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  • 1
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    The Performance of the Date-Randomization Test in Phylogenetic Analyses of Time-Structured Virus Data (2015)
    Oxford University Press
    Details
    Publication Date: 2015-06-22
    Description: Rates and timescales of viral evolution can be estimated using phylogenetic analyses of time-structured molecular sequences. This involves the use of molecular-clock methods, calibrated by the sampling times of the viral sequences. However, the spread of these sampling times is not always sufficient to allow the substitution rate to be estimated accurately. We conducted Bayesian phylogenetic analyses of simulated virus data to evaluate the performance of the date-randomization test, which is sometimes used to investigate whether time-structured data sets have temporal signal. An estimate of the substitution rate passes this test if its mean does not fall within the 95% credible intervals of rate estimates obtained using replicate data sets in which the sampling times have been randomized. We find that the test sometimes fails to detect rate estimates from data with no temporal signal. This error can be minimized by using a more conservative criterion, whereby the 95% credible interval of the estimate with correct sampling times should not overlap with those obtained with randomized sampling times. We also investigated the behavior of the test when the sampling times are not uniformly distributed throughout the tree, which sometimes occurs in empirical data sets. The test performs poorly in these circumstances, such that a modification to the randomization scheme is needed. Finally, we illustrate the behavior of the test in analyses of nucleotide sequences of cereal yellow dwarf virus . Our results validate the use of the date-randomization test and allow us to propose guidelines for interpretation of its results.
    Print ISSN: 0737-4038
    Electronic ISSN: 1537-1719
    Topics: Biology
    Published by Oxford University Press
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  • 2
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    INSECT PHYLOGENOMICS. Comment on "Phylogenomics resolves the timing and pattern of insect evolution" (2015)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2015-08-01
    Description: Misof et al. (Reports, 7 November 2014, p. 763) used a genome-scale data set to estimate the relationships among insect orders and the time scale of their evolution. Here, we reanalyze their data and show that their method has led to systematic underestimation of the evolutionary time scale. We find that key insect groups evolved up to 100 million years earlier than inferred in their study.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Tong, K Jun -- Duchene, Sebastian -- Ho, Simon Y W -- Lo, Nathan -- New York, N.Y. -- Science. 2015 Jul 31;349(6247):487. doi: 10.1126/science.aaa5460.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉School of Biological Sciences, University of Sydney, Sydney NSW 2006, Australia. ; School of Biological Sciences, University of Sydney, Sydney NSW 2006, Australia. nathan.lo@sydney.edu.au.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/26228137" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Insect Proteins/*classification ; Insects/*classification ; *Phylogeny
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
    Published by American Association for the Advancement of Science (AAAS)
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  • 3
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    Evolution, Expression, and Function of Nonneuronal Ligand-Gated Chloride Channels in Drosophila melanogaster (2016)
    Genetics Society of America (GSA)
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    Publication Date: 2016-07-08
    Description: Ligand-gated chloride channels have established roles in inhibitory neurotransmission in the nervous systems of vertebrates and invertebrates. Paradoxically, expression databases in Drosophila melanogaster have revealed that three uncharacterized ligand-gated chloride channel subunits, CG7589, CG6927, and CG11340, are highly expressed in nonneuronal tissues. Furthermore, subunit copy number varies between insects, with some orders containing one ortholog, whereas other lineages exhibit copy number increases. Here, we show that the Dipteran lineage has undergone two gene duplications followed by expression-based functional differentiation. We used promoter-GFP expression analysis, RNA-sequencing, and in situ hybridization to examine cell type and tissue-specific localization of the three D. melanogaster subunits. CG6927 is expressed in the nurse cells of the ovaries. CG7589 is expressed in multiple tissues including the salivary gland, ejaculatory duct, malpighian tubules, and early midgut. CG11340 is found in malpighian tubules and the copper cell region of the midgut. Overexpression of CG11340 increased sensitivity to dietary copper, and RNAi and ends-out knockout of CG11340 resulted in copper tolerance, providing evidence for a specific nonneuronal role for this subunit in D. melanogaster . Ligand-gated chloride channels are important insecticide targets and here we highlight copy number and functional divergence in insect lineages, raising the potential that order-specific receptors could be isolated within an effective class of insecticide targets.
    Electronic ISSN: 2160-1836
    Topics: Biology
    Published by Genetics Society of America (GSA)
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  • 4
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    Kinematic detection of a planet carving a gap in a protoplanetary disk (2019)
    Springer Nature
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    Publication Date: 2019
    Electronic ISSN: 2397-3366
    Topics: Physics
    Published by Springer Nature
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  • 5
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    Mammalian genome evolution is governed by multiple pacemakers (2015)
    Oxford University Press
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    Publication Date: 2015-06-27
    Description: Genomic evolution is shaped by a dynamic combination of mutation, selection and genetic drift. These processes lead to evolutionary rate variation across loci and among lineages. In turn, interactions between these two forms of rate variation can produce residual effects, whereby the pattern of among-lineage rate heterogeneity varies across loci. The nature of rate variation is encapsulated in the pacemaker models of genome evolution, which differ in the degree of importance assigned to residual effects: none (Universal Pacemaker), some (Multiple Pacemaker) or total (Degenerate Multiple Pacemaker). Here we use a phylogenetic method to partition the rate variation across loci, allowing comparison of these pacemaker models. Our analysis of 431 genes from 29 mammalian taxa reveals that rate variation across these genes can be explained by 13 pacemakers, consistent with the Multiple Pacemaker model. We find no evidence that these pacemakers correspond to gene function. Our results have important consequences for understanding the factors driving genomic evolution and for molecular-clock analyses. Availability and implementation: ClockstaR-G is freely available for download from github ( https://github.com/sebastianduchene/clockstarg ). Contact: simon.ho@sydney.edu.au Supplementary information: Supplementary data are available at Bioinformatics online.
    Print ISSN: 1367-4803
    Electronic ISSN: 1460-2059
    Topics: Biology , Computer Science , Medicine
    Published by Oxford University Press
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  • 6
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    Evaluating the Adequacy of Molecular Clock Models Using Posterior Predictive Simulations (2015)
    Oxford University Press
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    Publication Date: 2015-10-18
    Description: Molecular clock models are commonly used to estimate evolutionary rates and timescales from nucleotide sequences. The goal of these models is to account for rate variation among lineages, such that they are assumed to be adequate descriptions of the processes that generated the data. A common approach for selecting a clock model for a data set of interest is to examine a set of candidates and to select the model that provides the best statistical fit. However, this can lead to unreliable estimates if all the candidate models are actually inadequate. For this reason, a method of evaluating absolute model performance is critical. We describe a method that uses posterior predictive simulations to assess the adequacy of clock models. We test the power of this approach using simulated data and find that the method is sensitive to bias in the estimates of branch lengths, which tends to occur when using underparameterized clock models. We also compare the performance of the multinomial test statistic, originally developed to assess the adequacy of substitution models, but find that it has low power in identifying the adequacy of clock models. We illustrate the performance of our method using empirical data sets from coronaviruses, simian immunodeficiency virus, killer whales, and marine turtles. Our results indicate that methods of investigating model adequacy, including the one proposed here, should be routinely used in combination with traditional model selection in evolutionary studies. This will reveal whether a broader range of clock models to be considered in phylogenetic analysis.
    Print ISSN: 0737-4038
    Electronic ISSN: 1537-1719
    Topics: Biology
    Published by Oxford University Press
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  • 7
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    Probing nuclear structures in the vicinity of ^{78}Ni with β- and βn-decay spectroscopy of ^{84}Ga (2013)
    American Physical Society (APS)
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    Publication Date: 2013-10-15
    Description: Author(s): K. Kolos, D. Verney, F. Ibrahim, F. Le Blanc, S. Franchoo, K. Sieja, F. Nowacki, C. Bonnin, M. Cheikh Mhamed, P. V. Cuong, F. Didierjean, G. Duchêne, S. Essabaa, G. Germogli, L. H. Khiem, C. Lau, I. Matea, M. Niikura, B. Roussière, I. Stefan, D. Testov, and J.-C. Thomas The decay of 84 Ga has been reinvestigated at the PARRNe online mass separator of the electron-driven installation ALTO at IPN Orsay. The nominal primary electron beam of 10 μ A (50 MeV) on a 238 UC x target in combination with resonant laser ionization were used for the first time at ALTO. Improved lev... [Phys. Rev. C 88, 047301] Published Mon Oct 14, 2013
    Keywords: Nuclear Structure
    Print ISSN: 0556-2813
    Electronic ISSN: 1089-490X
    Topics: Physics
    Published by American Physical Society (APS)
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  • 8
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    ClockstaR: choosing the number of relaxed-clock models in molecular phylogenetic analysis (2014)
    Oxford University Press
    Details
    Publication Date: 2014-03-28
    Description: : Relaxed molecular clocks allow the phylogenetic estimation of evolutionary timescales even when substitution rates vary among branches. In analyses of large multigene datasets, it is often appropriate to use multiple relaxed-clock models to accommodate differing patterns of rate variation among genes. We present ClockstaR, a method for selecting the number of relaxed clocks for multigene datasets. Availability: ClockstaR is freely available for download at http://sydney.edu.au/science/biology/meep/software/ . Contact: sebastian.duchene@sydney.edu.au Supplementary information: Supplementary data are available at Bioinformatics online.
    Print ISSN: 1367-4803
    Electronic ISSN: 1460-2059
    Topics: Biology , Computer Science , Medicine
    Published by Oxford University Press
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  • 9
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    Estimating the number and assignment of clock models in analyses of multigene datasets (2016)
    Oxford University Press
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    Publication Date: 2016-04-29
    Description: Motivation: Molecular-clock methods can be used to estimate evolutionary rates and timescales from DNA sequence data. However, different genes can display different patterns of rate variation across lineages, calling for the employment of multiple clock models. Selecting the optimal clock-partitioning scheme for a multigene dataset can be computationally demanding, but clustering methods provide a feasible alternative. We investigated the performance of different clustering methods using data from chloroplast genomes and data generated by simulation. Results: Our results show that mixture models provide a useful alternative to traditional partitioning algorithms. We found only a small number of distinct patterns of among-lineage rate variation among chloroplast genes, which were consistent across taxonomic scales. This suggests that the evolution of chloroplast genes has been governed by a small number of genomic pacemakers. Our study also demonstrates that clustering methods provide an efficient means of identifying clock-partitioning schemes for genome-scale datasets. Availability and implementation: The code and data sets used in this study are available online at https://github.com/sebastianduchene/pacemaker_clustering_methods . Contact: sebastian.duchene@sydney.edu.au Supplementary information: Supplementary data are available at Bioinformatics online.
    Print ISSN: 1367-4803
    Electronic ISSN: 1460-2059
    Topics: Biology , Computer Science , Medicine
    Published by Oxford University Press
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  • 10
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    Structure of ^{80}Ge revealed by the β decay of isomeric states in ^{80}Ga: Triaxiality in the vicinity of ^{78}Ni (2013)
    American Physical Society (APS)
    Details
    Publication Date: 2013-05-10
    Description: Author(s): D. Verney, B. Tastet, K. Kolos, F. Le Blanc, F. Ibrahim, M. Cheikh Mhamed, E. Cottereau, P. V. Cuong, F. Didierjean, G. Duchêne, S. Essabaa, M. Ferraton, S. Franchoo, L. H. Khiem, C. Lau, J.-F. Le Du, I. Matea, B. Mouginot, M. Niikura, B. Roussière, I. Stefan, D. Testov, and J.-C. Thomas The decays of two long-lived low-lying isomeric states of 80 Ga were studied at the PARRNe mass separator of the ALTO ISOL facility. Over the 75 γ rays previously attributed to the 80 Ga decay, the decay time of 67 individual β -delayed γ activities were measured. This allowed the determination of the ... [Phys. Rev. C 87, 054307] Published Thu May 09, 2013
    Keywords: Nuclear Structure
    Print ISSN: 0556-2813
    Electronic ISSN: 1089-490X
    Topics: Physics
    Published by American Physical Society (APS)
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