The Influence of Gene Flow on Species Tree Estimation: A Simulation Study

Gene flow among populations or species and incomplete lineage sorting (ILS) are two evolutionary processes responsible for generating gene tree discordance and therefore hindering species tree estimation. Numerous studies have evaluated the impacts of ILS on species tree inference, yet the ramifications of gene flow on species trees remain less studied. Here, we simulate and analyse multilocus sequence data generated with ILS and gene flow to quantify their impacts on species tree inference. We characterize species tree estimation errors under various models of gene flow, such as the isolation-migration model, the n-island model, and gene flow between non-sister species or involving ancestral species, and species boundaries crossed by a single gene copy (allelic introgression) or by a single migrant individual. These patterns of gene flow are explored on species trees of different sizes (4 vs. 10 species), at different time scales (shallow vs. deep), and with different migration rates. Species trees are estimated with the multispecies coalescent model using Bayesian methods (BEST and *BEAST) and with a summary statistic approach (MPEST) that facilitates phylogenomic-scale analysis. Even in cases where the topology of the species tree is estimated with high accuracy, we find that gene flow can result in overestimates of population sizes (species tree dilation) and underestimates of species divergence times (species tree compression). Signatures of migration events remain present in the distribution of coalescent times for gene trees, and with sufficient data it is possible to identify those loci that have crossed species boundaries. These results highlight the need for careful sampling design in phylogeographic and species delimitation studies as gene flow, introgression, or incorrect sample assignments can bias the estimation of the species tree topology and of parameter estimates such as population sizes and divergence times

Redistribution of multi-phase particulate organic carbon in a marine shelf and canyon system during an exceptional river flood: Effects of Typhoon Morakot on the Gaoping River-Canyon system

This is the final published version of the article. It was originally published in Marine Geology (Sparkes RB, Lin I-T, Hovius N, Galy A, Liu JT, Xu X, Yang R, Marine Geology 2015, 363, 191–201, doi:10.1016/j.margeo.2015.02.013) http://dx.doi.org/10.1016/j.margeo.2015.02.013Volumetrically, turbidity currents are the prime suppliers of sediment to the deep sea, and conveyors of organic carbon from the terrestrial biosphere and submarine shelf into marine depositional basins. They result from complex processes of erosion, transport and deposition that can be difficult to study in detail. Here we present data from the Gaoping submarine canyon system, off SW Taiwan, which was perturbed in 2009 by the addition of flood deposits following Typhoon Morakot and sampled by gravity coring less than 2 months after the event. We use the different origins of organic carbon, distinguished by their carbon and nitrogen concentrations and δ13C and δ15N isotopic composition, to compare and contrast standard and extreme sedimentological conditions. Using well-constrained end-members, the results were de-convolved into inputs of metamorphic and sedimentary fossil organic carbon eroded within the Gaoping River basin, terrestrial non-fossil carbon and marine organic matter. In the upper Gaoping Canyon, sedimentation is dominated by the highly-localised hyperpycnal input of river washload and submarine sediment slumps, each associated with extensive flooding following Typhoon Morakot, whilst the shelf experienced deposition and reworking of hemi-pelagic marine sediments. A terrestrial signal is also found in the core-top of a fine-grained shelf sample over 20 km from the Gaoping Canyon, in a region normally dominated by marine carbon deposition, showing that Morakot was an unusually large flood event. Conversely, sediment from just above the canyon thalweg contains 0.23 wt.% depth-averaged marine organic carbon (37% of the TOC content) implying that terrestrial OC-dominated turbidites are tightly constrained within the canyon. Hyperpycnal processes can lead to the rapid and efficient transport of both terrestrial and submarine sediments to more permanent burial locations.RS was supported by an Engineering and Physical Sciences Research Council (EP/P502365/1 and EP/P504120/1) studentship. JTL was supported by grant number NSC95-2745-M-110-001 for the Fate of Terrestrial–Nonterrestrial Sediments in High Yield Particle–Export River–Sea Systems Program, which provided the cores in this study. We thank Peter Talling for his insightful and constructive comments on the manuscript and a further, anonymous reviewer for generous endorsement

Random-key cuckoo search for the travelling salesman problem

Combinatorial optimization problems are typically NP-hard, and thus very challenging to solve. In this paper, we present the random key cuckoo search (RKCS) algorithm for solving the famous Travelling Salesman Problem (TSP). We used a simplified random-key encoding scheme to pass from a continuous space (real numbers) to a combinatorial space. We also consider the displacement of a solution in both spaces using L\'evy flights. The performance of the proposed RKCS is tested against a set of benchmarks of symmetric TSP from the well-known TSPLIB library. The results of the tests show that RKCS is superior to some other metaheuristic algorithms

SUCI02 inhibits the erbB-2 tyrosine kinase receptor signaling pathway and arrests the cell cycle in G 1 phase in breast cancer cells

Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/73321/1/j.1349-7006.2006.00143.x.pd

Spectrum and Thermodynamics of the one-dimensional supersymmetric t-J model with 1/r21/r^2 exchange and hopping

We derive the spectrum and the thermodynamics of the one-dimensional supersymmetric t-J model with long range hopping and spin exchange using a set of maximal-spin eigenstates. This spectrum confirms the recent conjecture that the asymptotic Bethe-ansatz spectrum is exact. By empirical determining the spinon degeneracies of each state, we are able to explicitly construct the free energy.Comment: 13 pages, Latex, (published in PRB46, 6639 (1992)

Case Report: The Clinical Toxicity of Dimethylamine Borane

Context: Dimethylamine borane (DMAB) is a reducing agent used in nonelectric plating of semiconductors. Exposures are usually through occupational contact. We report here four cases of people who suffered from work-related exposure to DMAB. Case presentation: Three patients exposed to DMAB decontaminated immediately by drinking a lot of water; they reported dizziness, nausea, diarrhea 6–8 hr later. The other patient did not decontaminate at once, and he suffered from more severe symptoms, including dizziness, nausea, limb numbness, slurred speech, irritable mood, and ataxia 13 hr later. Magnetic resonance imaging showed symmetric lesions with hyperintensity on T2WI and FLAIR in bilateral cerebellar dantate nuclei. This patient was readmitted to the hospital due to difficulty in walking and climbing 18 days after exposure. Lower leg weakness and drop foot were found bilaterally. A nerve conduction study revealed polyneuropathy with motor-predominant axonal degeneration. This patient receives regular outpatient followups and still walks with a clumsy gait and has difficulty with hand-grasping activity. Discussion: This case study demonstrates that DMAB is highly toxic to humans through any route of exposure, and dermal absorption is the major route of neurotoxicity. DMAB induces acute cortical and cerebellar injuries and delayed peripheral neuropathy. Relevance: Further investigation of the toxic mechanism of DMAB is warranted. Early decontamination with copious water is the best current treatment for exposure to DMAB

Spectral weight transfer in a disorder-broadened Landau level

In the absence of disorder, the degeneracy of a Landau level (LL) is $N=BA/\phi_0$, where $B$ is the magnetic field, $A$ is the area of the sample and $\phi_0=h/e$ is the magnetic flux quantum. With disorder, localized states appear at the top and bottom of the broadened LL, while states in the center of the LL (the critical region) remain delocalized. This well-known phenomenology is sufficient to explain most aspects of the Integer Quantum Hall Effect (IQHE) [1]. One unnoticed issue is where the new states appear as the magnetic field is increased. Here we demonstrate that they appear predominantly inside the critical region. This leads to a certain ``spectral ordering'' of the localized states that explains the stripes observed in measurements of the local inverse compressibility [2-3], of two-terminal conductance [4], and of Hall and longitudinal resistances [5] without invoking interactions as done in previous work [6-8].Comment: 5 pages 3 figure

Measuring Coverage in MNCH:A Validation Study Linking Population Survey Derived Coverage to Maternal, Newborn, and Child Health Care Records in Rural China

Accurate data on coverage of key maternal, newborn, and child health (MNCH) interventions are crucial for monitoring progress toward the Millennium Development Goals 4 and 5. Coverage estimates are primarily obtained from routine population surveys through self-reporting, the validity of which is not well understood. We aimed to examine the validity of the coverage of selected MNCH interventions in Gongcheng County, China.We conducted a validation study by comparing women's self-reported coverage of MNCH interventions relating to antenatal and postnatal care, mode of delivery, and child vaccinations in a community survey with their paper- and electronic-based health care records, treating the health care records as the reference standard. Of 936 women recruited, 914 (97.6%) completed the survey. Results show that self-reported coverage of these interventions had moderate to high sensitivity (0.57 [95% confidence interval (CI): 0.50-0.63] to 0.99 [95% CI: 0.98-1.00]) and low to high specificity (0 to 0.83 [95% CI: 0.80-0.86]). Despite varying overall validity, with the area under the receiver operating characteristic curve (AUC) ranging between 0.49 [95% CI: 0.39-0.57] and 0.90 [95% CI: 0.88-0.92], bias in the coverage estimates at the population level was small to moderate, with the test to actual positive (TAP) ratio ranging between 0.8 and 1.5 for 24 of the 28 indicators examined. Our ability to accurately estimate validity was affected by several caveats associated with the reference standard. Caution should be exercised when generalizing the results to other settings.The overall validity of self-reported coverage was moderate across selected MNCH indicators. However, at the population level, self-reported coverage appears to have small to moderate degree of bias. Accuracy of the coverage was particularly high for indicators with high recorded coverage or low recorded coverage but high specificity. The study provides insights into the accuracy of self-reports based on a population survey in low- and middle-income countries. Similar studies applying an improved reference standard are warranted in the future

Fine-grained parallel RNAalifold algorithm for RNA secondary structure prediction on FPGA

<p>Abstract</p> <p>Background</p> <p>In the field of RNA secondary structure prediction, the RNAalifold algorithm is one of the most popular methods using free energy minimization. However, general-purpose computers including parallel computers or multi-core computers exhibit parallel efficiency of no more than 50%. Field Programmable Gate-Array (FPGA) chips provide a new approach to accelerate RNAalifold by exploiting fine-grained custom design.</p> <p>Results</p> <p>RNAalifold shows complicated data dependences, in which the dependence distance is variable, and the dependence direction is also across two dimensions. We propose a systolic array structure including one master Processing Element (PE) and multiple slave PEs for fine grain hardware implementation on FPGA. We exploit data reuse schemes to reduce the need to load energy matrices from external memory. We also propose several methods to reduce energy table parameter size by 80%.</p> <p>Conclusion</p> <p>To our knowledge, our implementation with 16 PEs is the only FPGA accelerator implementing the complete RNAalifold algorithm. The experimental results show a factor of 12.2 speedup over the RNAalifold (<it>ViennaPackage </it>– 1.6.5) software for a group of aligned RNA sequences with 2981-residue running on a Personal Computer (PC) platform with Pentium 4 2.6 GHz CPU.</p