Search results for "Likelihood Functions"
showing 10 items of 101 documents
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…
Widespread secondary contact and new glacial refugia in the halophilic rotifer Brachionus plicatilis in the Iberian Peninsula.
2011
Small aquatic organisms harbour deep phylogeographic patterns and highly structured populations even at local scales. These patterns indicate restricted gene flow, despite these organisms' high dispersal abilities, and have been explained by a combination of (1) strong founder effects due to rapidly growing populations and very large population sizes, and (2) the development of diapausing egg banks and local adaptation, resulting in low effective gene flow, what is known as the Monopolization hypothesis. In this study, we build up on our understanding of the mitochondrial phylogeography of the halophilic rotifer Brachionus plicatilis in the Iberian Peninsula by both increasing the number of…
The age and evolution of sociality in Stegodyphus spiders: a molecular phylogenetic perspective
2006
Social, cooperative breeding behaviour is rare in spiders and generally characterized by inbreeding, skewed sex ratios and high rates of colony turnover, processes that when combined may reduce genetic variation and lower individual fitness quickly. On these grounds, social spider species have been suggested to be unstable in evolutionary time, and hence sociality a rare phenomenon in spiders. Based on a partial molecular phylogeny of the genus Stegodyphus , we address the hypothesis that social spiders in this genus are evolutionary transient. We estimate the age of the three social species, test whether they represent an ancestral or derived state and assess diversification relative to s…
MLML2R: an R package for maximum likelihood estimation of DNA methylation and hydroxymethylation proportions.
2019
Abstract Accurately measuring epigenetic marks such as 5-methylcytosine (5-mC) and 5-hydroxymethylcytosine (5-hmC) at the single-nucleotide level, requires combining data from DNA processing methods including traditional (BS), oxidative (oxBS) or Tet-Assisted (TAB) bisulfite conversion. We introduce the R package MLML2R, which provides maximum likelihood estimates (MLE) of 5-mC and 5-hmC proportions. While all other available R packages provide 5-mC and 5-hmC MLEs only for the oxBS+BS combination, MLML2R also provides MLE for TAB combinations. For combinations of any two of the methods, we derived the pool-adjacent-violators algorithm (PAVA) exact constrained MLE in analytical form. For the…
Modeling temperature effects on mortality: multiple segmented relationships with common break points.
2008
We present a model for estimation of temperature effects on mortality that is able to capture jointly the typical features of every temperature-death relationship, that is, nonlinearity and delayed effect of cold and heat over a few days. Using a segmented approximation along with a doubly penalized spline-based distributed lag parameterization, estimates and relevant standard errors of the cold- and heat-related risks and the heat tolerance are provided. The model is applied to data from Milano, Italy.
Tailoring sparse multivariable regression techniques for prognostic single-nucleotide polymorphism signatures.
2011
When seeking prognostic information for patients, modern technologies provide a huge amount of genomic measurements as a starting point. For single-nucleotide polymorphisms (SNPs), there may be more than one million covariates that need to be simultaneously considered with respect to a clinical endpoint. Although the underlying biological problem cannot be solved on the basis of clinical cohorts of only modest size, some important SNPs might still be identified. Sparse multivariable regression techniques have recently become available for automatically identifying prognostic molecular signatures that comprise relatively few covariates and provide reasonable prediction performance. For illus…
Multitype spatial point patterns with hierarchical interactions.
2001
Multitype spatial point patterns with hierarchical interactions are considered. Here hierarchical interaction means directionality: points on a higher level of hierarchy affect the locations of points on the lower levels, but not vice versa. Such relations are common, for example, in ecological communities. Interacting point patterns are often modeled by Gibbs processes with pairwise interactions. However, these models are inherently symmetric, and the hierarchy can be acknowledged only when interpreting the results. We suggest the following in allowing the inclusion of the hierarchical structure in the model. Instead of regarding the pattern as a realization of a stationary multivariate po…