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"... A geographic survey, which requires much of working hours in the digital mapping process, is consisted with the complementary survey and the attribute survey of topography and topographic features, and depended on the field survey. In previous research, using the location-based image had been recomm ..."
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Cited by 60 (4 self)
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A geographic survey, which requires much of working hours in the digital mapping process, is consisted with the complementary survey and the attribute survey of topography and topographic features, and depended on the field survey. In previous research, using the location-based image had been recommended for diminishing the workload of field survey and post processing. For this research, we have developed the hardware and software for gathering and processing the location-based images with referencing results from the previous research. Those Geographic surveys were performed using developed system on 1/5,000 map sheets for Si and Gun area, respectively. The results have been evaluated as the mobile geographic survey system were able to replace the large part of field survey, and also the working hours were decreased by 37.5 % at Si area. However, the complementary survey was needed for the attributes of topography and topographic features that were occluded
Comparison of tree-child phylogenetic networks,
- IEEE/ACM Transactions on Computational Biology and Bioinformatics
, 2009
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Constructing level-2 phylogenetic networks from triplets
, 2009
"... Jansson and Sung showed that, given a dense set of input triplets T (representing hypotheses about the local evolutionary relationships of triplets of taxa), it is possible to determine in polynomial time whether there exists a level-1 network consistent with T, and if so, to construct such a netwo ..."
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Cited by 33 (9 self)
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Jansson and Sung showed that, given a dense set of input triplets T (representing hypotheses about the local evolutionary relationships of triplets of taxa), it is possible to determine in polynomial time whether there exists a level-1 network consistent with T, and if so, to construct such a network [24]. Here, we extend this work by showing that this problem is even polynomial time solvable for the construction of level-2 networks. This shows that, assuming density, it is tractable to construct plausible evolutionary histories from input triplets even when such histories are heavily nontree-like. This further strengthens the case for the use of triplet-based methods in the construction of phylogenetic networks. We also implemented the algorithm and applied it to yeast data.
Maximum likelihood of phylogenetic networks
- Bioinformatics
"... Motivation:Horizontal gene transfer (HGT) is believed tobeubiquitous amongbacteria,andplaysamajor role in their genomediversificationas well as their ability to develop resistance to antibiotics. In light of its evolutionary significanceand implications for humanhealth, developing accurate and effic ..."
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Cited by 33 (10 self)
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Motivation:Horizontal gene transfer (HGT) is believed tobeubiquitous amongbacteria,andplaysamajor role in their genomediversificationas well as their ability to develop resistance to antibiotics. In light of its evolutionary significanceand implications for humanhealth, developing accurate and efficient methods for detecting and reconstructing HGT is imperative. Results: In this article we provide a new HGT-oriented likelihood framework for many problems that involve phylogeny-based HGT detection and reconstruction. Beside the formulation of various like-lihood criteria, we show that most of these problems are NP-hard, and offer heuristics for efficient and accurate reconstruction of HGT under these criteria. We implemented our heuristics and used them to analyze biological as well as synthetic data. In both cases, our criteria and heuristics exhibited very good performance with respect to identifying the correct number of HGT events as well as inferring their correct location on the species tree. Availability: Implementation of the criteria as well as heuristics and hardnessproofs are available from theauthors upon request.Hardness proofs can also be downloaded at
Testing congruence in phylogenomic analysis. Systematic Biology
- The Journal of Biological Chemistry
, 1958
"... Abstract. — Phylogenomic analyses of large sets of genes or proteins have the potential to revolutionize our understanding of the tree of life. However, problems arise because estimated phylogenies from individual loci often differ because of different histories, systematic bias, or stochastic error ..."
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Cited by 30 (0 self)
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Abstract. — Phylogenomic analyses of large sets of genes or proteins have the potential to revolutionize our understanding of the tree of life. However, problems arise because estimated phylogenies from individual loci often differ because of different histories, systematic bias, or stochastic error. We have developed CONCATERPILLAR, a hierarchical clustering method based on likelihood-ratio testing that identifies congruent loci for phylogenomic analysis. CONCATERPILLAR also includes a test for shared relative evolutionary rates between genes indicating whether they should be analyzed separately or by concatenation. In simulation studies, the performance of this method is excellent when a multiple comparison correction is applied. We analyzed a phylogenomic data set of 60 translational protein sequences from the major supergroups of eukaryotes and identified three congruent subsets of proteins. Analysis of the largest set indicates improved congruence relative to the full data set and produced a phylogeny with stronger support for five eukaryote supergroups including the Opisthokonts, the Plantae, the stramenopiles + Apicomplexa (chromalveolates), the Amoebozoa, and the Excavata. In contrast, the phylogeny of the second largest set indicates a close relationship between stramenopiles and red algae, to the exclusion of alveolates, suggesting gene transfer from the red algal secondary symbiont to the ancestral stramenopile host nucleus during the origin of their chloroplast. Investigating phylogenomic data sets for conflicting signals has the potential to both improve phylogenetic accuracy and inform our understanding of genome evolution. [Concatenated analysis; endosymbiotic gene transfer; hierarchical clustering; lateral gene transfer; likelihood ratio testing; maximum likelihood; phylogenetic congruence;
Emergence and global spread of epidemic healthcare-associated Clostridium difficile. Nat Genet 45
- Coia JE, Douce G, Gerding D, Kim HJ, Koh TH, Kato H, Senoh M, Louie T, Michell S, Butt E, Peacock SJ, Brown NM, Riley T, Songer G, Wilcox M, Pirmohamed M, Kuijper E, Hawkey P, Wren BW, Dougan G, Parkhill J, Lawley TD
, 2013
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Prevalence and evolution of core photosystem II genes in marine cyanobacterial viruses and their hosts
, 2006
"... Cyanophages (cyanobacterial viruses) are important agents of horizontal gene transfer among marine cyanobacteria, the numerically dominant photosynthetic organisms in the oceans. Some cyanophage genomes carry and express host-like photosynthesis genes, presumably to augment the host photosynthetic m ..."
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Cited by 29 (8 self)
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Cyanophages (cyanobacterial viruses) are important agents of horizontal gene transfer among marine cyanobacteria, the numerically dominant photosynthetic organisms in the oceans. Some cyanophage genomes carry and express host-like photosynthesis genes, presumably to augment the host photosynthetic machinery during infection. To study the prevalence and evolutionary dynamics of this phenomenon, 33 cultured cyanophages of known family and host range and viral DNA from field samples were screened for the presence of two core photosystem reaction center genes, psbA and psbD. Combining this expanded dataset with published data for nine other cyanophages, we found that 88 % of the phage genomes contain psbA, and 50 % contain both psbA and psbD. The psbA gene was found in all myoviruses and Prochlorococcus podoviruses, but could not be amplified from Prochlorococcus siphoviruses or Synechococcus podoviruses. Nearly all of the phages that encoded both psbA and psbD had broad host ranges. We speculate that the presence or absence of psbA in a phage genome may be determined by the length of the latent period of infection. Whether it also carries psbD may reflect constraints on coupling of viral- and host-encoded PsbA–PsbD in the photosynthetic reaction center across divergent hosts. Phylogenetic clustering patterns of these genes from cultured phages suggest that whole genes have been transferred from host to phage in a discrete number of events over the course of evolution (four for psbA, and two for psbD), followed by horizontal and vertical transfer between cyanophages. Clustering patterns of psbA and psbD from Synechococcus cells were inconsistent with other molecular
A comparison of phylogenetic network methods using computer simulation
- Plos ONE
, 2008
"... Background: We present a series of simulation studies that explore the relative performance of several phylogenetic network approaches (statistical parsimony, split decomposition, union of maximum parsimony trees, neighbor-net, simulated history recombination upper bound, median-joining, reduced med ..."
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Cited by 24 (0 self)
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Background: We present a series of simulation studies that explore the relative performance of several phylogenetic network approaches (statistical parsimony, split decomposition, union of maximum parsimony trees, neighbor-net, simulated history recombination upper bound, median-joining, reduced median joining and minimum spanning network) compared to standard tree approaches, (neighbor-joining and maximum parsimony) in the presence and absence of recombination. Principal Findings: In the absence of recombination, all methods recovered the correct topology and branch lengths nearly all of the time when the substitution rate was low, except for minimum spanning networks, which did considerably worse. At a higher substitution rate, maximum parsimony and union of maximum parsimony trees were the most accurate. With recombination, the ability to infer the correct topology was halved for all methods and no method could accurately estimate branch lengths. Conclusions: Our results highlight the need for more accurate phylogenetic network methods and the importance of detecting and accounting for recombination in phylogenetic studies. Furthermore, we provide useful information for choosing a network algorithm and a framework in which to evaluate improvements to existing methods and novel
Visualizing differences in phylogenetic information content of alignments and distinction of three classes of long-branch effects.
- BMC Evol Biol
, 2007
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