Reconstructing phylogenies from nucleotide pattern probabilities : a survey and some new result

The variations between homologous nucleotide sequences representative of various species are, in part, a consequence of the evolutionary history of these species. Determining the evolutionary tree from patterns in the sequences depends on inverting the stochastic processes governing the substitutions from their ancestral sequence. We present a nl.J.mber of recent (and some new) results which allow for a tree to be reconstructed from the expected frequencies of patterns in its leaf colorations generated under various Markov models. We summarise recent work using Hadamard conjugation, which provides an analytic relation between the parameters of Kimura's 3ST model on a phylogenetic tree and the sequence patterns produced. We give two applications of the theory by describing new properties of the popular "maximum parsimony" method for tree reconstruction

PhyloNet: a software package for analyzing and reconstructing reticulate evolutionary relationships

<p>Abstract</p> <p>Background</p> <p>Phylogenies, i.e., the evolutionary histories of groups of taxa, play a major role in representing the interrelationships among biological entities. Many software tools for reconstructing and evaluating such phylogenies have been proposed, almost all of which assume the underlying evolutionary history to be a tree. While trees give a satisfactory first-order approximation for many families of organisms, other families exhibit evolutionary mechanisms that cannot be represented by trees. Processes such as horizontal gene transfer (HGT), hybrid speciation, and interspecific recombination, collectively referred to as <it>reticulate evolutionary events</it>, result in <it>networks</it>, rather than trees, of relationships. Various software tools have been recently developed to analyze reticulate evolutionary relationships, which include SplitsTree4, LatTrans, EEEP, HorizStory, and T-REX.</p> <p>Results</p> <p>In this paper, we report on the PhyloNet software package, which is a suite of tools for analyzing reticulate evolutionary relationships, or <it>evolutionary networks</it>, which are rooted, directed, acyclic graphs, leaf-labeled by a set of taxa. These tools can be classified into four categories: (1) evolutionary network representation: reading/writing evolutionary networks in a newly devised compact form; (2) evolutionary network characterization: analyzing evolutionary networks in terms of three basic building blocks – trees, clusters, and tripartitions; (3) evolutionary network comparison: comparing two evolutionary networks in terms of topological dissimilarities, as well as fitness to sequence evolution under a maximum parsimony criterion; and (4) evolutionary network reconstruction: reconstructing an evolutionary network from a species tree and a set of gene trees.</p> <p>Conclusion</p> <p>The software package, PhyloNet, offers an array of utilities to allow for efficient and accurate analysis of evolutionary networks. The software package will help significantly in analyzing large data sets, as well as in studying the performance of evolutionary network reconstruction methods. Further, the software package supports the proposed eNewick format for compact representation of evolutionary networks, a feature that allows for efficient interoperability of evolutionary network software tools. Currently, all utilities in PhyloNet are invoked on the command line.</p

Tracking Marsupial Evolution Using Archaic Genomic Retroposon Insertions

Genome-wide comparisons of shared retroposon insertion patterns resolve the phylogeny of marsupials, clearly distinguishing South American and Australian species and lending support to Didelphimorphia as the basal split

Universal Artifacts Affect the Branching of Phylogenetic Trees, Not Universal Scaling Laws

The superficial resemblance of phylogenetic trees to other branching structures allows searching for macroevolutionary patterns. However, such trees are just statistical inferences of particular historical events. Recent meta-analyses report finding regularities in the branching pattern of phylogenetic trees. But is this supported by evidence, or are such regularities just methodological artifacts? If so, is there any signal in a phylogeny?In order to evaluate the impact of polytomies and imbalance on tree shape, the distribution of all binary and polytomic trees of up to 7 taxa was assessed in tree-shape space. The relationship between the proportion of outgroups and the amount of imbalance introduced with them was assessed applying four different tree-building methods to 100 combinations from a set of 10 ingroup and 9 outgroup species, and performing covariance analyses. The relevance of this analysis was explored taking 61 published phylogenies, based on nucleic acid sequences and involving various taxa, taxonomic levels, and tree-building methods.All methods of phylogenetic inference are quite sensitive to the artifacts introduced by outgroups. However, published phylogenies appear to be subject to a rather effective, albeit rather intuitive control against such artifacts. The data and methods used to build phylogenetic trees are varied, so any meta-analysis is subject to pitfalls due to their uneven intrinsic merits, which translate into artifacts in tree shape. The binary branching pattern is an imposition of methods, and seldom reflects true relationships in intraspecific analyses, yielding artifactual polytomies in short trees. Above the species level, the departure of real trees from simplistic random models is caused at least by two natural factors--uneven speciation and extinction rates; and artifacts such as choice of taxa included in the analysis, and imbalance introduced by outgroups and basal paraphyletic taxa. This artifactual imbalance accounts for tree shape convergence of large trees.There is no evidence for any universal scaling in the tree of life. Instead, there is a need for improved methods of tree analysis that can be used to discriminate the noise due to outgroups from the phylogenetic signal within the taxon of interest, and to evaluate realistic models of evolution, correcting the retrospective perspective and explicitly recognizing extinction as a driving force. Artifacts are pervasive, and can only be overcome through understanding the structure and biological meaning of phylogenetic trees. Catalan Abstract in Translation S1

Recurrent selection for downy-mildew resistance in pearl millet

One population of pearl millet (Pennisetum glaucum (L.) R. Br.) highly susceptible to downy mildew (Sclerospora graminicola (Sacc.) Schroet.) was subjected to two cycles of recurrent selection for downy mildew resistance using a modified greenhouse screening method. The response to selection was evaluated under greenhouse and field conditions using 50 random S1 progenies and 50 random full-sib progenies from each cycle bulk. Significant progress over cycles of selection was observed in all evaluation trials. These results demonstrated that, in a susceptible population, recurrent selection effectively increased the level of resistance to downy mildew. The modified greenhouse method for assessing resistance to downy mildew effectively differentiated genotypes and had the advantages of greater rapidity and suitability for use throughout the year, independent of season. A rapid decline of genotypic variance was observed in advanced cycles of selection, indicating that a small number of genes controls downy-mildew resistance in this population. The comparison of genotypic and error variance components from S1 progenies and full-sib progenies suggested that full-sib progenies can be used successfully in recurrent selection for increased downy-mildew resistance

Two further links between MP and ML under the Poisson Model

Maximum parsimony and maximum likelihood are two contrasting approaches for reconstructing phylogenetic trees from sequence and character data. We establish analytic links between these methods (extending connections reported earlier) under the simple Poisson model of substitutions in two settings. First, we show that if the underlying state space is suffiently large then the maximum likelihood estimate phylogenetic tree is always a maximum parsimony tree for the data. Second, we show that a suffiently dense sampling of sequences ensures that the most parsimonious likelihood tree is always a maximum parsimony tree