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We present some experiences with the problem of multiple genome comparison, analogous to multiple sequence alignment in sequence comparison, under the inversion and transposition distance metrics, given a fixed phylogeny. We first describe a heuristic for the case in which phylogeny is a star on three vertices and then use this to approximate the multiple genome comparison problem via local search.

Trace elements in squid statoliths were analyzed by PIXE for the following fourteen species in five families of different habitat origin: Ommastrephidae, Ommastrephes bartrami, Dosidicus gigas, Sthenoteuthis oualaniensis; Gonatidae, Gonatopsis makko, G. borealis, Berryteuthis magister; Loliginidae, Loligo bleekeri, L. duvaucelii, L. chinensis, L. edulis and Sepioteuthis lessoniana; Sepiidae, Sepia aculeata and Sepiella inermis; Sepiolidae, Rossia pacifica, Manganese, iron, copper, zinc and strontium were detected from statoliths of all species examined. Among these trace elements, Sr is the highest in concentration. Variation of statoliths Sr concentration reflects taxonomic position and the habitat of specimens. In Ommastrephids and Gonatids, that have oceanic habitat, statoliths Sr concentration is relatively high whereas that of Loliginids and Sepiids, that have coastal habitat, is comparatively low. This fact supports our previous report on this subject. R. pacifica exceptionally shows high statoliths Sr concentration although this species inhabits in coastal water.

We present a brief review of a series of on-going work on bacterial phylogeny. We propose a new method to infer relatedness of prokaryotes from their complete genome data without using sequence alignment, leading to results comparable with the bacteriologist's systematics as reflected in the latest 2001 edition of Bergey's Manual of Systematic Bacteriology.¹ We only touch on the mathematical aspects of the method. The biological implications of our results will be published elsewhere.

Phylogenetic methods have recently been rediscovered in several interesting areas among which immunodynamics, epidemiology and many branches of evolutionary dynamics. In many interesting cases the reconstruction of a correct phylogeny is blurred by high mutation rates and/or horizontal transfer events. As a consequence, a divergence arises between the true evolutionary distances and the distances between pairs of taxa as inferred from the available data, making the phylogenetic reconstruction a challenging problem. Mathematically this divergence translates in the non-additivity of the actual distances between taxa and the quest for new algorithms able to efficiently cope with these effects is wide open. In distance-based reconstruction methods, two properties of additive distances were extensively exploited as antagonist criteria to drive phylogeny reconstruction: on the one hand a local property of quartets, i.e. sets of four taxa in a tree, the four-point condition; on the other hand, a recently proposed formula that allows to write the tree length as a function of the distances between taxa, the Pauplin's formula. A deeper comprehension of the effects of the non-additivity on the inspiring principles of the existing reconstruction algorithms is thus of paramount importance. In this paper we present a comparative analysis of the performances of the most important distance-based phylogenetic algorithms. We focus in particular on the dependence of their performances on two main sources of non-additivity: back-mutation processes and horizontal transfer processes. The comparison is carried out in the framework of a set of generative algorithms for phylogenies that incorporate non-additivity in a tunable way.

The crucial role played by the analysis of microbial diversity in biotechnology-based innovations has increased the interest in the microbial taxonomy research area. Phylogenetic sequence analyses have contributed significantly to the advances in this field, also in the view of the large amount of sequence data collected in recent years. Phylogenetic analyses could be realized on the basis of protein-encoding nucleotide sequences or encoded amino acid molecules: these two mechanisms present different peculiarities, still starting from two alternative representations of the same information. This complementarity could be exploited to achieve a multimodal phylogenetic scheme that is able to integrate gene and protein information in order to realize a single final tree. This aspect has been poorly addressed in the literature. In this paper, we propose to integrate the two phylogenetic analyses using basic schemes derived from the multimodality fusion theory (or multiclassifier systems theory), a well-founded and rigorous branch for which its powerfulness has already been demonstrated in other pattern recognition contexts. The proposed approach could be applied to distance matrix–based phylogenetic techniques (like neighbor joining), resulting in a smart and fast method. The proposed methodology has been tested in a real case involving sequences of some species of lactic acid bacteria. With this dataset, both nucleotide sequence– and amino acid sequence–based phylogenetic analyses present some drawbacks, which are overcome with the multimodal analysis.

Turkey coronavirus (TCoV) causes acute atrophic enteritis and uneven flock growth in turkey farms leading to economic loss. Since 1990's, turkey flocks have kept experiencing coronaviral enteritis sporadically in the United States, Canada, Europe, and Brazil. Poult enteritis and mortality syndrome (PEMS) caused by the co-infection of TCoV, astrovirus, and other viruses or bacteria resulted in significantly high mortality. Diagnosis of TCoV depends on reverse transcription polymerase chain reaction (RT-PCR), quantitative real-time PCR, immunohistochemistry (IHC), immunofluorescent antibody assay and virus isolation (VI). Genomic organization of TCoV is as follows: 5′ UTR-1a-1b-S-3a-3b-E-M-5a-5b-N-UTR 3′. Genomic analysis suggests the emergence of TCoV from infectious bronchitis virus (IBV) through the recombination of spike (S) gene. Both TCoV and IBV belong to species Avian coronavirus in genus Gammacoronavirus and have a single stranded RNA genome with a size about 27 kb. High similarity of S genes has been found between TCoV isolates in contrast to low similarity between IBV strains. TCoV infection induced strong humoral and cellular immune responses, characterized by high levels of antibody and interferon gamma. The fragment containing neutralizing epitopes in the S protein has been identified. Vaccines conferring protection against TCoV have not been developed and used in the fields but live attenuated, killed, DNA, and fowlpox virus vectored vaccines have been generated and their efficacies were evaluated. Molecular epidemiology of TCoV in recent outbreaks sheds more information on the evolution and transmission of TCoV, which will aid in developing effective vaccines or treatment to prevent, control, or eliminate TCoV infection.

Many models of genome rearrangement involve operations that are self-inverse, and hence generate a group acting on the space of genomes. This gives a correspondence between genome arrangements and the elements of a group, and consequently, between evolutionary paths and walks on the Cayley graph. Many common methods for phylogenetic reconstruction rely on calculating the minimal distance between two genomes; this omits much of the other information available from the Cayley graph. In this paper, we begin an exploration of some of this additional information, in particular describing the phylogeny as a Steiner tree within the Cayley graph, and exploring the “interval” between two genomes. While motivated by problems in systematic biology, many of these ideas are of independent group-theoretic interest.

Distinct mutational processes shape the genomes of the clones comprising a tumor. These processes result in distinct mutational patterns, summarized by a small number of mutational signatures. Current analyses of clone-specific exposures to mutational signatures do not fully incorporate a tumor’s evolutionary context, either inferring identical exposures for all tumor clones, or inferring exposures for each clone independently. Here, we introduce the Tree-constrained Exposure problem to infer a small number of exposure shifts along the edges of a given tumor phylogeny. Our algorithm, PhySigs, solves this problem and includes model selection to identify the number of exposure shifts that best explain the data. We validate our approach on simulated data and identify exposure shifts in lung cancer data, including at least one shift with a matching subclonal driver mutation in the mismatch repair pathway. Moreover, we show that our approach enables the prioritization of alternative phylogenies inferred from the same sequencing data. PhySigs is publicly available at https://github.com/elkebir-group/PhySigs.

Cancer results from an evolutionary process that yields a heterogeneous tumor with distinct subpopulations and varying sets of somatic mutations. This perspective discusses computational methods to infer models of evolutionary processes in cancer that aim to improve our understanding of tumorigenesis and ultimately enhance current clinical practice.

We begin with pervasive ultrametricity due to high dimensionality and/or spatial sparsity. How extent or degree of ultrametricity can be quantified leads us to the discussion of varied practical cases when ultrametricity can be partially or locally present in data. We show how the ultrametricity can be assessed in time series signals. An aspect of importance here is that to draw benefit from this perspective the data may need to be recoded. Such data recoding can also be powerful in proximity searching, as we will show, where the data is embedded globally and not locally in an ultrametric space.

Whole organism anatomical data are usually examined with specific hypotheses in mind: specifically that they are testing ideas about functional adaptations, convergences and parallels, or about primitivenesses, derivednesses and phylogeny. Presumably, of course, such data actually contain information about all of these factors. In addition, because they describe the end result of genetic mechanisms and developmental processes, they should be reflecting these in some degree. The separations of many such factors is very difficult as long as investigation is confined to individual anatomical observations (often called characters) because they will usually contain mixtures of information of various kinds. In data that are rendered quantitatively, however, it seems possible that statistical treatment might allow a degree of disentangling of these various factors. For studies of humans, the situation is especially complex because, though some investigations emphasises the adaptive uniqueness of humans from all other primates, related generally to their unique adaptations, other studies mirror the genetic closeness of humans to other primates, especially, of course, the African great apes.

This investigation looks at several quantitative studies of whole organism structure that, on the face of it, seem to present easily recognisable functional information. It tries to discover, both through the addition of individual studies into combined investigations, and by examining clusters of variables as well as clusters of animals, the degree to which the information content is really more complex. The various studies include morphometrics of the postcranium, cranium and teeth, but they also extend into the anatomy of the niche (hence nichemetrics) and into the form and proportions of the brain (hence ‘neurometrics’). The end result seems to be that a degree of disentanglement is indeed possible and that developmental phenomena obtained from studies of individual experimental animals are reflected in whole organism data from the adults of a wide diversity of related species. This result also speaks, therefore, about why humans hold paradoxical positions in different studies.

The aim of this study is focused in the evaluation of the genetic diversity of C. violaceum isolated from Brazilian ecosystems. Strains from Malaysia, Amazonas, Pernambuco, Ceará were analysed by the 16S rRNA gene (amplified 16S ribosomal DNA restriction analysis) to define their phylogenetic positions. All strains were grown overnight in LB medium at 30°C at 150 rpm, and cooled on ice, and the DNA was amplified in a thermocycler. The primers used were fD1 (AGAGTTTGATCCTGGCTC AG) and rD1 (AAGGAGGTGATCCAGCC) complementary to the ends of the 16S rDNA. The data obtained herein demonstrated that this method allowed grouping the C. violaceum isolates according to different Brazil States. However, the distances genetics between among all the isolated ones studied in this work demonstrated low variability but that the use of 16S rDNA gene tree revealed the good correlation between phylogenetic clustering and geographic origin.

Molecular methods have revolutionized insect systematic in Metarhizium genera. The importâãncia these entomopathogenic fungus in agriculture is enormous. . In Brazil, to control the sugar cane spittlebug, Mahanarva posticata (Homoptera: Cercopidae). Another very important factor for the selection of isolates of M. anisopliae for use in biological control of pests are particular virulence, reproductive aspects, the media of artificial culture and that the genetic variability of these entomopathogenic fungi have great potential for pest control and the lack of a link between isolate-host-site with the ability of fungal virulence. We studied 5 Metarhizium host (sugar cane spittlebug (IPA213, IPA215, IPA219 and IPA216) and the grasshopper (IPA217). The results obtained with the ITS1 and ITS4 markers showed that these isolates although they infect the same host, are genetically different, perhaps because of their origin as they do not know the origin of insects. However, the isolate IPA217 despite being isolated from grasshopper did not behave differently from the others showing that M. anisopliae complex is monophyletic. We conclude that the greater use of markers and morphological studies can yield good results that may corroborate the idea that this genus investigated phenotypic and molecular characteristics for its identification and typing a new species of Metarhizium.