Frequentist and Bayesian measures of confidence via multiscale bootstrap for testing three regions

A new computation method of frequentist $p$-values and Bayesian posterior probabilities based on the bootstrap probability is discussed for the multivariate normal model with unknown expectation parameter vector. The null hypothesis is represented as an arbitrary-shaped region. We introduce new parametric models for the scaling-law of bootstrap probability so that the multiscale bootstrap method, which was designed for one-sided test, can also computes confidence measures of two-sided test, extending applicability to a wider class of hypotheses. Parameter estimation is improved by the two-step multiscale bootstrap and also by including higher-order terms. Model selection is important not only as a motivating application of our method, but also as an essential ingredient in the method. A compromise between frequentist and Bayesian is attempted by showing that the Bayesian posterior probability with an noninformative prior is interpreted as a frequentist $p$-value of ``zero-sided'' test

Mitochondrial and nuclear genes suggest that stony corals are monophyletic but most families of stony corals are not (Order Scleractinia, Class Anthozoa, Phylum Cnidaria)

Modern hard corals (Class Hexacorallia; Order Scleractinia) are widely studied because of their fundamental role in reef building and their superb fossil record extending back to the Triassic. Nevertheless, interpretations of their evolutionary relationships have been in flux for over a decade. Recent analyses undermine the legitimacy of traditional suborders, families and genera, and suggest that a non-skeletal sister clade (Order Corallimorpharia) might be imbedded within the stony corals. However, these studies either sampled a relatively limited array of taxa or assembled trees from heterogeneous data sets. Here we provide a more comprehensive analysis of Scleractinia (127 species, 75 genera, 17 families) and various outgroups, based on two mitochondrial genes (cytochrome oxidase I, cytochrome b), with analyses of nuclear genes (ßtubulin, ribosomal DNA) of a subset of taxa to test unexpected relationships. Eleven of 16 families were found to be polyphyletic. Strikingly, over one third of all families as conventionally defined contain representatives from the highly divergent "robust" and "complex" clades. However, the recent suggestion that corallimorpharians are true corals that have lost their skeletons was not upheld. Relationships were supported not only by mitochondrial and nuclear genes, but also often by morphological characters which had been ignored or never noted previously. The concordance of molecular characters and more carefully examined morphological characters suggests a future of greater taxonomic stability, as well as the potential to trace the evolutionary history of this ecologically important group using fossils

Phylogenetic relationships of African Caecilians (Amphibia: Gymnophiona): insights from mitochondrial rRNA gene sequences

Africa (excluding the Seychelles) has a diverse caecilian fauna, including the endemic family Scolecomorphidae and six endemic genera of the more cosmopolitan Caeciliidae. Previous molecular phylogenetic studies have not included any caecilians from the African mainland. Partial 12S and 16S mitochondrial gene sequences were obtained for two species of the endemic African Scolecomorphidae and five species and four genera of African Caeciliids, aligned against previously reported sequences for 16 caecilian species, and analysed using parsimony, maximum likelihood, Bayesian and distance methods. Results are in agreement with traditional taxonomy in providing support for the monophyly of the African Caeciliid genera Boulengerula and Schistometopum and for the Scolecomorphidae. They disagree in indicating that the Caeciliidae is paraphyletic with respect to the Scolecomorphidae. Although more data from morphology and/or molecules will be required to resolve details of the interrelationships of the African caecilian genera, the data provide strong support for at least two origins of caecilians in which the eye is reduced and covered with bone, and do not support the hypotheses that the caecilian assemblages of Africa, and of East and of West Africa are monophyletic

Significance of chemokine receptor expression in aggressive NK cell leukemia

ArticleLEUKEMIA. 19(7): 1169-1174 (2005)journal articl

Quantifying Phenotypic Variation in Isogenic Caenorhabditis elegans Expressing Phsp-16.2::gfp by Clustering 2D Expression Patterns

Isogenic populations of animals still show a surprisingly large amount of phenotypic variation between individuals. Using a GFP reporter that has been shown to predict longevity and resistance to stress in isogenic populations of the nematode Caenorhabditis elegans, we examined residual variation in expression of this GFP reporter. We found that when we separated the populations into brightest 3% and dimmest 3% we also saw variation in relative expression patterns that distinguished the bright and dim worms. Using a novel image processing method which is capable of directly analyzing worm images, we found that bright worms (after normalization to remove variation between bright and dim worms) had expression patterns that correlated with other bright worms but that dim worms fell into two distinct expression patterns. We have analysed a small set of worms with confocal microscopy to validate these findings, and found that the activity loci in these clusters are caused by extremely bright intestine cells. We also found that the vast majority of the fluorescent signal for all worms came from intestinal cells as well, which may indicate that the activity of intestinal cells is responsible for the observed patterns. Phenotypic variation in C. elegans is still not well understood but our proposed novel method to analyze complex expression patterns offers a way to enable a better understanding

A Multi-Armed Bandit to Smartly Select a Training Set from Big Medical Data

With the availability of big medical image data, the selection of an adequate training set is becoming more important to address the heterogeneity of different datasets. Simply including all the data does not only incur high processing costs but can even harm the prediction. We formulate the smart and efficient selection of a training dataset from big medical image data as a multi-armed bandit problem, solved by Thompson sampling. Our method assumes that image features are not available at the time of the selection of the samples, and therefore relies only on meta information associated with the images. Our strategy simultaneously exploits data sources with high chances of yielding useful samples and explores new data regions. For our evaluation, we focus on the application of estimating the age from a brain MRI. Our results on 7,250 subjects from 10 datasets show that our approach leads to higher accuracy while only requiring a fraction of the training data.Comment: MICCAI 2017 Proceeding

Historic genetic structuring and paraphyly within the Great-tailed Grackle

The Great-tailed Grackle (Quiscalus mexicanus) and Boat-tailed Grackle (Q. major) are sister species that have expanded their ranges during historical times. This expansion has created an area of sympatry between these species in Texas and Louisiana, and between distinctive Great-tailed Grackle subspecies in the southwestern United States and northern Mexico. We investigated the evolutionary histories of both species using mitochondrial DNA sequence data and modern phylogenetic methods. Our results reveal genetic structure within Great-tailed, but not Boat-tailed Grackles. Great-tailed Grackles are separated into two clades, but range expansion in the north has led to secondary contact between them. Boat-tailed Grackles are monophyletic and are embedded within the Great-tailed Grackle assemblage, rendering the latter paraphyletic. These results reveal a complex phylogeographic pattern caused by recent range expansion and secondary contact of once allopatric units

Coalescent-based genome analyses resolve the early branches of the euarchontoglires

Despite numerous large-scale phylogenomic studies, certain parts of the mammalian tree are extraordinarily difficult to resolve. We used the coding regions from 19 completely sequenced genomes to study the relationships within the super-clade Euarchontoglires (Primates, Rodentia, Lagomorpha, Dermoptera and Scandentia) because the placement of Scandentia within this clade is controversial. The difficulty in resolving this issue is due to the short time spans between the early divergences of Euarchontoglires, which may cause incongruent gene trees. The conflict in the data can be depicted by network analyses and the contentious relationships are best reconstructed by coalescent-based analyses. This method is expected to be superior to analyses of concatenated data in reconstructing a species tree from numerous gene trees. The total concatenated dataset used to study the relationships in this group comprises 5,875 protein-coding genes (9,799,170 nucleotides) from all orders except Dermoptera (flying lemurs). Reconstruction of the species tree from 1,006 gene trees using coalescent models placed Scandentia as sister group to the primates, which is in agreement with maximum likelihood analyses of concatenated nucleotide sequence data. Additionally, both analytical approaches favoured the Tarsier to be sister taxon to Anthropoidea, thus belonging to the Haplorrhine clade. When divergence times are short such as in radiations over periods of a few million years, even genome scale analyses struggle to resolve phylogenetic relationships. On these short branches processes such as incomplete lineage sorting and possibly hybridization occur and make it preferable to base phylogenomic analyses on coalescent methods

The Apicomplexan Whole-Genome Phylogeny: An Analysis of Incongruence among Gene Trees

The protistan phylum Apicomplexa contains many important pathogens and is the subject of intense genome sequencing efforts. Based upon the genome sequences from seven apicomplexan species and a ciliate outgroup, we identified 268 single-copy genes suitable for phylogenetic inference. Both concatenation and consensus approaches inferred the same species tree topology. This topology is consistent with most prior conceptions of apicomplexan evolution based upon ultrastructural and developmental characters, that is, the piroplasm genera Theileria and Babesia form the sister group to the Plasmodium species, the coccidian genera Eimeria and Toxoplasma are monophyletic and are the sister group to the Plasmodium species and piroplasm genera, and Cryptosporidium forms the sister group to the above mentioned with the ciliate Tetrahymena as the outgroup. The level of incongruence among gene trees appears to be high at first glance; only 19% of the genes support the species tree, and a total of 48 different gene-tree topologies are observed. Detailed investigations suggest that the low signal-to-noise ratio in many genes may be the main source of incongruence. The probability of being consistent with the species tree increases as a function of the minimum bootstrap support observed at tree nodes for a given gene tree. Moreover, gene sequences that generate high bootstrap support are robust to the changes in alignment parameters or phylogenetic method used. However, caution should be taken in that some genes can infer a “wrong” tree with strong support because of paralogy, model violations, or other causes. The importance of examining multiple, unlinked genes that possess a strong phylogenetic signal cannot be overstated