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

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)

On-demand semiconductor single-photon source with near-unity indistinguishability

Single photon sources based on semiconductor quantum dots offer distinct advantages for quantum information, including a scalable solid-state platform, ultrabrightness, and interconnectivity with matter qubits. A key prerequisite for their use in optical quantum computing and solid-state networks is a high level of efficiency and indistinguishability. Pulsed resonance fluorescence (RF) has been anticipated as the optimum condition for the deterministic generation of high-quality photons with vanishing effects of dephasing. Here, we generate pulsed RF single photons on demand from a single, microcavity-embedded quantum dot under s-shell excitation with 3-ps laser pulses. The pi-pulse excited RF photons have less than 0.3% background contributions and a vanishing two-photon emission probability. Non-postselective Hong-Ou-Mandel interference between two successively emitted photons is observed with a visibility of 0.97(2), comparable to trapped atoms and ions. Two single photons are further used to implement a high-fidelity quantum controlled-NOT gate.Comment: 11 pages, 11 figure

Intra- and inter-individual genetic differences in gene expression

Genetic variation is known to influence the amount of mRNA produced by a gene. Given that the molecular machines control mRNA levels of multiple genes, we expect genetic variation in the components of these machines would influence multiple genes in a similar fashion. In this study we show that this assumption is correct by using correlation of mRNA levels measured independently in the brain, kidney or liver of multiple, genetically typed, mice strains to detect shared genetic influences. These correlating groups of genes (CGG) have collective properties that account for 40-90% of the variability of their constituent genes and in some cases, but not all, contain genes encoding functionally related proteins. Critically, we show that the genetic influences are essentially tissue specific and consequently the same genetic variations in the one animal may up-regulate a CGG in one tissue but down-regulate the same CGG in a second tissue. We further show similarly paradoxical behaviour of CGGs within the same tissues of different individuals. The implication of this study is that this class of genetic variation can result in complex inter- and intra-individual and tissue differences and that this will create substantial challenges to the investigation of phenotypic outcomes, particularly in humans where multiple tissues are not readily available.

&#xa

Combined In Silico, In Vivo, and In Vitro Studies Shed Insights into the Acute Inflammatory Response in Middle-Aged Mice

We combined in silico, in vivo, and in vitro studies to gain insights into age-dependent changes in acute inflammation in response to bacterial endotoxin (LPS). Time-course cytokine, chemokine, and NO2-/NO3- data from "middle-aged" (6-8 months old) C57BL/6 mice were used to re-parameterize a mechanistic mathematical model of acute inflammation originally calibrated for "young" (2-3 months old) mice. These studies suggested that macrophages from middle-aged mice are more susceptible to cell death, as well as producing higher levels of pro-inflammatory cytokines, vs. macrophages from young mice. In support of the in silico-derived hypotheses, resident peritoneal cells from endotoxemic middle-aged mice exhibited reduced viability and produced elevated levels of TNF-α, IL-6, IL-10, and KC/CXCL1 as compared to cells from young mice. Our studies demonstrate the utility of a combined in silico, in vivo, and in vitro approach to the study of acute inflammation in shock states, and suggest hypotheses with regard to the changes in the cytokine milieu that accompany aging. © 2013 Namas et al

Genetical genomics: spotlight on QTL hotspots

No abstract available

The extraordinary evolutionary history of the reticuloendotheliosis viruses

The reticuloendotheliosis viruses (REVs) comprise several closely related amphotropic retroviruses isolated from birds. These viruses exhibit several highly unusual characteristics that have not so far been adequately explained, including their extremely close relationship to mammalian retroviruses, and their presence as endogenous sequences within the genomes of certain large DNA viruses. We present evidence for an iatrogenic origin of REVs that accounts for these phenomena. Firstly, we identify endogenous retroviral fossils in mammalian genomes that share a unique recombinant structure with REVs—unequivocally demonstrating that REVs derive directly from mammalian retroviruses. Secondly, through sequencing of archived REV isolates, we confirm that contaminated Plasmodium lophurae stocks have been the source of multiple REV outbreaks in experimentally infected birds. Finally, we show that both phylogenetic and historical evidence support a scenario wherein REVs originated as mammalian retroviruses that were accidentally introduced into avian hosts in the late 1930s, during experimental studies of P. lophurae, and subsequently integrated into the fowlpox virus (FWPV) and gallid herpesvirus type 2 (GHV-2) genomes, generating recombinant DNA viruses that now circulate in wild birds and poultry. Our findings provide a novel perspective on the origin and evolution of REV, and indicate that horizontal gene transfer between virus families can expand the impact of iatrogenic transmission events