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PubMed1995

A new method of inference of ancestral nucleotide and amino acid sequences.

A statistical method was developed for reconstructing the nucleotide or amino acid sequences of extinct ancestors, given the phylogeny and sequences of the extant species. A model of nucleotide or amino acid substitution was employed to analyze data of the present-day sequences, and maximum likelihood estimates of parameters such as branch lengths were used to compare the posterior probabilities of assignments of character states (nucleotides or amino acids) to interior nodes of the tree; the assignment having the highest probability was the best reconstruction at the site. The lysozyme c sequences of six mammals were analyzed by using the likelihood and parsimony methods. The new likelihood-based method was found to be superior to the parsimony method. The probability that the amino acids for all interior nodes at a site reconstructed by the new method are correct was calculated to be 0.91, 0.86, and 0.73 for all, variable, and parsimony-informative sites, respectively, whereas the corresponding probabilities for the parsimony method were 0.84, 0.76, and 0.51, respectively. The probability that an amino acid in an ancestral sequence is correctly reconstructed by the likelihood analysis ranged from 91.3 to 98.7% for the four ancestral sequences.

Amino Acid Sequence↗

PubMed1997

Preservation of dendrites with the presence of reorganized mossy fiber collaterals in hippocampal dentate granule cells in patients with temporal lobe epilepsy.

Dendritic morphology was studied in human hippocampal dentate granule cells (DGCs) by intracellularly-injecting biocytin in slice preparations that were obtained from temporal lobe epilepsy patients who underwent a surgical treatment for medically-intractable seizures. These DGCs had a fan-shaped dendritic domain of 54.1 degrees +/- 4.1 S.E.M. with 13.8 +/- 1.1 branch points and an estimated total dendritic length of 11535.6 microns +/- 3045.4. Dendritic spines were counted, and spine density was calculated to be 0.25 spines/microns +/- 0.16 S.E.M.. However, when the cells were categorized into two groups based on the presence or absence of the aberrant mossy fiber collaterals, the number of dendritic branches was significantly lower and spine density was significantly higher in DGCs that had aberrant collaterals. In particular, in the proximal dendrite, the spine density was 5 times higher in DGCs whose own mossy fibers were reorganized sending aberrant collaterals to this dendritic region (0.750 spines/microns +/- 0.203 S.E.M.: P < 0.01) than the DGCs without such collaterals (0.082 spines/microns +/- p.021 S.E.M.). These results suggest that the axonal reorganization may have an effect on the morphology of DGC dendrites directly or indirectly in such a way that dendritic structure and spines could be protected from seizure-induced excitotoxic cell damage.

Dendrites↗

PubMed2004

Bayesian estimation of ancestral character states on phylogenies.

Biologists frequently attempt to infer the character states at ancestral nodes of a phylogeny from the distribution of traits observed in contemporary organisms. Because phylogenies are normally inferences from data, it is desirable to account for the uncertainty in estimates of the tree and its branch lengths when making inferences about ancestral states or other comparative parameters. Here we present a general Bayesian approach for testing comparative hypotheses across statistically justified samples of phylogenies, focusing on the specific issue of reconstructing ancestral states. The method uses Markov chain Monte Carlo techniques for sampling phylogenetic trees and for investigating the parameters of a statistical model of trait evolution. We describe how to combine information about the uncertainty of the phylogeny with uncertainty in the estimate of the ancestral state. Our approach does not constrain the sample of trees only to those that contain the ancestral node or nodes of interest, and we show how to reconstruct ancestral states of uncertain nodes using a most-recent-common-ancestor approach. We illustrate the methods with data on ribonuclease evolution in the Artiodactyla. Software implementing the methods (BayesMultiState) is available from the authors.

Animals↗

PubMed2003

Performance-based selection of likelihood models for phylogeny estimation.

Phylogenetic estimation has largely come to rely on explicitly model-based methods. This approach requires that a model be chosen and that that choice be justified. To date, justification has largely been accomplished through use of likelihood-ratio tests (LRTs) to assess the relative fit of a nested series of reversible models. While this approach certainly represents an important advance over arbitrary model selection, the best fit of a series of models may not always provide the most reliable phylogenetic estimates for finite real data sets, where all available models are surely incorrect. Here, we develop a novel approach to model selection, which is based on the Bayesian information criterion, but incorporates relative branch-length error as a performance measure in a decision theory (DT) framework. This DT method includes a penalty for overfitting, is applicable prior to running extensive analyses, and simultaneously compares all models being considered and thus does not rely on a series of pairwise comparisons of models to traverse model space. We evaluate this method by examining four real data sets and by using those data sets to define simulation conditions. In the real data sets, the DT method selects the same or simpler models than conventional LRTs. In order to lend generality to the simulations, codon-based models (with parameters estimated from the real data sets) were used to generate simulated data sets, which are therefore more complex than any of the models we evaluate. On average, the DT method selects models that are simpler than those chosen by conventional LRTs. Nevertheless, these simpler models provide estimates of branch lengths that are more accurate both in terms of relative error and absolute error than those derived using the more complex (yet still wrong) models chosen by conventional LRTs. This method is available in a program called DT-ModSel.

Bayes Theorem↗

PubMed2005

Branch-length prior influences Bayesian posterior probability of phylogeny.

The Bayesian method for estimating species phylogenies from molecular sequence data provides an attractive alternative to maximum likelihood with nonparametric bootstrap due to the easy interpretation of posterior probabilities for trees and to availability of efficient computational algorithms. However, for many data sets it produces extremely high posterior probabilities, sometimes for apparently incorrect clades. Here we use both computer simulation and empirical data analysis to examine the effect of the prior model for internal branch lengths. We found that posterior probabilities for trees and clades are sensitive to the prior for internal branch lengths, and priors assuming long internal branches cause high posterior probabilities for trees. In particular, uniform priors with high upper bounds bias Bayesian clade probabilities in favor of extreme values. We discuss possible remedies to the problem, including empirical and full Bayesian methods and subjective procedures suggested in Bayesian hypothesis testing. Our results also suggest that the bootstrap proportion and Bayesian posterior probability are different measures of accuracy, and that the bootstrap proportion, if interpreted as the probability that the clade is true, can be either too liberal or too conservative.

Bayes Theorem↗

PubMed2003

Pandit: a database of protein and associated nucleotide domains with inferred trees.

MOTIVATION: A large, high-quality database of homologous sequence alignments with good estimates of their corresponding phylogenetic trees will be a valuable resource to those studying phylogenetics. It will allow researchers to compare current and new models of sequence evolution across a large variety of sequences. The large quantity of data may provide inspiration for new models and methodology to study sequence evolution and may allow general statements about the relative effect of different molecular processes on evolution. RESULTS: The Pandit 7.6 database contains 4341 families of sequences derived from the seed alignments of the Pfam database of amino acid alignments of families of homologous protein domains (Bateman et al., 2002). Each family in Pandit includes an alignment of amino acid sequences that matches the corresponding Pfam family seed alignment, an alignment of DNA sequences that contain the coding sequence of the Pfam alignment when they can be recovered (overall, 82.9% of sequences taken from Pfam) and the alignment of amino acid sequences restricted to only those sequences for which a DNA sequence could be recovered. Each of the alignments has an estimate of the phylogenetic tree associated with it. The tree topologies were obtained using the neighbor joining method based on maximum likelihood estimates of the evolutionary distances, with branch lengths then calculated using a standard maximum likelihood approach.

Algorithms↗

PubMed2002

Regulation by glycogen synthase kinase-3beta of the arborization field and maturation of retinotectal projection in zebrafish.

The retinotectal projection is one of the best systems to study the molecular basis of synapse formation in the CNS because of the well characterized topographic connections and activity-dependent refinement. Here, we developed a presynaptic neuron-specific gene manipulation system in the zebrafish retinotectal projection in vivo using the nicotinic acetylcholine receptor beta3 (nAChRbeta3) gene promoter. Enhanced green fluorescent protein (EGFP) expression signals in living transgenic zebrafish lines carrying the nAChRbeta3 gene promoter-directed EGFP expression vector visualized the development of entire retinal ganglion cell (RGC) axon projection to the tectum. Microinjection of the nAChRbeta3 gene promoter-driven double-cassette vectors directing the expression of both dominant-negative glycogen synthase kinase-3beta (dnGSK-3beta) and EGFP enabled us to follow the development of individual RGCs and to examine the effect of the molecule on the axonal arborization and maturation of the same neurons in living zebrafish. We found that the expression of the dominant-negative form of zebrafish GSK-3beta suppressed the arborization field of RGC axon terminals in the tectum as estimated by the reduction of arbor branch length and arbor areas. Furthermore, the suppression of GSK-3beta activity increased the size of vesicle-associated membrane protein 2-EGFP puncta in RGC axon terminals at the early stage of innervation to the tectum. These results suggest that GSK-3beta regulates the arborization field and maturation of RGC axon terminals in vivo.

Animals↗

PubMed2003

When being "most likely" is not enough: examining the performance of three uses of the parametric bootstrap in phylogenetics.

I show that three parametric-bootstrap (PB) applications that have been proposed for phylogenetic analysis, can be misleading as currently implemented. First, I show that simulating a topology estimated from preliminary data in order to determine the sequence length that should allow the best tree obtained from more extensive data to be correct with a desired probability, delivers an accurate estimate of this length only in topological situations in which most preliminary trees are expected to be both correct and statistically significant, i.e. when no further analysis would be needed. Otherwise, one obtains strong underestimates of the length or similarly biased values for incorrect trees. Second, I show that PB-based topology tests that use as null hypothesis the most likely tree congruent with a pre-specified topological relationship alternative to the unconstrained most likely tree, and simulate this tree for P value estimation, produce excessive type I error (from 50% to 600% and higher) when they are applied to null data generated by star-shaped or dichotomous four-taxon topologies. Simulating the most likely star topology for P value estimation results instead in correct type-I-error production even when the null data are generated by a dichotomous topology. This is a strong indication that the star topology is the correct default null hypothesis for phylogenies. Third, I show that PB-estimated confidence intervals (CIs) for the length of a tree branch are generally accurate, although in some situations they can be strongly over- or under-estimated relative to the "true" CI. Attempts to identify a biased CI through a further round of simulations were unsuccessful. Tracing the origin and propagation of parameter estimate error through the CI estimation exercise, showed that the sparseness of site-patterns which are crucial to the estimation of pivotal parameters, can allow homoplasy to bias these estimates and ultimately the PB-based CI estimation. Concluding, I stress that statistical techniques that simulate models estimated from limited data need to be carefully calibrated, and I defend the point that pattern-sparseness assessment will be the next frontier in the statistical analysis of phylogenies, an effort that will require taking advantage of the merits of black-box maximum-likelihood approaches and of insights from intuitive, site-pattern-oriented approaches like parsimony.

Algorithms↗

PubMed2003

Testing for phylogenetic signal in comparative data: behavioral traits are more labile.

The primary rationale for the use of phylogenetically based statistical methods is that phylogenetic signal, the tendency for related species to resemble each other, is ubiquitous. Whether this assertion is true for a given trait in a given lineage is an empirical question, but general tools for detecting and quantifying phylogenetic signal are inadequately developed. We present new methods for continuous-valued characters that can be implemented with either phylogenetically independent contrasts or generalized least-squares models. First, a simple randomization procedure allows one to test the null hypothesis of no pattern of similarity among relatives. The test demonstrates correct Type I error rate at a nominal alpha = 0.05 and good power (0.8) for simulated datasets with 20 or more species. Second, we derive a descriptive statistic, K, which allows valid comparisons of the amount of phylogenetic signal across traits and trees. Third, we provide two biologically motivated branch-length transformations, one based on the Ornstein-Uhlenbeck (OU) model of stabilizing selection, the other based on a new model in which character evolution can accelerate or decelerate (ACDC) in rate (e.g., as may occur during or after an adaptive radiation). Maximum likelihood estimation of the OU (d) and ACDC (g) parameters can serve as tests for phylogenetic signal because an estimate of d or g near zero implies that a phylogeny with little hierarchical structure (a star) offers a good fit to the data. Transformations that improve the fit of a tree to comparative data will increase power to detect phylogenetic signal and may also be preferable for further comparative analyses, such as of correlated character evolution. Application of the methods to data from the literature revealed that, for trees with 20 or more species, 92% of traits exhibited significant phylogenetic signal (randomization test), including behavioral and ecological ones that are thought to be relatively evolutionarily malleable (e.g., highly adaptive) and/or subject to relatively strong environmental (nongenetic) effects or high levels of measurement error. Irrespective of sample size, most traits (but not body size, on average) showed less signal than expected given the topology, branch lengths, and a Brownian motion model of evolution (i.e., K was less than one), which may be attributed to adaptation and/or measurement error in the broad sense (including errors in estimates of phenotypes, branch lengths, and topology). Analysis of variance of log K for all 121 traits (from 35 trees) indicated that behavioral traits exhibit lower signal than body size, morphological, life-history, or physiological traits. In addition, physiological traits (corrected for body size) showed less signal than did body size itself. For trees with 20 or more species, the estimated OU (25% of traits) and/or ACDC (40%) transformation parameter differed significantly from both zero and unity, indicating that a hierarchical tree with less (or occasionally more) structure than the original better fit the data and so could be preferred for comparative analyses.

Animals↗

PubMed1998

Nucleotide substitution models and estimation of phylogeny.

The nucleotide substitution matrix inferred from avian data sets using cytochrome b differs considerably from the models commonly used in phylogenetic analyses. To analyze the possible effects of this particular pattern of change in phylogeny estimation we performed a computer simulation in which we started with a real sequence and used the inferred model of change to produce a tree of 10 species. Maximum parsimony (MP), maximum likelihood (ML), and various distance methods were then used to recover the topology and the branch lengths. We used two kinds of data with varying levels of variation. In addition, we tested with the removal of third positions and different weighting schemes. At low levels of variation, MP was outstanding in recovering the topology (90% correct), while unweighted pair-group method, arithmetic average (UPGMA), regardless of distances used, was poor (40%). At the higher level, most methods had a chance of around 40%-58% of finding the true tree. However, in most cases, the trees found were only slightly wrong, with only one or a few branches misplaced. On the other hand, the use of a "wrong" model had serious effects on the estimation of branch lengths (distances). Although precision was high, accuracy was poor with most methods, giving branch lengths that were biased downward. When seeded with the true distance matrix, Fitch and NJ always found the true tree, while UPGMA frequently failed to do so. The effect of removing third positions was dramatic at low levels of variation, because only one MP program was able to find a true tree at all, albeit rarely, while none of the others ever did so. At higher levels, the situation was better, but still much worse than with the whole data set.

Animals↗

PubMed2004

Using exon and intron sequences of the gene Mp20 to resolve basal relationships in Cicindela (Coleoptera:Cicindelidae).

The genus Cicindela (Coleoptera: Cicindelidae) is a species-rich cosmopolitan group of tiger beetles useful for comparing clade diversification worldwide. Knowledge about relationships of major groups is important for this analysis but basal nodes in Cicindela have been difficult to resolve with standard mtDNA markers. Here we developed the Mp20 gene, a single-copy nuclear marker coding for a muscle-associated protein in insects, for phylogenetic analysis of basal groups of Cicindela. Nearly full-length sequences were obtained for 51 cicindelids, including major taxonomic groups from all continents. Sequences of Mp20 were between 1.2 and 1.7 kb and spanning three introns. Phylogenetic signal of exon and intron sequences was compared with that from four gene regions of mtDNA (COI, COIII, Cytb, 16S rRNA; 2.4 kb total). Because introns differed in length, sequence alignment was conducted using various procedures of phenetic and parsimony-based character coding of indels to assess their phylogenetic information content, but major nodes were recovered consistently. Mp20 sequences contributed two thirds of the total support of the combined analysis, with most signal from the introns. We found major clades of Cicindela to be geographically largely coincident with continental regions, confined to Australasia, the Holarctic, the Indian subcontinent, Africa, and South and Central America. Clock estimates using various maximum-likelihood (ML) branch length calculations resulted in roughly similar divergence times whether Mp20 exon, introns, or mtDNA were used, and they were not greatly affected by different procedures for coding and optimizing indel characters. Based on existing clock calibrations in Cicindela, basal splits of continental lineages occurred in the mid-Miocene, placing the radiation of basal groups of Cicindela to a period when their open-vegetation habitats expanded globally.

Animals↗

PubMedDate not supplied

Placental morphogenesis and the star volumes of villous trees and intervillous pores.

In 27 human placentae collected at 13-39 weeks, the growth and morphogenesis of villi and of the maternal intervillous space were assessed using a design-based stereological approach for estimating star volume. The purpose was to quantify changes occurring during these processes and to derive parameters pertinent to physiological performance (notably transport capability and haemodynamics). Placentae were sampled by cutting paraffin sections at random locations and orientations. Estimates of the global volumes of peripheral (terminal and intermediate) villi and intervillous space were derived from placental volumes via point counting. Total villous surface was estimated by intersection counting and length by transection counting. Treating villi like the branches of tree-like networks and the intervillous space as a system of confluent pores, estimates of the star volumes of these compartments were also made. These volumes were calculated by measuring point-sampled intercept lengths. The total volumes of villi and intervillous space increased steadily throughout gestation. After the second trimester, the increase in volume of villi was accompanied by a decrease in villous star volume. This can be explained by the continued elaboration and maturation of terminal villi, the combined length of which increased whilst mean diameter declined. The star volume of the intervillous space also declined and this, too, is consistent with villous growth and proliferation.

Female↗

PubMed2006

A mitogenomic timescale for birds detects variable phylogenetic rates of molecular evolution and refutes the standard molecular clock.

Current understanding of the diversification of birds is hindered by their incomplete fossil record and uncertainty in phylogenetic relationships and phylogenetic rates of molecular evolution. Here we performed the first comprehensive analysis of mitogenomic data of 48 vertebrates, including 35 birds, to derive a Bayesian timescale for avian evolution and to estimate rates of DNA evolution. Our approach used multiple fossil time constraints scattered throughout the phylogenetic tree and accounts for uncertainties in time constraints, branch lengths, and heterogeneity of rates of DNA evolution. We estimated that the major vertebrate lineages originated in the Permian; the 95% credible intervals of our estimated ages of the origin of archosaurs (258 MYA), the amniote-amphibian split (356 MYA), and the archosaur-lizard divergence (278 MYA) bracket estimates from the fossil record. The origin of modern orders of birds was estimated to have occurred throughout the Cretaceous beginning about 139 MYA, arguing against a cataclysmic extinction of lineages at the Cretaceous/Tertiary boundary. We identified fossils that are useful as time constraints within vertebrates. Our timescale reveals that rates of molecular evolution vary across genes and among taxa through time, thereby refuting the widely used mitogenomic or cytochrome b molecular clock in birds. Moreover, the 5-Myr divergence time assumed between 2 genera of geese (Branta and Anser) to originally calibrate the standard mitochondrial clock rate of 0.01 substitutions per site per lineage per Myr (s/s/l/Myr) in birds was shown to be underestimated by about 9.5 Myr. Phylogenetic rates in birds vary between 0.0009 and 0.012 s/s/l/Myr, indicating that many phylogenetic splits among avian taxa also have been underestimated and need to be revised. We found no support for the hypothesis that the molecular clock in birds "ticks" according to a constant rate of substitution per unit of mass-specific metabolic energy rather than per unit of time, as recently suggested. Our analysis advances knowledge of rates of DNA evolution across birds and other vertebrates and will, therefore, aid comparative biology studies that seek to infer the origin and timing of major adaptive shifts in vertebrates.

Animals↗

PubMed2006

Cost and probability of flowering at the shoot level in relation to variability in shoot size within the crown of Vaccinium hirtum (Ericaceae).

Size-related variation in the cost and probability of flowering among shoots within a crown of Vaccinium hirtum was investigated to clarify patterns and regulation of flowering at the shoot-module level, below the level of the individual. The apices of previous-year shoots differentiated into current-year shoots vegetatively (vegetative branches) or became reproductive by developing inflorescences (reproductive branches). Length growth and fate of current-year shoots were determined, and the future potential for reproduction was estimated using a matrix model of shoot dynamics. Reproductive branches had fewer current-year shoots and shorter total shoot lengths and thus had a reduced potential for reproduction compared with vegetative branches, indicating the cost of flowering at the shoot level. This cost of flowering was higher in longer shoots. The probability of the initiation of flowering in a shoot increased with increasing shoot length in shorter shoots, reached a maximum in medium-sized shoots, and decreased in longer shoots. The size-related changes in the probability of flowering at the shoot level can be largely explained by the size-dependent changes in shoot-level resource availability and cost of flowering.

Flowers↗

PubMed1982

Accuracy of estimated phylogenetic trees from molecular data. I. Distantly related species.

The accuracies and efficiencies of four different methods for constructing phylogenetic trees from molecular data were examined by using computer simulation. The methods examined are UPGMA, Fitch and Margoliash's (1967) (F/M) method, Farris' (1972) method, and the modified Farris method (Tateno, Nei, and Tajima, this paper). In the computer simulation, eight OTUs (32 OTUs in one case) were assumed to evolve according to a given model tree, and the evolutionary change of a sequence of 300 nucleotides was followed. The nucleotide substitution in this sequence was assumed to occur following the Poisson distribution, negative binomial distribution or a model of temporally varying rate. Estimates of nucleotide substitutions (genetic distances) were then computed for all pairs of the nucleotide sequences that were generated at the end of the evolution considered, and from these estimates a phylogenetic tree was reconstructed and compared with the true model tree. The results of this comparison indicate that when the coefficient of variation of branch length is large the Farris and modified Farris methods tend to be better than UPGMA and the F/M method for obtaining a good topology. For estimating the number of nucleotide substitutions for each branch of the tree, however, the modified Farris method shows a better performance than the Farris method. When the coefficient of variation of branch length is small, however, UPGMA shows the best performance among the four methods examined. Nevertheless, any tree-making method is likely to make errors in obtaining the correct topology with a high probability, unless all branch lengths of the true tree are sufficiently long. It is also shown that the agreement between patristic and observed genetic distances is not a good indicator of the goodness of the tree obtained.

Base Sequence↗

PubMed2001

A putative insect intracellular endosymbiont stem clade, within the Enterobacteriaceae, infered from phylogenetic analysis based on a heterogeneous model of DNA evolution.

Insect intracellular symbiotic bacteria (intracellular endosymbionts, or endocytobionts) were positioned within the gamma 3-Proteobacteria using a non-homogeneous model of DNA evolution, allowing for rate variability among sites, for GC content heterogeneity among sequences, and applied to a maximum likelihood framework. Most of them were found to be closely related within the Enterobacteriaceae family, located between Proteus and Yersinia. These results suggest that such a bacterial group might possess several traits allowing for insect infection and the stable establishment of symbiotic relationships and that this could represent a stem clade for numerous insect endocytobionts. Based on the estimations of the equilibrium GC content and branch lengths in the phylogenetic tree, we have made comparisons of the relative ages of these different symbioses.

Animals↗

PubMed1984

Quantitative analysis of a vascular tree model with the dynamic spatial reconstructor.

The accuracy in determining the three-dimensional anatomy of a vessel network by computed tomography (CT) is evaluated using a glass model of a pulmonary artery. The dynamic spatial reconstructor (DSR), a high temporal resolution, volumetric, roentgenographic, CT scanner, was used to scan the model. The glass of the model had a roentgen attenuation coefficient mu = 0.55 cm-1, which is approximately equivalent to the 20% dilution of contrast medium to be expected in the pulmonary arterial tree following a contrast agent bolus injection of 2 ml/kg in the right atrium. The model was scanned inside a 20 cm diameter Plexiglas cylinder with a 1 cm thick wall (mu congruent to 0.2 cm-1) to simulate the chest wall of a 20 kg dog, and it was filled with potato flakes to simulate lung parenchyma (mu congruent to 0.06 cm-1). In one 0.011 s scan, information for reconstruction of a stack of images of transaxial sections was recorded. Sequential scans were performed to obtain data for either maximum transaxial resolution (14 angles of view every 0.0167 s, 120 parallel slices each 1.8 mm thick) or maximum axial resolution (eight angles of view every 0.0167 s, 240 parallel slices each 0.9 mm thick) reconstructions. Estimated detectable "vessel" size, cross-sectional area, branching angle, and interbranch segment length were determined as a function of imaged slice thickness, orientation of section image, and number of angles of view (i.e., scan duration) used to make images. Retrospective selection of 0.05 s duration scan apertures at sequential 0.5 s intervals was used to simulate a typical, retrospectively gated reconstruction from a DSR scan. Using these reconstructed images, 2 mm diameter "vessels" could be readily detected and their structure quantitated. Comparing direct measurements and DSR estimates, cross-sectional area (SEE = 3 mm2), branching angles (SEE = 2 degrees), and segment length (SEE = 1 mm) all had a correlation coefficient greater than 0.99, and the regression lines showed no significant differences from the lines of identity (p greater than 0.05).

Animals↗

PubMed2002

Rate4Site: an algorithmic tool for the identification of functional regions in proteins by surface mapping of evolutionary determinants within their homologues.

MOTIVATION: A number of proteins of known three-dimensional (3D) structure exist, with yet unknown function. In light of the recent progress in structure determination methodology, this number is likely to increase rapidly. A novel method is presented here: 'Rate4Site', which maps the rate of evolution among homologous proteins onto the molecular surface of one of the homologues whose 3D-structure is known. Functionally important regions often correspond to surface patches of slowly evolving residues. RESULTS: Rate4Site estimates the rate of evolution of amino acid sites using the maximum likelihood (ML) principle. The ML estimate of the rates considers the topology and branch lengths of the phylogenetic tree, as well as the underlying stochastic process. To demonstrate its potency, we study the Src SH2 domain. Like previously established methods, Rate4Site detected the SH2 peptide-binding groove. Interestingly, it also detected inter-domain interactions between the SH2 domain and the rest of the Src protein that other methods failed to detect.

Algorithms↗