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77
Reconstruction of organismal and gene phylogenies from data on multigene families: Concerted evolution
, 1992
"... Abstract.—The reliability of phylogenies reconstructed from data on multigene families is investigated via simulation. The evolutionary scenario used is a characterbased model of a twogene family in four species in which clocklike divergence is postulated but neither convergence nor reversal is al ..."
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Cited by 25 (0 self)
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is allowed except as a result of recombination and gene conversion. Thus, any homoplasy emerging from parsimony reconstructions from the simulated data matrices can be attributed to concerted evolution. The probabilities of correctly reconstructing two standard trees are estimated by replicate runs
Evaluating Hypotheses on the Origin and Evolution of the New Zealand Alpine Cicadas (Maoricicada) Using MultipleComparison Tests of Tree Topology
"... The statistical testing of alternative phylogenetic trees is central to evaluating competing evolutionary hypotheses. Fleming proposed that the New Zealand cicada species Maoricicada iolanthe is the sister species to the major radiation of both lowaltitude and montane Maoricicada species. However, ..."
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Cited by 20 (5 self)
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, using 1,520 bp of mitochondrial DNA sequence data from the cytochrome oxidase subunit I, tRNA aspartic acid, and the ATPase subunit 6 and 8 genes, we inferred that both M. iolanthe and another lowaltitude species, Maoricicada campbelli, are nested within the montane Maoricicada radiation. Therefore, we
SCALING OF ACCURACY IN EXTREMELY LARGE PHYLOGENETIC TREES
"... The accuracy of phylogenetic inference was examined in simulated data sets up to nearly 10,000 taxa, the size of the largest set of homologous genes in existing molecular sequence databases. Even with a simple search algorithm (maximum parsimony without branch swapping), the number of characters nee ..."
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needed to estimate 80 % of a tree correctly can scale remarkably well at optimal substitution rates (on the order of log N, where N is the number of taxa). In other words, the number of taxa in an analysis can be doubled and only an arithmetic increase in the number of characters is required to maintain
Research Articles Consistency Properties of Species Tree Inference by Minimizing Deep Coalescences
"... Methods for inferring species trees from sets of gene trees need to account for the possibility of discordance among the gene trees. Assuming that discordance is caused by incomplete lineage sorting, species tree estimates can be obtained by finding those species trees that minimize the number of ‘‘ ..."
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that the MDC criterion is not always guaranteed to infer the correct species tree estimate. In this article, we investigate the consistency of the MDC criterion. Using the multipscies coalescent model, we show that there are indeed anomaly zones for the MDC criterion for asymmetric fourtaxon species tree
USING MERIS FOR MOUNTAIN VEGETATION MAPPING AND MONITORING IN
"... The objective of this study is to apply ENVISAT MERIS data in mapping mountain vegetation in Sweden. The Swedish mountain vegetation is characterized by mosaics of different land cover types; a single MERIS pixel (300 meter IFOV) can consist of several of these different land cover types. “Hard” cla ..."
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and are nonparametric, and can be wellsuited for subpixel vegetation fraction estimation. Here, the soft classification methods of regression trees and linear regression are applied using spectral data from a MERIS Level 1B FR image. The image is corrected for atmosphere and illumination, and MTCI and PCA
Bayesian Nonparametric Modeling for Causal Inference
, 2007
"... Researchers have long struggled to identify causal effects in nonexperimental settings. Many recentlyproposed strategies assume ignorability of the treatment assignment mechanism and require fitting two models – one for the assignment mechanism and one for the response surface. We propose a strate ..."
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Cited by 18 (2 self)
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strategy that instead focuses on very flexibly modeling just the response surface using a Bayesian nonparametric modeling procedure, Bayesian Additive Regression Trees (BART). BART has several advantages: it is far simpler to use than many recent competitors, requires less guesswork in model fitting
1.1 Dominantly Inherited Gene Mutations
"... Estimation of rates of onset of rare, lateonset dominantly inherited genetic disorders is complicated by: (a) probable ascertainment bias resulting from the `recruitment ' of strongly aected families into studies; and (b) inability to identify the true `at risk ' population of mutation ca ..."
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carriers. To deal with the latter, Gui & Macdonald (2002a) proposed a nonparametric (NelsonAalen) estimate ̂(x) of a simple function (x) of the rate of onset at age x. (x) had a nite bound, which was an increasing function of the probability p that a child of an aected parent inherits the mutation
Measures of Clade Confidence Do Not Correlate with Accuracy of Phylogenetic Trees
"... Metrics of phylogenetic tree reliability, such as parametric bootstrap percentages or Bayesian posterior probabilities, represent internal measures of the topological reproducibility of a phylogenetic tree, while the recently introduced aLRT (approximate likelihood ratio test) assesses the likelihoo ..."
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Metrics of phylogenetic tree reliability, such as parametric bootstrap percentages or Bayesian posterior probabilities, represent internal measures of the topological reproducibility of a phylogenetic tree, while the recently introduced aLRT (approximate likelihood ratio test) assesses
Exploring the Relationship between Sequence Similarity and Accurate Phylogenetic Trees. Molecular Biology and Evolution
, 2006
"... We have characterized the relationship between accurate phylogenetic reconstruction and sequence similarity, testing whether high levels of sequence similarity can consistently produce accurate evolutionary trees. We generated protein families with known phylogenies using a modified version of the ..."
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trees, the likelihood of estimating an accurate tree is most dependent on whether radiation in the family was ancient or recent. Accuracy can be improved by combining genes from the same organism when creating species trees or by selecting protein families with the best bootstrap values in comprehensive
Dramatically elevated rate of mitochondrial substitution
 in lice (Insecta: Phthiraptera). Molecular Phylogenetics and Evolution
, 2003
"... Few estimates of relative substitution rates, and the underlying mutation rates, exist between mitochondrial and nuclear genes in insects. Previous estimates for insects indicate a 2–9 times faster substitution rate in mitochondrial genes relative to nuclear genes. Here we use novel methods for esti ..."
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Cited by 17 (2 self)
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in a phylogenetic tree. The branch length comparisons use maximum likelihood models to correct for multiple substitution. In addition, we estimate codonspecific rates under maximum likelihood for the different genes and compare these values. Estimates of the relative synonymous substitution rates
Results 11  20
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77