Differential Evolution Approach to Detect Recent Admixture

The genetic structure of human populations is extraordinarily complex and of fundamental importance to studies of anthropology, evolution, and medicine. As increasingly many individuals are of mixed origin, there is an unmet need for tools that can infer multiple origins. Misclassification of such individuals can lead to incorrect and costly misinterpretations of genomic data, primarily in disease studies and drug trials. We present an advanced tool to infer ancestry that can identify the biogeographic origins of highly mixed individuals. reAdmix is an online tool available at http://chcb.saban-chla.usc.edu/reAdmix/.Comment: presented at ISMB 2014, VariSI

Genetic Stratigraphy of Key Demographic Events in Arabia

The issue of admixture in human populations is normally addressed by genome-wide (GW) studies, and several approaches have been developed to date admixture events [1,2,3,4,5]. Admixed populations bear chromosomes with segments of DNA from all contributing source groups, the size of which decreases over successive generations until recombination renders them undetectably short. Several algorithms attempt to date admixture events by inferring the size of the nuclear ancestry segments, and these can work well when dating recent episodes in human history, such as the sub-Saharan African input into the New World [6], but they fail to detect several known episodes that took place at earlier times, such as the African input into Iberia [1] and genetic exchanges across the Red Sea [7]. Simulations with the suite of methods available at the ADMIXTOOLS package indicated that these methods could detect admixture events as early as 500 generation ago, but real data did not allow the tracing of such old events [8]. A recent improved algorithm, called GLOBETROTTER, has been used to tackle the detection of the co-occurrence of several mixture events by decomposing each chromosome into a series of haplotypic chunks and then analysing each chunk independently [3], but the problem of detecting ancient events remains. Its application to the systematic screening of worldwide admixture events was able to reveal around 100 events, but all occurring over only the past 4,000 years [3

Evidence-based gene models for structural and functional annotations of the oil palm genome

The advent of rapid and inexpensive DNA sequencing has led to an explosion of data waiting to be transformed into knowledge about genome organization and function. Gene prediction is customarily the starting point for genome analysis. This paper presents a bioinformatics study of the oil palm genome, including comparative genomics analysis, database and tools development, and mining of biological data for genes of interest. We have annotated 26,059 oil palm genes integrated from two independent gene-prediction pipelines, Fgenesh++ and Seqping. This integrated annotation constitutes a significant improvement in comparison to the preliminary annotation published in 2013. We conducted a comprehensive analysis of intronless, resistance and fatty acid biosynthesis genes, and demonstrated that the high quality of the current genome annotation. 3,658 intronless genes were identified in the oil palm genome, an important resource for evolutionary study. Further analysis of the oil palm genes revealed 210 candidate resistance genes involved in pathogen defense. Fatty acids have diverse applications ranging from food to industrial feedstocks, and we identified 42 key genes involved in fatty acid biosynthesis in oil palm. These results provide an important resource for studies of plant genomes and a theoretical foundation for marker-assisted breeding of oil palm and related crops

Separation of river network–scale nitrogen removal among the main channel and two transient storage compartments

Author Posting. © American Geophysical Union, 2011. This article is posted here by permission of American Geophysical Union for personal use, not for redistribution. The definitive version was published in Water Resources Research 47 (2011): W00J10, doi:10.1029/2010WR009896.Transient storage (TS) zones are important areas of dissolved inorganic nitrogen (DIN) processing in rivers. We assessed sensitivities regarding the relative impact that the main channel (MC), surface TS (STS), and hyporheic TS (HTS) have on network denitrification using a model applied to the Ipswich River in Massachusetts, United States. STS and HTS connectivity and size were parameterized using the results of in situ solute tracer studies in first- through fifth-order reaches. DIN removal was simulated in all compartments for every river grid cell using reactivity derived from Lotic Intersite Nitrogen Experiment (LINX2) studies, hydraulic characteristics, and simulated discharge. Model results suggest that although MC-to-STS connectivity is greater than MC-to-HTS connectivity at the reach scale, at basin scales, there is a high probability of water entering the HTS at some point along its flow path through the river network. Assuming our best empirical estimates of hydraulic parameters and reactivity, the MC, HTS, and STS removed approximately 38%, 21%, and 14% of total DIN inputs during a typical base flow period, respectively. There is considerable uncertainty in many of the parameters, particularly the estimates of reaction rates in the different compartments. Using sensitivity analyses, we found that the size of TS is more important for DIN removal processes than its connectivity with the MC when reactivity is low to moderate, whereas TS connectivity is more important when reaction rates are rapid. Our work suggests a network perspective is needed to understand how connectivity, residence times, and reactivity interact to influence DIN processing in hierarchical river systems.This work was supported by the National Science Foundation through DEB- 0614282, BCS-0709685 and the Plum Island Long Term Ecological Research site (NSF OCE-0423565)

Recent advances quantifying the large wood dynamics in river basins: New methods and remaining challenges

Citation: Ruiz-Villanueva, V., Piégay, H., Gurnell, A. A., Marston, R. A., & Stoffel, M. (2016). Recent advances quantifying the large wood dynamics in river basins: New methods and remaining challenges. Reviews of Geophysics. doi:10.1002/2015RG000514Large wood is an important physical component of woodland rivers and significantly influences river morphology. It is also a key component of stream ecosystems. However, large wood is also a source of risk for human activities as it may damage infrastructure, block river channels, and induce flooding. Therefore, the analysis and quantification of large wood and its mobility are crucial for understanding and managing wood in rivers. As the amount of large-wood-related studies by researchers, river managers, and stakeholders increases, documentation of commonly used and newly available techniques and their effectiveness has also become increasingly relevant as well. Important data and knowledge have been obtained from the application of very different approaches and have generated a significant body of valuable information representative of different environments. This review brings a comprehensive qualitative and quantitative summary of recent advances regarding the different processes involved in large wood dynamics in fluvial systems including wood budgeting and wood mechanics. First, some key definitions and concepts are introduced. Second, advances in quantifying large wood dynamics are reviewed; in particular, how measurements and modeling can be combined to integrate our understanding of how large wood moves through and is retained within river systems. Throughout, we present a quantitative and integrated meta-analysis compiled from different studies and geographical regions. Finally, we conclude by highlighting areas of particular research importance and their likely future trajectories, and we consider a particularly underresearched area so as to stress the future challenges for large wood research. ©2016. American Geophysical Union

Nucleotide patterns aiding in prediction of eukaryotic promoters.

Computational analysis of promoters is hindered by the complexity of their architecture. In less studied genomes with complex organization, false positive promoter predictions are common. Accurate identification of transcription start sites and core promoter regions remains an unsolved problem. In this paper, we present a comprehensive analysis of genomic features associated with promoters and show that probabilistic integrative algorithms-driven models allow accurate classification of DNA sequence into "promoters" and "non-promoters" even in absence of the full-length cDNA sequences. These models may be built upon the maps of the distributions of sequence polymorphisms, RNA sequencing reads on genomic DNA, methylated nucleotides, transcription factor binding sites, as well as relative frequencies of nucleotides and their combinations. Positional clustering of binding sites shows that the cells of Oryza sativa utilize three distinct classes of transcription factors: those that bind preferentially to the [-500,0] region (188 "promoter-specific" transcription factors), those that bind preferentially to the [0,500] region (282 "5' UTR-specific" TFs), and 207 of the "promiscuous" transcription factors with little or no location preference with respect to TSS. For the most informative motifs, their positional preferences are conserved between dicots and monocots

Strong Fluctuations Of Energetic Electrons At Low Altitudes

Strong fluctuations (SF) of energetic electrons within the local loss cone (LC) from high resolution data on Active, a low altitude, high inclination satellite, are reviewed. The pitch angle diffusion rate of electrons at L > 4 is rapidly changing by one order up to the isotropic pitch angle distribution, corresponding to strong diffusion. The duration of the spikes to nearly strong diffusion limit is increasing with latitude. The statistical study shows the maximum occurrence of fluctuations within LC is in the noon sector and at latitudes 65-70°. Strong geomagnetic activity increases the probability of SF occurrence. One of the possible mechanisms consistent with the observations is the nonlinear precipitation oscillator (Davidson 1986; Davidson and Chiu, 1991). © 1997 COSPAR. Published by Elsevier Science Ltd.203499503Davidson, G.T., Pitch angle diffusion in Morningside Aurorae 1. The role of the loss cone in the formation of impulsive bursts of precipitation (1986) J. Geophys. Res., 91, p. 4413Davidson, G.T., Pitch-angle diffusion and the origin of temporal and spatial structures in Morningside Aurorae (1990) Space Sci. Rev., 53, p. 45Davidson, G.T., Chiu, Y.T., An unusual nonlinear system in the magnetosphere: A possible driver for auroral pulsations (1991) J. Geophys. Res., 96, p. 19353Imhof, W.L., Characteristics of short-duration electron precipitation bursts and their relationship with VLF wave activity (1989) J. Geophys. Res., 94, p. 10079Imhof, W.L., Relativistic electron microbursts (1992) J. Geophys. Res., 97, p. 13829Imhof, W.L., Relativistic electron flux comparison at low and high altitudes with fast time resolution and broad spatial coverage (1994) J. Geophys. Res., 99 (9), p. 17241Kudela, K., Inner zone electron peaks observed by the active satellite (1992) J. Gephys. Res., 97, p. 8681Rycroft, R.J., Interactions between whistler-mode waves and energetic electrons in the coupled system formed by the magnetosphere, ionosphere and atmosphere (1991) J. Atmos. Terr. Physics, 53, p. 849Sandahl, I., (1984) Pitch Angle Scattering and Particle Precipitation in a Pulsating Aurora - An Experimental Study, , Rep. 185, Kiruna SRI, SwedenTrakhtengerts, V.Yu., Mechanism of formation of pulsating auroras (1992) Proceedings of the ICS-1 Conference on Subbstorms, pp. 463-468. , Kiruna, Sweden, ESA SP-335Vampola, A.L., Gorney, D.J., Electron energy deposition in the middle atmosphere (1983) J. Geophys. Res., 88, p. 6267Vampola, A.L., (1994) RADMODLS, Ver. 4.20, , Augus