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At least 19 recordsLinked to original sources

PubMed2004

Using Avida to test the effects of natural selection on phylogenetic reconstruction methods.

Phylogenetic trees group organisms by their ancestral relationships. There are a number of distinct algorithms used to reconstruct these trees from molecular sequence data, but different methods sometimes give conflicting results. Since there are few precisely known phylogenies, simulations are typically used to test the quality of reconstruction algorithms. These simulations randomly evolve strings of symbols to produce a tree, and then the algorithms are run with the tree leaves as inputs. Here we use Avida to test two widely used reconstruction methods, which gives us the chance to observe the effect of natural selection on tree reconstruction. We find that if the organisms undergo natural selection between branch points, the methods will be successful even on very large time scales. However, these algorithms often falter when selection is absent.

Phylogeny↗

PubMed2006

The Rieske protein: a case study on the pitfalls of multiple sequence alignments and phylogenetic reconstruction.

Previously published phylogenetic trees reconstructed on "Rieske protein" sequences frequently are at odds with each other, with those of other subunits of the parent enzymes and with small-subunit rRNA trees. These differences are shown to be at least partially if not completely due to problems in the reconstruction procedures. A major source of erroneous Rieske protein trees lies in the presence of a large, poorly conserved domain prone to accommodate very long insertions in well-defined structural hot spots substantially hampering multiple alignments. The remaining smaller domain, in contrast, is too conserved to allow distant phylogenies to be deduced with sufficient confidence. Three-dimensional structures of representatives from this protein family are now available from phylogenetically distant species and from diverse enzymes. Multiple alignments can thus be refined on the basis of these structures. We show that structurally guided alignments of Rieske proteins from Rieske-cytochrome b complexes and arsenite oxidases strongly reduce conflicts between resulting trees and those obtained on their companion enzyme subunits. Further problems encountered during this work, mainly consisting in database errors such as wrong annotations and frameshifts, are described. The obtained results are discussed against the background of hypotheses stipulating pervasive lateral gene transfer in prokaryotes.

Algorithms↗

PubMed1983

On a functional-morphological approach to phylogenetic reconstruction: a critique.

A method of phylogenetic reconstruction as proposed by a number of scientists of the Senckenberg Research Institute is discussed. The method is based on functional-morphological studies, the evolutionary adaptation principle of Bock and Von Wahlert (1965) and so-called model reconstruction. It is argued in this paper that direction of the adaptation process cannot be determined because of lack of knowledge about particular selective forces and that theories of model reconstruction are not open to contradiction in the sense of Popperian falsification. Although it has been claimed that the method provides the only valid directional argument for morphoclines in cladistic studies, it remains unclear how to proceed when morphoclines show contradictory polarities. Moreover, it is doubtful whether polarities of morphoclines can be determined independently of phylogenetic hypotheses, and also whether the use of multistate morphoclines is methodologically valid. By relying on a particular evolutionary theory, i.e. the neo-Darwinian theory, and consequently assigning natural selection as the major agent of directional progress, the Senckenburg method of phylogenetic reconstruction restricts itself to microevolutionary change and, therefore, cannot be used when other hypotheses on the evolutionary process appear to explain the speciation process more plausibly, i.e. hypotheses on macroevolution. Furthermore, it is an unproved statement that evolution always proceeds according to the principle of economy.

Animals↗

PubMed2000

[Methods of phylogenetic reconstruction and comparative functional morphology].

Cladistics is most prevalent method of phylogenetic reconstruction in the field of vertebrate paleontology, where it has been useful to overcome the weak points of previous evolutionary taxonomy and numerical phenetics. Its primary aim is to divide characters into two categories, old and new, and to bundle together taxonomic groups by their common derived characters (synapomorphies). In spite of such reasonable goals, the method also has limitations such as the premise for independency and equivalency of characters, deciding character polarity, and ignoring parallelism and convergence, as well as an inconsistency between phylogenetic positions and taxonomical names. It is important to understand the functional significance of the shape in question in order to eliminate mistakes in the quantitative treatment of morphology. Since the functions of various animals can be elucidated by mutual comparison of their morphologies, the author has termed this method "comparative functional morphology". One of the future trends for comparative morphology is a qualitative treatment of biological morphology that is more adapted to life, even in phylogenetic reconstructions.

Animals↗

PubMed2000

Control of insect pests with entomopathogenic nematodes: the impact of molecular biology and phylogenetic reconstruction.

Entomopathogenic nematodes are excellent biological control agents. Utilization of these nematodes is developing rapidly with almost a doubling of newly described species in the past five years. Advances in molecular biology and phylogenetic reconstruction have revolutionized understanding of population structure, identification, genetic improvement, systematics, and the symbiosis between entomopathogenic nematodes and their bacteria. Population structure provides the most fundamental information for reliable identification of species and unique genetic variants. Such information could be further assessed for nematode potential as biological control agents. Phylogenetic reconstruction is an important approach for understanding multitrophic interactions among entomopathogenic nematodes, symbiotic bacteria, and their insect hosts. Phylogenetic reconstruction is also important for the development of a natural and stable type of systematics, which can provide guidelines for selecting appropriate entomopathogenic nematode species for particular biological control programs.

Animals↗

PubMed2006

The impact of intragenic recombination on phylogenetic reconstruction at the sectional level in Eucalyptus when using a single copy nuclear gene (cinnamoyl CoA reductase).

Low copy number nuclear genes have been found to be useful for phylogenetic reconstruction at different taxonomic levels. This study investigated the utility of a single copy gene, cinnamoyl CoA reductase (CCR), for resolving phylogenetic relationships at the sectional level within Eucalyptus. The monophyly of sections Exsertaria and Latoangulatae was explored, using section Maidenaria as an outgroup, and the impact of intragenic recombination on phylogenetic reconstruction examined. Phylogenetic analysis did not resolve monophyletic groups. Latoangulatae and Maidenaria were polyphyletic or paraphyletic. Exsertaria species formed a clade but included a single Latoangulatae species (E. major). Recombination analysis identified two intragenic recombination events that involved species from different sections, which have probably been facilitated by inter-sectional hybridisation. One of the events most likely occurred prior to speciation, with several Latoangulatae species having the recombinant allele. The other event may have occurred after speciation, since only one of two E. globulus samples possessed the recombinant allele. This is the first detailed report of intragenic recombination in both CCR and Eucalyptus, and between species of different sections of a plant genus. The occurrence of intragenic recombination may explain the anomalous positions of some species within the phylogenetic tree, and indicates that phylogenetic analysis of Eucalyptus using nuclear genes will be problematic unless recombination is taken into account.

Aldehyde Oxidoreductases↗

PubMed1999

Potentials and limitations of histone repeat sequences for phylogenetic reconstruction of Sophophora.

Simplified DNA sequence acquisition has provided many new data sets that are useful for phylogenetic reconstruction, including single- and multiple-copy nuclear and organellar genes. Although transcribed regions receive much attention, nontranscribed regions have recently been added to the repertoire of sequences suitable for phylogenetic studies, especially for closely related taxa. We evaluated the efficacy of a small portion of the histone repeat for phylogenetic reconstruction among Drosophila species. Histone repeats in invertebrates offer distinct advantages similar to those of widely used ribosomal repeats. First, the units are tandemly repeated and undergo concerted evolution. Second, histone repeats include both highly conserved coding and variable intergenic regions. This composition facilitates application of "universal" primers spanning potentially informative sites. We examined a small region of the histone repeat, including the intergenic spacer segments of coding regions from the divergently transcribed H2A and H2B histone genes. The spacer (about 230 bp) exists as a mosaic with highly conserved functional motifs interspersed with rapidly diverging regions; the former aid in alignment of the spacer. There are no ambiguities in alignment of coding regions. Coding and noncoding regions were analyzed together and separately for phylogenetic information. Parsimony, distance, and maximum-likelihood methods successfully retrieve the corroborated phylogeny for the taxa examined. This study demonstrates the resolving power of a small histone region which may now be added to the growing collection of phylogenetically useful DNA sequences.

Animals↗

PubMed2003

Scaling up accurate phylogenetic reconstruction from gene-order data.

MOTIVATION: Phylogenetic reconstruction from gene-order data has attracted increasing attention from both biologists and computer scientists over the last few years. Methods used in reconstruction include distance-based methods (such as neighbor-joining), parsimony methods using sequence-based encodings, Bayesian approaches, and direct optimization. The latter, pioneered by Sankoff and extended by us with the software suite GRAPPA, is the most accurate approach, but cannot handle more than about 15 genomes of limited size (e.g. organelles). RESULTS: We report here on our successful efforts to scale up direct optimization through a two-step approach: the first step decomposes the dataset into smaller pieces and runs the direct optimization (GRAPPA) on the smaller pieces, while the second step builds a tree from the results obtained on the smaller pieces. We used the sophisticated disk-covering method (DCM) pioneered by Warnow and her group, suitably modified to take into account the computational limitations of GRAPPA. We find that DCM-GRAPPA scales gracefully to at least 1000 genomes of a few hundred genes each and retains surprisingly high accuracy throughout the range: in our experiments, the topological error rate rarely exceeded a few percent. Thus, reconstruction based on gene-order data can now be accomplished with high accuracy on datasets of significant size.

Algorithms↗

PubMed1996

Effects of RNA editing and gene processing on phylogenetic reconstruction.

RNA editing is a ubiquitous phenomenon affecting most mitochondrial and chloroplast, and some nuclear genomes, where mutations in genomic DNA are "corrected" in the mRNA during transcriptional processing. Most editing in plants and animals corrects T-to-C substitutions at nonsynonymous first or second base positions, and the overall effect is an mRNA and protein sequence that differs from that predicted by the DNA. It has been suggested that genomic sequences that undergo editing should not be used in phylogenetics. We contend that editing will have little or no effect on DNA-based phylogenetic reconstruction because it is an intrinsic transcriptional process that does not affect the historical information in the DNA sequence. The only effect of editing on protein-coding DNA should be an increase in the rate of T-to-C transitions. Here we test the effects of RNA editing on phylogenetic reconstruction, using two data sets with high levels of editing, plant coxII and coxIII. Even with high levels of editing, phylogenies based on DNA and edited mRNA are virtually identical. The two types of sequences should not be used in the same analysis, however, because the particular forms of the gene will tend to group together. We also examine the effects of processed paralogs--a term proposed for mRNA sequences that are reverse transcribed and reinserted into the genome as intact gene sequences. Processed paralogs result in a distinct and under-appreciated source of conflict among gene trees because of RNA editing. Analyses with unidentified processed paralogs may yield incorrect phylogenies, and the sequences may evolve at different rates if the gene has been transferred from one genetic compartment (nuclear, mitochondrial, chloroplast) to another. Although RNA editing itself is not a problem in phylogenetic reconstruction, analyses should not combine mRNAs with DNAs, and processed paralogs should be either excluded or analyzed with caution.

Cyclooxygenase 2↗

PubMed1999

Comparison of isoenzyme electrophoresis and morphometric analysis for phylogenetic reconstruction of the Rhodniini (Hemiptera: Reduviidae: Triatominae).

A phylogenetic reconstruction of the medically important tribe Rhodniini (Hemiptera: Reduviidae) based on multilocus isoenzyme electrophoresis is compared with phylogenetic patterns derived from a traditional morphometric analysis. Even with non-normality in the morphometric data, and some inequalities in population variances, discriminant analysis of size-free variables provided broadly similar phylogenetic information to that derived from isoenzyme analysis, revealing 3 main species groups within the genus Rhodnius.

Animals↗

PubMed1990

A simple graphic method for reconstructing phylogenetic trees from molecular data.

A simple graphic method is proposed for reconstructing phylogenetic trees from molecular data. This method is similar to the unweighted pair-group method with arithmetic mean, but the process of computation of average distances and reconstruction of new matrices, required in the latter method, is eliminated from this new method, so that one can reconstruct a phylogenetic tree without using a computer, unless the number of operational taxonomic units is very large. Furthermore, this method allows a phylogenetic tree to have multifurcating branches whenever there is ambiguity with bifurcation.

Algorithms↗

PubMed1994

Least squares estimation of molecular distance--noise abatement in phylogenetic reconstruction.

Zuckerkandl and Pauling (1962, "Horizons in Biochemistry," pp. 189-225, Academic Press, New York) first noticed that the degree of sequence similarity between the proteins of different species could be used to estimate their phylogenetic relationship. Since then models have been developed to improve the accuracy of phylogenetic inferences based on amino acid or DNA sequences. Most of these models were designed to yield distance measures that are linear with time, on average. The reliability of phylogenetic reconstruction, however, depends on the variance of the distance measure in addition to its expectation. In this paper we show how the method of generalized least squares can be used to combine data types, each most informative at different points in time, into a single distance measure. This measure reconstructs phylogenies more accurately than existing non-likelihood distance measures. We illustrate the approach for a two-rate mutation model and demonstrate that its application provides more accurate phylogenetic reconstruction than do currently available analytical distance measures.

Amino Acid Sequence↗

PubMed1994

Phylogenetic reconstruction of South American felids defined by protein electrophoresis.

Phylogenetic associations among six closely related South American felid species were defined by changes in protein-encoding gene loci. We analyzed proteins isolated from skin fibroblasts using two-dimensional electrophoresis and allozymes extracted from blood cells. Genotypes were determined for multiple individuals of ocelot, margay, tigrina, Geoffroy's cat, kodkod, and pampas cat at 548 loci resolved by two-dimensional electrophoresis and 44 allozyme loci. Phenograms were constructed using the methods of Fitch-Margoliash and neighbor-joining on a matrix of Nei's unbiased genetic distances for all pairs of species. Results of a relative-rate test indicate changes in two-dimensional electrophoresis data are constant among all South American felids with respect to a hyena outgroup. Allelic frequencies were transformed to discrete character states for maximum parsimony analysis. Phylogenetic reconstruction indicates a major split occurred approximately 5-6 million years ago, leading to three groups within the ocelot lineage. The earliest divergence led to Leopardus tigrina, followed by a split between an ancestor of an unresolved trichotomy of three species (Oncifelis guigna, O. geoffroyi, and Lynchailuris colocolo) and a recent common ancestor of Leopardus pardalis and L. wiedii. The results suggest that modern South American felids are monophyletic and evolved rapidly after the formation of the Panama land bridge between North and South America.

Alleles↗

PubMed1994

DNA-dependent RNA polymerase subunit B as a tool for phylogenetic reconstructions: branching topology of the archaeal domain.

The branching topology of the archaeal (archaebacterial) domain was inferred from sequence comparisons of the largest subunit (B) of DNA-dependent RNA polymerases (RNAP). Both the nucleic acid sequences of the genes coding for RNAP subunit B and the amino acid sequences of the derived gene products were used for phylogenetic reconstructions. Individual analysis of the three nucleotide positions of codons revealed significant inequalities with respect to guanosine and cytosine (GC) content and evolutionary rates. Only the nucleotides at the second codon positions were found to be unbiased by varied GC contents and sufficiently conserved for reliable phylogenetic reconstructions. A decision matrix was used for the combination of the results of distance matrix, maximum parsimony, and maximum likelihood methods. For this purpose the original results (sums of squares, steps, and logarithms of likelihoods) were transformed into comparable effective values and analyzed with methods known from the theory of statistical decisions. Phylogenetic invariants and statistical analysis with resampling techniques (bootstrap and jackknife) confirmed the preferred branching topology, which is significantly different from the topology known from phylogenetic trees based on 16S rRNA sequences. The preferred topology reconstructed by this analysis shows a common stem for the Methanococcales and Methanobacteriales and a separation of the thermophilic sulfur archaea from the methanogens and halophiles. The latter coincides with a unique phylogenetic location of a characteristic splitting event replacing the largest RNAP subunit of thermophilic sulfur archaea by two fragments in methanogens and halophiles. This topology is in good agreement with physiological and structural differences between the various archaea and demonstrates RNAP to be a suitable phylogenetic marker molecule.

Amino Acid Sequence↗

PubMed2005

Internal transcribed spacer rRNA gene-based phylogenetic reconstruction using algorithms with local and global sequence alignment for black yeasts and their relatives.

Sequences of rRNA gene internal transcribed spacer (ITS) of a standard set of black yeast-like fungal pathogens were compared using two methods: local and global alignments. The latter is based on DNA-walk divergence analysis. This method has become recently available as an algorithm (DNAWD program) which converts sequences into three-dimensional walks. The walks are compared with, or fit to, each other generating global alignments. The DNA-walk geometry defines a proper metric used to create a distance matrix appropriated for phylogenetic reconstruction. In this work, the analyses were carried out for species currently classified in Capronia, Cladophialophora, Exophiala, Fonsecaea, Phialophora, and Ramichloridium. Main groups were verified by small-subunit rRNA gene data. DNAWD applied to ITS2 alone enabled species recognition as well as phylogenetic reconstruction reflecting clades discriminated in small-subunit rRNA gene phylogeny, which was not possible with any other algorithm using local alignment for the same data set. It is concluded that DNAWD provides rapid insight into broader relationships between groups using genes that otherwise would be hardly usable for this purpose.

Algorithms↗

PubMed1987

The neighbor-joining method: a new method for reconstructing phylogenetic trees.

A new method called the neighbor-joining method is proposed for reconstructing phylogenetic trees from evolutionary distance data. The principle of this method is to find pairs of operational taxonomic units (OTUs [= neighbors]) that minimize the total branch length at each stage of clustering of OTUs starting with a starlike tree. The branch lengths as well as the topology of a parsimonious tree can quickly be obtained by using this method. Using computer simulation, we studied the efficiency of this method in obtaining the correct unrooted tree in comparison with that of five other tree-making methods: the unweighted pair group method of analysis, Farris's method, Sattath and Tversky's method, Li's method, and Tateno et al.'s modified Farris method. The new, neighbor-joining method and Sattath and Tversky's method are shown to be generally better than the other methods.

Animals↗

PubMed1999

Compositional bias may affect both DNA-based and protein-based phylogenetic reconstructions.

It is now well-established that compositional bias in DNA sequences can adversely affect phylogenetic analysis based on those sequences. Phylogenetic analyses based on protein sequences are generally considered to be more reliable than those derived from the corresponding DNA sequences because it is believed that the use of encoded protein sequences circumvents the problems caused by nucleotide compositional biases in the DNA sequences. There exists, however, a correlation between AT/GC bias at the nucleotide level and content of AT- and GC-rich codons and their corresponding amino acids. Consequently, protein sequences can also be affected secondarily by nucleotide compositional bias. Here, we report that DNA bias not only may affect phylogenetic analysis based on DNA sequences, but also drives a protein bias which may affect analyses based on protein sequences. We present a striking example where common phylogenetic tools fail to recover the correct tree from complete animal mitochondrial protein-coding sequences. The data set is very extensive, containing several thousand sites per sequence, and the incorrect phylogenetic trees are statistically very well supported. Additionally, neither the use of the LogDet/paralinear transform nor removal of positions in the protein alignment with AT- or GC-rich codons allowed recovery of the correct tree. Two taxa with a large compositional bias continually group together in these analyses, despite a lack of close biological relatedness. We conclude that even protein-based phylogenetic trees may be misleading, and we advise caution in phylogenetic reconstruction using protein sequences, especially those that are compositionally biased.

Animals↗

PubMed2001

Shared nucleotide composition biases among species and their impact on phylogenetic reconstructions of the Drosophilidae.

Compositional changes are a major feature of genome evolution. Overlooking nucleotide composition differences among sequences can seriously mislead phylogenetic reconstructions. Large compositional variation exists among the members of the family Drosophilidae. Until now, however, base composition differences have been largely neglected in the formulations of the nucleotide substitution process used to reconstruct the phylogeny of this important group of species. The present study adopts a maximum-likelihood framework of phylogenetic inference in order to analyze five nuclear gene regions and shows that (1) the pattern of compositional variation in the Drosophilidae does not match the phylogeny of the species; (2) accounting for the heterogeneous GC content with Galtier and Gouy's nucleotide substitution model leads to a tree that differs in significant aspects from the tree inferred when the nucleotide composition differences are ignored, even though both phylogenetic hypotheses attain strong nodal support in the bootstrap analyses; and (3) the LogDet distance correction cannot completely overcome the distorting effects of the compositional variation that exists among the species of the Drosophilidae. Our analyses confidently place the Chymomyza genus as an outgroup closer than the genus Scaptodrosophila to the Drosophila genus and conclusively support the monophyly of the Sophophora subgenus.

Alcohol Dehydrogenase↗