuss the limitations of these technologies and considerations to perform suitable analyses.

Description: Understanding the genetic basis of human traits/diseases and the underlying mechanisms of how these traits/diseases are affected by genetic variations is critical for public health. Current genome-wide functional genomics data uncovered a large number of functional elements in the noncoding regions of human genome, providing new opportunities to study regulatory variants (RVs). RVs play important roles in transcription factor bindings, chromatin states and epigenetic modifications. Here, we systematically review an array of methods currently used to map RVs as well as the computational approaches in annotating and interpreting their regulatory effects, with emphasis on regulatory single-nucleotide polymorphism. We also briefly introduce experimental methods to validate these functional RVs.

Description: The detection of parent-of-origin effects aims to identify whether the functionality of alleles, and in turn associated phenotypic traits, depends on the parental origin of the alleles. Different parent-of-origin effects have been identified through a variety of mechanisms and a number of statistical methodologies for their detection have been proposed, in particular for genome-wide association studies (GWAS). GWAS have had limited success in explaining the heritability of many complex disorders and traits, but successful identification of parent-of-origin effects using trio (mother, father and offspring) GWAS may help shed light on this missing heritability. However, it is important to choose the most appropriate parent-of-origin test or methodology, given knowledge of the phenotype, amount of available data and the type of parent-of-origin effect(s) being considered. This review brings together the parent-of-origin detection methodologies available, comparing them in terms of power and type I error for a number of different simulated data scenarios, and finally offering guidance as to the most appropriate choice for the different scenarios.

Description: With the increasing recognition of its role in trait and disease development, it is crucial to account for genetic imprinting to illustrate the genetic architecture of complex traits. Genetic mapping can be innovated to test and estimate effects of genetic imprinting in a segregating population derived from experimental crosses. Here, we describe and assess a design for imprinting detection in natural plant populations. This design is to sample maternal plants at random from a natural population and collect open-pollinated (OP) seeds randomly from each maternal plant and germinate them into seedlings. A two-stage hierarchical platform is constructed to jointly analyze maternal and OP progeny markers. Through tracing the segregation and transmission of alleles from the parental to progeny generation, this platform allows parent-of-origin-dependent gene expression to be discerned, providing an avenue to estimate the effect of imprinting genes on a quantitative trait. The design is derived to estimate imprinting effects expressed at the haplotype level. Its usefulness and utilization were validated through computer simulation. This OP-based design provides a tool to detect the genomic distribution and pattern of imprinting genes as an important component of heritable variation that is neglected in traditional genetic studies of complex traits.

Description: Breast cancer was traditionally perceived as a single disease; however, recent advances in gene expression and genomic profiling have revealed that breast cancer is in fact a collection of diseases exhibiting distinct anatomical features, responses to treatment and survival outcomes. Consequently, a number of schemes have been proposed for subtyping of breast cancer to bring out the biological and clinically relevant characteristics of the subtypes. Although some of these schemes capture underlying molecular differences, others predict variations in response to treatment and survival patterns. However, despite this diversity in the approaches, it is clear that molecular mechanisms drive clinical outcomes, and therefore an effective scheme should integrate molecular as well as clinical parameters to enable deeper understanding of cancer mechanisms and allow better decision making in the clinic. Here, using a large cohort of ~550 breast tumours from The Cancer Genome Atlas, we systematically evaluate a number of expression-based schemes including at least eight molecular pathways implicated in breast cancer and three prognostic signatures, across a variety of classification scenarios covering molecular characteristics, biomarker status, tumour stages and survival patterns. We observe that a careful combination of these schemes yields better classification results compared with using them individually, thus confirming that molecular mechanisms and clinical outcomes are related and that an effective scheme should therefore integrate both these parameters to enable a deeper understanding of the cancer.

Description: microRNAs (miRNAs) are important gene regulators. They control a wide range of biological processes and are involved in several types of cancers. Thus, exploring miRNA functions is important for diagnostics and therapeutics. To date, there are few feasible experimental techniques for discovering miRNA regulatory mechanisms. Alternatively, predictions of miRNA–mRNA regulatory relationships by computational methods have increasingly achieved promising results. Computational approaches are proving their ability as effective tools in reducing the number of biological experiments that must be conducted and to assist with the design of the experiments. In this review, we categorize and review different computational approaches to identify miRNA activities and functions, including the co-regulation of miRNAs and transcription factors. Our main focuses are on the recent approaches that use multiple data types for exploring miRNA functions. We discuss the remaining challenges in the evaluation and selection of models based on the results from a case study. Finally, we analyse the remaining challenges of each computational approach and suggest some future research directions.

Description: Technological advances in next-generation sequencing have uncovered a wide spectrum of aberrations in cancer genomes. The extreme diversity in cancer mutations necessitates computational approaches to differentiate between the ‘drivers’ with vital function in cancer progression and those nonfunctional ‘passengers’. Although individual driver mutations are routinely identified, mutational profiles of different tumors are highly heterogeneous. There is growing consensus that pathways rather than single genes are the primary target of mutations. Here we review extant bioinformatics approaches to identifying oncogenic drivers at different mutational levels, highlighting the strategies for discovering driver pathways and networks from cancer mutation data. These approaches will help reduce the mutation complexity, thus providing a simplified picture of cancer.

Description: Copy number variants (CNVs) play important roles in a number of human diseases and in pharmacogenetics. Powerful methods exist for CNV detection in whole genome sequencing (WGS) data, but such data are costly to obtain. Many disease causal CNVs span or are found in genome coding regions (exons), which makes CNV detection using whole exome sequencing (WES) data attractive. If reliably validated against WGS-based CNVs, exome-derived CNVs have potential applications in a clinical setting. Several algorithms have been developed to exploit exome data for CNV detection and comparisons made to find the most suitable methods for particular data samples. The results are not consistent across studies. Here, we review some of the exome CNV detection methods based on depth of coverage profiles and examine their performance to identify problems contributing to discrepancies in published results. We also present a streamlined strategy that uses a single metric, the likelihood ratio, to compare exome methods, and we demonstrated its utility using the VarScan 2 and eXome Hidden Markov Model (XHMM) programs using paired normal and tumour exome data from chronic lymphocytic leukaemia patients. We use array-based somatic CNV (SCNV) calls as a reference standard to compute prevalence-independent statistics, such as sensitivity, specificity and likelihood ratio, for validation of the exome-derived SCNVs. We also account for factors known to influence the performance of exome read depth methods, such as CNV size and frequency, while comparing our findings with published results.

Description: Publication date: Available online 23 May 2015 Source: Quaternary Research Author(s): Ari Matmon , Alan J. Hidy , Shlomy Vainer , Onn Crouvi , David Fink , Yigal Erel , Liora K. Horwitz , Michael Chazan Kalahari Group sediments accumulated in the Kalahari basin, which started forming during the breakup of Gondwana in the early Cretaceous. These sediments cover an extensive part of southern Africa and form a low-relief landscape. Current models assume that the Kalahari Group accumulated throughout the entire Cenozoic. However, chronology has been restricted to early–middle Cenozoic biostratigraphic correlations and to OSL dating of only the past ~ 300 ka. We present a new chronological framework that reveals a dynamic nature of sedimentation in the southern Kalahari. Cosmogenic burial ages obtained from a 55 m section of Kalahari Group sediments from the Mamatwan Mine, southern Kalahari, indicate that the majority of deposition at this location occurred rapidly at 1–1.2 Ma. This Pleistocene sequence overlies the Archaean basement, forming a significant hiatus that permits the possibility of many Phanerozoic cycles of deposition and erosion no longer preserved in the sedimentary record. Our data also establish the existence of a shallow early–middle Pleistocene water body that persisted for > 450 ka prior to this rapid period of deposition. Evidence from neighboring archeological excavations in southern Africa suggests an association of high-density hominin occupation with this water body.

Description: Publication date: Available online 10 June 2015 Source: Quaternary Research Author(s): Christoph Wißing , Simon Matzerath , Elaine Turner , Hervé Bocherens Climatic and ecological conditions during Marine Oxygen Isotope Stage (MIS) 3 are complex and the impact of cold spells on the ecosystems in Central Europe still needs to be investigated thoroughly. Ziegeleigrube Coenen (ZC) is a late Pleistocene MIS 3 locality in the Lower Rhine Embayment of Germany, radiocarbon-dated to > 34 14 C ka BP. The site yielded a broad spectrum of mammal species. We investigated the carbon (δ 13 C), nitrogen (δ 15 N) and sulfur (δ 34 S) isotope signatures of bone collagen, since these are valuable tools in characterizing ecological niches, environmental conditions and aspects of climate and mobility. By comparison with pre- and post-Last Glacial Maximum (LGM) sites in Central Europe we show that ZC belongs in a cold event of MIS 3 and was climatically more similar to post-LGM sites than to pre-LGM sites. However, the trophic structure resembled that of typical pre-LGM sites in Belgium. This cold event in MIS 3 changed the bottom of the foodweb, but do not seem to have had a direct impact on the occurrence of the mammalian species and their ecological distribution. Apparently the (mega-) faunal community could adapt also to harsher environmental conditions during MIS 3.

Description: Publication date: Available online 9 July 2016 Source: Quaternary Research Author(s): Martín Medina-Elizalde, Josué Moises Polanco-Martínez, Fernanda Lases-Hernández, Raymond Bradley, Stephen Burns We examine the “tropical storm” hypothesis that precipitation variability in the Yucatan Peninsula (YP) was linked to the frequency of tropical cyclones during the demise of the Classic Maya civilization, in the Terminal Classic Period (TCP, AD 750–950). Evidence that supports the hypothesis includes: (1) a positive relationship between tropical storm frequency and precipitation amount over the YP today (proof of feasibility), (2) a statistically significant correlation between a stalagmite (Chaac) quantitative precipitation record from the YP and the number of named tropical cyclones affecting this region today (1852–2004) (calibration sensu lato ), and, (3) correlations between the stalagmite Chaac precipitation record and an Atlantic basin tropical cyclone count record and two proxy records of shifts in macro-scale climate and ocean states that influence Atlantic tropical cyclongenesis. At face value, regional paleotempestology proxy records suggest that tropical storm activity in the YP was either similar or significantly lower than today during the TCP. The “tropical storm” hypothesis has implications for our understanding of the role the hydrological cycle played in the collapse of Classic Maya polities and the role of tropical storms in possibly ameliorating future drought in the YP and other tropical regions.

Description: The detailed, atomistic-level understanding of molecular signaling along the tumor-suppressive Hippo signaling pathway that controls tissue homeostasis by balancing cell proliferation and death through apoptosis is a promising avenue for the discovery of novel anticancer drug targets. The activation of kinases such as Mammalian STE20-Like Protein Kinases 1 and 2 (MST1 and MST2)—modulated through both homo- and heterodimerization (e.g. interactions with Ras association domain family, RASSF, enzymes)—is a key upstream event in this pathway and remains poorly understood. On the other hand, RASSFs (such as RASSF1A or RASSF5) act as important apoptosis activators and tumor suppressors, although their exact regulatory roles are also unclear. We present recent molecular studies of signaling along the Ras-RASSF-MST pathway, which controls growth and apoptosis in eukaryotic cells, including a variety of modern molecular modeling and simulation techniques. Using recently available structural information, we discuss the complex regulatory scenario according to which RASSFs perform dual signaling functions, either preventing or promoting MST2 activation, and thus control cell apoptosis. Here, we focus on recent studies highlighting the special role being played by the specific interactions between the helical Salvador/RASSF/Hippo (SARAH) domains of MST2 and RASSF1a or RASSF5 enzymes. These studies are crucial for integrating atomistic-level mechanistic information about the structures and conformational dynamics of interacting proteins, with information available on their system-level functions in cellular signaling.

Description: Big-data-based edge biomarker is a new concept to characterize disease features based on biomedical big data in a dynamical and network manner, which also provides alternative strategies to indicate disease status in single samples. This article gives a comprehensive review on big-data-based edge biomarkers for complex diseases in an individual patient, which are defined as biomarkers based on network information and high-dimensional data. Specifically, we firstly introduce the sources and structures of biomedical big data accessible in public for edge biomarker and disease study. We show that biomedical big data are typically ‘small-sample size in high-dimension space', i.e. small samples but with high dimensions on features (e.g. omics data) for each individual, in contrast to traditional big data in many other fields characterized as ‘large-sample size in low-dimension space', i.e. big samples but with low dimensions on features. Then, we demonstrate the concept, model and algorithm for edge biomarkers and further big-data-based edge biomarkers. Dissimilar to conventional biomarkers, edge biomarkers, e.g. module biomarkers in module network rewiring-analysis, are able to predict the disease state by learning differential associations between molecules rather than differential expressions of molecules during disease progression or treatment in individual patients. In particular, in contrast to using the information of the common molecules or edges (i.e.molecule-pairs) across a population in traditional biomarkers including network and edge biomarkers, big-data-based edge biomarkers are specific for each individual and thus can accurately evaluate the disease state by considering the individual heterogeneity. Therefore, the measurement of big data in a high-dimensional space is required not only in the learning process but also in the diagnosing or predicting process of the tested individual. Finally, we provide a case study on analyzing the temporal expression data from a malaria vaccine trial by big-data-based edge biomarkers from module network rewiring-analysis. The illustrative results show that the identified module biomarkers can accurately distinguish vaccines with or without protection and outperformed previous reported gene signatures in terms of effectiveness and efficiency.

Description: Molecular interrogation of a biological sample through DNA sequencing, RNA and microRNA profiling, proteomics and other assays, has the potential to provide a systems level approach to predicting treatment response and disease progression, and to developing precision therapies. Large publicly funded projects have generated extensive and freely available multi-assay data resources; however, bioinformatic and statistical methods for the analysis of such experiments are still nascent. We review multi-assay genomic data resources in the areas of clinical oncology, pharmacogenomics and other perturbation experiments, population genomics and regulatory genomics and other areas, and tools for data acquisition. Finally, we review bioinformatic tools that are explicitly geared toward integrative genomic data visualization and analysis. This review provides starting points for accessing publicly available data and tools to support development of needed integrative methods.

Description: One of the major challenges in biology concerns the integration of data across length and time scales into a consistent framework: how do macroscopic properties and functionalities arise from the molecular regulatory networks—and how can they change as a result of mutations? Morphogenesis provides an excellent model system to study how simple molecular networks robustly control complex processes on the macroscopic scale despite molecular noise, and how important functional variants can emerge from small genetic changes. Recent advancements in three-dimensional imaging technologies, computer algorithms and computer power now allow us to develop and analyse increasingly realistic models of biological control. Here, we present our pipeline for image-based modelling that includes the segmentation of images, the determination of displacement fields and the solution of systems of partial differential equations on the growing, embryonic domains. The development of suitable mathematical models, the data-based inference of parameter sets and the evaluation of competing models are still challenging, and current approaches are discussed.

Description: Owing greatly to the advancement of next-generation sequencing (NGS), the amount of NGS data is increasing rapidly. Although there are many NGS applications, one of the most commonly used techniques ‘RNA sequencing (RNA-seq)’ is rapidly replacing microarray-based techniques in laboratories around the world. As more and more of such techniques are standardized, allowing technicians to perform these experiments with minimal hands-on time and reduced experimental/operator-dependent biases, the bottleneck of such techniques is clearly visible; that is, data analysis. Further complicating the matter, increasing evidence suggests most of the genome is transcribed into RNA; however, the majority of these RNAs are not translated into proteins. These RNAs that do not become proteins are called ‘noncoding RNAs (ncRNAs)’. Although some time has passed since the discovery of ncRNAs, their annotations remain poor, making analysis of RNA-seq data challenging. Here, we examine the current limitations of RNA-seq analysis using case studies focused on the detection of novel transcripts and examination of their characteristics. Finally, we validate the presence of novel transcripts using biological experiments, showing novel transcripts can be accurately identified when a series of filters is applied. In conclusion, novel transcripts that are identified from RNA-seq must be examined carefully before proceeding to biological experiments.

Description: Functional genomics has enormous potential to facilitate our understanding of normal and disease-specific physiology. In the past decade, intensive research efforts have been focused on modeling functional relationship networks, which summarize the probability of gene co-functionality relationships. Such modeling can be based on either expression data only or heterogeneous data integration. Numerous methods have been deployed to infer the functional relationship networks, while most of them target the global (non-context-specific) functional relationship networks. However, it is expected that functional relationships consistently reprogram under different tissues or biological processes. Thus, advanced methods have been developed targeting tissue-specific or developmental stage-specific networks. This article brings together the state-of-the-art functional relationship network modeling methods, emphasizes the need for heterogeneous genomic data integration and context-specific network modeling and outlines future directions for functional relationship networks.

Description: Identification of drug–target interactions is an important process in drug discovery. Although high-throughput screening and other biological assays are becoming available, experimental methods for drug–target interaction identification remain to be extremely costly, time-consuming and challenging even nowadays. Therefore, various computational models have been developed to predict potential drug–target associations on a large scale. In this review, databases and web servers involved in drug–target identification and drug discovery are summarized. In addition, we mainly introduced some state-of-the-art computational models for drug–target interactions prediction, including network-based method, machine learning-based method and so on. Specially, for the machine learning-based method, much attention was paid to supervised and semi-supervised models, which have essential difference in the adoption of negative samples. Although significant improvements for drug–target interaction prediction have been obtained by many effective computational models, both network-based and machine learning-based methods have their disadvantages, respectively. Furthermore, we discuss the future directions of the network-based drug discovery and network approach for personalized drug discovery based on personalized medicine, genome sequencing, tumor clone-based network and cancer hallmark-based network. Finally, we discussed the new evaluation validation framework and the formulation of drug–target interactions prediction problem by more realistic regression formulation based on quantitative bioactivity data.

Description: Atherosclerosis is one of the principle pathologies of cardiovascular disease with blood cholesterol a significant risk factor. The World Health Organization estimates that approximately 2.5 million deaths occur annually because of the risk from elevated cholesterol, with 39% of adults worldwide at future risk. Atherosclerosis emerges from the combination of many dynamical factors, including haemodynamics, endothelial damage, innate immunity and sterol biochemistry. Despite its significance to public health, the dynamics that drive atherosclerosis remain poorly understood. As a disease that depends on multiple factors operating on different length scales, the natural framework to apply to atherosclerosis is mathematical and computational modelling. A computational model provides an integrated description of the disease and serves as an in silico experimental system from which we can learn about the disease and develop therapeutic hypotheses. Although the work completed in this area to date has been limited, there are clear signs that interest is growing and that a nascent field is establishing itself. This article discusses the current state of modelling in this area, bringing together many recent results for the first time. We review the work that has been done, discuss its scope and highlight the gaps in our understanding that could yield future opportunities.

Description: We present Bioinformatics Autodiscovery of Training Materials (BATMat), an open-source, Google-based, targeted, automatic search tool for training materials related to bioinformatics. BATMat helps gain access with one click to filtered and portable information containing links to existing materials (when present). It also offers functionality to sort results according to source site or title. Availability: http://imbatmat.com Contact: piar301@gmail.com

Description: Publication date: July 2016 Source: Quaternary Research, Volume 86, Issue 1 Author(s): Frédéric Quillévéré, Jean-Jacques Cornée, Pierre Moissette, Gatsby Emperatriz López-Otálvaro, Christiaan van Baak, Philippe Münch, Mihaela Carmen Melinte-Dobrinescu, Wout Krijgsman An integrated magneto-biostratigraphic study, based on calcareous nannofossils and foraminifers, together with the radiometric dating of a volcaniclastic layer found in several outcrops, was carried out on the hemipelagic deposits of the Lindos Bay Formation (LBF) at six localities on the island of Rhodes (Greece). Our highly refined chronostratigraphic framework indicates that the lower and upper lithostratigraphic boundaries of the LBF are diachronous. Associated with the 40 Ar/ 39 Ar age determination of 1.85 ± 0.08 Ma for the volcaniclastic layer, our data show that among the investigated outcrops, the Lindos Bay type locality section provides the longest record (1.1 Ma) of the LBF. Hemipelagic deposition occurred continuously from the late Gelasian (∼1.9 Ma) to the late Calabrian (∼0.8 Ma), i.e., from Chrons C2n (Olduvai) to C1r.1r (Matuyama) and from nannofossil Zones CNPL7 to CNPL10. This long record, together with the hemipelagic nature of the deposits, make the Lindos Bay type locality section a unique element in the eastern Mediterranean region, allowing future comparisons with other early Quaternary deep-sea sections available in the central and western Mediterranean regions.

Description: Publication date: Available online 29 July 2016 Source: Quaternary Research Author(s): Yanxia Liu, Haijun Huang, Yali Qi, Xiao Liu, Xiguang Yang Ground-penetrating radar (GPR) reflection profiles were interpreted and combined with sedimentological data to highlight the morpho-evolutionary history of the southwestern sector of the Bohai Sea. The internal structures in GPR images obtained near the Holocene maximum transgression boundary revealed concave-upward and onlap types of transgressive paleo-topography. The relationship between historical courses of the Yellow River and the distribution of shell ridges at three periods (6 ka, 2 ka, and recent times) showed that the concave-upward types derived from the marine sediments overlap the fluvial sediments, and the onlap types from the marine sediments cover the coastal lagoon sediments. Based on the above paleo-geographical setting, previous sea-level markers were corrected, taking into account uncertainties of their relationship to former water levels. The rates of vertical tectonic displacement, evaluated through comparison of the relative sea level (RSL) data from the GPR images and the Holocene predicted sea-level elevation, markedly affected RSL changes. The fitted RSL curves from the corrected sea-level indicators showed that the accuracy of former sea-level determinations can be improved by comparing with the maximum transgressive position of GPR detection. A topographic digital elevation model (DEM) for 6 ka is reconstructed based on the corrected data.

Description: Cancer is often driven by the accumulation of genetic alterations, including single nucleotide variants, small insertions or deletions, gene fusions, copy-number variations, and large chromosomal rearrangements. Recent advances in next-generation sequencing technologies have helped investigators generate massive amounts of cancer genomic data and catalog somatic mutations in both common and rare cancer types. So far, the somatic mutation landscapes and signatures of 〉10 major cancer types have been reported; however, pinpointing driver mutations and cancer genes from millions of available cancer somatic mutations remains a monumental challenge. To tackle this important task, many methods and computational tools have been developed during the past several years and, thus, a review of its advances is urgently needed. Here, we first summarize the main features of these methods and tools for whole-exome, whole-genome and whole-transcriptome sequencing data. Then, we discuss major challenges like tumor intra-heterogeneity, tumor sample saturation and functionality of synonymous mutations in cancer, all of which may result in false-positive discoveries. Finally, we highlight new directions in studying regulatory roles of noncoding somatic mutations and quantitatively measuring circulating tumor DNA in cancer. This review may help investigators find an appropriate tool for detecting potential driver or actionable mutations in rapidly emerging precision cancer medicine.

Description: Recent literature has highlighted the advantages of haplotype association methods for detecting rare variants associated with common diseases. As several new haplotype association methods have been proposed in the past few years, a comparison of new and standard methods is important and timely for guidance to the practitioners. We consider nine methods—Haplo.score, Haplo.glm, Hapassoc, Bayesian hierarchical Generalized Linear Model (BhGLM), Logistic Bayesian LASSO (LBL), regularized GLM (rGLM), Haplotype Kernel Association Test, wei-SIMc-matching and Weighted Haplotype and Imputation-based Tests. These can be divided into two types—individual haplotype-specific tests and global tests depending on whether there is just one overall test for a haplotype region (global) or there is an individual test for each haplotype in the region. Haplo.score is the only method that tests for both; Haplo.glm, Hapassoc, BhGLM and LBL are individual haplotype-specific, while the rest are global tests. For comparison, we also apply a popular collapsing method—Sequence Kernel Association Test (SKAT) and its two variants—SKAT-O (Optimal) and SKAT-C (Combined). We carry out an extensive comparison on our simulated data sets as well as on the Genetic Analysis Workshop (GAW) 18 simulated data. Further, we apply the methods to GAW18 real hypertension data and Dallas Heart Study sequence data. We find that LBL, Haplo.score (global test) and rGLM perform well over the scenarios considered here. Also, haplotype methods are more powerful (albeit more computationally intensive) than SKAT and its variants in scenarios where multiple causal variants act interactively to produce haplotype effects.

Description: The purpose of this article is to inform readers about technical challenges that we encountered when assembling exome sequencing data from the ‘Simplifying Complex Exomes' (SIMPLEXO) consortium—whose mandate is the discovery of novel genes predisposing to breast and ovarian cancers. Our motivation is to share these obstacles—and our solutions to them—as a means of communicating important technical details that should be discussed early in projects involving massively parallel sequencing.

Description: Predictive, preventive, personalized and participatory (P4) medicine is an emerging medical model that is based on the customization of all medical aspects (i.e. practices, drugs, decisions) of the individual patient. P4 medicine presupposes the elucidation of the so-called omic world, under the assumption that this knowledge may explain differences of patients with respect to disease prevention, diagnosis and therapies. Here, we elucidate the role of some selected omics sciences for different aspects of disease management, such as early diagnosis of diseases, prevention of diseases, selection of personalized appropriate and optimal therapies based on molecular profiling of patients. After introducing basic concepts of P4 medicine and omics sciences, we review some computational tools and approaches for analysing selected omics data, with a special focus on microarray and mass spectrometry data, which may be used to support P4 medicine. Some applications of biomarker discovery and pharmacogenomics and some experiences on the study of drug reactions are also described.

Description: A wide variety of large-scale data have been produced in bioinformatics. In response, the need for efficient handling of biomedical big data has been partly met by parallel computing. However, the time demand of many bioinformatics programs still remains high for large-scale practical uses because of factors that hinder acceleration by parallelization. Recently, new generations of storage devices have emerged, such as NAND flash-based solid-state drives (SSDs), and with the renewed interest in near-data processing, they are increasingly becoming acceleration methods that can accompany parallel processing. In certain cases, a simple drop-in replacement of hard disk drives by SSDs results in dramatic speedup. Despite the various advantages and continuous cost reduction of SSDs, there has been little review of SSD-based profiling and performance exploration of important but time-consuming bioinformatics programs. For an informative review, we perform in-depth profiling and analysis of 23 key bioinformatics programs using multiple types of devices. Based on the insight we obtain from this research, we further discuss issues related to design and optimize bioinformatics algorithms and pipelines to fully exploit SSDs. The programs we profile cover traditional and emerging areas of importance, such as alignment, assembly, mapping, expression analysis, variant calling and metagenomics. We explain how acceleration by parallelization can be combined with SSDs for improved performance and also how using SSDs can expedite important bioinformatics pipelines, such as variant calling by the Genome Analysis Toolkit and transcriptome analysis using RNA sequencing. We hope that this review can provide useful directions and tips to accompany future bioinformatics algorithm design procedures that properly consider new generations of powerful storage devices.

Description: Publication date: Available online 1 August 2016 Source: Quaternary Research Author(s): Rajeev Saraswat, Dinesh Kumar Naik, Rajiv Nigam, Anuruddh Singh Gaur We reconstruct centennial scale quantitative changes in surface seawater temperature (SST), evaporation-precipitation (from Mg/Ca and δ 18 O of surface dwelling planktic foraminifera), productivity (from relative abundance of Globigerina bulloides ), carbon burial (from %CaCO 3 and organic carbon [%C org ]) and dissolved oxygen at sediment–water interface, covering the entire Holocene, from a core collected from the eastern Arabian Sea. From the multi-proxy record, we define the timing, consequences and possible causes of the mid-Holocene climate transition (MHCT). A distinct shift in evaporation-precipitation (E-P) is observed at 6.4 ka, accompanied by a net cooling of SST. The shift in SST and E-P is synchronous with a change in surface productivity. A concurrent decrease is also noted in both the planktic foraminiferal abundance and coarse sediment fraction. A shift in carbon burial, as inferred from both the %CaCO 3 and %C org , coincides with a change in surface productivity. A simultaneous decrease in dissolved oxygen at the sediment–water interface, suggests that changes affected both the surface and subsurface water. A similar concomitant change is also observed in other cores from the Arabian Sea as well as terrestrial records, suggesting a widespread regional MHCT. The MHCT coincides with decreasing low-latitude summer insolation, perturbations in total solar intensity and an increase in atmospheric CO 2 .

Description: State-of-the-art next-generation sequencing, transcriptomics, proteomics and other high-throughput ‘omics' technologies enable the efficient generation of large experimental data sets. These data may yield unprecedented knowledge about molecular pathways in cells and their role in disease. Dimension reduction approaches have been widely used in exploratory analysis of single omics data sets. This review will focus on dimension reduction approaches for simultaneous exploratory analyses of multiple data sets. These methods extract the linear relationships that best explain the correlated structure across data sets, the variability both within and between variables (or observations) and may highlight data issues such as batch effects or outliers. We explore dimension reduction techniques as one of the emerging approaches for data integration, and how these can be applied to increase our understanding of biological systems in normal physiological function and disease.

Description: There is much interest in using high-throughput DNA sequencing methodology to monitor microorganisms, complex plant and animal communities. However, there are experimental and analytical issues to consider before applying a sequencing technology, which was originally developed for genome projects, to ecological projects. Many of these issues have been highlighted by recent microbial studies. Understanding how high-throughput sequencing is best implemented is important for the interpretation of recent results and the success of future applications. Addressing complex biological questions with metagenomics requires the interaction of researchers who bring different skill sets to problem solving. Educators can help by nurturing a collaborative interdisciplinary approach to genome science, which is essential for effective problem solving. Educators are in a position to help students, teachers, the public and policy makers interpret the new knowledge that metagenomics brings. To do this, they need to understand, not only the excitement of the science but also the pitfalls and shortcomings of methodology and research designs. We review these issues and some of the research directions that are helping to move the field forward.

Description: We believe that undergraduate biology students must acquire a foundational background in computing including how to formulate a computational problem; develop an algorithmic solution; implement their solution in software and then test, document and use their code to explore biological phenomena. Moreover, by learning these skills in the first year, students acquire a powerful tool set that they can use and build on throughout their studies. To address this need, we have developed a first-year undergraduate course that teaches students the foundations of computational thinking and programming in the context of problems in biology. This article describes the structure and content of the course and summarizes assessment data on both affective and learning outcomes.

Description: Bioinformatics is an integral part of modern life sciences. It has revolutionized and redefined how research is carried out and has had an enormous impact on biotechnology, medicine, agriculture and related areas. Yet, it is only rarely integrated into high school teaching and learning programs, playing almost no role in preparing the next generation of information-oriented citizens. Here, we describe the design principles of bioinformatics learning environments, including our own, that are aimed at introducing bioinformatics into senior high school curricula through engaging learners in scientifically authentic inquiry activities. We discuss the bioinformatics-related benefits and challenges that high school teachers and students face in the course of the implementation process, in light of previous studies and our own experience. Based on these lessons, we present a new approach for characterizing the questions embedded in bioinformatics teaching and learning units, based on three criteria: the type of domain-specific knowledge required to answer each question (declarative knowledge, procedural knowledge, strategic knowledge, situational knowledge), the scientific approach from which each question stems (biological, bioinformatics, a combination of the two) and the associated cognitive process dimension (remember, understand, apply, analyze, evaluate, create). We demonstrate the feasibility of this approach using a learning environment, which we developed for the high school level, and suggest some of its implications. This review sheds light on unique and critical characteristics related to broader integration of bioinformatics in secondary education, which are also relevant to the undergraduate level, and especially on curriculum design, development of suitable learning environments and teaching and learning processes.

Description: Next-generation sequencing (NGS) is increasingly being adopted as the backbone of biomedical research. With the commercialization of various affordable desktop sequencers, NGS will be reached by increasing numbers of cellular and molecular biologists, necessitating community consensus on bioinformatics protocols to tackle the exponential increase in quantity of sequence data. The current resources for NGS informatics are extremely fragmented. Finding a centralized synthesis is difficult. A multitude of tools exist for NGS data analysis; however, none of these satisfies all possible uses and needs. This gap in functionality could be filled by integrating different methods in customized pipelines, an approach helped by the open-source nature of many NGS programmes. Drawing from community spirit and with the use of the Wikipedia framework, we have initiated a collaborative NGS resource: The NGS WikiBook. We have collected a sufficient amount of text to incentivize a broader community to contribute to it. Users can search, browse, edit and create new content, so as to facilitate self-learning and feedback to the community. The overall structure and style for this dynamic material is designed for the bench biologists and non-bioinformaticians. The flexibility of online material allows the readers to ignore details in a first read, yet have immediate access to the information they need. Each chapter comes with practical exercises so readers may familiarize themselves with each step. The NGS WikiBook aims to create a collective laboratory book and protocol that explains the key concepts and describes best practices in this fast-evolving field.

Description: Publication date: Available online 24 September 2013 Source: Quaternary Research Author(s): Daniel E. Karig , Norton G. Miller Areal mapping of the middle Wisconsin varved clay site along Sixmile Creek near Ithaca, New York, has revealed a much more widespread and varied array of sediments than previously thought. Lacustrine clays, some varved, are interbedded with sands and gravels interpreted as sub-aqueous fan deposits, and both are overlain by a deformation till. Nine radiocarbon dates indicate a 34–37 14 C ka BP age for the lacustrine sediment, with the deformation till less than a few thousand years younger. Beneath this sequence is a deposit dated at ± 42 14 C ka BP. Both strata represent a tundra climate with a mean July temperature of about 10°C. The Sixmile Creek deformation till must correlate with the 35 14 C ka BP till along the Genesee River, 125 km to the NW, and defines a Cherrytree stade glacial advance into the Appalachian Plateau, much further south than what has generally been accepted. Such an advance would require drainage from a proglacial lake in the western Ontario basin to flow westward instead of northeastward. The Sixmile strata suggest a colder than accepted middle Wisconsin stage. Recent data indicate that this stage is one of progressive cooling, with large climatic fluctuations.

Description: Publication date: Available online 25 September 2013 Source: Quaternary Research Author(s): Denis Geraads , Fethi Amani , Abdelouahed Ben-Ncer , Shannon P. McPherron , Jean-Paul Raynal , Jean-Jacques Hublin The rodents from the late middle Pleistocene hominin-bearing locality of J'bel Irhoud include the following species: Meriones shawii , Gerbillus grandis , Dipodillus campestris , Paraethomys ras , Lemniscomys barbarus , Mus cf. spretus , and Eliomys sp. We consider M. shawii , a living species, as identical with the middle Pleistocene Meriones maghrebianus . The mouse differs from the domestic Mus musculus but does not clearly fit into Mus spretus , either. The rare G. grandis looks identical with the form from the middle Pleistocene of Thomas quarries, which may suggest a rather early age for Irhoud. This is in agreement with the occurrence of Paraethomys , a genus unknown in the upper Pleistocene of Morocco, but the absence of the arvicolid Ellobius suggests that the site is younger than other middle Pleistocene sites, Doukkala II, Sidi Abderrahmane D2, and Irhoud-Derbala-Virage. Paleoecological indicators, such as the taxonomic habitat spectrum, or the relative abundances of Gerbillinae and Murinae, suggest a less xeric environment than in many earlier and later sites. Diversity indices, comparable to those of other middle Pleistocene sites, point to similarly favorable conditions before the major climatic crisis close to the middle/upper Pleistocene boundary that drastically reduced rodent diversity in North Africa.

Description: With the advent of YouTube channels in bioinformatics, open platforms for problem solving in bioinformatics, active web forums in computing analyses and online resources for learning to code or use a bioinformatics tool, the more traditional continuing education bioinformatics training programs have had to adapt. Bioinformatics training programs that solely rely on traditional didactic methods are being superseded by these newer resources. Yet such face-to-face instruction is still invaluable in the learning continuum. Bioinformatics.ca, which hosts the Canadian Bioinformatics Workshops, has blended more traditional learning styles with current online and social learning styles. Here we share our growing experiences over the past 12 years and look toward what the future holds for bioinformatics training programs.

Description: Teaching students with very diverse backgrounds can be extremely challenging. This article uses the Bioinformatics and Systems Biology MSc in Amsterdam as a case study to describe how the knowledge gap for students with heterogeneous backgrounds can be bridged. We show that a mix in backgrounds can be turned into an advantage by creating a stimulating learning environment for the students. In the MSc Programme, conversion classes help to bridge differences between students, by mending initial knowledge and skill gaps. Mixing students from different backgrounds in a group to solve a complex task creates an opportunity for the students to reflect on their own abilities. We explain how a truly interdisciplinary approach to teaching helps students of all backgrounds to achieve the MSc end terms. Moreover, transferable skills obtained by the students in such a mixed study environment are invaluable for their later careers.

Description: The number of bioinformatics tools and resources that support molecular and cell biology approaches is continuously expanding. Moreover, systems and network biology analyses are accompanied more and more by integrated bioinformatics methods. Traditional information-centered university teaching methods often fail, as (1) it is impossible to cover all existing approaches in the frame of a single course, and (2) a large segment of the current bioinformation can become obsolete in a few years. Signaling network offers an excellent example for teaching bioinformatics resources and tools, as it is both focused and complex at the same time. Here, we present an outline of a university bioinformatics course with four sample practices to demonstrate how signaling network studies can integrate biochemistry, genetics, cell biology and network sciences. We show that several bioinformatics resources and tools, as well as important concepts and current trends, can also be integrated to signaling network studies. The research-type hands-on experiences we show enable the students to improve key competences such as teamworking, creative and critical thinking and problem solving. Our classroom course curriculum can be re-formulated as an e-learning material or applied as a part of a specific training course. The multi-disciplinary approach and the mosaic setup of the course have the additional benefit to support the advanced teaching of talented students.

Description: Today, Bioinformatics has become a scientific discipline with great relevance for the Molecular Biosciences and for the Omics sciences in general. Although developed countries have progressed with large strides in Bioinformatics education and research, in other regions, such as Central America, the advances have occurred in a gradual way and with little support from the Academia, either at the undergraduate or graduate level. To address this problem, the University of Costa Rica’s Medical School, a regional leader in Bioinformatics in Central America, has been conducting a series of Bioinformatics workshops, seminars and courses, leading to the creation of the region’s first Bioinformatics Master’s Degree. The recent creation of the Central American Bioinformatics Network (BioCANET), associated to the deployment of a supporting computational infrastructure (HPC Cluster) devoted to provide computing support for Molecular Biology in the region, is providing a foundational stone for the development of Bioinformatics in the area. Central American bioinformaticians have participated in the creation of as well as co-founded the Iberoamerican Bioinformatics Society (SOIBIO). In this article, we review the most recent activities in education and research in Bioinformatics from several regional institutions. These activities have resulted in further advances for Molecular Medicine, Agriculture and Biodiversity research in Costa Rica and the rest of the Central American countries. Finally, we provide summary information on the first Central America Bioinformatics International Congress, as well as the creation of the first Bioinformatics company (Indromics Bioinformatics), spin-off the Academy in Central America and the Caribbean.

Description: Pattern recognition is concerned with the development of systems that learn to solve a given problem using a set of example instances, each represented by a number of features. These problems include clustering, the grouping of similar instances; classification, the task of assigning a discrete label to a given instance; and dimensionality reduction, combining or selecting features to arrive at a more useful representation. The use of statistical pattern recognition algorithms in bioinformatics is pervasive. Classification and clustering are often applied to high-throughput measurement data arising from microarray, mass spectrometry and next-generation sequencing experiments for selecting markers, predicting phenotype and grouping objects or genes. Less explicitly, classification is at the core of a wide range of tools such as predictors of genes, protein function, functional or genetic interactions, etc., and used extensively in systems biology. A course on pattern recognition (or machine learning) should therefore be at the core of any bioinformatics education program. In this review, we discuss the main elements of a pattern recognition course, based on material developed for courses taught at the BSc, MSc and PhD levels to an audience of bioinformaticians, computer scientists and life scientists. We pay attention to common problems and pitfalls encountered in applications and in interpretation of the results obtained.

Description: Publication date: Available online 25 September 2013 Source: Quaternary Research Author(s): Mikael Ohlson , Isabella Kasin , Anveig Nordtug Wist , Anne E. Bjune Forest fires convert a proportion of the burning vegetation into charcoal that is stored in forest soils and lake sediments. In this paper we use a geostatistical approach to present a detailed analysis of the size of the charcoal pool and its spatial variation in a boreal forest watershed including its lake sediment. The amount of soil charcoal averaged 179 g/m 2 and ranged from 0 to 3600 g/m 2 in the watershed. There was an extreme variation in the size of the charcoal pool over fine (cm) spatial scales. For example, the amount of charcoal in the soil could range from 34 to 1646 g/m 2 within a distance of 10 cm. Individually dated soil charcoal particles had radiocarbon ages that varied from 630 to 2930 cal yr BP. The lake sediment began accumulating at 10,600 cal yr BP and charcoal accumulation has been practically continuous ever since then, with the largest peak occurring at 6900 cal yr BP. The lake sediment contained more charcoal, 360 g/m 2 , than the average for forest soil. We interpret this as an indication of a relatively rapid degradation of charcoal in boreal forest soils.

Description: Publication date: Available online 29 September 2013 Source: Quaternary Research Author(s): Julien Carcaillet , Isandra Angel , Eduardo Carrillo , Franck A. Audemard , Christian Beck In the tropical Mérida Andes (northwestern Venezuela), glacial landforms were found at altitudes between 2600 and 5000 m, corresponding to 600 km 2 of ice cover during the maximum glacial extension. However, the lack of sufficient absolute age data prevents detailed reconstruction of the timing of the last deglaciation. On the northwestern flank of the Mucuñuque Massif, successive moraines and striated eroded basement surfaces were sampled for cosmogenic 10 Be investigation. Their compilation with published data allows the establishment of a detailed chronology of the post-LGM glacier history. The oldest moraines (18.1 and 16.8 ka) correspond to the Oldest Dryas. Successive moraine ridges indicate stops in the overall retreat between the LGM and the Younger Dryas. The cold and short Older Dryas stadial has been identified. Results indicate that most of the ice withdrew during the Pleistocene. The dataset supports an intensification of the vertical retreat rate from ~ 25 m/ka during the late Pleistocene to ~ 310 m/ka during the Pleistocene/Holocene. Afterwards, the glacier was confined and located in the higher altitude zones. The altitude difference of the Younger Dryas moraines in the Mucubají, La Victoria and Los Zerpa valleys indicates a strong effect of valley orientation on the altitude of moraine development.

Description: Publication date: Available online 3 October 2013 Source: Quaternary Research Author(s): Nicole E. Spaulding , John A. Higgins , Andrei V. Kurbatov , Michael L. Bender , Steven A. Arcone , Seth Campbell , Nelia W. Dunbar , Laura M. Chimiak , Douglas S. Introne , Paul A. Mayewski Terrestrial meteorite ages indicate that some ice at the Allan Hills blue ice area (AH BIA) may be as old as 2.2 Ma. As such, ice from the AH BIA could potentially be used to extend the ice core record of paleoclimate beyond 800 ka. We collected samples from 5 to 10 cm depth along a 5 km transect through the main icefield and drilled a 225 m ice core (S27) at the midpoint of the transect to develop the climate archive of the AH BIA. Stable water isotope measurements (δD) of the surface chips and of ice core S27 yield comparable signals, indicating that the climate record has not been significantly altered in the surface ice. Measurements of 40 Ar atm and δ 18 O atm taken from ice core S27 and eight additional shallow ice cores constrain the age of the ice to approximately 90–250 ka. Our findings provide a framework around which future investigations of potentially older ice in the AH BIA could be based.

Description: Publication date: Available online 3 October 2013 Source: Quaternary Research Author(s): Yurena Yanes , María P. Asta , Miguel Ibáñez , María R. Alonso , Christopher S. Romanek Land snail shell δ 13 C value is often used as a paleovegetation proxy assuming that snails ingest all plants in relation to their abundance, and that plants are the only source of carbon. However, carbonate ingestion and variable metabolic rates complicate these relationships. We evaluate if live-collected snails from Lanzarote (Canary Islands) reflect the abundance of C 3 and CAM plants. Snails were collected on either CAM or C 3 plants for isotope analysis of shell and body, and shell size. Respective shell and body δ 13 C values of snails collected on CAM plants averaged − 8.5 ± 1.7‰ and − 22.8 ± 1.6‰, whereas specimens from C 3 plants averaged − 10.1 ± 0.7‰ and − 24.9 ± 1.1‰. A flux balance model suggests snails experienced comparable metabolic rates. A two-source mass balance equation implies that snails consumed ~ 10% of CAM, which agrees with their abundance in the landscape. Snails collected on CAM plant were smaller than those on C 3 plants. Conclusively: 1) snails consume CAM plants when they are available; 2) migration of snails among C 3 and CAM plants is a common phenomenon; and 3) C 3 plants may be a more energetic food for growth than CAM plants. This study shows that shell δ 13 C values offer approximate estimates of plants in C 3 –CAM mixed environments.

Description: Publication date: Available online 7 June 2013 Source: Quaternary Research Author(s): William R. Dickinson Unlike most tropical Pacific islands, which lie along island arcs or hotspot chains, the Loyalty Islands between New Caledonia and Vanuatu owe their existence and morphology to the uplift of pre-existing atolls on the flexural forebulge of the New Hebrides Trench. The configuration and topography of each island is a function of distance from the crest of the uplifted forebulge. Both Maré and Lifou are fully emergent paleoatolls upon which ancient barrier reefs form highstanding annular ridges that enclose interior plateaus representing paleolagoon floors, whereas the partially emergent Ouvea paleoatoll rim flanks a drowned remnant lagoon. Emergent paleoshoreline features exposed by island uplift include paleoreef flats constructed as ancient fringing reefs built to past low tide levels and emergent tidal notches incised at past high tide levels. Present paleoshoreline elevations record uplift rates of the islands since last-interglacial and mid-Holocene highstands in global and regional sea levels, respectively, and paleoreef stratigraphy reflects net Quaternary island emergence. The empirical uplift rates vary in harmony with theoretical uplift rates inferred from the different positions of the islands in transit across the trench forebulge at the trench subduction rate. The Loyalty Islands provide a case study of island environments controlled primarily by neotectonics.

Description: Publication date: Available online 7 June 2013 Source: Quaternary Research Author(s): Thomas R. Lakeman , John H. England The study revises the maximum extent of the northwest Laurentide Ice Sheet (LIS) in the western Canadian Arctic Archipelago (CAA) during the last glaciation and documents subsequent ice sheet retreat and glacioisostatic adjustments across western Banks Island. New geomorphological mapping and maximum-limiting radiocarbon ages indicate that the northwest LIS inundated western Banks Island after ~ 31 14 C ka BP and reached a terminal ice margin west of the present coastline. The onset of deglaciation and the age of the marine limit (22–40 m asl) are unresolved. Ice sheet retreat across western Banks Island was characterized by the withdrawal of a thin, cold-based ice margin that reached the central interior of the island by ~ 14 cal ka BP. The elevation of the marine limit is greater than previously recognized and consistent with greater glacioisostatic crustal unloading by a more expansive LIS. These results complement emerging bathymetric observations from the Arctic Ocean, which indicate glacial erosion during the Last Glacial Maximum (LGM) to depths of up to 450 m.

Description: Publication date: Available online 10 April 2013 Source: Quaternary Research The distribution of marine-influenced oxygen isotope stage (OIS) 5 to OIS 1 sediments was examined in several late Quaternary boreholes from the southern Changjiang (Yangtze) delta plain, China, using different dating methods including OSL, U-series, AMS 14 C and paleomagnetism. Results demonstrate that coastal and estuarine deposition during OIS 5 and OIS 3 occurred throughout the study area. However, Holocene transgressive sediments were absent on the Taihu block. The burial depth of intertidal to subtidal sediment deposited during OIS 5e records 30–80 m subsidence caused by sediment compaction and tectonic movement since that time. However, coastal sediments formed during the late phase of OIS 3 were buried to a depth of ca. 6–15 m in the Taihu Lake area, while the burial depth increased eastward to ca. 45–60 m on the coastal plain. This phenomenon, combined with the distribution of Holocene marine strata, indicates at least 25–30 m uplift of the Taihu block since the end of OIS 3. We suggest that this uplift was mainly caused by the differential subsidence due to substantial amount of post-glacial deposition by the Changjiang and Huanghe Rivers on the continental shelf of east China marginal sea.

Description: Publication date: Available online 5 September 2013 Source: Quaternary Research Author(s): Vachel A. Carter , Andrea Brunelle , Thomas A. Minckley , Philip E. Dennison , Mitchell J. Power Fire is one of the most important natural disturbances in the coniferous forests of the US Rocky Mountains. The Rocky Mountains are separated by a climatic boundary between 40° and 45° N, which we refer to as the central Rocky Mountains (CRM). To determine whether the fire regime from the CRM was more similar to the northern Rocky Mountains (NRM) or southern Rocky Mountains (SRM) during the Holocene, a 12,539-yr-old sediment core from Long Lake, Wyoming, located in the CRM was analyzed for charcoal and pollen. These data were then compared to charcoal records from the CRM, NRM and SRM. During the Younger Dryas chronozone, the fire regime was characterized as frequent at Long Lake. The early and middle Holocene fire regime was characterized as infrequent. A brief interval from 4000 to 3000 cal yr BP, termed the Populus period, had a frequent fire regime and remained frequent through the late Holocene at Long Lake. In comparison to sites from the NRM and SRM, the fire regime at Long Lake was most similar to the SRM during the past 12,539 cal yr BP. These results suggest the disturbance regime in the CRM has a greater affinity with those of the SRM.

Description: The mountains of data thrusting from the new landscape of modern high-throughput biology are irrevocably changing biomedical research and creating a near-insatiable demand for training in data management and manipulation and data mining and analysis. Among life scientists, from clinicians to environmental researchers, a common theme is the need not just to use, and gain familiarity with, bioinformatics tools and resources but also to understand their underlying fundamental theoretical and practical concepts. Providing bioinformatics training to empower life scientists to handle and analyse their data efficiently, and progress their research, is a challenge across the globe. Delivering good training goes beyond traditional lectures and resource-centric demos, using interactivity, problem-solving exercises and cooperative learning to substantially enhance training quality and learning outcomes. In this context, this article discusses various pragmatic criteria for identifying training needs and learning objectives, for selecting suitable trainees and trainers, for developing and maintaining training skills and evaluating training quality. Adherence to these criteria may help not only to guide course organizers and trainers on the path towards bioinformatics training excellence but, importantly, also to improve the training experience for life scientists.

Description: High-throughput technologies are widely used in the field of functional genomics and used in an increasing number of applications. For many ‘wet lab’ scientists, the analysis of the large amount of data generated by such technologies is a major bottleneck that can only be overcome through very specialized training in advanced data analysis methodologies and the use of dedicated bioinformatics software tools. In this article, we wish to discuss the challenges related to delivering training in the analysis of high-throughput sequencing data and how we addressed these challenges in the hands-on training courses that we have developed at the European Bioinformatics Institute.

Description: The widespread adoption of high-throughput next-generation sequencing (NGS) technology among the Australian life science research community is highlighting an urgent need to up-skill biologists in tools required for handling and analysing their NGS data. There is currently a shortage of cutting-edge bioinformatics training courses in Australia as a consequence of a scarcity of skilled trainers with time and funding to develop and deliver training courses. To address this, a consortium of Australian research organizations, including Bioplatforms Australia, the Commonwealth Scientific and Industrial Research Organisation and the Australian Bioinformatics Network, have been collaborating with EMBL-EBI training team. A group of Australian bioinformaticians attended the train-the-trainer workshop to improve training skills in developing and delivering bioinformatics workshop curriculum. A 2-day NGS workshop was jointly developed to provide hands-on knowledge and understanding of typical NGS data analysis workflows. The road show–style workshop was successfully delivered at five geographically distant venues in Australia using the newly established Australian NeCTAR Research Cloud. We highlight the challenges we had to overcome at different stages from design to delivery, including the establishment of an Australian bioinformatics training network and the computing infrastructure and resource development. A virtual machine image, workshop materials and scripts for configuring a machine with workshop contents have all been made available under a Creative Commons Attribution 3.0 Unported License. This means participants continue to have convenient access to an environment they had become familiar and bioinformatics trainers are able to access and reuse these resources.

Description: The patterns of variation within a molecular sequence data set result from the interplay between population genetic, molecular evolutionary and macroevolutionary processes—the standard purview of evolutionary biologists. Elucidating these patterns, particularly for large data sets, requires an understanding of the structure, assumptions and limitations of the algorithms used by bioinformatics software—the domain of mathematicians and computer scientists. As a result, bioinformatics often suffers a ‘two-culture’ problem because of the lack of broad overlapping expertise between these two groups. Collaboration among specialists in different fields has greatly mitigated this problem among active bioinformaticians. However, science education researchers report that much of bioinformatics education does little to bridge the cultural divide, the curriculum too focused on solving narrow problems (e.g. interpreting pre-built phylogenetic trees) rather than on exploring broader ones (e.g. exploring alternative phylogenetic strategies for different kinds of data sets). Herein, we present an introduction to the mathematics of tree enumeration, tree construction, split decomposition and sequence alignment. We also introduce off-line downloadable software tools developed by the BioQUEST Curriculum Consortium to help students learn how to interpret and critically evaluate the results of standard bioinformatics analyses.

Description: Publication date: Available online 13 September 2013 Source: Quaternary Research Author(s): Lyudmila S. Shumilovskikh , Helge W. Arz , Antje Wegwerth , Dominik Fleitmann , Fabienne Marret , Norbert Nowaczyk , Pavel Tarasov , Hermann Behling This multiproxy study on SE Black Sea sediments provides the first detailed reconstruction of vegetation and environmental history of Northern Anatolia between 134 and 119 ka. Here, the glacial–interglacial transition is characterized by several short-lived alternating cold and warm events preceding a meltwater pulse (~ 130.4–131.7 ka). The latter is reconstructed as a cold arid period correlated to Heinrich event 11. The initial warming is evidenced at ~ 130.4 ka by increased primary productivity in the Black Sea, disappearance of ice-rafted detritus, and spreading of oaks in Anatolia. A Younger Dryas-type event is not identifiable. The Eemian vegetation succession corresponds to the main climatic phases in Europe: i) the Quercus – Juniperus phase (128.7–126.4 ka) indicates a dry continental climate; ii) the Ostrya – Corylus – Quercus – Carpinus phase (126.4–122.9 ka) suggests warm summers, mild winters, and high year-round precipitation; iii) the Fagus – Carpinus phase (122.9–119.5 ka) indicates cooling and high precipitation; and iv) increasing Pinus at ~ 121 ka marks the onset of cooler/drier conditions. Generally, pollen reconstructions suggest altitudinal/latitudinal migrations of vegetation belts in Northern Anatolia during the Eemian caused by increased transport of moisture. The evidence for the wide distribution of Fagus around the Black Sea contrasts with the European records and is likely related to climatic and genetic factors.

Description: Publication date: Available online 26 September 2013 Source: Quaternary Research Author(s): Liubing Xu , Shangzhe Zhou The timing of terrace formation relative to the glacial–interglacial cycle and what factors control that timing, such as changes in climate and/or uplift, are controversial. Here we present a study of the terraces along the Yazheku River using electron spin resonance (ESR) dating and analysis of the sedimentary characteristics in order to establish the timing of terrace formation and to assess the forcing mechanisms that have been proposed. The Yazheku River flows in glacial trough leading from the Haizi Shan, on the eastern Tibetan Plateau. The range was uplifted during the Quaternary and repeatedly glaciated by ice caps. The four highest major terraces (T5, T4, T3, and T2) are the result of both climatic and tectonic influences. Strath terraces T5–T2 were created during Haizi Shan glacial expansions during MIS 16, 12, 6 and 3–4, respectively. The major aggradation phases of the four terraces occurred during the deglaciations at the ends of MIS 16, 12, 6, and 2. Down-cutting, which led to the generation of the four terraces, immediately followed the deposition of the T5–T2 gravel units. These incisions occurred during the transitions between MIS 16–15, MIS 12–11, MIS 6–5, and MIS 2–1.

Description: Publication date: Available online 6 May 2015 Source: Quaternary Research Author(s): Jaesoo Lim , Dong-Yoon Yang , Jin-Young Lee , Sei-Sun Hong , In Kwon Um To trace the surficial responses of lowlands to past climate change, we investigated δ 13 C in total organic carbon (TOC), C/N ratios, magnetic susceptibility (MS), and silicon (Si) intensity (directly proportional to concentration) in wetland sediments collected from the Gimpo area of central Korea, covering 6600–4600 cal yr BP. Two organic layers with high TOC%, negatively depleted δ 13 C TOC values (− 27 to − 29‰), low MS values, and low Si intensities were found at 6200–5900 and 5200–4800 cal yr BP, respectively. These middle Holocene wet periods corresponded to relatively intensified summer monsoon and solar activity periods. The intervening dry period (5900–5200 cal yr BP) with high MS, high Si, and low TOC% corresponded to an intensified dust-activity interval and stronger winter monsoon. This multi-centennial climatic fluctuation of wet periods (6200–5900 cal yr BP and 5200–4800 cal yr BP) and an intervening dry period (5900–5200 cal yr BP) in central Korea was more synchronous with climate change in the arid inner part of China than with that in South China, suggesting possible strong high-latitude-driven climatic influences (e.g., North Atlantic cooling events) during the middle Holocene.

Description: Publication date: Available online 8 May 2015 Source: Quaternary Research Author(s): Cheng-Bang An , Weimiao Dong , Yufeng Chen , Hu Li , Chao Shi , Wei Wang , Pingyu Zhang , Xueye Zhao Stable isotopic analysis of carbon and nitrogen in human and faunal remains has been widely used to reconstruct prehistoric diets and environmental changes. Isotopic analysis of plant remains allows for a more extensive consideration of paleodiets and can potentially provide information about the environment in which the crops were grown. This paper reports the results of δ 13 C and δ 15 N analyses performed on modern and charred archaeological foxtail millet samples collected from the western part of the Chinese Loess Plateau. The δ 13 C mean value of modern samples is lower than that of ancient samples. There is a significant difference between grain and leaf δ 15 N values. These results challenge the standard assumption in isotope studies that the nitrogen isotope signals of the different part of plants consumed by humans and animals are the same. The 3–5‰ difference between human and animal δ 15 N values is always regarded as an indicator of whether human diets contained considerable animal protein. The difference between grain and leaf δ 15 N values makes this assumption problematic in a foxtail millet-dominated society.

Description: Publication date: Available online 9 May 2015 Source: Quaternary Research Author(s): Glenn D. Thackray , Zhisheng An

Description: Publication date: Available online 14 May 2015 Source: Quaternary Research Author(s): Stephen W. Lokier , Mark D. Bateman , Nigel R. Larkin , Philip Rye , John R. Stewart Late Quaternary reflooding of the Persian Gulf climaxed with the mid-Holocene highstand previously variously dated between 6 and 3.4 ka. Examination of the stratigraphic and paleoenvironmental context of a mid-Holocene whale beaching allows us to accurately constrain the timing of the transgressive, highstand and regressive phases of the mid- to late Holocene sea-level highstand in the Persian Gulf. Mid-Holocene transgression of the Gulf surpassed today's sea level by 7100–6890 cal yr BP, attaining a highstand of > 1 m above current sea level shortly after 5290–4570 cal yr BP before falling back to current levels by 1440–1170 cal yr BP. The cetacean beached into an intertidal hardground pond during the transgressive phase (5300–4960 cal yr BP) with continued transgression interring the skeleton in shallow-subtidal sediments. Subsequent relative sea-level fall produced a forced regression with consequent progradation of the coastal system. These new ages refine previously reported timings for the mid- to late Holocene sea-level highstand published for other regions. By so doing, they allow us to constrain the timing of this correlatable global eustatic event more accurately.

Description: Publication date: Available online 13 May 2015 Source: Quaternary Research Author(s): Juan M. Rubiales , Mar Génova Macro- and megafossil studies are of great value in palaeoecology because such evidence is spatially precise, directly radiocarbon dated, and usually taxon-specific. Here, we present new macro- and megafossil data from ten sites from the Gredos Mountains, central Iberian Peninsula, that suggest persistent forest cover through the late Holocene, with a widespread belt of pinewoods in the highlands of the Central Iberian Mountains. Well-preserved pine cones found at several sites revealed that both Pinus sylvestris and Pinus nigra were present in the area during the middle and late Holocene at locations of important biogeographical interest. The P. sylvestris forests represent one of the southernmost locations of its entire range. P. nigra was not known to have occurred in central Spain during the Holocene; it was found at the westernmost edge of its range in siliceous soils, a rare environment compared with the rest of its distribution. Finally, we explored the potential for obtaining a long pine chronology from central Iberia using tree-ring measurements and radiocarbon dating of pine subfossil logs.

Description: Publication date: Available online 8 May 2015 Source: Quaternary Research Author(s): Isaac A. Hart , Jack M. Broughton , Ruth Gruhn The El Niño/Southern Oscillation (ENSO) is a major source of climatic variation worldwide, with significant impacts on modern human and animal populations. However, few detailed records exist on the long-term effects of ENSO on prehistoric vertebrate populations. Here we examine how lagomorph (rabbit and hare) deposition rate, population age structure and taxonomic composition from Abrigo de los Escorpiones, a well-dated, trans-Holocene vertebrate fauna from northern Baja California, Mexico, vary as a function of the frequency of wet El Niño events and eastern Pacific sea-surface temperatures (SSTs) derived from eastern Pacific geological records. Faunal indices vary significantly in response to El Niño-based precipitation and SST, with substantial moisture-driven variability in the middle and late Holocene. The late Holocene moisture pulse is coincident with previously documented changes in the population dynamics of other vertebrates, including humans. As the frequency and intensity of ENSO is anticipated to vary in the future, these results have important implications for change in future vertebrate populations.

Description: Publication date: Available online 16 December 2014 Source: Quaternary Research Author(s): Marith C. Reheis , David M. Miller , John P. McGeehin , Joanna R. Redwine , Charles G. Oviatt , Jordon Bright An outcrop-based lake-level curve, constrained by ~ 70 calibrated 14 C ages on Anodonta shells, indicates at least 8 highstands between 45 and 25 cal ka BP within 10 m of the 543-m upper threshold of Lake Manix in the Mojave Desert of southern California. Correlations of Manix highstands with ice, marine, and speleothem records suggest that at least the youngest three highstands coincide with Dansgaard–Oeschger (D–O) stadials and Heinrich events 3 and 4. The lake-level record is consistent with results from speleothem studies in the Southwest that indicate cool wet conditions during D–O stadials. Notably, highstands between 43 and 25 ka apparently occurred at times of generally low levels of pluvial lakes farther north as interpreted from core-based proxies. Mojave lakes may have been supported by tropical moisture sources during oxygen-isotope stage 3, perhaps controlled by southerly deflection of Pacific storm tracks due to weakening of the sea-surface temperature gradient in response to North Atlantic climate perturbations.

Description: Publication date: Available online 30 March 2015 Source: Quaternary Research Author(s): Kendrick J. Brown , Gerrit Schoups Holocene streamflow was reconstructed for two rivers on Vancouver Island, British Columbia, Canada in 500-yr intervals. The San Juan River watershed is located on the wetter western side of the island, whereas the Koksilah River watershed is positioned on the drier eastern side. Both watersheds are forested. To reconstruct streamflow, temporal changes in precipitation (estimated using a pollen-based transfer function) and evapotranspiration were established for each watershed and integrated into a water balance model, calibrated using modern data. While seasonal streamflow variability was maintained throughout the Holocene, with greater flow in the winter relative to the summer, the amount of discharge has changed markedly through time. Lowest simulated flow occurred in the earliest Holocene, with low-flow conditions beginning earlier in the year and extending later into the fall. Such conditions may have inhibited salmon from using many of the smaller rivers in the region. Streamflow steadily increased throughout the early Holocene so that by ca. 6500 cal yr before present near-modern flow regimes were established. As climate changes in the future, the San Juan and Koksilah watersheds are expected to remain as pluvial hydroclimatic regimes, though with an extended season of low flow similar to conditions during the early Holocene.

Description: Publication date: Available online 24 March 2015 Source: Quaternary Research Author(s): Lorita N. Mihindukulasooriya , Joseph D. Ortiz , David P. Pompeani , Byron A. Steinman , Mark B. Abbott Visible derivative spectroscopy (VDS) analysis of sediment from Cleland Lake, Southeastern British Columbia provides a reconstruction of paleolimnological productivity and hydrologic change during the past 14,000 calibrated 14 C years before present (cal yr BP). The first five principal components (PC) of the VDS data explain 97% of the variance in the VDS data set. Four PCs correlate with standard reflectance derivative spectra for diatom, dinoflagellate algae, and cyanophyte pigments that record ecological change, while two PCs are paleohydrologic indicators. Dinoflagellate algae are predominant from 11,600 to 8600 cal yr BP then decrease to low levels after ~ 8500 cal yr BP. PCs 3–5 represent variations in cyanophyte abundance and exhibit peaks from 14,000 to 11,600, 14,000 to 9500, and 6100 to 5400 cal yr BP, respectively. Conditions shifted toward favoring diatoms around 9400 and lasted until 170 cal yr BP. Higher dinoflagellate-related pigment concentrations suggest a lower lake level from 11,600 to 8600 cal yr BP, followed by higher water levels and wetter conditions after 8500 cal yr BP. We propose that drier conditions transitioning from the late glacial into the Holocene were caused by summer insolation-driven, non-linear feedbacks between the northern hemisphere subtropical high-pressure systems, vegetation, and soil moisture.

Description: Publication date: Available online 7 April 2015 Source: Quaternary Research Author(s): Yurena Yanes Land snails have been investigated isotopically in tropical islands and mid-latitude continental settings, while high-latitude locales, where snails grow only during the summer, have been overlooked. This study presents the first isotopic baseline of live snails from Fairbanks, Alaska (64°51′N), a proxy calibration necessary prior to paleoenvironmental inferences using fossils. δ 13 C values of the shell (− 10.4 ± 0.4‰) and the body (− 25.5 ± 1.0‰) indicate that snails consumed fresh and decayed C 3 -plants and fungi. A flux-balance mixing model suggests that specimens differed in metabolic rates, which may complicate paleovegetation inferences. Shell δ 18 O values (− 10.8 ± 0.4‰) were ~ 4‰ higher than local summer rain δ 18 O. If calcification occurred during summer, a flux-balance mixing model suggests that snails grew at temperatures of ~ 13°C, rainwater δ 18 O values of ~− 15‰ and relative humidity of ~ 93%. Results from Fairbanks were compared to shells from San Salvador (Bahamas), at 24°51′N. Average (annual) δ 18 O values of shells and rainwater samples from The Bahamas were both ~ 10‰ 18 O-enriched with respect to seasonal (summer) Alaskan samples. At a coarse latitudinal scale, shell δ 18 O values overwhelmingly record the signature of the rainfall during snail active periods. While tropical snails record annual average environmental information, high-latitude specimens only trace summer season climatic data.

Description: Publication date: Available online 22 March 2016 Source: Quaternary Research Author(s): Marie-Claude Fortin, Konrad Gajewski A study of chironomid remains in the sediments of Lake JR01 on the Boothia Peninsula in the central Canadian Arctic provides a high-resolution record of mean July air temperatures for the last 6.9 ka. Diatom and pollen studies have previously been published from this core. Peak Holocene temperatures occurred prior to 5.0 ka, a time when overall aquatic and terrestrial biological production was high. Chironomid-inferred summer air temperatures reached up to 7.5°C during this period. The region of Lake JR01 cooled over the mid- to late Holocene, with high biological production between 6.1 and 5.4 ka. Biological production decreased again at ~ 2 ka and the rate of cooling increased in the past 2 ka, with coolest temperatures occurring between 0.46 and 0.36 ka, coinciding with the Little Ice Age. Although biological production increased in the last 150 yr, the reconstructed temperatures do not indicate a warming during this time. During transitions, either warming or cooling, chironomid production increases, suggesting an ecosystem-level response to climate variability, seen at a number of lakes across the Arctic.

Description: Publication date: Available online 8 January 2016 Source: Quaternary Research Author(s): Cathy Whitlock, Julie K. Stein, Sherilyn Fritz

Description: Publication date: Available online 8 January 2016 Source: Quaternary Research Author(s): Philip D. Hughes, Neil F. Glasser, David Fink New 10 Be ages from the summits of three mountain areas of North Wales reveal a very similar exposure timing as the Welsh Ice Cap thinned after the global Last Glacial Maximum. Eight bedrock and one boulder sample gave a combined arithmetic mean exposure age of 19.08 ± 0.80 ka (4.2%, 1σ). Similar exposure ages over a 320 m vertical range (824 to 581 m altitude) show that ice cap thinning was very rapid and spatially uniform. Using the same production rate and scaling scheme, we recalculated six published 10 Be exposure ages from the nearby Arans, which also covered a similar elevation range from 608 to 901 m and obtained an arithmetic mean of 19.41 ± 1.45 ka (7.5%, 1σ). The average exposure age of all 15 accepted deglaciation ages is 19.21 ± 1.07 (5.6%, 1σ). The complete dataset from North Wales provides very strong evidence indicating that these summits became exposed as nunataks at 20–19 ka. This result provides important insight to the magnitude of ice surface lowering and behavior of the Welsh Ice Cap during the last deglaciation that can be compared to other ice masses that made up the British-Irish Ice Sheet.

Description: Publication date: Available online 8 January 2016 Source: Quaternary Research Author(s): Erin P. Fitch, Grant A. Meyer In the Jemez Mountains, tree-ring data indicate that low-severity fires characterized the 400 yr before Euro-American settlement, and that subsequent fire suppression promoted denser forests, recent severe fires, and erosion. Over longer timescales, climate change may alter fire regimes; thus, we used fire-related alluvial deposits to assess the timing of moderate- to high-severity fires, their geomorphic impact, and relation to climate over the last 4000 yr. Fire-related sedimentation does not clearly follow millennial-scale climatic changes, but probability peaks commonly correspond with severe drought, e.g., within the interval 1700–1400 cal yr BP, and ca. 650 and ca. 410 cal yr BP. The latter episodes were preceded by prolonged wet intervals that could promote dense stands. Estimated recurrence intervals for fire-related sedimentation are 250–400 yr. Climatic differences with aspect influenced Holocene post-fire response: fire-related deposits constitute 77% of fan sediments from north-facing basins but only 39% of deposits from drier southerly aspects. With sparser vegetation and exposed bedrock, south aspects can generate runoff and sediment when unburned, whereas soil-mantled north aspects produce minor sediment unless severely burned. Recent channel incision appears unprecedented over the last 2300 yr, suggesting that fuel loading and extreme drought produced an anomalously severe burn in 2002.

Description: Publication date: Available online 9 January 2016 Source: Quaternary Research Author(s): Matthieu Carré, Donald Jackson, Antonio Maldonado, Brian M. Chase, Julian P. Sachs The variability of radiocarbon marine reservoir age through time and space limits the accuracy of chronologies in marine paleo-environmental archives. We report here new radiocarbon reservoir ages (ΔR) from the central coast of Chile (~ 32°S) for the Holocene period and compare these values to existing reservoir age reconstructions from southern Peru and northern Chile. Late Holocene ΔR values show little variability from central Chile to Peru. Prior to 6000 cal yr BP, however, ΔR values were markedly increased in southern Peru and northern Chile, while similar or slightly lower-than-modern ΔR values were observed in central Chile. This extended dataset suggests that the early Holocene was characterized by a substantial increase in the latitudinal gradient of marine reservoir age between central and northern Chile. This change in the marine reservoir ages indicates that the early Holocene air–sea flux of CO 2 could have been up to five times more intense than in the late Holocene in the Peruvian upwelling, while slightly reduced in central Chile. Our results show that oceanic circulation changes in the Humboldt system during the Holocene have substantially modified the air–sea carbon flux in this region.

Description: Publication date: Available online 10 December 2015 Source: Quaternary Research Author(s): Steven G. Driese, Gail M. Ashley Paleosols record paleoclimatic processes in the Earth's Critical Zone and are archives of ancient landscapes associated with archeological sites. Detailed field, micromorphologic, and bulk geochemical analysis of paleosols were conducted near four sites at Olduvai Gorge, Tanzania within the same stratigraphic horizon as the Zinjanthropus ( Paranthropus ) boisei archeological site. Paleosols are thin (〈 35 cm), smectitic, and exhibit Vertisol shrink–swell features. Traced across the paleolandscape over 1 km and just beneath Tuff IC (1.845 Ma), the paleosols record a paleocatena in which soil moisture at the four sites was supplemented by seepage additions from adjacent springs, and soil development was enhanced by this additional moisture. Field evidence revealed an abrupt lateral transition in paleosol composition at the PTK site (〈 1.5 m apart) in which paleosol B, formed nearest the spring system, is highly siliceous, vs. paleosol A, formed in smectitic clay. Thin-section investigations combined with mass-balance geochemistry, using Chapati Tuff as parent material and assuming immobile Ti, show moderately intense weathering. Pedotransfer functions indicate a fertile soil system, but sodicity may have limited some plant growth. Paleosol bulk geochemical proxies used to estimate paleoprecipitation (733–944 mm/yr), are higher than published estimates of 250–700 mm/yr using δD values of lipid biomarkers.

Description: Publication date: Available online 4 January 2016 Source: Quaternary Research Author(s): Michael Dietze, Elisabeth Dietze, Johanna Lomax, Markus Fuchs, Arno Kleber, Stephen G. Wells Reconstructing the evolution of arid landscapes is challenged by limited availability of appropriate environmental archives. A widespread surface feature — stone pavement — traps aeolian fines and forms a special accretionary archive. Seven stone pavement-covered sections on basalt flows in the eastern Mojave Desert are condensed into a composite section, comprising five sedimentological units supported by an OSL-based chronology. Three of the units are of accretionary nature and each is covered by a stone pavement. They were deposited > 50.9–36.6 ka, 〈 36.6–14.2 ka and 〈 14.2 ka, and they are intimately coupled with the history of nearby Lake Mojave, which advances the current understanding of regional aeolian activity. End-member modeling analysis of grain-size distributions yielded seven sediment transport regimes. The accretionary system operates in two modes: A) episodic formation of a stone pavement by lateral processes once a vesicular horizon has formed on a barren surface; and B) accretion of dust and eventual burial of the clast layer. These findings improve current concepts about stone pavement evolution and their environmental proxy function in arid landscapes. Stone pavement-covered accretionary deposits are a new key archive that allows quantifying the relative importance of dust accretion, slope processes, soil formation and vegetation cover.

Description: Publication date: Available online 7 January 2016 Source: Quaternary Research Author(s): Tong He, Lianwen Liu, Yang Chen, Xuefen Sheng, Junfeng Ji Plagioclase mineral sub-species in the Lingtai Section in central Chinese Loess Plateau are examined using Mineral Liberation Analyzer techniques, showing that loess and paleosol samples exhibit similar patterns in terms of plagioclase feldspar sub-species content. This suggests that both loess and paleosol units have preserved their primary Ca-bearing plagioclase compositions of loess source regions. Weighted average CaO (%) in Ca-bearing plagioclase lies within a narrow range and is equivalent to the average plagioclase composition for upper continental crust. This fact supports the hypothesis that Chinese loess deposits are the result of a thorough mixing of dust sources. The sum of Ca-bearing plagioclase content exhibits a general increasing trend superimposed by glacial–interglacial oscillations. In combination with observed plagioclase data in the deserts, the variations of Ca-bearing plagioclase minerals might be used as a proxy for dust source migration and climate changes in the loess source regions. Furthermore, linear relationship between lithogenic magnetic susceptibility (MS) component input and contents of Ca-bearing plagioclase in loess units revises a MS proxy for reconstructing paleo-monsoon precipitation history. The revised MS and plagioclase sub-species records help in understanding the mechanism of glaciation across northern Tibetan Plateau.

Description: 〈div data-abstract-type="normal"〉〈p〉Moraines preserved around Mount Xuebaoding (5588 m above sea level) on the eastern margin of the Tibetan Plateau, represent past glacial activity in this area. The chronology of these moraines was established using 〈span〉10〈/span〉Be exposure dating. The dating results revealed multiple glacial events prior to the late glacial (〈span〉〉〈/span〉14.1±2.2 ka), the late glacial (15.6±1.6 to 11.2±3.0 ka), the early-middle Holocene (9.1±0.9 to 6.7±0.7 ka), and the Neoglacial periods (2.5±0.5 to 1.5±0.1 ka). These glacial stages are consistent with the recalculated ages from surrounding areas throughout the Indian and East Asian monsoon-influenced region on the eastern Tibetan Plateau. Comparing with other paleoclimate indexes, we suggest that the late glacial event was mainly driven by low temperature, the early–middle Holocene event by high precipitation, and the late Holocene/Neoglacial event by low temperature.〈/p〉〈/div〉

Description: 〈div data-abstract-type="normal"〉〈p〉The Channeled Scabland–Palouse region of the Pacific Northwest (PNW) of the United States preserves geomorphic and pedosedimentary records that inform understanding of late Pleistocene–Holocene paleoclimate change in a region proximal to the last glacial period Cordilleran Ice Sheet. We present a clumped (Δ〈span〉47〈/span〉) and conventional (δ〈span〉18〈/span〉O, δ〈span〉13〈/span〉C) isotopic study of Palouse loess–paleosol carbonates in combination with carbonate radiocarbon (〈span〉14〈/span〉C) dating to provide new measures of regional late–last glacial (~31–20 cal ka BP) and Holocene soil conditions. Average clumped isotope temperatures (T(Δ〈span〉47〈/span〉)) for last glacial Palouse loess–paleosol carbonates (9±4°C) are significantly lower than those for Holocene-aged carbonates (T(Δ〈span〉47〈/span〉)=18±2°C) in study sections. Calculated soil water δ〈span〉18〈/span〉O〈span〉VSMOW〈/span〉 values (−16±2‰) for last glacial carbonates are also offset relative to those for Holocene-aged samples (−11±1‰), whereas calculated soil CO〈span〉2〈/span〉 δ〈span〉13〈/span〉C〈span〉VPDB〈/span〉 values are similar for the Holocene (−16.9±0.2‰) and late–last glacial (−16.7±1.1‰) periods. Together, these paleoclimate metrics indicate late–last glacial conditions of pedogenic carbonate formation in the C〈span〉3〈/span〉 grassland soils of the Palouse were measurably colder (9±5°C) than during the Holocene and potentially reflect a more arid last glacial paleoclimate across the Palouse, findings in agreement with previous proxy studies and climate model simulations for the region.〈/p〉〈/div〉

Description: 〈div data-abstract-type="normal"〉〈p〉A precisely 〈span〉230〈/span〉Th-dated stalagmite δ〈span〉13〈/span〉C profile from Hulu Cave, China, is presented to characterize the frequency and pattern of millennial-scale Asian monsoon (AM) variability from 160.6 to 132.5 ka. Evidence for an antiphased relationship of the δ〈span〉13〈/span〉C and δ〈span〉18〈/span〉O on the millennial scale suggests that the δ〈span〉13〈/span〉C is indicative of the local hydrological cycle associated with changes in AM strength. Owing to the δ〈span〉13〈/span〉C responding to AM changes more sensitively than the δ〈span〉18〈/span〉O, we could identify 15 strong AM events that correlate to cold intervals recorded in Antarctic ice cores within 〈span〉230〈/span〉Th dating uncertainty. This result supports a dynamic link of AM strength and southern hemispheric climates via the cross-equatorial airflows. Power spectrum analysis shows a predominant periodicity of 1.5–2.5 ka for the δ〈span〉13〈/span〉C profile, similar to the Dansgaard-Oeschger frequency during the last glacial period. Moreover, the AM events are characterized by rapid transitions at the onset, suggesting that the observed millennial-scale AM variability is likely forced by northern high-latitude climates via north–south shifts of the Intertropical Convergence Zone associated with the bipolar seesaw mechanism. As evidence for a common mechanism for ice age terminations, a strong AM event (~134 ka) surrounding Termination II is analogous to the Bølling-Allerød warming interval.〈/p〉〈/div〉

Description: 〈div data-abstract-type="normal"〉〈p〉The Dead Sea Transform (DST) accounts for ~105 km of left-lateral slip between the Arabian plate and the Sinai subplate since the Miocene. Paleoseismic studies along the Arava Valley segment of the DST suggest that late Quaternary deformation has been primarily concentrated along the axis of the transform valley. Here, we examine late Quaternary changes in drainage system characteristics and attribute them to recent tectonic deformation in this region. Field-based geomorphic mapping, topographic cross sections, and optically stimulated luminescence (OSL) dating of fluvial deposits were used to map and date recent changes in the fluvial characteristics of catchments along the western margin of the southern Arava. Our results reveal coeval migration of channels, consistent with tectonically induced surface tilting caused by north–south compressional deformation along the western margin of the transform valley. OSL dating indicates this tilting was initiated in the late Pleistocene and continued at least into the mid-Holocene. The late Quaternary tectonic deformation along the southern Arava segment of the DST is distributed across a wider zone than previously considered and extends out to the margins of the transform valley. We associate the inferred wider deformation zone to possible changes in the geometry of motion along the DST.〈/p〉〈/div〉

Description: 〈div data-abstract-type="normal"〉〈p〉Reconstruction of lake-level fluctuations from landform and outcrop evidence typically involves characterizing periods with relative high stands. We developed a new approach to provide water-level estimates in the absence of shoreline evidence for Owens Lake in eastern California by integrating landform, outcrop, and existing lake-core data with wind-wave and sediment entrainment modeling of lake-core sedimentology. We also refined the late Holocene lake-level history of Owens Lake by dating four previously undated shoreline features above the water level (1096.4 m) in AD 1872. The new ages coincide with wetter and cooler climate during the Neopluvial (~3.6 ka), Medieval Pluvial (~0.8 ka), and Little Ice Age (~0.35 ka). Dates from stumps below 1096 m also indicate two periods of low stands at ~0.89 and 0.67 ka during the Medieval Climatic Anomaly. The timing of modeled water levels associated with 22 mud and sand units in lake cores agree well with shoreline records of Owens Lake and nearby Mono Lake, as well as with proxy evidence for relatively wet and dry periods from tree-ring and glacial records within the watershed. Our integrated analysis provides a continuous 4000-yr lake-level record showing the timing, duration, and magnitude of hydroclimate variability along the south-central Sierra Nevada.〈/p〉〈/div〉