5,382 research outputs found
Distinguishing regional from within-codon rate heterogeneity in DNA sequence alignments
We present an improved phylogenetic factorial hidden Markov model (FHMM) for detecting two types of mosaic structures in DNA sequence alignments, related to (1) recombination and (2) rate heterogeneity. The focus of the present work is on improving the modelling of the latter aspect. Earlier papers have modelled different degrees of rate heterogeneity with separate hidden states of the FHMM. This approach fails to appreciate the intrinsic difference between two types of rate heterogeneity: long-range regional effects, which are potentially related to differences in the selective pressure, and the short-term periodic patterns within the codons, which merely capture the signature of the genetic code. We propose an improved model that explicitly distinguishes between these two effects, and we assess its performance on a set of simulated DNA sequence alignments
The Fundamental Plane of Early-Type Galaxies as a Confounding Correlation
Early-type galaxies are characterized by many scaling relations. One of them,
the so-called fundamental plane is a relatively tight correlation between three
variables, and has resisted a clear physical understanding despite many years
of intensive research. Here, we show that the correlation between the three
variables of the fundamental plane can be the artifact of the effect of another
parameter influencing all, so that the fundamental plane may be understood as a
confounding correlation. Indeed, the complexity of the physics of galaxies and
of their evolution suggests that the main confounding parameter must be related
to the level of diversification reached by the galaxies. Consequently, many
scaling relations for galaxies are probably evolutionary correlations
Efficient FPT algorithms for (strict) compatibility of unrooted phylogenetic trees
In phylogenetics, a central problem is to infer the evolutionary
relationships between a set of species ; these relationships are often
depicted via a phylogenetic tree -- a tree having its leaves univocally labeled
by elements of and without degree-2 nodes -- called the "species tree". One
common approach for reconstructing a species tree consists in first
constructing several phylogenetic trees from primary data (e.g. DNA sequences
originating from some species in ), and then constructing a single
phylogenetic tree maximizing the "concordance" with the input trees. The
so-obtained tree is our estimation of the species tree and, when the input
trees are defined on overlapping -- but not identical -- sets of labels, is
called "supertree". In this paper, we focus on two problems that are central
when combining phylogenetic trees into a supertree: the compatibility and the
strict compatibility problems for unrooted phylogenetic trees. These problems
are strongly related, respectively, to the notions of "containing as a minor"
and "containing as a topological minor" in the graph community. Both problems
are known to be fixed-parameter tractable in the number of input trees , by
using their expressibility in Monadic Second Order Logic and a reduction to
graphs of bounded treewidth. Motivated by the fact that the dependency on
of these algorithms is prohibitively large, we give the first explicit dynamic
programming algorithms for solving these problems, both running in time
, where is the total size of the input.Comment: 18 pages, 1 figur
Nocardia kroppenstedtii sp. nov., a novel actinomycete isolated from a lung transplant patient with a pulmonary infection
An actinomycete, strain N1286T, isolated from a lung transplant patient with a pulmonary infection, was provisionally assigned to the genus Nocardia. The strain had chemotaxonomic and morphological properties typical of members of the genus Nocardia and formed a distinct phyletic line in the Nocardia 16S rRNA gene tree. It was most closely related to Nocardia farcinica DSM 43665T (99.8% gene similarity) but was distinguished from the latter by a low level of DNA:DNA relatedness. These strains were also distinguished by a broad range of phenotypic properties. On the basis of these data, it is proposed that isolate N1286T (=DSM 45810T = NCTC 13617T) should be classified as the type strain of a new Nocardia species for which the name Nocardia kroppenstedtii is proposed
Neighborhoods of trees in circular orderings
In phylogenetics, a common strategy used to construct an evolutionary tree for a set of species X is to search in the space of all such trees for one that optimizes some given score function (such as the minimum evolution, parsimony or likelihood score). As this can be computationally intensive, it was recently proposed to restrict such searches to the set of all those trees that are compatible with some circular ordering of the set X. To inform the design of efficient algorithms to perform such searches, it is therefore of interest to find bounds for the number of trees compatible with a fixed ordering in the neighborhood of a tree that is determined by certain tree operations commonly used to search for trees: the nearest neighbor interchange (nni), the subtree prune and regraft (spr) and the tree bisection and reconnection (tbr) operations. We show that the size of such a neighborhood of a binary tree associated with the nni operation is independent of the treeâs topology, but that this is not the case for the spr and tbr operations. We also give tight upper and lower bounds for the size of the neighborhood of a binary tree for the spr and tbr operations and characterize those trees for which these bounds are attained
Circular Networks from Distorted Metrics
Trees have long been used as a graphical representation of species
relationships. However complex evolutionary events, such as genetic
reassortments or hybrid speciations which occur commonly in viruses, bacteria
and plants, do not fit into this elementary framework. Alternatively, various
network representations have been developed. Circular networks are a natural
generalization of leaf-labeled trees interpreted as split systems, that is,
collections of bipartitions over leaf labels corresponding to current species.
Although such networks do not explicitly model specific evolutionary events of
interest, their straightforward visualization and fast reconstruction have made
them a popular exploratory tool to detect network-like evolution in genetic
datasets.
Standard reconstruction methods for circular networks, such as Neighbor-Net,
rely on an associated metric on the species set. Such a metric is first
estimated from DNA sequences, which leads to a key difficulty: distantly
related sequences produce statistically unreliable estimates. This is
problematic for Neighbor-Net as it is based on the popular tree reconstruction
method Neighbor-Joining, whose sensitivity to distance estimation errors is
well established theoretically. In the tree case, more robust reconstruction
methods have been developed using the notion of a distorted metric, which
captures the dependence of the error in the distance through a radius of
accuracy. Here we design the first circular network reconstruction method based
on distorted metrics. Our method is computationally efficient. Moreover, the
analysis of its radius of accuracy highlights the important role played by the
maximum incompatibility, a measure of the extent to which the network differs
from a tree.Comment: Submitte
Recombination dramatically speeds up evolution of finite populations
We study the role of recombination, as practiced by genetically-competent
bacteria, in speeding up Darwinian evolution. This is done by adding a new
process to a previously-studied Markov model of evolution on a smooth fitness
landscape; this new process allows alleles to be exchanged with those in the
surrounding medium. Our results, both numerical and analytic, indicate that for
a wide range of intermediate population sizes, recombination dramatically
speeds up the evolutionary advance
Taxonomy and chemical characterization of new antibiotics produced by Saccharothrix SA198 isolated from a Saharan soil
Actinomycete strain SA198, isolated from a Saharan soil sample of Algeria, exhibited antimicrobial activity
against Gram-positive and Gram-negative bacteria, and phytopathogenic and toxinogenic fungi. The
morphological and chemotaxonomic characteristics of the strain were consistent with those of the genus
Saccharothrix. Analysis of the 16S rRNA gene sequence of strain SA198 showed a similarity level ranging
between 97.2 and 98.8% within Saccharothrix species, S. australiensis being the most closely related. Two
new active products were isolated by reverse HPLC using a C18 column. The ultravioletâvisible (UVâVIS),
infrared (IR), mass, and 1Hand 14C nuclear magnetic resonance (NMR) spectra showed that these products
were new bioactive compounds. The minimum inhibitory concentrations of these antibiotics showed a
strong activity against fungi and moderate activities against Gram-positive and Gram-negative bacteria
Towards a Phylogenetic Analysis of Galaxy Evolution : a Case Study with the Dwarf Galaxies of the Local Group
Context: The Hubble tuning fork diagram has always been the preferred scheme
for classification of galaxies. It is based on morphology only. At the
opposite, biologists have long taken into account the genealogical relatedness
of living entities for classification purposes. Aims: Assuming branching
evolution of galaxies as a 'descent with modification', we show here that the
concepts and tools of phylogenetic systematics widely used in biology can be
heuristically transposed to the case of galaxies. Methods: This approach that
we call "astrocladistics" is applied to Dwarf Galaxies of the Local Group and
provides the first evolutionary tree for real galaxies. Results: The trees that
we present here are sufficiently solid to support the existence of a
hierarchical organization in the diversity of dwarf galaxies of the Local
Group. This also shows that these galaxies all derive from a common ancestral
kind of objects. We find that some kinds of dIrrs are progenitors of both dSphs
and other kinds of dIrrs.We also identify three evolutionary groups, each one
having its own characteristics and own evolution. Conclusions: The present work
opens a new way to analyze galaxy evolution and a path towards a new
systematics of galaxies. Work on other galaxies in the Universe is in progress.Comment: 13 pages 5 figures with 3 online onl
EVOLUTION FOR BIOINFORMATICIANS AND BIOINFORMATICS FOR EVOLUTIONISTS 1
Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/72826/1/j.0014-3820.2005.tb00937.x.pd
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