Search results for "likelihood function"
showing 10 items of 114 documents
Molecular phylogeny of Old World swifts (Aves: Apodiformes, Apodidae, Apus and Tachymarptis) based on mitochondrial and nuclear markers.
2011
We provide a molecular phylogeny for Old World swifts of genera Apus and Tachymarptis (tribe Apodini) based on a taxon-complete sampling at the species level. Phylogenetic reconstructions were based on two mitochondrial (cytochrome b, 12S rRNA) and three nuclear markers (introns of fibrinogen and glyceraldehyde 3-phosphate dehydrogenase plus anonymous marker 12884) while the myoglobin intron 2 did not show any intergeneric variation or phylogenetic signal among the target taxa at all. In contrast to previous hypotheses, the two genera Apus and Tachymarptis were shown as reciprocally monophyletic in all reconstructions. Apus was consistently divided into three major clades: (1) East Asian cl…
A novel family of tRNA-derived SINEs in the colugo and two new retrotransposable markers separating dermopterans from primates.
2003
Abstract Short interspersed nuclear elements (SINEs) provide a near homoplasy free and copious source of molecular evolutionary markers with precisely defined character polarity. Used as molecular cladistic markers in presence/absence analyses, they represent a powerful complement to phylogenetic reconstructions that are based on sequence comparisons on the level of nucleotide substitutions. Recent sequence comparisons of large data sets incorporating a broad eutherian taxonomic sample have led to considerations of the different primate infraorders to constitute a paraphyletic group. Statistically significant support against the monophyly of primates has been obtained by clustering the flyi…
Searching for localized cosmic particle sources with an unbinned maximum likelihood approach
2006
Abstract An unbinned method to search for localized cosmic particle sources is presented. The expected source shape, the measured background shape, and the estimated angular resolution of individual tracks are used to construct a likelihood function. Estimates of the flux, the position and—in particular—the significance of a source can be readily obtained. A full confidence belt construction to deduce flux limits is presented. General statistical issues when searching for sources of unknown position are discussed.
Partition function based analysis of cosmic microwave background maps
1999
We present an alternative method to analyse cosmic microwave background (CMB) maps. We base our analysis on the study of the partition function. This function is used to examine the CMB maps, making use of the different information embedded at different scales and moments. Using the partition function in a likelihood analysis in two dimensions (Qrms-PS, n), we find the best-fitting model to the best data available at present (the COBE–DMR 4 years data set). By means of this analysis we find a maximum in the likelihood function for n=1.8-0.65+0.35 and Qrms-PS = 10-2.5+3μ K (95 per cent confidence level) in agreement with the results of other similar analyses [Smoot et al. (1 yr), Bennet et a…
Benchmarking parameter-free AMaLGaM on functions with and without noise.
2013
We describe a parameter-free estimation-of-distribution algorithm (EDA) called the adapted maximum-likelihood Gaussian model iterated density-estimation evolutionary algorithm (AMaLGaM-ID[Formula: see text]A, or AMaLGaM for short) for numerical optimization. AMaLGaM is benchmarked within the 2009 black box optimization benchmarking (BBOB) framework and compared to a variant with incremental model building (iAMaLGaM). We study the implications of factorizing the covariance matrix in the Gaussian distribution, to use only a few or no covariances. Further, AMaLGaM and iAMaLGaM are also evaluated on the noisy BBOB problems and we assess how well multiple evaluations per solution can average ou…
Phylogenetic relationship among genera of Polymorphidae (Acanthocephala), inferred from nuclear and mitochondrial gene sequences.
2013
Abstract Acanthocephalans of the family Polymorphidae Meyer, 1931 are obligate endoparasites with complex life cycles. These worms use vertebrates (marine mammals, fish-eating birds and waterfowl) as definitive hosts and invertebrates (amphipods, decapods and euphausiids) as intermediate hosts to complete their life cycle. Polymorphidae has a wordwide distribution, containing 12 genera, with approximately 127 species. The family is diagnosed by having a spinose trunk, bulbose proboscis, double-walled proboscis receptacle, and usually four to eight tubular cement glands. To conduct a phylogenetic analysis, in the current study sequences of the small (18S) and large-subunit (28S) ribosomal RN…
Statistical properties of the site-frequency spectrum associated with lambda-coalescents.
2013
Abstract Statistical properties of the site-frequency spectrum associated with Λ-coalescents are our objects of study. In particular, we derive recursions for the expected value, variance, and covariance of the spectrum, extending earlier results of Fu (1995) for the classical Kingman coalescent. Estimating coalescent parameters introduced by certain Λ-coalescents for data sets too large for full-likelihood methods is our focus. The recursions for the expected values we obtain can be used to find the parameter values that give the best fit to the observed frequency spectrum. The expected values are also used to approximate the probability a (derived) mutation arises on a branch subtending a…
Gypsy endogenous retrovirus maintains potential infectivity in several species of Drosophilids.
2008
Abstract Background Sequences homologous to the gypsy retroelement from Drosophila melanogaster are widely distributed among drosophilids. The structure of gypsy includes an open reading frame resembling the retroviral gene env, which is responsible for the infectious properties of retroviruses. Results In this study we report molecular and phylogeny analysis of the complete env gene from ten species of the obscura group of the genus Drosophila and one species from the genus Scaptomyza. Conclusion The results indicate that in most cases env sequences could produce a functional Env protein and therefore maintain the infectious capability of gypsy in these species.
Support for the monophyletic origin of Gnathifera from phylogenomics
2009
The monophyletic origin of Spiralia within the metazoan tree of life is supported by many large-scale phylogenomic data. While there is now substantial molecular evidence for Lophotrochozoa being a monophyletic taxon within Spiralia, the phylogenetic affiliations of many other spiralian phyla remain unclear. Here we focus on the question of a monophyletic taxon Gnathifera, which was originally characterized by jaw morphology as comprising the taxa Rotifera, Acanthocephala and Gnathostomulida. Based on a large-scale molecular sequence dataset of 11,146 amino acid residues, we reconstructed phylogenetic trees of spiralian phyla using maximum-likelihood and Bayesian approaches. We obtain the f…
Evolutionary implications of intron-exon distribution and the properties and sequences of the RPL10A gene in eukaryotes.
2013
The RPL10A gene encodes the RPL10 protein, required for joining 40S and 60S subunits into a functional 80S ribosome. This highly conserved gene, ubiquitous across all eukaryotic super-groups, is characterized by a variable number of spliceosomal introns, present in most organisms. These properties facilitate the recognition of orthologs among distant taxa and thus comparative studies of sequences as well as the distribution and properties of introns in taxonomically distant groups of eukaryotes. The present study examined the multiple ways in which RPL10A conservation vs. sequence changes in the gene over the course of evolution, including in exons, introns, and the encoded proteins, can be…